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Sample records for error prone pcr

  1. Alcohol-mediated error-prone PCR.

    PubMed

    Claveau, S; Sasseville, M; Beauregard, M

    2004-11-01

    The effect of urea, isopropanol, propan-1-ol, and butan-1-ol on PCR using three different DNA polymerases was investigated. In the presence of these agents, polymerases were active as expected up to a critical concentration where they became progressively inhibited. Critical concentrations of alcohols generally increased with thermoresistance of the polymerases and decreased with the hydrophobicity of the alcohols. These results indicate that an important aspect of the inhibition involved conformational loosening due to a decrease in the hydrophobic effect. A mutagenic effect occurred with Vent(r) (exo-) DNA polymerase in the presence of 7.0 to 8.0% v/v propan-1-ol, affording mutation frequencies of up to 9.8 x 10(-3) mutation/bp/PCR. Under these conditions the preferential replacement of Gs and Cs was observed, in opposition to standard error-prone PCR that favors replacement of As and Ts. Comparison of various PCR conditions indicates that propanol and MnCl2 have different modes of action, and that the decrease in fidelity promoted by propanol is due to a finely tuned partial destabilization of the polymerase. The PCR conditions developed in this study provide a useful alternative for targeting different sequence space for directed evolution experiments. PMID:15585138

  2. [Directed evolution of aflatoxin detoxifzyme in vitro by error-prone PCR].

    PubMed

    Zhang, Sai; Xing, Keke; Hu, Yadong; Xie, Chunfang; Liu, Daling; Yao, Dongsheng

    2011-07-01

    The experiment was conducted by directed evolution strategy (error-prone PCR) to improve the activity of aflatoxin detoxifzyme with the high-throughput horse radish peroxidas and recessive brilliant green (HRP-RBG) screening system. We built up a mutant library to the order of 10(4). Two rounds of EP-PCR and HRP-RBG screening were used to obtain three optimum mutant strains A1773, A1476 and A2863. We found that mutant A1773 had upper temperature tolerance of 70 degrees C and that its enzyme activity was 6.5 times higher than that of the parent strain. Mutant strains A1476 worked well at pH 4.0 and its enzyme activity was 21 times higher than that of the parent strain. Mutant A2863 worked well at pH 4.0 and pH 7.5, and its enzyme activity was 12.6 times higher than that of the parent strain. With DNA sequencing we found that mutant A1773 revealed two amino acid substitutions, Glu127Lys and Gln613Arg. Mutant A1476 revealed four amino acid substitutions: Ser46Pro, Lys221Gln, Ile307Leu and Asn471lle. Mutant A2863 revealed four amino acid substitutions: Gly73Ser, Ile307Leu, Va1596Ala and Gln613Arg. The results provided a useful illustration for the deep understanding of the relationship between the function and structure of aflatoxin detoxifzyme. PMID:22016995

  3. Improvement of cyclodextrin glucanotransferase as an antistaling enzyme by error-prone PCR.

    PubMed

    Shim, Jae-Hoon; Kim, Young-Wan; Kim, Tae-Jip; Chae, Hye-Young; Park, Jin-Hee; Cha, Hyunju; Kim, Jung-Wan; Kim, Yong-Ro; Schaefer, Thomas; Spendler, Tina; Moon, Tae-Wha; Park, Kwan-Hwa

    2004-03-01

    In an effort to improve the properties of cyclodextrin glucanotransferase (CGTase) as an antistaling enzyme, error-prone PCR was used to introduce random mutations into a CGTase cloned from alkalophilic Bacillus sp. I-5 (CGTase I-5). A mutant CGTase[3-18] with the three mutations M234T, F259I and V591A was selected by agar plate assay. Sequence alignment of various CGTases indicated that M234 and F259 are located in the vicinity of the catalytic sites of the enzyme and V591 in the starch binding domain E. The cyclization activity of CGTase[3-18] was dramatically decreased by 10-fold, while the hydrolyzing activity was increased by up to 15-fold. These mutations near subsite +1 (M234T) and at subsite +2 (F259I) are likely to alter the enzyme activity in a concerted manner, promoting hydrolysis of substrate while retarding cyclization. The addition of CGTase[3-18] reduced the retrogradation rate of bread by as much as did the commercial antistaling enzyme Novamyl during 7-day storage at 4 degrees C. No cyclodextrin (CD) was detected in bread treated with CGTase[3-18], whereas 21 mg of CD per 10 g of bread was produced in bread treated with wild-type CGTase. PMID:15096580

  4. Thermostability improvement of maltogenic amylase MAUS149 by error prone PCR.

    PubMed

    Ben Mabrouk, Sameh; Ayadi, Dorra Zouari; Ben Hlima, Hajer; Bejar, Samir

    2013-12-01

    The thermostability of maltogenic amylase from Bacillus sp. US149 (MAUS149) was improved by random mutagenesis using error prone PCR. The library constructed for the mutants obtained was subjected to screening, leading to the selection of a thermostable mutant enzyme named MA-A27. The latter was noted to contain four single mutations, namely D46V, P78L, V145A, and K548E. The half-life times recorded for MA-A27 at 50°C and 55°C were 70 min and 25 min, compared to 30 min and 13 min for the wild type, respectively. The results from molecular modeling attributed the increase in thermostability observed for MA-A27 to P78L and K548E substitutions that led to new hydrogen bond and salt bridge formations. Further site-directed mutagenesis studies showed that the P78L and K548E single mutations underwent an increase in thermostability, thus confirming the joint contribution of both substitutions to the increase in thermostability observed for MA-A27. PMID:23994264

  5. 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

  6. Identification of the antigenic determinants of the American cockroach allergen Per a 1 by error-prone PCR.

    PubMed

    Tsai, Wei-Jen; Liu, Ching-Hang; Chen, Shu-Tsung; Yang, Chiou-Ying

    2003-05-01

    The group I allergen of cockroach is found in both American and German cockroaches, designated as Per a 1 and Bla g 1, respectively. Members of these allergens so far identified are composed of tandem repeats that may cause the high allergenicity of Per a 1 allergen. In this study, we used monoclonal antibodies HW-8 and HW-19, which can inhibit the binding of patient IgE to Per a 1 allergen, to define the structure of the antigenic determinants in Per a 1.0103 (designated C3), an isoallergen of Per a 1 allergen. Two recognition sites are present, one in the N-terminus (aa 1-208) and the other in the C-terminus (aa 208-395). The N-terminal epitope is not accessible to antibody molecules on the pET-expressed C3 protein. The C-terminal epitope was further localized to the aa 267-354 region (C3E) by colony immunoscreening of the cDNA epitope library. By negative screening of the mutated C3E expression library generated by error-prone PCR (ER-PCR), an approach which has rarely been applied in epitope mapping, the functional epitope was identified to lie in aa 318-337 with aa 323-331 being the core motif. The minimal region of the functional epitope was further delineated, by sequence alignment, to be D-x-[I, L]-A-[I, L]-L-P-V-D-E-[L, I]-x-A-[L, I], where x represents any amino acids. This motif is found in all Per a 1 allergens and may serve as a basis for designing a peptide vaccine for allergen-specific immunotherapy. To our knowledge, this is the first report for (1) detailed mapping of the cockroach allergens and (2) use of error-prone PCR random mutagenesis and negative selection in molecular allergology. PMID:12738370

  7. Improving the activity of the endoglucanase, Cel8M from Escherichia coli by error-prone PCR.

    PubMed

    Lin, Ling; Fu, Chenggen; Huang, Weiqian

    2016-05-01

    Endoglucanase is a key enzyme involved in cellulose hydrolysis and can be used in multiple industrial fields. In this study, we used error-prone PCR to engineer the endoglucanase, Cel8M, from Escherichia coli. The Cel8M belongs to the glycoside hydrolase family 8 and shows 99% identity with the reported endoglucanase from E. coli K12. Through screening of approximately 10,000Cel8M variants, two variants, Cel8ME15 and Cel8ME18, respectively showing 1.42 fold and 1.61 fold increased activities, were obtained. Through sequence analysis, it was found that Cel8ME15 had two mutations, with the residues Ala9 and Glu353 respectively substituting the residues Val9 and Lys353 of Cel8M; while Cel8ME18 had one mutation with the residue Ser117 replacing the residue Gly117 of Cel8M. Based on the analysis of the predicted 3D structure of Cel8M, it was suggested that changes of K353E and G117S might directly affect the substrate binding affinity and therefore contribute to the improved activities of Cel8ME15 and Cel8ME18. Based on all the results we had, it is believed that this study should provide a useful reference for the future engineering of other endoglucanases from glycoside hydrolase family 8. PMID:26992793

  8. 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 γ-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. PMID:26155461

  9. Directed Evolution and Resolution Mechanism of 1, 3-Propanediol Oxidoreductase from Klebsiella pneumoniae toward Higher Activity by Error-Prone PCR and Bioinformatics

    PubMed Central

    Jiang, Wei; Zhuang, Yuan; Wang, Shizhen; Fang, Baishan

    2015-01-01

    1, 3-propanediol oxidoreductase (PDOR) is a key enzyme in glycerol bioconversion to 1,3-propanediol (1, 3-PD) which is a valuable chemical and one of the six new petrochemical products. We used error-prone PCR and activity screening to identify mutants of Klebsiella pneumoniae (K. pneumoniae) PDOR with improved activity. The activity of one of the identified mutants, PDOR’-24, which includes a single mutation, A199S, was 48 U/mg, 4.9 times that of the wild-type enzyme. Molecular docking was performed to analyze the identified mutants; and amino acids S103, H271, N366, D106, N262 and D364 were predicted to bond with NADH. The origins of the improved activity of PDOR’-24, as well as three other mutants were analyzed by simulating the interaction mechanism of the mutants with the substrate and coenzyme, respectively. This research provides useful information about the use of safranine O plate screening for the directed evolution of oxidoreductases, identifies interesting sites for improving PDOR activity, and demonstrates the utility of using molecular docking to analyze the interaction mechanism of the mutants with the substrate and coenzyme, respectively. PMID:26528716

  10. Disruption of N terminus long range non covalent interactions shifted temp.opt 25°C to cold: Evolution of point mutant Bacillus lipase by error prone PCR.

    PubMed

    Goomber, Shelly; Kumar, Arbind; Kaur, Jagdeep

    2016-01-15

    Cold adapted enzymes have applications in detergent, textile, food, bioremediation and biotechnology processes. Bacillus lipases are 'generally recognized as safe' (GRAS) and hence are industrially attractive. Bacillus lipase of 1.4 subfamily are of lowest molecular weight and are reversibly unfolded due to absence of disulphide bonds. Therefore these are largely used to study energetic of protein stability that represents unfolding of native protein to fully unfolded state. In present study, metagenomically isolated Bacillus LipJ was laboratory evolved for cold adaptation by error Prone PCR. Library of variants were screened for high relative activity at low temperature of 10°C compared to native protein LipJ. Point mutant sequenced as Phe19→Leu was determined to be active at cold and was selected for extensive biochemical, biophysical characterization. Variant F19L showed its maximum activity at 10°C where parent protein LipJ had 20% relative activity. Psychrophilic nature of F19L was established with about 50% relative active at 5°C where native protein was frozen to act. Variant F19L showed no activity at temperature 40°C and above, establishing its thermolabile nature. Thermostability studies determined mutant to be unstable above 20°C and three fold decrease in its half life at 30°C compared to native protein. Far UV-CD and intrinsic fluorescence study demonstrated unstable tertiary structure of point variant F19L leading to its unfolding at low temperature of 20°C. Cold adaptation of mutant F19L is accompanied with increased specific activity. Mutant was catalytically more efficient with 1.3 fold increase in kcat. Homologue structure modelling predicted disruption of intersecondary hydrophobic core formed by aromatic ring of Phe19 with non polar residues placed at β3, β4, β5, β6, αF. Increased local flexibility of variant F19L explains molecular basis of its psychrophilic nature. PMID:26456196

  11. 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

  12. Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes.

    PubMed

    Creel, Scott; Spong, Goran; Sands, Jennifer L; Rotella, Jay; Zeigle, Janet; Joe, Lawrence; Murphy, Kerry M; Smith, Douglas

    2003-07-01

    Determining population sizes can be difficult, but is essential for conservation. By counting distinct microsatellite genotypes, DNA from noninvasive samples (hair, faeces) allows estimation of population size. Problems arise because genotypes from noninvasive samples are error-prone, but genotyping errors can be reduced by multiple polymerase chain reaction (PCR). For faecal genotypes from wolves in Yellowstone National Park, error rates varied substantially among samples, often above the 'worst-case threshold' suggested by simulation. Consequently, a substantial proportion of multilocus genotypes held one or more errors, despite multiple PCR. These genotyping errors created several genotypes per individual and caused overestimation (up to 5.5-fold) of population size. We propose a 'matching approach' to eliminate this overestimation bias. PMID:12803649

  13. Error-Prone Repair of DNA Double-Strand Breaks.

    PubMed

    Rodgers, Kasey; McVey, Mitch

    2016-01-01

    Preserving the integrity of the DNA double helix is crucial for the maintenance of genomic stability. Therefore, DNA double-strand breaks represent a serious threat to cells. In this review, we describe the two major strategies used to repair double strand breaks: non-homologous end joining and homologous recombination, emphasizing the mutagenic aspects of each. We focus on emerging evidence that homologous recombination, long thought to be an error-free repair process, can in fact be highly mutagenic, particularly in contexts requiring large amounts of DNA synthesis. Recent investigations have begun to illuminate the molecular mechanisms by which error-prone double-strand break repair can create major genomic changes, such as translocations and complex chromosome rearrangements. We highlight these studies and discuss proposed models that may explain some of the more extreme genetic changes observed in human cancers and congenital disorders. PMID:26033759

  14. Inducible error-prone repair in Escherichia coli.

    PubMed Central

    Sedgwick, S G

    1975-01-01

    A hypothesis that ultraviolet-induced mutagenesis arises from the induction of an error-prone mode of postreplication repair that requires the exrA+ recA+ genotype has been tested with alkaline sucrose gradient centrifugation coupled with assays of fixation determined by loss of photoreversibility. The inhibitor of protein synthesis, chloramphenicol, added before irradiation, prevented a small amount of postreplication repair and completely eliminated mutation fixation in E. coli WP2s uvrA. However, chloramphenicol did not affect strand joining: (a) in uvrA bacteria allowed 20 min of growth between irradiation and antibiotic treatment; (b) in nonmutable uvrA exrA bacteria; and (c) in uvrA tif bacteria grown at 42 degrees for 70 min before irradiation. These observations indicate that an inducible product is involved in a fraction of postreplication repair and is responsible for induced mutagenesis. PMID:1101265

  15. Error-prone polymerase activity causes multinucleotide mutations in humans

    PubMed Central

    Nielsen, Rasmus

    2014-01-01

    About 2% of human genetic polymorphisms have been hypothesized to arise via multinucleotide mutations (MNMs), complex events that generate SNPs at multiple sites in a single generation. MNMs have the potential to accelerate the pace at which single genes evolve and to confound studies of demography and selection that assume all SNPs arise independently. In this paper, we examine clustered mutations that are segregating in a set of 1092 human genomes, demonstrating that the signature of MNM becomes enriched as large numbers of individuals are sampled. We estimate the percentage of linked SNP pairs that were generated by simultaneous mutation as a function of the distance between affected sites and show that MNMs exhibit a high percentage of transversions relative to transitions, findings that are reproducible in data from multiple sequencing platforms and cannot be attributed to sequencing error. Among tandem mutations that occur simultaneously at adjacent sites, we find an especially skewed distribution of ancestral and derived alleles, with GC ? AA, GA ? TT, and their reverse complements making up 27% of the total. These mutations have been previously shown to dominate the spectrum of the error-prone polymerase Pol ?, suggesting that low-fidelity DNA replication by Pol ? is at least partly responsible for the MNMs that are segregating in the human population. We develop statistical estimates of MNM prevalence that can be used to correct phylogenetic and population genetic inferences for the presence of complex mutations. PMID:25079859

  16. Error-prone polyploid mitosis during normal Drosophila development

    PubMed Central

    Fox, Donald T.; Gall, Joseph G.; Spradling, Allan C.

    2010-01-01

    Endopolyploidy arises during normal development in many species when cells undergo endocycles—variant cell cycles in which DNA replicates but daughter cells do not form. Normally, polyploid cells do not divide mitotically after initiating endocycles; hence, little is known about their mitotic competence. However, polyploid cells are found in many tumors, and the enhanced chromosomal instability of polyploid cells in culture suggests that such cells contribute to tumor aneuploidy. Here, we describe a novel polyploid Drosophila cell type that undergoes normal mitotic cycles as part of a remodeling process that forms the adult rectal papillae. Similar polyploid mitotic divisions, but not depolyploidizing divisions, were observed during adult ileum development in the mosquito Culex pipiens. Extended anaphases, chromosome bridges, and lagging chromosomes were frequent during these polyploid divisions, despite normal expression of cell cycle regulators. Our results show that the switch to endocycles during development is not irreversible, but argue that the polyploid mitotic cycle is inherently error-prone, and that polyploid mitoses may help destabilize the cancer genome. PMID:20952538

  17. Preprocessing document images by resampling is error prone and unnecessary

    NASA Astrophysics Data System (ADS)

    Nagy, George

    2013-01-01

    Integrity tests are proposed for image processing algorithms that should yield essentially the same output under 90 degree rotations, edge-padding and monotonic gray-scale transformations of scanned documents. The tests are demonstrated on built-in functions of the Matlab Image Processing Toolbox. Only the routine that reports the area of the convex hull of foreground components fails the rotation test. Ensuring error-free preprocessing operations like size and skew normalization that are based on resampling an image requires more radical treatment. Even if faultlessly implemented, resampling is generally irreversible and may introduce artifacts. Fortunately, advances in storage and processor technology have all but eliminated any advantage of preprocessing or compressing document images by resampling them. Using floating point coordinate transformations instead of resampling images yields accurate run-length, moment, slope, and other geometric features.

  18. Prevalence of error-prone abbreviations used in medication prescribing for hospitalised patients: multi-hospital evaluation.

    PubMed

    Dooley, M J; Wiseman, M; Gu, G

    2012-03-01

    The use of error-prone abbreviations in prescribing is a potential cause of misinterpretation that may lead to medication error. This study determined frequency and type of error-prone abbreviations in inpatient medication prescribing across three Australian hospitals. Three hundred and sixty-nine (76.9%) patients had one or more error-prone abbreviations used in prescribing, with 8.4% of orders containing at least one error-prone abbreviation and 29.6% of these considered to be high risk for causing significant harm. PMID:22432997

  19. Designing an Algorithm to Preserve Privacy for Medical Record Linkage With Error-Prone Data

    PubMed Central

    Pal, Doyel; Chen, Tingting; Khethavath, Praveen

    2014-01-01

    Background Linking medical records across different medical service providers is important to the enhancement of health care quality and public health surveillance. In records linkage, protecting the patients’ privacy is a primary requirement. In real-world health care databases, records may well contain errors due to various reasons such as typos. Linking the error-prone data and preserving data privacy at the same time are very difficult. Existing privacy preserving solutions for this problem are only restricted to textual data. Objective To enable different medical service providers to link their error-prone data in a private way, our aim was to provide a holistic solution by designing and developing a medical record linkage system for medical service providers. Methods To initiate a record linkage, one provider selects one of its collaborators in the Connection Management Module, chooses some attributes of the database to be matched, and establishes the connection with the collaborator after the negotiation. In the Data Matching Module, for error-free data, our solution offered two different choices for cryptographic schemes. For error-prone numerical data, we proposed a newly designed privacy preserving linking algorithm named the Error-Tolerant Linking Algorithm, that allows the error-prone data to be correctly matched if the distance between the two records is below a threshold. Results We designed and developed a comprehensive and user-friendly software system that provides privacy preserving record linkage functions for medical service providers, which meets the regulation of Health Insurance Portability and Accountability Act. It does not require a third party and it is secure in that neither entity can learn the records in the other’s database. Moreover, our novel Error-Tolerant Linking Algorithm implemented in this software can work well with error-prone numerical data. We theoretically proved the correctness and security of our Error-Tolerant Linking Algorithm. We have also fully implemented the software. The experimental results showed that it is reliable and efficient. The design of our software is open so that the existing textual matching methods can be easily integrated into the system. Conclusions Designing algorithms to enable medical records linkage for error-prone numerical data and protect data privacy at the same time is difficult. Our proposed solution does not need a trusted third party and is secure in that in the linking process, neither entity can learn the records in the other’s database. PMID:25600786

  20. DNA polymerases are error-prone at RecA-mediated recombination intermediates.

    PubMed

    Pomerantz, Richard T; Goodman, Myron F; O'Donnell, Michael E

    2013-08-15

    Genetic studies have suggested that Y-family translesion DNA polymerase IV (DinB) performs error-prone recombination-directed replication (RDR) under conditions of stress due to its ability to promote mutations during double-strand break (DSB) repair in growth-limited E. coli cells. In recent studies we have demonstrated that pol IV is preferentially recruited to D-loop recombination intermediates at stress-induced concentrations and is highly mutagenic during RDR in vitro. These findings verify longstanding genetic data that have implicated pol IV in promoting stress-induced mutagenesis at D-loops. In this Extra View, we demonstrate the surprising finding that A-family pol I, which normally exhibits high-fidelity DNA synthesis, is highly error-prone at D-loops like pol IV. These findings indicate that DNA polymerases are intrinsically error-prone at RecA-mediated D-loops and suggest that auxiliary factors are necessary for suppressing mutations during RDR in non-stressed proliferating cells. PMID:23907132

  1. 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

  2. Inducible error-prone repair in B. subtilis. Final report, September 1, 1979-June 30, 1981

    SciTech Connect

    Yasbin, R. E.

    1981-06-01

    The research performed under this contract has been concentrated on the relationship between inducible DNA repair systems, mutagenesis and the competent state in the gram positive bacterium Bacillus subtilis. The following results have been obtained from this research: (1) competent Bacillus subtilis cells have been developed into a sensitive tester system for carcinogens; (2) competent B. subtilis cells have an efficient excision-repair system, however, this system will not function on bacteriophage DNA taken into the cell via the process of transfection; (3) DNA polymerase III is essential in the mechanism of the process of W-reactivation; (4) B. subtilis strains cured of their defective prophages have been isolated and are now being developed for gene cloning systems; (5) protoplasts of B. subtilis have been shown capable of acquiring DNA repair enzymes (i.e., enzyme therapy); and (6) a plasmid was characterized which enhanced inducible error-prone repair in a gram positive organism.

  3. Interactions and Localization of Escherichia coli Error-Prone DNA Polymerase IV after DNA Damage

    PubMed Central

    Mallik, Sarita; Popodi, Ellen M.; Hanson, Andrew J.

    2015-01-01

    ABSTRACT Escherichia coli's DNA polymerase IV (Pol IV/DinB), a member of the Y family of error-prone polymerases, is induced during the SOS response to DNA damage and is responsible for translesion bypass and adaptive (stress-induced) mutation. In this study, the localization of Pol IV after DNA damage was followed using fluorescent fusions. After exposure of E. coli to DNA-damaging agents, fluorescently tagged Pol IV localized to the nucleoid as foci. Stepwise photobleaching indicated ∼60% of the foci consisted of three Pol IV molecules, while ∼40% consisted of six Pol IV molecules. Fluorescently tagged Rep, a replication accessory DNA helicase, was recruited to the Pol IV foci after DNA damage, suggesting that the in vitro interaction between Rep and Pol IV reported previously also occurs in vivo. Fluorescently tagged RecA also formed foci after DNA damage, and Pol IV localized to them. To investigate if Pol IV localizes to double-strand breaks (DSBs), an I-SceI endonuclease-mediated DSB was introduced close to a fluorescently labeled LacO array on the chromosome. After DSB induction, Pol IV localized to the DSB site in ∼70% of SOS-induced cells. RecA also formed foci at the DSB sites, and Pol IV localized to the RecA foci. These results suggest that Pol IV interacts with RecA in vivo and is recruited to sites of DSBs to aid in the restoration of DNA replication. IMPORTANCE DNA polymerase IV (Pol IV/DinB) is an error-prone DNA polymerase capable of bypassing DNA lesions and aiding in the restart of stalled replication forks. In this work, we demonstrate in vivo localization of fluorescently tagged Pol IV to the nucleoid after DNA damage and to DNA double-strand breaks. We show colocalization of Pol IV with two proteins: Rep DNA helicase, which participates in replication, and RecA, which catalyzes recombinational repair of stalled replication forks. Time course experiments suggest that Pol IV recruits Rep and that RecA recruits Pol IV. These findings provide in vivo evidence that Pol IV aids in maintaining genomic stability not only by bypassing DNA lesions but also by participating in the restoration of stalled replication forks. PMID:26100038

  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 Enzyme Evolution in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426

    PubMed Central

    Kobayashi, Jyumpei; Wada, Keisuke; Furukawa, Megumi; Doi, Katsumi

    2014-01-01

    Thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. In this study, we constructed an error-prone strain of the thermophile Geobacillus kaustophilus HTA426 and investigated thermoadaptation-directed enzyme evolution using the strain. A mutation frequency assay using the antibiotics rifampin and streptomycin revealed that G. kaustophilus had substantially higher mutability than Escherichia coli and Bacillus subtilis. The predominant mutations in G. kaustophilus were A · T→G · C and C · G→T · A transitions, implying that the high mutability of G. kaustophilus was attributable in part to high-temperature-associated DNA damage during growth. Among the genes that may be involved in DNA repair in G. kaustophilus, deletions of the mutSL, mutY, ung, and mfd genes markedly enhanced mutability. These genes were subsequently deleted to construct an error-prone thermophile that showed much higher (700- to 9,000-fold) mutability than the parent strain. The error-prone strain was auxotrophic for uracil owing to the fact that the strain was deficient in the intrinsic pyrF gene. Although the strain harboring Bacillus subtilis pyrF was also essentially auxotrophic, cells became prototrophic after 2 days of culture under uracil starvation, generating B. subtilis PyrF variants with an enhanced half-denaturation temperature of >10°C. These data suggest that this error-prone strain is a promising host for thermoadaptation-directed evolution to generate thermostable variants from thermolabile enzymes. PMID:25326311

  6. Thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from Geobacillus kaustophilus HTA426.

    PubMed

    Suzuki, Hirokazu; Kobayashi, Jyumpei; Wada, Keisuke; Furukawa, Megumi; Doi, Katsumi

    2015-01-01

    Thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. In this study, we constructed an error-prone strain of the thermophile Geobacillus kaustophilus HTA426 and investigated thermoadaptation-directed enzyme evolution using the strain. A mutation frequency assay using the antibiotics rifampin and streptomycin revealed that G. kaustophilus had substantially higher mutability than Escherichia coli and Bacillus subtilis. The predominant mutations in G. kaustophilus were A · T→G · C and C · G→T · A transitions, implying that the high mutability of G. kaustophilus was attributable in part to high-temperature-associated DNA damage during growth. Among the genes that may be involved in DNA repair in G. kaustophilus, deletions of the mutSL, mutY, ung, and mfd genes markedly enhanced mutability. These genes were subsequently deleted to construct an error-prone thermophile that showed much higher (700- to 9,000-fold) mutability than the parent strain. The error-prone strain was auxotrophic for uracil owing to the fact that the strain was deficient in the intrinsic pyrF gene. Although the strain harboring Bacillus subtilis pyrF was also essentially auxotrophic, cells became prototrophic after 2 days of culture under uracil starvation, generating B. subtilis PyrF variants with an enhanced half-denaturation temperature of >10°C. These data suggest that this error-prone strain is a promising host for thermoadaptation-directed evolution to generate thermostable variants from thermolabile enzymes. PMID:25326311

  7. Inducible error-prone repair in B. subtilis. Progress report, September 1, 1981-April 30, 1985

    SciTech Connect

    Yasbin, R.E.

    1984-12-01

    The objective was to investigate and elucidate the molecular mechanisms responsible for (i) inducible DNA repair system(s) and for (ii) error-prone repair in the gram positive bacterium Bacillus subtilis. The SOS-like system of Bacillus subtilis consists of several coordinately induced phenomena (e.g., cellular filamentation, prophage induction, and Weigle reactivation of uv-damaged bacteriophage) which are expressed after cellular insult such as DNA damage or inhibition of DNA replication. Mutagenesis of the bacterial chromosome and the development or maintenance of competence also appear to be involved in the SOS-like response in this bacterium. The genetic characterization of the SOS-like system has involved an analysis of (i) the effects of various DNA repair mutations on the expression of inducible phenomena and (ii) the tsi-23 mutation, which renders host strains thermally inducible for each of the SOS-like functions. Bacterial filamentation was unaffected by any of the DNA repair mutations studied. In contrast, the induction of prophage after thermal or uv pretreatment was abolished in strains carrying the recE4, recA1, recB2, or recG13 mutation. Weigle reactivation was also inhibited by the recE4, recA1, recB2, or recG13 mutation, whereas levels of W-reactivation were lower in strains which carried the uvrA42, polA5, or rec-961 mutation than in the DNA repair-proficient strain. Strains which carried the recE4 allele were incapable of chromosomal DNA-mediated transformation, and the frequency of this event was decreased in strains carrying the recA1, recB2, or tsi-23 mutation. Plasmid DNA transformation efficiency was decreased only in strains carrying the tsi-23 mutation in addition to the recE4, recA1, recB2, mutation. The results indicate that the SOS-like or SOB system of B. subtilis is regulated at different levels by two or more gene products.

  8. Center of mass correction to an error-prone undergraduate centripetal force experiment

    NASA Astrophysics Data System (ADS)

    Ronhovde, Peter; Sirochman, Rudy

    2003-02-01

    In this undergraduate laboratory experiment we measure the centripetal force acting on a bob in uniform circular motion. As the experiment was originally designed, it consistently yielded large errors due to a subtle twist of the bob as the mass was increased incrementally. This error is due to the fact that the center of mass changes relative position as the mass is incremented; therefore, the spring that provides the centripetal force for the apparatus causes an unintended torque on the bob. A solution to the problem consists of positioning the incremental masses so that the center of mass does not change position. This simple correction provides a useful lesson on redesigning an undergraduate laboratory experiment to obtain better agreement with theory.

  9. Increased But Error-Prone Nonhomologous End Joining in Immortalized Lymphoblastoid Cell Extracts From Adult Cancer Patients With Late Radionecrosis

    SciTech Connect

    Tan, W.-M.; Paterson, Malcolm C.; Koo, Ghee Chong; Li Huihua; Price, Allan; Loong, Susan L.E.

    2008-09-01

    Purpose: To study nonhomologous end joining in extracts of two lymphoblastoid cell lines derived from patients with late radionecrosis after radiotherapy. Both cell lines were previously shown to exhibit impaired rejoining of DNA double-strand breaks in a pulse-field gel electrophoresis assay. Methods and Materials: We used a cell-free system and quantitative real-time polymerase chain reaction, as well as sequencing analysis of end joining products. Results: Paradoxically, extracts of the two cell lines display increased rates of in vitro end joining of noncohesive termini compared with normal cell extracts. This increase was seen in the absence of added deoxyribonucleoside triphosphates and was sensitive to inhibition by wortmannin. Sequencing of the joined products revealed that, despite increased rates of end joining, the process was error prone with a greater frequency of deletions compared with that observed in normal controls. Conclusion: These findings are consistent with the suggestion that a promiscuous, deletion-prone abnormality of nonhomologous end joining might underpin the predisposition of certain radiotherapy patients to late radionecrosis. We hypothesize that some individuals might harbor subclinical defects in nonhomologous end joining that clinically manifest on challenge with high-dose radiation. Because both quantitative and qualitative aspects of end joining have demonstrably been influenced, we recommend that the study of patient samples should involve a combination of quantitative methods (e.g., quantitative real-time polymerase chain reaction), sequencing analysis, and a comparison of multiple join types.

  10. 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

  11. 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.

    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.

  12. The DNA Ligase IV Syndrome R278H Mutation Impairs B Lymphopoiesis via Error-Prone Nonhomologous End-Joining.

    PubMed

    Park, Jihye; Welner, Robert S; Chan, Mei-Yee; Troppito, Logan; Staber, Philipp B; Tenen, Daniel G; Yan, Catherine T

    2016-01-01

    Hypomorphic mutations in the nonhomologous end-joining (NHEJ) DNA repair protein DNA ligase IV (LIG4) lead to immunodeficiency with varying severity. In this study, using a murine knock-in model, we investigated the mechanisms underlying abnormalities in class switch recombination (CSR) associated with the human homozygous Lig4 R278H mutation. Previously, we found that despite the near absence of Lig4 end-ligation activity and severely reduced mature B cell numbers, Lig4(R278H/R278H) (Lig4(R/R)) mice exhibit only a partial CSR block, producing near normal IgG1 and IgE but substantially reduced IgG3, IgG2b, and IgA serum levels. In this study, to address the cause of these abnormalities, we assayed CSR in Lig4(R/R) B cells generated via preassembled IgH and IgK V region exons (HL). This revealed that Lig4(R278H) protein levels while intact exhibited a higher turnover rate during activation of switching to IgG3 and IgG2b, as well as delays in CSR kinetics associated with defective proliferation during activation of switching to IgG1 and IgE. Activated Lig4(R/R)HL B cells consistently accumulated high frequencies of activation-induced cytidine deaminase-dependent IgH locus chromosomal breaks and translocations and were more prone to apoptosis, effects that appeared to be p53-independent, as p53 deficiency did not markedly influence these events. Importantly, NHEJ instead of alternative end-joining (A-EJ) was revealed as the predominant mechanism catalyzing robust CSR. Defective CSR was linked to failed NHEJ and residual A-EJ access to unrepaired double-strand breaks. These data firmly demonstrate that Lig4(R278H) activity renders NHEJ to be more error-prone, and they predict increased error-prone NHEJ activity and A-EJ suppression as the cause of the defective B lymphopoiesis in Lig4 patients. PMID:26608917

  13. Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid

    PubMed Central

    David, Vojtěch; Flegontov, Pavel; Gerasimov, Evgeny; Tanifuji, Goro; Hashimi, Hassan; Logacheva, Maria D.; Maruyama, Shinichiro; Onodera, Naoko T.; Gray, Michael W.; Archibald, John M.

    2015-01-01

    ABSTRACT Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts. PMID:26628723

  14. UmuDAb: An Error-Prone Polymerase Accessory Homolog Whose N-Terminal Domain Is Required for Repression of DNA Damage Inducible Gene Expression in Acinetobacter baylyi

    PubMed Central

    Stinnett, DeAnna B.; Wells, Whitney K.; Peterson, Megan A.; Hare, Janelle M.

    2016-01-01

    In many bacteria, the DNA damage response induces genes (SOS genes) that were repressed by LexA. LexA represses transcription by binding to SOS promoters via a helix-turn-helix motif in its N-terminal domain (NTD). Upon DNA damage, LexA cleaves itself and allows induction of transcription. In Acinetobacter baumannii and Acinetobacter baylyi, multiple genes are induced by DNA damage, and although the Acinetobacter genus lacks LexA, a homolog of the error-prone polymerase subunit UmuD, called UmuDAb, regulates some DNA damage-induced genes. The mechanism of UmuDAb regulation has not been determined. We constructed UmuDAb mutant strains of A. baylyi to test whether UmuDAb mediates gene regulation through LexA-like repressor actions consisting of relief of repression through self-cleavage after DNA damage. Real-time quantitative PCR experiments in both a null umuDAb mutant and an NTD mutant showed that the DNA damage-inducible, UmuDAb-regulated gene ddrR was highly expressed even in the absence of DNA damage. Protein modeling identified a potential LexA-like helix-turn-helix structure in the UmuDAb NTD, which when disrupted, also relieved ddrR and umuDAb repression under non-inducing conditions. Mutations in a putative SOS box in the shared umuDAb-ddrR promoter region similarly relieved these genes’ repression under non-inducing conditions. Conversely, cells possessing a cleavage-deficient UmuDAb were unable to induce gene expression after MMC-mediated DNA damage. This evidence of a UmuDAb repressor mechanism was contrasted with the failure of umuDAb to complement an Escherichia coli umuD mutant for UmuD error-prone DNA replication activity. Similarly, A. baumannii null umuDAb mutant cells did not have a reduced UmuDˊ2UmuC-mediated mutation rate after DNA damage, suggesting that although this UmuDAb protein may have evolved from a umuDC operon in this genus, it now performs a LexA-like repressor function for a sub-set of DNA damage-induced genes. PMID:27010837

  15. DNA Polymerase ?-Dependent Lesion Bypass in Saccharomyces cerevisiae Is Accompanied by Error-Prone Copying of Long Stretches of Adjacent DNA

    PubMed Central

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

    2015-01-01

    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

  16. 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…

  17. Removal of PCR error products and unincorporated primers by metal-chelate affinity chromatography.

    PubMed

    Kanakaraj, Indhu; Jewell, David L; Murphy, Jason C; Fox, George E; Willson, Richard C

    2011-01-01

    Immobilized Metal Affinity Chromatography (IMAC) has been used for decades to purify proteins on the basis of amino acid content, especially surface-exposed histidines and "histidine tags" genetically added to recombinant proteins. We and others have extended the use of IMAC to purification of nucleic acids via interactions with the nucleotide bases, especially purines, of single-stranded RNA and DNA. We also have demonstrated the purification of plasmid DNA from contaminating genomic DNA by IMAC capture of selectively-denatured genomic DNA. Here we describe an efficient method of purifying PCR products by specifically removing error products, excess primers, and unincorporated dNTPs from PCR product mixtures using flow-through metal-chelate affinity adsorption. By flowing a PCR product mixture through a Cu(2+)-iminodiacetic acid (IDA) agarose spin column, 94-99% of the dNTPs and nearly all the primers can be removed. Many of the error products commonly formed by Taq polymerase also are removed. Sequencing of the IMAC-processed PCR product gave base-calling accuracy comparable to that obtained with a commercial PCR product purification method. The results show that IMAC matrices (specifically Cu(2+)-IDA agarose) can be used for the purification of PCR products. Due to the generality of the base-specific mechanism of adsorption, IMAC matrices may also be used in the purification of oligonucleotides, cDNA, mRNA and micro RNAs. PMID:21264292

  18. Use of damaged DNA and dNTP substrates by the error-prone DNA polymerase X from African swine fever virus.

    PubMed

    Kumar, Sandeep; Lamarche, Brandon J; Tsai, Ming-Daw

    2007-03-27

    The structural specificity that translesion DNA polymerases often show for a particular class of lesions suggests that the predominant criterion of selection during their evolution has been the capacity for lesion tolerance and that the error-proneness they display when copying undamaged templates may simply be a byproduct of this adaptation. Regardless of selection criteria/evolutionary history, at present both of these properties coexist in these enzymes, and both properties confer a fitness advantage. The repair polymerase, Pol X, encoded by the African swine fever virus (ASFV) is one of the most error-prone polymerases known, leading us to previously hypothesize that it may work in tandem with the exceptionally error-tolerant ASFV DNA ligase to effect viral mutagenesis. Here, for the first time, we test whether the error-proneness of Pol X is coupled with a capacity for lesion tolerance by examining its ability to utilize the types of damaged DNA and dNTP substrates that are expected to be relevant to ASFV. We (i) test Pol X's ability to both incorporate opposite to and extend from ubiquitous oxidative purine (7,8-dihydro-8-oxoguanine), oxidative pyrimidine (5,6-dihydroxy-5,6-dihydrothymine), and noncoding (AP site) lesions, in addition to 5,6-dihydrothymine, (ii) determine the catalytic efficiency and dNTP specificity of Pol X when catalyzing incorporation opposite to, and when extending from, 7,8-dihydro-8-oxoguanine in a template/primer context, and (iii) quantitate Pol X-catalyzed incorporation of the damaged nucleotide 8-oxo-dGTP opposite to undamaged templates in the context of both template/primer and a single-nucleotide gap. Our findings are discussed in light of ASFV biology and the mutagenic DNA repair hypothesis described above. PMID:17335287

  19. Structural and Functional Elucidation of the Mechanism Promoting Error-prone Synthesis by Human DNA Polymerase [kappa] Opposite the 7,8-Dihydro-8-oxo-2'-deoxyguanosine Adduct

    SciTech Connect

    Irimia, Adriana; Eoff, Robert L.; Guengerich, F.Peter; Egli, Martin

    2009-09-25

    Human polymerase kappa (hPol {kappa}) is one of four eukaryotic Y-class DNA polymerases and may be an important element in the cellular response to polycyclic aromatic hydrocarbons such as benzo[a]pyrene, which can lead to reactive oxygenated metabolite-mediated oxidative stress. Here, we present a detailed analysis of the activity and specificity of hPol {kappa} bypass opposite the major oxidative adduct 7,8-dihydro-8-oxo-2{prime}-deoxyguanosine (8-oxoG). Unlike its archaeal homolog Dpo4, hPol {kappa} bypasses this lesion in an error-prone fashion by inserting mainly dATP. Analysis of transient-state kinetics shows diminished 'bursts' for dATP:8-oxoG and dCTP:8-oxoG incorporation, indicative of non-productive complex formation, but dATP:8-oxoG insertion events that do occur are 2-fold more efficient than dCTP:G insertion events. Crystal structures of ternary hPol {kappa} complexes with adducted template-primer DNA reveal non-productive (dGTP and dATP) alignments of incoming nucleotide and 8-oxoG. Structural limitations placed upon the hPol {kappa} by interactions between the N-clasp and finger domains combined with stabilization of the syn-oriented template 8-oxoG through the side chain of Met-135 both appear to contribute to error-prone bypass. Mutating Leu-508 in the little finger domain of hPol {kappa} to lysine modulates the insertion opposite 8-oxoG toward more accurate bypass, similar to previous findings with Dpo4. Our structural and activity data provide insight into important mechanistic aspects of error-prone bypass of 8-oxoG by hPol {kappa} compared with accurate and efficient bypass of the lesion by Dpo4 and polymerase {eta}.

  20. Differential expression of APE1 and APE2 in germinal centers promotes error-prone repair and A:T mutations during somatic hypermutation

    PubMed Central

    Stavnezer, Janet; Linehan, Erin K.; Thompson, Mikayla R.; Habboub, Ghaith; Ucher, Anna J.; Kadungure, Tatenda; Tsuchimoto, Daisuke; Nakabeppu, Yusaku; Schrader, Carol E.

    2014-01-01

    Somatic hypermutation (SHM) of antibody variable region genes is initiated in germinal center B cells during an immune response by activation-induced cytidine deaminase (AID), which converts cytosines to uracils. During accurate repair in nonmutating cells, uracil is excised by uracil DNA glycosylase (UNG), leaving abasic sites that are incised by AP endonuclease (APE) to create single-strand breaks, and the correct nucleotide is reinserted by DNA polymerase β. During SHM, for unknown reasons, repair is error prone. There are two APE homologs in mammals and, surprisingly, APE1, in contrast to its high expression in both resting and in vitro-activated splenic B cells, is expressed at very low levels in mouse germinal center B cells where SHM occurs, and APE1 haploinsufficiency has very little effect on SHM. In contrast, the less efficient homolog, APE2, is highly expressed and contributes not only to the frequency of mutations, but also to the generation of mutations at A:T base pair (bp), insertions, and deletions. In the absence of both UNG and APE2, mutations at A:T bp are dramatically reduced. Single-strand breaks generated by APE2 could provide entry points for exonuclease recruited by the mismatch repair proteins Msh2–Msh6, and the known association of APE2 with proliferating cell nuclear antigen could recruit translesion polymerases to create mutations at AID-induced lesions and also at A:T bp. Our data provide new insight into error-prone repair of AID-induced lesions, which we propose is facilitated by down-regulation of APE1 and up-regulation of APE2 expression in germinal center B cells. PMID:24927551

  1. Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase

    SciTech Connect

    Kirouac, Kevin N.; Ling, Hong

    2009-06-30

    Human DNA polymerase iota (pol iota) is a unique member of Y-family polymerases, which preferentially misincorporates nucleotides opposite thymines (T) and halts replication at T bases. The structural basis of the high error rates remains elusive. We present three crystal structures of pol complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides. A narrowed active site supports a pyrimidine to pyrimidine mismatch and excludes Watson-Crick base pairing by pol. The template thymine remains in an anti conformation irrespective of incoming nucleotides. Incoming ddATP adopts a syn conformation with reduced base stacking, whereas incorrect dGTP and dTTP maintain anti conformations with normal base stacking. Further stabilization of dGTP by H-bonding with Gln59 of the finger domain explains the preferential T to G mismatch. A template 'U-turn' is stabilized by pol and the methyl group of the thymine template, revealing the structural basis of T stalling. Our structural and domain-swapping experiments indicate that the finger domain is responsible for pol's high error rates on pyrimidines and determines the incorporation specificity.

  2. Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase ι

    PubMed Central

    Kirouac, Kevin N; Ling, Hong

    2009-01-01

    Human DNA polymerase ι (polι) is a unique member of Y-family polymerases, which preferentially misincorporates nucleotides opposite thymines (T) and halts replication at T bases. The structural basis of the high error rates remains elusive. We present three crystal structures of polι complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides. A narrowed active site supports a pyrimidine to pyrimidine mismatch and excludes Watson–Crick base pairing by polι. The template thymine remains in an anti conformation irrespective of incoming nucleotides. Incoming ddATP adopts a syn conformation with reduced base stacking, whereas incorrect dGTP and dTTP maintain anti conformations with normal base stacking. Further stabilization of dGTP by H-bonding with Gln59 of the finger domain explains the preferential T to G mismatch. A template ‘U-turn' is stabilized by polι and the methyl group of the thymine template, revealing the structural basis of T stalling. Our structural and domain-swapping experiments indicate that the finger domain is responsible for polι's high error rates on pyrimidines and determines the incorporation specificity. PMID:19440206

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

    SciTech Connect

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

    1990-07-01

    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.

  4. LEMming: A Linear Error Model to Normalize Parallel Quantitative Real-Time PCR (qPCR) Data as an Alternative to Reference Gene Based Methods

    PubMed Central

    Feuer, Ronny; Vlaic, Sebastian; Arlt, Janine; Sawodny, Oliver; Dahmen, Uta; Zanger, Ulrich M.; Thomas, Maria

    2015-01-01

    Background Gene expression analysis is an essential part of biological and medical investigations. Quantitative real-time PCR (qPCR) is characterized with excellent sensitivity, dynamic range, reproducibility and is still regarded to be the gold standard for quantifying transcripts abundance. Parallelization of qPCR such as by microfluidic Taqman Fluidigm Biomark Platform enables evaluation of multiple transcripts in samples treated under various conditions. Despite advanced technologies, correct evaluation of the measurements remains challenging. Most widely used methods for evaluating or calculating gene expression data include geNorm and ΔΔCt, respectively. They rely on one or several stable reference genes (RGs) for normalization, thus potentially causing biased results. We therefore applied multivariable regression with a tailored error model to overcome the necessity of stable RGs. Results We developed a RG independent data normalization approach based on a tailored linear error model for parallel qPCR data, called LEMming. It uses the assumption that the mean Ct values within samples of similarly treated groups are equal. Performance of LEMming was evaluated in three data sets with different stability patterns of RGs and compared to the results of geNorm normalization. Data set 1 showed that both methods gave similar results if stable RGs are available. Data set 2 included RGs which are stable according to geNorm criteria, but became differentially expressed in normalized data evaluated by a t-test. geNorm-normalized data showed an effect of a shifted mean per gene per condition whereas LEMming-normalized data did not. Comparing the decrease of standard deviation from raw data to geNorm and to LEMming, the latter was superior. In data set 3 according to geNorm calculated average expression stability and pairwise variation, stable RGs were available, but t-tests of raw data contradicted this. Normalization with RGs resulted in distorted data contradicting literature, while LEMming normalized data did not. Conclusions If RGs are coexpressed but are not independent of the experimental conditions the stability criteria based on inter- and intragroup variation fail. The linear error model developed, LEMming, overcomes the dependency of using RGs for parallel qPCR measurements, besides resolving biases of both technical and biological nature in qPCR. However, to distinguish systematic errors per treated group from a global treatment effect an additional measurement is needed. Quantification of total cDNA content per sample helps to identify systematic errors. PMID:26325269

  5. Error-Prone Processing of Apurinic/Apyrimidinic (AP) Sites by PolX Underlies a Novel Mechanism That Promotes Adaptive Mutagenesis in Bacillus subtilis

    PubMed Central

    Barajas-Ornelas, Rocío del Carmen; Ramírez-Guadiana, Fernando H.; Juárez-Godínez, Rafael; Ayala-García, Victor M.; Robleto, Eduardo A.; Yasbin, Ronald E.

    2014-01-01

    In growing cells, apurinic/apyrimidinic (AP) sites generated spontaneously or resulting from the enzymatic elimination of oxidized bases must be processed by AP endonucleases before they compromise cell integrity. Here, we investigated how AP sites and the processing of these noncoding lesions by the AP endonucleases Nfo, ExoA, and Nth contribute to the production of mutations (hisC952, metB5, and leuC427) in starved cells of the Bacillus subtilis YB955 strain. Interestingly, cells from this strain that were deficient for Nfo, ExoA, and Nth accumulated a greater amount of AP sites in the stationary phase than during exponential growth. Moreover, under growth-limiting conditions, the triple nfo exoA nth knockout strain significantly increased the amounts of adaptive his, met, and leu revertants produced by the B. subtilis YB955 parental strain. Of note, the number of stationary-phase-associated reversions in the his, met, and leu alleles produced by the nfo exoA nth strain was significantly decreased following disruption of polX. In contrast, during growth, the reversion rates in the three alleles tested were significantly increased in cells of the nfo exoA nth knockout strain deficient for polymerase X (PolX). Therefore, we postulate that adaptive mutations in B. subtilis can be generated through a novel mechanism mediated by error-prone processing of AP sites accumulated in the stationary phase by the PolX DNA polymerase. PMID:24914186

  6. Comparative Error-Free and Error-Prone Translesion Synthesis of N(2)-2'-Deoxyguanosine Adducts Formed by Mitomycin C and Its Metabolite, 2,7-Diaminomitosene, in Human Cells.

    PubMed

    Bose, Arindam; Surugihalli, Chaitra; Pande, Paritosh; Champeil, Elise; Basu, Ashis K

    2016-05-16

    Mitomycin C (MC) is a cytotoxic and mutagenic antitumor agent that alkylates DNA upon reductive activation. 2,7-Diaminomitosene (2,7-DAM) is a major metabolite of MC in tumor cells, which also alkylates DNA. MC forms seven DNA adducts, including monoadducts and inter- and intrastrand cross-links, whereas 2,7-DAM forms two monoadducts. Herein, the biological effects of the dG-N(2) adducts formed by MC and 2,7-DAM have been compared by constructing single-stranded plasmids containing these adducts and replicating them in human embryonic kidney 293T cells. Translesion synthesis (TLS) efficiencies of dG-N(2)-MC and dG-N(2)-2,7-DAM were 38 ± 3 and 27 ± 3%, respectively, compared to that of a control plasmid. This indicates that both adducts block DNA synthesis and that dG-N(2)-2,7-DAM is a stronger replication block than dG-N(2)-MC. TLS of each adducted construct was reduced upon siRNA knockdown of pol η, pol κ, or pol ζ. For both adducts, the most significant reduction occurred with knockdown of pol κ, which suggests that pol κ plays a major role in TLS of these dG-N(2) adducts. Analysis of the progeny showed that both adducts were mutagenic, and the mutation frequencies (MF) of dG-N(2)-MC and dG-N(2)-2,7-DAM were 18 ± 3 and 10 ± 1%, respectively. For both adducts, the major type of mutation was G → T transversions. Knockdown of pol η and pol ζ reduced the MF of dG-N(2)-MC and dG-N(2)-2,7-DAM, whereas knockdown of pol κ increased the MF of these adducts. This suggests that pol κ predominantly carries out error-free TLS, whereas pol η and pol ζ are involved in error-prone TLS. The largest reduction in MF by 78 and 80%, respectively, for dG-N(2)-MC and dG-N(2)-2,7-DAM constructs occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down. This result strongly suggests that, unlike pol κ, these three TLS polymerases cooperatively perform the error-prone TLS of these adducts. PMID:27082015

  7. Unique plasmids generated via pUC replicon mutagenesis in an error-prone thermophile derived from Geobacillus kaustophilus HTA426.

    PubMed

    Kobayashi, Jyumpei; Tanabiki, Misaki; Doi, Shohei; Kondo, Akihiko; Ohshiro, Takashi; Suzuki, Hirokazu

    2015-11-01

    The plasmid pGKE75-catA138T, which comprises pUC18 and the catA138T gene encoding thermostable chloramphenicol acetyltransferase with an A138T amino acid replacement (CATA138T), serves as an Escherichia coli-Geobacillus kaustophilus shuttle plasmid that confers moderate chloramphenicol resistance on G. kaustophilus HTA426. The present study examined the thermoadaptation-directed mutagenesis of pGKE75-catA138T in an error-prone thermophile, generating the mutant plasmid pGKE75(αβ)-catA138T responsible for substantial chloramphenicol resistance at 65°C. pGKE75(αβ)-catA138T contained no mutation in the catA138T gene but had two mutations in the pUC replicon, even though the replicon has no apparent role in G. kaustophilus. Biochemical characterization suggested that the efficient chloramphenicol resistance conferred by pGKE75(αβ)-catA138T is attributable to increases in intracellular CATA138T and acetyl-coenzyme A following a decrease in incomplete forms of pGKE75(αβ)-catA138T. The decrease in incomplete plasmids may be due to optimization of plasmid replication by RNA species transcribed from the mutant pUC replicon, which were actually produced in G. kaustophilus. It is noteworthy that G. kaustophilus was transformed with pGKE75(αβ)-catA138T using chloramphenicol selection at 60°C. In addition, a pUC18 derivative with the two mutations propagated in E. coli at a high copy number independently of the culture temperature and high plasmid stability. Since these properties have not been observed in known plasmids, the outcomes extend the genetic toolboxes for G. kaustophilus and E. coli. PMID:26319877

  8. Unique Plasmids Generated via pUC Replicon Mutagenesis in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426

    PubMed Central

    Kobayashi, Jyumpei; Tanabiki, Misaki; Doi, Shohei; Kondo, Akihiko; Ohshiro, Takashi

    2015-01-01

    The plasmid pGKE75-catA138T, which comprises pUC18 and the catA138T gene encoding thermostable chloramphenicol acetyltransferase with an A138T amino acid replacement (CATA138T), serves as an Escherichia coli-Geobacillus kaustophilus shuttle plasmid that confers moderate chloramphenicol resistance on G. kaustophilus HTA426. The present study examined the thermoadaptation-directed mutagenesis of pGKE75-catA138T in an error-prone thermophile, generating the mutant plasmid pGKE75αβ-catA138T responsible for substantial chloramphenicol resistance at 65°C. pGKE75αβ-catA138T contained no mutation in the catA138T gene but had two mutations in the pUC replicon, even though the replicon has no apparent role in G. kaustophilus. Biochemical characterization suggested that the efficient chloramphenicol resistance conferred by pGKE75αβ-catA138T is attributable to increases in intracellular CATA138T and acetyl-coenzyme A following a decrease in incomplete forms of pGKE75αβ-catA138T. The decrease in incomplete plasmids may be due to optimization of plasmid replication by RNA species transcribed from the mutant pUC replicon, which were actually produced in G. kaustophilus. It is noteworthy that G. kaustophilus was transformed with pGKE75αβ-catA138T using chloramphenicol selection at 60°C. In addition, a pUC18 derivative with the two mutations propagated in E. coli at a high copy number independently of the culture temperature and high plasmid stability. Since these properties have not been observed in known plasmids, the outcomes extend the genetic toolboxes for G. kaustophilus and E. coli. PMID:26319877

  9. [Mechanisms of targeted frameshift mutations--insertion formation under error-prone or SOS synthesis of DNA containing CIS-SYN cyncyclobutane thymine dimers].

    PubMed

    Grebneva, E A

    2014-01-01

    Up to now the mechanism of formation of frameshift mutations caused by cyclobutane pyrimidine dimers has not been yet explained satisfactorily. Mechanisms of different mutations are usually considered in polymerase model. Here, the alternative polymerase-tautomer model of ultraviolet mutagenesis is developed. The mechanism of targeted insertion formation caused by cis-syn cyclobutane thymine dimers is proposed. Insertions are mutations when one or several DNA bases are inserted.Targeted insertions are mutations of a frameshift type--when one or severalnucleotides are inserted opposite damageswhich may stop synthesis of DNA. Targeted insertions are induced bycyclobutane pyrimidine dimmers. Ultraviolet irradiation may result in a change of tautomer state of DNA bases. A thymine base may form 5 rare tautomer forms that are stable if the base is a part of cyclobutane dimer. As it was shown by structural analysis, one rare tautomeric form of thymine forms hydrogen bonds with no one canonical DNA base. Therefore, under SOS or error-prone synthesis of DNA containing cis-syn cyclobutane thymine dimers with such rare tautomeric_form a specialize or modified DNA polymerase leaves a single nucleotide gap opposite the cis-syn cyclobutane thymine dimer. According to Streisinger model, if the DNA composition within this region is homogeneous, the end of the growing DNA strand can slip and form complementary pairs with a template nucleotide neighboring to the dimer of such type a loop is formed. Further elongation of the daughter strand leads to the appearance of targeted insertion in the daughter strand. Here, it is first shown that cis-syn cyclobutane thymine dimers with one or both bases in the specific tautomer conformation--opposite which it is impossible to insert a canonical base with a hydrogen bond formation--results in targeted insertions. Moreover, the model of forming targeted single--and several-base insertions is developed. The polymerase-tautomer model of ultraviolet mutagenesis can explain a nature and mechanism of appearing not only hot and cold spots, targeted and untargeted base substitution mutations but also targeted frameshift mutations. PMID:25842840

  10. 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

  11. Addressing PCR Biases in Environmental Microbiology Studies

    NASA Astrophysics Data System (ADS)

    Sipos, Rita; Székely, Anna; Révész, Sára; Márialigeti, Károly

    Each step of a molecular environmental microbiology study is prone to errors, though the qualitative and quantitative biases of PCR amplification could result in the most serious biases. One has to be aware of this fact, and well-characterized PCR biases have to be avoided by using target-optimized PCR protocols. The most important tasks are primer and thermal profile optimization. We have shown that primer mismatches, even in the case of universal primers, can cause almost complete missing of common taxa from clone libraries, for example. Similarly high annealing temperatures can drastically distort community composition of the sample in the PCR product. Strategies of primer selection and PCR thermal profile design are discussed in detail.

  12. Groundtruthing Next-Gen Sequencing for Microbial EcologyBiases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

    PubMed Central

    Polson, Shawn W.; Wommack, K. Eric; Williamson, Shannon J.; McDonald, Ian R.; Cary, S. Craig

    2012-01-01

    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxaa phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure. PMID:22970184

  13. Errors in ribosomal sequence datasets generated using PCR-coupled 'panbacterial' pyrosequencing, and the establishment of an improved approach.

    PubMed

    Prosdocimi, Erica M; Novati, Stefano; Bruno, Raffaele; Bandi, Claudio; Mulatto, Patrizia; Giannico, Riccardo; Casiraghi, Maurizio; Ferri, Emanuele

    2013-02-01

    Universal bacterial primers are often used in PCR-coupled sequencing approaches to investigate environmental and host-associated bacterial communities. Some of these primers can also amplify eukaryotic DNA. This is leading to the submission of datasets to public databases which are erroneously annotated as prokaryotic sequences. The present note sends a message about the risk of submitting incorrectly annotated sequence data and suggests a reliable approach for the sequencing of 16S rRNA genes and identification of bacteria within complex communities. PMID:22824825

  14. Development of a high-throughput real time PCR based on a hot-start alternative for Pfu mediated by quantum dots

    NASA Astrophysics Data System (ADS)

    Sang, Fuming; Yang, Yang; Yuan, Lin; Ren, Jicun; Zhang, Zhizhou

    2015-09-01

    Hot start (HS) PCR is an excellent alternative for high-throughput real time PCR due to its ability to prevent nonspecific amplification at low temperature. Development of a cost-effective and simple HS PCR technique to guarantee high-throughput PCR specificity and consistency still remains a great challenge. In this study, we systematically investigated the HS characteristics of QDs triggered in real time PCR with EvaGreen and SYBR Green I dyes by the analysis of amplification curves, standard curves and melting curves. Two different kinds of DNA polymerases, Pfu and Taq, were employed. Here we showed that high specificity and efficiency of real time PCR were obtained in a plasmid DNA and an error-prone two-round PCR assay using QD-based HS PCR, even after an hour preincubation at 50 °C before real time PCR. Moreover, the results obtained by QD-based HS PCR were comparable to a commercial Taq antibody DNA polymerase. However, no obvious HS effect of QDs was found in real time PCR using Taq DNA polymerase. The findings of this study demonstrated that a cost-effective high-throughput real time PCR based on QD triggered HS PCR could be established with high consistency, sensitivity and accuracy.Hot start (HS) PCR is an excellent alternative for high-throughput real time PCR due to its ability to prevent nonspecific amplification at low temperature. Development of a cost-effective and simple HS PCR technique to guarantee high-throughput PCR specificity and consistency still remains a great challenge. In this study, we systematically investigated the HS characteristics of QDs triggered in real time PCR with EvaGreen and SYBR Green I dyes by the analysis of amplification curves, standard curves and melting curves. Two different kinds of DNA polymerases, Pfu and Taq, were employed. Here we showed that high specificity and efficiency of real time PCR were obtained in a plasmid DNA and an error-prone two-round PCR assay using QD-based HS PCR, even after an hour preincubation at 50 °C before real time PCR. Moreover, the results obtained by QD-based HS PCR were comparable to a commercial Taq antibody DNA polymerase. However, no obvious HS effect of QDs was found in real time PCR using Taq DNA polymerase. The findings of this study demonstrated that a cost-effective high-throughput real time PCR based on QD triggered HS PCR could be established with high consistency, sensitivity and accuracy. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03596a

  15. Virtual PCR

    SciTech Connect

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

    2006-02-23

    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. It is used in virtually every laboratory doing molecular, cellular, genetic, ecologic, forensic, or medical research. Despite its ubiquity, we lack the precise predictive capability that would enable detailed optimization of PCR reaction dynamics. In this LDRD, we proposed to develop Virtual PCR (VPCR) software, a computational method to model the kinetic, thermodynamic, and biological processes of PCR reactions. Given a successful completion, these tools will allow us to predict both the sequences and concentrations of all species that are amplified during PCR. The ability to answer the following questions will allow us both to optimize the PCR process and interpret the PCR results: What products are amplified when sequence mixtures are present, containing multiple, closely related targets and multiplexed primers, which may hybridize with sequence mismatches? What are the effects of time, temperature, and DNA concentrations on the concentrations of products? A better understanding of these issues will improve the design and interpretation of PCR reactions. The status of the VPCR project after 1.5 years of funding is consistent with the goals of the overall project which was scoped for 3 years of funding. At half way through the projected timeline of the project we have an early beta version of the VPCR code. We have begun investigating means to improve the robustness of the code, performed preliminary experiments to test the code and begun drafting manuscripts for publication. Although an experimental protocol for testing the code was developed, the preliminary experiments were tainted by contaminated products received from the manufacturer. Much knowledge has been gained in the development of the code thus far, but without final debugging, increasing its robustness and verifying it against experimental results, the papers which we have drafted to share our findings still require the final data necessary for publication. The following sections summarize our final progress on VPCR as it stands after 1.5 years of effort on an ambitious project scoped for a 3 year period. We have additional details of the methods than are provided here, but would like to have legal protection in place before releasing them. The result of this project, a suite of programs that predict PCR products as a function of reaction conditions and sequences, will be used to address outstanding questions in pathogen detection and forensics at LLNL. VPCR should enable scientists to optimize PCR protocols in terms of time, temperature, ion concentration, and primer sequences and concentrations, and to estimate products and error rates in advance of performing experiments. Our proposed capabilities are well ahead of all currently available technologies, which do not model non-equilibrium kinetics, polymerase extension, or predict multiple or undesired PCR products. We are currently seeking DHS funding to complete the project, at which time licensing opportunities will be explored, an updated patent application will be prepared, and a publication will be submitted. A provisional and a full patent application have already been filed (1).

  16. Peripheral blood antigen presenting cell responses in otitis-prone and non-otitis-prone infants.

    PubMed

    Surendran, Naveen; Nicolosi, Ted; Kaur, Ravinder; Pichichero, Michael E

    2016-01-01

    Stringently defined otitis-prone (sOP) children represent a new classification of the otitis-prone condition. Previous studies showed dysfunction in Ab, B-cell memory and T-cell memory responses. We sought to determine whether there are defects in numbers, phenotype and/or function of professional APC in the peripheral blood of sOP infants. APC phenotypic counts, MHC II expression and intracellular cytokine levels were determined in response to TLR7/8 (R848) stimulation by flow cytometry. Innate immune mRNA expression was measured using RT-PCR and cytokines were measured using Luminex technology. Significant (P < 0.05) increases in the phenotypic counts of monocytes and conventional dendritic cells but not plasmacytoid DCs were observed in sOP compared with non-otitis-prone (NOP) age-matched infants. No significant differences in APC activation or function were observed. Expression of various TLRs, intracellular signaling molecules and downstream cytokines was also not found to be significantly different between sOP and NOP infants. Higher numbers of APCs in sOP infants suggest the possibility of a persistent mucosal inflammatory status. Transcriptional and cytokine profiles of PBMCs among sOP infants suggest their systemic innate responses are not different compared to NOP infants. PMID:26566651

  17. Fission yeast Rad52 phosphorylation restrains error prone recombination pathways.

    PubMed

    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

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

    MedlinePlus

    ... unit dose (e.g., diltiazem 125 mg IV infusion “UD” misin- Use “as directed” terpreted as meaning to give the entire infusion as a unit [bolus] dose) Misinterpretation Correction Mistaken ...

  19. Propensity Score Weighting with Error-Prone Covariates

    ERIC Educational Resources Information Center

    McCaffrey, Daniel F.; Lockwood, J. R.; Setodji, Claude M.

    2011-01-01

    Inverse probability weighting (IPW) estimates are widely used in applications where data are missing due to nonresponse or censoring or in observational studies of causal effects where the counterfactuals cannot be observed. This extensive literature has shown the estimators to be consistent and asymptotically normal under very general conditions,…

  20. Replicative mechanisms for CNV formation are error prone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated 67 breakpoint junctions of gene copy number gains 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 (1...

  1. 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).

  2. Symmetric Biomechanically Guided Prone-to-Supine Breast Image Registration.

    PubMed

    Eiben, Björn; Vavourakis, Vasileios; Hipwell, John H; Kabus, Sven; Buelow, Thomas; Lorenz, Cristian; Mertzanidou, Thomy; Reis, Sara; Williams, Norman R; Keshtgar, Mohammed; Hawkes, David J

    2016-01-01

    Prone-to-supine breast image registration has potential application in the fields of surgical and radiotherapy planning, image guided interventions, and multi-modal cancer diagnosis, staging, and therapy response prediction. However, breast image registration of three dimensional images acquired in different patient positions is a challenging problem, due to large deformations induced to the soft breast tissue caused by the change in gravity loading. We present a symmetric, biomechanical simulation based registration framework which aligns the images in a central, virtually unloaded configuration. The breast tissue is modelled as a neo-Hookean material and gravity is considered as the main source of deformation in the original images. In addition to gravity, our framework successively applies image derived forces directly into the unloading simulation in place of a subsequent image registration step. This results in a biomechanically constrained deformation. Using a finite difference scheme avoids an explicit meshing step and enables simulations to be performed directly in the image space. The explicit time integration scheme allows the motion at the interface between chest and breast to be constrained along the chest wall. The feasibility and accuracy of the approach presented here was assessed by measuring the target registration error (TRE) using a numerical phantom with known ground truth deformations, nine clinical prone MRI and supine CT image pairs, one clinical prone-supine CT image pair and four prone-supine MRI image pairs. The registration reduced the mean TRE for the numerical phantom experiment from initially 19.3 to 0.9 mm and the combined mean TRE for all fourteen clinical data sets from 69.7 to 5.6 mm. PMID:26577254

  3. Mapping intended spinal site of care from the upright to prone position: an interexaminer reliability study

    PubMed Central

    2014-01-01

    Background Upright examination procedures like radiology, thermography, manual muscle testing, and spinal motion palpation may lead to spinal interventions with the patient prone. The reliability and accuracy of mapping upright examination findings to the prone position is unknown. This study had 2 primary goals: (1) investigate how erroneous spine-scapular landmark associations may lead to errors in treating and charting spine levels; and (2) study the interexaminer reliability of a novel method for mapping upright spinal sites to the prone position. Methods Experiment 1 was a thought experiment exploring the consequences of depending on the erroneous landmark association of the inferior scapular tip with the T7 spinous process upright and T6 spinous process prone (relatively recent studies suggest these levels are T8 and T9, respectively). This allowed deduction of targeting and charting errors. In experiment 2, 10 examiners (2 experienced, 8 novice) used an index finger to maintain contact with a mid-thoracic spinous process as each of 2 participants slowly moved from the upright to the prone position. Interexaminer reliability was assessed by computing Intraclass Correlation Coefficient, standard error of the mean, root mean squared error, and the absolute value of the mean difference for each examiner from the 10 examiner mean for each of the 2 participants. Results The thought experiment suggesting that using the (inaccurate) scapular tip landmark rule would result in a 3 level targeting and charting error when radiological findings are mapped to the prone position. Physical upright exam procedures like motion palpation would result in a 2 level targeting error for intervention, and a 3 level error for charting. The reliability experiment showed examiners accurately maintained contact with the same thoracic spinous process as the participant went from upright to prone, ICC (2,1) = 0.83. Conclusions As manual therapists, the authors have emphasized how targeting errors may impact upon manual care of the spine. Practitioners in other fields that need to accurately locate spinal levels, such as acupuncture and anesthesiology, would also be expected to draw important conclusions from these findings. PMID:24904747

  4. 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.

  5. Translationally optimal codons associate with aggregation-prone sites in proteins

    PubMed Central

    Lee, Yaelim; Zhou, Tong; Tartaglia, Gian Gaetano; Vendruscolo, Michele; Wilke, Claus O.

    2011-01-01

    We analyze the relationship between codon usage bias and residue aggregation propensity in the genomes of four model organisms, E. coli, yeast, fly, and mouse, as well as the archaeon Halobacterium species NRC-1. Using the Mantel-Haenszel procedure, we find that translationally optimal codons associate with aggregation-prone residues. Our results are qualitatively and quantitatively similar to those of an earlier study where we found an association between translationally optimal codons and buried residues. We also combine the aggregation-propensity data with solvent-accessibility data. Even though the resulting data set is small, and hence statistical power low, results indicate that the association between optimal codons and aggregation-prone residues exists both at buried and at exposed sites. By comparing codon usage at different combinations of sites (exposed, aggregation-prone sites vs. buried, non-aggregation-prone sites; buried, aggregation-prone sites vs. exposed, non-aggregation-prone sites), we find that aggregation propensity and solvent accessibility seem to have independent effects of (on average) comparable magnitude on codon usage. Finally, in fly, we assess whether optimal codons associate with sites at which amino-acid substitutions lead to an increase in aggregation propensity, and find only a very weak effect. These results suggest that optimal codons may be required to reduce the frequency of translation errors at aggregation-prone sites that coincide with certain functional sites, such as proteinprotein interfaces. Alternatively, optimal codons may be required for rapid translation of aggregation-prone regions. PMID:21046618

  6. Alternated Prone and Supine Whole-Breast Irradiation Using IMRT: Setup Precision, Respiratory Movement and Treatment Time

    SciTech Connect

    Veldeman, Liv; De Gersem, Werner; Speleers, Bruno; Truyens, Bart; Van Greveling, Annick; Van den Broecke, Rudy; De Neve, Wilfried

    2012-04-01

    Purpose: The objective of this study was to compare setup precision, respiration-related breast movement and treatment time between prone and supine positions for whole-breast irradiation. Methods and Materials: Ten patients with early-stage breast carcinoma after breast-conserving surgery were treated with prone and supine whole breast-irradiation in a daily alternating schedule. Setup precision was monitored using cone-beam computed tomography (CBCT) imaging. Respiration-related breast movement in the vertical direction was assessed by magnetic sensors. The time needed for patient setup and for the CBCT procedure, the beam time, and the length of the whole treatment slot were also recorded. Results: Random and systematic errors were not significantly different between positions in individual patients for each of the three axes (left-right, longitudinal, and vertical). Respiration-related movement was smaller in prone position, but about 80% of observations showed amplitudes <1 mm in both positions. Treatment slots were longer in prone position (21.2 {+-} 2.5 min) than in supine position (19.4 {+-} 0.8 min; p = 0.044). Conclusion: Comparison of setup precision between prone and supine position in the same patient showed no significant differences in random and systematic errors. Respiratory movement was smaller in prone position. The longer treatment slots in prone position can probably be attributed to the higher repositioning need.

  7. Suffocated prone: the iatrogenic tragedy of SIDS.

    PubMed

    Högberg, U; Bergström, E

    2000-04-01

    Epidemiologic research has shown that prone sleeping is a major risk factor for sudden infant death syndrome (SIDS). In a public health review from Sweden, we explored the historical background of the SIDS epidemic, starting with the view of the Catholic Church that sudden infant deaths were infanticides and ending with the slowly disseminated recommendation of a prone sleeping position during the 1960s, 1970s, and 1980s. The story of the SIDS epidemic illustrates a pitfall of preventive medicine--the translation of health care routines for patients to general health advice that targets the whole population. False advice, as well as correct advice, may have a profound effect on public health because of the many individuals concerned. Preventive measures must be based on scientific evidence, and systematic supervision and evaluations are necessary to identify the benefits or the harm of the measures. The discovery of the link between prone sleeping and SIDS has been called a success story for epidemiology, but the slow acceptance of the causal relationship between prone sleeping and SIDS illustrates the weak position of epidemiology and public health within the health care system. PMID:10754964

  8. Measurement error models with interactions.

    PubMed

    Midthune, Douglas; Carroll, Raymond J; Freedman, Laurence S; Kipnis, Victor

    2016-04-01

    An important use of measurement error models is to correct regression models for bias due to covariate measurement error. Most measurement error models assume that the observed error-prone covariate ([Formula: see text]) is a linear function of the unobserved true covariate ([Formula: see text]) plus other covariates ([Formula: see text]) in the regression model. In this paper, we consider models for [Formula: see text] that include interactions between [Formula: see text] and [Formula: see text]. We derive the conditional distribution of [Formula: see text] given [Formula: see text] and [Formula: see text] and use it to extend the method of regression calibration to this class of measurement error models. We apply the model to dietary data and test whether self-reported dietary intake includes an interaction between true intake and body mass index. We also perform simulations to compare the model to simpler approximate calibration models. PMID:26530858

  9. PCR thermocycler

    DOEpatents

    Benett, William J.; Richards, James B.

    2003-01-01

    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.

  10. 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.

  11. 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

  12. Prone versus supine thallium myocardial SPECT: A method to decrease artifactual inferior wall defects

    SciTech Connect

    Segall, G.M.; Davis, M.J.

    1989-04-01

    Artifactual inferior wall defects as a result of diaphragmatic attenuation of activity are a frequent source of error in thallium myocardial single photon emission computed tomography (SPECT) studies. Thirty-four patients and 11 clinically normal volunteers were studied prospectively to see if specificity of inferior wall defects for right coronary artery disease could be improved by scanning patients prone versus supine. All individuals were scanned both prone and supine, in random order, following symptom limited treadmill exercise. Images were acquired at 3 degrees steps, 25 sec per frame, in a 180 degrees elliptical orbit always beginning in the 45 degrees right anterior oblique position relative to the patient. Polar maps generated from the short axis slices were used to calculate the average regional activity. The prone studies showed consistently higher inferior wall activity compared to the supine studies on both the exercise (182 +/- 22 vs. 160 +/- 23, p less than or equal to 0.001) and 4-hr delay studies (183 +/- 20 vs. 175 +/- 21, p less than or equal to 0.001). Prone imaging resulted in a significantly higher specificity for RCA disease compared to supine imaging (90% vs. 66%, p less than 0.05) with an improvement in accuracy from 71% to 82%. Sensitivity, specificity, and accuracy for left anterior descending and left circumflex artery disease were not significantly affected by patient position during imaging. All patients having SPECT thallium myocardial perfusion studies should be imaged prone to minimize artifactual inferior wall defects and improve accuracy.

  13. Current Suicide Proneness and Past Suicidal Behavior in Adjudicated Adolescents

    ERIC Educational Resources Information Center

    Langhinrichsen-Rohling, Jennifer; Lamis, Dorian A.

    2008-01-01

    Youth recently assigned to probation (n = 233) were assessed for current suicide proneness, depression, and hopelessness, as well as for recent suicide ideation, previous suicide ideation, or suicide attempt(s). The Life Attitudes Schedule-Short Form (LAS-SF) was used to assess suicide proneness. As per the LAS-SF, suicide proneness was defined…

  14. Registration of prone and supine CT colonography scans using correlation optimized warping and canonical correlation analysis

    SciTech Connect

    Wang Shijun; Yao Jianhua; Liu Jiamin; Petrick, Nicholas; Van Uitert, Robert L.; Periaswamy, Senthil; Summers, Ronald M.

    2009-12-15

    Purpose: In computed tomographic colonography (CTC), a patient will be scanned twice--Once supine and once prone--to improve the sensitivity for polyp detection. To assist radiologists in CTC reading, in this paper we propose an automated method for colon registration from supine and prone CTC scans. Methods: We propose a new colon centerline registration method for prone and supine CTC scans using correlation optimized warping (COW) and canonical correlation analysis (CCA) based on the anatomical structure of the colon. Four anatomical salient points on the colon are first automatically distinguished. Then correlation optimized warping is applied to the segments defined by the anatomical landmarks to improve the global registration based on local correlation of segments. The COW method was modified by embedding canonical correlation analysis to allow multiple features along the colon centerline to be used in our implementation. Results: We tested the COW algorithm on a CTC data set of 39 patients with 39 polyps (19 training and 20 test cases) to verify the effectiveness of the proposed COW registration method. Experimental results on the test set show that the COW method significantly reduces the average estimation error in a polyp location between supine and prone scans by 67.6%, from 46.27{+-}52.97 to 14.98 mm{+-}11.41 mm, compared to the normalized distance along the colon centerline algorithm (p<0.01). Conclusions: The proposed COW algorithm is more accurate for the colon centerline registration compared to the normalized distance along the colon centerline method and the dynamic time warping method. Comparison results showed that the feature combination of z-coordinate and curvature achieved lowest registration error compared to the other feature combinations used by COW. The proposed method is tolerant to centerline errors because anatomical landmarks help prevent the propagation of errors across the entire colon centerline.

  15. Development of the Crying Proneness Scale: associations among crying proneness, empathy, attachment, and age.

    PubMed

    Denckla, Christy A; Fiori, Katherine L; Vingerhoets, Ad J J M

    2014-01-01

    Crying is a unique form of human emotional expression that is associated with both positive and negative evocative antecedents. This article investigates the psychometric properties of a newly developed Crying Proneness Scale by examining the factor structure, test-retest reliability, and theoretically hypothesized relationships with empathy, attachment, age, and gender. Based on an analysis of data provided by a Dutch panel (Time 1: N = 4,916, Time 2: N = 4,874), exploratory and confirmatory factor analyses suggest that crying proneness is a multidimensional construct best characterized by four factors called attachment tears, societal tears, sentimental/moral tears, and compassionate tears. Test-retest reliability of the scale was adequate and associations with age, gender, empathy, and attachment demonstrated expected relations. Results suggest that this scale can be used to measure crying proneness, and that it will be useful in future studies that aim to gain a better understanding of normal and pathological socioemotional development. PMID:24730588

  16. 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.

  17. Immunologic abnormalities in melanoma-prone families.

    PubMed

    Dean, J H; Greene, M H; Reimer, R R; LeSane, F V; McKeen, E A; Mulvihill, J J; Blattner, W A; Herberman, R B; Fraumeni, J F

    1979-11-01

    Sixty members of 4 families prone to cutaneous malignant melanoma (CMM) and a genetically determined precursor nevus syndrome underwent extensive immunologic evaluation. The most consistent finding was a diminished in vitro response to pooled alloantigens in the one-way mixed leukocyte culture (MLC) and a tendency to low T-lymphocyte and B-lymphocyte levels. When compared to controls, low B-lymphocyte levels and reduced MLC responses were found not only in family members with CMM and/or precursor nevi but also in unaffected blood relatives and spouses. The genesis of the immune dysfunction and its possible relationship to melanoma pathogenesis remain to be clarified. PMID:159376

  18. Comparison of Droplet Digital PCR and qPCR for the Quantification of Shiga Toxin-Producing Escherichia coli in Bovine Feces.

    PubMed

    Verhaegen, Bavo; De Reu, Koen; De Zutter, Lieven; Verstraete, Karen; Heyndrickx, Marc; Van Coillie, Els

    2016-01-01

    Cattle are considered to be the main reservoir for Shiga toxin-producing Escherichia coli (STEC) and are often the direct or indirect source of STEC outbreaks in humans. Accurate measurement of the concentration of shed STEC in cattle feces could be a key answer to questions concerning transmission of STEC, contamination sources and efficiency of treatments at farm level. Infected animals can be identified and the contamination level quantified by real-time quantitative PCR (qPCR), which has its specific limitations. Droplet digital PCR (ddPCR) has been proposed as a method to overcome many of the drawbacks of qPCR. This end-point amplification PCR is capable of absolute quantification independent from any reference material and is less prone to PCR inhibition than qPCR. In this study, the qPCR-based protocol described by Verstraete et al. (2014) for Shiga toxin genes stx1 and stx2 and the intimin gene eae quantification was optimized for ddPCR analysis. The properties of ddPCR and qPCR using two different mastermixes (EMM: TaqMan(®) Environmental Master Mix 2.0; UMM: TaqMan(®) Universal PCR Master Mix) were evaluated, using standard curves and both artificial and natural contaminated cattle fecal samples. In addition, the susceptibility of these assays to PCR-inhibitors was investigated. Evaluation of the standard curves and both artificial and natural contaminated cattle fecal samples suggested a very good agreement between qPCR using EMM and ddPCR. Furthermore, similar sensitivities and no PCR inhibition were recorded for both assays. On the other hand, qPCR using UMM was clearly prone to PCR inhibition. In conclusion, the ddPCR technique shows potential for the accurate absolute quantification of STEC on the farms, without relying on standardized reference material. PMID:27213452

  19. Comparison of Droplet Digital PCR and qPCR for the Quantification of Shiga Toxin-Producing Escherichia coli in Bovine Feces

    PubMed Central

    Verhaegen, Bavo; De Reu, Koen; De Zutter, Lieven; Verstraete, Karen; Heyndrickx, Marc; Van Coillie, Els

    2016-01-01

    Cattle are considered to be the main reservoir for Shiga toxin-producing Escherichia coli (STEC) and are often the direct or indirect source of STEC outbreaks in humans. Accurate measurement of the concentration of shed STEC in cattle feces could be a key answer to questions concerning transmission of STEC, contamination sources and efficiency of treatments at farm level. Infected animals can be identified and the contamination level quantified by real-time quantitative PCR (qPCR), which has its specific limitations. Droplet digital PCR (ddPCR) has been proposed as a method to overcome many of the drawbacks of qPCR. This end-point amplification PCR is capable of absolute quantification independent from any reference material and is less prone to PCR inhibition than qPCR. In this study, the qPCR-based protocol described by Verstraete et al. (2014) for Shiga toxin genes stx1 and stx2 and the intimin gene eae quantification was optimized for ddPCR analysis. The properties of ddPCR and qPCR using two different mastermixes (EMM: TaqMan® Environmental Master Mix 2.0; UMM: TaqMan® Universal PCR Master Mix) were evaluated, using standard curves and both artificial and natural contaminated cattle fecal samples. In addition, the susceptibility of these assays to PCR-inhibitors was investigated. Evaluation of the standard curves and both artificial and natural contaminated cattle fecal samples suggested a very good agreement between qPCR using EMM and ddPCR. Furthermore, similar sensitivities and no PCR inhibition were recorded for both assays. On the other hand, qPCR using UMM was clearly prone to PCR inhibition. In conclusion, the ddPCR technique shows potential for the accurate absolute quantification of STEC on the farms, without relying on standardized reference material. PMID:27213452

  20. Error Analysis

    NASA Astrophysics Data System (ADS)

    Scherer, Philipp O. J.

    Input data as well as the results of elementary operations have to be represented by machine numbers, the subset of real numbers which is used by the arithmetic unit of today's computers. Generally this generates rounding errors. This kind of numerical error can be avoided in principle by using arbitrary precision arithmetics or symbolic algebra programs. But this is unpractical in many cases due to the increase in computing time and memory requirements. Results from more complex operations like square roots or trigonometric functions can have even larger errors since series expansions have to be truncated and iterations accumulate the errors of the individual steps. In addition, the precision of input data from an experiment is limited. In this chapter we study the influence of numerical errors on the uncertainties of the calculated results and the stability of simple algorithms.

  1. Simplified primer design for PCR-based gene targeting and microarray primer database: two web tools for fission yeast.

    PubMed

    Penkett, Christopher J; Birtle, Zoë E; Bähler, Jürg

    2006-10-15

    PCR-based gene targeting is a popular method for manipulating yeast genes in their normal chromosomal locations. The manual design of primers, however, can be cumbersome and error-prone. We have developed a straightforward web-based tool that applies user-specified inputs to automate and simplify the task of primer selection for deletion, tagging and/or regulated expression of genes in Schizosaccharomyces pombe. This tool, named PPPP (for Pombe PCR Primer Programs), is available at http://www.sanger.ac.uk/PostGenomics/S_pombe/software/. We also present a searchable Microarray Primer Database to retrieve the sequences and accompanying information for primers and PCR products used to build our in-house Sz. pombe microarrays. This database contains information on both coding and intergenic regions to provide context for the microarray data, and it should be useful also for other applications, such as quantitative PCR. The database can be accessed at http://www.sanger.ac.uk/PostGenomics/S_pombe/microarray/. PMID:17072893

  2. 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 ...

  3. Neglected Children, Shame-Proneness, and Depressive Symptoms

    PubMed Central

    Bennett, David S.; Sullivan, Margaret Wolan; Lewis, Michael

    2013-01-01

    Neglected children may be at increased risk for depressive symptoms. This study examines shame-proneness as an outcome of child neglect and as a potential explanatory variable in the relation between neglect and depressive symptoms. Participants were 111 children (52 with a Child Protective Services [CPS] allegation of neglect) seen at age 7. Neglected children reported more shame-proneness and more depressive symptoms than comparison children. Guilt-proneness, in contrast, was unrelated to neglect and depressive symptoms, indicating specificity for shame-proneness. The potential role of shame as a process variable that can help explain how some neglected children exhibit depressive symptoms is discussed. PMID:20724372

  4. Sex Determination Using PCR

    ERIC Educational Resources Information Center

    Kima, Peter E.; Rasche, Madeline E.

    2004-01-01

    PCR has revolutionized many aspects of biochemistry and molecular biology research. In the following exercise, students learn PCR by isolating their own DNA, amplifying specific segments of the X and Y chromosomes, and estimating the sizes of the PCR products using agarose gel electrophoresis. Based on the pattern of PCR products, students can

  5. Sex Determination Using PCR

    ERIC Educational Resources Information Center

    Kima, Peter E.; Rasche, Madeline E.

    2004-01-01

    PCR has revolutionized many aspects of biochemistry and molecular biology research. In the following exercise, students learn PCR by isolating their own DNA, amplifying specific segments of the X and Y chromosomes, and estimating the sizes of the PCR products using agarose gel electrophoresis. Based on the pattern of PCR products, students can…

  6. Evening types are prone to depression.

    PubMed

    Merikanto, Ilona; Lahti, Tuuli; Kronholm, Erkki; Peltonen, Markku; Laatikainen, Tiina; Vartiainen, Erkki; Salomaa, Veikko; Partonen, Timo

    2013-06-01

    Certain preferences for the timing of daily activities (chronotype) may predispose an individual to sleep problems and mood disorders. In this study, we have examined the link between chronotypes and depression. Participants (N = 6071) were recruited from a random sample of the general population aged 25 to 74 yrs living in defined geographical areas, as part of the National FINRISK Study in 2007 in Finland. Chronotype assessment was based on six items from the original Horne-Östberg Morningness-Eveningness Questionnaire. Depression was assessed with four self-reported items, including two probes for a diagnosis of a major depressive episode, diagnosed or treated depression, and use of antidepressants. We also analyzed correlations between chronotype and several health indicators, such as systolic and diastolic blood pressures, resting heart rate, weight, and waist circumference. The odds ratios for a range of indicators of depression were higher for evening types (2.7- to 4.1-fold) and intermediate types (1.5- to 1.9-fold) than for morning types. Our results suggest that individuals having a preference for evening hours to carry out their daily activities are prone to depression. PMID:23688117

  7. Error Detection and Error Classification: Failure Awareness in Data Transfer Scheduling

    SciTech Connect

    Louisiana State University; Balman, Mehmet; Kosar, Tevfik

    2010-10-27

    Data transfer in distributed environment is prone to frequent failures resulting from back-end system level problems, like connectivity failure which is technically untraceable by users. Error messages are not logged efficiently, and sometimes are not relevant/useful from users point-of-view. Our study explores the possibility of an efficient error detection and reporting system for such environments. Prior knowledge about the environment and awareness of the actual reason behind a failure would enable higher level planners to make better and accurate decisions. It is necessary to have well defined error detection and error reporting methods to increase the usability and serviceability of existing data transfer protocols and data management systems. We investigate the applicability of early error detection and error classification techniques and propose an error reporting framework and a failure-aware data transfer life cycle to improve arrangement of data transfer operations and to enhance decision making of data transfer schedulers.

  8. Parent Proneness to Shame and the Use of Psychological Control

    ERIC Educational Resources Information Center

    Mills, Rosemary S. L.; Freeman, Wendy S.; Clara, Ian P.; Elgar, Frank J.; Walling, Bobbi R.; Mak, Leanne

    2007-01-01

    We examined the link between parent proneness to shame and two forms of psychological control, overprotection and critical/rejecting behavior, in parents of preschoolers. Because shame is self-condemning, proneness to shame affects intrapersonal and interpersonal functioning. We hypothesized that parents' emotion-regulatory responses to shame…

  9. Piezoelectric control of structures prone to instabilities

    NASA Astrophysics Data System (ADS)

    Kim, Sunjung

    Thin-walled structures such as stiffened panels fabricated out of high strength materials are ubiquitous in aerospace structures. These are prone to buckle in a variety of modes with strong possibility of adverse interaction under axial compression and/or bending. Optimally designed stiffened panels, at an appropriate combination of axial compression and suddenly applied lateral pressure undergo large amplitude oscillations and may experience divergence. Under aerodynamic loading, they can experience flutter instability with the amplitudes of oscillations attaining a limit (LCO) or escalating without any limit. Control of structures prone to these forms of instability using piezo-electric actuators is the theme of this dissertation. Issues involved in the control of stiffened panels under axial compression and liable to buckle simultaneously in local and overall modes are studied. The analytical approach employs finite elements in which are embedded periodic components of local buckling including the second order effects. It is shown that the adverse effects of mode interaction can be counteracted by simply controlling the overall bending of the stiffener by piezo-electric actuators attached its tips. Control is exercised by self-sensing actuators by direct negative feedback voltages proportional to the bending strains of the stiffener. In a dynamic loading environment, where vibrations are triggered by suddenly applied lateral pressure, negative velocity feedback is employed with voltages proportional to the bending strain-rate. The local plate oscillations are effectively controlled by a piezo-electric actuators placed along the longitudinal center line of the panel. The problem of flutter under aerodynamic pressure of stiffened panels in the linear and post-critical regimes is studied using modal analysis and finite strips. The analysis, control and interpretation of the response are facilitated by identification of two families of characteristic modes of vibration, viz. local and overall modes and by a classification of the local modes into two distinct categories, viz., symmetric and anti-symmetric modes respectively. The symmetric local modes interact with overall modes from the outset, i.e. in the linear flutter problem whereas both the sets of local modes interact with overall modes in the post-critical range via cubic terms in the elastic potential. However the effects of interaction in the flutter problem are far less dramatic in comparison to the interactive buckling problem unless the overall modes are activated, say by dynamic pressure on the plate. Control of the panel is exercised by piezo-electric patches placed on the plate at regions of maximum curvature as well as on the stiffener. Two types of control strategies were investigated for the panel subject to fluttering instability. The first is the direct negative velocity feedback control using a single gain factor for each of the sets of plate patches and stiffener patches respectively. A systematic method of determining the gains for the patches has been developed. This is based on the application of LQR algorithm in conjunction with a linearized stiffness matrix of the uncontrolled structure computed at a set of pre-selected times. This type of control was successful till the aerodynamic pressure coefficient reaches up to about six times its critical value, where after it simply failed. The second type of control is the multi-input and multi-output full state feedback control. The LQR algorithm and the linearized stiffness matrix are invoked again, but the gain matrix is computed at the beginning of every time step in the analysis and immediately implemented to control the structure. This type of control proved very effective the only limitation stemming from the maximum field strength that can be sustained by the piezo-electric material employed.

  10. Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements.

    PubMed

    Permina, Elizaveta A; Mironov, Andrey A; Gelfand, Mikhail S

    2002-06-26

    It is known that umuDC-like operons encoding DNA polymerase V are often found in plasmids of gamma-proteobacteria. Here we demonstrate that homologous operons are associated with mobile genomic elements in Gram-positive bacteria as well. Using the comparative analysis of transcriptional regulatory signals, we suggest that genes encoding homologs of UmuC in prophages of Bacillus subtilis and transposons of Enterococus faecalis are regulated by DinR (SOS repressor). We also predict a functional link between the polymerase V-like proteins of B. subtilis and the protein family containing YolD, YozL and YqjX. PMID:12137951

  11. Cdk1 phosphorylation of the kinetochore protein Nsk1 prevents error-prone chromosome segregation

    PubMed Central

    Chen, Jun-Song; Lu, Lucy X.; Ohi, Melanie D.; Creamer, Kevin M.; English, Chauca; Partridge, Janet F.; Ohi, Ryoma

    2011-01-01

    Cdk1 controls many aspects of mitotic chromosome behavior and spindle microtubule (MT) dynamics to ensure accurate chromosome segregation. In this paper, we characterize a new kinetochore substrate of fission yeast Cdk1, Nsk1, which promotes proper kinetochore–MT (k-MT) interactions and chromosome movements in a phosphoregulated manner. Cdk1 phosphorylation of Nsk1 antagonizes Nsk1 kinetochore and spindle localization during early mitosis. A nonphosphorylatable Nsk1 mutant binds prematurely to kinetochores and spindle, cementing improper k-MT attachments and leading to high rates of lagging chromosomes that missegregate. Accordingly, cells lacking nsk1 exhibit synthetic growth defects with mutations that disturb MT dynamics and/or kinetochore structure, and lack of proper phosphoregulation leads to even more severe defects. Intriguingly, Nsk1 is stabilized by binding directly to the dynein light chain Dlc1 independently of the dynein motor, and Nsk1–Dlc1 forms chainlike structures in vitro. Our findings establish new roles for Cdk1 and the Nsk1–Dlc1 complex in regulating the k-MT interface and chromosome segregation. PMID:22065639

  12. Timing matters: error-prone gap filling and translesion synthesis in immunoglobulin gene hypermutation

    PubMed Central

    Sale, Julian E.; Batters, Christopher; Edmunds, Charlotte E.; Phillips, Lara G.; Simpson, Laura J.; Szüts, Dávid

    2008-01-01

    By temporarily deferring the repair of DNA lesions encountered during replication, the bypass of DNA damage is critical to the ability of cells to withstand genomic insults. Damage bypass can be achieved either by recombinational mechanisms that are generally accurate or by a process called translesion synthesis. Translesion synthesis involves replacing the stalled replicative polymerase with one of a number of specialized DNA polymerases whose active sites are able to tolerate a distorted or damaged DNA template. While this property allows the translesion polymerases to synthesize across damaged bases, it does so with the trade-off of an increased mutation rate. The deployment of these enzymes must therefore be carefully regulated. In addition to their important role in general DNA damage tolerance and mutagenesis, the translesion polymerases play a crucial role in converting the products of activation induced deaminase-catalysed cytidine deamination to mutations during immunoglobulin gene somatic hypermutation. In this paper, we specifically consider the control of translesion synthesis in the context of the timing of lesion bypass relative to replication fork progression and arrest at sites of DNA damage. We then examine how recent observations concerning the control of translesion synthesis might help refine our view of the mechanisms of immunoglobulin gene somatic hypermutation. PMID:19008194

  13. Error-prone DNA repair activity during somatic hypermutation in shark B lymphocytes1

    PubMed Central

    Zhu, Catherine; Hsu, Ellen

    2010-01-01

    Sharks are representatives of the earliest vertebrates that possess an immune system utilizing V(D)J recombination to generate antigen receptors. Their antibody repertoire diversity is based in part on a somatic hypermutation process that introduces adjacent nucleotide substitutions of 2-5 bp. We have isolated mutant nonfunctional immunoglobulin rearrangements and intronic flank sequences in order to characterize the non-selected, intrinsic properties of this phenomenon; changes unique to shark were observed. Duplications and deletions were associated with N additions, suggesting participation of a DNA polymerase with some degree of template independence during the repair of DNA breaks initiated by activation-induced cytidine deaminase (AID). Other mutations were consistent with some in vitro activities of mammalian translesion DNA polymerase eta: tandem base substitutions, strand slippage, small insertions/deletions. The nature of substitution patterns shows that DNA lesions at shark immunoglobulin genes recruit DNA repair factors with a species-specific repertoire of activities. We speculate that the tandem mutations are introduced by direct sequential misinsertions and that, in shark B cells, the mispairs tend to be extended rather than proofread. Despite extensive changes undergone by some mutants, the physical range of mutational activity remained restricted to VDJ and within the first 2 kb portion of the 6.8 kb J-C intron, perhaps a self-regulating aspect of AID action that is conserved in evolution. PMID:20921520

  14. dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ε variants

    PubMed Central

    Williams, Lindsey N.; Marjavaara, Lisette; Knowels, Gary M.; Schultz, Eric M.; Fox, Edward J.; Chabes, Andrei; Herr, Alan J.

    2015-01-01

    Mutator phenotypes create genetic diversity that fuels tumor evolution. DNA polymerase (Pol) ε mediates leading strand DNA replication. Proofreading defects in this enzyme drive a number of human malignancies. Here, using budding yeast, we show that mutator variants of Pol ε depend on damage uninducible (Dun)1, an S-phase checkpoint kinase that maintains dNTP levels during a normal cell cycle and up-regulates dNTP synthesis upon checkpoint activation. Deletion of DUN1 (dun1Δ) suppresses the mutator phenotype of pol2-4 (encoding Pol ε proofreading deficiency) and is synthetically lethal with pol2-M644G (encoding altered Pol ε base selectivity). Although pol2-4 cells cycle normally, pol2-M644G cells progress slowly through S-phase. The pol2-M644G cells tolerate deletions of mediator of the replication checkpoint (MRC) 1 (mrc1Δ) and radiation sensitive (Rad) 9 (rad9Δ), which encode mediators of checkpoint responses to replication stress and DNA damage, respectively. The pol2-M644G mutator phenotype is partially suppressed by mrc1Δ but not rad9Δ; neither deletion suppresses the pol2-4 mutator phenotype. Thus, checkpoint activation augments the Dun1 effect on replication fidelity but is not required for it. Deletions of genes encoding key Dun1 targets that negatively regulate dNTP synthesis, suppress the dun1Δ pol2-M644G synthetic lethality and restore the mutator phenotype of pol2-4 in dun1Δ cells. DUN1 pol2-M644G cells have constitutively high dNTP levels, consistent with checkpoint activation. In contrast, pol2-4 and POL2 cells have similar dNTP levels, which decline in the absence of Dun1 and rise in the absence of the negative regulators of dNTP synthesis. Thus, dNTP pool levels correlate with Pol ε mutator severity, suggesting that treatments targeting dNTP pools could modulate mutator phenotypes for therapy. PMID:25827226

  15. Introduction to digital PCR.

    PubMed

    Bizouarn, Francisco

    2014-01-01

    Digital PCR (dPCR) is a molecular biology technique going through a renaissance. With the arrival of new instrumentation dPCR can now be performed as a routine molecular biology assay. This exciting new technique provides quantitative and detection capabilities that by far surpass other methods currently used. This chapter is an overview of some of the applications currently being performed using dPCR as well as the fundamental concepts and techniques this technology is based on. PMID:24740219

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

    SciTech Connect

    Ahn, Kang-Hyun Hargreaves, Brian A.; Alley, Marcus T.; Horst, Kathleen C.; Luxton, Gary; Daniel, Bruce L.; Hristov, Dimitre

    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.

  17. 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

  18. Effect of Reducing Abdominal Compression during Prone CT Colonography on Ascending Colonic Rotation during Supine-to-Prone Positional Change

    PubMed Central

    Jang, Jong Keon; Lee, Jong Seok; Kim, Hyun Jin; Kim, Ah Young; Ha, Hyun Kwon

    2016-01-01

    Objective To determine the effect of reduced abdominal compression in prone position on ascending colonic movement during supine-to-prone positional change during CT colonography (CTC). Materials and Methods Eighteen consecutive patients who had undergone prone CTC scanning with cushion blocks placed under the chest and hip/thigh to reduce abdominal compression and had confirmed sessile polyps ≥ 6 mm in the well-distended, straight, mid-ascending colon, were included. Radial location along the ascending colonic luminal circumference (°) was measured for 24 polyps and 54 colonic teniae on supine and prone CTC images. The supine-to-prone change ranging between -180° and +180° (- and + for internal and external colonic rotations, respectively), was determined. In addition, possible causes of any ascending colonic rotations were explored. Results Abdominal compression during prone CTC scanning completely disappeared with the use of cushion blocks in 17 of 18 patients. However, some degrees of ascending colonic rotation were still observed, with the radial location changes of -22° to 61° (median, 13.9°) for the polyps and similar degrees for teniae. Fifty-four percent and 56% of polyps and teniae, respectively, showed changes > 10°. The radial location change of the polyps was significantly associated with the degree of anterior shift of the small bowel and mesentery (r = 0.722, p < 0.001) and the degree of posterior displacement of the ascending colon (r = 0.566, p = 0.004) during supine-to-prone positional change. Conclusion Ascending colonic rotation upon supine-to-prone positional change during CTC, mostly in the form of external rotation, is not eliminated by removing abdominal compression in prone position. PMID:26798215

  19. Development and validation of the Adolescent Shame-Proneness Scale.

    PubMed

    Simonds, Laura M; John, Mary; Fife-Schaw, Chris; Willis, Susie; Taylor, Helen; Hand, Heidi; Rahim, Masuma; Winstanley, Harriet; Winton, Holly

    2016-05-01

    Like other self-conscious emotions, shame takes on particular significance during late childhood and adolescence because of a developing capacity for self-reflection, self-other comparisons, and sensitivity to the views of others. Shame is a potentially important variable in adolescent well-being given its established associations with depression, reduced feelings of self-worth, and problematic anger. Three studies are reported that describe the development and validation of the Adolescent Shame-Proneness Scale (ASPS), a novel semi-idiographic measure of shame-proneness. The ASPS is a 19-item measure assessing 3 components of shame-proneness-negative self-evaluation, externalization, and emotional discomfort. Taken together, the studies support the reliability and validity of the ASPS as a semi-idiographic measure of shame-proneness in adolescents aged 11 to 18 years. ASPS scores correlate as expected with scores on existing measure of shame-proneness and with measures of anger, negative affect, and self-esteem. More important, the data suggest that ASPS scores are related to, but distinct from, guilt. Confirmatory factor analysis supported the validity of the ASPS factor structure (RMSEA = .08, SRMR = .05, CFI = .97, NNFI = .97). The ASPS represents a unique contribution to existing options for measuring shame-proneness in research and clinical contexts. Further work is required to assess the ASPS' temporal stability and its viability and psychometric properties in more culturally diverse samples. (PsycINFO Database Record PMID:26302099

  20. 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

  1. PCR und Real-Time PCR

    NASA Astrophysics Data System (ADS)

    Konrad, Regina; Busch, Ulrich

    Die vielfältigen Anwendungsmöglichkeiten der Polymerasekettenreaktion (polymerase chain reaction, PCR) machen sie zu einer der wichtigsten und am häufigsten eingesetzten Methoden in der molekularbiologischen Forschung und Diagnostik. Für diese Technologie wurde der Erfinder der Methode, Kary Mullis, 1993 mit dem Nobelpreis ausgezeichnet. Die PCR erlaubt einen hochsensitiven und spezifischen in-vitro-Nachweis von Desoxyribonukleinsäuren (DNA), da im Zuge der Reaktion Sequenzabschnitte gezielt vermehrt werden. Innerhalb weniger Stunden können aus einem einzigen Zielmolekül 1012 identische Moleküle entstehen [1].

  2. 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.

  3. PEEP titration during prone positioning for acute respiratory distress syndrome.

    PubMed

    Beitler, Jeremy R; Guérin, Claude; Ayzac, Louis; Mancebo, Jordi; Bates, Dina M; Malhotra, Atul; Talmor, Daniel

    2015-01-01

    No major trial evaluating prone positioning for acute respiratory distress syndrome (ARDS) has incorporated a high-positive end-expiratory pressure (high-PEEP) strategy despite complementary physiological rationales. We evaluated generalizability of three recent proning trials to patients receiving a high-PEEP strategy. All trials employed a relatively low-PEEP strategy. After protocol ventilator settings were initiated and the patient was positioned per treatment assignment, post-intervention PEEP was not more than 5 cm H2O in 16.7 % and not more than 10 cm H2O in 66.0 % of patients. Post-intervention PEEP would have been nearly twice the set PEEP had a high-PEEP strategy been employed. Use of either proning or high-PEEP likely improves survival in moderate-severe ARDS; the role for both concomitantly remains unknown. PMID:26686509

  4. Fantasy proneness, creative capacity, and styles of creativity.

    PubMed

    Lack, Susanna A; Kumar, V K; Arevalo, Salvador

    2003-02-01

    The Creativity Styles Questionnaire-Revised was used to measure graduate psychology students' (N=173) self-perceptions of creative capacity and styles of creativity (beliefs about and strategies for going about being creative). Participants also completed the Inventory of Childhood Memories and Imaginings, a self-report measure of Fantasy Proneness. The Self-perceived Creative Capacity and Fantasy Proneness scores were significantly correlated (r=.36, p<.001), and these scores were positively correlated with the styles subscale scores of Belief in Unconscious Processes. Use of Techniques, Use of Senses, and negatively correlated with Final Product Orientation. Also, the Fantasy Proneness scores were positively correlated with the Superstition scores and the Environmental Control and Behavioral Self-regulation scores. PMID:12705504

  5. [Diagnostic Errors in Medicine].

    PubMed

    Buser, Claudia; Bankova, Andriyana

    2015-12-01

    The recognition of diagnostic errors in everyday practice can help improve patient safety. The most common diagnostic errors are the cognitive errors, followed by system-related errors and no fault errors. The cognitive errors often result from mental shortcuts, known as heuristics. The rate of cognitive errors can be reduced by a better understanding of heuristics and the use of checklists. The autopsy as a retrospective quality assessment of clinical diagnosis has a crucial role in learning from diagnostic errors. Diagnostic errors occur more often in primary care in comparison to hospital settings. On the other hand, the inpatient errors are more severe than the outpatient errors. PMID:26649954

  6. Transcription Errors Induce Proteotoxic Stress and Shorten Cellular Lifespan

    PubMed Central

    Vermulst, Marc; Denney, Ashley S.; Lang, Michael J.; Hung, Chao-Wei; Moore, Stephanie; Mosely, M. Arthur; Thompson, J. Will; Madden, Victoria; Gauer, Jacob; Wolfe, Katie J.; Summers, Daniel W.; Schleit, Jennifer; Sutphin, George L.; Haroon, Suraiya; Holczbauer, Agnes; Caine, Joanne; Jorgenson, James; Cyr, Douglas; Kaeberlein, Matt; Strathern, Jeffrey N.; Duncan, Mara C.; Erie, Dorothy A.

    2015-01-01

    Transcription errors occur in all living cells; however, it is unknown how these errors affect cellular health. To answer this question, we monitored yeast cells that were genetically engineered to display error-prone transcription. We discovered that these cells suffer from a profound loss in proteostasis, which sensitizes them to the expression of genes that are associated with protein-folding diseases in humans; thus, transcription errors represent a new molecular mechanism by which cells can acquire disease. We further found that the error rate of transcription increases as cells age, suggesting that transcription errors affect proteostasis particularly in aging cells. Accordingly, transcription errors accelerate the aggregation of a peptide that is implicated in Alzheimer’s disease, and shorten the lifespan of cells. These experiments reveal a novel, basic biological process that directly affects cellular health and aging. PMID:26304740

  7. First order error corrections in common introductory physics experiments

    NASA Astrophysics Data System (ADS)

    Beckey, Jacob; Baker, Andrew; Aravind, Vasudeva; Clarion Team

    As a part of introductory physics courses, students perform different standard lab experiments. Almost all of these experiments are prone to errors owing to factors like friction, misalignment of equipment, air drag, etc. Usually these types of errors are ignored by students and not much thought is paid to the source of these errors. However, paying attention to these factors that give rise to errors help students make better physics models and understand physical phenomena behind experiments in more detail. In this work, we explore common causes of errors in introductory physics experiment and suggest changes that will mitigate the errors, or suggest models that take the sources of these errors into consideration. This work helps students build better and refined physical models and understand physics concepts in greater detail. We thank Clarion University undergraduate student grant for financial support involving this project.

  8. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... flood-related erosion-prone areas. 60.24 Section 60.24 Emergency Management and Assistance FEDERAL..., Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning process for communities identified under part 65 of...

  9. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... flood-related erosion-prone areas. 60.24 Section 60.24 Emergency Management and Assistance FEDERAL..., Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning process for communities identified under part 65 of...

  10. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... flood-related erosion-prone areas. 60.24 Section 60.24 Emergency Management and Assistance FEDERAL..., Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning process for communities identified under part 65 of...

  11. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... flood-related erosion-prone areas. 60.24 Section 60.24 Emergency Management and Assistance FEDERAL..., Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning process for communities identified under part 65 of...

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... flood-related erosion-prone areas. 60.24 Section 60.24 Emergency Management and Assistance FEDERAL..., Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning process for communities identified under part 65 of...

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

    PubMed

    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 rate 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, Taq polymerase, AccuPrime-Taq High Fidelity, KOD Hot Start, cloned Pfu polymerase, Phusion Hot Start, and Pwo polymerase, we find the lowest error rates with Pfu, Phusion, and Pwo polymerases. Error rates are comparable for these 3 enzymes and are >10x lower than the error rate observed with Taq polymerase. 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. PMID:25197572

  14. Real-Time PCR

    NASA Astrophysics Data System (ADS)

    Evrard, A.; Boulle, N.; Lutfalla, G. S.

    Over the past few years there has been a considerable development of DNA amplification by polymerase chain reaction (PCR), and real-time PCR has now superseded conventional PCR techniques in many areas, e.g., the quantification of nucleic acids and genotyping. This new approach is based on the detection and quantification of a fluorescent signal proportional to the amount of amplicons generated by PCR. Real-time detection is achieved by coupling a thermocycler with a fluorimeter. This chapter discusses the general principles of quantitative real-time PCR, the different steps involved in implementing the technique, and some examples of applications in medicine. The polymerase chain reaction (PCR) provides a way of obtaining a large number of copies of a double-stranded DNA fragment of known sequence. This DNA amplification technique, developed in 1985 by K. Mullis (Cetus Corporation), saw a spectacular development over the space of a few years, revolutionising the methods used up to then in molecular biology. Indeed, PCR has many applications, such as the detection of small amounts of DNA, cloning, and quantitative analysis (assaying), each of which will be discussed further below.

  15. 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...

  16. 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

  17. 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

  18. The Social Antecedents of Anger Proneness in Young Adulthood

    ERIC Educational Resources Information Center

    Turner, R. Jay; Russell, David; Glover, Regan; Hutto, Pamela

    2007-01-01

    Anger has been shown to be an important factor in occupational maladjustment, family conflict, physical and sexual assault, criminal behavior, and substance abuse. It has also been linked with such adverse health outcomes as hypertension, heart disease, and cancer. Focusing on anger proneness, conceptualized as a relatively enduring propensity to

  19. Boredom Proneness in Young Adults: Gender and Cultural Comparisons.

    ERIC Educational Resources Information Center

    Sundberg, Norman D.; And Others

    Despite the widespread prevalence of boredom in many societies and of boredom-related problems in education, industry, and mental health, little research has been done on this emotion and no empirical cross-cultural research could be found. A Boredom Proneness (BP) Scale was developed and administered to college students in Australia, Hong Kong,…

  20. The Social Antecedents of Anger Proneness in Young Adulthood

    ERIC Educational Resources Information Center

    Turner, R. Jay; Russell, David; Glover, Regan; Hutto, Pamela

    2007-01-01

    Anger has been shown to be an important factor in occupational maladjustment, family conflict, physical and sexual assault, criminal behavior, and substance abuse. It has also been linked with such adverse health outcomes as hypertension, heart disease, and cancer. Focusing on anger proneness, conceptualized as a relatively enduring propensity to…

  1. 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.

  2. Utility of PCR in diagnosing pulmonary tuberculosis.

    PubMed Central

    Bennedsen, J; Thomsen, V O; Pfyffer, G E; Funke, G; Feldmann, K; Beneke, A; Jenkins, P A; Hegginbothom, M; Fahr, A; Hengstler, M; Cleator, G; Klapper, P; Wilkins, E G

    1996-01-01

    At present, the rapid diagnosis of pulmonary tuberculosis rests with microscopy. However, this technique is insensitive and many cases of pulmonary tuberculosis cannot be initially confirmed. Nucleic acid amplification techniques are extremely sensitive, but when they are applied to tuberculosis diagnosis, they have given variable results. Investigators at six centers in Europe compared a standardized PCR system (Amplicor; Roche) against conventional culture methods. Defined clinical information was collected. Discrepant samples were retested, and inhibition assays and backup amplification with a separate primer pair were performed. Mycobacterium tuberculosis complex organisms were recovered from 654 (9.1%) of 7,194 samples and 293 (7.8%) of 3,738 patients. Four hundred fifty-two of the M. tuberculosis isolates from 204 patients were smear positive and culture positive. Among the culture-positive specimens, PCR had a sensitivity of 91.4% for smear-positive specimens and 60.9% for smear-negative specimens, with a specificity of 96.1%. Analysis of 254 PCR-positive, culture-negative specimens with discrepant results revealed that 130 were from patients with recently diagnosed tuberculosis and 94 represented a presumed laboratory error. Similar analysis of 118 PCR-negative, culture-positive specimens demonstrated that 27 discrepancies were due to presumed uneven aliquot distribution and 11 were due to presumed laboratory error; PCR inhibitors were detected in 8 specimens. Amplicor enables laboratories with little previous experience with nucleic acid amplification to perform PCR. Disease in more than 60% of the patients with tuberculosis with smear-negative, culture-positive specimens can be diagnosed at the time of admission, and potentially all patients with smear-positive specimens can immediately be confirmed as being infected with M. tuberculosis, leading to improved clinical management. PMID:8735089

  3. Measurement error and dietary intake.

    PubMed

    Carroll, R J; Freedman, L S; Kipnis, V

    1998-01-01

    This chapter reviews work of Carroll, Freedman, Kipnis, and Li (1998) on the statistical analysis of the relationship between dietary intake and health outcomes. In the area of nutritional epidemiology, there is some evidence from biomarker studies that the usual statistical model for dietary measurements may break down due to two causes: (a) systematic biases depending on a person's body mass index; and (b) an additional random component of bias, so that the error structure is the same as a one-way random effects model. We investigate this problem, in the context of (1) the estimation of the distribution of usual nutrient intake; (2) estimating the correlation between a nutrient instrument and usual nutrient intake; and (3) estimating the true relative risk from an estimated relative risk using the error-prone covariate. While systematic bias due to body mass index appears to have little effect, the additional random effect in the variance structure is shown to have a potentially important impact on overall results, both on corrections for relative risk estimates and in estimating the distribution usual of nutrient intake. Our results point to a need for new experiments aimed at estimation of a crucial parameter. PMID:9781387

  4. Supine and prone registration of the colon for CT colonography based on dynamic programming technique

    NASA Astrophysics Data System (ADS)

    Oda, Masahiro; Fukano, Eiichiro; Kitasaka, Takayuki; Takayama, Tetsuji; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Nawano, Shigeru; Mori, Kensaku

    2013-02-01

    This paper proposes a registration method of the colon taken in two positions of CT images. CT colonographybased colon diagnosis using 3D CT images taken in supine and prone positions is time-consuming because a physician has to refer to many CT images for the diagnosis of a patient. Automated synchronization of the observing areas in the two positions is required to reduce the load on physicians. This paper proposes a novel registration method of the colon in two positions to synchronize the observing areas. The registration process utilizes the sharp curved points of the colon centerlines and haustral folds as landmarks. A dynamic programming technique finds correspondence between the haustral fold landmarks in the two positions. The experimental results using six pairs of CT images showed that the mean registration error was 4.70 [mm].

  5. 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. Errormore » rate 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, Taq polymerase, AccuPrime-Taq High Fidelity, KOD Hot Start, cloned Pfu polymerase, Phusion Hot Start, and Pwo polymerase, we find the lowest error rates with Pfu , Phusion, and Pwo polymerases. Error rates are comparable for these 3 enzymes and are >10x lower than the error rate observed with Taq polymerase. 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

  6. 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

  7. Help prevent hospital errors

    MedlinePlus

    A hospital error is when there is a mistake in your medical care. Errors can be made in your: ... Surgery Diagnosis Equipment Lab and other test reports Hospital errors are a leading cause of death. Doctors ...

  8. Rapid Optical Cavity PCR.

    PubMed

    Son, Jun Ho; Hong, SoonGweon; Haack, Amanda J; Gustafson, Lars; Song, Minsun; Hoxha, Ori; Lee, Luke P

    2016-01-01

    Recent outbreaks of deadly infectious diseases, such as Ebola and Middle East respiratory syndrome coronavirus, have motivated the research for accurate, rapid diagnostics that can be administered at the point of care. Nucleic acid biomarkers for these diseases can be amplified and quantified via polymerase chain reaction (PCR). In order to solve the problems of conventional PCR-speed, uniform heating and cooling, and massive metal heating blocks-an innovative optofluidic cavity PCR method using light-emitting diodes (LEDs) is accomplished. Using this device, 30 thermal cycles between 94 °C and 68 °C can be accomplished in 4 min for 1.3 μL (10 min for 10 μL). Simulation results show that temperature differences across the 750 μm thick cavity are less than 2 °C and 0.2 °C, respectively, at 94 °C and 68 °C. Nucleic acid concentrations as low as 10(-8) ng μL(-1) (2 DNA copies per μL) can be amplified with 40 PCR thermal cycles. This simple, ultrafast, precise, robust, and low-cost optofluidic cavity PCR is favorable for advanced molecular diagnostics and precision medicine. It is especially important for the development of lightweight, point-of-care devices for use in both developing and developed countries. PMID:26592501

  9. Ultrasound-guided central venous catheterization in prone position

    PubMed Central

    Sofi, Khalid; Arab, Samer

    2010-01-01

    Central venous catheterization (CVC) is a commonly performed intraoperative procedure. Traditionally, CVC placement is performed blindly using anatomic landmarks as a guide to vessel position. Real-time ultrasound provides the operator the benefit of visualizing the target vein and the surrounding anatomic structures prior to and during the catheter insertion, thereby minimizing complications and increasing speed of placement. A 22-year-old male underwent open reduction and internal fixation of acetabulum fracture in prone position. Excessive continuous bleeding intraoperatively warranted placement of CVC in right internal jugular vein (IJV), which was not possible in prone position without the help of ultrasound. Best view of right IJV was obtained and CVC was placed using real-time ultrasound without complications. Ultrasound-guided CVC placement can be done in atypical patient positions where traditional anatomic landmark technique has no role. Use of ultrasound not only increases the speed of placement but also reduces complications known with the traditional blind technique. PMID:20668564

  10. Enhancing disaster management by mapping disaster proneness and preparedness.

    PubMed

    Mishra, Vishal; Fuloria, Sanjay; Bisht, Shailendra Singh

    2012-07-01

    The focus of most disaster management programmes is to deploy resources-physical and human-from outside the disaster zone. This activity can produce a delay in disaster mitigation and recovery efforts, and a consequent loss of human lives and economic resources. It may be possible to expedite recovery and prevent loss of life by mapping out disaster proneness and the availability of resources in advance. This study proposes the development of two indices to do so. The Indian census data of 2001 is used to develop a methodology for creating one index on disaster proneness and one on resourcefulness for administrative units (tehsils). Findings reveal that tehsil residents face an elevated risk of disaster and that they are also grossly under-prepared for such events. The proposed indices can be used to map regional service provision facilities and to assist authorities in evaluating immediate, intermediate, and long-term disaster recovery needs and resource requirements. PMID:22092572

  11. Atypical diabetes in children: ketosis-prone type 2 diabetes

    PubMed Central

    Vaibhav, Atul; Mathai, Mathew; Gorman, Shaun

    2013-01-01

    Ketosis-prone type 2 diabetes mellitus also known as atypical or flatbush diabetes is being increasingly recognised worldwide. These patients are typically obese, middle-aged men with a strong family history of type 2 diabetes. The aetiology and pathophysiological mechanism is still unclear but some initial research suggests that patients with ketosis-prone type 2 diabetes have a unique predisposition to glucose desensitisation. These patients have negative autoantibodies typically associated with type 1 diabetes but have shown to have human leucocyte antigen (HLA) positivity. At initial presentation, there is an impairment of both insulin secretion and action. β Cell function and insulin sensitivity can be markedly improved by initiating aggressive diabetes management to allow for discontinuation of insulin therapy within a few months of treatment. These patients can be maintained on oral hypoglycaemic agents and insulin therapy can be safely discontinued after few months depending on their β cell function. PMID:23302548

  12. Accelerated failure time models with covariates subject to measurement error.

    PubMed

    He, Wenqing; Yi, Grace Y; Xiong, Juan

    2007-11-20

    It has been well known that ignoring measurement error may result in substantially biased estimates in many contexts including linear and nonlinear regressions. For survival data with measurement error in covariates there has been extensive discussion in the literature with the focus being on the Cox proportional hazards models. However, the impact of measurement error on accelerated failure time (AFT) models has received little attention, though AFT models are very useful in survival data analysis. In this paper, we discuss AFT models with error-prone covariates and study the bias induced by the naive approach of ignoring measurement error in covariates. To adjust for such a bias, we describe a simulation and extrapolation method. This method is appealing because it is simple to implement and it does not require modelling the true but error-prone covariate process that is often not observable. Asymptotic normality for the resulting estimators is established. Simulation studies are carried out to evaluate the performance of the proposed method as well as the impact of ignoring measurement error in covariates. The proposed method is applied to analyse a data set arising from the Busselton Health study (Australian J. Public Health 1994; 18:129-135). PMID:17436310

  13. Reward and Affective Regulation in Depression-Prone Smokers

    PubMed Central

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

    2014-01-01

    Background There is a disproportionately high smoking prevalence among individuals who are prone to depression. While depression has been conceptualized as a disorder of dysregulated positive affect and disrupted reward processing, little research has been conducted to determine the role of smoking in these processes among depression-prone smokers. Methods Depression-prone smokers (DP+; n = 34) and smokers not depression-prone (DP-; n=49) underwent two laboratory sessions, once while smoking abstinent and once while smoking ad-libitum, to assess the relative reinforcing value of smoking and reward sensitivity. Using experience sampling methods, participants completed self-report measures of subjective reward, positive affect, and negative affect across three days while smoking as usual and three days while smoking abstinent. Results DP+ were two times more likely to work for cigarette puffs versus money in a progressive ratio, choice task (OR 2.05; CI 95% 1.04 to 4.06, p=0.039) compared to DP-. Reward sensitivity as measured by the signal detection task did not yield any significant findings. Mixed models regressions revealed a 3-way interaction (depression group, smoking phase, and time) for subjective reward, negative affect and positive affect. For all three of these outcomes, the slopes for DP- and DP+ differed significantly from each other (p's < 0.05), and the effect of smoking (vs. abstinence) over time was greater for DP+ than DP- smokers (p's <0.05). Conclusions These findings indicate that the effects of smoking on reward and positive affect regulation are specific to DP+ smokers and highlight novel targets for smoking cessation treatment in this population. PMID:24947541

  14. Prediction of aggregation prone regions of therapeutic proteins.

    PubMed

    Chennamsetty, Naresh; Voynov, Vladimir; Kayser, Veysel; Helk, Bernhard; Trout, Bernhardt L

    2010-05-20

    Therapeutic proteins such as antibodies are playing an increasingly prominent role in the treatment of numerous diseases including cancer and rheumatoid arthritis. However, these proteins tend to degrade due to aggregation during manufacture and storage. Aggregation decreases protein activity and raises concerns about an immunological response. We have recently developed a method based on full antibody atomistic simulations to predict antibody aggregation prone regions [Proc. Natl. Acac. Sci. 2009, 106, 11937]. This method is based on "spatial-aggregation-propensity (SAP)", a measure of the dynamic exposure of hydrophobic patches. In the present paper, we expand on this method to analyze the aggregation prone regions over a wide parameter range. We also explore the effect of different hydrophilic mutations on these predicted aggregation prone regions to engineer antibodies with enhanced stability. The mutation to lysine is more effective than serine but less effective than glutamic acid in enhancing antibody stability. Furthermore, we show that multiple simultaneous mutations on different SAP peaks can have a cumulative effect on enhancing protein stability. We also investigate the accuracy of various cheaper alternatives for SAP evaluation because the full antibody atomistic simulations are highly computationally expensive. These cheaper alternatives include antibody fragment (Fab, Fc) simulations, implicit solvent models, or direct computations from a static structure (i.e., a structure from X-ray or homology modeling). The SAP evaluation from the static structure is 200,000 times faster but less accurate compared to the SAP from explicit atom simulations. Nevertheless, the SAP from a static structure still predicts most of the major aggregation prone regions, making it a potential approach for use in high-throughput applications. Thus, the SAP technology described here could be employed either in high-throughput developability screening of therapeutic protein candidates or to improve their stability at later stages of manufacturing. PMID:20411962

  15. Supine and prone colon registration using quasi-conformal mapping.

    PubMed

    Zeng, Wei; Marino, Joseph; Chaitanya Gurijala, Krishna; Gu, Xianfeng; Kaufman, Arie

    2010-01-01

    In virtual colonoscopy, CT scans are typically acquired with the patient in both supine (facing up) and prone (facing down) positions. The registration of these two scans is desirable so that the user can clarify situations or confirm polyp findings at a location in one scan with the same location in the other, thereby improving polyp detection rates and reducing false positives. However, this supine-prone registration is challenging because of the substantial distortions in the colon shape due to the patient's change in position. We present an efficient algorithm and framework for performing this registration through the use of conformal geometry to guarantee that the registration is a diffeomorphism (a one-to-one and onto mapping). The taeniae coli and colon flexures are automatically extracted for each supine and prone surface, employing the colon geometry. The two colon surfaces are then divided into several segments using the flexures, and each segment is cut along a taenia coli and conformally flattened to the rectangular domain using holomorphic differentials. The mean curvature is color encoded as texture images, from which feature points are automatically detected using graph cut segmentation, mathematic morphological operations, and principal component analysis. Corresponding feature points are found between supine and prone and are used to adjust the conformal flattening to be quasi-conformal, such that the features become aligned. We present multiple methods of visualizing our results, including 2D flattened rendering, corresponding 3D endoluminal views, and rendering of distortion measurements. We demonstrate the efficiency and efficacy of our registration method by illustrating matched views on both the 2D flattened colon images and in the 3D volume rendered colon endoluminal view. We analytically evaluate the correctness of the results by measuring the distance between features on the registered colons. PMID:20975175

  16. Aggression proneness: Transdiagnostic processes involving negative valence and cognitive systems.

    PubMed

    Verona, Edelyn; Bresin, Konrad

    2015-11-01

    Aggressive behavior is observed in persons with various mental health problems and has been studied from the perspectives of neuroscience and psychophysiology. The present research reviews some of the extant experimental literature to help clarify the interplay between domains of functioning implicated in aggression proneness. We then convey a process-oriented model that elucidates how the interplay of the Negative Valence and Cognitive System domains of NIMH's Research Domain Criteria (RDoC) helps explain aggression proneness, particularly reactive aggression. Finally, we report on a study involving event-related potential (ERP) indices of emotional and inhibitory control processing during an emotional-linguistic go/no-go task among 67 individuals with histories of violence and criminal offending (30% female, 44% African-American) who reported on their aggressive tendencies using the Buss-Perry Aggression Questionnaire. Results provide evidence that tendencies toward angry and aggressive behavior relate to reduced inhibitory control processing (no-go P3) specifically during relevant threat-word blocks, suggesting deterioration of cognitive control by acute or sustained threat sensitivity. These findings highlight the value of ERP methodologies for clarifying the interplay of Negative Valence and Cognitive System processes in aggression proneness. PMID:25816797

  17. Anger Proneness, Gender, and the Risk of Heart Failure

    PubMed Central

    Kucharska-Newton, Anna M.; Williams, Janice E.; Chang, Patricia P.; Stearns, Sally C.; Sueta, Carla A.; Blecker, Saul B.; Mosley, Thomas H.

    2014-01-01

    Background Evidence concerning the association of anger-proneness with incidence of heart failure is lacking. Methods Anger proneness was ascertained among 13,171 black and white participants of the Atherosclerosis Risk in Communities (ARIC) Study cohort using the Spielberger Trait Anger Scale. Incident heart failure events, defined as occurrence of ICD-9-CM code 428.x, were ascertained from participants’ medical records during follow-up 1990–2010. Relative hazard of heart failure across categories of trait anger was estimated from Cox proportional hazard models. Results Study participants (mean age 56.9 (SD 5.7) years) experienced 1,985 incident HF events during 18.5 (SD 4.9) years of follow-up. Incidence of HF was greater among those with high, as compared to those with low or moderate trait anger, with higher incidence observed for men as compared to women. The relative hazard of incident HF was modestly high among those with high trait anger, as compared to those with low or moderate trait anger (age-adjusted HR for men=1.44 (95% CI 1.23, 1.69). Adjustment for comorbidities and depressive symptoms attenuated the estimated age-adjusted relative hazard in men to 1.26 (95% CI 1.00, 1.60). Conclusion Assessment of anger proneness may be necessary in successful prevention and clinical management of heart failure, especially in men. PMID:25284390

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

    PubMed Central

    Granata, Kevin P.; Lockhart, Thurmon E.

    2010-01-01

    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 three speeds. From this data, we estimated the vector from the center-of-mass to the center of pressure at each foot-strike. Dynamic stability of walking was computed by methods of Poincare analyses of these vectors. Results revealed that the fall-prone group demonstrated poorer dynamic stability than the healthy elderly and young adult groups. Stability was not influenced by walking velocity, indicating that group differences in walking speed could not fully explain the differences in stability. This pilot study supports the need for future investigations using larger population samples to study fall-prone individuals using nonlinear dynamic analyses of movement kinematics. PMID:17686633

  19. Lumbar Lordosis of Spinal Stenosis Patients during Intraoperative Prone Positioning

    PubMed Central

    Lee, Su-Keon; Song, Kyung-Sub; Park, Byung-Moon; Lim, Sang-Youn; Jang, Geun; Lee, Beom-Seok; Moon, Seong-Hwan; Lee, Hwan-Mo

    2016-01-01

    Background To evaluate the effect of spondylolisthesis on lumbar lordosis on the OSI (Jackson; Orthopaedic Systems Inc.) frame. Restoration of lumbar lordosis is important for maintaining sagittal balance. Physiologic lumbar lordosis has to be gained by intraoperative prone positioning with a hip extension and posterior instrumentation technique. There are some debates about changing lumbar lordosis on the OSI frame after an intraoperative prone position. We evaluated the effect of spondylolisthesis on lumbar lordosis after an intraoperative prone position. Methods Sixty-seven patients, who underwent spinal fusion at the Department of Orthopaedic Surgery of Gwangmyeong Sungae Hospital between May 2007 and February 2012, were included in this study. The study compared lumbar lordosis on preoperative upright, intraoperative prone and postoperative upright lateral X-rays between the simple stenosis (SS) group and spondylolisthesis group. The average age of patients was 67.86 years old. The average preoperative lordosis was 43.5° (± 14.9°), average intraoperative lordosis was 48.8° (± 13.2°), average postoperative lordosis was 46.5° (± 16.1°) and the average change on the frame was 5.3° (± 10.6°). Results Among all patients, 24 patients were diagnosed with simple spinal stenosis, 43 patients with spondylolisthesis (29 degenerative spondylolisthesis and 14 isthmic spondylolisthesis). Between the SS group and spondylolisthesis group, preoperative lordosis, intraoperative lordosis and postoperative lordosis were significantly larger in the spondylolisthesis group. The ratio of patients with increased lordosis on the OSI frame compared to preoperative lordosis was significantly higher in the spondylolisthesis group. The risk of increased lordosis on frame was significantly higher in the spondylolisthesis group (odds ratio, 3.325; 95% confidence interval, 1.101 to 10.039; p = 0.033). Conclusions Intraoperative lumbar lordosis on the OSI frame with a prone position was larger in the SS patients than the spondylolisthesis patients, which also produced a larger postoperative lordosis angle after posterior spinal fusion surgery. An increase in lumbar lordosis on the OSI frame should be considered during posterior spinal fusion surgery, especially in spondylolisthesis patients. PMID:26929801

  20. Use of Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA Surveys

    PubMed Central

    Doi, Hideyuki; Uchii, Kimiko; Takahara, Teruhiko; Matsuhashi, Saeko; Yamanaka, Hiroki; Minamoto, Toshifumi

    2015-01-01

    An environmental DNA (eDNA) analysis method has been recently developed to estimate the distribution of aquatic animals by quantifying the number of target DNA copies with quantitative real-time PCR (qPCR). A new quantitative PCR technology, droplet digital PCR (ddPCR), partitions PCR reactions into thousands of droplets and detects the amplification in each droplet, thereby allowing direct quantification of target DNA. We evaluated the quantification accuracy of qPCR and ddPCR to estimate species abundance and biomass by using eDNA in mesocosm experiments involving different numbers of common carp. We found that ddPCR quantified the concentration of carp eDNA along with carp abundance and biomass more accurately than qPCR, especially at low eDNA concentrations. In addition, errors in the analysis were smaller in ddPCR than in qPCR. Thus, ddPCR is better suited to measure eDNA concentration in water, and it provides more accurate results for the abundance and biomass of the target species than qPCR. We also found that the relationship between carp abundance and eDNA concentration was stronger than that between biomass and eDNA by using both ddPCR and qPCR; this suggests that abundance can be better estimated by the analysis of eDNA for species with fewer variations in body mass. PMID:25799582

  1. An enriched environment improves cognitive performance in mice from the senescence-accelerated prone mouse 8 strain

    PubMed Central

    Yuan, Zhenyun; Wang, Mingwei; Yan, Baoyong; Gu, Ping; Jiang, Xiangming; Yang, Xiufen; Cui, Dongsheng

    2012-01-01

    In this study, we examined 3-month-old female mice from the senescence-accelerated prone mouse 8 strain and age-matched homologous normal aging female mice from the senescence accelerated- resistant mouse 1 strain. Mice from each strain were housed in an enriched environment (including a platform, running wheels, tunnel, and some toys) or a standard environment for 3 months. The mice housed in the enriched environment exhibited shorter escape latencies and a greater percentage of time in the target quadrant in the Morris water maze test, and they exhibited reduced errors and longer latencies in step-down avoidance experiments compared with mice housed in the standard environment. Correspondently, brain-derived neurotrophic factor mRNA and protein expression in the hippocampus was significantly higher in mice housed in the enriched environment compared with those housed in the standard environment, and the level of hippocampal brain-derived neurotrophic factor protein was positively correlated with the learning and memory abilities of mice from the senescence-accelerated prone mouse 8 strain. These results suggest that an enriched environment improved cognitive performance in mice form the senescence-accelerated prone mouse 8 strain by increasing brain-derived neurotrophic factor expression in the hippocampus. PMID:25624804

  2. 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...

  3. 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...

  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. 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

  6. Apta-PCR.

    PubMed

    Pinto, Alessandro; Polo, Pedro Nadal; Rubio, Miriam Jauest; Svobodova, Marketa; Lerga, Teresa Mairal; O'Sullivan, Ciara K

    2016-01-01

    Real-time Apta-PCR is a methodology that can be used for a wide variety of applications ranging from food quality control to clinical diagnostics. This method takes advantage of the combination of the sensitivity of nucleic acid amplification with the selectivity of aptamers. Ultra-low detection of target analyte can potentially be achieved, or, improved detection limits can be achieved with aptamers of low-medium affinity. Herein, we describe a generic methodology coined real-time Apta-PCR, using a model target (β-conglutin) and a competitive format, which can be adapted for the detection of any target which an aptamer has been selected for. PMID:26552825

  7. Prone Breast Intensity Modulated Radiation Therapy: 5-Year Results

    SciTech Connect

    Osa, Etin-Osa O.; DeWyngaert, Keith; Roses, Daniel; Speyer, James; Guth, Amber; Axelrod, Deborah; Fenton Kerimian, Maria; Goldberg, Judith D.; Formenti, Silvia C.

    2014-07-15

    Purpose: To report the 5-year results of a technique of prone breast radiation therapy delivered by a regimen of accelerated intensity modulated radiation therapy with a concurrent boost to the tumor bed. Methods and Materials: Between 2003 and 2006, 404 patients with stage I-II breast cancer were prospectively enrolled into 2 consecutive protocols, institutional trials 03-30 and 05-181, that used the same regimen of 40.5 Gy/15 fractions delivered to the index breast over 3 weeks, with a concomitant daily boost to the tumor bed of 0.5 Gy (total dose 48 Gy). All patients were treated after segmental mastectomy and had negative margins and nodal assessment. Patients were set up prone: only if lung or heart volumes were in the field was a supine setup attempted and chosen if found to better spare these organs. Results: Ninety-two percent of patients were treated prone, 8% supine. Seventy-two percent had stage I, 28% stage II invasive breast cancer. In-field lung volume ranged from 0 to 228.27 cm{sup 3}, mean 19.65 cm{sup 3}. In-field heart volume for left breast cancer patients ranged from 0 to 21.24 cm{sup 3}, mean 1.59 cm{sup 3}. There was no heart in the field for right breast cancer patients. At a median follow-up of 5 years, the 5-year cumulative incidence of isolated ipsilateral breast tumor recurrence was 0.82% (95% confidence interval [CI] 0.65%-1.04%). The 5-year cumulative incidence of regional recurrence was 0.53% (95% CI 0.41%-0.69%), and the 5-year overall cumulative death rate was 1.28% (95% CI 0.48%-3.38%). Eighty-two percent (95% CI 77%-85%) of patients judged their final cosmetic result as excellent/good. Conclusions: Prone accelerated intensity modulated radiation therapy with a concomitant boost results in excellent local control and optimal sparing of heart and lung, with good cosmesis. Radiation Therapy Oncology Group protocol 1005, a phase 3, multi-institutional, randomized trial is ongoing and is evaluating the equivalence of a similar dose and fractionation approach to standard 6-week radiation therapy with a sequential boost.

  8. Microseismic study of an outburst-prone coal seam

    SciTech Connect

    MacDonald, P.; Brown, K.M.

    1984-01-01

    Outbursts of coal and gas present a danger to life and can severely inhibit production. This paper describes the development of a microseismic monitoring technique as an aid to outburst prediction and its application at an anthracite colliery in the UK. Results of initial laboratory and field trials are presented and show that the method is feasible. A review is made of previous work in the field of microseismic monitoring at outburst-prone mines and indicates the varied degree of success hitherto achieved with this technique.

  9. Boredom proneness and emotion regulation predict emotional eating.

    PubMed

    Crockett, Amanda C; Myhre, Samantha K; Rokke, Paul D

    2015-05-01

    Emotional eating is considered a risk factor for eating disorders and an important contributor to obesity and its associated health problems. It has been suggested that boredom may be an important contributor to overeating, but has received relatively little attention. A sample of 552 college students was surveyed. Linear regression analyses found that proneness to boredom and difficulties in emotion regulation simultaneously predicted inappropriate eating behavior, including eating in response to boredom, other negative emotions, and external cues. The unique contributions of these variables to emotional eating were discussed. These findings help to further identify which individuals could be at risk for emotional eating and potentially for unhealthy weight gain. PMID:25903253

  10. Field error lottery

    SciTech Connect

    Elliott, C.J.; McVey, B. ); Quimby, D.C. )

    1990-01-01

    The level of field errors in an FEL is an important determinant of its performance. We have computed 3D performance of a large laser subsystem subjected to field errors of various types. These calculations have been guided by simple models such as SWOOP. The technique of choice is utilization of the FELEX free electron laser code that now possesses extensive engineering capabilities. Modeling includes the ability to establish tolerances of various types: fast and slow scale field bowing, field error level, beam position monitor error level, gap errors, defocusing errors, energy slew, displacement and pointing errors. Many effects of these errors on relative gain and relative power extraction are displayed and are the essential elements of determining an error budget. The random errors also depend on the particular random number seed used in the calculation. The simultaneous display of the performance versus error level of cases with multiple seeds illustrates the variations attributable to stochasticity of this model. All these errors are evaluated numerically for comprehensive engineering of the system. In particular, gap errors are found to place requirements beyond mechanical tolerances of {plus minus}25{mu}m, and amelioration of these may occur by a procedure utilizing direct measurement of the magnetic fields at assembly time. 4 refs., 12 figs.

  11. Field error lottery

    NASA Astrophysics Data System (ADS)

    James Elliott, C.; McVey, Brian D.; Quimby, David C.

    1991-07-01

    The level of field errors in a free electron laser (FEL) is an important determinant of its performance. We have computed 3D performance of a large laser subsystem subjected to field errors of various types. These calculations have been guided by simple models such as SWOOP. The technique of choice is use of the FELEX free electron laser code that now possesses extensive engineering capabilities. Modeling includes the ability to establish tolerances of various types: fast and slow scale field bowing, field error level, beam position monitor error level, gap errors, defocusing errors, energy slew, displacement and pointing errors. Many effects of these errors on relative gain and relative power extraction are displayed and are the essential elements of determining an error budget. The random errors also depend on the particular random number seed used in the calculation. The simultaneous display of the performance versus error level of cases with multiple seeds illustrates the variations attributable to stochasticity of this model. All these errors are evaluated numerically for comprehensive engineering of the system. In particular, gap errors are found to place requirements beyond convenient mechanical tolerances of ± 25 μm, and amelioration of these may occur by a procedure using direct measurement of the magnetic fields at assembly time.

  12. Field error lottery

    NASA Astrophysics Data System (ADS)

    Elliott, C. James; McVey, Brian D.; Quimby, David C.

    1990-11-01

    The level of field errors in an FEL is an important determinant of its performance. We have computed 3D performance of a large laser subsystem subjected to field errors of various types. These calculations have been guided by simple models such as SWOOP. The technique of choice is utilization of the FELEX free electron laser code that now possesses extensive engineering capabilities. Modeling includes the ability to establish tolerances of various types: fast and slow scale field bowing, field error level, beam position monitor error level, gap errors, defocusing errors, energy slew, displacement, and pointing errors. Many effects of these errors on relative gain and relative power extraction are displayed and are the essential elements of determining an error budget. The random errors also depend on the particular random number seed used in the calculation. The simultaneous display of the performance versus error level of cases with multiple seeds illustrates the variations attributable to stochasticity of this model. All these errors are evaluated numerically for comprehensive engineering of the system. In particular, gap errors are found to place requirements beyond mechanical tolerances of (plus minus)25(mu)m, and amelioration of these may occur by a procedure utilizing direct measurement of the magnetic fields at assembly time.

  13. MAMMALIAN DNA IN PCR REAGENTS

    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 t...

  14. Predicting Fault-Prone Modules: A Comparative Study

    NASA Astrophysics Data System (ADS)

    Jia, Hao; Shu, Fengdi; Yang, Ye; Wang, Qing

    Offshore and outsourced software development is a rapidly increasing trend in global software business environment. Predicting fault-prone modules in outsourced software product may allow both parties to establish mutually satisfactory, cost-effective testing strategies and product acceptance criteria, especially in iterative transitions. In this paper, based on industrial software releases data, we conduct an empirical study to compare ten classifiers over eight sets of code attributes, and provide recommendations to aid both the client and vendor to assess the products quality through defect prediction. Overall, a generally high accuracy is observed, which confirms the usefulness of the metric-based classification. Furthermore, two classification techniques, Random Forest and Bayesian Belief Network, outperform the others in terms of predictive accuracy; in more detail, the former is the most cost-effective and the latter is of the lowest fault-prone module escaping rate. Our study also concludes that code metrics including size, traditional complexity, and object-oriented complexity perform fairly well.

  15. Coping Mechanisms for Crop Plants in Drought-prone Environments

    PubMed Central

    Neumann, Peter M.

    2008-01-01

    Background Drought is a major limitation to plant productivity. Various options are available for increasing water availability and sustaining growth of crop plants in drought-prone environments. Scope After a general introduction to the problems of water availability, this review focuses on a critical evaluation of recent progress in unravelling mechanisms for modifying plant growth responses to drought. Conclusions Investigations of key regulatory mechanisms integrating plant growth responses to water deficits at the whole-organism, cellular and genomic levels continue to provide novel and exiting research findings. For example, recent reports contradict the widespread conception that root-derived abscisic acid is necessarily involved in signalling for stomatal and shoot-growth responses to soil water deficits. The findings bring into question the theoretical basis for alternate-side root-irrigation techniques. Similarly, recent reports indicate that increased ABA production or increased aquaporin expression did not lead to improved drought resistance. Other reports have concerned key genes and proteins involved in regulation of flowering (FT), vegetative growth (DELLA), leaf senescence (IPT) and desiccation tolerance (LEA). Introgression of such genes, with suitable promoters, can greatly impact on whole-plant responses to drought. Further developments could facilitate the introduction by breeders of new crop varieties with growth physiologies tailored to improved field performance under drought. Parallel efforts to encourage the introduction of supplementary irrigation with water made available by improved conservation measures and by sea- or brackish-water desalination, will probably provide comprehensive solutions to coping with drought-prone environments. PMID:18252764

  16. Inborn errors of metabolism

    MedlinePlus

    Metabolism - inborn errors of ... Bodamer OA. Approach to inborn errors of metabolism. In: Goldman L, Schafer AI, eds. Goldman's Cecil Medicine . 25th ed. Philadelphia, PA: Elsevier Saunders; 2015:chap 205. Rezvani I, Rezvani G. An ...

  17. 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.

    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.

  18. Systematic errors in strong lens modeling

    NASA Astrophysics Data System (ADS)

    Johnson, Traci Lin; Sharon, Keren; Bayliss, Matthew B.

    2015-08-01

    The lensing community has made great strides in quantifying the statistical errors associated with strong lens modeling. However, we are just now beginning to understand the systematic errors. Quantifying these errors is pertinent to Frontier Fields science, as number counts and luminosity functions are highly sensitive to the value of the magnifications of background sources across the entire field of view. We are aware that models can be very different when modelers change their assumptions about the parameterization of the lensing potential (i.e., parametric vs. non-parametric models). However, models built while utilizing a single methodology can lead to inconsistent outcomes for different quantities, distributions, and qualities of redshift information regarding the multiple images used as constraints in the lens model. We investigate how varying the number of multiple image constraints and available redshift information of those constraints (ex., spectroscopic vs. photometric vs. no redshift) can influence the outputs of our parametric strong lens models, specifically, the mass distribution and magnifications of background sources. We make use of the simulated clusters by M. Meneghetti et al. and the first two Frontier Fields clusters, which have a high number of multiply imaged galaxies with spectroscopically-measured redshifts (or input redshifts, in the case of simulated clusters). This work will not only inform upon Frontier Field science, but also for work on the growing collection of strong lensing galaxy clusters, most of which are less massive and are capable of lensing a handful of galaxies, and are more prone to these systematic errors.

  19. 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.

  20. Improved temporal error concealment algorithm for H.264

    NASA Astrophysics Data System (ADS)

    Hou, Yan-yan

    2013-03-01

    The compressed video stream transmission is a challenging task due to loss-prone, time-varying and limitation bandwidth characteristics. In this paper, improved temporal error concealment based on boundary matching algorithm is presented, we use an optimized mode selection for the lost macroblock based on candidate motion vector set, and adopt an improved BMA to estimate lost macroblock motion vectors for H.264 coded video. Experimental results show that improved temporal error concealment algorithm gets better video quality over a large set of operating conditions.

  1. Programming Errors in APL.

    ERIC Educational Resources Information Center

    Kearsley, Greg P.

    This paper discusses and provides some preliminary data on errors in APL programming. Data were obtained by analyzing listings of 148 complete and partial APL sessions collected from student terminal rooms at the University of Alberta. Frequencies of errors for the various error messages are tabulated. The data, however, are limited because they…

  2. How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments

    PubMed Central

    Svec, David; Tichopad, Ales; Novosadova, Vendula; Pfaffl, Michael W.; Kubista, Mikael

    2015-01-01

    We have examined the imprecision in the estimation of PCR efficiency by means of standard curves based on strategic experimental design with large number of technical replicates. In particular, how robust this estimation is in terms of a commonly varying factors: the instrument used, the number of technical replicates performed and the effect of the volume transferred throughout the dilution series. We used six different qPCR instruments, we performed 1–16 qPCR replicates per concentration and we tested 2–10 μl volume of analyte transferred, respectively. We find that the estimated PCR efficiency varies significantly across different instruments. Using a Monte Carlo approach, we find the uncertainty in the PCR efficiency estimation may be as large as 42.5% (95% CI) if standard curve with only one qPCR replicate is used in 16 different plates. Based on our investigation we propose recommendations for the precise estimation of PCR efficiency: (1) one robust standard curve with at least 3–4 qPCR replicates at each concentration shall be generated, (2) the efficiency is instrument dependent, but reproducibly stable on one platform, and (3) using a larger volume when constructing serial dilution series reduces sampling error and enables calibration across a wider dynamic range. PMID:27077029

  3. How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments.

    PubMed

    Svec, David; Tichopad, Ales; Novosadova, Vendula; Pfaffl, Michael W; Kubista, Mikael

    2015-03-01

    We have examined the imprecision in the estimation of PCR efficiency by means of standard curves based on strategic experimental design with large number of technical replicates. In particular, how robust this estimation is in terms of a commonly varying factors: the instrument used, the number of technical replicates performed and the effect of the volume transferred throughout the dilution series. We used six different qPCR instruments, we performed 1-16 qPCR replicates per concentration and we tested 2-10 μl volume of analyte transferred, respectively. We find that the estimated PCR efficiency varies significantly across different instruments. Using a Monte Carlo approach, we find the uncertainty in the PCR efficiency estimation may be as large as 42.5% (95% CI) if standard curve with only one qPCR replicate is used in 16 different plates. Based on our investigation we propose recommendations for the precise estimation of PCR efficiency: (1) one robust standard curve with at least 3-4 qPCR replicates at each concentration shall be generated, (2) the efficiency is instrument dependent, but reproducibly stable on one platform, and (3) using a larger volume when constructing serial dilution series reduces sampling error and enables calibration across a wider dynamic range. PMID:27077029

  4. Simulation of between Repeat Variability in Real Time PCR Reactions

    PubMed Central

    Lievens, Antoon; Van Aelst, Stefan; Van den Bulcke, Marc; Goetghebeur, Els

    2012-01-01

    While many decisions rely on real time quantitative PCR (qPCR) analysis few attempts have hitherto been made to quantify bounds of precision accounting for the various sources of variation involved in the measurement process. Besides influences of more obvious factors such as camera noise and pipetting variation, changing efficiencies within and between reactions affect PCR results to a degree which is not fully recognized. Here, we develop a statistical framework that models measurement error and other sources of variation as they contribute to fluorescence observations during the amplification process and to derived parameter estimates. Evaluation of reproducibility is then based on simulations capable of generating realistic variation patterns. To this end, we start from a relatively simple statistical model for the evolution of efficiency in a single PCR reaction and introduce additional error components, one at a time, to arrive at stochastic data generation capable of simulating the variation patterns witnessed in repeated reactions (technical repeats). Most of the variation in values was adequately captured by the statistical model in terms of foreseen components. To recreate the dispersion of the repeats' plateau levels while keeping the other aspects of the PCR curves within realistic bounds, additional sources of reagent consumption (side reactions) enter into the model. Once an adequate data generating model is available, simulations can serve to evaluate various aspects of PCR under the assumptions of the model and beyond. PMID:23189123

  5. 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

  6. 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.

  7. 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.

  8. Sources of PCR-induced distortions in high-throughput sequencing data sets.

    PubMed

    Kebschull, Justus M; Zador, Anthony M

    2015-12-01

    PCR permits the exponential and sequence-specific amplification of DNA, even from minute starting quantities. PCR is a fundamental step in preparing DNA samples for high-throughput sequencing. However, there are errors associated with PCR-mediated amplification. Here we examine the effects of four important sources of error-bias, stochasticity, template switches and polymerase errors-on sequence representation in low-input next-generation sequencing libraries. We designed a pool of diverse PCR amplicons with a defined structure, and then used Illumina sequencing to search for signatures of each process. We further developed quantitative models for each process, and compared predictions of these models to our experimental data. We find that PCR stochasticity is the major force skewing sequence representation after amplification of a pool of unique DNA amplicons. Polymerase errors become very common in later cycles of PCR but have little impact on the overall sequence distribution as they are confined to small copy numbers. PCR template switches are rare and confined to low copy numbers. Our results provide a theoretical basis for removing distortions from high-throughput sequencing data. In addition, our findings on PCR stochasticity will have particular relevance to quantification of results from single cell sequencing, in which sequences are represented by only one or a few molecules. PMID:26187991

  9. 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.).

  10. Software error detection

    NASA Technical Reports Server (NTRS)

    Buechler, W.; Tucker, A. G.

    1981-01-01

    Several methods were employed to detect both the occurrence and source of errors in the operational software of the AN/SLQ-32. A large embedded real time electronic warfare command and control system for the ROLM 1606 computer are presented. The ROLM computer provides information about invalid addressing, improper use of privileged instructions, stack overflows, and unimplemented instructions. Additionally, software techniques were developed to detect invalid jumps, indices out of range, infinte loops, stack underflows, and field size errors. Finally, data are saved to provide information about the status of the system when an error is detected. This information includes I/O buffers, interrupt counts, stack contents, and recently passed locations. The various errors detected, techniques to assist in debugging problems, and segment simulation on a nontarget computer are discussed. These error detection techniques were a major factor in the success of finding the primary cause of error in 98% of over 500 system dumps.

  11. 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.

  12. Model Error Budgets

    NASA Technical Reports Server (NTRS)

    Briggs, Hugh C.

    2008-01-01

    An error budget is a commonly used tool in design of complex aerospace systems. It represents system performance requirements in terms of allowable errors and flows these down through a hierarchical structure to lower assemblies and components. The requirements may simply be 'allocated' based upon heuristics or experience, or they may be designed through use of physics-based models. This paper presents a basis for developing an error budget for models of the system, as opposed to the system itself. The need for model error budgets arises when system models are a principle design agent as is increasingly more common for poorly testable high performance space systems.

  13. 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

  14. Structural Dynamics as a Contributor to Error-prone Replication by an RNA-dependent RNA Polymerase*

    PubMed Central

    Moustafa, Ibrahim M.; Korboukh, Victoria K.; Arnold, Jamie J.; Smidansky, Eric D.; Marcotte, Laura L.; Gohara, David W.; Yang, Xiaorong; Sánchez-Farrán, María Antonieta; Filman, David; Maranas, Janna K.; Boehr, David D.; Hogle, James M.; Colina, Coray M.; Cameron, Craig E.

    2014-01-01

    RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity. PMID:25378410

  15. In vitro characterization of pol I*, an SOS inducible, error-prone from of Escherichia coli DNA polymerase I

    SciTech Connect

    Hodes, C.S.

    1987-01-01

    E. coli strains carrying mutations in the SOS regulon were screened for the presence of pol I*. Use of pol I* in assays of polymerase fidelity and selectivity has been limited by the low concentration and purity of the enzyme. Therefore, attempts were made to further concentrate and purify pol I*. The template selectivity of pol I* was compared to that of pol I using three models of damaged DNA. UV-irradiated M13 DNA was used in a two-stage termination reaction to determine if pol I* could bypass putative pyrimidine dimers to a greater extent than pol I. In the gel system no reproducibly significant bypass could be detected by either pol I* or pol I. However, the degree of replication by pol I* utilizing UV-irradiated M13 DNA template, was up to 5-fold greater than for pol I. OsO{sub 4}-oxidized M13 DNA was used as a model substrate for oxidative DNA damage. Opposite this substrate incorporation by pol I* is less inhibited than incorporation by pol I. However, in a test of nucleotide selectivity neither pol I*, pol I, nor terminal deoxyribonucleotidyl transferase will incorporate ({alpha}-{sup 32}P)thymine glycol deoxyribonucleotide. The activity of pol I* was compared to that of pol I on the synthetic templates, poly (dA) and poly((dA)+2-AP). Pol I* misincorporated both dCMP and dGMP to a greater extent than pol I when utilizing templates containing 2-aminopurine deoxyribonucleotide.

  16. The Discovery of Error-prone DNA Polymerase V and Its Unique Regulation by RecA and ATP

    PubMed Central

    Goodman, Myron F.

    2014-01-01

    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

  17. Structural dynamics as a contributor to error-prone replication by an RNA-dependent RNA polymerase.

    PubMed

    Moustafa, Ibrahim M; Korboukh, Victoria K; Arnold, Jamie J; Smidansky, Eric D; Marcotte, Laura L; Gohara, David W; Yang, Xiaorong; Sánchez-Farrán, María Antonieta; Filman, David; Maranas, Janna K; Boehr, David D; Hogle, James M; Colina, Coray M; Cameron, Craig E

    2014-12-26

    RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity. PMID:25378410

  18. TRIP13 promotes error-prone nonhomologous end joining and induces chemoresistance in head and neck cancer

    PubMed Central

    Banerjee, Rajat; Russo, Nickole; Liu, Min; Basrur, Venkatesha; Bellile, Emily; Palanisamy, Nallasivam; Scanlon, Christina S.; van Tubergen, Elizabeth; Inglehart, Ronald C.; Metwally, Tarek; Mani, Ram-Shankar; Yocum, Anastasia; Nyati, Mukesh K.; Castilho, Rogerio M.; Varambally, Sooryanarayana; Chinnaiyan, Arul M.

    2014-01-01

    Head and neck cancer (SCCHN) is a common, aggressive, treatment-resistant cancer with a high recurrence rate and mortality, but the mechanism of treatment-resistance remains unclear. Here we describe a mechanism where the AAA-ATPase TRIP13 promotes treatment-resistance. Overexpression of TRIP13 in non-malignant cells results in malignant transformation. High expression of TRIP13 in SCCHN leads to aggressive, treatment-resistant tumors and enhanced repair of DNA damage. Using mass spectrometry, we identify DNA-PKcs complex proteins that mediate non homologous end joining (NHEJ), as TRIP13 binding partners. Using repair-deficient reporter systems, we show that TRIP13 promotes NHEJ, even when homologous recombination is intact. Importantly, overexpression of TRIP13 sensitizes SCCHN to an inhibitor of DNA-PKcs. Thus, this study defines a new mechanism of treatment resistance in SCCHN and underscores the importance of targeting NHEJ to overcome treatment failure in SCCHN and potentially in other cancers that overexpress TRIP13. PMID:25078033

  19. Procrastination and suicide proneness: A moderated-mediation model for cognitive schemas and gender.

    PubMed

    Klibert, Jeffrey; LeLeux-LaBarge, Kayla; Tarantino, Nicholas; Yancey, Thresa; Lamis, Dorian A

    2016-07-01

    This study examined the direct and indirect paths between procrastination and suicide proneness while considering gender differences. Participants included 547 undergraduates from a southeastern university. Procrastination was positively related to suicide proneness for both genders, although this relation was stronger for women. Moderated-mediation analyses with bootstrapping highlighted insufficient self-control schemas as a mediator in the relation between procrastination and suicide proneness. However, indirect pathways did not vary by gender. Results represent an extension of the Procrastination-Health Model by highlighting the contribution of cognitive factors in explaining the relation between procrastination and suicide proneness. PMID:26766597

  20. Digital droplet PCR on disk.

    PubMed

    Schuler, Friedrich; Trotter, Martin; Geltman, Marcel; Schwemmer, Frank; Wadle, Simon; Domínguez-Garrido, Elena; López, María; Cervera-Acedo, Cristina; Santibáñez, Paula; von Stetten, Felix; Zengerle, Roland; Paust, Nils

    2016-01-01

    Existing systems for digital droplet PCR (ddPCR) either suffer from low integration or are difficult to introduce to mass fabrication. Here we present an integrated system that is compatible to mass fabrication and combines emulsification, PCR, and fluorescence readout in a single chamber within a disposable cartridge (disk). Droplets are generated by injecting the sample into fluorinated oil via centrifugal step emulsification. The resulting emulsion is aligned in the PCR and readout zone by capillary action. During thermocycling, gas bubbles generated by degassing are removed by capillary driven transport through tapered regions in the PCR chamber. Thereby, the positioning of the emulsion within the readout zone of the PCR chamber is ensured at any time and no bubbles are present during readout. Manual handling of the disk solely requires pipetting of oil and PCR mix into the inlet structures, placing the disk into the thermocycler and subsequently into a microarray scanner. The functionality of the ddPCR process chain is demonstrated by quantitative detection of the cystic fibrosis causing mutation p.Phe508del, which is of interest for non-invasive prenatal testing (NIPT). The mutation was detected in a concentration range spanning four orders of magnitude. We envision that this work will lay the base for the development of highly integrated sample-to-digital-answer PCR systems that can be employed in routine clinical diagnosis. PMID:26610263

  1. Investigation on reference value error in multivariate calibration

    NASA Astrophysics Data System (ADS)

    Li, Qingbo; Zhang, Guangjun; Li, Xiang; Xu, Kexin; Wang, Yan

    2008-10-01

    Near infrared spectral analysis is a kind of indirect measuring technology, that is, calibration model is established by using sample spectra and the reference value of the interested concentration, and then predict the interested concentration of the unknown sample by using its spectrum and calibration model. Generally, the quality of calibration model is evaluated by the deviation between the predicted value and the reference value of the measured concentration. Reference value measurement error of the calibration set samples and model error are the main error source of multivariate calibration. When there was reference value measurement error, the regression model would cause great prediction deviation. However in practical application, apparent prediction error caused by reference value measurement error is always considered as the faultiness of calibration model. So it is falsely regarded that the prediction error of multivariate calibration model would be greater than that of reference method. In this paper, effect of reference value measurement error on prediction error was analyzed, and the relationship among apparent prediction error, actual prediction error and reference value measurement error was discussed. At the same time, the applicability and rationality of a computation formula was also discussed, which could estimate the true prediction error in a more precise way. It was proved that the prediction accuracy of an excellent calibration model was greater than that of the reference method by analyzing the reference value measurement error. An experiment of glucose aqueous solution samples was given in this paper. In this example, the effect of reference value measurement error on the prediction error of multivariate calibration model was investigated, and the estimating formula of the corrected prediction error was evaluated. The conclusion could be universally applied to not only multivariate calibration MLR, PCR, PLS and so on, but also in much more complex samples.

  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. 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

  4. Individual differences in error tolerance in humans: Neurophysiological evidences.

    PubMed

    Padrao, Gonçalo; Mallorquí, Aida; Cucurell, David; Rodriguez-Fornells, Antoni

    2015-12-01

    When interacting in error-prone environments, humans display different tolerances to changing their decisions when faced with erroneous feedback information. Here, we investigated whether these individual differences in error tolerance (ET) were reflected in neurophysiological mechanisms indexing specific motivational states related to feedback monitoring. To explore differences in ET, we examined the performance of 80 participants in a probabilistic reversal-learning task. We then compared event-related brain responses (ERPs) of two extreme groups of participants (High ET and Low ET), which showed radical differences in their propensity to maintain newly learned rules after receiving spurious negative feedback. We observed that High ET participants showed reduced anticipatory activity prior to the presentation of incoming feedback, informing them of the correctness of their performance. This was evidenced by measuring the amplitude of the stimulus-preceding negativity (SPN), an ERP component indexing attention and motivational engagement of incoming informative feedback. Postfeedback processing ERP components (the so-called Feedback-Related Negativity and the P300) also showed reduced amplitude in this group (High ET). The general decreased responsiveness of the High ET group to external feedback suggests a higher proneness to favor internal(rule)-based strategies, reducing attention to external cues and the consequent impact of negative evaluations on decision making. We believe that the present findings support the existence of specific cognitive and motivational processes underlying individual differences on error-tolerance among humans, contributing to the ongoing research focused on understanding the mental processes behind human fallibility in error-prone scenarios. PMID:26018781

  5. Dry-reagent-based PCR as a novel tool for the rapid detection of Clostridium spp.

    PubMed

    Seise, Barbara; Pollok, Sibyll; Seyboldt, Christian; Weber, Karina

    2013-10-01

    Improved conventional PCR techniques are required for the rapid on-site detection of human and animal diseases. In this context, a PCR method using dry-stored reagents intended for the detection of Clostridium spp. is presented. Basic PCR reagents (BSA, PCR buffer, MgCl₂ and primers), which were dried on polyolefin matrices, showed stability at ambient temperatures for up to 10 months without any loss of functionality. An outstanding advantage of our amelioration is the elimination of PCR process errors caused by the improper storage and handling of liquid reagents. Moreover, our PCR-based amplification can be performed in less than 30 min, saving time compared with conventional detection methods. Thus, dry-reagent-based PCR is implementable in a suitcase-like modular device for the rapid on-site detection of microbial pathogens such as blackleg of ruminants caused by Clostridium chauvoei. PMID:23904074

  6. Disgust proneness and associated neural substrates in obesity.

    PubMed

    Watkins, Tristan J; Di Iorio, Christina R; Olatunji, Bunmi O; Benningfield, Margaret M; Blackford, Jennifer U; Dietrich, Mary S; Bhatia, Monisha; Theiss, Justin D; Salomon, Ronald M; Niswender, Kevin; Cowan, Ronald L

    2016-03-01

    Defects in experiencing disgust may contribute to obesity by allowing for the overconsumption of food. However, the relationship of disgust proneness and its associated neural locus has yet to be explored in the context of obesity. Thirty-three participants (17 obese, 16 lean) completed the Disgust Propensity and Sensitivity Scale-Revised and a functional magnetic resonance imaging paradigm where images from 4 categories (food, contaminates, contaminated food or fixation) were randomly presented. Independent two-sample t-tests revealed significantly lower levels of Disgust Sensitivity for the obese group (mean score = 14.7) compared with the lean group (mean score = 17.6, P = 0.026). The obese group had less activation in the right insula than the lean group when viewing contaminated food images. Multiple regression with interaction analysis revealed one left insula region where the association of Disgust Sensitivity scores with activation differed by group when viewing contaminated food images. These interaction effects were driven by the negative correlation of Disgust Sensitivity scores with beta values extracted from the left insula in the obese group (r = -0.59) compared with a positive correlation in the lean group (r = 0.65). Given these body mass index-dependent differences in Disgust Sensitivity and neural responsiveness to disgusting food images, it is likely that altered Disgust Sensitivity may contribute to obesity. PMID:26454815

  7. Epidermal injury promotes nephritis flare in lupus-prone mice.

    PubMed

    Clark, Kaitlyn L; Reed, Tamra J; Wolf, Sonya J; Lowe, Lori; Hodgin, Jeffrey B; Kahlenberg, J Michelle

    2015-12-01

    Systemic lupus erythematosus is clinically characterized by episodes of flare and remission. In patients, cutaneous exposure to ultraviolet light has been proposed as a flare trigger. However, induction of flare secondary to cutaneous exposure has been difficult to emulate in many murine lupus models. Here, we describe a system in which epidermal injury is able to trigger the development of a lupus nephritis flare in New Zealand Mixed (NZM) 2328 mice. 20-week old NZM2328 female mice underwent removal of the stratum corneum via duct tape, which resulted in rapid onset of proteinuria and death when compared to sham-stripped littermate control NZM2328 mice. This was coupled with a drop in serum C3 concentrations and dsDNA antibody levels and enhanced immune complex deposition in the glomeruli. Recruitment of CD11b(+)CD11c(+)F4/80(high) macrophages and CD11b(+)CD11c(+)F4/80(low) dendritic cells was noted prior to the onset of proteinuria in injured mice. Transcriptional changes within the kidney suggest a burst of type I IFN-mediated and inflammatory signaling which is followed by upregulation of CXCL13 following epidermal injury. Thus, we propose that tape stripping of lupus-prone NZM2328 mice is a novel model of lupus flare induction that will allow for the study of the role of cutaneous inflammation in lupus development and how crosstalk between dermal and systemic immune systems can lead to lupus flare. PMID:26305061

  8. Male predominance in ketosis-prone diabetes mellitus

    PubMed Central

    WANG, XIAOHAO; TAN, HUIWEN

    2015-01-01

    The incidence of ketosis-prone diabetes mellitus (KPDM) shows a higher prevalence in men. The clear male predominance of this syndrome and its underlying pathogenesis mechanisms are unclear. KPDM, once described as atypical diabetes mellitus, idiopathetic type 1 diabetes (type 1B diabetes) and flatbush diabetes, is an uncommon form of diabetes characterized by severe reversible insulin deficiency. KPDM was first described and mostly observed in males of African-American descent and recently in Asian populations, including Japanese and Chinese. Patients with KPDM often present acutely with diabetic ketoacidosis without any immunological autoantibody to islet antigens of classic type 1 diabetes but demonstrate clinical and metabolic features of type 2 diabetes. Accumulating data indicated that gender-related body fat distribution, hormonal and genetic factors are associated with the diabetic process and the human glucose homeostasis and metabolism. A controversial question is whether and to what degree those factors contribute to the phenomenon of male predominance in KPDM. The present review focuses on the role of gender hormones and other potential precipitating factors in explaining the male predominance in KPDM patients. PMID:26171144

  9. Multidisciplinary approach to converting power chair into motorized prone cart.

    PubMed

    Brose, Steven W; Wali, Eisha

    2014-01-01

    Pressure ulcers remain a major source of morbidity and mortality in veterans with neurologic impairment. Management of pressure ulcers typically involves pressure relief over skin regions containing wounds, but this can lead to loss of mobility and independence when the wounds are located in regions that receive pressure from sitting. An innovative, low-cost, multidisciplinary effort was undertaken to maximize quality of life in a veteran with a thoracic-4 level complete spinal cord injury and a stage 4 ischial wound. The person's power wheelchair was converted into a motorized prone cart, allowing navigation of the Department of Veterans Affairs spinal cord injury hospital ward and improved socialization while relieving pressure on the wound. Physical and occupational therapy assisted with the reconfiguration of the power chair and verified safe transfers into the chair and driving of the device. Psychology verified positive psychosocial benefit, while nursing and physician services verified an absence of unwanted pain or skin injury resulting from use of the device. Further investigation of ways to apply this technique is warranted to improve the quality of life of persons with pressure ulcers. PMID:25786192

  10. Development of Korean Smartphone addiction proneness scale for youth.

    PubMed

    Kim, Dongil; Lee, Yunhee; Lee, Juyoung; Nam, JeeEun Karin; Chung, Yeoju

    2014-01-01

    This study developed a Smartphone Addiction Proneness Scale (SAPS) based on the existing internet and cellular phone addiction scales. For the development of this scale, 29 items (1.5 times the final number of items) were initially selected as preliminary items, based on the previous studies on internet/phone addiction as well as the clinical experience of involved experts. The preliminary scale was administered to a nationally representative sample of 795 students in elementary, middle, and high schools across South Korea. Then, final 15 items were selected according to the reliability test results. The final scale consisted of four subdomains: (1) disturbance of adaptive functions, (2) virtual life orientation, (3) withdrawal, and (4) tolerance. The final scale indicated a high reliability with Cronbach's α of .880. Support for the scale's criterion validity has been demonstrated by its relationship to the internet addiction scale, KS-II (r  =  .49). For the analysis of construct validity, we tested the Structural Equation Model. The results showed the four-factor structure to be valid (NFI  =  .943, TLI  =  .902, CFI  =  .902, RMSEA  =  .034). Smartphone addiction is gaining a greater spotlight as possibly a new form of addiction along with internet addiction. The SAPS appears to be a reliable and valid diagnostic scale for screening adolescents who may be at risk of smartphone addiction. Further implications and limitations are discussed. PMID:24848006

  11. Development of Korean Smartphone Addiction Proneness Scale for Youth

    PubMed Central

    Kim, Dongil; Lee, Yunhee; Lee, Juyoung; Nam, JeeEun Karin; Chung, Yeoju

    2014-01-01

    This study developed a Smartphone Addiction Proneness Scale (SAPS) based on the existing internet and cellular phone addiction scales. For the development of this scale, 29 items (1.5 times the final number of items) were initially selected as preliminary items, based on the previous studies on internet/phone addiction as well as the clinical experience of involved experts. The preliminary scale was administered to a nationally representative sample of 795 students in elementary, middle, and high schools across South Korea. Then, final 15 items were selected according to the reliability test results. The final scale consisted of four subdomains: (1) disturbance of adaptive functions, (2) virtual life orientation, (3) withdrawal, and (4) tolerance. The final scale indicated a high reliability with Cronbach's α of .880. Support for the scale's criterion validity has been demonstrated by its relationship to the internet addiction scale, KS-II (r  =  .49). For the analysis of construct validity, we tested the Structural Equation Model. The results showed the four-factor structure to be valid (NFI  =  .943, TLI  =  .902, CFI  =  .902, RMSEA  =  .034). Smartphone addiction is gaining a greater spotlight as possibly a new form of addiction along with internet addiction. The SAPS appears to be a reliable and valid diagnostic scale for screening adolescents who may be at risk of smartphone addiction. Further implications and limitations are discussed. PMID:24848006

  12. 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

  13. Are brain and heart tissue prone to the development of thiamine deficiency?

    PubMed

    Klooster, Astrid; Larkin, James R; Wiersema-Buist, Janneke; Gans, Reinold O B; Thornalley, Paul J; Navis, Gerjan; van Goor, Harry; Leuvenink, Henri G D; Bakker, Stephan J L

    2013-05-01

    Thiamine deficiency is a continuing problem leading to beriberi and Wernicke's encephalopathy. The symptoms of thiamine deficiency develop in the heart, brain and neuronal tissue. Yet, it is unclear how rapid thiamine deficiency develops and which organs are prone to development of thiamine deficiency. We investigated these issues in a thiamine deficient animal model. Twenty-four male Lewis rats were fed a thiamine deficient diet, which contained 0.04% of normal thiamine intake. Six control rats were fed 200 μg of thiamine per day. Every week a group of six rats on the thiamine-deficient diet was sacrificed and blood, urine and tissue were stored. Blood and tissue transketolase activity, thiamine and thiamine metabolites were measured and PCR of thiamine transporter-1 (ThTr-1) was performed. Transketolase activity was significantly reduced in red blood cells, liver, lung, kidney and spleen tissue after two weeks of thiamine deficient diet. In brain tissue, transketolase activity was not reduced after up to four weeks of thiamine deficient diet. The amount of thiamine pyrophosphate was also significantly conserved in brain and heart tissue (decrease of 31% and 28% respectively), compared to other tissues (decrease of ~70%) after four weeks of thiamine deficient diet. There was no difference between tissues in ThTr-1 expression after four weeks of thiamine deficient diet. Despite the fact that the heart and the brain are predilection sites for complications from thiamine deficiency, these tissues are protected against thiamine deficiency. Other organs could be suffering from thiamine deficiency without resulting in clinical signs of classic thiamine deficiency in beriberi and Wernicke's encephalopathy. PMID:23357554

  14. Uncorrected refractive errors.

    PubMed

    Naidoo, Kovin S; Jaggernath, Jyoti

    2012-01-01

    Global estimates indicate that more than 2.3 billion people in the world suffer from poor vision due to refractive error; of which 670 million people are considered visually impaired because they do not have access to corrective treatment. Refractive errors, if uncorrected, results in an impaired quality of life for millions of people worldwide, irrespective of their age, sex and ethnicity. Over the past decade, a series of studies using a survey methodology, referred to as Refractive Error Study in Children (RESC), were performed in populations with different ethnic origins and cultural settings. These studies confirmed that the prevalence of uncorrected refractive errors is considerably high for children in low-and-middle-income countries. Furthermore, uncorrected refractive error has been noted to have extensive social and economic impacts, such as limiting educational and employment opportunities of economically active persons, healthy individuals and communities. The key public health challenges presented by uncorrected refractive errors, the leading cause of vision impairment across the world, require urgent attention. To address these issues, it is critical to focus on the development of human resources and sustainable methods of service delivery. This paper discusses three core pillars to addressing the challenges posed by uncorrected refractive errors: Human Resource (HR) Development, Service Development and Social Entrepreneurship. PMID:22944755

  15. Uncorrected refractive errors

    PubMed Central

    Naidoo, Kovin S; Jaggernath, Jyoti

    2012-01-01

    Global estimates indicate that more than 2.3 billion people in the world suffer from poor vision due to refractive error; of which 670 million people are considered visually impaired because they do not have access to corrective treatment. Refractive errors, if uncorrected, results in an impaired quality of life for millions of people worldwide, irrespective of their age, sex and ethnicity. Over the past decade, a series of studies using a survey methodology, referred to as Refractive Error Study in Children (RESC), were performed in populations with different ethnic origins and cultural settings. These studies confirmed that the prevalence of uncorrected refractive errors is considerably high for children in low-and-middle-income countries. Furthermore, uncorrected refractive error has been noted to have extensive social and economic impacts, such as limiting educational and employment opportunities of economically active persons, healthy individuals and communities. The key public health challenges presented by uncorrected refractive errors, the leading cause of vision impairment across the world, require urgent attention. To address these issues, it is critical to focus on the development of human resources and sustainable methods of service delivery. This paper discusses three core pillars to addressing the challenges posed by uncorrected refractive errors: Human Resource (HR) Development, Service Development and Social Entrepreneurship. PMID:22944755

  16. Emulsion PCR: Techniques and Applications.

    PubMed

    Kanagal-Shamanna, Rashmi

    2016-01-01

    Emulsion PCR (EmPCR) is a commonly employed method for template amplification in multiple NGS-based sequencing platforms. The basic principle of emPCR is dilution and compartmentalization of template molecules in water droplets in a water-in-oil emulsion. Ideally, the dilution is to a degree where each droplet contains a single template molecule and functions as a micro-PCR reactor. Here, we discuss the basic principles, advantages, and challenges of applications of emPCR in clinical testing. We describe the methods of preparation and enrichment of template-positive Ion PGM™ Template OT2 200 Ion Sphere™ Particles (ISPs) on the Ion Personal Genome Machine(®) (PGM™) System. For routine clinical testing, following library generation, we employ the automated Ion OneTouch™ System that includes the Ion OneTouch™ 2 and the Ion OneTouch™ ES instruments for template generation and enrichment of template-positive ISPs, respectively. PMID:26843044

  17. 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…

  18. 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.

  19. Suicide Proneness in College Students: Relationships with Gender, Procrastination, and Achievement Motivation

    ERIC Educational Resources Information Center

    Klibert, Jeffrey; Langhinrichsen-Rohling, Jennifer; Luna, Amy; Robichaux, Michelle

    2011-01-01

    This study examined the relationships between 2 academic dispositions (i.e., procrastination and achievement motivation) and 2 indices of suicidal proneness in college women and men. The degree these 2 academic dispositions could predict unique variance in suicide proneness scores, above and beyond the influence of depression and self-esteem was…

  20. Body Image, Self-Esteem, and Depression-Proneness: Closing the Gender Gap.

    ERIC Educational Resources Information Center

    McCaulay, Marci; And Others

    1988-01-01

    Examines gender differences in body image and its relationship to depression-proneness and self-esteem. Findings indicate a preoccupation with body weight and appearance for both men and women, and a relationship between body satisfaction and depression-proneness. (FMW)

  1. Suicide Proneness in College Students: Relationships with Gender, Procrastination, and Achievement Motivation

    ERIC Educational Resources Information Center

    Klibert, Jeffrey; Langhinrichsen-Rohling, Jennifer; Luna, Amy; Robichaux, Michelle

    2011-01-01

    This study examined the relationships between 2 academic dispositions (i.e., procrastination and achievement motivation) and 2 indices of suicidal proneness in college women and men. The degree these 2 academic dispositions could predict unique variance in suicide proneness scores, above and beyond the influence of depression and self-esteem was

  2. 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.…

  3. The Relationship of Stress Arousal and Stress Prone Personality Traits to Menstrual Distress.

    ERIC Educational Resources Information Center

    Marini, David C.

    The various relationships of stress arousal and stress-prone personality traits to menstrual distress were investigated in order to quantify psychophysiological arousal differences between high and low menstrual distress symptom reporters and examine differences in stress-prone personality traits between high and low menstrual distress symptom…

  4. Medication Errors in Cardiopulmonary Arrest and Code-Related Situations.

    PubMed

    Flannery, Alexander H; Parli, Sara E

    2016-01-01

    PubMed/MEDLINE (1966-November 2014) was searched to identify relevant published studies on the overall frequency, types, and examples of medication errors during medical emergencies involving cardiopulmonary resuscitation and related situations, and the breakdown by type of error. The overall frequency of medication errors during medical emergencies, specifically situations related to resuscitation, is highly variable. Medication errors during such emergencies, particularly cardiopulmonary resuscitation and surrounding events, are not well characterized in the literature but may be more frequent than previously thought. Depending on whether research methods included database mining, simulation, or prospective observation of clinical practice, reported occurrence of medication errors during cardiopulmonary resuscitation and surrounding events has ranged from less than 1% to 50%. Because of the chaos of the resuscitation environment, errors in prescribing, dosing, preparing, labeling, and administering drugs are prone to occur. System-based strategies, such as infusion pump policies and code cart management, as well as personal strategies exist to minimize medication errors during emergency situations. PMID:26724288

  5. Error Prevention Aid

    NASA Technical Reports Server (NTRS)

    1987-01-01

    In a complex computer environment there is ample opportunity for error, a mistake by a programmer, or a software-induced undesirable side effect. In insurance, errors can cost a company heavily, so protection against inadvertent change is a must for the efficient firm. The data processing center at Transport Life Insurance Company has taken a step to guard against accidental changes by adopting a software package called EQNINT (Equations Interpreter Program). EQNINT cross checks the basic formulas in a program against the formulas that make up the major production system. EQNINT assures that formulas are coded correctly and helps catch errors before they affect the customer service or its profitability.

  6. Insulin use: preventable errors.

    PubMed

    2014-01-01

    Insulin is vital for patients with type 1 diabetes and useful for certain patients with type 2 diabetes. The serious consequences of insulin-related medication errors are overdose, resulting in severe hypoglycaemia, causing seizures, coma and even death; or underdose, resulting in hyperglycaemia and sometimes ketoacidosis. Errors associated with the preparation and administration of insulin are often reported, both outside and inside the hospital setting. These errors are preventable. By analysing reports from organisations devoted to medication error prevention and from poison control centres, as well as a few studies and detailed case reports of medication errors, various types of error associated with insulin use have been identified, especially in the hospital setting. Generally, patients know more about the practicalities of their insulin treatment than healthcare professionals with intermittent involvement. Medication errors involving insulin can occur at each step of the medication-use process: prescribing, data entry, preparation, dispensing and administration. When prescribing insulin, wrong-dose errors have been caused by the use of abbreviations, especially "U" instead of the word "units" (often resulting in a 10-fold overdose because the "U" is read as a zero), or by failing to write the drug's name correctly or in full. In electronic prescribing, the sheer number of insulin products is a source of confusion and, ultimately, wrong-dose errors, and often overdose. Prescribing, dispensing or administration software is rarely compatible with insulin prescriptions in which the dose is adjusted on the basis of the patient's subsequent capillary blood glucose readings, and can therefore generate errors. When preparing and dispensing insulin, a tuberculin syringe is sometimes used instead of an insulin syringe, leading to overdose. Other errors arise from confusion created by similar packaging, between different insulin products or between insulin and other drugs, such as heparin. Sometimes patients receive insulin intended for another patient. A risk of viral contamination exists when the same injection pen is used for several patients. In practice, many of these errors, which expose diabetic patients to sometimes serious blood glucose fluctuations, can be prevented by involving patients in the details of their treatment, by making use of their experience in managing their diabetes, and by implementing certain preventive measures. PMID:24516905

  7. PCR detection of Tritrichomonas foetus in preputial bull fluid without prior DNA isolation.

    PubMed

    Mutto, A A; Giambiaggi, S; Angel, S O

    2006-03-31

    Tritrichomonosis is a widespread, economically important venereal disease caused by Tritrichomonas foetus. The traditional diagnosis of this disease, which causes infertility and abortion in cattle, is based on the culture of the parasite. This process is time consuming, has low sensitivity, and is prone to contamination with intestinal or coprophilic trichomonadid protozoa, resulting in false positive diagnostics of T. foetus. In order to avoid the shortcomings of the traditional method, we developed a simple PCR assay based on TFR3 and TFR4 primers, which does not require parasite culturing. The sensitivity of the PCR assay resulted comparable to that of the classical method, being able to detect as few as five T. foetus parasites. In addition the method is highly specific. The analysis of preputial fluid washing samples showed that 58 out of 203 samples were positive by both, the PCR and the culture method (+/+), 9 samples were positive by PCR and negative by the traditional method (+/-) and only one sample resulted negative by PCR and negative by culture (-/+). The samples for the PCR assay can be stored for a week at 4 degrees C or 72h at room temperature. In summary, our study demonstrated that the PCR assay is an effective method for the diagnosis of T. foetus from preputial samples, and that it compares advantageously to the classical method. PMID:16386373

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

    SciTech Connect

    Veldeman, Liv; Speleers, Bruno; Bakker, Marlies; Jacobs, Filip; Coghe, Marc; De Gersem, Werner; Impens, Aline; Nechelput, Sarah; De Wagter, Carlos

    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.

  9. Errors in prenatal diagnosis.

    PubMed

    Anumba, Dilly O C

    2013-08-01

    Prenatal screening and diagnosis are integral to antenatal care worldwide. Prospective parents are offered screening for common fetal chromosomal and structural congenital malformations. In most developed countries, prenatal screening is routinely offered in a package that includes ultrasound scan of the fetus and the assay in maternal blood of biochemical markers of aneuploidy. Mistakes can arise at any point of the care pathway for fetal screening and diagnosis, and may involve individual or corporate systemic or latent errors. Special clinical circumstances, such as maternal size, fetal position, and multiple pregnancy, contribute to the complexities of prenatal diagnosis and to the chance of error. Clinical interventions may lead to adverse outcomes not caused by operator error. In this review I discuss the scope of the errors in prenatal diagnosis, and highlight strategies for their prevention and diagnosis, as well as identify areas for further research and study to enhance patient safety. PMID:23725900

  10. 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.

  11. 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

  12. Evidence, errors, and ethics.

    PubMed

    Miller, Franklin G; Joffe, Steven; Kesselheim, Aaron S

    2014-01-01

    Evidence-based decisions relating to the development and use of novel medical interventions are liable to false positive and false negative errors: adverse consequences that ensue from making or omitting to make a given decision. In this article we examine the propensity to false positive and false negative errors in light of competing value judgments in the areas of designing randomized controlled trials, pharmaceutical licensing, coverage of medical treatments, and clinical practice. PMID:25959345

  13. Quantum Error Correction

    NASA Astrophysics Data System (ADS)

    Lidar, Daniel A.; Brun, Todd A.

    2013-09-01

    Prologue; Preface; Part I. Background: 1. Introduction to decoherence and noise in open quantum systems Daniel Lidar and Todd Brun; 2. Introduction to quantum error correction Dave Bacon; 3. Introduction to decoherence-free subspaces and noiseless subsystems Daniel Lidar; 4. Introduction to quantum dynamical decoupling Lorenza Viola; 5. Introduction to quantum fault tolerance Panos Aliferis; Part II. Generalized Approaches to Quantum Error Correction: 6. Operator quantum error correction David Kribs and David Poulin; 7. Entanglement-assisted quantum error-correcting codes Todd Brun and Min-Hsiu Hsieh; 8. Continuous-time quantum error correction Ognyan Oreshkov; Part III. Advanced Quantum Codes: 9. Quantum convolutional codes Mark Wilde; 10. Non-additive quantum codes Markus Grassl and Martin Rötteler; 11. Iterative quantum coding systems David Poulin; 12. Algebraic quantum coding theory Andreas Klappenecker; 13. Optimization-based quantum error correction Andrew Fletcher; Part IV. Advanced Dynamical Decoupling: 14. High order dynamical decoupling Zhen-Yu Wang and Ren-Bao Liu; 15. Combinatorial approaches to dynamical decoupling Martin Rötteler and Pawel Wocjan; Part V. Alternative Quantum Computation Approaches: 16. Holonomic quantum computation Paolo Zanardi; 17. Fault tolerance for holonomic quantum computation Ognyan Oreshkov, Todd Brun and Daniel Lidar; 18. Fault tolerant measurement-based quantum computing Debbie Leung; Part VI. Topological Methods: 19. Topological codes Héctor Bombín; 20. Fault tolerant topological cluster state quantum computing Austin Fowler and Kovid Goyal; Part VII. Applications and Implementations: 21. Experimental quantum error correction Dave Bacon; 22. Experimental dynamical decoupling Lorenza Viola; 23. Architectures Jacob Taylor; 24. Error correction in quantum communication Mark Wilde; Part VIII. Critical Evaluation of Fault Tolerance: 25. Hamiltonian methods in QEC and fault tolerance Eduardo Novais, Eduardo Mucciolo and Harold Baranger; 26. Critique of fault-tolerant quantum information processing Robert Alicki; References; Index.

  14. Alcohol and error processing.

    PubMed

    Holroyd, Clay B; Yeung, Nick

    2003-08-01

    A recent study indicates that alcohol consumption reduces the amplitude of the error-related negativity (ERN), a negative deflection in the electroencephalogram associated with error commission. Here, we explore possible mechanisms underlying this result in the context of two recent theories about the neural system that produces the ERN - one based on principles of reinforcement learning and the other based on response conflict monitoring. PMID:12900168

  15. Thermodynamics of Error Correction

    NASA Astrophysics Data System (ADS)

    Sartori, Pablo; Pigolotti, Simone

    2015-10-01

    Information processing at the molecular scale is limited by thermal fluctuations. This can cause undesired consequences in copying information since thermal noise can lead to errors that can compromise the functionality of the copy. For example, a high error rate during DNA duplication can lead to cell death. Given the importance of accurate copying at the molecular scale, it is fundamental to understand its thermodynamic features. In this paper, we derive a universal expression for the copy error as a function of entropy production and work dissipated by the system during wrong incorporations. Its derivation is based on the second law of thermodynamics; hence, its validity is independent of the details of the molecular machinery, be it any polymerase or artificial copying device. Using this expression, we find that information can be copied in three different regimes. In two of them, work is dissipated to either increase or decrease the error. In the third regime, the protocol extracts work while correcting errors, reminiscent of a Maxwell demon. As a case study, we apply our framework to study a copy protocol assisted by kinetic proofreading, and show that it can operate in any of these three regimes. We finally show that, for any effective proofreading scheme, error reduction is limited by the chemical driving of the proofreading reaction.

  16. Recovery at the edge of error: debunking the myth of the infallible expert.

    PubMed

    Patel, Vimla L; Cohen, Trevor; Murarka, Tripti; Olsen, Joanne; Kagita, Srujana; Myneni, Sahiti; Buchman, Timothy; Ghaemmaghami, Vafa

    2011-06-01

    The notion that human error should not be tolerated is prevalent in both the public and personal perception of the performance of clinicians. However, researchers in other safety-critical domains have long since abandoned the quest for zero defects as an impractical goal, choosing to focus instead on the development of strategies to enhance the ability to recover from error. This paper presents a cognitive framework for the study of error recovery, and the results of our empirical research into error detection and recovery in the critical care domain, using both laboratory-based and naturalistic approaches. Both attending physicians and residents were prone to commit, detect and recover from errors, but the nature of these errors was different. Experts corrected the errors as soon as they detected them and were better able to detect errors requiring integration of multiple elements in the case. Residents were more cautious in making decisions showing a slower error recovery pattern, and the detected errors were more procedural in nature with specific patient outcomes. Error detection and correction are shown to be dependent on expertise, and on the nature of the everyday tasks of the clinicians concerned. Understanding the limits and failures of human decision-making is important if we are to build robust decision-support systems to manage the boundaries of risk of error in decision-making. Detection and correction of potential error is an integral part of cognitive work in the complex, critical care workplace. PMID:20869466

  17. Predicted Errors In Children's Early Sentence Comprehension

    PubMed Central

    Gertner, Yael; Fisher, Cynthia

    2012-01-01

    Children use syntax to interpret sentences and learn verbs; this is syntactic bootstrapping. The structure-mapping account of early syntactic bootstrapping proposes that a partial representation of sentence structure, the set of nouns occurring with the verb, guides initial interpretation and provides an abstract format for new learning. This account predicts early successes, but also telltale errors: Toddlers should be unable to tell transitive sentences from other sentences containing two nouns. In testing this prediction, we capitalized on evidence that 21-month-olds use what they have learned about noun order in English sentences to understand new transitive verbs. In two experiments, 21-month-olds applied this noun-order knowledge to two-noun intransitive sentences, mistakenly assigning different interpretations to “The boy and the girl are gorping!” and “The girl and the boy are gorping!”. This suggests that toddlers exploit partial representations of sentence structure to guide sentence interpretation; these sparse representations are useful, but error-prone. PMID:22525312

  18. Error monitoring in musicians

    PubMed Central

    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

  19. 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…

  20. Is decreased diameter of renal pelvis in prone position an indicator of successful pyeloplasty?

    PubMed Central

    Sharma, Gyanendra; Sharma, Anshu; Leung, Vivian Yee-Fong; Chu, Winnie Chiu-Wing

    2016-01-01

    Objective: To evaluate patients who had undergone pyeloplasty for pelviureteric junction obstruction, by measuring the anteroposterior diameter (APD) of the renal pelvis in supine and prone positions, and determine whether a decrease in APD in prone position can exclude obstruction in dilated renal system. Materials and Methods: From January 2012 to December 2013, patients who had undergone pyeloplasty were evaluated by ultrasound in two centers. The difference of APD of the renal pelvis in supine and prone positions was obtained. Correlation was made with the pre- and post-pyeloplasty renal function by radionuclide renogram. Results: There were 42 patients (31 males, 11 females; age range 5 months to 18 years). Residual hydronephrosis was detected in 41 patients of whom 35 patients (85%) showed decrease in APD by >10% in prone position. These patients and the one without hydronephrosis showed either no deterioration or improvement in renal function. Six patients (15%) showed either no change or increase in APD in prone position. Three patients (7.5%) were confirmed to have decrease in renal function indicating obstruction. Three patients (7.5%) showed no deterioration of renal function, but sluggish drainage on radionuclide renogram. Conclusion: Demonstration of decreased APD of renal pelvis in prone position by ultrasound is useful to differentiate obstructed from non-obstructed dilated renal system, and it correctly identified 85% candidates with successful pyeloplasty. In patients with no decrease or increase in APD at prone position, further follow-up is recommended to rule out obstruction. PMID:27081219

  1. Regional ventilation-perfusion distribution is more uniform in the prone position

    NASA Technical Reports Server (NTRS)

    Mure, M.; Domino, K. B.; Lindahl, S. G.; Hlastala, M. P.; Altemeier, W. A.; Glenny, R. W.

    2000-01-01

    The arterial blood PO(2) is increased in the prone position in animals and humans because of an improvement in ventilation (VA) and perfusion (Q) matching. However, the mechanism of improved VA/Q is unknown. This experiment measured regional VA/Q heterogeneity and the correlation between VA and Q in supine and prone positions in pigs. Eight ketamine-diazepam-anesthetized, mechanically ventilated pigs were studied in supine and prone positions in random order. Regional VA and Q were measured using fluorescent-labeled aerosols and radioactive-labeled microspheres, respectively. The lungs were dried at total lung capacity and cubed into 603-967 small ( approximately 1.7-cm(3)) pieces. In the prone position the homogeneity of the ventilation distribution increased (P = 0.030) and the correlation between VA and Q increased (correlation coefficient = 0.72 +/- 0.08 and 0.82 +/- 0.06 in supine and prone positions, respectively, P = 0.03). The homogeneity of the VA/Q distribution increased in the prone position (P = 0.028). We conclude that the improvement in VA/Q matching in the prone position is secondary to increased homogeneity of the VA distribution and increased correlation of regional VA and Q.

  2. [Rapid PCR authentication Lonicera japanica].

    PubMed

    Jiang, Chao; Hou, Jing-Yi; Huang, Lu-Qi; Yuan, Yuan; Chen, Min; Jin, Yan

    2014-10-01

    To simply and rapid authenticate Lonicera japanica. Rapid allele-specific PCR primer was designed base on trnL-trnF 625 G/T Single nucleotide polymorphism and the PCR reaction systems including annealing temperature was optimized; optimized results were performed to authenticate L. japanica and its 9 adulterants. When 100 x SYBR Green I was added in the PCR product of 87 degrees C initial denatured 1 min; 87 degrees C denatured 5 s, 68 degrees C annealing 5 s, 30 cycle; L. japanica visualize strong green fluorescence under 365 nm UV lamp whereas adulterants without. The results indicate rapid allele-specific PCR could authenticate L. japanica and its adulterants rapidly and simply. PMID:25612418

  3. Smoothing error pitfalls

    NASA Astrophysics Data System (ADS)

    von Clarmann, T.

    2014-09-01

    The difference due to the content of a priori information between a constrained retrieval and the true atmospheric state is usually represented by a diagnostic quantity called smoothing error. In this paper it is shown that, regardless of the usefulness of the smoothing error as a diagnostic tool in its own right, the concept of the smoothing error as a component of the retrieval error budget is questionable because it is not compliant with Gaussian error propagation. The reason for this is that the smoothing error does not represent the expected deviation of the retrieval from the true state but the expected deviation of the retrieval from the atmospheric state sampled on an arbitrary grid, which is itself a smoothed representation of the true state; in other words, to characterize the full loss of information with respect to the true atmosphere, the effect of the representation of the atmospheric state on a finite grid also needs to be considered. The idea of a sufficiently fine sampling of this reference atmospheric state is problematic because atmospheric variability occurs on all scales, implying that there is no limit beyond which the sampling is fine enough. Even the idealization of infinitesimally fine sampling of the reference state does not help, because the smoothing error is applied to quantities which are only defined in a statistical sense, which implies that a finite volume of sufficient spatial extent is needed to meaningfully discuss temperature or concentration. Smoothing differences, however, which play a role when measurements are compared, are still a useful quantity if the covariance matrix involved has been evaluated on the comparison grid rather than resulting from interpolation and if the averaging kernel matrices have been evaluated on a grid fine enough to capture all atmospheric variations that the instruments are sensitive to. This is, under the assumptions stated, because the undefined component of the smoothing error, which is the effect of smoothing implied by the finite grid on which the measurements are compared, cancels out when the difference is calculated. If the effect of a retrieval constraint is to be diagnosed on a grid finer than the native grid of the retrieval by means of the smoothing error, the latter must be evaluated directly on the fine grid, using an ensemble covariance matrix which includes all variability on the fine grid. Ideally, the averaging kernels needed should be calculated directly on the finer grid, but if the grid of the original averaging kernels allows for representation of all the structures the instrument is sensitive to, then their interpolation can be an adequate approximation.

  4. Compact disk error measurements

    NASA Technical Reports Server (NTRS)

    Howe, D.; Harriman, K.; Tehranchi, B.

    1993-01-01

    The objectives of this project are as follows: provide hardware and software that will perform simple, real-time, high resolution (single-byte) measurement of the error burst and good data gap statistics seen by a photoCD player read channel when recorded CD write-once discs of variable quality (i.e., condition) are being read; extend the above system to enable measurement of the hard decision (i.e., 1-bit error flags) and soft decision (i.e., 2-bit error flags) decoding information that is produced/used by the Cross Interleaved - Reed - Solomon - Code (CIRC) block decoder employed in the photoCD player read channel; construct a model that uses data obtained via the systems described above to produce meaningful estimates of output error rates (due to both uncorrected ECC words and misdecoded ECC words) when a CD disc having specific (measured) error statistics is read (completion date to be determined); and check the hypothesis that current adaptive CIRC block decoders are optimized for pressed (DAD/ROM) CD discs. If warranted, do a conceptual design of an adaptive CIRC decoder that is optimized for write-once CD discs.

  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; Kahan, Zsuzsanna

    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. Experimental investigation of observation error in anuran call surveys

    USGS Publications Warehouse

    McClintock, B.T.; Bailey, L.L.; Pollock, K.H.; Simons, T.R.

    2010-01-01

    Occupancy models that account for imperfect detection are often used to monitor anuran and songbird species occurrence. However, presenceabsence data arising from auditory detections may be more prone to observation error (e.g., false-positive detections) than are sampling approaches utilizing physical captures or sightings of individuals. We conducted realistic, replicated field experiments using a remote broadcasting system to simulate simple anuran call surveys and to investigate potential factors affecting observation error in these studies. Distance, time, ambient noise, and observer abilities were the most important factors explaining false-negative detections. Distance and observer ability were the best overall predictors of false-positive errors, but ambient noise and competing species also affected error rates for some species. False-positive errors made up 5 of all positive detections, with individual observers exhibiting false-positive rates between 0.5 and 14. Previous research suggests false-positive errors of these magnitudes would induce substantial positive biases in standard estimators of species occurrence, and we recommend practices to mitigate for false positives when developing occupancy monitoring protocols that rely on auditory detections. These recommendations include additional observer training, limiting the number of target species, and establishing distance and ambient noise thresholds during surveys. ?? 2010 The Wildlife Society.

  7. 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.

  8. Mapping radon-prone areas using γ-radiation dose rate and geological information.

    PubMed

    García-Talavera, M; García-Pérez, A; Rey, C; Ramos, L

    2013-09-01

    Identifying radon-prone areas is key to policies on the control of this environmental carcinogen. In the current paper, we present the methodology followed to delineate radon-prone areas in Spain. It combines information from indoor radon measurements with γ-radiation and geological maps. The advantage of the proposed approach is that it lessens the requirement for a high density of measurements by making use of commonly available information. It can be applied for an initial definition of radon-prone areas in countries committed to introducing a national radon policy or to improving existing radon maps in low population regions. PMID:23803560

  9. Seismogram ``Picking Error'' Experiment

    NASA Astrophysics Data System (ADS)

    Zeiler, Cleat P.; Velasco, Aaron; Pingitore, Nicholas E.; Anderson, Dale

    2008-10-01

    The Seismogram Picking Error From Analyst Review (SPEAR) project is looking for input from analysts with experience in picking earthquake or other seismic data. The project, begun in February 2008 as a grassroots effort among the authors' institutions, will aid the seismological community in producing more reliable results for hypocenter locations and in establishing Earth models that are more accurate. The project could develop into a continuous forum for the seismological community to better understand the errors, biases, and mental processes or steps involved in picking seismic data, and to establish standards for how to pick and assess seismic data.

  10. Error Free Software

    NASA Technical Reports Server (NTRS)

    1985-01-01

    A mathematical theory for development of "higher order" software to catch computer mistakes resulted from a Johnson Space Center contract for Apollo spacecraft navigation. Two women who were involved in the project formed Higher Order Software, Inc. to develop and market the system of error analysis and correction. They designed software which is logically error-free, which, in one instance, was found to increase productivity by 600%. USE.IT defines its objectives using AXES -- a user can write in English and the system converts to computer languages. It is employed by several large corporations.

  11. 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

  12. A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae.

    PubMed

    Kramer, Emily B; Vallabhaneni, Haritha; Mayer, Lauren M; Farabaugh, Philip J

    2010-09-01

    The process of protein synthesis must be sufficiently rapid and sufficiently accurate to support continued cellular growth. Failure in speed or accuracy can have dire consequences, including disease in humans. Most estimates of the accuracy come from studies of bacterial systems, principally Escherichia coli, and have involved incomplete analysis of possible errors. We recently used a highly quantitative system to measure the frequency of all types of misreading errors by a single tRNA in E. coli. That study found a wide variation in error frequencies among codons; a major factor causing that variation is competition between the correct (cognate) and incorrect (near-cognate) aminoacyl-tRNAs for the mutant codon. Here we extend that analysis to measure the frequency of missense errors by two tRNAs in a eukaryote, the yeast Saccharomyces cerevisiae. The data show that in yeast errors vary by codon from a low of 4 x 10(-5) to a high of 6.9 x 10(-4) per codon and that error frequency is in general about threefold lower than in E. coli, which may suggest that yeast has additional mechanisms that reduce missense errors. Error rate again is strongly influenced by tRNA competition. Surprisingly, missense errors involving wobble position mispairing were much less frequent in S. cerevisiae than in E. coli. Furthermore, the error-inducing aminoglycoside antibiotic, paromomycin, which stimulates errors on all error-prone codons in E. coli, has a more codon-specific effect in yeast. PMID:20651030

  13. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... Management Regulations § 60.5 Flood plain management criteria for flood-related erosion-prone areas. The... flood-related erosion-prone areas shall be based. If the Federal Insurance Administrator has...

  14. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... Management Regulations § 60.5 Flood plain management criteria for flood-related erosion-prone areas. The... flood-related erosion-prone areas shall be based. If the Federal Insurance Administrator has...

  15. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... Management Regulations § 60.5 Flood plain management criteria for flood-related erosion-prone areas. The... flood-related erosion-prone areas shall be based. If the Federal Insurance Administrator has...

  16. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... Management Regulations § 60.5 Flood plain management criteria for flood-related erosion-prone areas. The... flood-related erosion-prone areas shall be based. If the Federal Insurance Administrator has...

  17. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... Management Regulations § 60.5 Flood plain management criteria for flood-related erosion-prone areas. The... flood-related erosion-prone areas shall be based. If the Federal Insurance Administrator has...

  18. Orwell's Instructive Errors

    ERIC Educational Resources Information Center

    Julian, Liam

    2009-01-01

    In this article, the author talks about George Orwell, his instructive errors, and the manner in which Orwell pierced worthless theory, faced facts and defended decency (with fluctuating success), and largely ignored the tradition of accumulated wisdom that has rendered him a timeless teacher--one whose inadvertent lessons, while infrequently…

  19. 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...

  20. When feeling bad leads to feeling good: guilt-proneness and affective organizational commitment.

    PubMed

    Flynn, Francis J; Schaumberg, Rebecca L

    2012-01-01

    The authors posit that higher levels of guilt-proneness are associated with higher levels of affective organizational commitment. To explain this counterintuitive link, the authors suggest that a dispositional tendency to feel guilt motivates individuals to exert greater effort on their work-related tasks that, in turn, strengthens their affinity for the organization. The authors tested this idea using a laboratory study and field data from 2 samples of working adults. Individuals who are more guilt-prone reported higher levels of organizational attachment compared with less guilt-prone individuals. Furthermore, mediation analyses indicate that the link between guilt-proneness and affective commitment is driven by greater task effort. The authors discuss the implications of these findings for understanding the affective drivers of commitment in organizations. PMID:21728398

  1. FDA: Wait a Month to Donate Blood After Travel to Zika-Prone Areas

    MedlinePlus

    ... medlineplus/news/fullstory_157278.html FDA: Wait a Month to Donate Blood After Travel to Zika-Prone ... have symptoms that suggest infection, should wait a month before donating blood, the U.S. Food and Drug ...

  2. Check Newborns of Women Who Visited Zika-Prone Areas for Infection: CDC

    MedlinePlus

    ... 157361.html Check Newborns of Women Who Visited Zika-Prone Areas for Infection: CDC Advisory is for ... who traveled in an area affected by the Zika virus within two weeks of delivery, or whose ...

  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. Car Crash Risk May Nearly Double in People Prone to Fainting

    MedlinePlus

    ... nlm.nih.gov/medlineplus/news/fullstory_157512.html Car Crash Risk May Nearly Double in People Prone to ... as likely as others to get into a car crash, a new study finds. The researchers say the ...

  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. Inborn Errors of Metabolism.

    PubMed

    Ezgu, Fatih

    2016-01-01

    Inborn errors of metabolism are single gene disorders resulting from the defects in the biochemical pathways of the body. Although these disorders are individually rare, collectively they account for a significant portion of childhood disability and deaths. Most of the disorders are inherited as autosomal recessive whereas autosomal dominant and X-linked disorders are also present. The clinical signs and symptoms arise from the accumulation of the toxic substrate, deficiency of the product, or both. Depending on the residual activity of the deficient enzyme, the initiation of the clinical picture may vary starting from the newborn period up until adulthood. Hundreds of disorders have been described until now and there has been a considerable clinical overlap between certain inborn errors. Resulting from this fact, the definite diagnosis of inborn errors depends on enzyme assays or genetic tests. Especially during the recent years, significant achievements have been gained for the biochemical and genetic diagnosis of inborn errors. Techniques such as tandem mass spectrometry and gas chromatography for biochemical diagnosis and microarrays and next-generation sequencing for the genetic diagnosis have enabled rapid and accurate diagnosis. The achievements for the diagnosis also enabled newborn screening and prenatal diagnosis. Parallel to the development the diagnostic methods; significant progress has also been obtained for the treatment. Treatment approaches such as special diets, enzyme replacement therapy, substrate inhibition, and organ transplantation have been widely used. It is obvious that by the help of the preclinical and clinical research carried out for inborn errors, better diagnostic methods and better treatment approaches will high likely be available. PMID:26975974

  7. Prone versus supine position for adjuvant breast radiotherapy: a prospective study in patients with pendulous breasts

    PubMed Central

    2013-01-01

    Purpose To analyze dosimetric parameters of patients receiving adjuvant breast radiotherapy (RT) in the prone versus supine position. Methods and materials Forty-one out of 55 patients with pendulous breasts and candidates for adjuvant RT were enrolled in the study after informed consent. They underwent computed tomography (CT)-simulation in both prone and supine position. Target and non target volumes were outlined on CT images. Prescribed dose was 50 Gy delivered by two tangential photon fields followed by 10 Gy electron boost. Target coverage and dose homogeneity to clinical target volume (CTV) and planning target volume (PTV) were assessed by V95, V105 and V107 and dose to lung, heart and left anterior descending coronary artery (LAD) by V5, V10, V20, and mean and maximum dose. Data were analyzed by Student’s t-test. Results CTV and PTV coverage was significantly better in supine than in prone position. Lung V5, V10, and V20 were significantly lower in prone than in supine position. Heart V5, V10, V20, and LAD mean and maximum dose, in the 17 patients with left breast tumor, were lower in prone than in supine position, but without statistical significance. Based on treatment planning data and on treatment feasibility, 29/41 patients (70.7%) were treated in prone position. Acute and late toxicities of patients treated in prone and in supine position were not statistically different. Conclusion Prone position is a favorable alternative for irradiation of mammary gland in patients with pendulous breasts and in our series was adopted in 71% of the cases. PMID:24103708

  8. "I'd only let you down": Guilt proneness and the avoidance of harmful interdependence.

    PubMed

    Wiltermuth, Scott S; Cohen, Taya R

    2014-11-01

    Five studies demonstrated that highly guilt-prone people may avoid forming interdependent partnerships with others whom they perceive to be more competent than themselves, as benefitting a partner less than the partner benefits one's self could trigger feelings of guilt. Highly guilt-prone people who lacked expertise in a domain were less willing than were those low in guilt proneness who lacked expertise in that domain to create outcome-interdependent relationships with people who possessed domain-specific expertise. These highly guilt-prone people were more likely than others both to opt to be paid on their performance alone (Studies 1, 3, 4, and 5) and to opt to be paid on the basis of the average of their performance and that of others whose competence was more similar to their own (Studies 2 and 5). Guilt proneness did not predict people's willingness to form outcome-interdependent relationships with potential partners who lacked domain-specific expertise (Studies 4 and 5). It also did not predict people's willingness to form relationships when poor individual performance would not negatively affect partner outcomes (Study 4). Guilt proneness therefore predicts whether, and with whom, people develop interdependent relationships. The findings also demonstrate that highly guilt-prone people sacrifice financial gain out of concern about how their actions would influence others' welfare. As such, the findings demonstrate a novel way in which guilt proneness limits free-riding and therefore reduces the incidence of potentially unethical behavior. Lastly, the findings demonstrate that people who lack competence may not always seek out competence in others when choosing partners. PMID:25133718

  9. 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.

  10. Sources of PCR-induced distortions in high-throughput sequencing data sets

    PubMed Central

    Kebschull, Justus M.; Zador, Anthony M.

    2015-01-01

    PCR permits the exponential and sequence-specific amplification of DNA, even from minute starting quantities. PCR is a fundamental step in preparing DNA samples for high-throughput sequencing. However, there are errors associated with PCR-mediated amplification. Here we examine the effects of four important sources of error—bias, stochasticity, template switches and polymerase errors—on sequence representation in low-input next-generation sequencing libraries. We designed a pool of diverse PCR amplicons with a defined structure, and then used Illumina sequencing to search for signatures of each process. We further developed quantitative models for each process, and compared predictions of these models to our experimental data. We find that PCR stochasticity is the major force skewing sequence representation after amplification of a pool of unique DNA amplicons. Polymerase errors become very common in later cycles of PCR but have little impact on the overall sequence distribution as they are confined to small copy numbers. PCR template switches are rare and confined to low copy numbers. Our results provide a theoretical basis for removing distortions from high-throughput sequencing data. In addition, our findings on PCR stochasticity will have particular relevance to quantification of results from single cell sequencing, in which sequences are represented by only one or a few molecules. PMID:26187991

  11. Efficacy of prone position in acute respiratory distress syndrome patients: A pathophysiology-based review

    PubMed Central

    Koulouras, Vasilios; Papathanakos, Georgios; Papathanasiou, Athanasios; Nakos, Georgios

    2016-01-01

    Acute respiratory distress syndrome (ARDS) is a syndrome with heterogeneous underlying pathological processes. It represents a common clinical problem in intensive care unit patients and it is characterized by high mortality. The mainstay of treatment for ARDS is lung protective ventilation with low tidal volumes and positive end-expiratory pressure sufficient for alveolar recruitment. Prone positioning is a supplementary strategy available in managing patients with ARDS. It was first described 40 years ago and it proves to be in alignment with two major ARDS pathophysiological lung models; the “sponge lung” - and the “shape matching” -model. Current evidence strongly supports that prone positioning has beneficial effects on gas exchange, respiratory mechanics, lung protection and hemodynamics as it redistributes transpulmonary pressure, stress and strain throughout the lung and unloads the right ventricle. The factors that individually influence the time course of alveolar recruitment and the improvement in oxygenation during prone positioning have not been well characterized. Although patients’ response to prone positioning is quite variable and hard to predict, large randomized trials and recent meta-analyses show that prone position in conjunction with a lung-protective strategy, when performed early and in sufficient duration, may improve survival in patients with ARDS. This pathophysiology-based review and recent clinical evidence strongly support the use of prone positioning in the early management of severe ARDS systematically and not as a rescue maneuver or a last-ditch effort. PMID:27152255

  12. Children’s Proneness to Shame and Guilt Predict Risky and Illegal Behaviors in Young Adulthood

    PubMed Central

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

    2014-01-01

    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

  13. Efficacy of prone position in acute respiratory distress syndrome patients: A pathophysiology-based review.

    PubMed

    Koulouras, Vasilios; Papathanakos, Georgios; Papathanasiou, Athanasios; Nakos, Georgios

    2016-05-01

    Acute respiratory distress syndrome (ARDS) is a syndrome with heterogeneous underlying pathological processes. It represents a common clinical problem in intensive care unit patients and it is characterized by high mortality. The mainstay of treatment for ARDS is lung protective ventilation with low tidal volumes and positive end-expiratory pressure sufficient for alveolar recruitment. Prone positioning is a supplementary strategy available in managing patients with ARDS. It was first described 40 years ago and it proves to be in alignment with two major ARDS pathophysiological lung models; the "sponge lung" - and the "shape matching" -model. Current evidence strongly supports that prone positioning has beneficial effects on gas exchange, respiratory mechanics, lung protection and hemodynamics as it redistributes transpulmonary pressure, stress and strain throughout the lung and unloads the right ventricle. The factors that individually influence the time course of alveolar recruitment and the improvement in oxygenation during prone positioning have not been well characterized. Although patients' response to prone positioning is quite variable and hard to predict, large randomized trials and recent meta-analyses show that prone position in conjunction with a lung-protective strategy, when performed early and in sufficient duration, may improve survival in patients with ARDS. This pathophysiology-based review and recent clinical evidence strongly support the use of prone positioning in the early management of severe ARDS systematically and not as a rescue maneuver or a last-ditch effort. PMID:27152255

  14. Prediction of Fault-Prone Software Modules Using a Generic Text Discriminator

    NASA Astrophysics Data System (ADS)

    Mizuno, Osamu; Kikuno, Tohru

    This paper describes a novel approach for detecting fault-prone modules using a spam filtering technique. Fault-prone module detection in source code is important for the assurance of software quality. Most previous fault-prone detection approaches have been based on using software metrics. Such approaches, however, have difficulties in collecting the metrics and constructing mathematical models based on the metrics. Because of the increase in the need for spam e-mail detection, the spam filtering technique has progressed as a convenient and effective technique for text mining. In our approach, fault-prone modules are detected in such a way that the source code modules are considered text files and are applied to the seam filter directly. To show the applicability of our approach, we conducted experimental applications using source code repositories of Java based open source developments. The result of experiments shows that our approach can correctly predict 78% of actual fault-prone modules as fault-prone.

  15. 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

  16. The effect of prone positioning with surgical bolsters on liver blood flow in healthy volunteers.

    PubMed

    Chikhani, M; Evans, D L; Blatcher, A W; Jackson, A P; Guha, I N; Aithal, G P; Moppett, I K

    2016-05-01

    This study sought to identify changes in hepatic flood flow and cardiac output during prone positioning on surgical bolsters in awake volunteers, and was prompted by a local incident of significant hepatic dysfunction following surgery in the prone position. Cardiac output was determined using the non-invasive Peñáz technique, and plasma disappearance rate of indocyanine green (ICG-PDR) was measured as a surrogate maker for hepatic blood flow along with serum hepatic enzyme assays. Measurements were made after one hour in supine, prone and returned supine positions. Ten volunteers completed the study. There were significant changes in the disappearance rate of indocyanine green, which decreased this from mean (SD) 31.1 (9.70) supine to 19.6 (4.37)%.min prone, respectively (p = 0.02), increasing on return to the supine position to 24.6 (5.54)%.min (p = 0.019). Cardiac output was also significantly reduced when changing from the supine to the prone position, from mean (SD) 4.7 (1.0 to 3.5 (1.1) (l.min(-1) ), respectively (p = 0.002). We demonstrated an acute and reversible change in both hepatocellular function and cardiac output associated with the prone position. PMID:26948476

  17. 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…

  18. Enhanced Named Entity Extraction via Error-Driven Aggregation

    SciTech Connect

    Lemmond, T D; Perry, N C; Guensche, J W; Nitao, J J; Glaser, R E; Kidwell, P; Hanley, W G

    2010-02-22

    Despite recent advances in named entity extraction technologies, state-of-the-art extraction tools achieve insufficient accuracy rates for practical use in many operational settings. However, they are not generally prone to the same types of error, suggesting that substantial improvements may be achieved via appropriate combinations of existing tools, provided their behavior can be accurately characterized and quantified. In this paper, we present an inference methodology for the aggregation of named entity extraction technologies that is founded upon a black-box analysis of their respective error processes. This method has been shown to produce statistically significant improvements in extraction relative to standard performance metrics and to mitigate the weak performance of entity extractors operating under suboptimal conditions. Moreover, this approach provides a framework for quantifying uncertainty and has demonstrated the ability to reconstruct the truth when majority voting fails.

  19. Control by model error estimation

    NASA Technical Reports Server (NTRS)

    Likins, P. W.; Skelton, R. E.

    1976-01-01

    Modern control theory relies upon the fidelity of the mathematical model of the system. Truncated modes, external disturbances, and parameter errors in linear system models are corrected by augmenting to the original system of equations an 'error system' which is designed to approximate the effects of such model errors. A Chebyshev error system is developed for application to the Large Space Telescope (LST).

  20. Automatic Error Analysis Using Intervals

    ERIC Educational Resources Information Center

    Rothwell, E. J.; Cloud, M. J.

    2012-01-01

    A technique for automatic error analysis using interval mathematics is introduced. A comparison to standard error propagation methods shows that in cases involving complicated formulas, the interval approach gives comparable error estimates with much less effort. Several examples are considered, and numerical errors are computed using the INTLAB…

  1. Imagery of Errors in Typing

    ERIC Educational Resources Information Center

    Rieger, Martina; Martinez, Fanny; Wenke, Dorit

    2011-01-01

    Using a typing task we investigated whether insufficient imagination of errors and error corrections is related to duration differences between execution and imagination. In Experiment 1 spontaneous error imagination was investigated, whereas in Experiment 2 participants were specifically instructed to imagine errors. Further, in Experiment 2 we…

  2. Automatic Error Analysis Using Intervals

    ERIC Educational Resources Information Center

    Rothwell, E. J.; Cloud, M. J.

    2012-01-01

    A technique for automatic error analysis using interval mathematics is introduced. A comparison to standard error propagation methods shows that in cases involving complicated formulas, the interval approach gives comparable error estimates with much less effort. Several examples are considered, and numerical errors are computed using the INTLAB

  3. Sequetyping: Serotyping Streptococcus pneumoniae by a Single PCR Sequencing Strategy

    PubMed Central

    Leung, Marcus H.; Bryson, Kevin; Freystatter, Kathrin; Pichon, Bruno; Edwards, Giles; Gillespie, Stephen H.

    2012-01-01

    The introduction of pneumococcal conjugate vaccines necessitates continued monitoring of circulating strains to assess vaccine efficacy and replacement serotypes. Conventional serological methods are costly, labor-intensive, and prone to misidentification, while current DNA-based methods have limited serotype coverage requiring multiple PCR primers. In this study, a computer algorithm was developed to interrogate the capsulation locus (cps) of vaccine serotypes to locate primer pairs in conserved regions that border variable regions and could differentiate between serotypes. In silico analysis of cps from 92 serotypes indicated that a primer pair spanning the regulatory gene cpsB could putatively amplify 84 serotypes and differentiate 46. This primer set was specific to Streptococcus pneumoniae, with no amplification observed for other species, including S. mitis, S. oralis, and S. pseudopneumoniae. One hundred thirty-eight pneumococcal strains covering 48 serotypes were tested. Of 23 vaccine serotypes included in the study, most (19/22, 86%) were identified correctly at least to the serogroup level, including all of the 13-valent conjugate vaccine and other replacement serotypes. Reproducibility was demonstrated by the correct sequetyping of different strains of a serotype. This novel sequence-based method employing a single PCR primer pair is cost-effective and simple. Furthermore, it has the potential to identify new serotypes that may evolve in the future. PMID:22553238

  4. Sequetyping: serotyping Streptococcus pneumoniae by a single PCR sequencing strategy.

    PubMed

    Leung, Marcus H; Bryson, Kevin; Freystatter, Kathrin; Pichon, Bruno; Edwards, Giles; Charalambous, Bambos M; Gillespie, Stephen H

    2012-07-01

    The introduction of pneumococcal conjugate vaccines necessitates continued monitoring of circulating strains to assess vaccine efficacy and replacement serotypes. Conventional serological methods are costly, labor-intensive, and prone to misidentification, while current DNA-based methods have limited serotype coverage requiring multiple PCR primers. In this study, a computer algorithm was developed to interrogate the capsulation locus (cps) of vaccine serotypes to locate primer pairs in conserved regions that border variable regions and could differentiate between serotypes. In silico analysis of cps from 92 serotypes indicated that a primer pair spanning the regulatory gene cpsB could putatively amplify 84 serotypes and differentiate 46. This primer set was specific to Streptococcus pneumoniae, with no amplification observed for other species, including S. mitis, S. oralis, and S. pseudopneumoniae. One hundred thirty-eight pneumococcal strains covering 48 serotypes were tested. Of 23 vaccine serotypes included in the study, most (19/22, 86%) were identified correctly at least to the serogroup level, including all of the 13-valent conjugate vaccine and other replacement serotypes. Reproducibility was demonstrated by the correct sequetyping of different strains of a serotype. This novel sequence-based method employing a single PCR primer pair is cost-effective and simple. Furthermore, it has the potential to identify new serotypes that may evolve in the future. PMID:22553238

  5. Error-free DNA-damage tolerance in Saccharomyces cerevisiae.

    PubMed

    Xu, Xin; Blackwell, Susan; Lin, Aiyang; Li, Fangfang; Qin, Zhoushuai; Xiao, Wei

    2015-01-01

    DNA-damage tolerance (DDT) is an important mechanism for living cells to bypass replication blocks on the template strand. In Saccharomyces cerevisiae, DDT is mediated by the RAD6 epistasis group of genes, consisting of two parallel pathways: error-prone translesion DNA synthesis (TLS), and error-free lesion bypass. The two pathways are activated by sequential ubiquitination of PCNA on the Lys164 residue. When a replication fork is stalled at a lesion, PCNA is first monoubiquitinated by Rad6-Rad18, which leads to the TLS pathway. The subsequent ubiquitination by the Mms2-Ubc13-Rad5 complex on the monoubiquitinated PCNA is to form a Lys63-linked polyubiquitin chain that promotes error-free lesion bypass. While the TLS pathway has been extensively characterized, the molecular events leading to error-free lesion bypass by polyubiquitinated PCNA are largely obscure. Furthermore, PCNA can also be sumoylated at the same Lys164 residue, which helps to recruit Srs2, a helicase and anti-recombinase. This review summarizes recent advances in our understanding of error-free DDT and its interplay with Srs2 and homologous recombination. PMID:26041265

  6. 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.

  7. 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.

  8. Modular error embedding

    DOEpatents

    Sandford, II, Maxwell T.; Handel, Theodore G.; Ettinger, J. Mark

    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.

  9. Error-Free Software

    NASA Technical Reports Server (NTRS)

    1989-01-01

    001 is an integrated tool suited for automatically developing ultra reliable models, simulations and software systems. Developed and marketed by Hamilton Technologies, Inc. (HTI), it has been applied in engineering, manufacturing, banking and software tools development. The software provides the ability to simplify the complex. A system developed with 001 can be a prototype or fully developed with production quality code. It is free of interface errors, consistent, logically complete and has no data or control flow errors. Systems can be designed, developed and maintained with maximum productivity. Margaret Hamilton, President of Hamilton Technologies, also directed the research and development of USE.IT, an earlier product which was the first computer aided software engineering product in the industry to concentrate on automatically supporting the development of an ultrareliable system throughout its life cycle. Both products originated in NASA technology developed under a Johnson Space Center contract.

  10. Error-correction coding

    NASA Technical Reports Server (NTRS)

    Hinds, Erold W. (Principal Investigator)

    1996-01-01

    This report describes the progress made towards the completion of a specific task on error-correcting coding. The proposed research consisted of investigating the use of modulation block codes as the inner code of a concatenated coding system in order to improve the overall space link communications performance. The study proposed to identify and analyze candidate codes that will complement the performance of the overall coding system which uses the interleaved RS (255,223) code as the outer code.

  11. Memory efficient error diffusion

    NASA Astrophysics Data System (ADS)

    Chang, Ti-chiun; Allebach, Jan P.

    2003-01-01

    Li and Allebach recently proposed parameter-trainable tone dependent error diffusion (TDED) which yields outstanding halftone quality among error diffusion based algorithms. In TDED, the tone dependent weights and thresholds as well as a halftone bitmap for threshold modulation are implemented as look-up tables (LUTs) which consume on-chip memory. In addition, the diffused errors must be buffered in on-chip memory and in most cases, transferred to off-chip memory. However, off-chip memory access considerably deteriorates system performance. In this paper, we propose two approaches to improve memory efficiency. First, we use deterministic bit flipping to replace threshold modulation, and linearize the weights and thresholds of TDED. This reduces the memory requirement by using only a few constants, rather than full LUTs, and generates halftones whose quality is nearly indistinguishable from that of standard TDED. Secondly, we propose a block-based processing strategy which significantly reduces off-chip memory access. We devise a novel scan-path which enables our algorithm to process any input image block-by-block without yielding block-boundary artifacts. Special filters are designed and optimized for the block diagonals so that the resulting halftone quality is comparable to that of standard TDED.

  12. 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

  13. Bayesian Error Estimation Functionals

    NASA Astrophysics Data System (ADS)

    Jacobsen, Karsten W.

    The challenge of approximating the exchange-correlation functional in Density Functional Theory (DFT) has led to the development of numerous different approximations of varying accuracy on different calculated properties. There is therefore a need for reliable estimation of prediction errors within the different approximation schemes to DFT. The Bayesian Error Estimation Functionals (BEEF) have been developed with this in mind. The functionals are constructed by fitting to experimental and high-quality computational databases for molecules and solids including chemisorption and van der Waals systems. This leads to reasonably accurate general-purpose functionals with particual focus on surface science. The fitting procedure involves considerations on how to combine different types of data, and applies Tikhonov regularization and bootstrap cross validation. The methodology has been applied to construct GGA and metaGGA functionals with and without inclusion of long-ranged van der Waals contributions. The error estimation is made possible by the generation of not only a single functional but through the construction of a probability distribution of functionals represented by a functional ensemble. The use of the functional ensemble is illustrated on compound heat of formation and by investigations of the reliability of calculated catalytic ammonia synthesis rates.

  14. The Diagnosis of Error in Histories of Science

    NASA Astrophysics Data System (ADS)

    Thomas, William

    Whether and how to diagnose error in the history of science is a contentious issue. For many scientists, diagnosis is appealing because it allows them to discuss how knowledge can progress most effectively. Many historians disagree. They consider diagnosis inappropriate because it may discard features of past actors' thought that are important to understanding it, and may have even been intellectually productive. Ironically, these historians are apt to diagnose flaws in scientists' histories as proceeding from a misguided desire to idealize scientific method, and from their attendant identification of deviations from the ideal as, ipso facto, a paramount source of error in historical science. While both views have some merit, they should be reconciled if a more harmonious and productive relationship between the disciplines is to prevail. In To Explain the World, Steven Weinberg narrates the slow but definite emergence of what we call science from long traditions of philosophical and mathematical thought. This narrative follows in a historiographical tradition charted by historians such as Alexandre Koyre and Rupert Hall about sixty years ago. It is essentially a history of the emergence of reliable (if fallible) scientific method from more error-prone thought. While some historians such as Steven Shapin view narratives of this type as fundamentally error-prone, I do not view such projects as a priori illegitimate. They are, however, perhaps more difficult than Weinberg supposes. In this presentation, I will focus on two of Weinberg's strong historical claims: that physics became detached from religion as early as the beginning of the eighteenth century, and that physics proved an effective model for placing other fields on scientific grounds. While I disagree with these claims, they represent at most an overestimation of vintage science's interest in discarding theological questions, and an overestimation of that science's ability to function at all reliably.

  15. Human Error In Complex Systems

    NASA Technical Reports Server (NTRS)

    Morris, Nancy M.; Rouse, William B.

    1991-01-01

    Report presents results of research aimed at understanding causes of human error in such complex systems as aircraft, nuclear powerplants, and chemical processing plants. Research considered both slips (errors of action) and mistakes (errors of intention), and influence of workload on them. Results indicated that: humans respond to conditions in which errors expected by attempting to reduce incidence of errors; and adaptation to conditions potent influence on human behavior in discretionary situations.

  16. Error equations of inertial navigation

    NASA Astrophysics Data System (ADS)

    Arshal, George

    1987-08-01

    This paper derives basic error equations of inertial navigation which apply to any properly constructed inertial navigator. The equations are deduced from the integral equations of inertial navigation by a vectorial analysis. A major result of this analysis is a set of fundamental error propagation equations that has apparently been missed. These equations regard the absolute navigational errors. The conventional velocity and position errors are shown to be transfer errors.

  17. A semiparametric copula method for Cox models with covariate measurement error.

    PubMed

    Kim, Sehee; Li, Yi; Spiegelman, Donna

    2016-01-01

    We consider measurement error problem in the Cox model, where the underlying association between the true exposure and its surrogate is unknown, but can be estimated from a validation study. Under this framework, one can accommodate general distributional structures for the error-prone covariates, not restricted to a linear additive measurement error model or Gaussian measurement error. The proposed copula-based approach enables us to fit flexible measurement error models, and to be applicable with an internal or external validation study. Large sample properties are derived and finite sample properties are investigated through extensive simulation studies. The methods are applied to a study of physical activity in relation to breast cancer mortality in the Nurses' Health Study. PMID:25504515

  18. A non-orthogonal SVD-based decomposition for phase invariant error-related potential estimation.

    PubMed

    Phlypo, Ronald; Jrad, Nisrine; Rousseau, Sandra; Congedo, Marco

    2011-01-01

    The estimation of the Error Related Potential from a set of trials is a challenging problem. Indeed, the Error Related Potential is of low amplitude compared to the ongoing electroencephalographic activity. In addition, simple summing over the different trials is prone to errors, since the waveform does not appear at an exact latency with respect to the trigger. In this work, we propose a method to cope with the discrepancy of these latencies of the Error Related Potential waveform and offer a framework in which the estimation of the Error Related Potential waveform reduces to a simple Singular Value Decomposition of an analytic waveform representation of the observed signal. The followed approach is promising, since we are able to explain a higher portion of the variance of the observed signal with fewer components in the expansion. PMID:22255940

  19. Prone positioning improves pulmonary function in obese patients during general anesthesia.

    PubMed

    Pelosi, P; Croci, M; Calappi, E; Mulazzi, D; Cerisara, M; Vercesi, P; Vicardi, P; Gattinoni, L

    1996-09-01

    We investigated the effects of prone position on functional residual capacity (FRC), the mechanical properties (compliance and resistance) of the total respiratory system, lung and chest wall, and the gas exchange in 10 anesthetized and paralyzed obese (body mass index more than 30 kg/m2) patients, undergoing elective surgery. We used the esophageal balloon technique together with rapid airway occlusions during constant inspiratory flow to partition the mechanics of the respiratory system into its pulmonary and chest wall components. FRC was measured by the helium dilution technique. Measurements were taken in the supine position and after 15-30 min of prone position maintaining the same respiratory pattern (tidal volume 12 mL/kg ideal body weight, respiratory rate 14 breaths/ min, fraction of inspired oxygen [FIO2]0.4). We found that FRC and lung compliance significantly (P < 0.01) increased from the supine to prone position (0.894 +/- 0.327 L vs 1.980 +/- 0.856 L and 91.4 +/- 55.2 mL/cm H2O vs 109.6 +/- 52.4 mL/cm H2O, respectively). On the contrary, the prone position reduced chest wall compliance (199.5 +/- 58.7 mL/cm H2O vs 160.5 +/- 45.4 mL/cm H2O, P < 0.01), thus total respiratory system compliance did not change. Resistance of the total respiratory system, lung, and chest wall were not modified on turning the patients prone. The increase in FRC and lung compliance was paralleled by a significant (P < 0.01) improvement of PaO2 from supine to prone position (130 +/- 31 vs 181 +/- 28 mm Hg, P < 0.01), while PaCO2 was unchanged. We conclude that, in anesthetized and paralyzed obese subjects, the prone position improves pulmonary function, increasing FRC, lung compliance, and oxygenation. PMID:8780285

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

    SciTech Connect

    Ramella, Sara; Trodella, Lucio; Ippolito, Edy; Fiore, Michele; Cellini, Francesco; Stimato, Gerardina; Gaudino, Diego; Greco, Carlo; Ramponi, Sara; Cammilluzzi, Eugenio; Cesarini, Claudio; Piermattei, Angelo; Cesario, Alfredo; D'Angelillo, Rolando Maria

    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.

  1. Evaluating a medical error taxonomy.

    PubMed Central

    Brixey, Juliana; Johnson, Todd R.; Zhang, Jiajie

    2002-01-01

    Healthcare has been slow in using human factors principles to reduce medical errors. The Center for Devices and Radiological Health (CDRH) recognizes that a lack of attention to human factors during product development may lead to errors that have the potential for patient injury, or even death. In response to the need for reducing medication errors, the National Coordinating Council for Medication Errors Reporting and Prevention (NCC MERP) released the NCC MERP taxonomy that provides a standard language for reporting medication errors. This project maps the NCC MERP taxonomy of medication error to MedWatch medical errors involving infusion pumps. Of particular interest are human factors associated with medical device errors. The NCC MERP taxonomy of medication errors is limited in mapping information from MEDWATCH because of the focus on the medical device and the format of reporting. PMID:12463789

  2. 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

  3. Wavefront error sensing

    NASA Technical Reports Server (NTRS)

    Tubbs, Eldred F.

    1986-01-01

    A two-step approach to wavefront sensing for the Large Deployable Reflector (LDR) was examined as part of an effort to define wavefront-sensing requirements and to determine particular areas for more detailed study. A Hartmann test for coarse alignment, particularly segment tilt, seems feasible if LDR can operate at 5 microns or less. The direct measurement of the point spread function in the diffraction limited region may be a way to determine piston error, but this can only be answered by a detailed software model of the optical system. The question of suitable astronomical sources for either test must also be addressed.

  4. Hip rotation range of motion in sitting and prone positions in healthy Japanese adults

    PubMed Central

    Han, Heonsoo; Kubo, Akira; Kurosawa, Kazuo; Maruichi, Shizuka; Maruyama, Hitoshi

    2015-01-01

    [Purpose] The aim of this study was to elucidate the difference in hip external and internal rotation ranges of motion (ROM) between the prone and sitting positions. [Subjects] The subjects included 151 students. [Methods] Hip rotational ROM was measured with the subjects in the prone and sitting positions. Two-way repeated measures analysis of variance (ANOVA) was used to analyze ipsilateral hip rotation ROM in the prone and sitting positions in males and females. The total ipsilateral hip rotation ROM was calculated by adding the measured values for external and internal rotations. [Results] Ipsilateral hip rotation ROM revealed significant differences between two positions for both left and right internal and external rotations. Hip rotation ROM was significantly higher in the prone position than in the sitting position. Hip rotation ROM significantly differed between the men and women. Hip external rotation ROM was significantly higher in both positions in men; conversely, hip internal rotation ROM was significantly higher in both positions in women. [Conclusion] Hip rotation ROM significantly differed between the sexes and between the sitting and prone positions. Total ipsilateral hip rotation ROM, total angle of external rotation, and total angle of internal rotation of the left and right hips greatly varied, suggesting that hip joint rotational ROM is widely distributed. PMID:25729186

  5. Prone versus Modified Supine Position in Percutaneous Nephrolithotomy: a Prospective Randomized Study

    PubMed Central

    Wang, Yanbo; Wang, Yan; Yao, Yunming; Xu, Ning; Zhang, Haifeng; Chen, Qihui; Lu, Zhihua; Hu, Jinghai; Wang, Xiaoqing; Lu, Ji; Hao, Yuanyuan; Jiang, Fengming; Hou, Yuchuan; Wang, Chunxi

    2013-01-01

    Objective: To perform a prospective randomized trial comparing the efficacy and safety of percutaneous nephrolithotomy (PCNL) in the prone and modified supine positions. Methods: Between August 2010 and August 2011, 102 patients with renal calculi and 20 patients with ureteral calculi were randomized to undergo fluoroscopy and ultrasound-guided PCNL procedures in the prone or modified supine position. Baseline characteristics, puncture position, numbers of punctures, operation time, stone free rate, loss of blood, hospital stay and second phase PCNL were compared in the two groups. Results: There were no significant differences in gender, age, body mass index, stone location, stone size and the presence of hydronephrosis between the two groups. The rate of second PCNL was significantly higher and the stone clearance rate was significantly lower in the modified supine than in the prone position group. Mean operation time was significantly lower in the prone than in the modified supine position group (78 min vs 88 min, P<0.05). There were no significant differences in rates of rib and calyx puncture, numbers of punctures, mean blood loss, and mean hospital stay between the two groups. Conclusions: Both the prone and modified supine positions are effective and safe for PCNL. Operation time was longer in the modified supine group, and patients undergoing PCNL in the modified supine position more frequently required a second operation due to a lower stone clearance rate. PMID:24046526

  6. 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

  7. Assessing Jail Inmates’ Proneness to Shame and Guilt: Feeling Bad About the Behavior or the Self?

    PubMed Central

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

    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 (TOSCA-SD; Hanson & Tangney, 1996) 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 of blame, anger, psychological symptoms, and substance use problems) was supported, paralleling results from community samples. Further, proneness to shame and guilt were differentially related to widely used risk measures from the field of criminal justice (e.g., criminal history, psychopathy, violence risk, antisocial personality). Guilt-proneness appears to be a protective factor, whereas there was no evidence that shame-proneness serves an inhibitory function. Subsequent analyses indicate these findings generalize quite well across gender and race. Implications for intervention and sentencing practices are discussed. PMID:21743757

  8. 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.

  9. Short-term effects of combining upright and prone positions in patients with ARDS: a prospective randomized study

    PubMed Central

    2011-01-01

    Introduction Prone position is known to improve oxygenation in patients with acute lung injury (ALI) and the acute respiratory distress syndrome (ARDS). Supine upright (semirecumbent) position also exerts beneficial effects on gas exchange in this group of patients. We evaluated the effect of combining upright and prone position on oxygenation and respiratory mechanics in patients with ALI or ARDS in a prospective randomized cross-over study. Methods After turning them prone from a supine position, we randomized the patients to a prone position or combined prone and upright position. After 2 hours, the position was changed to the other one for another 6 hours. The gas exchange and static compliance of the respiratory system, lungs, and chest wall were assessed in the supine position as well as every hour in the prone position. Results Twenty patients were enrolled in the study. The PaO2/FiO2 ratio improved significantly from the supine to the prone position and further significantly increased with additional upright position. Fourteen (70%) patients were classified as responders to the prone position, whereas 17 (85%) patients responded to the prone plus upright position compared with the supine position (P = n.s.). No statistically significant changes were found with respect to compliance. Conclusions Combining the prone position with the upright position in patients with ALI or ARDS leads to further improvement of oxygenation. Trial registration Clinical Trials No. NCT00753129 PMID:21955757

  10. SU-E-T-538: Does Abdominal Compression Through Prone Patient Position Reduce Respiratory Motion in Lung Cancer Radiotherapy?

    SciTech Connect

    Catron, T; Rosu, M; Weiss, E

    2014-06-01

    Purpose: This study assesses the effect of physiological abdominal compression from prone positioning by comparing respiratory-induced tumor movements in supine and prone positions. Methods: 19 lung cancer patients underwent repeated supine and prone free-breathing 4DCT scans. The effect of patient position on motion magnitude was investigated for tumors, lymph nodes (9 cases), and subgroups of central (11 cases), peripheral (8 cases) and small peripheral tumors (5 cases), by evaluating the population average excursions, absolute and relative to a carina-point. Results: Absolute motion analysis: In prone, motion increased by ~20% for tumors and ~25% for lymph nodes. Central tumors moved more compared to peripheral tumors in both supine and prone (~22%, and ~4% respectively). Central tumors movement increased by ~12% in prone. For peripheral tumors the increase in prone position was ~25% (~40% and 29% changes on along RL and AP directions). Motion relative to carina-point analysis: Overall, tumor excursions relative to carina-point increased by ~17% in prone. Lymph node relative magnitudes were lower by ~4%. Likewise, the central tumors moved ~7% less in prone. The subgroup of peripheral tumors exhibited increased amplitudes by ~44%; the small peripheral tumors had even larger relative displacements in prone (~46%). Conclusion: Tumor and lymph node movement in the patient population from this study averaged to be higher in prone than in supine position. Results from carina analysis also suggest that peripheral tissues have more physiologic freedom of motility when placed in the prone position, regardless of size. From these observations we should continue to avoid prone positioning for all types of primary lung tumor, suggesting that patients should receive radiotherapy for primary lung cancer in supine position to minimize target tissue mobility during normal respiratory effort. Further investigation will include more patients with peripheral tumors to validate our observations.

  11. Error Analysis in Mathematics Education.

    ERIC Educational Resources Information Center

    Rittner, Max

    1982-01-01

    The article reviews the development of mathematics error analysis as a means of diagnosing students' cognitive reasoning. Errors specific to addition, subtraction, multiplication, and division are described, and suggestions for remediation are provided. (CL)

  12. Skylab water balance error analysis

    NASA Technical Reports Server (NTRS)

    Leonard, J. I.

    1977-01-01

    Estimates of the precision of the net water balance were obtained for the entire Skylab preflight and inflight phases as well as for the first two weeks of flight. Quantitative estimates of both total sampling errors and instrumentation errors were obtained. It was shown that measurement error is minimal in comparison to biological variability and little can be gained from improvement in analytical accuracy. In addition, a propagation of error analysis demonstrated that total water balance error could be accounted for almost entirely by the errors associated with body mass changes. Errors due to interaction between terms in the water balance equation (covariances) represented less than 10% of the total error. Overall, the analysis provides evidence that daily measurements of body water changes obtained from the indirect balance technique are reasonable, precise, and relaible. The method is not biased toward net retention or loss.

  13. Standard Errors for Matrix Correlations.

    ERIC Educational Resources Information Center

    Ogasawara, Haruhiko

    1999-01-01

    Derives the asymptotic standard errors and intercorrelations for several matrix correlations assuming multivariate normality for manifest variables and derives the asymptotic standard errors of the matrix correlations for two factor-loading matrices. (SLD)

  14. Attitudes Toward Divorce, Commitment, and Divorce Proneness in First Marriages and Remarriages.

    PubMed

    Whitton, Sarah W; Stanley, Scott M; Markman, Howard J; Johnson, Christine A

    2013-04-01

    A random multistate sample of married individuals (N = 1,931) was used to explore whether more positive attitudes toward divorce and weaker commitment to marriage may contribute to the greater instability of remarriages than first marriages. Remarried adults, whether or not they brought children from a previous union into the remarriage, reported marital quality (happiness and conflict) equal to those in first marriages. They also reported more positive attitudes toward divorce, which were associated with higher divorce proneness (i.e., thinking about and taking actions toward divorce). Marriage type interacted with marital quality to predict divorce proneness, such that the association between low marital quality and divorce proneness was stronger for remarried individuals than for those in first marriages. This suggests that remarried adults may be more likely than adults in first marriages to take steps toward divorce when experiencing marital distress, possibly reflecting a weaker commitment to marriage. PMID:23630405

  15. Dysmorphic concern is related to delusional proneness and negative affect in a community sample.

    PubMed

    Keating, Charlotte; Thomas, Neil; Stephens, Jessie; Castle, David J; Rossell, Susan L

    2016-06-30

    Body image concerns are common in the general population and in some mental illnesses reach pathological levels. We investigated whether dysmorphic concern with appearance (a preoccupation with minor or imagined defects in appearance) is explained by psychotic processes in a community sample. In a cross-sectional design, two hundred and twenty six participants completed an online survey battery including: The Dysmorphic Concern Questionnaire; the Peters Delusional inventory; the Aberrant Salience Inventory; and the Depression, Anxiety, Stress Scale. Participants were native English speakers residing in Australia. Dysmorphic concern was positively correlated with delusional proneness, aberrant salience and negative emotion. Regression established that negative emotion and delusional proneness predicted dysmorphic concern, whereas, aberrant salience did not. Although delusional proneness was related to body dysmorphia, there was no evidence that it was related to aberrant salience. Understanding the contribution of other psychosis processes, and other health related variables to the severity of dysmorphic concern will be a focus of future research. PMID:27085667

  16. Suicide proneness in college students: relationships with gender, procrastination, and achievement motivation.

    PubMed

    Klibert, Jeffrey; Langhinrichsen-Rohling, Jennifer; Luna, Amy; Robichaux, Michelle

    2011-08-01

    This study examined the relationships between 2 academic dispositions (i.e., procrastination and achievement motivation) and 2 indices of suicidal proneness in college women and men. The degree these 2 academic dispositions could predict unique variance in suicide proneness scores, above and beyond the influence of depression and self-esteem was also examined for each gender. Participants included 475 (336 women, 139 men) undergraduates from a southeastern university. For both genders, procrastination and achievement motivation were significantly correlated at the univarate level with the suicide proneness indices. However, for college women, but not men, procrastination significantly accounted for unique amounts of variance in both suicide indices above and beyond the influence of depression and self-esteem. Implications for suicide intervention efforts directed toward college women and men are offered. PMID:24501841

  17. Prone positioning for ARDS following blunt chest trauma in late pregnancy.

    PubMed

    Kenn, S; Weber-Carstens, S; Weizsaecker, K; Bercker, S

    2009-07-01

    After a road traffic accident a pregnant patient at 34 weeks of gestation developed ARDS following blunt chest trauma, for which she required mechanical ventilation. Twenty-four hours after the accident, ongoing severe hypoxaemia with atelectasis mainly in the dorsal parts of the lung led to the decision to manage the patient in the prone position. Prone positioning over 8h resulted in a persistent improvement of oxygenation, which allowed extubation the following day. At term, however, our patient was admitted with dyspnoea, chest pain, haemodynamic instability and fetal bradycardia, for which she required emergency caesarean section followed by thoracotomy for haemothorax, from which she eventually made a full recovery. We have demonstrated that prone positioning can be used safely and effectively in a pregnant patient. It might be superior to other therapeutic options for improvement of oxygenation in pregnant patients. Careful positioning avoiding any external abdominal pressure and continuous fetal monitoring are mandatory. PMID:19464876

  18. Error Sources in Asteroid Astrometry

    NASA Technical Reports Server (NTRS)

    Owen, William M., Jr.

    2000-01-01

    Asteroid astrometry, like any other scientific measurement process, is subject to both random and systematic errors, not all of which are under the observer's control. To design an astrometric observing program or to improve an existing one requires knowledge of the various sources of error, how different errors affect one's results, and how various errors may be minimized by careful observation or data reduction techniques.

  19. 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.

  20. Prone Sleeping Impairs Circulatory Control During Sleep in Healthy Term Infants: Implications for SIDS

    PubMed Central

    Yiallourou, Stephanie R.; Walker, Adrian M.; Horne, Rosemary S. C.

    2008-01-01

    Study Objectives: To determine the effects of sleeping position on development of circulatory control in infants over the first 6 months of postnatal age (PNA). Design: Effects of sleeping position, sleep state and PNA on beat-beat heart rate (HR) and mean arterial pressure (MAP) responses to a head-up tilt (HUT) were assessed during sleep in infants at 2–4 wks, 2–3 mo and 5–6 mo PNA. Measurements: Daytime polysomnography was performed on 20 full-term infants (12 F/8 M) and MAP was recorded continuously and noninvasively (Finometer™). HUTs of 15° were performed during active sleep (AS) and quiet sleep (QS) in both the prone and supine sleeping positions. MAP and HR data were expressed as the percentage change from baseline, and responses were divided into initial, middle and late phases. Results: In the supine position HUT usually resulted in an initial increase (P < 0.05) in HR and MAP, followed by decreases (P < 0.05) in HR and MAP in the middle phase; subsequently HR and MAP returned to baseline in the late phase. By contrast, in the prone position the initial HUT-induced rises in HR and MAP were usually absent, and at 2–3 mo MAP actually decreased (P < 0.05); subsequently HR but not MAP returned to baseline. At 2–3 mo, MAP was lower (P < 0.05) in prone than supine sleeping throughout the HUT. Conclusions: Prone sleeping alters MAP responses to a HUT during QS at 2–3 mo PNA. Decreased autonomic responsiveness may contribute to the increased risk for SIDS of infants sleeping in the prone position. Citation: Yiallourou SR, Walker AM; Horne RSC. Prone sleeping impairs circulatory control during sleep in healthy term infants: implications for SIDS. SLEEP 2008;31(8):1139-1146. PMID:18714786

  1. Effects of the prone position on respiratory mechanics and gas exchange during acute lung injury.

    PubMed

    Pelosi, P; Tubiolo, D; Mascheroni, D; Vicardi, P; Crotti, S; Valenza, F; Gattinoni, L

    1998-02-01

    We studied 16 patients with acute lung injury receiving volume-controlled ventilation to assess the relationships between gas exchange and respiratory mechanics before, during, and after 2 h in the prone position. We measured the end-expiratory lung volume (EELV, helium dilution), the total respiratory system (Cst,rs), the lung (Cst,L) and the thoracoabdominal cage (Cst,w) compliances (end-inspiratory occlusion technique and esophageal balloon), the hemodynamics, and gas exchange. In the prone position, PaO2 increased from 103.2 +/- 23.8 to 129.3 +/- 32.9 mm Hg (p < 0.05) without significant changes of Cst,rs and EELV. However, Cst,w decreased from 204.8 +/- 97.4 to 135.9 +/- 52.5 ml/cm H2O (p < 0.01) and the decrease was correlated with the oxygenation increase (r = 0.62, p < 0.05). Furthermore, the greater the baseline supine Cst,w, the greater its decrease in the prone position (r = 0.82, p < 0.01). Consequently, the oxygenation changes in the prone position were predictable from baseline supine Cst,w (r = 0.80, p < 0.01). Returning to the supine position, Cst,rs increased compared with baseline (42.3 +/- 14.4 versus 38.4 +/- 13.7 ml/cm H2O; p < 0.01), mainly because of the lung component (57.5 +/- 25.1 versus 52.4 +/- 23.3 ml/cm H2O; p < 0.01). Thus, (1) baseline Cst,w and its changes may play a role in determining the oxygenation response in the prone position; (2) the prone position improves Cst,rs and Cst,L when the supine position is resumed. PMID:9476848

  2. 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

  3. Uncertainty quantification and error analysis

    SciTech Connect

    Higdon, Dave M; Anderson, Mark C; Habib, Salman; Klein, Richard; Berliner, Mark; Covey, Curt; Ghattas, Omar; Graziani, Carlo; Seager, Mark; Sefcik, Joseph; Stark, Philip

    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.

  4. Is homologous recombination really an error-free process?

    PubMed Central

    Guirouilh-Barbat, Josée; Lambert, Sarah; Bertrand, Pascale; Lopez, Bernard S.

    2014-01-01

    Homologous recombination (HR) is an evolutionarily conserved process that plays a pivotal role in the equilibrium between genetic stability and diversity. HR is commonly considered to be error-free, but several studies have shown that HR can be error-prone. Here, we discuss the actual accuracy of HR. First, we present the product of genetic exchanges (gene conversion, GC, and crossing over, CO) and the mechanisms of HR during double strand break repair and replication restart. We discuss the intrinsic capacities of HR to generate genome rearrangements by GC or CO, either during DSB repair or replication restart. During this process, abortive HR intermediates generate genetic instability and cell toxicity. In addition to genome rearrangements, HR also primes error-prone DNA synthesis and favors mutagenesis on single stranded DNA, a key DNA intermediate during the HR process. The fact that cells have developed several mechanisms protecting against HR excess emphasize its potential risks. Consistent with this duality, several pro-oncogenic situations have been consistently associated with either decreased or increased HR levels. Nevertheless, this versatility also has advantages that we outline here. We conclude that HR is a double-edged sword, which on one hand controls the equilibrium between genome stability and diversity but, on the other hand, can jeopardize the maintenance of genomic integrity. Therefore, whether non-homologous end joining (which, in contrast with HR, is not intrinsically mutagenic) or HR is the more mutagenic process is a question that should be re-evaluated. Both processes can be “Dr. Jekyll” in maintaining genome stability/variability and “Mr. Hyde” in jeopardizing genome integrity. PMID:24966870

  5. 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.

  6. Vicarious trial and error.

    PubMed

    Redish, A David

    2016-02-19

    When rats come to a decision point, they sometimes pause and look back and forth as if deliberating over the choice; at other times, they proceed as if they have already made their decision. In the 1930s, this pause-and-look behaviour was termed 'vicarious trial and error' (VTE), with the implication that the rat was 'thinking about the future'. The discovery in 2007 that the firing of hippocampal place cells gives rise to alternating representations of each of the potential path options in a serial manner during VTE suggested a possible neural mechanism that could underlie the representations of future outcomes. More-recent experiments examining VTE in rats suggest that there are direct parallels to human processes of deliberative decision making, working memory and mental time travel. PMID:26891625

  7. 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.

  8. Errors inducing radiation overdoses.

    PubMed

    Grammaticos, Philip C

    2013-01-01

    There is no doubt that equipments exposing radiation and used for therapeutic purposes should be often checked for possibly administering radiation overdoses to the patients. Technologists, radiation safety officers, radiologists, medical physicists, healthcare providers and administration should take proper care on this issue. "We must be beneficial and not harmful to the patients", according to the Hippocratic doctrine. Cases of radiation overdose are often reported. A series of cases of radiation overdoses have recently been reported. Doctors who were responsible, received heavy punishments. It is much better to prevent than to treat an error or a disease. A Personal Smart Card or Score Card has been suggested for every patient undergoing therapeutic and/or diagnostic procedures by the use of radiation. Taxonomy may also help. PMID:24251304

  9. Validity and internal consistency reliability of a computerized test to assess prone extension in children ages four to six years.

    PubMed

    Lin, Chin-Kai; Wu, Huey-Min; Kuo, Bor-Chen; Li, Cheng-Hsaun

    2010-08-01

    The objective of this study was to develop a computerized test of prone extension to measure performance of prone extension in children 4 to 6 years of age. The participants were selected from kindergartens, comprising 132 boys and 107 girls with a mean age of 5 yr. 2 mo. (SD = 6 mo.). Sensitivity and specificity of the computerized test of prone extension were assessed by comparison with the judgments of an expert, an occupational therapist with more than 20 yr. of pediatric experience, as the criterion standard. The computerized test of prone extension identified children with poor outcomes with a sensitivity of 0.83, a specificity of 0.88, and an accuracy of 0.87. The internal reliability index was 0.81. The computerized test of prone extension could be of value in detecting problems of antigravity posture in prone extension and permitting early intervention to correct it. PMID:21058600

  10. Register file soft error recovery

    DOEpatents

    Fleischer, Bruce M.; Fox, Thomas W.; Wait, Charles D.; Muff, Adam J.; Watson, III, Alfred T.

    2013-10-15

    Register file soft error recovery including a system that includes a first register file and a second register file that mirrors the first register file. The system also includes an arithmetic pipeline for receiving data read from the first register file, and error detection circuitry to detect whether the data read from the first register file includes corrupted data. The system further includes error recovery circuitry to insert an error recovery instruction into the arithmetic pipeline in response to detecting the corrupted data. The inserted error recovery instruction replaces the corrupted data in the first register file with a copy of the data from the second register file.

  11. PALATAL DYSMORPHOGENESIS: QUANTITATIVE RT-PCR

    EPA Science Inventory

    ABSTRACT

    Palatal Dysmorphogenesis : Quantitative RT-PCR

    Gary A. Held and Barbara D. Abbott

    Reverse transcription PCR (RT-PCR) is a very sensitive method for detecting mRNA in tissue samples. However, as it is usually performed it is does not yield quantitativ...

  12. 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.

  13. Standard Deviation and Intra Prediction Mode Based Adaptive Spatial Error Concealment (SEC) in H.264/AVC

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Wang, Lei; Ikenaga, Takeshi; Goto, Satoshi

    Transmission of compressed video over error prone channels may result in packet losses or errors, which can significantly degrade the image quality. Therefore an error concealment scheme is applied at the video receiver side to mask the damaged video. Considering there are 3 types of MBs (Macro Blocks) in natural video frame, i. e., Textural MB, Edged MB, and Smooth MB, this paper proposes an adaptive spatial error concealment which can choose 3 different methods for these 3 different MBs. For criteria of choosing appropriate method, 2 factors are taken into consideration. Firstly, standard deviation of our proposed edge statistical model is exploited. Secondly, some new features of latest video compression standard H.264/AVC, i. e., intra prediction mode is also considered for criterion formulation. Compared with previous works, which are only based on deterministic measurement, proposed method achieves the best image recovery. Subjective and objective image quality evaluations in experiments confirmed this.

  14. 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)

  15. Effect of Indirect Teacher Influence on Dependent-Prone Students' Learning Outcomes in Secondary School Mathematics

    ERIC Educational Resources Information Center

    Adegoke, Benson Adesina

    2011-01-01

    Introduction: Student's personality orientation and teacher's classroom behavior are among the many factors that influence student's learning. In this study, the author examined the effect of indirect teacher influence on dependent-prone students' learning outcomes (achievement) in mathematics at the senior secondary school level. Method: The…

  16. Change in trunk muscle activities with prone bridge exercise in patients with chronic low back pain

    PubMed Central

    Kong, Yong-soo; Park, Seol; Kweon, Mi-Gyong; Park, Ji-won

    2016-01-01

    [Purpose] The aim of this study was to determine the effect of three different bridge exercises on internal oblique, external oblique, transverse abdominis, and erector spinae activities. [Subjects and Methods] Forty-five subjects with chronic low back pain participated in this study. The training outcome was evaluated with three different testing methods: supine bridge exercise, supine bridge on Swiss ball exercise, and prone bridge exercise. The activities of the transverse abdominis, internal oblique, external oblique, and erector spinae were measured using surface electromyography. [Results] There were significant differences in the internal oblique, external oblique, and erector spinae according to the three kinds of bridging exercises. The internal oblique, external oblique and transverse abdominis activities were highest in the prone bridge exercise, followed by those in the supine bridge on Swiss ball exercise, and supine bridge exercises. The activity of erector spine was highest in the supine bridge on Swiss ball exercise followed by the supine bridge exercise and prone bridge exercise. [Conclusion] These results suggest that prone bridge exercise is more effective than conventional supine bridge exercise and supine bridge on Swiss ball in increasing trunk muscle activity of chronic low back pain patients. PMID:26957771

  17. A Modified Obesity Proneness Model Predicts Adolescent Weight Concerns and Inability to Self-Regulate Eating

    ERIC Educational Resources Information Center

    Nickelson, Jen; Bryant, Carol A.; McDermott, Robert J.; Buhi, Eric R.; DeBate, Rita D.

    2012-01-01

    Background: The prevalence of obesity among high school students has risen in recent decades. Many high school students report trying to lose weight and some engage in disordered eating to do so. The obesity proneness model suggests that parents may influence their offspring's development of disordered eating. This study examined the…

  18. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... hazards; (5) Require within flood-prone areas new and replacement water supply systems to be designed to... facilities, be designed so that below the base flood level the structure is watertight with walls... designed to automatically equalize hydrostatic flood forces on exterior walls by allowing for the entry...

  19. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... hazards; (5) Require within flood-prone areas new and replacement water supply systems to be designed to... facilities, be designed so that below the base flood level the structure is watertight with walls... designed to automatically equalize hydrostatic flood forces on exterior walls by allowing for the entry...

  20. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... hazards; (5) Require within flood-prone areas new and replacement water supply systems to be designed to... facilities, be designed so that below the base flood level the structure is watertight with walls... designed to automatically equalize hydrostatic flood forces on exterior walls by allowing for the entry...

  1. Shame and Guilt-Proneness in Adolescents: Gene-Environment Interactions

    PubMed Central

    Szentágotai-Tătar, Aurora; Chiș, Adina; Vulturar, Romana; Dobrean, Anca; Cândea, Diana Mirela; Miu, Andrei C.

    2015-01-01

    Rooted in people’s preoccupation with how they are perceived and evaluated, shame and guilt are self-conscious emotions that play adaptive roles in social behavior, but can also contribute to psychopathology when dysregulated. Shame and guilt-proneness develop during childhood and adolescence, and are influenced by genetic and environmental factors that are little known to date. This study investigated the effects of early traumatic events and functional polymorphisms in the brain-derived neurotrophic factor (BDNF) gene and the serotonin transporter gene promoter (5-HTTLPR) on shame and guilt in adolescents. A sample of N = 271 healthy adolescents between 14 and 17 years of age filled in measures of early traumatic events and proneness to shame and guilt, and were genotyped for the BDNF Val66Met and 5-HTTLPR polymorphisms. Results of moderator analyses indicated that trauma intensity was positively associated with guilt-proneness only in carriers of the low-expressing Met allele of BDNF Val66Met. This is the first study that identifies a gene-environment interaction that significantly contributes to guilt proneness in adolescents, with potential implications for developmental psychopathology. PMID:26230319

  2. 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…

  3. A Modified Obesity Proneness Model Predicts Adolescent Weight Concerns and Inability to Self-Regulate Eating

    ERIC Educational Resources Information Center

    Nickelson, Jen; Bryant, Carol A.; McDermott, Robert J.; Buhi, Eric R.; DeBate, Rita D.

    2012-01-01

    Background: The prevalence of obesity among high school students has risen in recent decades. Many high school students report trying to lose weight and some engage in disordered eating to do so. The obesity proneness model suggests that parents may influence their offspring's development of disordered eating. This study examined the

  4. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 44 Emergency Management and Assistance 1 2014-10-01 2014-10-01 false Planning considerations for mudslide (i.e., mudflow)-prone areas. 60.23 Section 60.23 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR...

  5. "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…

  6. The association between psychosis proneness and sensory gating in cocaine-dependent patients and healthy controls.

    PubMed

    Gooding, Diane C; Gjini, Klevest; Burroughs, Scott A; Boutros, Nash N

    2013-12-30

    This was a naturalistic study of 23 abstinent cocaine-dependent patients and 38 controls who were studied using a paired-stimulus paradigm to elicit three mid-latency auditory evoked responses (MLAERs), namely, the P50, N100, and P200. Sensory gating was defined as the ratio of the S2 amplitude to the S1 amplitude. Psychosis-proneness was assessed using four Chapman psychosis proneness scales measuring perceptual aberration, magical ideation, social anhedonia, and physical anhedonia. Omnibus correlations based upon the entire sample revealed significant and differential relationships between the MLAER components and psychosis-proneness. Social Anhedonia scale scores accounted for the largest proportion of variance in the P50 gating ratio, while Perceptual Aberration scores accounted for the largest proportion of variance in P200 gating. Psychosis proneness and sensory gating appear to be associated. In particular, poorer P50 gating is related to higher scores on the Social Anhedonia scale in healthy controls and across mixed samples of cocainede-pendent patients and controls. These findings hold significance for the further understanding of the relationship between deficient sensory gating ability and the propensity to developing psychotic symptoms in a vulnerable population like cocaine-dependent individuals. PMID:24064464

  7. [A case of endotracheal intubation in prone position utilizing PENTAX-Airwayscope for morbidly obese patient].

    PubMed

    Suzuki, Hiroto; Nakajima, Waka; Aoyagi, Mitsuo; Takahashi, Minori; Kuzuta, Toshimichi; Osaki, Mami

    2012-04-01

    We experienced the airway management of a morbidly obese patient in prone position utilizing PENTAX-Airwayscope (AWS) which is a novel airway device for endotracheal intubation. A 29-year-old man, who was 150 kg in weight and 51.9 kg x m(-2) in body mass index, was scheduled for the discectomy for lumbar disc herniation. After the topical anesthesia with lidocaine spray, the patient lay on his stomach by himself on the table. Following the induction of general anesthesia with ketamine and dexmedetomidine in prone position, an anatomically curved blade (INTLOCK) was inserted to his oral cavity first, then the body of AWS was attached. With the patient breathing spontaneously, we successfully inserted the reinforced endotracheal tube. After the maintenance of anesthesia with continuous infusion of dexmedetomidine, ketamin and remifentanil, the patient awoke clearly without pain and endotracheal tube was removed safely in the prone position. Although the prone position is not the standard position for endotracheal intubation under general anesthesia, our technique could be performed in emergency situations. PMID:22590940

  8. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 44 Emergency Management and Assistance 1 2013-10-01 2013-10-01 false Planning considerations for mudslide (i.e., mudflow)-prone areas. 60.23 Section 60.23 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National...

  9. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 44 Emergency Management and Assistance 1 2012-10-01 2011-10-01 true Planning considerations for mudslide (i.e., mudflow)-prone areas. 60.23 Section 60.23 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National...

  10. No-tillage Improvement of Soil Physical Quality in Calcareous, Degradation-prone, Semiarid Soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many soils in the semiarid Mediterranean Ebro Valley of Spain are prone to physical and chemical degradation due to their silty texture, low organic matter contents, and presence of carbonates, gypsum, and other soluble salts. Rainfed agriculture on these soils is also hindered by the scarcity of wa...

  11. Do Guilt- and Shame-Proneness Differentially Predict Prosocial, Aggressive, and Withdrawn Behaviors during Early Adolescence?

    ERIC Educational Resources Information Center

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

    2014-01-01

    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…

  12. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... flood damage; (6) Flood warning and emergency preparedness plans; (7) Provision for alternative... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance...

  13. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... flood damage; (6) Flood warning and emergency preparedness plans; (7) Provision for alternative... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance...

  14. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... flood damage; (6) Flood warning and emergency preparedness plans; (7) Provision for alternative... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance...

  15. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... flood damage; (6) Flood warning and emergency preparedness plans; (7) Provision for alternative... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance...

  16. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... flood damage; (6) Flood warning and emergency preparedness plans; (7) Provision for alternative... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance...

  17. "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

  18. Female Coronary-Prone Behaviors: Relationship to Alpha and Self-Concept.

    ERIC Educational Resources Information Center

    Comer, David W.; And Others

    Researchers have been working toward isolating a set of psychological risk factors that would reliably predict coronary problems. This coronary-prone behavior pattern, Type A, is characterized by extremes of competitiveness, striving for achievement, impatience, and hostility. Differences were examined between 20 Type A and 20 Type B…

  19. Differentiating fall-prone and healthy adults using local dynamic stability

    PubMed Central

    Lockhart, Thurmon E.; Liu, Jian

    2010-01-01

    Variability in kinematic and spatio-temporal gait parameters has long been equated with stability and used to differentiate fallers from non-fallers. Recently, a mathematically rigorous measure of local dynamic stability has been proposed based on the non-linear dynamics theory to differentiate fallers from non-fallers. This study investigated whether the assessment of local dynamic stability can identify fall-prone elderly individuals who were unable to successfully avoid slip-induced falls. Five healthy young, four healthy elderly and four fall-prone elderly individuals participated in a walking experiment. Local dynamic stability was quantified by the maximum Lyapunov exponent. The fall-prone elderly were found to exhibit significantly lower local dynamic stability (i.e. greater sensitivity to local perturbations), as compared to their healthy counterparts. In addition to providing evidence that the increased falls of the elderly may be due to the inability to attenuate/control stride-to-stride disturbances during locomotion, the current study proposed the opportunity of using local dynamic stability as a potential indicator of risk of falling. Early identification of individuals with a higher risk of falling is important for effective fall prevention. The findings from this study suggest that local dynamic stability may be used as a potential fall predictor to differentiate fall-prone adults. PMID:19034782

  20. The effects of prone bridge exercise on trunk muscle thickness in chronic low back pain patients

    PubMed Central

    Kong, Yong-Soo; Lee, Woo-Jin; Park, Seol; Jang, Gwon-Uk

    2015-01-01

    [Purpose] This study aimed to investigate the effects of prone bridge exercise on trunk muscle thickness. [Subjects and Methods] Thirty-seven chronic low back pain patients participated in this study. Each participant was randomly assigned to one of three exercise groups, namely, a prone bridge exercise group, supine bridge exercise on a Swiss ball group, and supine bridge exercise group. The thicknesses of the transverse abdominis (TrA), internal oblique (IO), and external oblique (EO) were measured using ultrasound. [Results] After eight weeks of training, the three groups showed significant increases in the thicknesses of the TrA, IO, and EO. Among the groups, TrA and IO showed significantly different muscle thicknesses. [Conclusion] The prone bridge exercise significantly affected the thicknesses of the TrA, IO, and EO unlike the supine bridge exercises. Based on the results of this study, the prone bridge exercise is a more effective method to improve trunk stability than conventional supine bridge exercises. PMID:26311928

  1. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., see the List of CFR Sections Affected, which appears in the Finding Aids section of the printed volume... 44 Emergency Management and Assistance 1 2012-10-01 2011-10-01 true Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency Management and Assistance FEDERAL...

  2. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., see the List of CFR Sections Affected, which appears in the Finding Aids section of the printed volume... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency Management and Assistance FEDERAL...

  3. Clinical applications using digital PCR.

    PubMed

    Bizouarn, Francisco

    2014-01-01

    Molecular diagnostics and disease-specific tailored treatments are now being introduced to patients at many hospitals and clinics throughout the world (Strain and Richman, Curr Opin HIV AIDS 8:106-110, 2013) and becoming prevalent in the nonscientific literature. Instead of generically using a "one treatment fits all" approach that may have varying levels of effectiveness to different patients, patient-specific molecular profiling based on the genetic makeup of the disease and/or a more accurate pathogen titer could provide more effective treatments with fewer unwanted side effects. One commonly known example of this scenario is epidermal growth factor receptor (EGFR). EGFR is upregulated in many cancers, including many lung and colorectal cancers. Commonly used treatments for these include the receptor blockers cetuximab or panitumumab and tyrosine kinase inhibitors erlotinib or gefitinib. These agents are effective at reducing out-of-control cell cycling and tumor proliferation, but only if downstream signaling kinases and phosphatases are not mutated. Known oncogenes such as BRAF V600E and KRAS G12/13 that are constitutively activated render these treatments ineffective. The use of known ineffective drugs and treatments can thus be avoided reducing time to more effective treatments, reducing cost, and increasing patient well-being. Although digital PCR is for all practical purposes a "new" technology, there is already tremendous interest in its potential for the clinical diagnostics arena. Specificity of the information acquired, accuracy of results, time to results, and cost per sample analyzed are making dPCR an attractive tool for this field. Three areas where dPCR will have a noticeable impact are pathogen/viral detection and quantitation, copy number variations, and rare mutation detection and abundance, but it will inevitably expand from these as the technology becomes more and more prevalent. This chapter discusses digital PCR assay optimization and validation, pathogen/viral detection and quantitation, copy number variation, and rare mutation abundance assays. The sample methods described below utilize the QX100/QX200 methodologies, but with the exception of reaction sub-partitioning (dependent on the instrumentation used) most other parameters remain the same. PMID:24740231

  4. The 13 errors.

    PubMed

    Flower, J

    1998-01-01

    The reality is that most change efforts fail. McKinsey & Company carried out a fascinating research project on change to "crack the code" on creating and managing change in large organizations. One of the questions they asked--and answered--is why most organizations fail in their efforts to manage change. They found that 80 percent of these failures could be traced to 13 common errors. They are: (1) No winning strategy; (2) failure to make a compelling and urgent case for change; (3) failure to distinguish between decision-driven and behavior-dependent change; (4) over-reliance on structure and systems to change behavior; (5) lack of skills and resources; (6) failure to experiment; (7) leaders' inability or unwillingness to confront how they and their roles must change; (8) failure to mobilize and engage pivotal groups; (9) failure to understand and shape the informal organization; (10) inability to integrate and align all the initiatives; (11) no performance focus; (12) excessively open-ended process; and (13) failure to make the whole process transparent and meaningful to individuals. PMID:10351717

  5. Contour Error Map Algorithm

    NASA Technical Reports Server (NTRS)

    Merceret, Francis; Lane, John; Immer, Christopher; Case, Jonathan; Manobianco, John

    2005-01-01

    The contour error map (CEM) algorithm and the software that implements the algorithm are means of quantifying correlations between sets of time-varying data that are binarized and registered on spatial grids. The present version of the software is intended for use in evaluating numerical weather forecasts against observational sea-breeze data. In cases in which observational data come from off-grid stations, it is necessary to preprocess the observational data to transform them into gridded data. First, the wind direction is gridded and binarized so that D(i,j;n) is the input to CEM based on forecast data and d(i,j;n) is the input to CEM based on gridded observational data. Here, i and j are spatial indices representing 1.25-km intervals along the west-to-east and south-to-north directions, respectively; and n is a time index representing 5-minute intervals. A binary value of D or d = 0 corresponds to an offshore wind, whereas a value of D or d = 1 corresponds to an onshore wind. CEM includes two notable subalgorithms: One identifies and verifies sea-breeze boundaries; the other, which can be invoked optionally, performs an image-erosion function for the purpose of attempting to eliminate river-breeze contributions in the wind fields.

  6. Sepsis: Medical errors in Poland.

    PubMed

    Rorat, Marta; Jurek, Tomasz

    2016-01-01

    Health, safety and medical errors are currently the subject of worldwide discussion. The authors analysed medico-legal opinions trying to determine types of medical errors and their impact on the course of sepsis. The authors carried out a retrospective analysis of 66 medico-legal opinions issued by the Wroclaw Department of Forensic Medicine between 2004 and 2013 (at the request of the prosecutor or court) in cases examined for medical errors. Medical errors were confirmed in 55 of the 66 medico-legal opinions. The age of victims varied from 2 weeks to 68 years; 49 patients died. The analysis revealed medical errors committed by 113 health-care workers: 98 physicians, 8 nurses and 8 emergency medical dispatchers. In 33 cases, an error was made before hospitalisation. Hospital errors occurred in 35 victims. Diagnostic errors were discovered in 50 patients, including 46 cases of sepsis being incorrectly recognised and insufficient diagnoses in 37 cases. Therapeutic errors occurred in 37 victims, organisational errors in 9 and technical errors in 2. In addition to sepsis, 8 patients also had a severe concomitant disease and 8 had a chronic disease. In 45 cases, the authors observed glaring errors, which could incur criminal liability. There is an urgent need to introduce a system for reporting and analysing medical errors in Poland. The development and popularisation of standards for identifying and treating sepsis across basic medical professions is essential to improve patient safety and survival rates. Procedures should be introduced to prevent health-care workers from administering incorrect treatment in cases. PMID:26113542

  7. Comparison of next-generation droplet digital PCR (ddPCR) with quantitative PCR (qPCR) for enumeration of Cryptosporidium oocysts in faecal samples.

    PubMed

    Yang, Rongchang; Paparini, Andrea; Monis, Paul; Ryan, Una

    2014-12-01

    Clinical microbiology laboratories rely on quantitative PCR for its speed, sensitivity, specificity and ease-of-use. However, quantitative PCR quantitation requires the use of a standard curve or normalisation to reference genes. Droplet digital PCR provides absolute quantitation without the need for calibration curves. A comparison between droplet digital PCR and quantitative PCR-based analyses was conducted for the enteric parasite Cryptosporidium, which is an important cause of gastritis in both humans and animals. Two loci were analysed (18S rRNA and actin) using a range of Cryptosporidium DNA templates, including recombinant plasmids, purified haemocytometer-counted oocysts, commercial flow cytometry-counted oocysts and faecal DNA samples from sheep, cattle and humans. Each method was evaluated for linearity, precision, limit of detection and cost. Across the same range of detection, both methods showed a high degree of linearity and positive correlation for standards (R(2)⩾0.999) and faecal samples (R(2)⩾0.9750). The precision of droplet digital PCR, as measured by mean Relative Standard Deviation (RSD;%), was consistently better compared with quantitative PCR, particularly for the 18S rRNA locus, but was poorer as DNA concentration decreased. The quantitative detection of quantitative PCR was unaffected by DNA concentration, but droplet digital PCR quantitative PCR was less affected by the presence of inhibitors, compared with quantitative PCR. For most templates analysed including Cryptosporidium-positive faecal DNA, the template copy numbers, as determined by droplet digital PCR, were consistently lower than by quantitative PCR. However, the quantitations obtained by quantitative PCR are dependent on the accuracy of the standard curve and when the quantitative PCR data were corrected for pipetting and DNA losses (as determined by droplet digital PCR), then the sensitivity of both methods was comparable. A cost analysis based on 96 samples revealed that the overall cost (consumables and labour) of droplet digital PCR was two times higher than quantitative PCR. Using droplet digital PCR to precisely quantify standard dilutions used for high-throughput and cost-effective amplifications by quantitative PCR would be one way to combine the advantages of the two technologies. PMID:25229177

  8. Real-Time PCR (qPCR) Primer Design Using Free Online Software

    ERIC Educational Resources Information Center

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

    Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most

  9. Real-Time PCR (qPCR) Primer Design Using Free Online Software

    ERIC Educational Resources Information Center

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

    Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most…

  10. Phenotypic and functional alterations of pDCs in lupus-prone mice

    PubMed Central

    Zhou, Zhenyuan; Ma, Jianyang; Xiao, Chunyuan; Han, Xiao; Qiu, Rong; Wang, Yan; Zhou, Yingying; Wu, Li; Huang, Xinfang; Shen, Nan

    2016-01-01

    Plasmacytoid dendritic cells (pDCs) were considered to be the major IFNα source in systemic lupus erythematosus (SLE) but their phenotype and function in different disease status have not been well studied. To study the function and phenotype of pDCs in lupus-prone mice we used 7 strains of lupus-prone mice including NZB/W F1, NZB, NZW, NZM2410, B6.NZMSle1/2/3, MRL/lpr and BXSB/Mp mice and C57BL/6 as control mice. Increased spleen pDC numbers were found in most lupus mice compared to C57BL/6 mice. The IFNα-producing ability of BM pDCs was similar between lupus and C57BL/6 mice, whereas pDCs from the spleens of NZB/W F1 and NZB mice produced more IFNα than pDCs from the spleens of C57BL/6 mice. Furthermore, spleen pDCs from MRL-lpr and NZM2410 mice showed increased responses to Tlr7 and Tlr9, respectively. As the disease progressed, IFN signature were evaluated in both BM and spleen pDC from lupus prone mice and the number of BM pDCs and their ability to produce IFNα gradually decreased in lupus-prone mice. In conclusion, pDC are activated alone with disease development and its phenotype and function differ among lupus-prone strains, and these differences may contribute to the development of lupus in these mice. PMID:26879679

  11. A Prospective Study of Intrafraction Prostate Motion in the Prone vs. Supine Position

    SciTech Connect

    Wilder, Richard B.; Chittenden, Lucy; Mesa, Albert V.; Bunyapanasarn, Jane; Agustin, Jeff; Lizarde, Jessica; Ravera, John; Tokita, Kenneth M.

    2010-05-01

    Purpose: To prospectively analyze prostate intrafraction motion in the prone vs. supine position and to assess patient satisfaction with these two positions. Methods and Materials: Fifteen prostate cancer patients underwent implantation of five fiducial gold seeds in their prostate for localization. Patients were treated with high-dose-rate brachytherapy to 2,200 cGy followed by intensity-modulated radiation therapy (IMRT) to 5,040 cGy. Patients underwent computed tomography simulation and IMRT in the prone position. For the first five IMRT treatments, an electronic portal imaging system was used to acquire anteroposterior (AP) and lateral images pretreatment and posttreatment. We then repositioned each patient supine and repeated the process, resulting in 600 images. Results: Mean +- standard deviation intrafraction prostate motion was 2.1 +- 1.2 mm and 1.7 +- 1.4 mm (AP, p = 0.47), 2.2 +- 2.0 mm and 1.6 +- 1.8 mm (superoinferior, p = 0.16), and 1.0 +- 1.2 mm and 0.6 +- 0.9 mm (left-right, p = 0.03) in the prone and supine positions, respectively. Eighty percent of patients stated that they were more comfortable in the supine position (p = 0.02). Conclusions: Prone and supine positions resulted in a similar magnitude of AP and superoinferior intrafraction prostate motion (2 mm). Because there was no significant difference in the magnitude of AP and superoinferior prostate motion prone vs. supine and patients were more comfortable in the supine position, patients now undergo IMRT to the prostate and seminal vesicles at our center in the supine position.

  12. Direct in situ rt-PCR.

    PubMed

    Lossi, Laura; Gambino, Graziana; Salio, Chiara; Merighi, Adalberto

    2011-01-01

    In situ polymerase chain reaction (PCR) is a histological technique that exploits the advantages of PCR for detection of mRNA directly in tissue sections. It somehow conjugates together PCR and in situ hybridization that is more traditionally employed for mRNA localization in cell organelles, intact cells, or tissue sections. This chapter describes the application of in situ PCR for neuropeptide mRNA localization. We provide here a detailed protocol for direct in situ reverse transcription (RT) PCR (RT-PCR) with nonradioactive probes after fixation and paraffin embedding or cryosectioning. Digoxigenin-labeled nucleotides (digoxigenin-11-dUTP) are incorporated in the PCR product after RT and subsequently detected with an anti-digoxigenin antibody conjugated with alkaline phosphatase. The procedure can be modified for use with fluorescent probes and employed in combination with enzyme/fluorescence immunocytochemical labeling. PMID:21922403

  13. A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells

    PubMed Central

    Berman, Jennifer R.; Postovit, Lynne-Marie

    2016-01-01

    The rapid adoption of gene editing tools such as CRISPRs and TALENs for research and eventually therapeutics necessitates assays that can rapidly detect and quantitate the desired alterations. Currently, the most commonly used assay employs “mismatch nucleases” T7E1 or “Surveyor” that recognize and cleave heteroduplexed DNA amplicons containing mismatched base-pairs. However, this assay is prone to false positives due to cancer-associated mutations and/or SNPs and requires large amounts of starting material. Here we describe a powerful alternative wherein droplet digital PCR (ddPCR) can be used to decipher homozygous from heterozygous mutations with superior levels of both precision and sensitivity. We use this assay to detect knockout inducing alterations to stem cell associated proteins, NODAL and SFRP1, generated using either TALENs or an “all-in-one” CRISPR/Cas plasmid that we have modified for one-step cloning and blue/white screening of transformants. Moreover, we highlight how ddPCR can be used to assess the efficiency of varying TALEN-based strategies. Collectively, this work highlights how ddPCR-based screening can be paired with CRISPR and TALEN technologies to enable sensitive, specific, and streamlined approaches to gene editing and validation. PMID:27089539

  14. Random errors in egocentric networks

    PubMed Central

    Almquist, Zack W.

    2013-01-01

    The systematic errors that are induced by a combination of human memory limitations and common survey design and implementation have long been studied in the context of egocentric networks. Despite this, little if any work exists in the area of random error analysis on these same networks; this paper offers a perspective on the effects of random errors on egonet analysis, as well as the effects of using egonet measures as independent predictors in linear models. We explore the effects of false-positive and false-negative error in egocentric networks on both standard network measures and on linear models through simulation analysis on a ground truth egocentric network sample based on facebook-friendships. Results show that 5–20% error rates, which are consistent with error rates known to occur in ego network data, can cause serious misestimation of network properties and regression parameters. PMID:23878412

  15. Dopamine reward prediction error coding

    PubMed Central

    Schultz, Wolfram

    2016-01-01

    Reward prediction errors consist of the differences between received and predicted rewards. They are crucial for basic forms of learning about rewards and make us strive for more rewards—an evolutionary beneficial trait. Most dopamine neurons in the midbrain of humans, monkeys, and rodents signal a reward prediction error; they are activated by more reward than predicted (positive prediction error), remain at baseline activity for fully predicted rewards, and show depressed activity with less reward than predicted (negative prediction error). The dopamine signal increases nonlinearly with reward value and codes formal economic utility. Drugs of addiction generate, hijack, and amplify the dopamine reward signal and induce exaggerated, uncontrolled dopamine effects on neuronal plasticity. The striatum, amygdala, and frontal cortex also show reward prediction error coding, but only in subpopulations of neurons. Thus, the important concept of reward prediction errors is implemented in neuronal hardware. PMID:27069377

  16. Medical errors: overcoming the challenges.

    PubMed

    Kalra, Jawahar

    2004-12-01

    The issue of medical errors has received substantial attention in recent years. The Institute of Medicine (IOM) report released in 1999 has several implications for health care systems in all disciplines of medicine. Notwithstanding the plethora of available information on the subject, little, by way of substantive action, is done toward medical error reduction. A principal reason for this may be the stigma associated with medical errors. An educational program with a practical, informed, and longitudinal approach offers realistic solutions toward this end. Effective reporting systems need to be developed as a medium of learning from the errors and modifying behaviors appropriately. The presence of a strong leadership supported by organizational commitment is essential in driving these changes. A national, provincial or territorial quality care council dedicated solely for the purpose of enhancing patient safety and medical error reduction may be formed to oversee these efforts. The bioethical and emotional components associated with medical errors also deserve attention and focus. PMID:15589811

  17. Real-time PCR in Food Science: PCR Diagnostics.

    PubMed

    Rodriguez-Lazaro, David; Cook, Nigel; Hernandez, Marta

    2013-01-01

    A principal consumer demand is a guarantee of the safety and quality of food. The presence of foodborne pathogens and their potential hazard, the use of genetically modified organisms (GMOs) in food production, and the correct labelling in foods suitable for vegetarians are among the subjects where society demands total transparency. The application of controls within the quality assessment programmes of the food industry is a way to satisfy these demands, and is necessary to ensure efficient analytical methodologies are possessed and correctly applied by the Food Sector. The use of real-time PCR has become a promising alternative approach in food diagnostics. It possesses a number of advantages over conventional culturing approaches, including rapidity, excellent analytical sensitivity and selectivity, and potential for quantification. However, the use of expensive equipment and reagents, the need for qualified personnel, and the lack of standardized protocols are impairing its practical implementation for food monitoring and control. PMID:23513039

  18. Teratogenic inborn errors of metabolism.

    PubMed Central

    Leonard, J. V.

    1986-01-01

    Most children with inborn errors of metabolism are born healthy without malformations as the fetus is protected by the metabolic activity of the placenta. However, certain inborn errors of the fetus have teratogenic effects although the mechanisms responsible for the malformations are not generally understood. Inborn errors in the mother may also be teratogenic. The adverse effects of these may be reduced by improved metabolic control of the biochemical disorder. PMID:3540927

  19. 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.

  20. Confidence limits and their errors

    SciTech Connect

    Rajendran Raja

    2002-03-22

    Confidence limits are common place in physics analysis. Great care must be taken in their calculation and use especially in cases of limited statistics. We introduce the concept of statistical errors of confidence limits and argue that not only should limits be calculated but also their errors in order to represent the results of the analysis to the fullest. We show that comparison of two different limits from two different experiments becomes easier when their errors are also quoted. Use of errors of confidence limits will lead to abatement of the debate on which method is best suited to calculate confidence limits.

  1. 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.

  2. Anxiety and Error Monitoring: Increased Error Sensitivity or Altered Expectations?

    ERIC Educational Resources Information Center

    Compton, Rebecca J.; Carp, Joshua; Chaddock, Laura; Fineman, Stephanie L.; Quandt, Lorna C.; Ratliff, Jeffrey B.

    2007-01-01

    This study tested the prediction that the error-related negativity (ERN), a physiological measure of error monitoring, would be enhanced in anxious individuals, particularly in conditions with threatening cues. Participants made gender judgments about faces whose expressions were either happy, angry, or neutral. Replicating prior studies, midline…

  3. Prescription errors in cancer chemotherapy: Omissions supersede potentially harmful errors

    PubMed Central

    Mathaiyan, Jayanthi; Jain, Tanvi; Dubashi, Biswajit; Reddy, K Satyanarayana; Batmanabane, Gitanjali

    2015-01-01

    Objective: To estimate the frequency and type of prescription errors in patients receiving cancer chemotherapy. Settings and Design: We conducted a cross-sectional study at the day care unit of the Regional Cancer Centre (RCC) of a tertiary care hospital in South India. Materials and Methods: All prescriptions written during July to September 2013 for patients attending the out-patient department of the RCC to be treated at the day care center were included in this study. The prescriptions were analyzed for omission of standard information, usage of brand names, abbreviations and legibility. The errors were further classified into potentially harmful ones and not harmful based on the likelihood of resulting in harm to the patient. Descriptive analysis was performed to estimate the frequency of prescription errors and expressed as total number of errors and percentage. Results: A total of 4253 prescribing errors were found in 1500 prescriptions (283.5%), of which 47.1% were due to omissions like name, age and diagnosis and 22.5% were due to usage of brand names. Abbreviations of pre-medications and anticancer drugs accounted for 29.2% of the errors. Potentially harmful errors that were likely to result in serious consequences to the patient were estimated to be 11.7%. Conclusions: Most of the errors intercepted in our study are due to a high patient load and inattention of the prescribers to omissions in prescription. Redesigning prescription forms and sensitizing prescribers to the importance of writing prescriptions without errors may help in reducing errors to a large extent. PMID:25969654

  4. DEVELOPMENT OF AN INTERNAL POSITIVE CONTROL FOR RAPID DIAGNOSIS OF AVIAN INFLUENZA VIRAL INFECTIONS BY REAL-TIME RT-PCR WITH LYOPHILIZED REAGENTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Real time RT-PCR (RRT-PCR) has been widely adopted as a diagnostic screening test for Avian Influenza (AI) in the U.S. However, concerns about false negative results due to inhibition or human error have been an issue. We developed an internal positive control (IPC) in the nucleic acid amplificati...

  5. 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.

  6. Multiplexed Primer Prediction for PCR

    Energy Science and Technology Software Center (ESTSC)

    2007-07-23

    MPP predicts sets of multiplex-compatible primers for Polymerase Chain Reaction (PCR), finding a near minimal set of primers such that at least one amplicon will be generated from every target sequence in the input file. The code finds highly conserved oligos that are suitable as primers, according to user-specified desired primer characteristics such as length, melting temperature, and amplicon length. The primers are predicted not to form unwanted dimer or hairpin structures. The target sequencesmore » used as input can be diverse, since no multiple sequence alighment is required. The code is scalable, taking up to tens of thousands of sequences as input, and works, for example, to find a "universal primer set" for all viral genomes provided as a single input file. The code generates a periodic check-point file, thus in the event of premature execution termination, the application can be restarted from the last check-point file.« less

  7. Human Error: A Concept Analysis

    NASA Technical Reports Server (NTRS)

    Hansen, Frederick D.

    2007-01-01

    Human error is the subject of research in almost every industry and profession of our times. This term is part of our daily language and intuitively understood by most people however, it would be premature to assume that everyone's understanding of human error s the same. For example, human error is used to describe the outcome or consequence of human action, the causal factor of an accident, deliberate violations,a nd the actual action taken by a human being. As a result, researchers rarely agree on the either a specific definition or how to prevent human error. The purpose of this article is to explore the specific concept of human error using Concept Analysis as described by Walker and Avant (1995). The concept of human error is examined as currently used in the literature of a variety of industries and professions. Defining attributes and examples of model, borderline, and contrary cases are described. The antecedents and consequences of human error are also discussed and a definition of human error is offered.

  8. Barriers to Medical Error Reporting

    PubMed Central

    Poorolajal, Jalal; Rezaie, Shirin; Aghighi, Negar

    2015-01-01

    Background: This study was conducted to explore the prevalence of medical error underreporting and associated barriers. Methods: This cross-sectional study was performed from September to December 2012. Five hospitals, affiliated with Hamadan University of Medical Sciences, in Hamedan, Iran were investigated. A self-administered questionnaire was used for data collection. Participants consisted of physicians, nurses, midwives, residents, interns, and staffs of radiology and laboratory departments. Results: Overall, 50.26% of subjects had committed but not reported medical errors. The main reasons mentioned for underreporting were lack of effective medical error reporting system (60.0%), lack of proper reporting form (51.8%), lack of peer supporting a person who has committed an error (56.0%), and lack of personal attention to the importance of medical errors (62.9%). The rate of committing medical errors was higher in men (71.4%), age of 50–40 years (67.6%), less-experienced personnel (58.7%), educational level of MSc (87.5%), and staff of radiology department (88.9%). Conclusions: This study outlined the main barriers to reporting medical errors and associated factors that may be helpful for healthcare organizations in improving medical error reporting as an essential component for patient safety enhancement. PMID:26605018

  9. 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,…

  10. Children's Scale Errors with Tools

    ERIC Educational Resources Information Center

    Casler, Krista; Eshleman, Angelica; Greene, Kimberly; Terziyan, Treysi

    2011-01-01

    Children sometimes make "scale errors," attempting to interact with tiny object replicas as though they were full size. Here, we demonstrate that instrumental tools provide special insight into the origins of scale errors and, moreover, into the broader nature of children's purpose-guided reasoning and behavior with objects. In Study 1, 1.5- to…

  11. 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,

  12. 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,…

  13. Twenty questions about student errors

    NASA Astrophysics Data System (ADS)

    Fisher, Kathleen M.; Lipson, Joseph Isaac

    Errors in science learning (errors in expression of organized, purposeful thought within the domain of science) provide a window through which glimpses of mental functioning can be obtained. Errors are valuable and normal occurrences in the process of learning science. A student can use his/her errors to develop a deeper understanding of a concept as long as the error can be recognized and appropriate, informative feedback can be obtained. A safe, non-threatening, and nonpunitive environment which encourages dialogue helps students to express their conceptions and to risk making errors. Pedagogical methods that systematically address common student errors produce significant gains in student learning. Just as the nature-nurture interaction is integral to the development of living things, so the individual-environment interaction is basic to thought processes. At a minimum, four systems interact: (1) the individual problem solver (who has a worldview, relatively stable cognitive characteristics, relatively malleable mental states and conditions, and aims or intentions), (2) task to be performed (including relative importance and nature of the task), (3) knowledge domain in which task is contained, and (4) the environment (including orienting conditions and the social and physical context).Several basic assumptions underlie research on errors and alternative conceptions. Among these are: Knowledge and thought involve active, constructive processes; there are many ways to acquire, organize, store, retrieve, and think about a given concept or event; and understanding is achieved by successive approximations. Application of these ideas will require a fundamental change in how science is taught.

  14. 20 Tips to Help Prevent Medical Errors

    MedlinePlus

    ... Errors > 20 Tips to Help Prevent Medical Errors 20 Tips to Help Prevent Medical Errors: Patient Fact ... care. Page last reviewed December 2014 Internet Citation: 20 Tips to Help Prevent Medical Errors. December 2014. ...

  15. Quantization of accumulated diffused errors in error diffusion

    NASA Astrophysics Data System (ADS)

    Chang, Ti-chiun; Allebach, Jan P.

    2005-01-01

    Due to its high image quality and moderate computational complexity, error diffusion is a popular halftoning algorithm for use with inkjet printers. However, error diffusion is an inherently serial algorithm that requires buffering a full row of accumulated diffused error (ADE) samples. For the best performance when the algorithm is implemented in hardware, the ADE data should be stored on the chip on which the error diffusion algorithm is implemented. However, this may result in an unacceptable hardware cost. In this paper, we examine the use of quantization of the ADE to reduce the amount of data that must be stored. We consider both uniform and non-uniform quantizers. For the non-uniform quantizer, we propose a novel feature-dependent quantizer that yield improved image quality at a given bit rate, compared to memoryless quantizers. The optimal design of these quantizers is coupled with the design of the tone-dependent parameters associated with error diffusion. This is done via a combination of the classical Lloyd-Max algorithm and the training framework for tone-dependent error diffusion (TDED). Our results show that 4-bit uniform quantization of the ADE yields the same halftone quality as error diffusion without quantization of the ADE. At rate 2 bits per pixel, the feature-dependent quantizer achieves comparable quality as 3-bit uniform quantization.

  16. Quantization of accumulated diffused errors in error diffusion

    NASA Astrophysics Data System (ADS)

    Chang, Ti-chiun; Allebach, Jan P.

    2004-12-01

    Due to its high image quality and moderate computational complexity, error diffusion is a popular halftoning algorithm for use with inkjet printers. However, error diffusion is an inherently serial algorithm that requires buffering a full row of accumulated diffused error (ADE) samples. For the best performance when the algorithm is implemented in hardware, the ADE data should be stored on the chip on which the error diffusion algorithm is implemented. However, this may result in an unacceptable hardware cost. In this paper, we examine the use of quantization of the ADE to reduce the amount of data that must be stored. We consider both uniform and non-uniform quantizers. For the non-uniform quantizer, we propose a novel feature-dependent quantizer that yield improved image quality at a given bit rate, compared to memoryless quantizers. The optimal design of these quantizers is coupled with the design of the tone-dependent parameters associated with error diffusion. This is done via a combination of the classical Lloyd-Max algorithm and the training framework for tone-dependent error diffusion (TDED). Our results show that 4-bit uniform quantization of the ADE yields the same halftone quality as error diffusion without quantization of the ADE. At rate 2 bits per pixel, the feature-dependent quantizer achieves comparable quality as 3-bit uniform quantization.

  17. Reducing latent errors, drift errors, and stakeholder dissonance.

    PubMed

    Samaras, George M

    2012-01-01

    Healthcare information technology (HIT) is being offered as a transformer of modern healthcare delivery systems. Some believe that it has the potential to improve patient safety, increase the effectiveness of healthcare delivery, and generate significant cost savings. In other industrial sectors, information technology has dramatically influenced quality and profitability - sometimes for the better and sometimes not. Quality improvement efforts in healthcare delivery have not yet produced the dramatic results obtained in other industrial sectors. This may be that previously successful quality improvement experts do not possess the requisite domain knowledge (clinical experience and expertise). It also appears related to a continuing misconception regarding the origins and meaning of work errors in healthcare delivery. The focus here is on system use errors rather than individual user errors. System use errors originate in both the development and the deployment of technology. Not recognizing stakeholders and their conflicting needs, wants, and desires (NWDs) may lead to stakeholder dissonance. Mistakes translating stakeholder NWDs into development or deployment requirements may lead to latent errors. Mistakes translating requirements into specifications may lead to drift errors. At the sharp end, workers encounter system use errors or, recognizing the risk, expend extensive and unanticipated resources to avoid them. PMID:22317001

  18. 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

  19. 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.

  20. Comparison of two real-time PCR assays for the detection of malaria parasites from hemolytic blood samples – Short communication

    PubMed Central

    Hagen, Ralf Matthias; Hinz, Rebecca; Tannich, Egbert; Frickmann, Hagen

    2015-01-01

    We compared the performance of an in-house and a commercial malaria polymerase chain reaction (PCR) assay using freeze–thawed hemolytic blood samples. A total of 116 freeze–thawed ethylenediamine tetraacetic acid (EDTA) blood samples of patients with suspicion of malaria were analyzed by an in-house as well as by a commercially available real-time PCR. Concordant malaria negative PCR results were reported for 39 samples and malaria-positive PCR results for 67 samples. The in-house assay further detected one case of Plasmodium falciparum infection, which was negative in the commercial assay as well as five cases of P. falciparum malaria and three cases of Plasmodium vivax malaria, which showed sample inhibition in the commercial assay. The commercial malaria assay was positive in spite of a negative in-house PCR result in one case. In all concordant results, cycle threshold values of P. falciparum-positive samples were lower in the commercial PCR than in the in-house assay. Although Ct values of the commercial PCR kit suggest higher sensitivity in case of concordant results, it is prone to inhibition if it is applied to hemolytic freeze–thawed blood samples. The number of misidentifications was, however, identical for both real-time PCR assays. PMID:26185684

  1. Exceptional error minimization in putative primordial genetic codes

    PubMed Central

    2009-01-01

    Background The standard genetic code is redundant and has a highly non-random structure. Codons for the same amino acids typically differ only by the nucleotide in the third position, whereas similar amino acids are encoded, mostly, by codon series that differ by a single base substitution in the third or the first position. As a result, the code is highly albeit not optimally robust to errors of translation, a property that has been interpreted either as a product of selection directed at the minimization of errors or as a non-adaptive by-product of evolution of the code driven by other forces. Results We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage as the measure of a code's robustness to mistranslation. It is shown that, when the 16-supercodon table is populated with 10 putative primordial amino acids, inferred from the results of abiotic synthesis experiments and other evidence independent of the code's evolution, and with minimal assumptions used to assign the remaining supercodons, the resulting 2-letter codes are nearly optimal in terms of the error minimization level. Conclusion The results of the computational experiments with putative primordial genetic codes that contained only two meaningful letters in all codons and encoded 10 to 16 amino acids indicate that such codes are likely to have been nearly optimal with respect to the minimization of translation errors. This near-optimality could be the outcome of extensive early selection during the co-evolution of the code with the primordial, error-prone translation system, or a result of a unique, accidental event. Under this hypothesis, the subsequent expansion of the code resulted in a decrease of the error minimization level that became sustainable owing to the evolution of a high-fidelity translation system. Reviewers This article was reviewed by Paul Higgs (nominated by Arcady Mushegian), Rob Knight, and Sandor Pongor. For the complete reports, go to the Reviewers' Reports section. PMID:19925661

  2. LANDSAT imagery analysis: An aid for predicting landslide prone areas for highway construction. [in Arkansas

    NASA Technical Reports Server (NTRS)

    Macdonald, H. C.; Grubbs, R. S.

    1975-01-01

    The most obvious landform features of geologic significance revealed on LANDSAT imagery are linear trends or lineaments. These trends were found to correspond, at least to a large degree, with unmapped faults or complex fracture zones. LANDSAT imagery analysis in northern Arkansas revealed a lineament complex which provides a remarkable correlation with landslide-prone areas along major highway routes. The weathering properties of various rock types, which are considered in designing stable cut slopes and drainage structures, appear to be adversely influenced by the location and trends of LANDSAT defined lineaments. Geologic interpretation of LANDSAT imagery, where applicable and utilized effectively, provides the highway engineer with a tool for predicting and evaluating landslide-prone areas.

  3. Simple shielding reduces dose to the contralateral breast during prone breast cancer radiotherapy.

    PubMed

    Goyal, Uma; Locke, Angela; Smith-Raymond, Lexie; Georgiev, Georgi N

    2016-01-01

    Our goal was to design a prone breast shield for the contralateral breast and study its efficacy in decreasing scatter radiation to the contralateral breast in a prone breast phantom setup receiving radiation therapy designed for breast cancer. We constructed a prone breast phantom setup consisting of (1) A thermoplastic mask with a left-sided depression created by a water balloon for a breast shape; (2) 2 plastic bags to hold water in the thermoplastic mask depression; (3) 2000mL of water to fill the thermoplastic mask depression to create a water-based false breast; (4) 1-cm thick bolus placed in the contralateral breast holder; (5) 2 lead (Pb) sheets, each 0.1-cm thick for blocking scatter radiation in the contralateral bolus-based false breast; (6) a prone breast board to hold the thermoplastic mask, water, bolus, and lead; (7) 9cm solid water on top of the breast board to simulate body; (8) a diode was used to verify dose for each treatment field of the treated water-based breast; (9) metal-oxide-semiconductor-field effect transistor (MOSFET) dosimeters to measure dose to the contralateral bolus-based breast. The phantom prone breast setup was CT simulated and treatment was designed with 95% isodose line covering the treated breast. The maximum dose was 107.1%. Megavoltage (MV) port images ensured accurate setup. Measurements were done using diodes on the treated water-based breast and MOSFET dosimeters at the medial and lateral sides of the contralateral bolus-based breast without and with the Pb shield. Five treatments were done for each of the 3 data sets and recorded individually for statistical purposes. All treatments were completed with 6MV photons at 200cGy per treatment. The dose contributions from each of the 3 data sets including 15 treatments total without and with the prone lead shield to the medial and lateral portions of contralateral bolus-based breast were averaged individually. Unshielded dose means were 37.11 and 2.94cGy, and shielded dose means were 12.68 and 1.54cGy, respectively. When comparing medial and lateral portions of the contralateral bolus-based doses without and with Pb, the shield significantly reduced dose to both sides of the contralateral breast (medial p = 2.64 × 10(-14), lateral p = 4.91 × 10(-6)). The prone 0.2-cm Pb shield significantly reduced scatter dose to the contralateral breast on the order of 2 to 3 times. Reductions may be clinically relevant for women younger than 45 years by decreasing the risk of contralateral radiation-induced breast cancer in patients receiving radiation therapy for breast cancer. This shield is simple as it would be a part of the prone breast board during treatments, but future studies are warranted for safety and efficacy clinically. PMID:26994826

  4. Evaluating the fakability of a conditional reasoning test of addiction proneness.

    PubMed

    Bowler, Jennifer L; Bowler, Mark C

    2014-10-01

    The quest to assess personality objectively is riddled with challenges. However, conditional reasoning (CR) methodology takes an innovative approach to personality measurement by indirectly evaluating the cognitive biases associated with specific dispositional traits. In addition to demonstrating strong criterion-related validities, the CR format has been shown to be more resistant to response distortion than traditional self-report measures so long as indirect measurement is maintained. The present study evaluated the necessity of maintaining the indirect nature of a CR-based measure of addiction proneness. Results indicated that disclosing the purpose of assessment yielded significant mean shifts on a CR-based measure of addiction proneness compared to those of an uninformed group. Specifically, when the construct of interest was made explicit, participants could identify the keyed response options when instructed to do so. These findings further underscore the necessity of maintaining indirect measurement when administering CR measures. PMID:25178965

  5. Acute ischemic optic neuropathy with extended prone position ventilation in a lung transplant recipient.

    PubMed

    Panchabhai, Tanmay S; Bandyopadhyay, Debabrata; Kapoor, Aanchal; Akindipe, Olufemi; Lane, Charles; Krishnan, Sudhir

    2016-01-01

    Prone position ventilation (PPV) improves mortality in severe acute respiratory distress syndrome (ARDS), but outcomes following its use in lung transplant recipients are not known. We report the case of a 42-year-old Caucasian man who presented with severe ARDS from Bordetella pertussis, 5 years after bilateral sequential lung transplant for cystic fibrosis. He was managed with PPV for 22 days and had a prolonged ICU stay complicated by hypoxic ischemic optic neuropathy leading to blindness. Since his discharge from the ICU 6 months ago, his FEV1 has recovered to 47% predicted compared to his pre-ICU peak FEV1 of 85% predicted, suggesting recovery of lung function. This is the first report of optic nerve damage and vision loss in patients undergoing PPV. Our report also suggests that, in appropriately selected lung transplant recipients, severe hypoxemia could potentially be managed with prone ventilation. PMID:27051622

  6. Acute ischemic optic neuropathy with extended prone position ventilation in a lung transplant recipient

    PubMed Central

    Panchabhai, Tanmay S; Bandyopadhyay, Debabrata; Kapoor, Aanchal; Akindipe, Olufemi; Lane, Charles; Krishnan, Sudhir

    2016-01-01

    Prone position ventilation (PPV) improves mortality in severe acute respiratory distress syndrome (ARDS), but outcomes following its use in lung transplant recipients are not known. We report the case of a 42-year-old Caucasian man who presented with severe ARDS from Bordetella pertussis, 5 years after bilateral sequential lung transplant for cystic fibrosis. He was managed with PPV for 22 days and had a prolonged ICU stay complicated by hypoxic ischemic optic neuropathy leading to blindness. Since his discharge from the ICU 6 months ago, his FEV1 has recovered to 47% predicted compared to his pre-ICU peak FEV1 of 85% predicted, suggesting recovery of lung function. This is the first report of optic nerve damage and vision loss in patients undergoing PPV. Our report also suggests that, in appropriately selected lung transplant recipients, severe hypoxemia could potentially be managed with prone ventilation.

  7. Posterior callosotomy using a parietooccipital interhemispheric approach in the semi-prone park-bench position.

    PubMed

    Ito, Hirotaka; Morino, Michiharu; Niimura, Manabu; Takamizawa, Sachiko; Shimizu, Yoshie

    2015-11-01

    A 2-stage corpus callosotomy is accepted as a palliative procedure for patients older than 16 years with, in particular, medically intractable generalized epilepsy and drop attack seizures and is preferable for a lower risk of disconnection syndrome. Although the methods by which a previously performed craniotomy can be reopened for posterior callosotomy have already been reported, posterior corpus callosotomy using a parietooccipital interhemispheric approach with the patient in a semi-prone park-bench position has not been described in the literature. Here, the authors present a surgical technique for posterior callosotomy using a parietooccipital interhemispheric approach with a semi-prone park-bench position as a second surgery. Although this procedure requires an additional skin incision in the parietooccipital region, it makes the 2-stage callosotomy safer and easier to perform because of reduced intracranial adhesion, less bleeding, and an easier approach to the splenium of the corpus callosum. PMID:26047417

  8. p63 heterozygous mutant mice are not prone to spontaneous or chemically induced tumors

    PubMed Central

    Keyes, William M.; Vogel, Hannes; Koster, Maranke I.; Guo, Xuecui; Qi, Yi; Petherbridge, Kristin M.; Roop, Dennis R.; Bradley, Allan; Mills, Alea A.

    2006-01-01

    Homology between p63 and p53 has suggested that these proteins might function similarly. However, the majority of data from human tumors have not supported a similar role for p63 in tumor suppression. To investigate this issue, we studied spontaneous tumorigenesis in p63+/? mice in both WT and p53-compromised backgrounds. We found that p63+/? mice were not tumor prone and mice heterozygous for both p63 and p53 had fewer tumors than p53+/? mice. The rare tumors that developed in mice with compromised p63 were also distinct from those of p53+/? mice. Furthermore, p63+/? mice were not prone to chemically induced tumorigenesis, and p63 expression was maintained in carcinomas. These findings demonstrate that, in agreement with data from human tumors, p63 plays a markedly different biological role in cancer than p53. PMID:16714381

  9. 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.

  10. Multimodal nonlinear optical imaging of atherosclerotic plaque development in myocardial infarction-prone rabbits

    NASA Astrophysics Data System (ADS)

    Ko, Alex C. T.; Ridsdale, Andrew; Smith, Michael S. D.; Mostaço-Guidolin, Leila B.; Hewko, Mark D.; Pegoraro, Adrian F.; Kohlenberg, Elicia K.; Schattka, Bernie; Shiomi, Masashi; Stolow, Albert; Sowa, Michael G.

    2010-03-01

    Label-free imaging of bulk arterial tissue is demonstrated using a multimodal nonlinear optical microscope based on a photonic crystal fiber and a single femtosecond oscillator operating at 800 nm. Colocalized imaging of extracellular elastin fibers, fibrillar collagen, and lipid-rich structures within aortic tissue obtained from atherosclerosis-prone myocardial infarction-prone Watanabe heritable hyperlipidemic (WHHLMI) rabbits is demonstrated through two-photon excited fluorescence, second harmonic generation, and coherent anti-Stokes Raman scattering, respectively. These images are shown to differentiate healthy arterial wall, early atherosclerotic lesions, and advanced plaques. Clear pathological changes are observed in the extracellular matrix of the arterial wall and correlated with progression of atherosclerotic disease as represented by the age of the WHHLMI rabbits.

  11. The Prone Position During Surgery and its Complications: A Systematic Review and Evidence-Based Guidelines

    PubMed Central

    Kwee, Melissa M.; Ho, Yik-Hong; Rozen, Warren M.

    2015-01-01

    Surgery in the prone position is often a necessity when access to posterior anatomic structures is required. However, many complications are known to be associated with this type of surgery, as physiologic changes occur with increased pressure to anterior structures. While several studies have discussed postoperative vision loss, much fewer studies with lower levels of evidence have addressed other complications. A systematic literature review was conducted using 2 different databases, and 53 papers were regarded as appropriate for inclusion. Qualitative and quantitative analysis was performed. Thirteen complications were identified. Postoperative vision loss and cardiovascular complications, including hypovolemia and cardiac arrest, had the most number of studies and highest level of evidence. Careful planning for optimal positioning, padding, timing, as well as increased vigilance are evidence-based recommendations where operative prone positioning is required. PMID:25692433

  12. Identification of patients prone to hypotension during hemodialysis based on the analysis of cardiovascular signals.

    PubMed

    Hernando, D; Sörnmo, L; Sandberg, F; Laguna, P; Llamedo, M; Bailón, R

    2015-12-01

    Intradialytic hypotension (IDH) is a major complication during hemodialysis treatment, and therefore it is highly desirable to identify, at an early stage during treatment, whether the patient is prone to IDH. Heart rate variability (HRV), blood pressure variability (BPV) and baroreflex sensitivity (BRS) were analyzed during the first 30 min of treatment to assess information on the autonomic nervous system. Using the sequential floating forward selection method and linear classification, the set of features with the best discriminative power was selected, resulting in an accuracy of 92.1%. Using a classifier based on the HRV features only, thereby avoiding that continuous blood pressure has to be recorded, accuracy decreased to 90.2%. The results suggest that an HRV-based classifier is useful for determining whether a patient is prone to IDH at the beginning of the treatment. PMID:26525780

  13. Decorin and biglycan retain LDL in disease-prone valvular and aortic subendothelial intimal matrix

    PubMed Central

    Neufeld, Edward B.; Zadrozny, Leah M.; Phillips, Darci; Aponte, Angel; Yu, Zu-Xi; Balaban, Robert S.

    2014-01-01

    Objective Subendothelial LDL retention by intimal matrix proteoglycans is an initial step in atherosclerosis and calcific aortic valve disease. Herein, we identify decorin and biglycan as the proteoglycans that preferentially retain LDL in intimal matrix at disease-prone sites in normal valve and vessel wall. Methods The porcine aortic valve and renal artery ostial diverter, initiation sites of calcific valve disease and renal atherosclerosis, respectively, from normal non-diseased animals were used as models in these studies. Results Fluorescent human LDL was selectively retained on the lesion-prone collagen/proteoglycan-enriched aortic surface of the valve, where the elastic lamina is depleted, as previously observed in lesion-prone sites in the renal ostium. iTRAQ mass spectrometry of valve and diverter protein extracts identified decorin and biglycan as the major subendothelial intimal matrix proteoglycans electrostatically retained on human LDL affinity columns. Decorin levels correlated with LDL binding in lesion-prone sites in both tissues. Collagen binding to LDL was shown to be proteoglycan-mediated. All known basement membrane proteoglycans bound LDL suggesting they may modulate LDL uptake into the subendothelial matrix. The association of purified decorin with human LDL in an in vitro microassay was blocked by serum albumin and heparin suggesting anti-atherogenic roles for these proteins in vivo. Conclusions LDL electrostatic interactions with decorin and biglycan in the valve leaflets and vascular wall is a major source of LDL retention. The complementary electrostatic sites on LDL or these proteoglycans may provide a novel therapeutic target for preventing one of the earliest events in these cardiovascular diseases. PMID:24529131

  14. Anesthetic Management of the Parturient for Lumbar Disc Surgery in the Prone Position

    PubMed Central

    Martel, Colleen G.; Volpi-Abadie, Jacqueline; Ural, Kelly

    2015-01-01

    Background While back pain is common in pregnancy, urgent surgical intervention is rarely required. Case Report A parturient in the third trimester presented with foot drop and sensory deficits. Surgical intervention was deemed necessary and was performed in the prone position to facilitate exposure. A multidisciplinary approach was vital to the management plan. Conclusion For any pregnant patient undergoing nonobstetric surgery, the care provided should be individualized and thoughtful, keeping in mind both the mother and fetus. PMID:26412999

  15. The effect of auditory verbal imagery on signal detection in hallucination-prone individuals

    PubMed Central

    Moseley, Peter; Smailes, David; Ellison, Amanda; Fernyhough, Charles

    2016-01-01

    Cognitive models have suggested that auditory hallucinations occur when internal mental events, such as inner speech or auditory verbal imagery (AVI), are misattributed to an external source. This has been supported by numerous studies indicating that individuals who experience hallucinations tend to perform in a biased manner on tasks that require them to distinguish self-generated from non-self-generated perceptions. However, these tasks have typically been of limited relevance to inner speech models of hallucinations, because they have not manipulated the AVI that participants used during the task. Here, a new paradigm was employed to investigate the interaction between imagery and perception, in which a healthy, non-clinical sample of participants were instructed to use AVI whilst completing an auditory signal detection task. It was hypothesized that AVI-usage would cause participants to perform in a biased manner, therefore falsely detecting more voices in bursts of noise. In Experiment 1, when cued to generate AVI, highly hallucination-prone participants showed a lower response bias than when performing a standard signal detection task, being more willing to report the presence of a voice in the noise. Participants not prone to hallucinations performed no differently between the two conditions. In Experiment 2, participants were not specifically instructed to use AVI, but retrospectively reported how often they engaged in AVI during the task. Highly hallucination-prone participants who retrospectively reported using imagery showed a lower response bias than did participants with lower proneness who also reported using AVI. Results are discussed in relation to prominent inner speech models of hallucinations. PMID:26435050

  16. Genetic and environmental influences on the relationship between flow proneness, locus of control and behavioral inhibition.

    PubMed

    Mosing, Miriam A; Pedersen, Nancy L; Cesarini, David; Johannesson, Magnus; Magnusson, Patrik K E; Nakamura, Jeanne; Madison, Guy; Ullén, Fredrik

    2012-01-01

    Flow is a psychological state of high but subjectively effortless attention that typically occurs during active performance of challenging tasks and is accompanied by a sense of automaticity, high control, low self-awareness, and enjoyment. Flow proneness is associated with traits and behaviors related to low neuroticism such as emotional stability, conscientiousness, active coping, self-esteem and life satisfaction. Little is known about the genetic architecture of flow proneness, behavioral inhibition and locus of control--traits also associated with neuroticism--and their interrelation. Here, we hypothesized that individuals low in behavioral inhibition and with an internal locus of control would be more likely to experience flow and explored the genetic and environmental architecture of the relationship between the three variables. Behavioral inhibition and locus of control was measured in a large population sample of 3,375 full twin pairs and 4,527 single twins, about 26% of whom also scored the flow proneness questionnaire. Findings revealed significant but relatively low correlations between the three traits and moderate heritability estimates of .41, .45, and .30 for flow proneness, behavioral inhibition, and locus of control, respectively, with some indication of non-additive genetic influences. For behavioral inhibition we found significant sex differences in heritability, with females showing a higher estimate including significant non-additive genetic influences, while in males the entire heritability was due to additive genetic variance. We also found a mainly genetically mediated relationship between the three traits, suggesting that individuals who are genetically predisposed to experience flow, show less behavioral inhibition (less anxious) and feel that they are in control of their own destiny (internal locus of control). We discuss that some of the genes underlying this relationship may include those influencing the function of dopaminergic neural systems. PMID:23133606

  17. The effect of auditory verbal imagery on signal detection in hallucination-prone individuals.

    PubMed

    Moseley, Peter; Smailes, David; Ellison, Amanda; Fernyhough, Charles

    2016-01-01

    Cognitive models have suggested that auditory hallucinations occur when internal mental events, such as inner speech or auditory verbal imagery (AVI), are misattributed to an external source. This has been supported by numerous studies indicating that individuals who experience hallucinations tend to perform in a biased manner on tasks that require them to distinguish self-generated from non-self-generated perceptions. However, these tasks have typically been of limited relevance to inner speech models of hallucinations, because they have not manipulated the AVI that participants used during the task. Here, a new paradigm was employed to investigate the interaction between imagery and perception, in which a healthy, non-clinical sample of participants were instructed to use AVI whilst completing an auditory signal detection task. It was hypothesized that AVI-usage would cause participants to perform in a biased manner, therefore falsely detecting more voices in bursts of noise. In Experiment 1, when cued to generate AVI, highly hallucination-prone participants showed a lower response bias than when performing a standard signal detection task, being more willing to report the presence of a voice in the noise. Participants not prone to hallucinations performed no differently between the two conditions. In Experiment 2, participants were not specifically instructed to use AVI, but retrospectively reported how often they engaged in AVI during the task. Highly hallucination-prone participants who retrospectively reported using imagery showed a lower response bias than did participants with lower proneness who also reported using AVI. Results are discussed in relation to prominent inner speech models of hallucinations. PMID:26435050

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

    SciTech Connect

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

  19. Pitfalls in PCR troubleshooting: Expect the unexpected?

    PubMed Central

    Schrick, Livia; Nitsche, Andreas

    2015-01-01

    PCR is a well-understood and established laboratory technique often used in molecular diagnostics. Huge experience has been accumulated over the last years regarding the design of PCR assays and their set-up, including in-depth troubleshooting to obtain the optimal PCR assay for each purpose. Here we report a PCR troubleshooting that came up with a surprising result never observed before. With this report we hope to sensitize the reader to this peculiar problem and to save troubleshooting efforts in similar situations, especially in time-critical and ambitious diagnostic settings. PMID:27077041

  20. Real-time PCR in microfluidic devices

    NASA Astrophysics Data System (ADS)

    Becker, Holger; Hlawatsch, Nadine; Klemm, Richard; Moche, Christian; Hansen-Hagge, Thomas; Gärtner, Claudia

    2014-03-01

    A central method in a standard biochemical laboratory is represented by the polymerase chain reaction (PCR), therefore many attempts have been performed so far to implement this technique in lab-on-a-chip (LOC) devices. PCR is an ideal candidate for miniaturization because of a reduction of assay time and decreased costs for expensive bio-chemicals. In case of the "classical" PCR, detection is done by identification of DNA fragments electrophoretically separated in agarose gels. This method is meanwhile frequently replaced by the so-called Real-Time-PCR because here the exponential increase of amplificates can be observed directly by measurement of DNA interacting fluorescent dyes. Two main methods for on-chip PCRs are available: traditional "batch" PCR in chambers on a chip using thermal cycling, requiring about 30 minutes for a typical PCR protocol and continuous-flow PCR, where the liquid is guided over stationary temperature zones. In the latter case, the PCR protocol can be as fast as 5 minutes. In the presented work, a proof of concept is demonstrated for a real-time-detection of PCR products in microfluidic systems.

  1. Emerging and reemerging epidemic-prone diseases among settling nomadic pastoralists in Uganda.

    PubMed

    Cummings, Matthew J; Wamala, Joseph F; Komakech, Innocent; Malimbo, Mugagga; Lukwago, Luswa

    2014-09-01

    Epidemic-prone diseases have traditionally been uncommon among nomadic pastoralists as mobility allows already dispersed populations to migrate away from epidemic threats. In the Karamoja region of Uganda, nomadic pastoralists are transitioning to an increasingly settled lifestyle due to cattle raiding and associated civil insecurity. In attempts to reduce conflict in the region, the Ugandan government has instituted disarmament campaigns and encouraged sedentism in place of mobility. In Karamoja, this transition to sedentism has contributed to the emergence and reemergence of epidemic-prone diseases such as cholera, hepatitis E, yellow fever, and meningococcal meningitis. The incidence of these diseases remains difficult to measure and several challenges exist to their control. Challenges to communicable disease surveillance and control among settling nomadic pastoralists are related to nomadic mobility, remote geography, vaccination and immunity, and poor sanitation and safe water access. In addition to improving gaps in infrastructure, attracting well-trained government health workers to Karamoja and similar areas with longstanding human resource limitations is critical to address the challenges to epidemic-prone disease surveillance and control among settling nomadic pastoralists. In conjunction with government health workers, community health teams provide a sustainable method by which public health programs can be improved in the austere environments inhabited by mobile and settling pastoralists. PMID:24784434

  2. Rosuvastatin Treatment Prevents Progressive Kidney Inflammation and Fibrosis in Stroke-Prone Rats

    PubMed Central

    Gianella, Anita; Nobili, Elena; Abbate, Mauro; Zoja, Carla; Gelosa, Paolo; Mussoni, Luciana; Bellosta, Stefano; Canavesi, Monica; Rottoli, Daniela; Guerrini, Uliano; Brioschi, Maura; Banfi, Cristina; Tremoli, Elena; Remuzzi, Giuseppe; Sironi, Luigi

    2007-01-01

    Salt-loaded, spontaneously hypertensive stroke-prone rats show progressive increases in blood pressure and proteinuria and accumulate acute-phase proteins in body fluids, modeling events during renal damage. The aim of this study was to assess the pathological events occurring in the kidney of spontaneously hypertensive stroke-prone rats over time and evaluate the effects of statin treatment, which is known to improve renal and cardiovascular outcomes. Kidneys of male spontaneously hypertensive stroke-prone rats euthanized at different stages of proteinuria showed progressive inflammatory cell infiltration, the accumulation of α-smooth muscle actin-positive cells, degenerative changes in podocytes, and severe fibrosis. These were accompanied by an imbalance in the plasminogen/plasmin and metalloprotease systems characterized by the increased renal expression of plasminogen activator inhibitor-1, tissue plasminogen activator, and urokinase plasminogen activator; the net result was an increase in plasmin and matrix metalloproteinase (MMP)-2 and a reduction in MMP-9 activity. Chronic treatment with the hydrophilic rosuvastatin had renoprotective effects in terms of morphology and inflammation and prevented the changes in plasmin, MMP-2, and MMP-9 activity. These effects were independent of the changes in blood pressure and plasma lipid levels. Treatment with the lipophilic simvastatin was not renoprotective. These data suggest that rosuvastatin may have potential utility as a therapeutic option in renal diseases that are characterized by inflammation and fibrosis. PMID:17392157

  3. Changes in cerebral blood flow under the prone condition with and without massage.

    PubMed

    Ouchi, Yasuomi; Kanno, Toshihiko; Okada, Hiroyuki; Yoshikawa, Etsuji; Shinke, Tomomi; Nagasawa, Shingo; Minoda, Keiji; Doi, Hiroyuki

    2006-10-23

    To investigate changes in regional cerebral blood flow (rCBF) under the prone condition with and without light massage on the back, we measured rCBF quantitatively in healthy human subjects using positron emission tomography with H(2)15O. Biochemical tests showed that the light massage (palm-pressure) reduced levels of stress-related serum cortisol and salivary stress protein chromogranin-A measured after the PET examination. Absolute rCBF significantly increased in the parietal cortex (precuneus) under the prone condition compared with the supine condition, and this rCBF increase was in parallel with comfortable sensation and slowing heart rate during the massage. Correlation analysis in statistical parametric mapping showed that the amygdalar and basal forebrain rCBF correlated with parasympathetic function (heart rate reduction), indicating involvement of the forebrain-amygdala system in mediating activities in the autonomic nervous system in the presence of comfortable sensation. To conclude, prone posture itself can stimulate the precuneus region to raise awareness, and the light massage on the back may help accommodate the brain to comfortable stimulation. PMID:16973270

  4. 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

  5. Factors Associated with Larval Control Practices in a Dengue Outbreak Prone Area

    PubMed Central

    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

  6. Brain structural correlates of schizotypy and psychosis proneness in a non-clinical healthy volunteer sample.

    PubMed

    Nenadic, Igor; Lorenz, Carsten; Langbein, Kerstin; Dietzek, Maren; Smesny, Stefan; Schönfeld, Nils; Fañanás, Lourdes; Sauer, Heinrich; Gaser, Christian

    2015-10-01

    Schizotypal traits are phenotypic risk factors for schizophrenia, associated with biological changes across a putative schizophrenia spectrum. In this study, we tested the hypothesis that brain structural changes in key brain areas relevant to this spectrum (esp. medial and lateral prefrontal cortex) would vary across different degrees of schizotypal trait expression and/or phenotypic markers of psychosis proneness in healthy non-clinical volunteers. We analysed high-resolution 3Tesla magnetic resonance images (MRI) of 59 healthy volunteers using voxel-based morphometry (VBM), correlating grey matter values to the positive and negative symptom factors of the schizotypal personality questionnaire (SPQ, German version) and a measure of psychosis proneness (community assessment of psychic experiences, CAPE). We found positive correlations between positive SPQ dimension and bilateral inferior and right superior frontal cortices, and positive CAPE dimension and left inferior frontal cortex, as well as CAPE negative dimension and right supplementary motor area (SMA) and left inferior parietal cortex. However, only the positive correlation of the right precuneus with negative schizotypy scores was significant after FWE correction for multiple comparisons. Our findings confirm an effect of schizotypal traits and psychosis proneness on brain structure in healthy subjects, providing further support to a biological continuum model. PMID:26164819

  7. Influence of Hip Joint Position on Muscle Activity during Prone Hip Extension with Knee Flexion

    PubMed Central

    Suehiro, Tadanobu; Mizutani, Masatoshi; Okamoto, Mitsuhisa; Ishida, Hiroshi; Kobara, Kenichi; Fujita, Daisuke; Osaka, Hiroshi; Takahashi, Hisashi; Watanabe, Susumu

    2014-01-01

    [Purpose] This study investigated the selective activation of the gluteus maximus during a prone hip extension with knee flexion exercise, with the hip joint in different positions. [Subjects] The subjects were 21 healthy, male volunteers. [Methods] Activities of the right gluteus maximus, right hamstrings, bilateral lumbar erector spinae, and bilateral lumbar multifidus were measured using surface electromyography during a prone hip extension with knee flexion exercise. Measurements were made with the hip joint in each of 3 positions: (1) a neutral hip joint position, (2) an abduction hip joint position, and (3) an abduction with external rotation hip joint position. [Results] Gluteus maximus activity was significantly higher when the hip was in the abduction with external rotation hip joint position than when it was in the neutral hip joint and abduction hip joint positions. Gluteus maximus activity was also significantly higher in the abduction hip joint position than in the neutral hip joint position. Hamstring activity was significantly lower when the hip was in the abduction with external rotation hip joint position than when it was in the neutral hip joint and abduction hip joint positions. [Conclusion] Abduction and external rotation of the hip during prone hip extension with knee flexion exercise selectively activates the gluteus maximus. PMID:25540492

  8. Error rates in a clinical data repository: lessons from the transition to electronic data transfer—a descriptive study

    PubMed Central

    Hong, Matthew K H; Yao, Henry H I; Pedersen, John S; Peters, Justin S; Costello, Anthony J; Murphy, Declan G; Hovens, Christopher M; Corcoran, Niall M

    2013-01-01

    Objective Data errors are a well-documented part of clinical datasets as is their potential to confound downstream analysis. In this study, we explore the reliability of manually transcribed data across different pathology fields in a prostate cancer database and also measure error rates attributable to the source data. Design Descriptive study. Setting Specialist urology service at a single centre in metropolitan Victoria in Australia. Participants Between 2004 and 2011, 1471 patients underwent radical prostatectomy at our institution. In a large proportion of these cases, clinicopathological variables were recorded by manual data-entry. In 2011, we obtained electronic versions of the same printed pathology reports for our cohort. The data were electronically imported in parallel to any existing manual entry record enabling direct comparison between them. Outcome measures Error rates of manually entered data compared with electronically imported data across clinicopathological fields. Results 421 patients had at least 10 comparable pathology fields between the electronic import and manual records and were selected for study. 320 patients had concordant data between manually entered and electronically populated fields in a median of 12 pathology fields (range 10–13), indicating an outright accuracy in manually entered pathology data in 76% of patients. Across all fields, the error rate was 2.8%, while individual field error ranges from 0.5% to 6.4%. Fields in text formats were significantly more error-prone than those with direct measurements or involving numerical figures (p<0.001). 971 cases were available for review of error within the source data, with figures of 0.1–0.9%. Conclusions While the overall rate of error was low in manually entered data, individual pathology fields were variably prone to error. High-quality pathology data can be obtained for both prospective and retrospective parts of our data repository and the electronic checking of source pathology data for error is feasible. PMID:23793682

  9. Quantum rms error and Heisenberg's error-disturbance relation

    NASA Astrophysics Data System (ADS)

    Busch, Paul

    2014-09-01

    Reports on experiments recently performed in Vienna [Erhard et al, Nature Phys. 8, 185 (2012)] and Toronto [Rozema et al, Phys. Rev. Lett. 109, 100404 (2012)] include claims of a violation of Heisenberg's error-disturbance relation. In contrast, a Heisenberg-type tradeoff relation for joint measurements of position and momentum has been formulated and proven in [Phys. Rev. Lett. 111, 160405 (2013)]. Here I show how the apparent conflict is resolved by a careful consideration of the quantum generalization of the notion of root-mean-square error. The claim of a violation of Heisenberg's principle is untenable as it is based on a historically wrong attribution of an incorrect relation to Heisenberg, which is in fact trivially violated. We review a new general trade-off relation for the necessary errors in approximate joint measurements of incompatible qubit observables that is in the spirit of Heisenberg's intuitions. The experiments mentioned may directly be used to test this new error inequality.

  10. Propidium monoazide reverse transcriptase PCR and RT-qPCR for detecting infectious enterovirus and norovirus.

    PubMed

    Karim, Mohammad R; Fout, G Shay; Johnson, Clifford H; White, Karen M; Parshionikar, Sandhya U

    2015-07-01

    Presently there is no established cell line or small animal model that allows for the detection of infectious human norovirus. Current methods based on RT-PCR and RT-qPCR detect both infectious and non-infectious virus and thus the conclusions that may be drawn regarding the public health significance of positive findings are limited. In this study, PMA RT-PCR and RT-qPCR assays were evaluated for selective detection of infectious poliovirus, murine norovirus (MNV-1), and Norwalk virus. Viruses were inactivated using heat, chlorine, and ultraviolet light (UV). Infectious and non-infectious viruses were treated with PMA before RT-PCR and RT-qPCR. PMA RT-PCR was able to differentiate selectively between infectious and heat and chlorine inactivated poliovirus. PMA RT-PCR was able to differentiate selectively between infectious and noninfectious murine norovirus only when inactivated by chlorine. However, PMA RT-PCR could not differentiate infectious Norwalk virus from virus particles rendered non-infectious by any treatment. PMA RT-PCR assay was not able to differentiate between infectious and UV inactivated viruses suggesting that viral capsid damage may be necessary for PMA to enter and bind to the viral genome. PMA RT-PCR on naked MNV-1 and Norwalk virus RNA suggest that PMA RT-PCR can be used to detect intact, potentially infectious MNV-1 and Norwalk viruses and can be used to exclude the detection of free viral RNA by PCR assay. PMID:25796356

  11. 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.

  12. Role of Computerized Physician Order Entry Usability in the Reduction of Prescribing Errors

    PubMed Central

    Zakaria, Mohamad Shanudin; Yasin, Norjaya M.; Shah, Mahmood Hussain; Elhissi, Abdelbary

    2013-01-01

    Objectives Some hospitals have implemented computerized physician order entry (CPOE) systems to reduce the medical error rates. However, research in this area has been very limited, especially regarding the impact of CPOE use on the reduction of prescribing errors. Moreover, the past studies have dealt with the overall impact of CPOE on the reduction of broadly termed "medical errors", and they have not specified which medical errors have been reduced by CPOE. Furthermore, the majority of the past research in this field has been either qualitative or has not used robust empirical techniques. This research examined the impacts of usability of CPOE systems on the reduction of doctors' prescribing errors. Methods One hundred and sixty-six questionnaires were used for quantitative data analyses. Since the data was not normally distributed, partial least square path modelling-as the second generation of multivariate data analyses-was applied to analyze data. Results It was found that the ease of use of the system and information quality can significantly reduce prescribing errors. Moreover, the user interface consistency and system error prevention have a significant positive impact on the perceived ease of use. More than 50% of the respondents believed that CPOE reduces the likelihood of drug allergy, drug interaction, and drug dosing errors thus improving patient safety. Conclusions Prescribing errors in terms of drug allergy, drug interaction, and drug dosing errors are reduced if the CPOE is not error-prone and easy to use, if the user interface is consistent, and if it provides quality information to doctors. PMID:23882414

  13. 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, σP = σT (12 / (N3-N))1 / 2, where σP is the period error, σT 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.

  14. 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

  15. Errors, error detection, error correction and hippocampal-region damage: data and theories.

    PubMed

    MacKay, Donald G; Johnson, Laura W

    2013-11-01

    This review and perspective article outlines 15 observational constraints on theories of errors, error detection, and error correction, and their relation to hippocampal-region (HR) damage. The core observations come from 10 studies with H.M., an amnesic with cerebellar and HR damage but virtually no neocortical damage. Three studies examined the detection of errors planted in visual scenes (e.g., a bird flying in a fish bowl in a school classroom) and sentences (e.g., I helped themselves to the birthday cake). In all three experiments, H.M. detected reliably fewer errors than carefully matched memory-normal controls. Other studies examined the detection and correction of self-produced errors, with controls for comprehension of the instructions, impaired visual acuity, temporal factors, motoric slowing, forgetting, excessive memory load, lack of motivation, and deficits in visual scanning or attention. In these studies, H.M. corrected reliably fewer errors than memory-normal and cerebellar controls, and his uncorrected errors in speech, object naming, and reading aloud exhibited two consistent features: omission and anomaly. For example, in sentence production tasks, H.M. omitted one or more words in uncorrected encoding errors that rendered his sentences anomalous (incoherent, incomplete, or ungrammatical) reliably more often than controls. Besides explaining these core findings, the theoretical principles discussed here explain H.M.'s retrograde amnesia for once familiar episodic and semantic information; his anterograde amnesia for novel information; his deficits in visual cognition, sentence comprehension, sentence production, sentence reading, and object naming; and effects of aging on his ability to read isolated low frequency words aloud. These theoretical principles also explain a wide range of other data on error detection and correction and generate new predictions for future test. PMID:23999403

  16. 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.

  17. ADEPT, a dynamic next generation sequencing data error-detection program with trimming

    DOE PAGESBeta

    Feng, Shihai; Lo, Chien-Chi; Li, Po-E; Chain, Patrick S. G.

    2016-02-29

    Illumina is the most widely used next generation sequencing technology and produces millions of short reads that contain errors. These sequencing errors constitute a major problem in applications such as de novo genome assembly, metagenomics analysis and single nucleotide polymorphism discovery. In this study, we present ADEPT, a dynamic error detection method, based on the quality scores of each nucleotide and its neighboring nucleotides, together with their positions within the read and compares this to the position-specific quality score distribution of all bases within the sequencing run. This method greatly improves upon other available methods in terms of the truemore » positive rate of error discovery without affecting the false positive rate, particularly within the middle of reads. We conclude that ADEPT is the only tool to date that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution of quality scores for the dataset being analyzed. The result is a method that is less prone to position-dependent under-prediction, which is one of the most prominent issues in error prediction. The outcome is that ADEPT improves upon prior efforts in identifying true errors, primarily within the middle of reads, while reducing the false positive rate.« less

  18. Progressive and Error-Resilient Transmission Strategies for VLC Encoded Signals over Noisy Channels

    NASA Astrophysics Data System (ADS)

    Jégou, Hervé; Guillemot, Christine

    2006-12-01

    This paper addresses the issue of robust and progressive transmission of signals (e.g., images, video) encoded with variable length codes (VLCs) over error-prone channels. This paper first describes bitstream construction methods offering good properties in terms of error resilience and progressivity. In contrast with related algorithms described in the literature, all proposed methods have a linear complexity as the sequence length increases. The applicability of soft-input soft-output (SISO) and turbo decoding principles to resulting bitstream structures is investigated. In addition to error resilience, the amenability of the bitstream construction methods to progressive decoding is considered. The problem of code design for achieving good performance in terms of error resilience and progressive decoding with these transmission strategies is then addressed. The VLC code has to be such that the symbol energy is mainly concentrated on the first bits of the symbol representation (i.e., on the first transitions of the corresponding codetree). Simulation results reveal high performance in terms of symbol error rate (SER) and mean-square reconstruction error (MSE). These error-resilience and progressivity properties are obtained without any penalty in compression efficiency. Codes with such properties are of strong interest for the binarization of[InlineEquation not available: see fulltext.]-ary sources in state-of-the-art image, and video coding systems making use of, for example, the EBCOT or CABAC algorithms. A prior statistical analysis of the signal allows the construction of the appropriate binarization code.

  19. Error recovery in asynchronous systems

    NASA Technical Reports Server (NTRS)

    Campbell, R. H.; Randell, B.

    1986-01-01

    Techniques for structuring forward error recovery measures in asynchronous systems are proposed, and recent ideas of atomic actions are generalized so as to support fault-tolerant interactions between processes. In particular, the proposal generalizes the form of simple recovery facilities supported by nested atomic actions in which the exception mechanisms only permit backward error recovery. It allows for construction of systems employing both forward and backward error recovery and thus allows for exploitation of the complementary benefits of the two schemes. Backward recovery, forward recovery, and normal processing activities can occur concurrently within the organization proposed.

  20. 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.

  1. Error bounds in cascading regressions

    USGS Publications Warehouse

    Karlinger, M.R.; Troutman, B.M.

    1985-01-01

    Cascading regressions is a technique for predicting a value of a dependent variable when no paired measurements exist to perform a standard regression analysis. Biases in coefficients of a cascaded-regression line as well as error variance of points about the line are functions of the correlation coefficient between dependent and independent variables. Although this correlation cannot be computed because of the lack of paired data, bounds can be placed on errors through the required properties of the correlation coefficient. The potential meansquared error of a cascaded-regression prediction can be large, as illustrated through an example using geomorphologic data. ?? 1985 Plenum Publishing Corporation.

  2. 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

  3. Errors in dynamically tunable gyroscopes

    NASA Astrophysics Data System (ADS)

    Abramov, R. A.

    The various errors occurring in dynamically tunable gyroscopes are examined in a systematic manner. First, equations of motion are presented for various types of dynamically tunable gyroscopes, and the errors resulting from combination resonances and their compensation are discussed. Attention is then given to the theory of deformation of the elastic elements of dynamically tunable gyroscopes and the effect of the nonlinear characteristics of elastic deformations on the gyroscope accuracy. The discussion also covers the dynamic accuracy of dynamically tunable gyroscopes and errors due to interactions through the platform.

  4. PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

    PubMed Central

    Pinto, Ameet J.; Raskin, Lutgarde

    2012-01-01

    As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of sequencing and chimeric PCR artifacts through rigorous quality control measures. However, there has been little effort towards understanding the effect of multi-template PCR biases on microbial community structure. In this study, we used three bacterial and three archaeal mock communities consisting of, respectively, 33 bacterial and 24 archaeal 16S rRNA gene sequences combined in different proportions to compare the influences of (1) sequencing depth, (2) sequencing artifacts (sequencing errors and chimeric PCR artifacts), and (3) biases in multi-template PCR, towards the interpretation of community structure in pyrosequencing datasets. We also assessed the influence of each of these three variables on ?- and ?-diversity metrics that rely on the number of OTUs alone (richness) and those that include both membership and the relative abundance of detected OTUs (diversity). As part of this study, we redesigned bacterial and archaeal primer sets that target the V3V5 region of the 16S rRNA gene, along with multiplexing barcodes, to permit simultaneous sequencing of PCR products from the two domains. We conclude that the benefits of deeper sequencing efforts extend beyond greater OTU detection and result in higher precision in ?-diversity analyses by reducing the variability between replicate libraries, despite the presence of more sequencing artifacts. Additionally, spurious OTUs resulting from sequencing errors have a significant impact on richness or shared-richness based ?- and ?-diversity metrics, whereas metrics that utilize community structure (including both richness and relative abundance of OTUs) are minimally affected by spurious OTUs. However, the greatest obstacle towards accurately evaluating community structure are the errors in estimated mean relative abundance of each detected OTU due to biases associated with multi-template PCR reactions. PMID:22905208

  5. The Benefits of Prone SPECT Myocardial Perfusion Imaging in Reducing Both Artifact Defects and Patient Radiation Exposure

    PubMed Central

    Stathaki, Maria; Koukouraki, Sophia; Papadaki, Emmanouela; Tsaroucha, Angeliki; Karkavitsas, Nikolaos

    2015-01-01

    Background Prone imaging has been demonstrated to minimize diaphragmatic and breast tissue attenuation. Objectives To determine the role of prone imaging on the reduction of unnecessary rest perfusion studies and coronary angiographies performed, thus decreasing investigation time and radiation exposure. Methods We examined 139 patients, 120 with an inferior wall and 19 with an anterior wall perfusion defect that might represented attenuation artifact. Post-stress images were acquired in both the supine and prone position. Coronary angiography was used as the “gold standard” for evaluating coronary artery patency. The study was terminated and rest imaging was obviated in the presence of complete improvement of the defect in the prone position. Quantitative interpretation was performed. Results were compared with clinical data and coronary angiographic findings. Results Prone acquisition correctly revealed defect improvement in 89 patients (89/120) with inferior wall and 12 patients (12/19) with anterior wall attenuation artifact. Quantitative analysis demonstrated statistically significant difference in the mean summed stress scores (SSS) of supine and mean SSS of prone studies in patients with disappearing inferior wall defect in the prone position and patent right coronary artery (true negative results). The mean difference between SSS in supine and in prone position was higher with disappearing than with remaining defects. Conclusion Technetium-99m (Tc-99m) tetrofosmin myocardial perfusion imaging with the patient in the prone position overcomes soft tissue attenuation; moreover it provides an inexpensive, accurate approach to limit the number of unnecessary rest perfusion studies and coronary angiographies performed. PMID:26559981

  6. Increased B Cell ADAM10 in Allergic Patients and Th2 Prone Mice

    PubMed Central

    Cooley, Lauren Folgosa; Martin, Rebecca K.; Zellner, Hannah B.; Irani, Anne-Marie; Uram-Tuculescu, Cora; El Shikh, Mohey Eldin; Conrad, Daniel H.

    2015-01-01

    ADAM10, as the sheddase of the low affinity IgE receptor (CD23), promotes IgE production and thus is a unique target for attenuating allergic disease. Herein, we describe that B cell levels of ADAM10, specifically, are increased in allergic patients and Th2 prone WT mouse strains (Balb/c and A/J). While T cell help augments ADAM10 expression, Balb WT B cells exhibit increased ADAM10 in the naïve state and even more dramatically increased ADAM10 after anti-CD40/IL4 stimulation compared C57 (Th1 prone) WT B cells. Furthermore, ADAM17 and TNF are reduced in allergic patients and Th2 prone mouse strains (Balb/c and A/J) compared to Th1 prone controls. To further understand this regulation, ADAM17 and TNF were studied in C57Bl/6 and Balb/c mice deficient in ADAM10. C57-ADAM10B-/- were more adept at increasing ADAM17 levels and thus TNF cleavage resulting in excess follicular TNF levels and abnormal secondary lymphoid tissue architecture not noted in Balb-ADAM10B-/-. Moreover, the level of B cell ADAM10 as well as Th context is critical for determining IgE production potential. Using a murine house dust mite airway hypersensitivity model, we describe that high B cell ADAM10 level in a Th2 context (Balb/c WT) is optimal for disease induction including bronchoconstriction, goblet cell metaplasia, mucus, inflammatory cellular infiltration, and IgE production. Balb/c mice deficient in B cell ADAM10 have attenuated lung and airway symptoms compared to Balb WT and are actually most similar to C57 WT (Th1 prone). C57-ADAM10B-/- have even further reduced symptomology. Taken together, it is critical to consider both innate B cell levels of ADAM10 and ADAM17 as well as Th context when determining host susceptibility to allergic disease. High B cell ADAM10 and low ADAM17 levels would help diagnostically in predicting Th2 disease susceptibility; and, we provide support for the use ADAM10 inhibitors in treating Th2 disease. PMID:25933166

  7. Removal of between-run variation in a multi-plate qPCR experiment

    PubMed Central

    Ruijter, Jan M.; Ruiz Villalba, Adrián; Hellemans, Jan; Untergasser, Andreas; van den Hoff, Maurice J.B.

    2015-01-01

    Quantitative PCR (qPCR) is the method of choice in gene expression analysis. However, the number of groups or treatments, target genes and technical replicates quickly exceeds the capacity of a single run on a qPCR machine and the measurements have to be spread over more than 1 plate. Such multi-plate measurements often show similar proportional differences between experimental conditions, but different absolute values, even though the measurements were technically carried out with identical procedures. Removal of this between-plate variation will enhance the power of the statistical analysis on the resulting data. Inclusion and application of calibrator samples, with replicate measurements distributed over the plates, assumes a multiplicative difference between plates. However, random and technical errors in these calibrators will propagate to all samples on the plate. To avoid this effect, the systematic bias between plates can be removed with a correction factor based on all overlapping technical and biological replicates between plates. This approach removes the requirement for all calibrator samples to be measured successfully on every plate. This paper extends an already published factor correction method to the use in multi-plate qPCR experiments. The between-run correction factor is derived from the target quantities which are calculated from the quantification threshold, PCR efficiency and observed Cq value. To enable further statistical analysis in existing qPCR software packages, an efficiency-corrected Cq value is reported, based on the corrected target quantity and a PCR efficiency per target. The latter is calculated as the mean of the PCR efficiencies taking the number of reactions per amplicon per plate into account. Export to the RDML format completes an RDML-supported analysis pipeline of qPCR data ranging from raw fluorescence data, amplification curve analysis and application of reference genes to statistical analysis.

  8. Performance of a multiplex PCR for the determination of Haemophilus influenzae capsular types in the clinical microbiology laboratory.

    PubMed

    Gonin, P; Lorange, M; Delage, G

    2000-05-01

    To improve tools for the surveillance of invasive H. influenzae in the context of the drastic decrease of type b infections following the implementation of vaccination, a two-step PCR technique was developed to detect the capsule and type specific regions of H. influenzae. The technique of Falla et al (1994) was modified to amplify in a first step the capsule and type b regions by multiplex PCR. For non-b capsulated strains, the type a, c, d, e, and f loci were afterward detected simultaneously by an optimized touch-down PCR technique. An internal control of extraction and amplification (16S rDNA) was included for both PCR techniques. Overall, this technique was shown to perform as efficiently or better than the slide agglutination without risks of interpretation errors. Of the 138 H. influenzae strains tested, seven that had given doubtful results by the agglutination technique were unequivocally typed by PCR. PMID:10794932

  9. 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.

    2015-07-01

    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 and which error characteristics are most important. Here we employ global sensitivity analysis to explore how (1) different error types (i.e., bias, random errors), (2) different error probability distributions, and (3) different error magnitudes influence physically based simulations of four snow variables (snow water equivalent, ablation rates, snow disappearance, and sublimation). We use the Sobol' global sensitivity analysis, which is typically used for model parameters but adapted here for testing model sensitivity to coexisting errors in all forcings. We quantify the Utah Energy Balance model's sensitivity to forcing errors with 1 840 000 Monte Carlo simulations across four sites and five different scenarios. Model outputs were (1) consistently more sensitive to forcing biases than random errors, (2) generally less sensitive to forcing error distributions, and (3) critically sensitive to different forcings depending on the relative magnitude of errors. For typical error magnitudes found in areas with drifting snow, precipitation bias was the most important factor for snow water equivalent, ablation rates, and snow disappearance timing, but other forcings had a more dominant impact when precipitation uncertainty was due solely to gauge undercatch. 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.

  10. Error Analysis in Mathematics Education.

    ERIC Educational Resources Information Center

    Radatz, Hendrik

    1979-01-01

    Five types of errors in an information-processing classification are discussed: language difficulties; difficulties in obtaining spatial information; deficient mastery of prerequisite skills, facts, and concepts; incorrect associations; and application of irrelevant rules. (MP)

  11. Robust characterization of leakage errors

    NASA Astrophysics Data System (ADS)

    Wallman, Joel J.; Barnhill, Marie; Emerson, Joseph

    2016-04-01

    Leakage errors arise when the quantum state leaks out of some subspace of interest, for example, the two-level subspace of a multi-level system defining a computational ‘qubit’, the logical code space of a quantum error-correcting code, or a decoherence-free subspace. Leakage errors pose a distinct challenge to quantum control relative to the more well-studied decoherence errors and can be a limiting factor to achieving fault-tolerant quantum computation. Here we present a scalable and robust randomized benchmarking protocol for quickly estimating the leakage rate due to an arbitrary Markovian noise process on a larger system. We illustrate the reliability of the protocol through numerical simulations.

  12. Orbital and Geodetic Error Analysis

    NASA Technical Reports Server (NTRS)

    Felsentreger, T.; Maresca, P.; Estes, R.

    1985-01-01

    Results that previously required several runs determined in more computer-efficient manner. Multiple runs performed only once with GEODYN and stored on tape. ERODYN then performs matrix partitioning and linear algebra required for each individual error-analysis run.

  13. 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.

  14. Static Detection of Disassembly Errors

    SciTech Connect

    Krishnamoorthy, Nithya; Debray, Saumya; Fligg, Alan K.

    2009-10-13

    Static disassembly is a crucial first step in reverse engineering executable files, and there is a consider- able body of work in reverse-engineering of binaries, as well as areas such as semantics-based security anal- ysis, that assumes that the input executable has been correctly disassembled. However, disassembly errors, e.g., arising from binary obfuscations, can render this assumption invalid. This work describes a machine- learning-based approach, using decision trees, for stat- ically identifying possible errors in a static disassem- bly; such potential errors may then be examined more closely, e.g., using dynamic analyses. Experimental re- sults using a variety of input executables indicate that our approach performs well, correctly identifying most disassembly errors with relatively few false positives.

  15. Developing checklists to prevent diagnostic error in Emergency Room settings

    PubMed Central

    Graber, Mark L.; Sorensen, Asta V.; Biswas, Jon; Modi, Varsha; Wackett, Andrew; Johnson, Scott; Lenfestey, Nancy; Meyer, Ashley N.D.; Singh, Hardeep

    2016-01-01

    Background Checklists have been shown to improve performance of complex, error-prone processes. To develop a checklist with potential to reduce the likelihood of diagnostic error for patients presenting to the Emergency Room (ER) with undiagnosed conditions. Methods Participants included 15 staff ER physicians working in two large academic centers. A rapid cycle design and evaluation process was used to develop a general checklist for high-risk situations vulnerable to diagnostic error. Physicians used the general checklists and a set of symptom-specific checklists for a period of 2 months. We conducted a mixed methods evaluation that included interviews regarding user perceptions and quantitative assessment of resource utilization before and after checklist use. Results A general checklist was developed iteratively by obtaining feedback from users and subject matter experts, and was trialed along with a set of specific checklists in the ER. Both the general and the symptom-specific checklists were judged to be helpful, with a slight preference for using symptom-specific lists. Checklist use commonly prompted consideration of additional diagnostic possibilities, changed the working diagnosis in approximately 10% of cases, and anecdotally was thought to be helpful in avoiding diagnostic errors. Checklist use was prompted by a variety of different factors, not just diagnostic uncertainty. None of the physicians used the checklists in collaboration with the patient, despite being encouraged to do so. Checklist use did not prompt large changes in test ordering or consultation. Conclusions In the ER setting, checklists for diagnosis are helpful in considering additional diagnostic possibilities, thus having potential to prevent diagnostic errors. Inconsistent usage and using the checklists privately, instead of with the patient, are factors that may detract from obtaining maximum benefit. Further research is needed to optimize checklists for use in the ER, determine how to increase usage, to evaluate the impact of checklist utilization on error rates and patient outcomes, to determine how checklist usage affects test ordering and consultation, and to compare checklists generally with other approaches to reduce diagnostic error.

  16. Digital PCR for detection of citrus pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus trees are often infected with multiple pathogens of economic importance, especially those with insect or mite vectors. Real-time/quantitative PCR (qPCR) has been used for high-throughput detection and relative quantification of pathogens; however, target reference or standards are required. I...

  17. Testing for Genetically Modified Foods Using PCR

    ERIC Educational Resources Information Center

    Taylor, Ann; Sajan, Samin

    2005-01-01

    The polymerase chain reaction (PCR) is a Nobel Prize-winning technique that amplifies a specific segment of DNA and is commonly used to test for the presence of genetic modifications. Students use PCR to test corn meal and corn-muffin mixes for the presence of a promoter commonly used in genetically modified foods, the cauliflower mosaic virus 35S

  18. Testing for Genetically Modified Foods Using PCR

    ERIC Educational Resources Information Center

    Taylor, Ann; Sajan, Samin

    2005-01-01

    The polymerase chain reaction (PCR) is a Nobel Prize-winning technique that amplifies a specific segment of DNA and is commonly used to test for the presence of genetic modifications. Students use PCR to test corn meal and corn-muffin mixes for the presence of a promoter commonly used in genetically modified foods, the cauliflower mosaic virus 35S…

  19. 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 ...

  20. Memory efficient hierarchical error diffusion

    NASA Astrophysics Data System (ADS)

    He, Zhen; Fan, Zhigang

    2010-01-01

    Hierarchical Error Diffusion (HED) developed in [14] yields high-quality color halftone by explicitly designing three critical factors: dot overlapping, positioning, and coloring. However, HED requires more error memory buffer than the conventional error diffusion algorithms since the pixel error is diffused in dot-color domain, instead of colorant domain. This can potentially be an issue for certain low-cost hardware implementation. This paper develops a memory-efficient HED algorithm (MEHED). To achieve this goal, the pixel error in dot-color domain is converted backward and diffused to future pixels in input colorant domain, say, CMYK for print applications. Since the error-augmented pixel value is no longer bounded within the range [0, 1.0], the dot overlapping control algorithm developed in [14] needs to be generalized to coherently handle the pixel density of outside the normal range. The key is to carefully split the modified pixel density into three parts: negative, regular, and surplus densities. The determination of regular and surplus densities needs to be dependent on the density of K channel, in order to maintain local color and avoid halftone texture artifact. The resulting dot-color densities are serves as the input to hierarchical thresholding and coloring steps to generate final halftone output. Experimental results demonstrate that MEHED achieves similar image quality compared to HED.

  1. Error thresholds in genetic algorithms.

    PubMed

    Ochoa, Gabriela

    2006-01-01

    The error threshold of replication is an important notion in the quasispecies evolution model; it is a critical mutation rate (error rate) beyond which structures obtained by an evolutionary process are destroyed more frequently than selection can reproduce them. With mutation rates above this critical value, an error catastrophe occurs and the genomic information is irretrievably lost. Therefore, studying the factors that alter this magnitude has important implications in the study of evolution. Here we use a genetic algorithm, instead of the quasispecies model, as the underlying model of evolution, and explore whether the phenomenon of error thresholds is found on finite populations of bit strings evolving on complex landscapes. Our empirical results verify the occurrence of error thresholds in genetic algorithms. In this way, this notion is brought from molecular evolution to evolutionary computation. We also study the effect of modifying the most prominent evolutionary parameters on the magnitude of this critical value, and found that error thresholds depend mainly on the selection pressure and genotype length. PMID:16831105

  2. Error image aware content restoration

    NASA Astrophysics Data System (ADS)

    Choi, Sungwoo; Lee, Moonsik; Jung, Byunghee

    2015-12-01

    As the resolution of TV significantly increased, content consumers have become increasingly sensitive to the subtlest defect in TV contents. This rising standard in quality demanded by consumers has posed a new challenge in today's context where the tape-based process has transitioned to the file-based process: the transition necessitated digitalizing old archives, a process which inevitably produces errors such as disordered pixel blocks, scattered white noise, or totally missing pixels. Unsurprisingly, detecting and fixing such errors require a substantial amount of time and human labor to meet the standard demanded by today's consumers. In this paper, we introduce a novel, automated error restoration algorithm which can be applied to different types of classic errors by utilizing adjacent images while preserving the undamaged parts of an error image as much as possible. We tested our method to error images detected from our quality check system in KBS(Korean Broadcasting System) video archive. We are also implementing the algorithm as a plugin of well-known NLE(Non-linear editing system), which is a familiar tool for quality control agent.

  3. A modified error correction protocol for CCITT signalling system no. 7 on satellite links

    NASA Astrophysics Data System (ADS)

    Kreuer, Dieter; Quernheim, Ulrich

    1991-10-01

    Comite Consultatif International des Telegraphe et Telephone (CCITT) Signalling System No. 7 (SS7) provides a level 2 error correction protocol particularly suited for links with propagation delays higher than 15 ms. Not being originally designed for satellite links, however, the so called Preventive Cyclic Retransmission (PCR) Method only performs well on satellite channels when traffic is low. A modified level 2 error control protocol, termed Fix Delay Retransmission (FDR) method is suggested which performs better at high loads, thus providing a more efficient use of the limited carrier capacity. Both the PCR and the FDR methods are investigated by means of simulation and results concerning throughput, queueing delay, and system delay, respectively. The FDR method exhibits higher capacity and shorter delay than the PCR method.

  4. Efficient error correction for next-generation sequencing of viral amplicons

    PubMed Central

    2012-01-01

    Background Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing. Results In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET). Both were compared to a previously published clustering algorithm (SHORAH), in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones. Conclusions Both algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses. The implementations of the algorithms and data sets used for their testing are available at: http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm PMID:22759430

  5. Identification of stable reference genes for quantitative PCR in cells derived from chicken lymphoid organs.

    PubMed

    Borowska, D; Rothwell, L; Bailey, R A; Watson, K; Kaiser, P

    2016-02-01

    Quantitative polymerase chain reaction (qPCR) is a powerful technique for quantification of gene expression, especially genes involved in immune responses. Although qPCR is a very efficient and sensitive tool, variations in the enzymatic efficiency, quality of RNA and the presence of inhibitors can lead to errors. Therefore, qPCR needs to be normalised to obtain reliable results and allow comparison. The most common approach is to use reference genes as internal controls in qPCR analyses. In this study, expression of seven genes, including β-actin (ACTB), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-glucuronidase (GUSB), TATA box binding protein (TBP), α-tubulin (TUBAT) and 28S ribosomal RNA (r28S), was determined in cells isolated from chicken lymphoid tissues and stimulated with three different mitogens. The stability of the genes was measured using geNorm, NormFinder and BestKeeper software. The results from both geNorm and NormFinder were that the three most stably expressed genes in this panel were TBP, GAPDH and r28S. BestKeeper did not generate clear answers because of the highly heterogeneous sample set. Based on these data we will include TBP in future qPCR normalisation. The study shows the importance of appropriate reference gene normalisation in other tissues before qPCR analysis. PMID:26872627

  6. 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

  7. 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.

  8. [PCR MP (PCR melting profile) technique--possibilities of application in epidemiological studies].

    PubMed

    Krawczyk, Beata; Leibner, Justyna; Samet, Alfred; Kur, Józef

    2007-01-01

    The performance and convenience of a PCR melting profile (PCR MP) technique based on using low denaturation temperatures during ligation mediated PCR (LM PCR) of bacterial DNA is shown. We found that PCR MP technique is a rapid method that offers good discriminatory power, excellent reproducibility and may be applied for epidemiological studies. Results from strain genotyping illustrate that PCR MP is useful for the study of intraspecific genetic relatedness of strains and is as effective in discriminating closely related strains as the PFGE method, which is currently considered to be the gold standard for epidemiological studies. The usefulness of the PCR MP for molecular typing was shown for clinical strains of Escherichia coli, Enterococcus faecium VRE and Stapylococcus aureus. PMID:17601026

  9. Nanomaterial Containing Wall Paints Can Increase Radon Concentration in Houses Located in Radon Prone Areas

    PubMed Central

    Haghani, M.; Mortazavi, S. M. J.; Faghihi, R.; Mehdizadeh, S.; Moradgholi, J.; Darvish, L.; Fathi-Pour, E.; Ansari, L.; Ghanbar-pour, M. R.

    2013-01-01

    Background: Nowadays, extensive technological advancements have made it possible to use nanopaints which show exciting properties. In IR Iran excessive radon levels (up to 3700 Bq m–3) have been reported in homes located in radon prone areas. Over the past decades, concerns have been raised about the risk posed by residential radon exposure. Objective: This study aims at investigating the effect of using nanomaterial containing wall paints on radon concentration in homes. Methods: Two wooden model houses were used in this study. Soil samples from Ramsar high background radiation areas were used for simulating the situation of a typical house in radon-prone areas. Conventional water-soluble wall paint was used for painting the walls of the 1st house model; while the 2nd house model was painted with the same wall paint with montmorillonitenanoclay. Results: Three days after sealing the house models, radon level was measured by using a portable radon survey meter. The mean radon level inside the 1st house model (conventional paint) was 515.3 ± 17.8 Bq/m3 while the mean radon concentration in the 2nd house model (nano-painted house model) was 570.8 ± 18.5 Bq/m3. The difference between these means was statistically significant (P<0.001). Conclusion: To the best of our knowledge, this study is the first investigation on the effect of nano-material containing wall paints on indoor radon concentrations.  It can be concluded that nano-material-containing wall paints should not be used in houses with wooden walls located in radon prone areas. Although the mechanism of this effect is not clearly known, decreased porosity in nano-paints might be a key factor in increasing the radon concentration in homes. PMID:25505754

  10. Accelerated Whole Breast Irradiation With Intensity-Modulated Radiotherapy to the Prone Breast

    SciTech Connect

    Croog, Victoria J.; Wu, Abraham J.; McCormick, Beryl; Beal, Kathryn P.

    2009-01-01

    Purpose: Whole breast irradiation (WBI) is the standard of care for patients with early-stage breast cancer who opt for breast conservation. After a randomized trial demonstrated equivalent cosmesis and disease control with accelerated WBI (AWBI), our institution began to offer AWBI to appropriate patients. The aim of this study was to examine our unique experience with AWBI using prone positioning and simplified intensity-modulated radiotherapy (IMRT) planning with a sequential boost to the tumor bed. Methods and Materials: We identified 356 patients who had been treated with prone WBI using IMRT in our department between January 2004 and December 2006. Of these, 128 (36%) patients had received AWBI (representing 131 treated breasts), consisting of 16 daily fractions of 265 cGy to a total dose of 4,240 cGy followed by a conventionally fractionated boost. Results: Patients who opted for AWBI were similar demographically to the patients undergoing conventional WBI. In the AWBI cohort, 83% of the patients had Stage T1 disease and 22% had nodal involvement (N1). The tumors were estrogen receptor-positive, progesterone receptor-positive and Her-2/Neu-amplified in 82%, 69%, and 11%, respectively. The median duration of AWBI plus a boost was 29 days, and no patient required a toxicity-related treatment break. No Grade 3 or greater acute toxicity developed. At a median follow-up of 18 months, one ipsilateral breast recurrence developed that was salvaged with mastectomy and immediate reconstruction. Conclusion: AWBI to the prone breast using simplified IMRT with a sequential boost offers women requiring breast-only adjuvant radiotherapy an abbreviated treatment with early tumor control and cosmesis comparable to that with standard fractionation.

  11. Correlates of the multidimensional construct of hypnotizability: paranormal belief, fantasy proneness, magical ideation, and dissociation.

    PubMed

    Dasse, Michelle N; Elkins, Gary R; Weaver, Charles A

    2015-01-01

    Hypnotizability is a multifaceted construct that may relate to multiple aspects of personality and beliefs. This study sought to address 4 known correlates of hypnotizability to aid in its understanding. Eighty undergraduates completed the Magical Ideation Scale (MIS), the Creative Experiences Questionnaire (CEQ), the Australian Sheep-Goat Scale (ASGS), and the Dissociative Experiences Scale (DES) and then were administered the Creative Imagination Scale (CIS). All 5 scales were significantly correlated. Participants higher in hypnotizability scored higher on the CEQ and the MIS. The findings demonstrate the influence of fantasy proneness and magical thinking on hypnotizability and support the theory that hypnotizability is a complex interaction of multiple traits. PMID:25978081

  12. Short-term absence from industry: III The inference of `proneness' and a search for causes

    PubMed Central

    Froggatt, P.

    1970-01-01

    Froggatt, P. (1970).Brit. J. industr. Med.,27, 297-312. Short-term absence from industry. III. The inference of `proneness' and a search for causes. The abilities of five hypotheses (`chance', `proneness', and three of `true contagion' - as defined in the text) to explain the distributions of one-day and two-day absences among groups of male and female industrial personnel and clerks in government service are examined by curve-fitting and correlation methods. The five hypotheses generate (in order) the Poisson, negative binomial, Neyman type A, Short, and Hermite (two-parameter form) distributions which are fitted to the data using maximum-likelihood estimates. The conclusion is drawn that `proneness', i.e., a stable `liability', compounded from several though unquantifiable factors, and constant for each individual over the period of the study, is markedly successful in explaining the data. It is emphasized that some of the other hypotheses under test cannot be unequivocably rejected; and there is in theory an infinite number, still unformulated or untested, which may be acceptable or even fit the data better. Correlation coefficients for the numbers of one-day (and two-day) absences taken by the same individuals in two equal non-overlapping periods of time are of the order 0·5 to 0·7 (0·3 to 0·5 for two-day absences) and the corresponding regressions fulfil linear requirements. These correlations are higher than any between `personal characteristics' and their overt consequence in contingent fields of human enquiry. For one-day absences the predictive power for the future from the past record could in some circumstances justify executive action. When freely available, overtime was greatest among junior married men and least among junior married women. The validity of the inference of `proneness' and the implications of its acceptance are fully discussed. While interpretation is not unequivocal, one-day absences seemingly have many causes; two-day absences are also heterogeneous but in some ways resemble longer certified absence. It is concluded that short-term absence, particularly of one day, may be largely the overt expression of a traditional desire, even need, to work discontinuously which, though it can be mitigated by often identifiable general and individual circumstances, is consistently more marked in some individuals than in others. PMID:5488689

  13. Estimation of stapes piston motion from uniaxial interferometer measurements along observation directions at an angle with the piston axis is prone to substantial errors

    NASA Astrophysics Data System (ADS)

    Decraemer, Willem F. S.; Khanna, Shyam M.; Dirckx, Joris J. J.

    2006-06-01

    We have shown that the vibration of the stapes in human, cat and gerbil exhibits all 3-D components of translation and rotation, but also that non-piston components do not contribute to the transmission path. In most experiments access for direct measurement of stapes motion in line with the piston axis is not available and piston motion is estimated from single component interferometric measurements done under observation directions that make angles up to 50° with the piston axis. We used a heterodyne microscope/interferometer to measure the vibration velocity of the stapes in human, cat and gerbil from different observation angles and calculated the complete set of 3-D motion components for the stapes. Using micro CT scans of the experimental ears, we could express the components in an intrinsic reference system and foretell the motion component that will be obtained when a single axis interferometric measurement is done under various angles with the piston axis. For low frequencies (f<2kHz) a cosine factor provides a good correction for the axis off-set, at higher frequencies the piston component can not correctly be estimated from a single off-axis observation. We will show that this may lead to serious misinterpretations of experimental results.

  14. 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

  15. Error-prone mutagenesis detected in mammalian cells by a shuttle vector containing the supF gene of Escherichia coli.

    PubMed Central

    Sarkar, S; Dasgupta, U B; Summers, W C

    1984-01-01

    When a shuttle vector containing a tyrosine suppressor tRNA (supF) gene as a target for mutagenesis replicated in a monkey kidney cell line, the frequency of SupF+ mutations was 2.3 +/- 0.5 x 10(-3). When the host cells were treated with ethyl methanesulfonate 40 h before transfection, a 10-fold increase in SupF+ mutation frequency was observed. These results supported the hypothesis that a damage-inducible mutagenic pathway exists in mammalian cells and also demonstrated the utility of this shuttle vector for the study of mutagenesis in mammalian cells. Images PMID:6095049

  16. Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein

    PubMed Central

    Yuan, Ying; Britton, Sébastien; Delteil, Christine; Coates, Julia; Jackson, Stephen P.; Barboule, Nadia; Frit, Philippe; Calsou, Patrick

    2015-01-01

    In humans, DNA double-strand breaks (DSBs) are repaired by two mutually-exclusive mechanisms, homologous recombination or end-joining. Among end-joining mechanisms, the main process is classical non-homologous end-joining (C-NHEJ) which relies on Ku binding to DNA ends and DNA Ligase IV (Lig4)-mediated ligation. Mostly under Ku- or Lig4-defective conditions, an alternative end-joining process (A-EJ) can operate and exhibits a trend toward microhomology usage at the break junction. Homologous recombination relies on an initial MRN-dependent nucleolytic degradation of one strand at DNA ends. This process, named DNA resection generates 3′ single-stranded tails necessary for homologous pairing with the sister chromatid. While it is believed from the current literature that the balance between joining and recombination processes at DSBs ends is mainly dependent on the initiation of resection, it has also been shown that MRN activity can generate short single-stranded DNA oligonucleotides (ssO) that may also be implicated in repair regulation. Here, we evaluate the effect of ssO on end-joining at DSB sites both in vitro and in cells. We report that under both conditions, ssO inhibit C-NHEJ through binding to Ku and favor repair by the Lig4-independent microhomology-mediated A-EJ process. PMID:26350212

  17. Real-time PCR detection chemistry.

    PubMed

    Navarro, E; Serrano-Heras, G; Castaño, M J; Solera, J

    2015-01-15

    Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review. PMID:25451956

  18. Integrating a calibrated groundwater flow model with error-correcting data-driven models to improve predictions

    NASA Astrophysics Data System (ADS)

    Demissie, Yonas K.; Valocchi, Albert J.; Minsker, Barbara S.; Bailey, Barbara A.

    2009-01-01

    SummaryPhysically-based groundwater models (PBMs), such as MODFLOW, contain numerous parameters which are usually estimated using statistically-based methods, which assume that the underlying error is white noise. However, because of the practical difficulties of representing all the natural subsurface complexity, numerical simulations are often prone to large uncertainties that can result in both random and systematic model error. The systematic errors can be attributed to conceptual, parameter, and measurement uncertainty, and most often it can be difficult to determine their physical cause. In this paper, we have developed a framework to handle systematic error in physically-based groundwater flow model applications that uses error-correcting data-driven models (DDMs) in a complementary fashion. The data-driven models are separately developed to predict the MODFLOW head prediction errors, which were subsequently used to update the head predictions at existing and proposed observation wells. The framework is evaluated using a hypothetical case study developed based on a phytoremediation site at the Argonne National Laboratory. This case study includes structural, parameter, and measurement uncertainties. In terms of bias and prediction uncertainty range, the complementary modeling framework has shown substantial improvements (up to 64% reduction in RMSE and prediction error ranges) over the original MODFLOW model, in both the calibration and the verification periods. Moreover, the spatial and temporal correlations of the prediction errors are significantly reduced, thus resulting in reduced local biases and structures in the model prediction errors.

  19. Attentional Capture by Irrelevant Transients Leads to Perceptual Errors in a Competitive Change Detection Task

    PubMed Central

    Schneider, Daniel; Beste, Christian; Wascher, Edmund

    2012-01-01

    Theories on visual change detection imply that attention is a necessary but not sufficient prerequisite for aware perception. Misguidance of attention due to salient irrelevant distractors can therefore lead to severe deficits in change detection. The present study investigates the mechanisms behind such perceptual errors and their relation to error processing on higher cognitive levels. Participants had to detect a luminance change that occasionally occurred simultaneously with an irrelevant orientation change in the opposite hemi-field (conflict condition). By analyzing event-related potentials in the EEG separately in those error prone conflict trials for correct and erroneous change detection, we demonstrate that only correct change detection was associated with the allocation of attention to the relevant luminance change. Erroneous change detection was associated with an initial capture of attention toward the irrelevant orientation change in the N1 time window and a lack of subsequent target selection processes (N2pc). Errors were additionally accompanied by an increase of the fronto-central N2 and a kind of error negativity (Ne or ERN), which, however, peaked prior to the response. These results suggest that a strong perceptual conflict by salient distractors can disrupt the further processing of relevant information and thus affect its aware perception. Yet, it does not impair higher cognitive processes for conflict and error detection, indicating that these processes are independent from awareness. PMID:22654780

  20. Comparison of prone versus supine 18F-FDG-PET of locally advanced breast cancer: Phantom and preliminary clinical studies

    SciTech Connect

    Williams, Jason M.; Rani, Sudheer D.; Li, Xia; Whisenant, Jennifer G.; Abramson, Richard G.; Arlinghaus, Lori R.; Lee, Tzu-Cheng; MacDonald, Lawrence R.; Partridge, Savannah C.; Kang, Hakmook; Linden, Hannah M.; Kinahan, Paul E.; Yankeelov, Thomas E.

    2015-07-15

    Purpose: Previous studies have demonstrated how imaging of the breast with patients lying prone using a supportive positioning device markedly facilitates longitudinal and/or multimodal image registration. In this contribution, the authors’ primary objective was to determine if there are differences in the standardized uptake value (SUV) derived from [{sup 18}F]fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) in breast tumors imaged in the standard supine position and in the prone position using a specialized positioning device. Methods: A custom positioning device was constructed to allow for breast scanning in the prone position. Rigid and nonrigid phantom studies evaluated differences in prone and supine PET. Clinical studies comprised 18F-FDG-PET of 34 patients with locally advanced breast cancer imaged in the prone position (with the custom support) followed by imaging in the supine position (without the support). Mean and maximum values (SUV{sub peak} and SUV{sub max}, respectively) were obtained from tumor regions-of-interest for both positions. Prone and supine SUV were linearly corrected to account for the differences in 18F-FDG uptake time. Correlation, Bland–Altman, and nonparametric analyses were performed on uptake time-corrected and uncorrected data. Results: SUV from the rigid PET breast phantom imaged in the prone position with the support device was 1.9% lower than without the support device. In the nonrigid PET breast phantom, prone SUV with the support device was 5.0% lower than supine SUV without the support device. In patients, the median (range) difference in uptake time between prone and supine scans was 16.4 min (13.4–30.9 min), which was significantly—but not completely—reduced by the linear correction method. SUV{sub peak} and SUV{sub max} from prone versus supine scans were highly correlated, with concordance correlation coefficients of 0.91 and 0.90, respectively. Prone SUV{sub peak} and SUV{sub max} were significantly lower than supine in both original and uptake time-adjusted data across a range of index times (P < < 0.0001, Wilcoxon signed rank test). Before correcting for uptake time differences, Bland–Altman analyses revealed proportional bias between prone and supine measurements (SUV{sub peak} and SUV{sub max}) that increased with higher levels of FDG uptake. After uptake time correction, this bias was significantly reduced (P < 0.01). Significant prone-supine differences, with regard to the spatial distribution of lesions relative to isocenter, were observed between the two scan positions, but this was poorly correlated with the residual (uptake time-corrected) prone-supine SUV{sub peak} difference (P = 0.78). Conclusions: Quantitative 18F-FDG-PET/CT of the breast in the prone position is not deleteriously affected by the support device but yields SUV that is consistently lower than those obtained in the standard supine position. SUV differences between scans arising from FDG uptake time differences can be substantially reduced, but not removed entirely, with the current correction method. SUV from the two scan orientations is quantitatively different and should not be assumed equivalent or interchangeable within the same subject. These findings have clinical relevance in that they underscore the importance of patient positioning while scanning as a clinical variable that must be accounted for with longitudinal PET measurement, for example, in the assessment of treatment response.

  1. 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.

  2. Patterns of pronoun case error.

    PubMed

    Rispoli, M

    1998-10-01

    This paper addresses the question of whether the rate and patterns of pronoun case error are influenced by the composition of an individual pronoun's paradigm. Twenty-nine children, aged 2;6 to 4;0 were audiotaped for two 1-hour sessions, interacting with their primary caregivers engaged in free play, book reading and family album viewing. It was found that her was overextended for she at a significantly higher rate than him for he and them for they, providing evidence of a 'double-cell' effect that increases the incidence of error in the feminine pronoun. It was also found that the overextension of nominative forms (e.g. he for him), were antagonistic to the more frequently occurring type of overextension, objective for nominative (e.g. him for he). These findings indicate that the composition of a pronoun's paradigm influenced the patterns of pronoun case error observed. PMID:10095324

  3. Error Field Correction in ITER

    SciTech Connect

    Park, Jong-kyu; Boozer, Allen H.; Menard, Jonathan E.; Schaffer, Michael J.

    2008-05-22

    A new method for correcting magnetic field errors in the ITER tokamak is developed using the Ideal Perturbed Equilibrium Code (IPEC). The dominant external magnetic field for driving islands is shown to be localized to the outboard midplane for three ITER equilibria that represent the projected range of operational scenarios. The coupling matrices between the poloidal harmonics of the external magnetic perturbations and the resonant fields on the rational surfaces that drive islands are combined for different equilibria and used to determine an ordered list of the dominant errors in the external magnetic field. It is found that efficient and robust error field correction is possible with a fixed setting of the correction currents relative to the currents in the main coils across the range of ITER operating scenarios that was considered.

  4. Orbit IMU alignment: Error analysis

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    A comprehensive accuracy analysis of orbit inertial measurement unit (IMU) alignments using the shuttle star trackers was completed and the results are presented. Monte Carlo techniques were used in a computer simulation of the IMU alignment hardware and software systems to: (1) determine the expected Space Transportation System 1 Flight (STS-1) manual mode IMU alignment accuracy; (2) investigate the accuracy of alignments in later shuttle flights when the automatic mode of star acquisition may be used; and (3) verify that an analytical model previously used for estimating the alignment error is a valid model. The analysis results do not differ significantly from expectations. The standard deviation in the IMU alignment error for STS-1 alignments was determined to the 68 arc seconds per axis. This corresponds to a 99.7% probability that the magnitude of the total alignment error is less than 258 arc seconds.

  5. Motion errors and compensation possibilities

    NASA Astrophysics Data System (ADS)

    Hounam, David

    1992-08-01

    The synthetic aperture radar (SAR) technique relies on knowledge of the relative motion between the sensor and the target. If the flight path of the sensor is not accurately known or the SAR processor is limited in its ability to take the flight data into account, the SAR image will be degraded. Motion errors are particularly critical for SAR sensors on small, low-flying aircraft, due to turbulence, and where high spatial resolution is required. The lecture discusses the effects of motion errors on image quality and the requirements on the sensor and processor to compensate for motion errors. The DLR airborne sensor, E-SAR, and associated image processor will be used as examples. Techniques using a priori knowledge of the flight path from independent sensors, e.g., inertial navigation systems (INS), and by extracting the flight data from the SAR data, e.g., autofocus and reflectivity displacement method (RDM), are treated.

  6. Spacecraft and propulsion technician error

    NASA Astrophysics Data System (ADS)

    Schultz, Daniel Clyde

    Commercial aviation and commercial space similarly launch, fly, and land passenger vehicles. Unlike aviation, the U.S. government has not established maintenance policies for commercial space. This study conducted a mixed methods review of 610 U.S. space launches from 1984 through 2011, which included 31 failures. An analysis of the failure causal factors showed that human error accounted for 76% of those failures, which included workmanship error accounting for 29% of the failures. With the imminent future of commercial space travel, the increased potential for the loss of human life demands that changes be made to the standardized procedures, training, and certification to reduce human error and failure rates. Several recommendations were made by this study to the FAA's Office of Commercial Space Transportation, space launch vehicle operators, and maintenance technician schools in an effort to increase the safety of the space transportation passengers.

  7. Assessment of surfactants for efficient droplet PCR in mineral oil using the pendant drop technique.

    PubMed

    Pandit, Kunal R; Rueger, Paul E; Calabrese, Richard V; Raghavan, Srinivasa R; White, Ian M

    2015-02-01

    Amplification and detection of nucleic acid sequences within integrated microsystems is routinely conducted using the technique of droplet PCR, wherein the polymerase chain reaction (PCR) is performed in microscale water-in-oil droplets (nanoliter to picoliter volumes). During droplet PCR, interactions at the interface of the droplet tend to dominate. Specifically, adsorption of the polymerase at the droplet interface leads to inefficient amplification. To reduce polymerase adsorption, surfactants such as the silicone-based ABIL EM90 have been commonly used. However, these surfactants have been selected largely through trial and error, and have been only somewhat effective. For example, when using ABIL EM90, 8 times (8 ×) the manufacturer prescribed concentration of polymerase was necessary for amplification. In this report, we use the pendant drop technique to measure adsorption and loss of enzyme at droplet interfaces for various surfactant-oil combinations. Dynamic interfacial tension and surface pressure measurements showed that significant polymerase adsorption occurs when using ABIL EM90. In contrast, much lower polymerase adsorption is observed when using Brij L4, a nonionic surfactant with a C12 tail and an oxyethylene headgroup, which has not yet been reported for droplet PCR. These results correlate strongly with droplet PCR efficiency. Brij L4 enables highly efficient PCR at 2 × polymerase concentration, and still enables effective PCR at 1 × polymerase concentration. Overall, this work introduces a methodology for quantitatively assessing surfactants for use with droplet microreactors, and it demonstrates the practical value of this new approach by identifying a surfactant that can dramatically improve the efficiency of droplet PCR. PMID:25620443

  8. Analysis of Medication Error Reports

    SciTech Connect

    Whitney, Paul D.; Young, Jonathan; Santell, John; Hicks, Rodney; Posse, Christian; Fecht, Barbara A.

    2004-11-15

    In medicine, as in many areas of research, technological innovation and the shift from paper based information to electronic records has created a climate of ever increasing availability of raw data. There has been, however, a corresponding lag in our abilities to analyze this overwhelming mass of data, and classic forms of statistical analysis may not allow researchers to interact with data in the most productive way. This is true in the emerging area of patient safety improvement. Traditionally, a majority of the analysis of error and incident reports has been carried out based on an approach of data comparison, and starts with a specific question which needs to be answered. Newer data analysis tools have been developed which allow the researcher to not only ask specific questions but also to “mine” data: approach an area of interest without preconceived questions, and explore the information dynamically, allowing questions to be formulated based on patterns brought up by the data itself. Since 1991, United States Pharmacopeia (USP) has been collecting data on medication errors through voluntary reporting programs. USP’s MEDMARXsm reporting program is the largest national medication error database and currently contains well over 600,000 records. Traditionally, USP has conducted an annual quantitative analysis of data derived from “pick-lists” (i.e., items selected from a list of items) without an in-depth analysis of free-text fields. In this paper, the application of text analysis and data analysis tools used by Battelle to analyze the medication error reports already analyzed in the traditional way by USP is described. New insights and findings were revealed including the value of language normalization and the distribution of error incidents by day of the week. The motivation for this effort is to gain additional insight into the nature of medication errors to support improvements in medication safety.

  9. Six-port error propagation

    NASA Astrophysics Data System (ADS)

    Stelzer, Andreas; Diskus, Christian G.

    2000-07-01

    In this contribution the various influences on the accuracy of a near range precision radar are described. The front-end is a monostatic design operating at 34 - 36.2 GHz. The hardware configuration enables different modes of operation including FM-CW and interferometric modes. To achieve a highly accurate distance measurement, attention must be paid to various error sources. Due to the use of a six-port it is rather complicated to determine the corresponding error propagation. In the following the results of investigations on how to achieve an exceptional accuracy of +/- 0.1 mm are described.

  10. 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

  11. Automatic-repeat-request error control schemes

    NASA Technical Reports Server (NTRS)

    Lin, S.; Costello, D. J., Jr.; Miller, M. J.

    1983-01-01

    Error detection incorporated with automatic-repeat-request (ARQ) is widely used for error control in data communication systems. This method of error control is simple and provides high system reliability. If a properly chosen code is used for error detection, virtually error-free data transmission can be attained. Various types of ARQ and hybrid ARQ schemes, and error detection using linear block codes are surveyed.

  12. SU-E-J-227: Breathing Pattern Consistency and Reproducibility: Comparative Analysis for Supine and Prone Body Positioning

    SciTech Connect

    Laugeman, E; Weiss, E; Chen, S; Hugo, G; Rosu, M

    2014-06-01

    Purpose: Evaluate and compare the cycle-to-cycle consistency of breathing patterns and their reproducibility over the course of treatment, for supine and prone positioning. Methods: Respiratory traces from 25 patients were recorded for sequential supine/prone 4DCT scans acquired prior to treatment, and during the course of the treatment (weekly or bi-weekly). For each breathing cycle, the average(AVE), end-of-exhale(EoE) and end-of-inhale( EoI) locations were identified using in-house developed software. In addition, the mean values and variations for the above quantities were computed for each breathing trace. F-tests were used to compare the cycle-to-cycle consistency of all pairs of sequential supine and prone scans. Analysis of variances was also performed using population means for AVE, EoE and EoI to quantify differences between the reproducibility of prone and supine respiration traces over the treatment course. Results: Consistency: Cycle-to-cycle variations are less in prone than supine in the pre-treatment and during-treatment scans for AVE, EoE and EoI points, for the majority of patients (differences significant at p<0.05). The few cases where the respiratory pattern had more variability in prone appeared to be random events. Reproducibility: The reproducibility of breathing patterns (supine and prone) improved as treatment progressed, perhaps due to patients becoming more comfortable with the procedure. However, variability in supine position continued to remain significantly larger than in prone (p<0.05), as indicated by the variance analysis of population means for the pretreatment and subsequent during-treatment scans. Conclusions: Prone positioning stabilizes breathing patterns in most subjects investigated in this study. Importantly, a parallel analysis of the same group of patients revealed a tendency towards increasing motion amplitude of tumor targets in prone position regardless of their size or location; thus, the choice for body positioning during radiation therapy will have to consider the clinical relevance of the two opposing trends - breathing consistency and motion amplitude.

  13. Detection of potential microbial antigens by immuno-PCR (PCR-amplified immunoassay).

    PubMed

    Mehta, Promod K; Raj, Ankush; Singh, Netra Pal; Khuller, Gopal K

    2014-05-01

    Immuno-PCR (PCR-amplified immunoassay; I-PCR) is a novel ultrasensitive method combining the versatility of ELISA with the sensitivity of nucleic acid amplification of PCR. The enormous exponential amplification power of PCR in an I-PCR assay leads to at least a 10(2)-10(4)-fold increase in sensitivity compared with an analogous ELISA. I-PCR has been used to detect many biological molecules such as proto-oncogenes, toxins, cytokines, hormones, and biomarkers for autoimmune and Alzheimer's diseases, as well as microbial antigens and antibodies, and it can be adapted as a novel diagnostic tool for various infectious and non-infectious diseases. Quantitative real-time I-PCR has the potential to become the most analytically sensitive method for the detection of proteins. The sensitivity and specificity of a real-time I-PCR assay can be enhanced further with the use of magnetic beads and nanoparticles. This review is primarily focused on the detection of potential viral, bacterial and parasitic antigens by I-PCR assay, thus enabling their application for immunological research and for early diagnosis of infectious diseases. PMID:24568881

  14. Detection and screening of chromosomal rearrangements in uterine leiomyomas by long-distance inverse PCR.

    PubMed

    Pradhan, Barun; Sarvilinna, Nanna; Matilainen, Juha; Aska, Elli; Sjöberg, Jari; Kauppi, Liisa

    2016-03-01

    Genome instability is a hallmark of many tumors and recently, next-generation sequencing methods have enabled analyses of tumor genomes at an unprecedented level. Studying rearrangement-prone chromosomal regions (putative "breakpoint hotspots") in detail, however, necessitates molecular assays that can detect de novo DNA fusions arising from these hotspots. Here we demonstrate the utility of a long-distance inverse PCR-based method for the detection and screening of de novo DNA rearrangements in uterine leiomyomas, one of the most common types of human neoplasm. This assay allows in principle any genomic region suspected of instability to be queried for DNA rearrangements originating there. No prior knowledge of the identity of the fusion partner chromosome is needed. We used this method to screen uterine leiomyomas for rearrangements at genomic locations known to be rearrangement-prone in this tumor type: upstream HMGA2 and within RAD51B. We identified a novel DNA rearrangement upstream of HMGA2 that had gone undetected in an earlier whole-genome sequencing study. In more than 30 additional uterine leiomyoma samples, not analyzed by whole-genome sequencing previously, no rearrangements were observed within the 1,107 bp and 1,996 bp assayed in the RAD51B and HMGA2 rearrangement hotspots. Our findings show that long-distance inverse PCR is a robust, sensitive, and cost-effective method for the detection and screening of DNA rearrangements from solid tumors that should be useful for many diagnostic applications. © 2015 Wiley Periodicals, Inc. PMID:26608380

  15. Digital stereo photogrammetry for grain-scale monitoring of fluvial surfaces: Error evaluation and workflow optimisation

    NASA Astrophysics Data System (ADS)

    Bertin, Stephane; Friedrich, Heide; Delmas, Patrice; Chan, Edwin; Gimel'farb, Georgy

    2015-03-01

    Grain-scale monitoring of fluvial morphology is important for the evaluation of river system dynamics. Significant progress in remote sensing and computer performance allows rapid high-resolution data acquisition, however, applications in fluvial environments remain challenging. Even in a controlled environment, such as a laboratory, the extensive acquisition workflow is prone to the propagation of errors in digital elevation models (DEMs). This is valid for both of the common surface recording techniques: digital stereo photogrammetry and terrestrial laser scanning (TLS). The optimisation of the acquisition process, an effective way to reduce the occurrence of errors, is generally limited by the use of commercial software. Therefore, the removal of evident blunders during post processing is regarded as standard practice, although this may introduce new errors. This paper presents a detailed evaluation of a digital stereo-photogrammetric workflow developed for fluvial hydraulic applications. The introduced workflow is user-friendly and can be adapted to various close-range measurements: imagery is acquired with two Nikon D5100 cameras and processed using non-proprietary "on-the-job" calibration and dense scanline-based stereo matching algorithms. Novel ground truth evaluation studies were designed to identify the DEM errors, which resulted from a combination of calibration errors, inaccurate image rectifications and stereo-matching errors. To ensure optimum DEM quality, we show that systematic DEM errors must be minimised by ensuring a good distribution of control points throughout the image format during calibration. DEM quality is then largely dependent on the imagery utilised. We evaluated the open access multi-scale Retinex algorithm to facilitate the stereo matching, and quantified its influence on DEM quality. Occlusions, inherent to any roughness element, are still a major limiting factor to DEM accuracy. We show that a careful selection of the camera-to-object and baseline distance reduces errors in occluded areas and that realistic ground truths help to quantify those errors.

  16. DIRECT DNA SEQUENCING OF PCR PRODUCTS

    EPA Science Inventory

    Experiments are described which elucidate some of the technical problems associated with the direct sequencing of polymerase chain reaction (PCR) amplified DNA. Sequencing primer purity, labeling methodology, and template preparation were explored. onditions are presented for the...

  17. Construction of synthetic genes using PCR after automated DNA synthesis of their entire top and bottom strands.

    PubMed Central

    Ciccarelli, R B; Gunyuzlu, P; Huang, J; Scott, C; Oakes, F T

    1991-01-01

    A new method is described for the direct construction of synthetic genes by applying a modified version of the polymerase chain reaction (PCR) to crude oligonucleotide mixtures made by automated solid phase DNA synthesis. Construction of the HIV-1 393 bp rev gene and the 655 bp nef gene by this method is illustrated. The sequences for the entire top and bottom strands of rev were each programmed into an automated DNA synthesizer. Following DNA synthesis, the two crude oligonucleotide solutions were mixed together, specific primers were added, and the target gene was amplified by a modified PCR technique. Although the longer (greater than 200 bases) strands comprise a very small percentage of the total DNA after solid phase synthesis, this method uses PCR to 'find' and amplify such strands to create the target gene. The rev gene constructed by this method was found to contain 4 sequence errors, which were subsequently corrected by site-directed mutagenesis. In order to evaluate the source of sequence errors, several nef genes were made from the top and bottom strand DNA synthesis solutions using independent PCR's. Results suggest that sequence errors arose from both DNA synthesis and PCR. The utility of this method in producing a functional gene is demonstrated by expression of rev in E.coli. Images PMID:1945885

  18. qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

    SciTech Connect

    Jackson, Christopher B.; Gallati, Sabina; Schaller, Andre

    2012-07-06

    Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two genomes is demonstrated and which evaluates systematically the impact of DNA degradation on quantification of mtDNA copy number.

  19. A bifactor model of disgust proneness: examination of the Disgust Emotion Scale.

    PubMed

    Olatunji, Bunmi O; Ebesutani, Chad; Reise, Steven P

    2015-04-01

    The current research evaluated a bifactor model for the Disgust Emotion Scale (DES) in three samples: N = 1,318 nonclinical participants, N = 152 clinic-referred patients, and N = 352 nonclinical participants. The primary goals were to (a) use bifactor modeling to examine the latent structure of the DES and in turn (b) evaluate whether the DES should be scored as a unidimensional scale or whether subscales should also be interpreted. Results suggested that a bifactor model fit the DES data well and that all DES items were strongly influenced by a general disgust proneness dimension and by five content dimensions. Moreover, model-based reliability analyses suggested that scoring a general disgust dimension is justified despite the confirmed multidimensional structure. However, subscales were found to be unreliable after controlling for the general disgust factor with the potential exception of the Mutilation/Death and Animals subscale. Subsequent analysis also showed that only the general disgust factor robustly predicted an obsessive-compulsive disorder symptom latent factor-a clinical condition closely related to disgust proneness; latent variables representing DES domains displayed weak relations with an obsessive-compulsive disorder factor above and beyond the general disgust factor. Implications for better understanding the structure of DES responses and its use in clinical research are discussed. PMID:25006025

  20. Gene expression profiling of white adipose tissue reveals paternal transmission of proneness to obesity.

    PubMed

    Morita, Sumiyo; Nakabayashi, Kazuhiko; Kawai, Tomoko; Hayashi, Keiko; Horii, Takuro; Kimura, Mika; Kamei, Yasutomi; Ogawa, Yoshihiro; Hata, Kenichiro; Hatada, Izuho

    2016-01-01

    Previously, we found that C57BL/6J (B6) mice are more prone to develop obesity than PWK mice. In addition, we analyzed reciprocal crosses between these mice and found that (PWK × B6) F1 mice, which have B6 fathers, are more likely to develop dietary obesity than (B6 × PWK) F1 mice, which have B6 mothers. These results suggested that diet-induced obesity is paternally transmitted. In this study, we performed transcriptome analysis of adipose tissues of B6, PWK, (PWK × B6) F1, and (B6 × PWK) F1 mice using next-generation sequencing. We found that paternal transmission of diet-induced obesity was correlated with genes involved in adipose tissue inflammation, metal ion transport, and cilia. Furthermore, we analyzed the imprinted genes expressed in white adipose tissue (WAT) and obesity. Expression of paternally expressed imprinted genes (PEGs) was negatively correlated with body weight, whereas expression of maternally expressed imprinted genes (MEGs) was positively correlated. In the obesity-prone B6 mice, expression of PEGs was down-regulated by a high-fat diet, suggesting that abnormally low expression of PEGs contributes to high-fat diet-induced obesity in B6 mice. In addition, using single-nucleotide polymorphisms that differ between B6 and PWK, we identified candidate imprinted genes in WAT. PMID:26868178

  1. Gene expression profiling of white adipose tissue reveals paternal transmission of proneness to obesity

    PubMed Central

    Morita, Sumiyo; Nakabayashi, Kazuhiko; Kawai, Tomoko; Hayashi, Keiko; Horii, Takuro; Kimura, Mika; Kamei, Yasutomi; Ogawa, Yoshihiro; Hata, Kenichiro; Hatada, Izuho

    2016-01-01

    Previously, we found that C57BL/6J (B6) mice are more prone to develop obesity than PWK mice. In addition, we analyzed reciprocal crosses between these mice and found that (PWK × B6) F1 mice, which have B6 fathers, are more likely to develop dietary obesity than (B6 × PWK) F1 mice, which have B6 mothers. These results suggested that diet-induced obesity is paternally transmitted. In this study, we performed transcriptome analysis of adipose tissues of B6, PWK, (PWK × B6) F1, and (B6 × PWK) F1 mice using next-generation sequencing. We found that paternal transmission of diet-induced obesity was correlated with genes involved in adipose tissue inflammation, metal ion transport, and cilia. Furthermore, we analyzed the imprinted genes expressed in white adipose tissue (WAT) and obesity. Expression of paternally expressed imprinted genes (PEGs) was negatively correlated with body weight, whereas expression of maternally expressed imprinted genes (MEGs) was positively correlated. In the obesity-prone B6 mice, expression of PEGs was down-regulated by a high-fat diet, suggesting that abnormally low expression of PEGs contributes to high-fat diet-induced obesity in B6 mice. In addition, using single-nucleotide polymorphisms that differ between B6 and PWK, we identified candidate imprinted genes in WAT. PMID:26868178

  2. 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

  3. Risk Perception in Flood-Prone Lands of Costa Brava, Spain

    NASA Astrophysics Data System (ADS)

    Serra Llobet, A.; Kondolf, G. M.

    2009-12-01

    How well residents of flood-prone lands understand the risks of flooding is a question with profound implications for public policies to manage flood risk and land use on floodplains. Surveys of 300 residents of rapidly urbanizing floodplains in three coastal cities (100-135 km north of Barcelona), supplanted by interviews with public officials and government agency staff, indicate that most residents underestimate the probability and extent of flooding, unless they have experienced a flood within the previous three years. However, most dwelling units are now in multistory buildings, so residents of upper stories are vertically removed from floodwaters. Moreover, unlike the poor fishermen who formerly inhabited villages along this coast and who were devastated by periodic floods, the new inhabitants are mostly affluent and well-insured, so they can recover quickly from flood damage. Thus, while exposure to flooding has increased through urbanization of flood-prone lands, resistance to flooding has increased due to multistory buildings and sump pumps in lower floors, and resilience is much greater thanks to the financial resources of new residents.

  4. Use of thermal inertia determined by HCMM to predict nocturnal cold prone areas in Florida

    NASA Technical Reports Server (NTRS)

    Allen, L. H., Jr. (Principal Investigator)

    1983-01-01

    Pairs of HCMM day-night thermal infrared (IR) data were selected during the 1978-79 winter to examine patterns of surface temperature and thermal inertia (TI) of peninsular Florida. The GOES and NOAA-6 thermal IR, as well as National Climatic Center temperatures and rainfall, were also used. The HCMM apparent thermal inertia (ATI) images closely corresponded to the general soil map of Florida, based on soil drainage classes. Areas with low ATI overlay well-drained soils, such as deep sands and drained organic soils, whereas with high ATI overlay areas with wetlands and bodies of water. The HCMM ATI images also corresponded well with GOES-detected winter nocturnal cold-prone areas. Use of HCMM data with Carlson's energy balance model showed both high moisture availability (MA) and high thermal inertia (TI) of wetland-type surfaces and low MA and low TI of upland, well-drained soils. Since soil areas with low TI develop higher temperatures during the day, then antecedent patterns of highest maximum daytime surface temperature can also be used to predict nocturnal cold-prone areas in Florida.

  5. Generation in Human Plasma of Misfolded, Aggregation-Prone Electronegative Low Density Lipoprotein

    PubMed Central

    Greco, Giulia; Balogh, Gabor; Brunelli, Roberto; Costa, Graziella; De Spirito, Marco; Lenzi, Laura; Mei, Giampiero; Ursini, Fulvio; Parasassi, Tiziana

    2009-01-01

    Abstract Human plasma contains small amounts of a low density lipoprotein in which apoprotein is misfolded. Originally identified and isolated by means of anion-exchange chromatography, this component was subsequently described as electronegative low density lipoprotein (LDL)(−), with increased concentrations associated with elevated cardiovascular disease risk. It has been recognized recently as the trigger of LDL amyloidogenesis, which produces aggregates similar to subendothelial droplets observed in vivo in early atherogenesis. Although LDL(−) has been produced in vitro through various manipulations, the mechanisms involved in its generation in vivo remain obscure. By using a more physiological model, we demonstrate spontaneous, sustained and noticeable production of LDL(−) during incubation of unprocessed human plasma at 37°C. In addition to a higher fraction of amyloidogenic LDL(−), LDL purified from incubated plasma contains an increased level of lysophospholipids and free fatty acids; analysis of LDL lipids packing shows their loosening. As a result, during plasma incubation, lipid destabilization and protein misfolding take place, and aggregation-prone particles are generated. All these phenomena can be prevented by inhibiting calcium-dependent secretory phospholipases A2. Our plasma incubation model, without removal of reaction products, effectively shows a lipid-protein interplay in LDL, where lipid destabilization after lipolysis threatens the apoprotein's structure, which misfolds and becomes aggregation-prone. PMID:19619478

  6. Clearance of senescent hepatocytes in a neoplastic-prone microenvironment delays the emergence of hepatocellular carcinoma

    PubMed Central

    Sini, Marcella; Angius, Fabrizio; Laconi, Ezio

    2014-01-01

    Increasing evidence indicates that carcinogenesis is dependent on the tissue context in which it occurs, implying that the latter can be a target for preventive or therapeutic strategies. We tested the possibility that re-normalizing a senescent, neoplastic-prone tissue microenvironment would exert a modulatory effect on the emergence of neoplastic disease. Rats were exposed to a protocol for the induction of hepatocellular carcinoma (HCC). Using an orthotopic and syngeneic system for cell transplantation, one group of animal was then delivered 8 million normal hepatocytes, via the portal circulation. Hepatocytes transplantation resulted in a prominent decrease in the incidence of both pre-neoplastic and neoplastic lesions. At the end of 1 year 50% of control animals presented with HCC, while no HCC were observed in the transplanted group. Extensive hepatocyte senescence was induced by the carcinogenic protocol in the host liver; however, senescent cells were largely cleared following infusion of normal hepatocytes. Furthermore, levels of Il-6 increased in rats exposed to the carcinogenic protocol, while they returned to near control values in the group receiving hepatocyte transplantation. These results support the concept that strategies aimed at normalizing a neoplastic-prone tissue landscape can modulate progression of neoplastic disease. PMID:24464501

  7. Too Little Oxygen: Ventilation, Prone Positioning, and Extracorporeal Membrane Oxygenation for Severe Hypoxemia.

    PubMed

    Park, Pauline K

    2016-02-01

    Severe hypoxemia is associated with untoward outcomes in acute respiratory distress syndrome patients. Nevertheless, in and of itself, correction of hypoxemia is not an adequate surrogate outcome for mortality and clear evidence-based targets for correction of hypoxemia remain to be determined. At present, clinical management is directed toward achieving sufficient oxygenation while minimizing toxicity of ventilator-induced lung injury. The gold standard remains lung-protective mechanical ventilation, using lower-tidal volumes and pressure-limited ventilator titration. Notable progress in care includes further refinements in mechanical ventilation, consideration of salutatory effects of early prone positioning and neuromuscular blockade, and exploration of adjunctive extrapulmonary support with extracorporeal membrane oxygenation. This review focuses on three specific aspects: the evolving trend toward open lung ventilation, tempered by the recent cautionary experience with high-frequency oscillation ventilation; the evolution of prone positioning as a treatment for the most hypoxemic patients; and the continued future promise of extracorporeal support as a true rescue therapy. PMID:26820269

  8. Acute exacerbations of asthma: epidemiology, biology and the exacerbation-prone phenotype.

    PubMed

    Dougherty, R H; Fahy, J V

    2009-02-01

    Asthma is a highly prevalent chronic respiratory disease affecting 300 million people world-wide. A significant fraction of the cost and morbidity of asthma derives from acute care for asthma exacerbations. In the United States alone, there are approximately 15 million outpatient visits, 2 million emergency room visits, and 500,000 hospitalizations each year for management of acute asthma. Common respiratory viruses, especially rhinoviruses, cause the majority of exacerbations in children and adults. Infection of airway epithelial cells with rhinovirus causes the release of pro-inflammatory cytokines and chemokines, as well as recruitment of inflammatory cells, particularly neutrophils, lymphocytes, and eosinophils. The host response to viral infection is likely to influence susceptibility to asthma exacerbation. Having had at least one exacerbation is an important risk factor for recurrent exacerbations suggesting an 'exacerbation-prone' subset of asthmatics. Factors underlying the 'exacerbation-prone' phenotype are incompletely understood but include extrinsic factors: cigarette smoking, medication non-compliance, psychosocial factors, and co-morbidities such as gastroesophageal reflux disease, rhinosinusitis, obesity, and intolerance to non-steroidal anti-inflammatory medications; as well as intrinsic factors such as deficient epithelial cell production of the anti-viral type I interferons (IFN-alpha and IFN-beta). A better understanding of the biologic mechanisms of host susceptibility to recurrent exacerbations will be important for developing more effective preventions and treatments aimed at reducing the significant cost and morbidity associated with this important global health problem. PMID:19187331

  9. Hydrological and hydraulic models for determination of flood-prone and flood inundation areas

    NASA Astrophysics Data System (ADS)

    Aksoy, Hafzullah; Sadan Ozgur Kirca, Veysel; Burgan, Halil Ibrahim; Kellecioglu, Dorukhan

    2016-05-01

    Geographic Information Systems (GIS) are widely used in most studies on water resources. Especially, when the topography and geomorphology of study area are considered, GIS can ease the work load. Detailed data should be used in this kind of studies. Because of, either the complication of the models or the requirement of highly detailed data, model outputs can be obtained fast only with a good optimization. The aim in this study, firstly, is to determine flood-prone areas in a watershed by using a hydrological model considering two wetness indexes; the topographical wetness index, and the SAGA (System for Automated Geoscientific Analyses) wetness index. The wetness indexes were obtained in the Quantum GIS (QGIS) software by using the Digital Elevation Model of the study area. Flood-prone areas are determined by considering the wetness index maps of the watershed. As the second stage of this study, a hydraulic model, HEC-RAS, was executed to determine flood inundation areas under different return period-flood events. River network cross-sections required for this study were derived from highly detailed digital elevation models by QGIS. Also river hydraulic parameters were used in the hydraulic model. Modelling technology used in this study is made of freely available open source softwares. Based on case studies performed on watersheds in Turkey, it is concluded that results of such studies can be used for taking precaution measures against life and monetary losses due to floods in urban areas particularly.

  10. Detection of individuals prone to develop hypertension in their future life.

    PubMed

    Pramanik, T; Regmi, P; Shrestha, P

    2008-03-01

    Hypertension is a global burning health problem. Early detection of proneness to hypertension may help an individual to lead a healthy life by altering the life style (by diet restriction, exercise etc.). Subjects at high risk of future hypertension e.g. the persons of hypertensive family and/or having high resting heart rate etc. show blood pressure hyper-responsiveness to stress. Elevated blood pressure due to sympathetic stimulation prevailed longer time in susceptible persons. In the present study sympathetic stimulation exerted through cold pressor test (hand immersion up to the wrist in 4 degrees C water) resulted in elevation of blood pressure and heart rate in all young male normotensive individuals (age 18-35 years, n=72). Nevertheless, blood pressure and heart rate returned to baseline, following 5 minutes of withdrawal of the stressor, in case of volunteers from normotensive families. On the other hand, the subjects whose parents, either or both were reported to be hypertensive showed elevated diastolic blood pressure even after 5 minutes of withdrawal of the said stressor- indicating that the autonomic nervous system in them was not competent enough for lowering the diastolic pressure quickly to baseline as observed in the volunteers from the normotensive families. The present study revealed that the young subjects who showed greater and prolonged responsiveness to diastolic blood pressure due to sympathetic stimulation through cold pressor test are prone to develop hypertension in future. PMID:18700629

  11. Triage of oxidation-prone proteins by Sqstm1/p62 within the mitochondria

    SciTech Connect

    Lee, Minjung; Shin, Jaekyoon

    2011-09-16

    Highlights: {yields} The mitochondrion contains its own protein quality control system. {yields} p62 localizes within the mitochondria and forms mega-dalton sized complexes. {yields} p62 interacts with oxidation-prone proteins and the proteins of quality control. {yields} In vitro delivery of p62 improves mitochondrial functions. {yields} p62 is implicated as a participant in mitochondrial protein quality control. -- Abstract: As the mitochondrion is vulnerable to oxidative stress, cells have evolved several strategies to maintain mitochondrial integrity, including mitochondrial protein quality control mechanisms and autophagic removal of damaged mitochondria. Involvement of an autophagy adaptor, Sqstm1/p62, in the latter process has been recently described. In the present study, we provide evidence that a portion of p62 directly localizes within the mitochondria and supports stable electron transport by forming heterogeneous protein complexes. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) of mitochondrial proteins co-purified with p62 revealed that p62 interacts with several oxidation-prone proteins, including a few components of the electron transport chain complexes, as well as multiple chaperone molecules and redox regulatory enzymes. Accordingly, p62-deficient mitochondria exhibited compromised electron transport, and the compromised function was partially restored by in vitro delivery of p62. These results suggest that p62 plays an additional role in maintaining mitochondrial integrity at the vicinity of target machineries through its function in relation to protein quality control.

  12. Determination of PCR efficiency in chelex-100 purified clinical samples and comparison of real-time quantitative PCR and conventional PCR for detection of Chlamydia pneumoniae

    PubMed Central

    Mygind, Tina; Birkelund, Svend; Birkebæk, Niels H; Østergaard, Lars; Jensen, Jørgen Skov; Christiansen, Gunna

    2002-01-01

    Background Chlamydia pneumoniae infection has been detected by serological methods, but PCR is gaining more interest. A number of different PCR assays have been developed and some are used in combination with serology for diagnosis. Real-time PCR could be an attractive new PCR method; therefore it must be evaluated and compared to conventional PCR methods. Results We compared the performance of a newly developed real-time PCR with a conventional PCR method for detection of C. pneumoniae. The PCR methods were tested on reference samples containing C. pneumoniae DNA and on 136 nasopharyngeal samples from patients with a chronic cough. We found the same detection limit for the two methods and that clinical performance was equal for the real-time PCR and for the conventional PCR method, although only three samples tested positive. To investigate whether the low prevalence of C. pneumoniae among patients with a chronic cough was caused by suboptimal PCR efficiency in the samples, PCR efficiency was determined based on the real-time PCR. Seventeen of twenty randomly selected clinical samples had a similar PCR efficiency to samples containing pure genomic C. pneumoniae DNA. Conclusions These results indicate that the performance of real-time PCR is comparable to that of conventional PCR, but that needs to be confirmed further. Real-time PCR can be used to investigate the PCR efficiency which gives a rough estimate of how well the real-time PCR assay works in a specific sample type. Suboptimal PCR efficiency of PCR is not a likely explanation for the low positivity rate of C. pneumoniae in patients with a chronic cough. PMID:12106506

  13. Transgene Detection by Digital Droplet PCR

    PubMed Central

    Moser, Dirk A.; Braga, Luca; Raso, Andrea; Zacchigna, Serena; Giacca, Mauro; Simon, Perikles

    2014-01-01

    Somatic gene therapy is a promising tool for the treatment of severe diseases. Because of its abuse potential for performance enhancement in sports, the World Anti-Doping Agency (WADA) included the term gene doping in the official list of banned substances and methods in 2004. Several nested PCR or qPCR-based strategies have been proposed that aim at detecting long-term presence of transgene in blood, but these strategies are hampered by technical limitations. We developed a digital droplet PCR (ddPCR) protocol for Insulin-Like Growth Factor 1 (IGF1) detection and demonstrated its applicability monitoring 6 mice injected into skeletal muscle with AAV9-IGF1 elements and 2 controls over a 33-day period. A duplex ddPCR protocol for simultaneous detection of Insulin-Like Growth Factor 1 (IGF1) and Erythropoietin (EPO) transgenic elements was created. A new DNA extraction procedure with target-orientated usage of restriction enzymes including on-column DNA-digestion was established. In vivo data revealed that IGF1 transgenic elements could be reliably detected for a 33-day period in DNA extracted from whole blood. In vitro data indicated feasibility of IGF1 and EPO detection by duplex ddPCR with high reliability and sensitivity. On-column DNA-digestion allowed for significantly improved target detection in downstream PCR-based approaches. As ddPCR provides absolute quantification, it ensures excellent day-to-day reproducibility. Therefore, we expect this technique to be used in diagnosing and monitoring of viral and bacterial infection, in detecting mutated DNA sequences as well as profiling for the presence of foreign genetic material in elite athletes in the future. PMID:25375130

  14. Transgene detection by digital droplet PCR.

    PubMed

    Moser, Dirk A; Braga, Luca; Raso, Andrea; Zacchigna, Serena; Giacca, Mauro; Simon, Perikles

    2014-01-01

    Somatic gene therapy is a promising tool for the treatment of severe diseases. Because of its abuse potential for performance enhancement in sports, the World Anti-Doping Agency (WADA) included the term 'gene doping' in the official list of banned substances and methods in 2004. Several nested PCR or qPCR-based strategies have been proposed that aim at detecting long-term presence of transgene in blood, but these strategies are hampered by technical limitations. We developed a digital droplet PCR (ddPCR) protocol for Insulin-Like Growth Factor 1 (IGF1) detection and demonstrated its applicability monitoring 6 mice injected into skeletal muscle with AAV9-IGF1 elements and 2 controls over a 33-day period. A duplex ddPCR protocol for simultaneous detection of Insulin-Like Growth Factor 1 (IGF1) and Erythropoietin (EPO) transgenic elements was created. A new DNA extraction procedure with target-orientated usage of restriction enzymes including on-column DNA-digestion was established. In vivo data revealed that IGF1 transgenic elements could be reliably detected for a 33-day period in DNA extracted from whole blood. In vitro data indicated feasibility of IGF1 and EPO detection by duplex ddPCR with high reliability and sensitivity. On-column DNA-digestion allowed for significantly improved target detection in downstream PCR-based approaches. As ddPCR provides absolute quantification, it ensures excellent day-to-day reproducibility. Therefore, we expect this technique to be used in diagnosing and monitoring of viral and bacterial infection, in detecting mutated DNA sequences as well as profiling for the presence of foreign genetic material in elite athletes in the future. PMID:25375130

  15. 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.

  16. Error Processing in Huntington's Disease

    PubMed Central

    Andrich, Jürgen; Gold, Ralf; Falkenstein, Michael

    2006-01-01

    Background Huntington's disease (HD) is a genetic disorder expressed by a degeneration of the basal ganglia inter alia accompanied with dopaminergic alterations. These dopaminergic alterations are related to genetic factors i.e., CAG-repeat expansion. The error (related) negativity (Ne/ERN), a cognitive event-related potential related to performance monitoring, is generated in the anterior cingulate cortex (ACC) and supposed to depend on the dopaminergic system. The Ne is reduced in Parkinson's Disease (PD). Due to a dopaminergic deficit in HD, a reduction of the Ne is also likely. Furthermore it is assumed that movement dysfunction emerges as a consequence of dysfunctional error-feedback processing. Since dopaminergic alterations are related to the CAG-repeat, a Ne reduction may furthermore also be related to the genetic disease load. Methodology/Principle Findings We assessed the error negativity (Ne) in a speeded reaction task under consideration of the underlying genetic abnormalities. HD patients showed a specific reduction in the Ne, which suggests impaired error processing in these patients. Furthermore, the Ne was closely related to CAG-repeat expansion. Conclusions/Significance The reduction of the Ne is likely to be an effect of the dopaminergic pathology. The result resembles findings in Parkinson's Disease. As such the Ne might be a measure for the integrity of striatal dopaminergic output function. The relation to the CAG-repeat expansion indicates that the Ne could serve as a gene-associated “cognitive” biomarker in HD. PMID:17183717

  17. Amplify Errors to Minimize Them

    ERIC Educational Resources Information Center

    Stewart, Maria Shine

    2009-01-01

    In this article, the author offers her experience of modeling mistakes and writing spontaneously in the computer classroom to get students' attention and elicit their editorial response. She describes how she taught her class about major sentence errors--comma splices, run-ons, and fragments--through her Sentence Meditation exercise, a rendition…

  18. Theory of Test Translation Error

    ERIC Educational Resources Information Center

    Solano-Flores, Guillermo; Backhoff, Eduardo; Contreras-Nino, Luis Angel

    2009-01-01

    In this article, we present a theory of test translation whose intent is to provide the conceptual foundation for effective, systematic work in the process of test translation and test translation review. According to the theory, translation error is multidimensional; it is not simply the consequence of defective translation but an inevitable fact…

  19. What Is a Reading Error?

    ERIC Educational Resources Information Center

    Labov, William; Baker, Bettina

    2010-01-01

    Early efforts to apply knowledge of dialect differences to reading stressed the importance of the distinction between differences in pronunciation and mistakes in reading. This study develops a method of estimating the probability that a given oral reading that deviates from the text is a true reading error by observing the semantic impact of the…

  20. Having Fun with Error Analysis

    ERIC Educational Resources Information Center

    Siegel, Peter

    2007-01-01

    We present a fun activity that can be used to introduce students to error analysis: the M&M game. Students are told to estimate the number of individual candies plus uncertainty in a bag of M&M's. The winner is the group whose estimate brackets the actual number with the smallest uncertainty. The exercise produces enthusiastic discussions and…