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1

Error-Prone PCR Mutagenesis Reveals Functional Domains of a Bacterial Transcriptional Activator, TraJ  

PubMed Central

TraJ is the essential activator of PY, the promoter of the F and F-like plasmid tra operon that encodes the majority of the proteins for bacterial conjugation. By combining error-prone PCR mutagenesis with a two-plasmid screen, we isolated 55 missense mutations in traJ, each affecting the ability of TraJ to activate PY. These mutations define two distinct functional clusters (amino acids [aa] 21 to 117 and aa 150 to 219). Limited proteolytic analysis of TraJ suggested that the N- and C-terminal functional clusters are two structurally distinct domains. Most TraJ mutants exhibited decreased intracellular protein levels, and the HslVU protease-chaperone pair was found to be responsible for degrading those mutants without extracytoplasmic stress-induced overexpression. In vivo cross-linking analysis of TraJ mutants indicated that the N-terminal domain is responsible for dimerization. This was confirmed by the finding that the purified N-terminal region of TraJ forms dimers in solution. The levels of dimerization and in vivo activities of TraJ mutants are well correlated, suggesting that dimerization of TraJ is required for its biological function. We propose that the regulation of TraJ dimerization and/or its susceptibility to HslVU could be a key mechanism in various signaling processes for controlling bacterial conjugation in response to physiological or environmental stimuli.

Lu, Jun; Peng, Yun; Arutyunov, Denis; Frost, Laura S.

2012-01-01

2

[Enhanced thermostability of Rhizopus chinensis lipase by error-prone PCR].  

PubMed

Directed evolution was conducted to improve the thermostability of lipase from Rhizopus chinensis CCTCC M201021. Mutations were introduced by two rounds of error-prone PCR and mutant lipase was selected by fast-blue RR top agar screening. Two positive variants were selected in the first-round and four in the second-round screening process. Ep2-4 was proved as the most thermostable lipase and its DNA sequencing revealed three amino acid substitutions: A129S, P168L and V329A. Compared with the parent, its half-life at 60 degrees C was 5.4- times longer and T50 was 7.8 degrees higher. Purified lipase of Ep2-4 was characterized and the result shows that its thermostability improved without compromising enzyme activity. According to the mimicked protein structure, mutation A129S formed a hydrogen bond with Gln133 and improved the thermostability by increasing the hydrophilicity and polarity of protein; mutation P168L by forming a hydrophobic bond with the nearby Leu164. PMID:24660623

Wang, Rui; Yu, Xiaowei; Xu, Yan

2013-12-01

3

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

PubMed Central

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

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

2013-01-01

4

Improved activity and pH stability of E. coli ATCC 11105 penicillin acylase by error-prone PCR.  

PubMed

Penicillin G acylase is the key enzyme used in the industrial production of ?-lactam antibiotics. This enzyme hydrolyzes penicillin G and related ?-lactam antibiotics releasing 6-aminopenicillanic acid, which is an intermediate in the production of semisynthetic penicillins. To improve the enzymatic activity of Escherichia coli penicillin acylase, sequential rounds of error-prone polymerase chain reaction were applied to the E. coli pac gene. After the second round of evolution, the best mutant M2234 with enhanced activity was selected and analyzed. DNA sequence analyses of M2234 revealed that one amino acid residue (K297I), located far from the center of the catalytic pocket, was changed. This mutant (M2234) has a specific activity 4.0 times higher than the parent enzyme and also displayed higher stability at pH 10. PMID:24389703

Balci, Huseyin; Ozturk, Merve Tuzlakoglu; Pijning, Tjaard; Ozturk, Saliha Issever; Gumusel, Fusun

2014-05-01

5

Improving phytase enzyme activity in a recombinant phyA mutant phytase from Aspergillus niger N25 by error-prone PCR.  

PubMed

The mutant acid phytase (phyA ( m )) gene was modified by random mutagenesis to improve enzymatic activity by using an error-prone PCR (ep-PCR) strategy. The mutated gene was linearized and inserted into plasmid vector pPIC9K and transformed by electroporation into Pichia pastoris GS115. A single transformant, PP-NP(ep)-6A, showing the strongest phytase activity from among the 5,500 transformants, was selected for detailed analyses. Southern blot analysis of the mutant yeast transformant showed that phyA ( ep ) gene was integrated into the chromosome genome through single crossover with one copy of phyA. The kinetic parameters indicated that the mutant one showed 61% higher specific activity and 53% lower k (m) value than that of PP-NP(m)-8 (P?PCR somehow reorganized or remodeled the active site, which could lead to increasing catalytic efficiency. PMID:22101445

Liao, Yan; Zeng, Min; Wu, Zhen-Fang; Chen, Hui; Wang, Hong-Ning; Wu, Qi; Shan, Zhi; Han, Xue-Yi

2012-02-01

6

Inhibiting HER3-Mediated Tumor Cell Growth with Affibody Molecules Engineered to Low Picomolar Affinity by Position-Directed Error-Prone PCR-Like Diversification  

PubMed Central

The HER3 receptor is implicated in the progression of various cancers as well as in resistance to several currently used drugs, and is hence a potential target for development of new therapies. We have previously generated Affibody molecules that inhibit heregulin-induced signaling of the HER3 pathways. The aim of this study was to improve the affinity of the binders to hopefully increase receptor inhibition efficacy and enable a high receptor-mediated uptake in tumors. We explored a novel strategy for affinity maturation of Affibody molecules that is based on alanine scanning followed by design of library diversification to mimic the result from an error-prone PCR reaction, but with full control over mutated positions and thus less biases. Using bacterial surface display and flow-cytometric sorting of the maturation library, the affinity for HER3 was improved more than 30-fold down to 21 pM. The affinity is among the higher that has been reported for Affibody molecules and we believe that the maturation strategy should be generally applicable for improvement of affinity proteins. The new binders also demonstrated an improved thermal stability as well as complete refolding after denaturation. Moreover, inhibition of ligand-induced proliferation of HER3-positive breast cancer cells was improved more than two orders of magnitude compared to the previously best-performing clone. Radiolabeled Affibody molecules showed specific targeting of a number of HER3-positive cell lines in vitro as well as targeting of HER3 in in vivo mouse models and represent promising candidates for future development of targeted therapies and diagnostics.

Malm, Magdalena; Kronqvist, Nina; Lindberg, Hanna; Gudmundsdotter, Lindvi; Bass, Tarek; Frejd, Fredrik Y.; Hoiden-Guthenberg, Ingmarie; Varasteh, Zohreh; Orlova, Anna; Tolmachev, Vladimir; Stahl, Stefan; Lofblom, John

2013-01-01

7

AIDing antibody diversity by error-prone mismatch repair  

PubMed Central

The creation of a highly diverse antibody repertoire requires the synergistic activity of a DNA mutator, known as activation-induced deaminase (AID), coupled with an error-prone repair process that recognizes the DNA mismatch catalyzed by AID. Instead of facilitating the canonical error-free response, which generally occurs throughout the genome, DNA mismatch repair (MMR) participates in an error-prone repair mode that promotes A:T mutagenesis and double-strand breaks at the immunoglobulin (Ig) genes. As such, MMR is capable of compounding the mutation frequency of AID activity as well as broadening the spectrum of base mutations; thereby increasing the efficiency of antibody maturation. We here review the current understanding of this MMR-mediated process and describe how the MMR signaling cascade downstream of AID diverges in a locus dependent manner and even within the Ig locus itself to differentially promote somatic hypermutation (SHM) and class switch recombination (CSR) in B cells.

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

2012-01-01

8

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

PubMed

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

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

2003-07-01

9

Replicative mechanisms for CNV formation are error prone.  

PubMed

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 (13%), at or flanking the breakpoint junctions of complex copy number variants. These single-nucleotide variants were generated concomitantly with the de novo complex genomic rearrangement (CGR) event. Our findings implicate low-fidelity, error-prone DNA polymerase activity in synthesis associated with DNA repair mechanisms as the cause of local increase in point mutation burden associated with human CGR. PMID:24056715

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

2013-11-01

10

Replicative mechanisms for CNV formation are error prone  

PubMed Central

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

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

2013-01-01

11

Random mutagenesis by error-prone Pol I plasmid replication in Escherichia coli  

PubMed Central

Summary Directed evolution is an approach that mimics natural evolution in the laboratory with the goal of modifying existing enzymatic activities or of generating new ones. The identification of mutants with desired properties involves the generation of genetic diversity coupled with a functional selection or screen. Genetic diversity can be generated using PCR or using in vivo methods such as chemical mutagenesis or error-prone replication of the desired sequence in a mutator strain. In vivo mutagenesis methods facilitate iterative selection because they do not require cloning, but generally produce a low mutation density with mutations not restricted to specific genes or areas within a gene. For this reason, this approach is typically used to generate new biochemical properties when large numbers of mutants can be screened or selected. Here we describe protocols for an advanced in vivo mutagenesis method that is based on error-prone replication of a ColE1 plasmid bearing the gene of interest. Compared to other in vivo mutagenesis methods, this plasmid-targeted approach allows increased mutation loads and facilitates iterative selection approaches. We also describe the mutation spectrum for this mutagenesis methodology in detail and, using cycle 3 GFP as a target for mutagenesis, we illustrate the phenotypic diversity that can be generated using our method. In sum, error-prone Pol I replication is a mutagenesis method that is ideally suited for the evolution of new biochemical activities when a functional selection is available.

Alexander, David L.; Lilly, Joshua; Hernandez, Jaime; Romsdahl, Jillian; Troll, Christopher J.; Camps, Manel

2014-01-01

12

Random Mutagenesis by Error-Prone Pol Plasmid Replication in Escherichia coli.  

PubMed

Directed evolution is an approach that mimics natural evolution in the laboratory with the goal of modifying existing enzymatic activities or of generating new ones. The identification of mutants with desired properties involves the generation of genetic diversity coupled with a functional selection or screen. Genetic diversity can be generated using PCR or using in vivo methods such as chemical mutagenesis or error-prone replication of the desired sequence in a mutator strain. In vivo mutagenesis methods facilitate iterative selection because they do not require cloning, but generally produce a low mutation density with mutations not restricted to specific genes or areas within a gene. For this reason, this approach is typically used to generate new biochemical properties when large numbers of mutants can be screened or selected. Here we describe protocols for an advanced in vivo mutagenesis method that is based on error-prone replication of a ColE1 plasmid bearing the gene of interest. Compared to other in vivo mutagenesis methods, this plasmid-targeted approach allows increased mutation loads and facilitates iterative selection approaches. We also describe the mutation spectrum for this mutagenesis methodology in detail, and, using cycle 3 GFP as a target for mutagenesis, we illustrate the phenotypic diversity that can be generated using our method. In sum, error-prone Pol I replication is a mutagenesis method that is ideally suited for the evolution of new biochemical activities when a functional selection is available. PMID:25055769

Alexander, David L; Lilly, Joshua; Hernandez, Jaime; Romsdahl, Jillian; Troll, Christopher J; Camps, Manel

2014-01-01

13

Increase of ethanol tolerance of Saccharomyces cerevisiae by error-prone whole genome amplification.  

PubMed

Saccharomyces cerevisiae was transformed for higher ethanol tolerance by error-prone whole genome amplification. The resulting PCR products were transformed back to the parental strain for homologous recombination to create a library of mutants with the perturbed genomic networks. A few rounds of transformation led to the isolation of mutants that grew in 9% (v/v) ethanol and 100 g glucose l(-1) compared to untransformed yeast which grew only at 6% (v/v) ethanol and 100 g glucose l(-1). PMID:21246255

Luhe, Annette Lin; Tan, Lily; Wu, Jinchuan; Zhao, Hua

2011-05-01

14

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

Microsoft Academic Search

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

Charles R. Litecky; Gordon B. Davis

1976-01-01

15

Eukaryotic error-prone DNA polymerases: The presumed roles in replication, repair, and mutagenesis  

Microsoft Academic Search

A number of error-prone DNA polymerases have been found in various eukaryotes, ranging from yeasts to mammals, including humans.\\u000a According to partial homology of the primary structure, they are grouped into families B, X, and Y. These enzymes display\\u000a a high infidelity on an intact DNA template, but they are accurate on a damaged template. Error-prone DNA polymerases are\\u000a characterized

V. M. Krutyakov

2006-01-01

16

Inverse probability weighting with error-prone covariates  

PubMed Central

Summary Inverse probability-weighted estimators are widely used in applications where data are missing due to nonresponse or censoring and in the estimation of causal effects from observational studies. Current estimators rely on ignorability assumptions for response indicators or treatment assignment and outcomes being conditional on observed covariates which are assumed to be measured without error. However, measurement error is common for the variables collected in many applications. For example, in studies of educational interventions, student achievement as measured by standardized tests is almost always used as the key covariate for removing hidden biases, but standardized test scores may have substantial measurement errors. We provide several expressions for a weighting function that can yield a consistent estimator for population means using incomplete data and covariates measured with error. We propose a method to estimate the weighting function from data. The results of a simulation study show that the estimator is consistent and has no bias and small variance.

McCAFFREY, DANIEL F.; LOCKWOOD, J. R.; SETODJI, CLAUDE M.

2014-01-01

17

Preferential D-loop Extension by a Translesion DNA Polymerase Underlies Error-Prone Recombination  

PubMed Central

Summary Although homologous recombination (HR) is considered an accurate form of DNA repair, genetics suggest that Escherichia coli (E. coli) translesion DNA polymerase (pol) IV (DinB) promotes error-prone recombination during stress which allows cells to overcome adverse conditions. How pol IV functions and is regulated during recombination under stress, however, is unknown. We show that pol IV is highly proficient in error-prone recombination, and is preferentially recruited to D-loops at stress-induced concentrations in vitro. Unexpectedly, we find that high-fidelity pol II switches to exonuclease mode at D-loops which is stimulated by topological stress and reduced deoxy-ribonucleotide pools observed during stationary-phase. The exonuclease activity of pol II enables it to compete with pol IV which likely suppresses error-prone recombination. These findings indicate that preferential D-loop extension by pol IV facilitates error-prone recombination and explain how pol II reduces such errors in vivo.

Pomerantz, Richard T.; Kurth, Isabel; Goodman, Myron F.; O'Donnell, Mike

2013-01-01

18

Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination.  

PubMed

Although homologous recombination is considered an accurate form of DNA repair, genetics suggest that the Escherichia coli translesion DNA polymerase IV (Pol IV, also known as DinB) promotes error-prone recombination during stress, which allows cells to overcome adverse conditions. However, how Pol IV functions and is regulated during recombination under stress is unknown. We show that Pol IV is highly proficient in error-prone recombination and is preferentially recruited to displacement loops (D loops) at stress-induced concentrations in vitro. We also found that high-fidelity Pol II switches to exonuclease mode at D loops, which is stimulated by topological stress and reduced deoxyribonucleotide pool concentration during stationary phase. The exonuclease activity of Pol II enables it to compete with Pol IV, which probably suppresses error-prone recombination. These findings indicate that preferential D-loop extension by Pol IV facilitates error-prone recombination and explain how Pol II reduces such errors in vivo. PMID:23686288

Pomerantz, Richard T; Kurth, Isabel; Goodman, Myron F; O'Donnell, Mike E

2013-06-01

19

Regulation of error-prone translesion synthesis by Spartan/C1orf124.  

PubMed

Translesion synthesis (TLS) employs low fidelity polymerases to replicate past damaged DNA in a potentially error-prone process. Regulatory mechanisms that prevent TLS-associated mutagenesis are unknown; however, our recent studies suggest that the PCNA-binding protein Spartan plays a role in suppression of damage-induced mutagenesis. Here, we show that Spartan negatively regulates error-prone TLS that is dependent on POLD3, the accessory subunit of the replicative DNA polymerase Pol ?. We demonstrate that the putative zinc metalloprotease domain SprT in Spartan directly interacts with POLD3 and contributes to suppression of damage-induced mutagenesis. Depletion of Spartan induces complex formation of POLD3 with Rev1 and the error-prone TLS polymerase Pol ?, and elevates mutagenesis that relies on POLD3, Rev1 and Pol ?. These results suggest that Spartan negatively regulates POLD3 function in Rev1/Pol ?-dependent TLS, revealing a previously unrecognized regulatory step in error-prone TLS. PMID:23254330

Kim, Myoung Shin; Machida, Yuka; Vashisht, Ajay A; Wohlschlegel, James A; Pang, Yuan-Ping; Machida, Yuichi J

2013-02-01

20

Error-prone bypass of certain DNA lesions by the human DNA polymerase ?  

PubMed Central

The Escherichia coli protein DinB is a newly identified error-prone DNA polymerase. Recently, a human homolog of DinB was identified and named DINB1. We report that the DINB1 gene encodes a DNA polymerase (designated pol?), which incorporates mismatched bases on a nondamaged template with a high frequency. Moreover, pol? bypasses an abasic site and N-2–acetylaminofluorene (AAF)-adduct in an error-prone manner but does not bypass a cis–syn or (6-4) thymine–thymine dimer or a cisplatin-adduct. Therefore, our results implicate an important role for pol? in the mutagenic bypass of certain types of DNA lesions.

Ohashi, Eiji; Ogi, Tomoo; Kusumoto, Rika; Iwai, Shigenori; Masutani, Chikahide; Hanaoka, Fumio; Ohmori, Haruo

2000-01-01

21

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

PubMed

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

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

2013-08-15

22

Inducible error-prone repair in B. subtilis. Progress report, September 1, 1979-February 28, 1981  

SciTech Connect

The mechanism of activation and the mode of action of the SOS system in Bacillus subtilis are being investigated. Interesting aspects of the SOS system in B. subtilis include: (1) the differences between the SOS functions in this bacterium and in the enteric bacteria; (2) the spontaneous activation of SOS functions in competent cells; and (3) the difficulty in establishing the presence of error-prone repair in this bacterium. In order to characterize the SOS system of B. subtilis, attempts will be made to: (1) isolate bacteria mutated in genes controlling various repair functions; (2) investigate inducible repair; (3) determine the role of endogenous prophages in DNA repair phenomena; and (4) utilize competent B. subtilis as a tester system for the detection of potential carcinogens. Data obtained during the past 18 months demonstrate: (1) the ability of the B. subtilis Comptest to detect potential environmental carcinogens; (2) the importance of DNA polymerase III in W-reactivation in B. subtilis; and (3) the control the bacteriophage SP..beta.. has over the inducible DNA modification system in B. subtilis. Furthermore, the data also suggests the lack of error-prone repair in B. subtilis, and the differences which exist between the Bacilli and the enteric bacteria with regards to SOS phenomena. In order to further characterize inducible repair functions in B. subtilis, results will also be presented on attempts to mobilize error-prone repair systems of other bacterial species.

Yasbin, R E

1980-10-01

23

Change of Bacillus cereus flavonoid O-triglucosyltransferase into flavonoid O-monoglucosyltransferase by error-prone polymerase chain reaction.  

PubMed

The attachment of sugar to flavonoids enhances their solubility. Glycosylation is performed primarily by uridine diphosphate-dependent glycosyltransferases (UGTs). The UGT from Bacillus cereus, BcGT-1 transferred three glucose molecules into kaempferol. The structural analysis of BcGT-1 showed that its substrate binding site is wider than that of flavonoid monoglucosyltransferase of plant. In order to create monoglucosyltransferase from BcGT-1, error-prone polymerase chain reaction (PCR) was performed. We analyzed 150 clones. Among them, two mutants generated only kaempferol O-monoglucoside, albeit with reduced reactivity. Unexpectedly, the two mutants harbored mutations in the amino acids located outside of the active sites. Based on the modeled structure of BcGT-1, it was proposed that the local change in the secondary structure of BcGT-1 caused the alteration of triglucosyltransferase into monoglucosyltransferase. PMID:21030823

Jung, Na Ri; Joe, Eun Ji; Kim, Bong-Gyu; Ahn, Byoung Chan; Park, Jun Cheol; Chong, Youhoon; Ahn, Joong-Hoon

2010-10-01

24

Recovery of Arrested Replication Forks by Homologous Recombination Is Error-Prone  

PubMed Central

Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletions and translocations. Fork-arrest-induced gross chromosomal rearrangements are mediated by inappropriate ectopic recombination events at the site of collapsed forks. Inverted repeats near the site of fork collapse stimulate large-scale genomic changes up to 1,500 times over spontaneous events. We also show that the high accuracy of DNA replication during S-phase is impaired by impediments to fork progression, since fork-arrest-induced mutation is due to erroneous DNA synthesis during recovery of replication forks. The mutations caused are small insertions/duplications between short tandem repeats (micro-homology) indicative of replication slippage. Our data establish that collapsed forks, but not stalled forks, recovered by homologous recombination are prone to replication slippage. The inaccuracy of DNA synthesis does not rely on PCNA ubiquitination or trans-lesion-synthesis DNA polymerases, and it is not counteracted by mismatch repair. We propose that deletions/insertions, mediated by micro-homology, leading to copy number variations during replication stress may arise by progression of error-prone replication forks restarted by homologous recombination.

Pietrobon, Violena; Freon, Karine; Costes, Audrey; Lambert, Sarah A. E.

2012-01-01

25

Recovery of arrested replication forks by homologous recombination is error-prone.  

PubMed

Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletions and translocations. Fork-arrest-induced gross chromosomal rearrangements are mediated by inappropriate ectopic recombination events at the site of collapsed forks. Inverted repeats near the site of fork collapse stimulate large-scale genomic changes up to 1,500 times over spontaneous events. We also show that the high accuracy of DNA replication during S-phase is impaired by impediments to fork progression, since fork-arrest-induced mutation is due to erroneous DNA synthesis during recovery of replication forks. The mutations caused are small insertions/duplications between short tandem repeats (micro-homology) indicative of replication slippage. Our data establish that collapsed forks, but not stalled forks, recovered by homologous recombination are prone to replication slippage. The inaccuracy of DNA synthesis does not rely on PCNA ubiquitination or trans-lesion-synthesis DNA polymerases, and it is not counteracted by mismatch repair. We propose that deletions/insertions, mediated by micro-homology, leading to copy number variations during replication stress may arise by progression of error-prone replication forks restarted by homologous recombination. PMID:23093942

Iraqui, Ismail; Chekkal, Yasmina; Jmari, Nada; Pietrobon, Violena; Fréon, Karine; Costes, Audrey; Lambert, Sarah A E

2012-01-01

26

Error-prone translesion replication of damaged DNA suppresses skin carcinogenesis by controlling inflammatory hyperplasia  

PubMed Central

The induction of skin cancer involves both mutagenic and proliferative responses of the epidermis to ultraviolet (UV) light. It is believed that tumor initiation requires the mutagenic replication of damaged DNA by translesion synthesis (TLS) pathways. The mechanistic basis for the induction of proliferation, providing tumor promotion, is poorly understood. Here, we have investigated the role of TLS in the initiation and promotion of skin carcinogenesis, using a sensitive nucleotide excision repair-deficient mouse model that carries a hypomorphic allele of the error-prone TLS gene Rev1. Despite a defect in UV-induced mutagenesis, skin carcinogenesis was accelerated in these mice. This paradoxical phenotype was caused by the induction of inflammatory hyperplasia of the mutant skin that provides strong tumor promotion. The induction of hyperplasia was associated with mild and transient replicational stress of the UV-damaged genome, triggering DNA damage signaling and senescence. The concomitant expression of Interleukin-6 (IL-6) is in agreement with an executive role for IL-6 and possibly other cytokines in the autocrine induction of senescence and the paracrine induction of inflammatory hyperplasia. In conclusion, error-prone TLS suppresses tumor-promoting activities of UV light, thereby controlling skin carcinogenesis.

Tsaalbi-Shtylik, Anastasia; Verspuy, Johan W. A.; Jansen, Jacob G.; Rebel, Heggert; Carlee, Leone M.; van der Valk, Martin A.; Jonkers, Jos; de Gruijl, Frank R.; de Wind, Niels

2009-01-01

27

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

PubMed Central

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

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

2014-01-01

28

Improved acid tolerance of Lactobacillus pentosus by error-prone whole genome amplification.  

PubMed

Acid tolerance of Lactobacillus pentosus ATCC 8041 was improved by error-prone amplification of its genomic DNA using random primers and Taq DNA polymerase. The resulting amplification products were transferred into wild-type L. pentosus by electroporation and the transformants were screened for growth on low-pH agar plates. After only one round of mutation, one mutant (MT3) was identified that was able to completely consume 20 g/L of glucose to produce lactic acid at a yield of 95% in 1L MRS medium at pH 3.8 within 36 h, whereas no growth or lactic acid production was observed for the wild-type strain under the same conditions. The acid tolerance of mutant MT3 remained genetically stable for at least 25 subcultures. Therefore, the error-prone whole genome amplification technique is a very powerful tool for improving phenotypes of this lactic acid bacterium and may also be applicable for other microorganisms. PMID:23182040

Ye, Lidan; Zhao, Hua; Li, Zhi; Wu, Jin Chuan

2013-05-01

29

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

PubMed Central

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.

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

2014-01-01

30

The Saccharomyces cerevisiae RAD6 Group Is Composed of an Error-Prone and Two Error-Free Postreplication Repair Pathways  

Microsoft Academic Search

The RAD6 postreplication repair and mutagenesis pathway is the only major radiation repair pathway yet to be extensively characterized. It has been previously speculated that the RAD6 pathway consists of two parallel subpathways, one error free and another error prone (mutagenic). Here we show that the RAD6 group genes can be exclusively divided into three rather than two independent subpathways

Wei Xiao; Barbara L. Chow; Stacey Broomfield; Michelle Hanna

2000-01-01

31

The Advantage of Arriving First: Characteristic Times in Finite Size Populations of Error-Prone Replicators  

PubMed Central

We study the evolution of a finite size population formed by mutationally isolated lineages of error-prone replicators in a two-peak fitness landscape. Computer simulations are performed to gain a stochastic description of the system dynamics. More specifically, for different population sizes, we compute the probability of each lineage being selected in terms of their mutation rates and the amplification factors of the fittest phenotypes. We interpret the results as the compromise between the characteristic time a lineage takes to reach its fittest phenotype by crossing the neutral valley and the selective value of the sequences that form the lineages. A main conclusion is drawn: for finite population sizes, the survival probability of the lineage that arrives first to the fittest phenotype rises significantly.

Marin, Arturo; Tejero, Hector; Nuno, Juan Carlos; Montero, Francisco

2013-01-01

32

Meiosis I in Xenopus oocytes is not error-prone despite lacking spindle assembly checkpoint.  

PubMed

The spindle assembly checkpoint, SAC, is a surveillance mechanism to control the onset of anaphase during cell division. SAC prevents anaphase initiation until all chromosome pairs have achieved bipolar attachment and aligned at the metaphase plate of the spindle. In doing so, SAC is thought to be the key mechanism to prevent chromosome nondisjunction in mitosis and meiosis. We have recently demonstrated that Xenopus oocyte meiosis lacks SAC control. This prompted the question of whether Xenopus oocyte meiosis is particularly error-prone. In this study, we have karyotyped a total of 313 Xenopus eggs following in vitro oocyte maturation. We found no hyperploid egg, out of 204 metaphase II eggs with countable chromosome spreads. Therefore, chromosome nondisjunction is very rare during Xenopus oocyte meiosis I, despite the lack of SAC. PMID:24646611

Liu, Dandan; Shao, Hua; Wang, Hongmei; Liu, X Johné

2014-05-15

33

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

SciTech Connect

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.

Yasbin, R. E.

1981-06-01

34

[Medication safety in the home care setting: error-prone process steps].  

PubMed

So far, little is known about drug-related problems in the homecare setting. It is estimated that up to 30% of homecare patients experience a potential medication error, most frequently happening during preparation and administration of drugs. In order to identify error-prone process steps in a Swiss homecare organisation caring for 1854 patients per year, direct observation of the medication use process, including the analysis of 10% of all prescriptions, was executed. Three complimentary methods were combined for the assessment of qualitative aspects of the medication use process: the analysis of a critical incident reporting system, a survey among homecare nurses, and a failure, mode and effects analysis. The medication use process is complex, consisting of 20 individual steps. Patients are prescribed an average of 7.5 ± 3.5 drugs per day, including 1 to 9 doses not suitable for deblistering into weekly dispensing systems. Of 84 reported errors, 74% happened during drug preparation. Communication with physicians, patients interrupting drug preparation and not transmitted changes of the drug regimen were considered the most critical process steps. PMID:22811293

Meyer-Massetti, C; Kaiser, E; Hedinger-Grogg, B; Luterbacher, S; Hersberger, K

2012-08-01

35

Error-free RAD52 pathway and error-prone REV3 pathway determines spontaneous mutagenesis in Saccharomyces cerevisiae.  

PubMed

Using the CAN1 gene in haploid cells or heterozygous diploid cells, we characterized the effects of mutations in the RAD52 and REV3 genes of Saccharomyces cerevisiae in spontaneous mutagenesis. The mutation rate was 5-fold higher in the haploid rad52 strain and 2.5-fold lower in rev3 than in the wild-type strain. The rate in the rad52 rev3 strain was as low as in the wild-type strain, indicating the rad52 mutator phenotype to be dependent on REV3. Sequencing indicated that G:C-->T:A and G:C-->C:G transversions increased in the rad52 strain and decreased in the rev3 and rad52 rev3 strains, suggesting a role for REV3 in transversion mutagenesis. In diploid rev3 cells, frequencies of can1Delta::LEU2/can1Delta::LEU2 from CAN1/can1Delta::LEU2 due to recombination were increased over the wild-type level. Overall, in the absence of RAD52, REV3-dependent base-substitutions increased, while in the absence of REV3, RAD52-dependent recombination events increased. We further found that the rad52 mutant had an increased rate of chromosome loss and the rad52 rev3 double mutant had an enhanced chromosome loss mutator phenotype. Taken together, our study indicates that the error-free RAD52 pathway and error-prone REV3 pathway for rescuing replication fork arrest determine spontaneous mutagenesis, recombination, and genome instability. PMID:17396018

Endo, Kingo; Tago, Yu-ichiro; Daigaku, Yasukazu; Yamamoto, Kazuo

2007-02-01

36

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

PubMed Central

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

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

1984-01-01

37

Modification of PCNA by ISG15 Plays a Crucial Role in Termination of Error-Prone Translesion DNA Synthesis.  

PubMed

In response to DNA damage, PCNA is mono-ubiquitinated and triggers translesion DNA synthesis (TLS) by recruiting polymerase-?. However, it remained unknown how error-prone TLS is turned off after DNA lesion bypass to prevent mutagenesis. Here we showed that ISG15 modification (ISGylation) of PCNA plays a key role in TLS termination. Upon UV irradiation, EFP, an ISG15 E3 ligase, bound to mono-ubiquitinated PCNA and promoted its ISGylation. ISGylated PCNA then tethered USP10 for deubiquitination and in turn the release of polymerase-? from PCNA. Eventually, PCNA was deISGylated by UBP43 for reloading of replicative DNA polymerases and resuming normal DNA replication. However, ISGylation-defective Lys-to-Arg mutations in PCNA or knockdown of any of ISG15, EFP, or USP10 led to persistent recruitment of mono-ubiquitinated PCNA and polymerase-? to nuclear foci, causing an increase in mutation frequency. These findings establish a crucial role of PCNA ISGylation in termination of error-prone TLS for preventing excessive mutagenesis. PMID:24768535

Park, Jung Mi; Yang, Seung Wook; Yu, Kyung Ryun; Ka, Seung Hyun; Lee, Seong Won; Seol, Jae Hong; Jeon, Young Joo; Chung, Chin Ha

2014-05-22

38

ASFV DNA Polymerase X is Extremely Error-Prone Under Diverse Assay Conditions and Within Multiple DNA Sequence Contexts†  

PubMed Central

We previously demonstrated that the DNA repair system encoded by the African swine fever virus (ASFV) is both extremely error-prone during the single-nucleotide gap-filling step (catalyzed by ASFV DNA Polymerase X) and extremely error-tolerant during the nick-sealing step (catalyzed by ASFV DNA ligase). On the basis of these findings we have suggested that at least some of the diversity known to exist among ASFV isolates may be a consequence of mutagenic DNA repair – wherein damaged nucleotides are replaced with undamaged but incorrect nucleotides by Pol X and the resultant mismatched nicks are sealed by ASFV DNA ligase. Recently, this hypothesis appeared to be discredited by Salas and coworkers [J. Mol. Biol. 2003, 326, 1403–1412.] who reported the fidelity of Pol X to be, on average, two orders of magnitude higher than what we previously published. In an effort to address this discrepancy and provide a definitive conclusion about the fidelity of Pol X, herein we examine the fidelity of Pol X-catalyzed single-nucleotide gap-filling in both the steady state and the pre-steady state under a diverse array of assay conditions (varying pH and ionic strength) and within different DNA sequence contexts. These studies corroborate our previously published data (demonstrating the low-fidelity of Pol X to be independent of assay condition/sequence context), do not reproduce the data of Salas et al., and therefore confirm Pol X to be one of the most error-prone polymerases known. These results are discussed in light of ASFV biology and the mutagenic DNA repair hypothesis described above.

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

2008-01-01

39

Survival analysis with error-prone time-varying covariates: a risk set calibration approach  

PubMed Central

Summary Occupational, environmental, and nutritional epidemiologists are often interested in estimating the prospective effect of time-varying exposure variables such as cumulative exposure or cumulative updated average exposure, in relation to chronic disease endpoints such as cancer incidence and mortality. From exposure validation studies, it is apparent that many of the variables of interest are measured with moderate to substantial error. Although the ordinary regression calibration approach is approximately valid and efficient for measurement error correction of relative risk estimates from the Cox model with time-independent point exposures when the disease is rare, it is not adaptable for use with time-varying exposures. By re-calibrating the measurement error model within each risk set, a risk set regression calibration method is proposed for this setting. An algorithm for a bias-corrected point estimate of the relative risk using an RRC approach is presented, followed by the derivation of an estimate of its variance, resulting in a sandwich estimator. Emphasis is on methods applicable to the main study/external validation study design, which arises in important applications. Simulation studies under several assumptions about the error model were carried out, which demonstrated the validity and efficiency of the method in finite samples. The method was applied to a study of diet and cancer from Harvard’s Health Professionals Follow-up Study (HPFS).

Liao, Xiaomei; Zucker, David M.; Li, Yi; Spiegelman, Donna

2010-01-01

40

The Error Prone Model and the Basic Grants Validation Selection System. Draft Final Report.  

ERIC Educational Resources Information Center

An evaluation of existing and proposed mechanisms to ensure data accuracy for the Pell Grant program is reported, and recommendations for efficient detection of fraud and error in the program are offered. One study objective was to examine the existing system of pre-established criteria (PEC), which are validation criteria that select students on…

System Development Corp., Falls Church, VA.

41

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

SciTech Connect

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.

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

2012-10-25

42

The preference for error-free or error-prone postreplication repair in Saccharomyces cerevisiae exposed to low-dose methyl methanesulfonate is cell cycle dependent.  

PubMed

Cells employ error-free or error-prone postreplication repair (PRR) processes to tolerate DNA damage. Here, we present a genome-wide screen for sensitivity to 0.001% methyl methanesulfonate (MMS). This relatively low dose is of particular interest because wild-type cells exhibit no discernible phenotypes in response to treatment, yet PRR mutants are unique among repair mutants in their exquisite sensitivity to 0.001% MMS; thus, low-dose MMS treatment provides a distinctive opportunity to study postreplication repair processes. We show that upon exposure to low-dose MMS, a PRR-defective rad18? mutant stalls into a lengthy G2 arrest associated with the accumulation of single-stranded DNA (ssDNA) gaps. Consistent with previous results following UV-induced damage, reactivation of Rad18, even after prolonged G2 arrest, restores viability and genome integrity. We further show that PRR pathway preference in 0.001% MMS depends on timing and context; cells preferentially employ the error-free pathway in S phase and do not require MEC1-dependent checkpoint activation for survival. However, when PRR is restricted to the G2 phase, cells utilize REV3-dependent translesion synthesis, which requires a MEC1-dependent delay and results in significant hypermutability. PMID:23382077

Huang, Dongqing; Piening, Brian D; Paulovich, Amanda G

2013-04-01

43

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

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…

Saavedra, Pedro; And Others

44

Error-Prone ZW Pairing and No Evidence for Meiotic Sex Chromosome Inactivation in the Chicken Germ Line  

PubMed Central

In the male mouse the X and Y chromosomes pair and recombine within the small pseudoautosomal region. Genes located on the unsynapsed segments of the X and Y are transcriptionally silenced at pachytene by Meiotic Sex Chromosome Inactivation (MSCI). The degree to which MSCI is conserved in other vertebrates is currently unclear. In the female chicken the ZW bivalent is thought to undergo a transient phase of full synapsis at pachytene, starting from the homologous ends and spreading through the heterologous regions. It has been proposed that the repair of the ZW DNA double-strand breaks (DSBs) is postponed until diplotene and that the ZW bivalent is subject to MSCI, which is independent of its synaptic status. Here we present a distinct model of meiotic pairing and silencing of the ZW pair during chicken oogenesis. We show that, in most oocytes, DNA DSB foci on the ZW are resolved by the end of pachytene and that the ZW desynapses in broad synchrony with the autosomes. We unexpectedly find that ZW pairing is highly error prone, with many oocytes failing to engage in ZW synapsis and crossover formation. Oocytes with unsynapsed Z and W chromosomes nevertheless progress to the diplotene stage, suggesting that a checkpoint does not operate during pachytene in the chicken germ line. Using a combination of epigenetic profiling and RNA–FISH analysis, we find no evidence for MSCI, associated with neither the asynaptic ZW, as described in mammals, nor the synaptic ZW. The lack of conservation of MSCI in the chicken reopens the debate about the evolution of MSCI and its driving forces.

Guioli, Silvana; Lovell-Badge, Robin; Turner, James M. A.

2012-01-01

45

hREV3 is essential for error-prone translesion synthesis past UV or benzo[a]pyrene diol epoxide-induced DNA lesions in human fibroblasts  

Microsoft Academic Search

In S. cerevisiae, the REV3 gene, encoding the catalytic subunit of polymerase zeta, is involved in translesion synthesis and required for the production of mutations induced by ultraviolet radiation (UV) photoproducts and other DNA fork-blocking lesions, and for the majority of spontaneous mutations. To determine whether hREV3, the human homolog of yeast REV3, is similarly involved in error-prone translesion synthesis

Ziqiang Li; Hong Zhang; Terrence P McManus; J. Justin McCormick; Christopher W Lawrence; Veronica M Maher

2002-01-01

46

Interactions in the Error-prone Postreplication Repair Proteins hREV1, hREV3, and hREV7  

Microsoft Academic Search

Most mutations after DNA damage in yeast Saccharo- myces cerevisiae are induced by error-prone translesion DNA synthesis employing scRev1 and DNA polymerase that consists of scRev3 and scRev7 proteins. Recently, the human REV1 (hREV1) and REV3 (hREV3) genes were identified, and their products were revealed to be in- volved in UV-induced mutagenesis, as observed for their yeast counterparts. Human REV7

Yoshiki Murakumo; Yukiko Ogura; Hideshi Ishii; Shin-ichiro Numata; Masatoshi Ichihara; Carlo M. Croce; Richard Fishel; Masahide Takahashi

2001-01-01

47

Corrupted Speech Data Considered Useful: Improving Perceived Speech Quality of VoIP over Error-Prone Channels  

Microsoft Academic Search

Summary The provisioning of an appropriate level of perceptual speech quality is crucial for the successful deployment of Vo ice over the Internet Protocol (VoIP). Today's heterogeneous multimedia networks include links that introduce bit errors into the voice data stream. These errors are detected by the IP packet transport protocol and result in packet losses which eventually degrade the speech

Florian Hammer; Peter Reichl; Tomas Nordstrom; Gernot Kubin

2004-01-01

48

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

PubMed

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 ?. 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

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

2014-06-24

49

PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data  

PubMed Central

Background Ultra-deep pyrosequencing (UDPS) is used to identify rare sequence variants. The sequence depth is influenced by several factors including the error frequency of PCR and UDPS. This study investigated the characteristics and source of errors in raw and cleaned UDPS data. Results UDPS of a 167-nucleotide fragment of the HIV-1 SG3?env plasmid was performed on the Roche/454 platform. The plasmid was diluted to one copy, PCR amplified and subjected to bidirectional UDPS on three occasions. The dataset consisted of 47,693 UDPS reads. Raw UDPS data had an average error frequency of 0.30% per nucleotide site. Most errors were insertions and deletions in homopolymeric regions. We used a cleaning strategy that removed almost all indel errors, but had little effect on substitution errors, which reduced the error frequency to 0.056% per nucleotide. In cleaned data the error frequency was similar in homopolymeric and non-homopolymeric regions, but varied considerably across sites. These site-specific error frequencies were moderately, but still significantly, correlated between runs (r?=?0.15–0.65) and between forward and reverse sequencing directions within runs (r?=?0.33–0.65). Furthermore, transition errors were 48-times more common than transversion errors (0.052% vs. 0.001%; p<0.0001). Collectively the results indicate that a considerable proportion of the sequencing errors that remained after data cleaning were generated during the PCR that preceded UDPS. Conclusions A majority of the sequencing errors that remained after data cleaning were introduced by PCR prior to sequencing, which means that they will be independent of platform used for next-generation sequencing. The transition vs. transversion error bias in cleaned UDPS data will influence the detection limits of rare mutations and sequence variants.

Brodin, Johanna; Mild, Mattias; Hedskog, Charlotte; Sherwood, Ellen; Leitner, Thomas; Andersson, Bjorn; Albert, Jan

2013-01-01

50

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

ERIC Educational Resources Information Center

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

Saavedra, Pedro; Kuchak, JoAnn

51

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

PubMed

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

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

2014-08-15

52

Systemic Errors In Quantitative PCR Titration of Self-Complementary AAV Vectors and Improved Alternative Methods  

PubMed Central

Self-complementary AAV (scAAV) vector genomes contain a covalently closed hairpin derived from a mutated inverted terminal repeat which connects the two monomer single stranded genomes into a head-to-head or tail-to-tail dimer. We found that during quantitative PCR (qPCR) this structure inhibits the amplification of proximal amplicons and causes the systemic underreporting of copy number by as much as 10-fold. We show that cleavage of scAAV vector genomes with restriction endonuclease to liberate amplicons from the covalently closed terminal hairpin restores quantitative amplification, and we implement this procedure in a simple, modified qPCR titration method for scAAV vectors. Additionally, we developed and present an AAV genome titration procedure based on gel electrophoresis that requires minimal sample processing and has very low inter assay variability, and as such is well suited for the rigorous quality control demands of clinical vector production facilities.

Fagone, Paolo; Wright, J. Fraser; Nathwani, Amit C.; Nienhuis, Arthur W.; Davidoff, Andrew M.; Gray, John T.

2013-01-01

53

MsDpo4--a DinB Homolog from Mycobacterium smegmatis--Is an Error-Prone DNA Polymerase That Can Promote G:T and T:G Mismatches  

PubMed Central

Error-prone DNA synthesis in prokaryotes imparts plasticity to the genome to allow for evolution in unfavorable environmental conditions, and this phenomenon is termed adaptive mutagenesis. At a molecular level, adaptive mutagenesis is mediated by upregulating the expression of specialized error-prone DNA polymerases that generally belong to the Y-family, such as the polypeptide product of the dinB gene in case of E. coli. However, unlike E. coli, it has been seen that expression of the homologs of dinB in Mycobacterium tuberculosis are not upregulated under conditions of stress. These studies suggest that DinB homologs in Mycobacteria might not be able to promote mismatches and participate in adaptive mutagenesis. We show that a representative homolog from Mycobacterium smegmatis (MsDpo4) can carry out template-dependent nucleotide incorporation and therefore is a DNA polymerase. In addition, it is seen that MsDpo4 is also capable of misincorporation with a significant ability to promote G:T and T:G mismatches. The frequency of misincorporation for these two mismatches is similar to that exhibited by archaeal and prokaryotic homologs. Overall, our data show that MsDpo4 has the capacity to facilitate transition mutations and can potentially impart plasticity to the genome.

Sharma, Amit; Nair, Deepak T.

2012-01-01

54

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

Microsoft Academic Search

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

2004-01-01

55

Chemotherapy-related secondary leukemias: A role for DNA repair by error-prone non-homologous end joining in topoisomerase II - Induced chromosomal rearrangements.  

PubMed

Chromosome rearrangements are believed to cause the secondary leukemias which constitute frequent complications of antitumor chemotherapy with topoisomerase II-specific drugs. Here we show that inhibition of DNA topoisomerase II in cultured cells stimulates association of components of the non-homologous end joining system with a known breakpoint cluster region of the human AML1 gene, suggesting that errors of DNA repair during NHEJ may be the cause of illegitimate recombination in cells treated with topoisomerase II poisons. PMID:17234368

Kantidze, Omar L; Razin, Sergey V

2007-04-15

56

Digital Droplet PCR: CNV Analysis and Other Applications.  

PubMed

Digital droplet PCR (ddPCR) is an assay that combines state-of-the-art microfluidics technology with TaqMan-based PCR to achieve precise target DNA quantification at high levels of sensitivity and specificity. Because quantification is achieved without the need for standard assays in an easy to interpret, unambiguous digital readout, ddPCR is far simpler, faster, and less error prone than real-time qPCR. The basic protocol can be modified with minor adjustments to suit a wide range of applications, such as CNV analysis, rare variant detection, SNP genotyping, and transcript quantification. This unit describes the ddPCR workflow in detail for the Bio-Rad QX100 system, but the theory and data interpretation are generalizable to any ddPCR system. Curr. Protoc. Hum. Genet. 82:7.24.1-7.24.13. © 2014 by John Wiley & Sons, Inc. PMID:25042719

Mazaika, Erica; Homsy, Jason

2014-01-01

57

PCR-Based Ordered Genomic Libraries: a New Approach to Drug Target Identification for Streptococcus pneumoniae  

Microsoft Academic Search

Described here are the development and validation of a novel approach to identify genes encoding drug targets in Streptococcus pneumoniae. The method relies on the use of an ordered genomic library composed of PCR amplicons that were generated under error-prone conditions so as to introduce random mutations into the DNA. Since some of the mutations occur in drug target-encoding genes

Aimee E. Belanger; Angel Lai; Marcia A. Brackman; Donald J. LeBlanc

2002-01-01

58

Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications  

Microsoft Academic Search

Quantitative real-time PCR has revolutionized many aspects of genetic research, biomedical diagnostics and pathogen detection. Nevertheless, the full poten- tial of this technology has yet to be realized, primarily due to the limitations of the threshold-based meth- odologies that are currently used for quantitative analysis. Prone to errors caused by variations in reac- tion preparation and amplification conditions, these approaches

R. G. Rutledge

2004-01-01

59

Upscaled CTAB-Based DNA Extraction and Real-Time PCR Assays for Fusarium culmorum and F. graminearum DNA in Plant Material with Reduced Sampling Error  

PubMed Central

Fusarium graminearum Schwabe (Gibberella zeae Schwein. Petch.) and F. culmorum W.G. Smith are major mycotoxin producers in small-grain cereals afflicted with Fusarium head blight (FHB). Real-time PCR (qPCR) is the method of choice for species-specific, quantitative estimation of fungal biomass in plant tissue. We demonstrated that increasing the amount of plant material used for DNA extraction to 0.5–1.0 g considerably reduced sampling error and improved the reproducibility of DNA yield. The costs of DNA extraction at different scales and with different methods (commercial kits versus cetyltrimethylammonium bromide-based protocol) and qPCR systems (doubly labeled hybridization probes versus SYBR Green) were compared. A cost-effective protocol for the quantification of F. graminearum and F. culmorum DNA in wheat grain and maize stalk debris based on DNA extraction from 0.5–1.0 g material and real-time PCR with SYBR Green fluorescence detection was developed.

Brandfass, Christoph; Karlovsky, Petr

2008-01-01

60

Prone positioning for surgery.  

PubMed

The role of the registered perioperative practitioner (Operating Department Practitioner or Registered Nurse) includes the responsibility for safely positioning patients for surgery. The prone position is in common use for a variety of surgical procedures. The formal term for this surgical position is ventral decubitus (meaning laying face down). PMID:22720505

Bowers, Mark

2012-05-01

61

A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR  

Microsoft Academic Search

BACKGROUND: Based upon defining a common reference point, current real-time quantitative PCR technologies compare relative differences in amplification profile position. As such, absolute quantification requires construction of target-specific standard curves that are highly resource intensive and prone to introducing quantitative errors. Sigmoidal modeling using nonlinear regression has previously demonstrated that absolute quantification can be accomplished without standard curves; however, quantitative

Robert G Rutledge; Don Stewart

2008-01-01

62

A Computerized Methodology for Improved Virus Typing by PCR-RFLP Gel Electrophoresis  

Microsoft Academic Search

The analysis of digitized images from polymerase chain reaction-restriction fragment length polymorphism (PCR- RFLP) gel electrophoresis examinations is a popular method for virus typing, i.e., for identifying the virus type(s) that have in- fected an investigated biological sample. However, being mostly manual, the conventional virus typing protocol remains laborious, time consuming, and error prone. In order to overcome these short-

Christos F. Maramis; Anastasios N. Delopoulos; Alexandros F. Lambropoulos

2011-01-01

63

A system for automatic HPV typing via PCR-RFLP gel electrophoresis  

Microsoft Academic Search

The identification of the types of the human papil- lomavirus (HPV) that have infected a female patient provides valuable information as regards to her risk for developing cervical cancer. A widely used method for performing the above task (namely HPV typing) is PCR-RFLP gel electrophoresis. However, the conventional HPV typing protocol is error-prone and resource-ineffective due to lack of interaction

Christos F. Maramis; Anastasios N. Delopoulos; Alexandros F. Lambropoulos; Sokratis P. Katafigiotis

2011-01-01

64

Blast Displacement of Prone Dummies.  

National Technical Information Service (NTIS)

Dummies were placed prone on the surface at ground ranges of 560 and 650 feet from a 500-ton charge. Dummies were also placed in slit trenches at these ranges. The overpressure measured at the 560- and 650-foot range was 37 and 21 p.s.i., respectively, an...

D. R. Richmond E. R. Fletcher R. K. Jones

1971-01-01

65

Ethnic and gender differences in boredom proneness.  

National Technical Information Service (NTIS)

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 (...

G. S. Gibson Morales

1996-01-01

66

Fission yeast Rad52 phosphorylation restrains error prone recombination pathways.  

PubMed

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

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

2014-01-01

67

Fission Yeast Rad52 Phosphorylation Restrains Error Prone Recombination Pathways  

PubMed Central

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.

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

2014-01-01

68

Propensity Score Weighting with Error-Prone Covariates  

ERIC Educational Resources Information Center

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,…

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

2011-01-01

69

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

MedlinePLUS

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

70

Fantasy Proneness: Hypnosis, Developmental Antecedents, and Psychopathology  

Microsoft Academic Search

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

Steven Jay Lynn; Judith W. Rhue

1988-01-01

71

Temporal Error Concealment Using Self-Organizing Map  

Microsoft Academic Search

The performance of MPEG video transmission over error-prone channels is limited by the channel noise. An efficient error concealment (EC) scheme is essential for diminishing the impact of transmission errors in a compressed video. A number of error concealment (EC) techniques have been developed to combat the transmission errors. However, the techniques are always inefficient when the motions of object

Yu-Len Huang; Hsiu-Yi Lien

2004-01-01

72

Operationalizing Proneness to Externalizing Psychopathology as a Multivariate Psychophysiological Phenotype  

PubMed Central

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

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

2010-01-01

73

Intra- and Interfractional Variations for Prone Breast Irradiation: An Indication for Image-Guided Radiotherapy  

SciTech Connect

Purpose: Intra- and interfractional errors for breast cancer patients undergoing breast irradiation in the prone position were analyzed. Methods and Materials: To assess intrafractional error resulting from respiratory motion, four-dimensional computed tomography scans were acquired for 3 prone and 3 supine patients, and the respiratory motion was compared for the two positions. To assess the interfractional error caused by daily set-up variations, daily electronic portal images of one of the treatment beams were taken for 15 prone-positioned patients. Portal images were then overlaid with images from the planning system that included the breast contour and the isocenter, treatment beam portal, and isocenter. The shift between the planned and actual isocenter was recorded for each portal image, and descriptive statistics were collected for each patient. The margins were calculated using the 2{sigma}+0.7{sigma} recipe, as well as 95% confidence interval based on the pooled standard deviation of the datasets. Results: Respiratory motion of the chest wall is drastically reduced from 2.3 {+-} 0.9 mm in supine position to -0.1 {+-} 0.4 mm in prone position. The daily set-up errors vary in magnitude from 0.0 cm to 1.65 cm and are patient dependent. The margins were defined by considering only the standard deviation to be 1.1 cm, and 2.0 cm when the systematic errors were considered using the 2{sigma}+0.7{sigma} recipe. Conclusions: Prone positioning of patients for breast irradiation significantly reduces the uncertainty introduced by intrafractional respiratory motion. The presence of large systematic error in the interfractional variations necessitates a large clinical target volume-to-planning target volume margin and indicates the importance of image guidance for partial breast irradiation in the prone position, particularly using imaging modality capable of identifying the lumpectomy cavity.

Morrow, Natalya V.; Stepaniak, Christopher; White, Julia; Wilson, J. Frank [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States); Li, X. Allen [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States)], E-mail: ali@radonc.mcw.edu

2007-11-01

74

Deriving models of software fault-proneness  

Microsoft Academic Search

The effectiveness of the software testing process is a key issue for meeting the increasing demand of quality without augmenting the overall costs of software development. The estimation of software fault-proneness is important for assessing costs and quality and thus better planning and tuning the testing process. Unfortunately, no general techniques are available for estimating software fault-proneness and the distribution

Giovanni Denaro; Sandro Morasca; Mauro Pezzè

2002-01-01

75

Isometric elbow extensors strength in supine- and prone-lying positions.  

PubMed

The purpose of this study was to compare isometric strength of elbow extensors measured in supine- and prone-lying positions at elbow flexion angles of 45 and 90 degrees. Twenty-two male subjects under single-blind procedures participated in the study. Each subject participated in both supine-lying and prone-lying measuring protocols. Calibrated cable tensiometer was used to measure isometric strength of the right elbow extensors and a biofeedback electromyography was used to assure no substitution movements from shoulder girdle muscles. The mean values of isometric strength of elbow extensors measured from supine-lying position at elbow flexion angles of 45 and 90 degrees were 11.1 ?±? 4.2 kg and 13.1 ?±? 4.6 kg, while those measured from prone-lying position were 9.9 ?±? 3.6 kg and 12 ?±? 4.2 kg, respectively. There is statistical significant difference between the isometric strength of elbow extensors measured from supine-lying position at elbow flexion angles of 45 and 90 degrees compared to that measured from prone-lying position (p ?prone-lying starting position. PMID:22489839

Abdelzaher, Ibrahim E; Ababneh, Anas F; Alzyoud, Jehad M

2013-01-01

76

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

PubMed Central

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.

2014-01-01

77

Fully automated prone-supine coregistration in computed tomographic colonography  

NASA Astrophysics Data System (ADS)

A fully automated, anatomically-based procedure is developed for the coregistration of prone and supine scans in computed tomographic colonography (CTC). Haustral folds, teniae coli and other anatomic landmarks are extracted from the segmented colonic lumen and serve as the basis for iterative optimization-based matching of the colonic surfaces. The three-dimensional coregistration is computed efficiently using a two-dimensional filet representation of the colon. The circumferential positions of longitudinal structures such as teniae coli are used to estimate a rotational prone-to-supine deformation, haustral folds give a longitudinal (stretching) deformation, while other landmarks and anatomical considerations are used to constrain the allowable deformations. The proposed method is robust to changes in the detected anatomical landmarks such as the obscuration or apparent bifurcation of teniae coli. Preliminary validation in the Walter Reed CTC data set shows excellent coregistration accuracy-57 manually identified features (such as polyps and diverticula) are automatically coregistered with a mean three-dimensional error of 16.4 mm. In phantom studies, 210 fiducial pairs are coregistered to a mean three-dimensional error of 8.6 mm. The coregistration allows points of interest in one scan to be automatically located in the other, leading to an expected improvement in per-patient read time and a significant reduction in the cost of CTC.

Davis, Brynmor J.; Norris, James A.; Bieszczad, Jerry Y.; Soto, Jorge A.; Kynor, David B.

2011-03-01

78

Routine intubation in the prone position  

PubMed Central

Background. Tracheal intubation in the prone position has previously been reported only as a necessity in a very few emergency situations. It emerged at our clinic as a routine after invention of a test aimed at pinpointing a painful motion segment in patients with chronic low back pain who were candidates for lumbar fusion operation. Material and methods. During a 6-year period 247 consecutive patients were treated at our clinic, 91 men and 156 women, mean age 42.8 years, range 25.3–62.8. Classification of the pharyngeal structures according to Mallampati et al. was done the day before surgery, and grading of visualization of the glottis as described by Cormack and Lehane was done during intubation, with the aim of revealing factors of importance for the possibility of performing tracheal intubation in the prone position. Results. The large majority of patients classified preoperatively as Mallampati class 1 had Cormack and Lehane grade 1 at laryngoscopy, although some patients had grades 2, 3, and 4. Most problems with intubation in the prone position were anticipated among those classified preoperatively as Mallampati class 3, but tracheal intubation in the prone position was still possible in 21 of the 23 patients in this group. In all, tracheal intubation in the prone position was successful in 244 of the 247 patients (98.8%). Conclusion. Routine tracheal intubation in the prone position can be performed effectively by experienced anaesthesiologists, but this requires continuous training and good support from the anaesthesiology staff.

Baer, Klaus

2012-01-01

79

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

SciTech Connect

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.

Veldeman, Liv, E-mail: Liv.Veldeman@uzgent.be [Department of Radiotherapy, Ghent University Hospital, Ghent (Belgium); De Gersem, Werner; Speleers, Bruno; Truyens, Bart; Van Greveling, Annick [Department of Radiotherapy, Ghent University Hospital, Ghent (Belgium); Van den Broecke, Rudy [Department of Gynecology, Ghent University Hospital, Ghent (Belgium); De Neve, Wilfried [Department of Radiotherapy, Ghent University Hospital, Ghent (Belgium)

2012-04-01

80

[Successful cardiopulmonary resuscitation in prone position].  

PubMed

In certain surgical positions standard cardiopulmonary resuscitation (CPR) cannot be carried out. It is sometimes impossible or time-consuming to establish a supine position without increasing the no-flow-time and therefore creating a negative outcome of the patient. The case of CPR in a prone position during an emergency evacuation of a cerebellar hematoma is reported. The resuscitation was initiated in the prone position to decrease the no-flow-time. This was very effective because the return of spontaneous circulation (ROSC) started before turning the patient to the supine position. Resuscitation in the prone position in this case was equally as effective as in the traditional supine position. PMID:20852835

Haffner, E; Sostarich, A M; Fösel, T

2010-12-01

81

PCR Methodology  

Microsoft Academic Search

\\u000a PCR methodologies have become firmly entrenched in many clinical laboratories for the detection of a wide range of organisms,\\u000a because they offer major advantages of improved sensitivity and rapidity over traditional diagnostic methods. However, many\\u000a variables need to be considered in performing a reliable PCR assay, ranging from nucleic acid extraction, storage, composition\\u000a of the PCR reaction mix used, to

Ian Carter; Catriona Halliday; Theo P. Sloots; Todd M. Pryce; Ian D. Kay; Gerald B. Harnett; Glenys R. Chidlow; Philip M. Giffard

82

General PCR.  

PubMed

The primary purpose of polymerase chain reaction (PCR) is to rapidly make many copies of a specific region of DNA or RNA so that it can be adequately detected, often by agarose gel electrophoresis. PCR is routinely used to amplify, modify, and clone genes for expression studies. There are many other applications for PCR, including paternity testing, biological relationships, mouse genotyping, diagnosing genetic diseases, forensics, and finding bacteria and viruses. PMID:24011055

Canene-Adams, Kirstie

2013-01-01

83

Virtual PCR.  

National Technical Information Service (NTIS)

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 for...

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

2006-01-01

84

Why is psychiatry prone to fads?  

PubMed

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

Paris, Joel

2013-10-01

85

Potential aggregation prone regions in biotherapeutics  

PubMed Central

Aggregation of a biotherapeutic is of significant concern and judicious process and formulation development is required to minimize aggregate levels in the final product. Aggregation of a protein in solution is driven by intrinsic and extrinsic factors. In this work we have focused on aggregation as an intrinsic property of the molecule. We have studied the sequences and Fab structures of commercial and non-commercial antibody sequences for their vulnerability towards aggregation by using sequence based computational tools to identify potential aggregation-prone motifs or regions. The mAbs in our dataset contain 2 to 8 aggregation-prone motifs per heavy and light chain pair. Some of these motifs are located in variable domains, primarily in CDRs. Most aggregation-prone motifs are rich in ? branched aliphatic and aromatic residues. Hydroxyl-containing Ser/Thr residues are also found in several aggregation-prone motifs while charged residues are rare. The motifs found in light chain CDR3 are glutamine (Q)/asparagine (N) rich. These motifs are similar to the reported aggregation promoting regions found in prion and amyloidogenic proteins that are also rich in Q/N, aliphatic and aromatic residues. The implication is that one possible mechanism for aggregation of mAbs may be through formation of cross-? structures and fibrils. Mapping on the available Fab—receptor/antigen complex structures reveals that these motifs in CDRs might also contribute significantly towards receptor/antigen binding. Our analysis identifies the opportunity and tools for simultaneous optimization of the therapeutic protein sequence for potency and specificity while reducing vulnerability towards aggregation.

Wang, Xiaoling; Das, Tapan K; Singh, Satish K

2009-01-01

86

Systematic lossy forward error protection for error-resilient digital video broadcasting  

Microsoft Academic Search

We present a novel scheme for error-resilient digital video broadcasting,using the Wyner-Ziv coding paradigm. We apply the general framework of systematic lossy source-channel coding to generate a supplementary bitstream that can correct transmission errors in the decoded video waveform up to a certain residual distortion. The systematic portion consists of a conventional MPEG-coded bitstream, which is transmitted over the error-prone

Shantanu D. Rane; Anne Aaron; Bernd Girod

2004-01-01

87

Action simulation in hallucination-prone adolescents  

PubMed Central

Theoretical and empirical accounts suggest that impairments in self-other discrimination processes are likely to promote the expression of hallucinations. Studies using a variety of paradigms involving self-performed actions argue in favor of perspective taking confusion in hallucination-prone subjects. However, our understanding of such processes during adolescence is still at an early stage. The present study thus aims (1) to delineate the neural correlates sustaining mental simulation of actions involving self-performed actions (first-person perspective; 1PP) and other-performed actions (third-person perspective; 3PP) during adolescence (2) to identify atypical activation patterns during 1PP/3PP mental simulation of actions in hallucination-prone adolescents (3) to examine whether differential risk for schizophrenia (clinical vs. genetic) is also associated with differential impairments in the 1PP/3PP mental simulation of actions during adolescence. Twenty-two typically developing controls (Control group; 6 females), 12 hallucination-prone adolescents [auditory hallucination (AH) group; 7 females] and 13 adolescents with 22q11.2 Deletion Syndrome (22q11.2DS group; 4 females) were included in the study. During the fMRI task, subjects were presented with a cue (self-other priming cues) indicating to perform the task using either a first person perspective (“you”-1PP) or a third person perspective (“best friend”-3PP) and then they were asked to mentally simulate actions based on the type of cue. Hallucination-proneness was assessed using a self-report questionnaire [Cardiff Anomalous Perception Scale (CAPS)]. Our results indicated that atypical patterns of cerebral activation, particularly in the key areas of self-other distinction, were found in both groups at risk for auditory hallucinations (AHs and 22q11.2DS). More precisely, adolescents in the AH group presented decreased activations in the right middle occipital gyrus BA19, left cingulate gyrus BA31, and right precuneus BA31 for the 3PP > 1PP contrast. Adolescents in the 22q11.2DS group presented decreased activations in the right superior occipital gyrus BA19, left caudate tail and left precuneus BA7 for the 3PP > 1PP contrast. In comparison to the Control group, only the 22q11.2DS adolescents showed a decreased activation for other-related cues (prime other > prime self contrast) in areas of visual imagery, episodic memory and social cognition. This study characterizes the neural correlates of mental imagery for actions during adolescence, and suggests that a differential risk for hallucination-proneness (clinical vs. genetic) is associated to similar patterns of atypical activations in key areas sustaining self-other discrimination processes. These observations may provide relevant information for future research and prevention strategies with regards to hallucination-proneness during adolescence.

Dahoun, Tarik; Eliez, Stephan; Chen, Fei; Badoud, Deborah; Schneider, Maude; Lar?i, Frank; Debbane, Martin

2013-01-01

88

Action simulation in hallucination-prone adolescents.  

PubMed

Theoretical and empirical accounts suggest that impairments in self-other discrimination processes are likely to promote the expression of hallucinations. Studies using a variety of paradigms involving self-performed actions argue in favor of perspective taking confusion in hallucination-prone subjects. However, our understanding of such processes during adolescence is still at an early stage. The present study thus aims (1) to delineate the neural correlates sustaining mental simulation of actions involving self-performed actions (first-person perspective; 1PP) and other-performed actions (third-person perspective; 3PP) during adolescence (2) to identify atypical activation patterns during 1PP/3PP mental simulation of actions in hallucination-prone adolescents (3) to examine whether differential risk for schizophrenia (clinical vs. genetic) is also associated with differential impairments in the 1PP/3PP mental simulation of actions during adolescence. Twenty-two typically developing controls (Control group; 6 females), 12 hallucination-prone adolescents [auditory hallucination (AH) group; 7 females] and 13 adolescents with 22q11.2 Deletion Syndrome (22q11.2DS group; 4 females) were included in the study. During the fMRI task, subjects were presented with a cue (self-other priming cues) indicating to perform the task using either a first person perspective ("you"-1PP) or a third person perspective ("best friend"-3PP) and then they were asked to mentally simulate actions based on the type of cue. Hallucination-proneness was assessed using a self-report questionnaire [Cardiff Anomalous Perception Scale (CAPS)]. Our results indicated that atypical patterns of cerebral activation, particularly in the key areas of self-other distinction, were found in both groups at risk for auditory hallucinations (AHs and 22q11.2DS). More precisely, adolescents in the AH group presented decreased activations in the right middle occipital gyrus BA19, left cingulate gyrus BA31, and right precuneus BA31 for the 3PP > 1PP contrast. Adolescents in the 22q11.2DS group presented decreased activations in the right superior occipital gyrus BA19, left caudate tail and left precuneus BA7 for the 3PP > 1PP contrast. In comparison to the Control group, only the 22q11.2DS adolescents showed a decreased activation for other-related cues (prime other > prime self contrast) in areas of visual imagery, episodic memory and social cognition. This study characterizes the neural correlates of mental imagery for actions during adolescence, and suggests that a differential risk for hallucination-proneness (clinical vs. genetic) is associated to similar patterns of atypical activations in key areas sustaining self-other discrimination processes. These observations may provide relevant information for future research and prevention strategies with regards to hallucination-proneness during adolescence. PMID:23847502

Dahoun, Tarik; Eliez, Stephan; Chen, Fei; Badoud, Deborah; Schneider, Maude; Larøi, Frank; Debbane, Martin

2013-01-01

89

Sampling Error  

NSDL National Science Digital Library

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

2009-01-07

90

Digital PCR  

Microsoft Academic Search

The identification of predefined mutations expected to be present in a minor fraction of a cell population is important for a variety of basic research and clinical applications. Here, we describe an approach for transforming the exponential, analog nature of the PCR into a linear, digital signal suitable for this purpose. Single molecules are isolated by dilution and individually amplified

Bert Vogelstein; Kenneth W. Kinzler

1999-01-01

91

New fire-prone areas in Europe  

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

92

Temporal error concealment for MPEG coded video using a self-organizing map  

Microsoft Academic Search

The performance of MPEG video transmission over error-prone channels is limited by the channel noise. An efficient error concealment (EC) scheme is essential for diminishing the impact of transmission errors in a compressed video, A number of EC techniques have been developed to combat the transmission errors. However, the previous techniques are always inefficient when the motions of video object

Yu-Len Huang; Hsiu-Yi Lien

2006-01-01

93

INCORPORATING INHERENT MAP ERROR INTO FLOOD-HAZARD ANALYSIS  

Microsoft Academic Search

Maps are an important source of data for planning and land use analysis of flood-prone areas. Map users with inadequate training are not aware that map errors can lead to ineffective decisions. Although inherent errors introduced by transformation, map construction, and symbolization are never identified on maps, they limit the effectiveness of maps as sources of data. Additional vertical and

John D. Vitek; Donald G. Richards

1978-01-01

94

PCR thermocycler  

DOEpatents

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.

Benett, William J. (Livermore, CA); Richards, James B. (Danville, CA)

2003-01-01

95

Delusion-prone individuals: stuck in their ways?  

PubMed

Although false memories and confabulation have been linked to both executive dysfunction and greater suggestibility, similar associations with the emergence of delusional thinking remain unexamined. We therefore compared healthy individuals who scored high and low on the Peters Delusional Inventory (PDI: Peters et al., 1999) on measures of set-shifting (the intra-extradimensional set shift task: IED) planning (the Stockings of Cambridge Task: SOC). Additionally, we examined whether high delusion-prone individuals show greater suggestibility on the Gudjonsson Suggestibility Scale (GSS 2: Gudjonsson, 1987). On the IED task, the high group made more pre-extradimensional shift errors than the low PDI group, and this was especially notable for reversal learning. By contrast, no differences emerged on any aspect of the SOC. Finally, and intriguingly, the high PDI group was less likely than the low PDI group to change their responses after receiving suggestive negative feedback. We propose that delusional-style thinking may be underpinned by an orbitofrontal-based reversal learning difficulty affecting the flexibility to adapt responses to changing contingencies and external pressure. PMID:21035195

Laws, Keith Richard; Kondel, Tejinder Kaur; Clarke, Richard; Nillo, Anne-Marie

2011-04-30

96

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 ...

97

FANTASY PRONENESS AND OTHER PSYCHOLOGICAL CORRELATES OF UFO EXPERIENCE  

Microsoft Academic Search

This study examined the psychological variables that underpin the reporting of UFO (unidentified flying objects) experiences of 198 subjects (155 controls, 19 UFO sightees, 12 UFO contactees, and 12 UFO abductees). Findings demonstrate that reporting of UFO experiences is related to heightened levels of fantasy proneness and paranormal belief and that the relationship between fantasy proneness and UFO experiences is

Kathryn Gow; Janine Lurie; Stuart Coppin; Ari Popper; Anthony Powell; Keith Basterfield

98

Pathogenesis of A??+ Ketosis-Prone Diabetes  

PubMed Central

A??+ ketosis-prone diabetes (KPD) is an emerging syndrome of obesity, unprovoked ketoacidosis, reversible ?-cell dysfunction, and near-normoglycemic remission. We combined metabolomics with targeted kinetic measurements to investigate its pathophysiology. Fasting plasma fatty acids, acylcarnitines, and amino acids were quantified in 20 KPD patients compared with 19 nondiabetic control subjects. Unique signatures in KPD—higher glutamate but lower glutamine and citrulline concentrations, increased ?-hydroxybutyryl-carnitine, decreased isovaleryl-carnitine (a leucine catabolite), and decreased tricarboxylic acid (TCA) cycle intermediates—generated hypotheses that were tested through stable isotope/mass spectrometry protocols in nine new-onset, stable KPD patients compared with seven nondiabetic control subjects. Free fatty acid flux and acetyl CoA flux and oxidation were similar, but KPD had slower acetyl CoA conversion to ?-hydroxybutyrate; higher fasting ?-hydroxybutyrate concentration; slower ?-hydroxybutyrate oxidation; faster leucine oxidative decarboxylation; accelerated glutamine conversion to glutamate without increase in glutamate carbon oxidation; and slower citrulline flux, with diminished glutamine amide–nitrogen transfer to citrulline. The confluence of metabolomic and kinetic data indicate a distinctive pathogenic sequence: impaired ketone oxidation and fatty acid utilization for energy, leading to accelerated leucine catabolism and transamination of ?-ketoglutarate to glutamate, with impaired TCA anaplerosis of glutamate carbon. They highlight a novel process of defective energy production and ketosis in A??+ KPD.

Patel, Sanjeet G.; Hsu, Jean W.; Jahoor, Farook; Coraza, Ivonne; Bain, James R.; Stevens, Robert D.; Iyer, Dinakar; Nalini, Ramaswami; Ozer, Kerem; Hampe, Christiane S.; Newgard, Christopher B.; Balasubramanyam, Ashok

2013-01-01

99

Syndromes of Ketosis-Prone Diabetes Mellitus  

PubMed Central

Ketosis-prone diabetes (KPD) is a widespread, emerging, heterogeneous syndrome characterized by patients who present with diabetic ketoacidosis or unprovoked ketosis but do not necessarily have the typical phenotype of autoimmune type 1 diabetes. Multiple, severe forms of ?-cell dysfunction appear to underlie the pathophysiology of KPD. Until recently, the syndrome has lacked an accurate, clinically relevant and etiologically useful classification scheme. We have utilized a large, longitudinally followed, heterogeneous, multiethnic cohort of KPD patients to identify four clinically and pathophysiologically distinct subgroups that are separable by the presence or absence of ?-cell autoimmunity and the presence or absence of ?-cell functional reserve. The resulting “A?” classification system of KPD has proven to be highly accurate and predictive of such clinically important outcomes as glycemic control and insulin dependence, as well as an aid to biochemical and molecular investigations into novel causes of ?-cell dysfunction. In this review, we describe the current state of knowledge in regard to the natural history, pathophysiology, and treatment of the subgroups of KPD, with an emphasis on recent advances in understanding their immunological and genetic bases.

Balasubramanyam, Ashok; Nalini, Ramaswami; Hampe, Christiane S.; Maldonado, Mario

2008-01-01

100

Modified prone position to dissect the popliteal fossa  

PubMed Central

Introduction Traditionally, the prone position is used for dissecting the popliteal fossa, which requires endotracheal intubation. Access to the airway in this position is limited, hence the complications. It is not surprising that the prone position is not favoured by the anaesthetists, especially in patients with a high body mass index. We describe a safe and novel alternative to the prone position. Methods The modified prone position (MPP) is described as an alternative position that facilitates access to the airway. Results Between October 2007 and May 2010, 12 patients underwent popliteal fossa dissection using the MPP. All patients had general anaesthesia using a laryngeal mask airway with the exception of one, who had an epidural anaesthesia. There were no airway or haemodynamic complications. The surgical access to the popliteal fossa was as good as with the traditional prone position. Conclusions The MPP was satisfactory for both the surgeon and the anaesthetists. The authors now use this position routinely for dissecting the popliteal fossa.

Boulemden, A; Ritzmann, T; Liptrot, S; Abbas, A

2013-01-01

101

Total genome polymorphism and low frequency of intra-genomic variation in the uspA1 and uspA2 genes of Moraxella catarrhalis in otitis prone and non-prone children up to 2 years of age. Consequences for vaccine design?  

PubMed

Intra-genomic variation in the uspA1 and uspA2 genes of Moraxella catarrhalis was studied using pulsed field gel electrophoresis (PFGE) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. From a set of 91 M. catarrhalis isolates, 19 pairs of PFGE identical isolates were found. Five pairs originated from otitis non-prone children, 11 pairs from otitis prone children and for 3 pairs, one of the pair originated from an otitis prone and the other from an otitis non-prone child. No particular M. catarrhalis isolate was associated with either the otitis prone or non-prone children. One of these 19 pairs of isolates was found to exhibit both uspA1 and uspA2 intra-genomic variation, whilst another pair exhibited uspA2 intra-genomic variation only. Sequence data obtained from these variants showed that PCR-RFLP pattern differences reflected actual changes in predicted amino acid composition and that minor amino acid changes in a 23 base pair "NINNIY" repeat region (a conserved UspA1 and UspA2 binding site for the neutralising antibody mAb17C7) occurred. Variation in the uspA2 5' non-coding "AGAT" repeat region was also observed. These results may have implications for future M. catarrhalis vaccines comprising UspA1 or UspA2 components. PMID:12559789

Hays, John P; van der Schee, Cindy; Loogman, Anita; Eadie, Kim; Verduin, Cees; Faden, Howard; Verbrugh, Henri; van Belkum, Alex

2003-03-01

102

Controlling misdiagnosis errors in preimplantation genetic diagnosis: a comprehensive model encompassing extrinsic and intrinsic sources of error  

Microsoft Academic Search

We have developed a mathematical model to explore accuracy of preimplantation genetic diagnosis (PGD) using single cell polymerase chain reaction (PCR). The model encompasses both extrinsic technical errors and intrinsic errors related to nuclear and chromosomal abnormalities. Using estimates for these errors, we have calculated the probability of a serious error (affected embryo diagnosed as unaffected) using a variety of

C. M. Lewis; T. Pinel; J. C. Whittaker; A. H. Handyside

2001-01-01

103

Systematic lossy forward error protection for error-resilient digital video broadcasting  

NASA Astrophysics Data System (ADS)

We present a novel scheme for error-resilient digital video broadcasting,using the Wyner-Ziv coding paradigm. We apply the general framework of systematic lossy source-channel coding to generate a supplementary bitstream that can correct transmission errors in the decoded video waveform up to a certain residual distortion. The systematic portion consists of a conventional MPEG-coded bitstream, which is transmitted over the error-prone channel without forward error correction.The supplementary bitstream is a low rate representation of the transmitted video sequence generated using Wyner-Ziv encoding. We use the conventionally decoded error-concealed MPEG video sequence as side information to decode the Wyner-Ziv bits. The decoder combines the error-prone side information and the Wyner-Ziv description to yield an improved decoded video signal. Our results indicate that, over a large range of channel error probabilities, this scheme yields superior video quality when compared with traditional forward error correction techniques employed in digital video broadcasting.

Rane, Shantanu D.; Aaron, Anne; Girod, Bernd

2004-01-01

104

Automatic Error Correction of Java Programs  

NASA Astrophysics Data System (ADS)

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

Kern, Christian; Esparza, Javier

105

Refractive Errors  

MedlinePLUS

... Errors En Español How does the eye focus light? In order to see clearly, light rays from an object must focus onto the ... a focusing lens inside (crystalline lens), and a light-sensing portion at the back (the retina). If ...

106

Discovering motifs that induce sequencing errors  

PubMed Central

Background Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS). Beyond routinely handled generic sources of errors, certain base calling errors relate to specific sequence patterns. Statistically principled ways to associate sequence patterns with base calling errors have not been previously described. Extant approaches either incur decisive losses in power, due to relating errors with individual genomic positions rather than motifs, or do not properly distinguish between motif-induced and sequence-unspecific sources of errors. Results Here, for the first time, we describe a statistically rigorous framework for the discovery of motifs that induce sequencing errors. We apply our method to several datasets from Illumina GA IIx, HiSeq 2000, and MiSeq sequencers. We confirm previously known error-causing sequence contexts and report new more specific ones. Conclusions Checking for error-inducing motifs should be included into SNP calling pipelines to avoid false positives. To facilitate filtering of sets of putative SNPs, we provide tracks of error-prone genomic positions (in BED format). Availability http://discovering-cse.googlecode.com

2013-01-01

107

MultiPriDe: automated batch development of quantitative real-time PCR primers  

PubMed Central

Quantitative reverse transcriptase polymerase chain reaction (qRT–PCR) is a commonly employed gene expression quantification technique. This requires the development of appropriately targeted oligonucleotide primers, which necessitates the identification of ideal amplicons, development of optimized oligonucleotide sequences under most favorable pre-determined reaction conditions, and management of the resultant target-oligonucleotide pair information for each gene to be studied. The Primer3 utility exists for development of oligonucleotide primers and fills that role effectively. However, the manual process of identifying target sites and individually generating primers is inefficient and prone to user-introduced error, especially when a large number of genes are to be examined. We have developed MultiPriDe (Multiple Primer Design), a Perl utility that accepts batch lists of Gene database identifiers, collects available intron and exon position data critical to qRT–PCR primer development, and supplies these sites as identified targets for the Primer3 utility. This automated ‘gene to primer’ procedure is coupled with a set of optimized hybridization conditions used by the Primer3 utility to maximize successful primer design. MultiPriDe and assembled repeat libraries are available upon request. Please direct requests to aziesel@emory.edu.

Ziesel, A. C.; Chrenek, M. A.; Wong, P. W.

2008-01-01

108

Correlates of prone infant sleeping position by period of birth.  

PubMed

Intervention to avoid the prone sleeping position during infancy has occurred in various countries after evidence that it increases the risk of sudden infant death syndrome (SIDS). This study examined cohort data to determine if correlates of the prone position differed by period of birth, before intervention (1 May 1988 to 30 April 1991) compared with after intervention (1 May 1991 to 30 April 1992). The usual prone sleeping position was more closely associated with the following factors after intervention: teenage motherhood, low maternal education, paternal unemployment, unmarried motherhood, non-specialist antenatal care, not reading books to prepare for a baby, poor smoking hygiene, and bottle feeding. For example, the association of usual prone position with being unmarried shown by the odds ratio (95% confidence interval) was 0.54 (0.47 to 0.63) in the period before intervention and 1.92 (1.18 to 3.15) in the period after intervention. The alteration in correlates of the prone position reported here provide an example to support the theoretical concept that well known 'modifiable' risk factors for disease tend to be associated with each other in both populations and individuals. This phenomenon was not evident in the population before intervention, that is, before the prone sleeping position became a well known SIDS risk factor. PMID:7741564

Ponsonby, A L; Dwyer, T; Kasl, S V; Couper, D; Cochrane, J A

1995-03-01

109

The Fanconi Anaemia Gene FANCC Promotes Homologous Recombination and Error-Prone DNA Repair  

Microsoft Academic Search

The Fanconi anemia (FA) protein FANCC is essential for chromosome stability in vertebrate cells, a feature underscored by the extreme sensitivity of FANCC-deficient cells to agents that crosslink DNA. However, it is not known how this FA protein facilitates the repair of both endogenously acquired and mutagen-induced DNA damage. Here, we use the model vertebrate cell line DT40 to address

Wojciech Niedzwiedz; Georgina Mosedale; Mark Johnson; Chong Yi Ong; Paul Pace; Ketan J. Patel

2004-01-01

110

Inducible Error-Prone Repair in Bacillus Subtilis. Progress Report, May 1, 1985-April 30, 1986.  

National Technical Information Service (NTIS)

DNA damage-inducible star operon fusions were generated in B. subtilis by transpositional mutagenesis. These fusion isolates produce increased beta-galactosidase when exposed to mitomycin C, uv radiation, or ethyl methanesulfonate, indicating that the lac...

R. E. Yasbin

1986-01-01

111

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

PubMed Central

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.

Zhu, Catherine; Hsu, Ellen

2010-01-01

112

Error-prone initiation factor 2 mutations reduce the fitness cost of antibiotic resistance.  

PubMed

Mutations in the fmt gene (encoding formyl methionine transferase) that eliminate formylation of initiator tRNA (Met-tRNA(i)) confer resistance to the novel antibiotic class of peptide deformylase inhibitors (PDFIs) while concomitantly reducing bacterial fitness. Here we show in Salmonella typhimurium that novel mutations in initiation factor 2 (IF2) located outside the initiator tRNA binding domain can partly restore fitness of fmt mutants without loss of antibiotic resistance. Analysis of initiation of protein synthesis in vitro showed that with non-formylated Met-tRNA(i) IF2 mutants initiated much faster than wild-type IF2, whereas with formylated fMet-tRNA(i) the initiation rates were similar. Moreover, the increase in initiation rates with Met-tRNA(i) conferred by IF2 mutations in vitro correlated well with the increase in growth rate conferred by the same mutations in vivo, suggesting that the mutations in IF2 compensate formylation deficiency by increasing the rate of in vivo initiation with Met-tRNA(i). IF2 mutants had also a high propensity for erroneous initiation with elongator tRNAs in vitro, which could account for their reduced fitness in vivo in a formylation-proficient strain. More generally, our results suggest that bacterial protein synthesis is mRNA-limited and that compensatory mutations in IF2 could increase the persistence of PDFI-resistant bacteria in clinical settings. PMID:20132454

Zorzet, Anna; Pavlov, Michael Y; Nilsson, Annika I; Ehrenberg, Måns; Andersson, Dan I

2010-03-01

113

DEM-based Approaches for the Identification of Flood Prone Areas  

NASA Astrophysics Data System (ADS)

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.

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

2013-04-01

114

Neighbourhood Effects on Error Rates in Speech Production  

ERIC Educational Resources Information Center

Models of speech production differ on whether phonological neighbourhoods should affect processing, and on whether effects should be facilitatory or inhibitory. Inhibitory effects of large neighbourhoods have been argued to underlie apparent anti-frequency effects, whereby high-frequency default features are more prone to mispronunciation errors

Stemberger, Joseph Paul

2004-01-01

115

Software errors and complexity: an empirical investigation0  

Microsoft Academic Search

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

Victor R. Basili; Barry T. Perricone

1984-01-01

116

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

Code of Federal Regulations, 2010 CFR

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

2010-10-01

117

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

Code of Federal Regulations, 2010 CFR

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

2009-10-01

118

Steroid sulfatase activity in epidermis of acne-prone and non-acne-prone skin of patients with acne vulgaris.  

PubMed

Abnormal keratinization of hair follicles appears to be intimately associated with acne vulgaris. Whether steroid metabolism in follicular wall keratinocytes of acne-prone skin plays a role in the development and maintenance of acne vulgaris is unknown at this time. The enzymatic hydrolysis of dehydroepiandrosterone sulfate to dehydroepiandrosterone and of estrone sulfate to estrone in cultured epidermal keratinocytes has been demonstrated. Thus, we sought to establish whether steroid sulfatase activity in freshly obtained epidermal tissue (greater than 90% keratinocytes) from acne-prone skin in patients with acne vulgaris was altered when compared with that in epidermal tissue from non-acne-prone skin in the same individuals. We found that there were no differences in the rates of enzymatic hydrolysis of steroid sulfates in epidermis of acne-prone and non-acne-prone skin; however, the rate of estrone sulfate hydrolysis was two to eight times greater than that of dehydroepiandrosterone sulfate in all of the tissues evaluated in this study. PMID:2145810

Milewich, L; Sontheimer, R D; Herndon, J H

1990-10-01

119

Hemispheric Asymmetries in the Activation and Monitoring of Memory Errors  

PubMed Central

Previous research on the lateralization of memory errors suggests that the right hemisphere’s tendency to produce more memory errors than the left hemisphere reflects hemispheric differences in semantic activation. However, all prior research that has examined the lateralization of memory errors has used self-paced recognition judgments. Because activation occurs early in memory retrieval, with more time to make a decision, other memory processes, like strategic monitoring processes, may affect memory errors. By manipulating the time subjects were given to make memory decisions, this study separated the influence of automatic memory processes (activation) from strategic memory processes (monitoring) on the production of false memories. The results indicated that when retrieval was fast, the right hemisphere produced more memory errors than the left hemisphere. However, when retrieval was slow, the left hemisphere’s error-proneness increased compared to the fast retrieval condition, while the right hemisphere’s error-proneness remained the same. These results suggest that the right hemisphere’s errors are largely due to activation, while the left hemisphere’s errors are influenced by both activation and monitoring.

Giammattei, Jeannette; Arndt, Jason

2012-01-01

120

Test effort optimization by prediction and ranking of fault-prone software modules  

Microsoft Academic Search

Identification of fault-prone or not fault-prone modules is very essential to improve the reliability and quality of a software system. Once modules are categorized as fault-prone or not fault-prone, test effort are allocated accordingly. Testing effort and efficiency are primary concern and can be optimized by prediction and ranking of fault-prone modules. This paper discusses a new model for prediction

Ajeet Kumar Pandey; Neeraj Kumar Goyal

2010-01-01

121

Video transmission technology with effective error protection and tough synchronization for wireless channels  

Microsoft Academic Search

Video transmission over error-prone mobile communication channels requires higher error resiliency than required in other channels. However, most video coding schemes utilize some form of variable length data structure in order to achieve high coding efficiency, and this can result in large drops in transmission quality in mobile channels due to loss of data structure synchronization or variable length code

Toshiro Kawahara; Satoru Adachi

1996-01-01

122

Comparison of Outlier Detection Methods in Fault-proneness Models  

Microsoft Academic Search

In this paper, we experimentally evaluated the effect of outlier detection methods to improve the prediction performance of fault-proneness models. Detected outliers were removed from a fit dataset before building a model. In the experiment, we compared three outlier detection methods (Mahalanobis outlier analysis (MOA), local outlier factor method (LOFM) and rule based modeling (RBM)) each applied to three well-known

Shinsuke MATSUMOTO; Yasutaka KAMEI; Akito MONDEN; Ken-ichi MATSUMOTO

2007-01-01

123

Comparison of Outlier Detection Methods in Fault-proneness Models  

Microsoft Academic Search

In this paper, we experimentally evaluated the effect of outlier detection methods to improve the prediction perfor- mance of fault-proneness models. Detected outliers were removed from a fit dataset before building a model. In the experiment, we compared three outlier detection methods (Mahalanobis outlier analysis (MOA), local outlier factor method (LOFM) and rule based modeling (RBM)) each ap- plied to

Shinsuke Matsumoto; Yasutaka Kamei; Akito Monden; Ken-ichi Matsumoto

2007-01-01

124

The Social Antecedents of Anger Proneness in Young Adulthood  

ERIC Educational Resources Information Center

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…

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

2007-01-01

125

Accident proneness among street car motormen and motor coach operators  

Microsoft Academic Search

The accident records of 59 trolley car motormen and 34 motor coach operators were studied over a period of 18 months. The correlation coefficients between various types of accidents are small. Therefore, the theory that accident proneness is a general trait of an individual is not substantiated since a high rate of accidents of one kind does not indicate necessarily

Clarence W. Brown; Edwin E. Ghiselli

1948-01-01

126

Managing fire-prone forests in the western United States  

Microsoft Academic Search

5 The management of fire-prone forests is one of the most controversial natural resource issues in the US today, particularly in the west of the country. Although vegetation and wildlife in these forests are adapted to fire, the historical range of fire frequency and severity was huge. When fire regimes are altered by human activity, major effects on biodiversity and

Reed F. Noss; Jerry F. Franklin; William L. Baker; Tania Schoennagel; Peter B. Moyle

2006-01-01

127

Using early stage project data to predict change-proneness  

Microsoft Academic Search

Several previous studies have suggested methods for predicting change-proneness based on software complexity metrics. We hypothesise that data from the early stages of a development project such as requirements and design could also be used to make such predictions. We define here a set of new metrics to capture data from the requirements and\\/or design stages, and derive values for

Claire Ingram; Steve Riddle

2012-01-01

128

Coronary-prone behavior pattern and interpersonal aggression  

Microsoft Academic Search

An overt behavior pattern called Type A has been implicated in the etiology of coronary heart disease. Pattern A is often characterized in terms of 3 components: competitive achievement striving, time urgency, and aggressiveness. The noncoronary-prone Pattern B is defined as the relative absence of Type A characteristics. Experimentation has shown that 2 of the components of Pattern A––achievement striving

Charles S. Carver; David C. Glass

1978-01-01

129

Stress, Symptom Proneness, and General Adaptational Distress During Pregnancy  

Microsoft Academic Search

Symptom proneness (SP), the 20 psychiatric items of the Cornell Medical Index, here called the Cornell Psychiatric Items (CPI), and a test developed partially from the Schedule of Recent Experiences called the Utah Stress Scales (STRESS) were used to predict general adaptational distress (GAD) symptoms during pregnancy on a sample of 1306 primigravidas. The causal model explored in seven path

Nancy Fagley; Paul Miller; John Sullivan

1982-01-01

130

Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications  

PubMed Central

Quantitative real-time PCR has revolutionized many aspects of genetic research, biomedical diagnostics and pathogen detection. Nevertheless, the full potential of this technology has yet to be realized, primarily due to the limitations of the threshold-based methodologies that are currently used for quantitative analysis. Prone to errors caused by variations in reaction preparation and amplification conditions, these approaches necessitate construction of standard curves for each target sequence, significantly limiting the development of high-throughput applications that demand substantive levels of reliability and automation. In this study, an alternative approach based upon fitting of fluorescence data to a four-parametric sigmoid function is shown to dramatically increase both the utility and reliability of quantitative real-time PCR. By mathematically modeling individual amplification reactions, quantification can be achieved without the use of standard curves and without prior knowledge of amplification efficiency. Combined with provision of quantitative scale via optical calibration, sigmoidal curve-fitting could confer the capability for fully automated quantification of nucleic acids with unparalleled accuracy and reliability.

Rutledge, R. G.

2004-01-01

131

Development and application of a PCR diagnostic assay for the accurate and rapid identification of the nematophagous fungus Duddingtonia flagrans.  

PubMed

The nematophagous fungus, Duddingtonia flagrans is a potential biocontrol agent against nematode parasites of ruminants. Improved methods for the rapid and accurate detection of D. flagrans would aid the evaluation of this fungus as a biocontrol agent and its suitability for environmental release. To date, detection and identification of D. flagrans is reliant on morphological methods, which can be laborious, time-consuming, and error prone. In this study, a PCR assay using species-specific primers located in the ITS regions was developed for the rapid and accurate identification of D. flagrans. The PCR assay was specific to five different isolates of D. flagrans and was capable of detecting a minimum concentration of 100 chlamydospores per gram of soil. In contrast to cultured-based detection and identification methods, this assay is amenable to high throughput screening of environmental samples. The assay detected D. flagrans in faecal, leaf litter, and soil samples collected from 80% of the Irish farms tested indicating that the fungus is abundant in Ireland. PMID:18692372

Kelly, Paula; Good, Barbara; Fitzpatrick, Richard; Hanrahan, J P; de Waal, Theo D T

2008-09-01

132

A PCR Based Protocol for Detecting Indel Mutations Induced by TALENs and CRISPR/Cas9 in Zebrafish  

PubMed Central

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

Yao, Shaohua; Wei, Yuquan

2014-01-01

133

The pathophysiology of medication errors: how and where they arise  

PubMed Central

Errors arise when an action is intended but not performed; errors that arise from poor planning or inadequate knowledge are characterized as mistakes; those that arise from imperfect execution of well-formulated plans are called slips when an erroneous act is committed and lapses when a correct act is omitted. Some tasks are intrinsically prone to error. Examples are tasks that are unfamiliar to the operator or performed under pressure. Tasks that require the calculation of a dosage or dilution are especially susceptible to error. The tasks of prescribing, preparation, and administration of medicines are complex, and are carried out within a complex system; errors can occur at each of many steps and the error rate for the overall process is therefore high. The error rate increases when health-care professionals are inexperienced, inattentive, rushed, distracted, fatigued, or depressed; orthopaedic surgeons and nurses may be more likely than other health-care professionals to make medication errors. Medication error rates in hospital are higher in paediatric departments and intensive care units than elsewhere. Rates of medication errors may be higher in very young or very old patients. Intravenous antibiotics are the drugs most commonly involved in medication errors in hospital; antiplatelet agents, diuretics, and non-steroidal anti-inflammatory drugs are most likely to account for ‘preventable admissions’. Computers effectively reduce the rates of easily counted errors. It is not clear whether they can save lives lost through rare but dangerous errors in the medication process.

McDowell, Sarah E; Ferner, Harriet S; Ferner, Robin E

2009-01-01

134

Patient safety & post-analytical error.  

PubMed

Post-analytical laboratory processes have been considered to be less prone to error than preanalytical processes because of the widespread adoption of laboratory automation and interfaced laboratory reporting. Quality monitors and controls for the post-analytical process have focused on critical result notification, meeting established turnaround time goals, and review of changed reports. The rapid increase in the adoption of electronic health records has created a new role for laboratory professionals in the management of patient test results. Laboratory professionals must interface with the clinical side of the health care team in establishing quality control for post-analytical processes, particularly in high-risk transitions of care. PMID:23331737

Walz, Stacy E; Darcy, Teresa P

2013-03-01

135

Systematic lossy error protection versus layered coding with unequal error protection  

NASA Astrophysics Data System (ADS)

In this paper we compare two schemes for error-resilient video transmission, viz., systematic lossy error protection, and scalable coding with unequal error protection. In the first scheme, the systematic portion consists of the compressed video signal transmitted without channel coding. For error-resilience, an additional bitstream generated by Wyner-Ziv encoding of the video signal is transmitted. In the event of channel errors, the Wyner-Ziv description is decoded using the error-prone systematic description as side-information. In the second scheme, the video bitstream is partitioned into two or more layers, and each layer is assigned different amounts of parity information depending upon its relative significance. Since the base layer has heavy protection, a certain minimum video quality is guaranteed at the receiver. We compare experimentally, the performance of the competing schemes, for a particular application, i.e., Error-resilient digital video broadcasting. It is shown that systematic lossy error protection ensures graceful degradation of video quality without incurring the loss in rate-distortion performance characteristic of practical layered video coding schemes.

Rane, Shantanu D.; Girod, Bernd

2005-03-01

136

Sun compass error model  

NASA Technical Reports Server (NTRS)

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.

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

1971-01-01

137

Single error correction and errors detection system  

NASA Astrophysics Data System (ADS)

A system for correcting single bit error and detecting burst errors is provided. A check bit generator generates partition check bits and burst check bits based on a H-parity matrix data regeneration scheme which provides an error correction and multiple bit error detection code which is linear and has the property of mutual orthogonality within a subclass of mutually orthogonal codes exclusive of Latin square codes. These check bits provide two independent sources for ascertaining the correct value for any given data bit. An error corrector and detector takes as input the data bits and check bits and provides a corrected data bit output as well as a set of error status lines. The error corrector and detector consists of error corrector, error corrector/detector, and error status modules. The error corrector and error corrector/detector modules run in parallel providing a high speed error correction and detection implementation, and providing a simplicity of logic structure compatible with application specific integrated circuit (ASIC) design and production processes.

Williams, Everett L.; Lo, Jien

1993-11-01

138

Error resilient macroblock rate control for H.264\\/AVC video coding  

Microsoft Academic Search

In this paper, an error resilient rate control scheme for the H.264\\/AVC standard is proposed. This scheme differs from traditional rate control schemes in that macroblock mode decisions are not made only to minimize their rate-distortion cost, but also take into account that the bitstream will have to be transmitted through an error-prone network. Since channel errors will probably occur,

Paulo Nunes; Luis Ducla Soares; Fernando Pereira

2008-01-01

139

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

PubMed

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. ? 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 ? cell function. PMID:23302548

Vaibhav, Atul; Mathai, Mathew; Gorman, Shaun

2013-01-01

140

A general anxiety-prone cognitive style in anxiety disorders  

Microsoft Academic Search

Objective: This study compared scores on the Anxious Thoughts & Tendencies (AT&T) questionnaire, a putative measure of a general anxiety-prone cognitive style, among patients with panic disorder without agoraphobia (PD, n=62), panic disorder with agoraphobia (PDA, n=29), generalized anxiety disorder (GAD, n=43), limited social phobia (LSP, n=34), generalized social phobia (GSP, n=33), and community residents (n=319). Method: Candidates for treatment

E. H Uhlenhuth; Vladan Starcevic; Teddy D Warner; William Matuzas; Teresita McCarty; Brian Roberts; Steven Jenkusky

2002-01-01

141

A General Software Defect-Proneness Prediction Framework  

Microsoft Academic Search

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

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

2011-01-01

142

Predicting Fault-Prone Modules: A Comparative Study  

Microsoft Academic Search

Offshore and outsourced software development is a rapidly increasing trend in global software business environment. Predicting\\u000a fault-prone modules in outsourced software product may allow both parties to establish mutually satisfactory, cost-effective\\u000a testing strategies and product acceptance criteria, especially in iterative transitions. In this paper, based on industrial\\u000a software releases data, we conduct an empirical study to compare ten classifiers over

Hao Jia; Fengdi Shu; Ye Yang; Qing Wang

2009-01-01

143

Melatonin improves inflammation processes in liver of senescence-accelerated prone male mice (SAMP8).  

PubMed

Aging is associated with an increase in oxidative stress and inflammation. The aim of this study was to investigate the effect of aging on various physiological parameters related to inflammation in livers obtained from two types of male mice models: Senescence-accelerated prone (SAMP8) and senescence-accelerated-resistant (SAMR1) mice, and to study the influence of the administration of melatonin (1mg/kg/day) for one month on old SAMP8 mice on these parameters. The parameters studied have been the mRNA expression of TNF-?, iNOS, IL-1?, HO-1, HO-2, MCP1, NFkB1, NFkB2, NFkB protein or NKAP and IL-10. All have been measured by real-time reverse transcription polymerase chain reaction RT-PCR. Furthermore we analyzed the protein expression of TNF-?, iNOS, IL-1?, HO-1, HO-2, and IL-10 by Western-blot. Aging increased oxidative stress and inflammation especially in the liver of SAMP8 mice. Treatment with melatonin decreased the mRNA expression of TNF-?, IL-1?, HO (HO-1 and HO-2), iNOS, MCP1, NF?B1, NF?B2 and NKAP in old male mice. The protein expression of TNF-?, IL-1? was also decreased and IL-10 increased with melatonin treatment and no significant differences were observed in the rest of parameters analyzed. The present study showed that aging was related to inflammation in livers obtained from old male senescence prone mice (SAMP8) and old male senescence resistant mice (SAMR1) being the alterations more evident in the former. Exogenous administration of melatonin was able to reduce inflammation. PMID:20817086

Cuesta, Sara; Kireev, Roman; Forman, Katherine; García, Cruz; Escames, Germaine; Ariznavarreta, Carmen; Vara, Elena; Tresguerres, Jesús A F

2010-12-01

144

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

Code of Federal Regulations, 2013 CFR

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

2013-10-01

145

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

Code of Federal Regulations, 2010 CFR

... false Planning considerations for flood-prone areas. 60.22 Section...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

2009-10-01

146

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

Code of Federal Regulations, 2013 CFR

... false Planning considerations for flood-prone areas. 60.22 Section...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

2013-10-01

147

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

Code of Federal Regulations, 2010 CFR

... false Planning considerations for flood-prone areas. 60.22 Section...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

2010-10-01

148

Dynamic stability differences in fall-prone and healthy adults  

PubMed Central

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.

Granata, Kevin P.; Lockhart, Thurmon E.

2010-01-01

149

Single Error Correction and Errors Detection System.  

National Technical Information Service (NTIS)

A system for correcting single bit error and detecting burst errors is provided. A check bit generator generates partition check bits and burst check bits based on a H-parity matrix data regeneration scheme which provides an error correction and multiple ...

E. L. Williams J. Lo

1993-01-01

150

Uncertainties and Error Propagation  

NSDL National Science Digital Library

This item is a tutorial on Uncertainties and Error Propagation. Topics covered include Systematic versus Random Error, Determining Random Errors, Relative and Absolute error, Propagation of errors, Rounding answers properly, and Significant figures. A list of well illustrated problems are embedded throughout the tutorial.

Lindberg, Vern

2008-07-22

151

Use of the prone oblique position in surgery for posterior fossa lesions  

Microsoft Academic Search

Summary Background. The lateral suboccipital approach has been conventionally performed with the lateral, park-bench, or sitting position and the midline suboccipital approach has been performed in the prone position. We attempt to show the advantages of the prone oblique position in the surgery for posterior fossa lesions. Methods. Twenty-two patients with posterior fossa lesions underwent surgery in the prone oblique

K.-I. Kikuta; S. Miyamoto; H. Kataoka; T. Satow; K. Yamada; N. Hashimoto

2004-01-01

152

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

ERIC Educational Resources Information Center

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

Calamari, Elena; Pini, Mauro

2003-01-01

153

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 ...

154

Computing chronodisruption: how to avoid potential chronobiological errors in epidemiological studies of shift work and cancer.  

PubMed

We ask if epidemiological studies into shift work and cancer may be prone to chronobiological errors. We illustrate how ignoring internal time (IT), or chronotype, may lead to what we call IT errors. Errors from truncating relevant external time (ET) information (activities start before and do not end with the shift) we call ET errors. We develop how observational research may avoid potential chronobiological biases and how chronodisruption can be computed. We assess how IT and ET errors may have affected studies published so far with a focus on those that considered chronobiological information but were confined to night work. PMID:24417520

Erren, Thomas C; Morfeld, Peter

2014-05-01

155

Structural inference in transition measurement error models for longitudinal data.  

PubMed

We propose a new class of models, transition measurement error models, to study the effects of covariates and the past responses on the current response in longitudinal studies when one of the covariates is measured with error. We show that the response variable conditional on the error-prone covariate follows a complex transition mixed effects model. The naive model obtained by ignoring the measurement error correctly specifies the transition part of the model, but misspecifies the covariate effect structure and ignores the random effects. We next study the asymptotic bias in naive estimator obtained by ignoring the measurement error for both continuous and discrete outcomes. We show that the naive estimator of the regression coefficient of the error-prone covariate is attenuated, while the naive estimators of the regression coefficients of the past responses are generally inflated. We then develop a structural modeling approach for parameter estimation using the maximum likelihood estimation method. In view of the multidimensional integration required by full maximum likelihood estimation, an EM algorithm is developed to calculate maximum likelihood estimators, in which Monte Carlo simulations are used to evaluate the conditional expectations in the E-step. We evaluate the performance of the proposed method through a simulation study and apply it to a longitudinal social support study for elderly women with heart disease. An additional simulation study shows that the Bayesian information criterion (BIC) performs well in choosing the correct transition orders of the models. PMID:16918904

Pan, Wenqin; Lin, Xihong; Zeng, Donglin

2006-06-01

156

Nicotine effects on affective response in depression-prone smokers  

Microsoft Academic Search

Rationale  Comorbidity between cigarette smoking and depression is thought to arise because depression-prone smokers self-administer\\u000a nicotine to improve mood. Yet little evidence supports this view, and nicotine’s effect on positive affect deficiency in depression\\u000a remains largely unstudied.\\u000a \\u000a \\u000a \\u000a Objectives  We hypothesized that (1) nicotine would dispel negative affect and enhance positive affect and (2) effects would be stronger\\u000a for smokers vulnerable to depression,

Bonnie Spring; Jessica Werth Cook; Bradley Appelhans; Anne Maloney; Malia Richmond; Jocelyn Vaughn; Joseph Vanderveen; Donald Hedeker

2008-01-01

157

Real-Time PCR  

NASA Astrophysics Data System (ADS)

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.

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

158

Learning From Performance Errors  

Microsoft Academic Search

A theory of how people detect and correct their own performance errors during skill practice is proposed. The basic principles of the theory are that errors are caused by overly general knowledge structures, that error detection requires domain-specific declarative knowledge, that errors are experienced as conflicts between what the learner believes ought to be true and what he or she

Stellan Ohlsson

1996-01-01

159

Errors in autobiographical memory  

Microsoft Academic Search

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

Ira E. Hyman; Elizabeth F. Loftus

1998-01-01

160

Towards error-free profiling of immune repertoires.  

PubMed

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

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

2014-06-01

161

When soft controls get slippery: User interfaces and human error  

SciTech Connect

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.

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

1998-12-01

162

Denoising PCR-amplified metagenome data  

PubMed Central

Background PCR amplification and high-throughput sequencing theoretically enable the characterization of the finest-scale diversity in natural microbial and viral populations, but each of these methods introduces random errors that are difficult to distinguish from genuine biological diversity. Several approaches have been proposed to denoise these data but lack either speed or accuracy. Results We introduce a new denoising algorithm that we call DADA (Divisive Amplicon Denoising Algorithm). Without training data, DADA infers both the sample genotypes and error parameters that produced a metagenome data set. We demonstrate performance on control data sequenced on Roche’s 454 platform, and compare the results to the most accurate denoising software currently available, AmpliconNoise. Conclusions DADA is more accurate and over an order of magnitude faster than AmpliconNoise. It eliminates the need for training data to establish error parameters, fully utilizes sequence-abundance information, and enables inclusion of context-dependent PCR error rates. It should be readily extensible to other sequencing platforms such as Illumina.

2012-01-01

163

Learning from prescribing errors  

PubMed Central

?? The importance of learning from medical error has recently received increasing emphasis. This paper focuses on prescribing errors and argues that, while learning from prescribing errors is a laudable goal, there are currently barriers that can prevent this occurring. Learning from errors can take place on an individual level, at a team level, and across an organisation. Barriers to learning from prescribing errors include the non-discovery of many prescribing errors, lack of feedback to the prescriber when errors are discovered by other healthcare professionals, and a culture that does not encourage reflection on errors together with why they occurred and how they can be prevented. Changes are needed in both systems and culture to provide an environment in which lessons can be learnt from errors and put into practice.

Dean, B

2002-01-01

164

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

NASA Technical Reports Server (NTRS)

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.

Hobbs, Alan; Williamson, Ann

2002-01-01

165

Field error lottery  

SciTech Connect

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.

Elliott, C.J.; McVey, B. (Los Alamos National Lab., NM (USA)); Quimby, D.C. (Spectra Technology, Inc., Bellevue, WA (USA))

1990-01-01

166

Dynein mutations impair autophagic clearance of aggregate-prone proteins.  

PubMed

Mutations that affect the dynein motor machinery are sufficient to cause motor neuron disease. It is not known why there are aggregates or inclusions in affected tissues in mice with such mutations and in most forms of human motor neuron disease. Here we identify a new mechanism of inclusion formation by showing that decreased dynein function impairs autophagic clearance of aggregate-prone proteins. We show that mutations of the dynein machinery enhanced the toxicity of the mutation that causes Huntington disease in fly and mouse models. Furthermore, loss of dynein function resulted in premature aggregate formation by mutant huntingtin and increased levels of the autophagosome marker LC3-II in both cell culture and mouse models, compatible with impaired autophagosome-lysosome fusion. PMID:15980862

Ravikumar, Brinda; Acevedo-Arozena, Abraham; Imarisio, Sara; Berger, Zdenek; Vacher, Coralie; O'Kane, Cahir J; Brown, Steve D M; Rubinsztein, David C

2005-07-01

167

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

ERIC Educational Resources Information Center

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

Shang, Yi

2012-01-01

168

Prone position during ECMO is safe and improves oxygenation.  

PubMed

Purpose: Combination of prone positioning (PrP) and extracorporeal membrane oxygenation (ECMO) might be beneficial in severe acute respiratory distress syndrome (ARDS), because both approaches are recommended. However, PrP during ECMO might be associated with complications such as dislocation of ECMO cannulae. We investigated complications and change of oxygenation effects of PrP during ECMO to identify "responders" and discuss our results considering different definitions of response in the literature.?Methods: Retrospective analysis of complications, gas exchange, and invasiveness of mechanical ventilation during first and second PrP on ECMO at specified time points (before, during, and after PrP). We used multivariate nonparametric analysis of longitudinal data (MANOVA) to compare changes of mechanical ventilation and hemodynamics associated with the first and second procedures.?Results: In 12 ECMO patients, 74 PrPs were performed (median ECMO duration: 10 days (IQR: 6.3-?15.5 days)). No dislocations of intravascular catheters/cannulae, endotracheal tubes or chest tubes were observed. Two PrPs had to be interrupted (endotracheal tube obstruction, acute pulmonary embolism). PaO2/FiO2-ratio increased associated with the first and second PrP (p = 0.002) and lasted after PrP in 58% of these turning procedures ("responders") without changes in ECMO blood flow, respiratory pressures, minute ventilation, portion of spontaneously triggered breathing, and compliance. Hemodynamics did not change with exception of increased mean pulmonary arterial pressure during PrP and decrease after PrP (p<0.001), while norepinephrine dosage decreased (p = 0.03) (MANOVA).?Conclusions: Prone position during ECMO is safe and improves oxygenation even after repositioning. This might ameliorate hypoxemia and reduce the harm from mechanical ventilation. PMID:24338657

Kipping, Valesca; Weber-Carstens, Steffen; Lojewski, Christian; Feldmann, Paul; Rydlewski, Antje; Boemke, Willehad; Spies, Claudia; Kastrup, Marc; Kaisers, Udo X; Wernecke, Klaus-D; Deja, Maria

2013-12-12

169

Behavioral Dependency Measurement for Change-Proneness Prediction in UML 2.0 Design Models  

Microsoft Academic Search

During the development and maintenance of object-oriented (OO) software, the information on the classes which are more prone to be changed is very useful. Developers and maintainers can make a more flexible software by modifying the part of classes which are sensitive to changes. Traditionally, most change-proneness prediction has been studied based on source codes. However, change-proneness prediction in the

Ah-rim Han; Sang-uk Jeon; Doo-hwan Bae; Jang-eui Hong

2008-01-01

170

An Integrated Approach to Detect Fault-Prone Modules Using Complexity and Text Feature Metrics  

Microsoft Academic Search

\\u000a Early detection of fault-prone products is necessary to assure the quality of software product. Therefore, fault-prone module\\u000a detection is one of the major and traditional area of software engineering. Although there are many approaches to detect fault-prone\\u000a modules, they have their own pros and cons. Consequently, it is recommended to use appropriate approach on the various situations.\\u000a This paper tries

Osamu Mizuno; Hideaki Hata

2010-01-01

171

Delay Constraint Error Control Protocol for Real-Time Video Communication  

Microsoft Academic Search

Real-time video communication over wireless channels is subject to information loss since wireless links are error-prone and susceptible to noise. Popular wireless link-layer protocols, such as retransmission (ARQ) based 802.11 and hybrid ARQ methods provide some level of reliability while largely ignoring the latency issue which is critical for real-time applications. Therefore, they suffer from low throughput (under high-error rates)

Sohraab Soltani; Kiran Misra; Hayder Radha

2009-01-01

172

A framework for H.264 with video enhancement components for minimizing errors and noise  

Microsoft Academic Search

Video transmission over error prone networks, such as the Internet and wireless networks, requires some methods of receiver-side video enhancement to achieve good quality. In this paper, we present a receiver-side video enhancement component to be augmented on the receiver (decoder) side to minimize errors and noise that exist in the received video. This component is characterized by using light-weight

Mohamed T. Faheem Saidahmd; A. Sarhan; R. O. Mahmoud

2010-01-01

173

Spatio-temporal video error concealment with perceptually optimized mode selection  

Microsoft Academic Search

We propose a spatio-temporal error concealment algorithm for video transmission in an error-prone environment. The proposed technique employs motion vector estimation, edge-preserving interpolation, and texture analysis\\/synthesis. It has two main advantages with respect to existing methods, namely: (i) it aims at optimizing the visual quality of the restored video, and not only PSNR; and (ii) it employs an automatic mode

S. Belfiore; M. Grangetto; E. Magli; G. Olmo

2003-01-01

174

The HUMAN Project: Model-Based Analysis of Human Errors During Aircraft Cockpit System Design  

Microsoft Academic Search

\\u000a The objective of the HUMAN project is to develop a methodology with techniques and prototypical tools supporting the prediction\\u000a of human errors in ways that are usable and practical for human-centred design of systems operating in complex cockpit environments.\\u000a The current approach of analysing systems is error prone as well as costly and time-consuming (based on engineering judgement,\\u000a operational feedback

Andreas Lüdtke; Denis Javaux

175

MOPITT Error 2012  

MOPITT Error 2012 Versions 3, 4, and 5; Levels 1 and 2 A small systematic error in the MOPITT geolocation values (latitude and longitude) has been ... overpasses do not appear to be biased. The longitudinal error is similar to the size of a single MOPITT field of view (~22 km). ...

2013-08-06

176

A theory of error  

Microsoft Academic Search

Ideas developed in A Theory of Error explore notions of art and corporality, and in particular art representing the brain and mechanisms of thought, reflections about exploring the creative process and considering thought when the brain is simulated through digital imaging.Using personal thought processes as a model, this project explores the creative process resulting from error. Error, not in the

Kellyann Geurts

2005-01-01

177

MS2 VLP-based delivery of microRNA-146a inhibits autoantibody production in lupus-prone mice  

PubMed Central

Background Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by the presence of pathogenic autoantibodies. Recent studies suggest that microRNAs (miRNAs) play an essential role in immunoregulation and may be involved in the pathogenesis of SLE. Therefore, it was of interest to investigate the potential therapeutic application of miRNAs in SLE, a concept that has not been thoroughly investigated thus far. Virus-like particles (VLPs) are a type of recombinant nanoparticle enveloped by certain proteins derived from the outer coat of a virus. Herein, we describe a novel miRNA-delivery approach via bacteriophage MS2 VLPs and investigate the therapeutic effects of miR-146a, a well-studied and SLE-related miRNA, in BXSB lupus-prone mice. Methods VLPs containing miR-146a, and the control VLPs, were prepared using an Escherichia coli expression system and then administered to lupus-prone mice over a 12-day period. We performed an enzyme-linked immunosorbent assay to evaluate the anti-dsDNA antibody, autoantibody to nuclear antigen (ANA), total IgG and total IgM levels in serum. The expression of miR-146a was analyzed by qRT-PCR. SLE-related cytokines as well as some toll-like receptor signaling pathway molecules were also measured. Results Treatment with MS2-miR146a VLP showed profound effects on lupus-prone BXSB mice, including an increased level of mature miR-146a, which led to a significant reduction in the expression of autoantibodies and total IgG. Remarkably, these mice also exhibited reduced levels of proinflammatorycytokines, including IFN-Interferon-? (IFN-?), Interleukin-1? (Il-1?) and Interleukin-6 (Il-6). Moreover, we showed that the toll-like receptor pathway was involved in this regulation. Conclusion Restoring the loss of miR-146a was effective in eliminating the production of autoantibodies and ameliorating SLE progression in lupus-prone mice. Thus, the induction of dysregulated miRNAs by an MS2 VLP-based delivery system may lead to novel therapies.

Pan, Yang; Jia, Tingting; Zhang, Yuan; Zhang, Kuo; Zhang, Rui; Li, Jinming; Wang, Lunan

2012-01-01

178

Absolute reliability of isokinetic knee flexion and extension measurements adopting a prone position.  

PubMed

The main purpose of this study was to determine the absolute and relative reliability of isokinetic peak torque (PT), angle of peak torque (APT), average power (PW) and total work (TW) for knee flexion and extension during concentric and eccentric actions measured in a prone position at 60, 180 and 240° s(-1). A total of 50 recreational athletes completed the study. PT, APT, PW and TW for concentric and eccentric knee extension and flexion were recorded at three different angular velocities (60, 180 and 240° s(-1)) on three different occasions with a 72- to 96-h rest interval between consecutive testing sessions. Absolute reliability was examined through typical percentage error (CV(TE)), percentage change in the mean (ChM) and relative reliability with intraclass correlations (ICC(3,1)). For both the knee extensor and flexor muscle groups, all strength data (except APT during knee flexion movements) demonstrated moderate absolute reliability (ChM < 3%; ICCs > 0·70; and CV(TE) < 20%) independent of the knee movement (flexion and extension), type of muscle action (concentric and eccentric) and angular velocity (60, 180 and 240° s(-1)). Therefore, the current study suggests that the CV(TE) values reported for PT (8-20%), APT (8-18%) (only during knee extension movements), PW (14-20%) and TW (12-28%) may be acceptable to detect the large changes usually observed after rehabilitation programmes, but not acceptable to examine the effect of preventative training programmes in healthy individuals. PMID:23216765

Ayala, F; De Ste Croix, M; Sainz de Baranda, P; Santonja, F

2013-01-01

179

In vitro adherence of radioactively labeled Escherichia coli in normal and cystitis-prone females.  

PubMed Central

Numerous investigators report data obtained using an in vitro quantitative assay for measuring bacterial adherence to epithelial cells. We found this assay to contain significant sources of error in the large variation in number of bacteria bound per cell and in the dependence on the investigator's visual counting of bacteria bound per cell. In the modified assay described here, we eliminated the need for visual counting of bacteria by incorporating the use of radioactively labeled Escherichia coli. This allowed quantitation of bacterial adherence to as many as 50,000 vaginal cells, whereas the visual counting system limits the determination to perhaps 50 cells. We feel that the use of radioactively labeled bacteria in place of the visual counting system increases the validity and sensitivity of this assay. Using the modified method, we found no statistically significant differences among values for adherence of E. coli type 04 to the vaginal cells of control and cystitis-prone women at either pH 6.4 or 4.0.

Parsons, C L; Anwar, H; Stauffer, C; Schmidt, J D

1979-01-01

180

Supine chest compression: alternative to prone ventilation in acute respiratory distress syndrome.  

PubMed

Prone ventilation is usually used for severe acute respiratory distress syndrome. We applied an alternative method to prone position. We described 2 cases of trauma where prone position could not be done. Chest wall compression was performed by 2-kg weight in front of the chest wall bilaterally while the patient was in a supine position. Respiratory mechanics work to improve oxygenation almost as same as the mechanism proposed for prone position without any major adverse effects and serious complications. We suggest a larger randomized study to determine the efficacy and also to find out the optimum weight required to compress the chest. PMID:24332252

Samanta, Sukhen; Samanta, Sujay; Soni, Kapil Dev

2014-05-01

181

Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution  

Microsoft Academic Search

This paper assesses the quantitative resolution of qPCR using copy number variation (CNV) as a paradigm. An error model is developed for real-time qPCR data showing how the precision of CNV determination varies with the number of replicates. Using samples with varying numbers of X chromosomes, experimental data demonstrates that real-time qPCR can readily distinguish four copes from five copies,

Suzanne Weaver; Simant Dube; Alain Mir; Jian Qin; Gang Sun; Ramesh Ramakrishnan; Robert C. Jones; Kenneth J. Livak

2010-01-01

182

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...

183

Aircraft system modeling error and control error  

NASA Technical Reports Server (NTRS)

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.

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

2012-01-01

184

Differential Effectiveness of Paradoxical Interventions for More Versus Less Stress-Prone Individuals.  

ERIC Educational Resources Information Center

Forty-three undergraduates underwent stress induction and were then assigned to a paradoxical, stress management, or self-help treatment. In the stress management and self-help groups, better performance was exhibited by less stress-prone subjects. Initial stress proneness, continued stress, and resistance facilitated performance in the…

Shoham-Salomon, Varda; Jancourt, Annick

1985-01-01

185

Premorbid personality differentiation of cancer and noncancer groups: A test of the hypothesis of cancer proneness  

Microsoft Academic Search

The question of a cancer-prone personality has been extensively researched, yet few if any studies have employed a premorbid data base. Thus, nearly all evidence has been confounded, most importantly by alterations of psychological functioning due to the disease itself. The present study provides a more equitable test of the cancer proneness hypothesis. Premorbid MMPI records were collected from 75

Patrick J. Dattore; Franklin C. Shontz; Lolafaye Coyne

1980-01-01

186

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

ERIC Educational Resources Information Center

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)

McCaulay, Marci; And Others

1988-01-01

187

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

ERIC Educational Resources Information Center

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…

Cassel, Russell N.; Cassel, Susie L.

1984-01-01

188

Effects of the supine and prone position on diaphragm thickness in healthy term infants  

Microsoft Academic Search

BACKGROUNDThe physiological basis underlying the decline in the incidence of sudden infant death syndrome (SIDS) associated with changing the sleep position from prone to supine remains unknown.AIMSTo evaluate diaphragm thickness (tdi) and shortening in healthy term infants in the prone and supine positions in order to determine whether changes in body position would affect diaphragm resting length and the degree

Virender K Rehan; James M Nakashima; Aliza Gutman; Lewis P Rubin; F Dennis McCool

2000-01-01

189

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

ERIC Educational Resources Information Center

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…

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

2011-01-01

190

Software error detection  

NASA Technical Reports Server (NTRS)

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.

Buechler, W.; Tucker, A. G.

1981-01-01

191

GCF HSD error control  

NASA Technical Reports Server (NTRS)

A selective repeat automatic repeat request (ARQ) system was implemented under software control in the Ground Communications Facility error detection and correction (EDC) assembly at JPL and the comm monitor and formatter (CMF) assembly at the DSSs. The CMF and EDC significantly improved real time data quality and significantly reduced the post-pass time required for replay of blocks originally received in error. Since the remote mission operation centers (RMOCs) do not provide compatible error correction equipment, error correction will not be used on the RMOC-JPL high speed data (HSD) circuits. The real time error correction capability will correct error burst or outage of two loop-times or less for each DSS-JPL HSD circuit.

Hung, C. K.

1978-01-01

192

The extent of error-prone replication restart by homologous recombination is controlled by Exo1 and checkpoint proteins.  

PubMed

Genetic instability, a hallmark of cancer, can occur when the replication machinery encounters a barrier. The intra-S-phase checkpoint maintains stalled replication forks in a replication-competent configuration by phosphorylating replisome components and DNA repair proteins to prevent forks from catastrophically collapsing. Here, we report a novel function of the core Schizosaccharomyces pombe checkpoint sensor kinase, Rad3 (an ATR orthologue), that is independent of Chk1 and Cds1 (a CHK2 orthologue); Rad3(ATR) regulates the association of recombination factors with collapsed forks, thus limiting their genetic instability. We further reveal antagonistic roles for Rad3(ATR) and the 9-1-1 clamp - Rad3(ATR) restrains MRN- and Exo1-dependent resection, whereas the 9-1-1 complex promotes Exo1 activity. Interestingly, the MRN complex, but not its nuclease activity, promotes resection and the subsequent association of recombination factors at collapsed forks. The biological significance of this regulation is revealed by the observation that Rad3(ATR) prevents Exo1-dependent genome instability upstream of a collapsed fork without affecting the efficiency of recombination-mediated replication restart. We propose that the interplay between Rad3(ATR) and the 9-1-1 clamp functions to fine-tune the balance between the need for the recovery of replication through recombination and the risk of increased genome instability. PMID:24806966

Tsang, Ellen; Miyabe, Izumi; Iraqui, Ismail; Zheng, Jiping; Lambert, Sarah A E; Carr, Antony M

2014-07-01

193

Genomic instability in myeloid malignancies: Increased reactive oxygen species (ROS), DNA double strand breaks (DSBs) and error-prone repair  

Microsoft Academic Search

Disease progression in myeloid malignancies results from the accumulation of “mutations” in genes that control cellular growth and differentiation. Many types of genetic alterations have been identified in myeloid diseases. However, the mechanism(s) by which these cells acquire genetic alterations or “Genomic instability”, is less well understood. Increasing evidence suggests that the genetic changes in myeloid malignancies lead to increased

Annahita Sallmyr; Jinshui Fan; Feyruz Virgilia Rassool

2008-01-01

194

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

Microsoft Academic Search

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

P. Koutsakis

2005-01-01

195

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

PubMed

Squamous cell carcinoma of the head and neck (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 nonhomologous 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

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; D'Silva, Nisha J

2014-01-01

196

Genome-Wide Association Study of Proneness to Anger  

PubMed Central

Background Community samples suggest that approximately 1 in 20 children and adults exhibit clinically significant anger, hostility, and aggression. Individuals with dysregulated emotional control have a greater lifetime burden of psychiatric morbidity, severe impairment in role functioning, and premature mortality due to cardiovascular disease. Methods With publically available data secured from dbGaP, we conducted a genome-wide association study of proneness to anger using the Spielberger State-Trait Anger Scale in the Atherosclerosis Risk in Communities (ARIC) study (n?=?8,747). Results Subjects were, on average, 54 (range 45–64) years old at baseline enrollment, 47% (n?=?4,117) were male, and all were of European descent by self-report. The mean Angry Temperament and Angry Reaction scores were 5.8±1.8 and 7.6±2.2. We observed a nominally significant finding (p?=?2.9E-08, ??=?1.027 - corrected pgc?=?2.2E-07, ??=?1.0015) on chromosome 6q21 in the gene coding for the non-receptor protein-tyrosine kinase, Fyn. Conclusions Fyn interacts with NDMA receptors and inositol-1,4,5-trisphosphate (IP3)-gated channels to regulate calcium influx and intracellular release in the post-synaptic density. These results suggest that signaling pathways regulating intracellular calcium homeostasis, which are relevant to memory, learning, and neuronal survival, may in part underlie the expression of Angry Temperament.

Mick, Eric; McGough, James; Deutsch, Curtis K.; Frazier, Jean A.; Kennedy, David; Goldberg, Robert J.

2014-01-01

197

Development of Korean Smartphone Addiction Proneness Scale for Youth  

PubMed Central

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 ? 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.

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

2014-01-01

198

Psychosis-proneness correlates with expression levels of dopaminergic genes.  

PubMed

Psychosis-proneness or schizotypy is a personality organisation mirroring individual risk for schizophrenia-development. Believed to be a fully dimensional construct sharing considerable geno- and phenotypal variance with clinical schizophrenia, it has become an increasingly promising tool for basic psychosis-research. Although many studies show genetic commonalities between schizotypy and schizophrenia, changes in regulation of gene expression have never been examined in schizotypy before. We therefore extracted RNA from the blood, a valid surrogate for brain tissue, of a large sample of 67 healthy male volunteers and correlated the activities of all genes relevant for dopaminergic neurotransmission with the positive schizotypy-scale of the O-LIFE. We found significant negative correlations regarding the expression of the genes COMT, MAOB, DRD4, DRD5 and FOS, indicating that increased schizotypy coincides with higher levels of dopaminergic dysregulation on the mRNA-level. Considering the advantages of this method, we suggest that it be applied more often in fundamental psychosis-research. PMID:24630741

Grant, P; Gabriel, F; Kuepper, Y; Wielpuetz, C; Hennig, J

2014-06-01

199

Model Error Budgets  

NASA Technical Reports Server (NTRS)

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.

Briggs, Hugh C.

2008-01-01

200

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...

201

Prone Positioning can be Safely Performed in Critically Ill Infants and Children  

PubMed Central

Objective To describe the effects of prone positioning on airway management, mechanical ventilation, enteral nutrition, pain and sedation management and staff utilization in infants and children with acute lung injury (ALI). Design Secondary analysis of data collected in a multi-center, randomized, controlled clinical trial of supine versus prone positioning. Patients and Setting 102 pediatric patients (51 prone and 51 supine) with ALI from seven pediatric intensive care units located in the Untied States. Interventions Patients randomized to the supine group remained supine. Patients randomized to the prone group were positioned prone per protocol during the acute phase of their illness for a maximum of 7 days. Both groups were managed using ventilator and sedation protocols and nutrition and skin care guidelines. Measurements Airway management and mechanical ventilatory parameters pre and post repositioning, enteral nutrition management, pain and sedation management, staff utilization, and adverse event data collected for up to 28 days after enrollment. Main Results There were a total of 202 supine-prone-supine cycles. There were no differences in the incidence of endotracheal tube leak between the two groups (p=0.30). Per protocol, 95% of patients remained connected to the ventilator during repositioning. The inadvertent extubation rate was 0.85 for the prone group and 1.03 for the supine group per 100 ventilator days (p=1.00). There were no significant differences in the initiation of trophic (p=0.24), advancing (p=0.82) or full enteral feeds (p=0.80) between the prone and supine groups and in the average pain (p=0.81) and sedation (p=0.18) scores over the acute phase and in the amount of comfort medications received between the two groups. (p=.91). There were no critical events during a turn procedure. While prone, two patients experienced an obstructed ETT. One patient, supported on HFOV, experienced persistent hypercapnea when prone and was withdrawn from the study. The occurrence of pressure ulcers was similar between the two groups (p=0.71). Compared to the supine group, more staff (p ?0.001) and more time were necessary to reposition patients in the prone group. Conclusions Our data show that prone positioning can be safely performed in critically ill pediatric patients and that these patients can be safely managed while in the prone position for prolonged periods of time.

Fineman, Lori D.; LaBrecque, Michelle A.; Shih, Mei-Chiung; Curley, Martha A.Q.

2006-01-01

202

Field error lottery.  

National Technical Information Service (NTIS)

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. ...

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

1990-01-01

203

Refractive error blindness.  

PubMed

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

Dandona, R; Dandona, L

2001-01-01

204

Approximation Error Maps.  

National Technical Information Service (NTIS)

In order to analyze the accuracy of a fixed, finite-dimensional approximation space which is not uniform over its domain Omega, we define approximation error map, a description of how the error is distributed over Omega-not for a single test function but ...

A. Gomide J. Stolfi

2001-01-01

205

Error Correction by Design  

Microsoft Academic Search

\\u000a This chapter discusses published DAC correction methods that do not use error measurements to improve the DAC performance.\\u000a It overviews main state-of-the art mechanisms to reduce DAC expected errors. Recent publications are referenced to support\\u000a the overview.

Georgi Radulov; Patrick Quinn; Hans Hegt; Arthur Roermund

206

Medication error prevalence  

Microsoft Academic Search

Purpose – Healthcare risk epidemiology identifies medication error as the commonest cause of adverse effects on patients. Medication error can occur at any phase of the complex medication process so prevalence rates need to be estimated at each drug treatment phase: prescription, transcription and administration along with their clinical repercussions. This paper aims to investigate this issue. Design\\/methodology\\/approach – Medication

Ana Belén Jiménez Muñoz; Antonio Muiño Miguez; María Paz Rodriguez Pérez; María Dolores Vigil Escribano; María Esther Durán Garcia; María Sanjurjo Saez

2010-01-01

207

Development of a strand-specific RT-PCR based assay to detect the replicative form of hepatitis C virus RNA  

Microsoft Academic Search

The recent development of tagged RT-PCR and rTth RT-PCR has greatly improved strand-specific detection of hepatitis C virus (HCV) RNA but these assays are still prone to some false detection of the incorrect strand of RNA. In this study we aimed to address additional factors which contribute towards false detection of HCV RNA. Firstly the benefits of both tagged primers

Joanna K Craggs; Jonathan K Ball; Brian J Thomson; William L Irving; Anna M Grabowska

2001-01-01

208

Effect of Head Rotation on Cerebral Blood Velocity in the Prone Position  

PubMed Central

Background. The prone position is applied to facilitate surgery of the back and to improve oxygenation in the respirator-treated patient. In particular, with positive pressure ventilation the prone position reduces venous return to the heart and in turn cardiac output (CO) with consequences for cerebral blood flow. We tested in healthy subjects the hypothesis that rotating the head in the prone position reduces cerebral blood flow. Methods. Mean arterial blood pressure (MAP), stroke volume (SV), and CO were determined, together with the middle cerebral artery mean blood velocity (MCA Vmean) and jugular vein diameters bilaterally in 22 healthy subjects in the prone position with the head centered, respectively, rotated sideways, with and without positive pressure breathing (10?cmH2O). Results. The prone position reduced SV (by 5.4 ± 1.5%; P < 0.05) and CO (by 2.3 ± 1.9 %), and slightly increased MAP (from 78 ± 3 to 80 ± 2?mmHg) as well as bilateral jugular vein diameters, leaving MCA Vmean unchanged. Positive pressure breathing in the prone position increased MAP (by 3.6 ± 0.8?mmHg) but further reduced SV and CO (by 9.3 ± 1.3 % and 7.2 ± 2.4 % below baseline) while MCA Vmean was maintained. The head-rotated prone position with positive pressure breathing augmented MAP further (87 ± 2?mmHg) but not CO, narrowed both jugular vein diameters, and reduced MCA Vmean (by 8.6 ± 3.2 %). Conclusion. During positive pressure breathing the prone position with sideways rotated head reduces MCA Vmean ~10% in spite of an elevated MAP. Prone positioning with rotated head affects both CBF and cerebrovenous drainage indicating that optimal brain perfusion requires head centering.

H?jlund, Jakob; Sandmand, Marie; Sonne, Morten; Mantoni, Teit; J?rgensen, Henrik L.; Belhage, Bo; van Lieshout, Johannes J.; Pott, Frank C.

2012-01-01

209

Uncorrected refractive errors  

PubMed Central

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.

Naidoo, Kovin S; Jaggernath, Jyoti

2012-01-01

210

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

PubMed

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 ?-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

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

2013-09-01

211

Prone cross-table lateral view: an alternative to the invertogram in imperforate anus  

SciTech Connect

The prone cross-table lateral radiograph provides equal or sometimes better information, compared to the invertogram, for demonstration of the level of rectal atresia in neonates. Easy positioning, better cooperation of the patient, elimination of the effect of gravity, and better delineation of the rectal gas shadow are the advantages of the prone lateral view. Among the 45 cases compared, equal findings were noted in 37, but in eight babies the level of rectal atresia was more caudal in the prone radiograph than in the invertogram.

Narasimharao, K.L.; Prasad, G.R.; Katariya, S.; Yadav, K.; Mitra, S.K.; Pathak, I.C.

1983-02-01

212

Error Prevention Aid  

NASA Technical Reports Server (NTRS)

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.

1987-01-01

213

The importance of robust error control in data compression applications  

NASA Technical Reports Server (NTRS)

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.

Woolley, S. I.

1993-01-01

214

Experimental investigation of observation error in anuran call surveys  

USGS Publications Warehouse

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.

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

2010-01-01

215

Methylation-specific PCR.  

PubMed

Defining DNA methylation patterns in the genome has become essential for understanding diverse biological processes including the regulation of gene expression, imprinted genes, and X chromosome inactivation and how these patterns are deregulated in human diseases. Methylation-specific (MS)-PCR is a useful tool for qualitative DNA methylation analysis with multiple advantages, including ease of design and execution, sensitivity in the ability to detect small quantities of methylated DNA, and the ability to rapidly screen a large number of samples without the need for purchase of expensive laboratory equipment. This assay requires modification of the genomic DNA by sodium bisulfite and two independent primer sets for PCR amplification, one pair designed to recognize the methylated and the other pair the unmethylated versions of the bisulfite-modified sequence. The amplicons are visualized using ethidium bromide staining following agarose gel electrophoresis. Amplicons of the expected size produced from either primer pair are indicative of the presence of DNA in the original sample with the respective methylation status. PMID:23913210

Huang, Zhiqing; Bassil, Christopher F; Murphy, Susan K

2013-01-01

216

Low delay, error resilient error control for mobile video communication  

Microsoft Academic Search

This paper proposes a low delay, error resilient video transmission scheme for mobile radio channels. Compressed video data is sensitive to channel error. Channel error can fatally degraded the reconstructed video sequence by causing intra-frame and inter-frame error propagation. Using ARQ to prevent all forms of error propagation, significantly increases the transmission delay of the video frame. We propose a

Naoto Matoba; Yasushi Kondo; Toshiaki Tanaka

1997-01-01

217

Factors Affecting Coding Errors.  

National Technical Information Service (NTIS)

This Memorandum describes experiments which sought to identify the factors that contribute to coding errors. The experiments used code-stimulus materials: numeric codes, consisting only of numbers; alpha codes, consisting only of letters; alpha-numeric co...

S. Owsowtiz, A. Sweetland

1965-01-01

218

Inborn errors of metabolism  

MedlinePLUS

Inborn errors of metabolism are rare genetic disorders in which the body cannot properly turn food into energy. The disorders are usually caused by defects in specific proteins (enzymes) that help break down (metabolize) parts ...

219

Estimating Bias Error Distributions  

NASA Technical Reports Server (NTRS)

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.

Liu, Tian-Shu; Finley, Tom D.

2001-01-01

220

Measurement Error Webinar Series  

Cancer.gov

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

221

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

PubMed Central

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 × 10?5 to a high of 6.9 × 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.

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

2010-01-01

222

Quantum Error Correction  

NASA Astrophysics Data System (ADS)

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.

Lidar, Daniel A.; Brun, Todd A.

2013-09-01

223

Proximity in agreement errors  

Microsoft Academic Search

Across languages subject-verb agreement errors have been established when subjects are producing complex (NP PP) noun-phrases (see Bock, 1995, for an overview). Very recently, Haskell & MacDonalds (2002) proposed a locality-based principle, the principle of proximity, to explain a variety of agreement errors in production. They base they argument partly on preferences in verb number marking in sentences with disjunctive

Barbara Hemforth; Robert Schuman

224

Smoothing error pitfalls  

NASA Astrophysics Data System (ADS)

The difference due to the content of a priori information between a constrained retrieval and the true atmospheric state is usually represented by the so-called smoothing error. In this paper it is shown that the concept of the smoothing error 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. The idea of a sufficiently fine sampling of this reference atmospheric state is untenable 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 talk about temperature or concentration. Smoothing differences, however, which play a role when measurements are compared, are still a useful quantity if the involved a priori covariance matrix has been evaluated on the comparison grid rather than resulting from interpolation. This is, 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.

von Clarmann, T.

2014-04-01

225

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

Code of Federal Regulations, 2013 CFR

... 1 2013-10-01 2013-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency...SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...

2013-10-01

226

Insight into mental illness and self-stigma: the mediating role of shame proneness.  

PubMed

Insight into mental illness and self-stigma among persons with serious mental illness (SMI) have been found to be related, but the process behind this relation is still unclear. The current study examined whether shame and guilt proneness mediates or moderates the relation between insight into mental illness and self-stigma among persons with SMI. Sixty persons with SMI completed questionnaires that assessed their insight, shame, guilt proneness, and self-stigma. Results reveal that shame proneness but not guilt proneness mediates the relation between insight and self-stigma. The theoretical and clinical implications of the differences between shame and guilt and their relation to the development of self-stigma are discussed. PMID:22889545

Hasson-Ohayon, Ilanit; Ehrlich-Ben Or, Shir; Vahab, Kobi; Amiaz, Revital; Weiser, Mark; Roe, David

2012-12-30

227

Intracranial delivery of metrizamide from the lumbar subarachnoid space: prone versus supine positioning.  

PubMed

Forty patients undergoing metrizamide computed tomographic cisternography (MCTC) were prospectively evaluated for the relative merits of prone and supine positioning for the intracranial delivery of the subarachnoid contrast material. Twenty patients were prone and 20 supine when tilted head downward. The degree of opacification was deemed satisfactory or unsatisfactory in each case for the various ventricles and for the suprasellar, quadrigeminal, perimesencephalic, and cerebellopontine angle cisterns. The visualization of the suprasellar and perimesencephalic cisterns was much more often satisfactory using a prone delivery (p less than or equal to 0.05 by Fisher exact test). None of these structures was opacified significantly better with the patient supine. A prone delivery is therefore recommended for most of the common indications for MCTC. PMID:7142507

Lotz, P R

1982-10-01

228

Likelihood-based genetic mark–recapture estimates when genotype samples are incomplete and contain typing errors  

Microsoft Academic Search

Genotypes produced from samples collected non-invasively in harsh field conditions often lack the full complement of data from the selected microsatellite loci. The application to genetic mark–recapture methodology in wildlife species can therefore be prone to misidentifications leading to both ‘true non-recaptures’ being falsely accepted as recaptures (Type I errors) and ‘true recaptures’ being undetected (Type II errors). Here we

Gilbert M. Macbeth; Damien Broderick; Jennifer R. Ovenden; Rik C. Buckworth

2011-01-01

229

Source monitoring and proneness to auditory-verbal hallucinations: A signal detection analysis  

Microsoft Academic Search

Introduction. It has been suggested that a bias to misattribute self-generated thoughts to a nonself source underlies the experience of auditory-verbal hallucinations (AVH). We tested this hypothesis with healthy participants prone or not prone to AVH.Method. Participants (N=133) were presented with 96 words for subsequent recognition (half positively, half negatively valenced). For self-generated trials, participants generated a sentence containing the

Meredith McKague; Ken I. McAnally; Marissa Skovron; Sarah Bendall; Henry J. Jackson

2012-01-01

230

Historical Change in the Link between Adolescent Deviance Proneness and Marijuana Use, 1979–2004  

Microsoft Academic Search

We examined historical change in the association between adolescent deviance proneness and marijuana use using 26 years (from\\u000a 1979 through 2004) of national 12th grade data from the Monitoring the Future (MTF) study. “Deviance proneness” was measured\\u000a using a latent factor model of behavioral and personality characteristics that underlie both substance use and antisocial\\u000a disorders. Marijuana use was measured both in

Michelle Little; Scott R. Weaver; Kevin M. King; Freda Liu; Laurie Chassin

2008-01-01

231

Fantasy-proneness dimensionalized: Dissociative component is related to psychopathology, daydreaming as such is not  

Microsoft Academic Search

Studies of “fantasy-proneness” have suggested a modest relationship with psychopathology, contradicting previous findings of daydreaming as a normal part of human consciousness. To resolve this inconsistency, principal-components analyses of the chief fantasy-proneness measure, the Inventory of Childhood Memories and Imaginings (ICMI), produced 18 weak ICMI dimensions. Only a two-component solution accounting for 20% of variance was moderately stable. Component 1

Eric Klinger; Vincent R. Henning; Jonathan M. Janssen

2009-01-01

232

Dosimetric effects of prone and supine positions on post-implant assessments for prostate brachytherapy  

PubMed Central

Purpose Post-implant dosimetric assessment is essential for optimal care of patients receiving prostate brachytherapy. In most institutions, post-implant computed tomography (CT) is performed in the supine position. This study aimed to assess variability in dosimetric parameters with postural changes during acquisition of post-implant CT scans. Material and methods In total, 85 consecutive patients were enrolled in this study. Fifty-three patients underwent seed implantation alone, and the remaining 32 received a combination of seed implantation and external beam radiotherapy. For post-implant analyses, CT scans were obtained in two patient positions, supine and prone. To evaluate differences in dosimetric parameters associated with postural change, the dosimetric data obtained in the supine position were defined as the standard. Results The median prostate volume was 22.4 ml in the supine and 22.5 ml in the prone position (p = 0.51). The median prostate D90 was 120.1% in the supine and 120.3% in the prone position, not significantly different. The mean prostate V100 was 97.1% in the supine and 97.0% in the prone position, again not significantly different. Median rectal V100 in supine and prone positions were 0.42 ml and 0.33 ml, respectively (p < 0.01). Rectal D2cc was also significantly decreased in the prone as compared with the supine position (median, 59.1% vs. 63.6%; p < 0.01). A larger post-implant prostate volume was associated with decreased rectal doses in the prone position. Conclusions Though there were no significant differences among prostate D90 assessments according to postural changes, our results suggest that post-implant rectal doses decreased in the prone position.

Momma, Tetsuo; Yamashita, Shoji; Kanai, Kunimitsu; Watanabe, Yusuke; Hanada, Takashi; Shigematsu, Naoyuki

2013-01-01

233

ROLE OF ALDOSTERONE IN RENAL VASCULAR INJURY IN STROKE-PRONE HYPERTENSIVE RATS  

Microsoft Academic Search

Background: Stroke-prone spontaneously hypertensive rats (SHRSP) on 1% NaCl drinking solution and Stroke-Prone Rodent Diet develop severe hypertension and glomerular and vascular lesions characteristic of thrombotic microangiopathy seen in malignant nephrosclerosis. We recently reported that spironolactone, a mineralocorticoid receptor antagonist, markedly reduced proteinuria and malignant nephrosclerotic lesions in these animals. This observation, together with our previous findings that angiotensin-converting enzyme

Ricardo Rocha; Praveen N. Chander; Andrea Zuckerman; Charles T. Stier

2010-01-01

234

Speech errors across the lifespan  

Microsoft Academic Search

Dell, Burger, and Svec (1997) proposed that the proportion of speech errors classified as anticipations (e.g., “moot and mouth”) can be predicted solely from the overall error rate, such that the greater the error rate, the lower the anticipatory proportion (AP) of errors. We report a study examining whether this effect applies to changes in error rates that occur developmentally

Janet I. Vousden; Elizabeth A. Maylor

2006-01-01

235

Speech Errors across the Lifespan  

ERIC Educational Resources Information Center

Dell, Burger, and Svec (1997) proposed that the proportion of speech errors classified as anticipations (e.g., "moot and mouth") can be predicted solely from the overall error rate, such that the greater the error rate, the lower the anticipatory proportion (AP) of errors. We report a study examining whether this effect applies to changes in error

Vousden, Janet I.; Maylor, Elizabeth A.

2006-01-01

236

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

NASA Astrophysics Data System (ADS)

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.

Mizuno, Osamu; Kikuno, Tohru

237

Historical Change in the Link between Adolescent Deviance Proneness and Marijuana Use, 1979-2004  

PubMed Central

We examined historical change in the association between adolescent deviance proneness and marijuana use using 26 years (from 1979 through 2004) of national 12th grade data from the Monitoring the Future (MTF) study. “Deviance proneness” was measured using a latent factor model of behavioral and personality characteristics that underlie both substance use and antisocial disorders. Marijuana use outcomes were measured in terms of youths’ annual frequency of use, and youths’ degree of involvement with marijuana. Separate within-gender structural equation models were used to determine whether links between deviance proneness and marijuana use were consistently significant and invariant in magnitude across 13 2-year historical cohorts. Overall results affirmed the established association between adolescent deviance proneness and both the frequency of marijuana use as well as regular use. Among male youth, the size of the association between deviance proneness and marijuana use was significantly smaller at the cohort of lowest population prevalence (1991/92) compared to cohorts marking peaks in marijuana use prevalence, thus suggesting a “softening” historical trend. By contrast, the prediction of female marijuana use from deviance proneness was not consistently related to historical shifts in population prevalence of marijuana use. Study findings point to the utility of risk-focused prevention programming that targets early precursors of both antisocial and substance use disorders.

Little, Michelle; Weaver, Scott R.; King, Kevin M.; Liu, Freda; Chassin, Laurie

2009-01-01

238

Compact disk error measurements  

NASA Technical Reports Server (NTRS)

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.

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

1993-01-01

239

Theoretical Considerations on Error Management.  

National Technical Information Service (NTIS)

A definition of system reliability and failure of a system is presented. Erroneous states, errors and faults are discussed. Reliability requirements and types of faults are reviewed. Techniques for error management: error detection, damage assessment and ...

J. Stigter

1990-01-01

240

Molecular detection of Mycoplasma pneumoniae by quantitative real-time PCR in patients with community acquired pneumonia  

PubMed Central

Background & objectives: Mycoplasma pneumoniae is the most important and common cause of community-acquired pneumonia (CAP). The conventional detection methods (culture and serology) lack sensitivity. PCR offers a better approach for rapid detection but is prone to carry over contamination during manipulation of amplification products. Quantitative real-time PCR (qRT-PCR) method offers an attractive alternative detection method. In the present study, qRT-PCR, PCR and serology methods were used to detect M. pneumoniae infection in cases of pneumonias and findings compared. Methods: A total of 134 samples consisting of blood (for serology) and respiratory secretions (for PCR and qRT-PCR) from 134 patients were collected. The blood samples were tested for IgG, IgM and IgA using commercially available kits. For standardization of PCR of M. pneumoniae P1 gene was cloned in pGEMTEasy vector. Specific primers and reporter sequence were designed and procured for this fragment. The qRT-PCR assay was performed to prepare the standard curve for M. pneumoniae positive control DNA template and detection in patient samples. Results: Of the 134 patients, 26 (19%) were positive for antibodies against M. pneumoniae. IgG was positive in 14.92 per cent (20) cases, IgM in 4.47 per cent (6) and IgA was positive in 5.22 per cent (7) cases. In the qRT-PCR assay 19 per cent (26) samples were positive. Of the 26 qRT-PCR positive samples, nine could be detected by serology. PCR was positive for 25 samples. An extra sample negative by PCR was detected by qRT-PCR. Thus, real-time PCR assay, PCR and serology in combination could detect M. pneumoniae infection in 43 patients. Interpretation & conclusions: The study shows that 17 patients were detected by serology alone, 17 were detected by qRT-PCR only and nine patients were positive by both serology and real-time PCR. Of the 134 samples tested, 25 were positive by conventional PCR, but qRT-PCR could detect one more sample that was negative by PCR and serology. These results suggest that a combination of two or three methods may be required for reliable identification of CAP due to M. pneumoniae.

Chaudhry, Rama; Sharma, Sutikshan; Javed, Sabah; Passi, Kapil; Dey, A.B.; Malhotra, Pawan

2013-01-01

241

Experimental Quantum Error Detection  

NASA Astrophysics Data System (ADS)

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

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

2012-09-01

242

Estimating GPS Positional Error  

NSDL National Science Digital Library

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

Witte, Bill

243

Surprise beyond prediction error.  

PubMed

Surprise drives learning. Various neural "prediction error" signals are believed to underpin surprise-based reinforcement learning. Here, we report a surprise signal that reflects reinforcement learning but is neither un/signed reward prediction error (RPE) nor un/signed state prediction error (SPE). To exclude these alternatives, we measured surprise responses in the absence of RPE and accounted for a host of potential SPE confounds. This new surprise signal was evident in ventral striatum, primary sensory cortex, frontal poles, and amygdala. We interpret these findings via a normative model of surprise. Hum Brain Mapp 35:4805-4814, 2014. © 2014 The Authors. Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:24700400

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

2014-09-01

244

Experimental Quantum Error Detection  

PubMed Central

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

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

2012-01-01

245

Observation and Representativity Errors in historical Upper-Air Observations  

NASA Astrophysics Data System (ADS)

Upper-air observations are a fundamental data source for global atmospheric data products, but uncertainties, particularly in the early years, are not well known. Most of the early observations, which have now been digitized, are prone to a large variety of undocumented errors that need to be quantified e.g., for their assimilation in reanalysis projects. Here we present a novel approach for systematically estimating observation and representativity errors in upper-air observations. The method is based on a buddy approach that is largely independent of metadata, making it applicable to a wide scope of observational datasets. We assume a linear dependency between the magnitude of the errors and station distance. The method is applied to upper-air temperature, geopotential height and wind observations of the Comprehensive Historical Upper-Air Network (CHUAN; 1930 - 1966). The estimated mean non-systematic observation errors are 1.3 K for air temperature, 0.9 hPa for pressure, 3.4 ms-1 for wind speed, and 34 ° for wind direction. All errors have physically meaningful vertical profiles and depend on both the geographical location as well as on time. Next to its usefulness for future reanalysis products, the results are valuable for data homogenization efforts by highlighting suspicious observations.

Wartenburger, Richard; Brönnimann, Stefan; Stickler, Alexander

2013-04-01

246

Cerebrovascular Control is Altered in Healthy Term Infants When They Sleep Prone  

PubMed Central

Study Objectives: Sudden infant death syndrome (SIDS) is a leading cause of infant death, and prone sleeping is the major risk factor. Prone sleeping impairs arousal from sleep and cardiovascular control in infants at 2-3 months, coinciding with the highest risk period for SIDS. We hypothesized that prone sleeping would also alter cerebrovascular control, and aimed to test this hypothesis by examining responses of cerebral oxygenation to head-up tilts (HUTs) over the first 6 months after birth. Study Design and Participants: Seventeen healthy full-term infants were studied at 2-4 weeks, 2-3 months, and 5-6 months of age using daytime polysomnography, with the additional measurements of blood pressure (BP, FinometerTM, Finometer Medical Systems, The Netherlands) and cerebral tissue oxygenation index (TOI, NIRO 200, Hamamatsu Photonics KK, Japan). HUTs were performed in active sleep (AS) and quiet sleep (QS) in both prone and supine positions. Results: When infants slept in the prone position, a sustained increase in TOI (P < 0.05) occurred following HUTs, except in QS at 2-3 months when TOI was unchanged. BP was either unchanged or fell below baseline during the sustained TOI increase, signifying cerebro-vasodilatation. In contrast, when infants slept supine, TOI did not change after HUTs, except in QS at 2-3 and 5-6 months when TOI dropped below baseline (P < 0.05). Conclusions: When infants slept in the prone position, cerebral arterial vasodilation and increased cerebral oxygenation occurred during head-up tilts, possibly as a protection against cerebral hypoxia. Absence of the vasodilatory response during quiet sleep at 2-3 months possibly underpins the decreased arousability from sleep and increased risk for sudden infant death syndrome at this age. Citation: Wong F; Yiallourou SR; Odoi A; Browne P; Walker AM; Horne RSC. Cerebrovascular control is altered in healthy term infants when they sleep prone. SLEEP 2013;36(12):1911-1918.

Wong, Flora; Yiallourou, Stephanie R.; Odoi, Alexsandria; Browne, Pamela; Walker, Adrian M.; Horne, Rosemary S. C.

2013-01-01

247

Dosimetric and toxicity comparison between prone and supine position IMRT for endometrial cancer  

SciTech Connect

Purpose: To determine the dosimetric and toxicity differences between prone and supine position intensity-modulate radiotherapy in endometrial cancer patients treated with adjuvant radiotherapy. Methods: Forty-seven consecutive endometrial cancer patients treated with adjuvant RT were analyzed. Of these, 21 were treated in prone position and 26 in the supine position. Dose-volume histograms for normal tissue structures and targets were compared between the two groups. Acute and chronic toxicity were also compared between the cohorts. Results: The percentage of volume receiving 10, 20, 30, 40, 45, and 50 Gy for small bowel was 89.5%, 69%, 33%, 12.2%, 5%, and 0% in the prone group and 87.5%, 62.7%, 26.4%, 8%, 4.3%, and 0% in the supine group, respectively. The difference was not statistically significant. The dose-volume histograms for bladder and rectum were also comparable, except for a slightly greater percentage of volume receiving 10 Gy (1.5%) and 20 Gy (5%) for the rectum in the prone group. Acute small bowel toxicities were Grade 1 in 7 patients and Grade 2 in 14 patients in the prone group vs. Grade 1 in 6 patients and Grade 2 in 19 patients in the supine group. Chronic toxicity was Grade 1 in 7 patients and Grade 3 in 1 patient in the prone group and Grade 1 in 5 patients in the supine group. Conclusion: These preliminary results suggest that no difference exists in the dose to the normal tissue and toxicity between prone and supine intensity-modulated radiotherapy for endometrial cancer. Longer follow-up and more outcome studies are needed to determine whether any differences exist between the two approaches.

Beriwal, Sushil [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States) and University of Pittsburgh School of Medicine, Pittsburgh, PA (United States)]. E-mail: beriwals@upmc.edu; Jain, Sheena K. [University of Pittsburgh School of Medicine, Pittsburgh, PA (United States); Heron, Dwight E. [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); University of Pittsburgh School of Medicine, Pittsburgh, PA (United States); De Andrade, Regiane S. [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); Lin, Chyonghiou J. [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); Kim, Hayeon [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); University of Pittsburgh School of Medicine, Pittsburgh, PA (United States)

2007-02-01

248

PCR amplification reactions in parasitology  

Microsoft Academic Search

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

Henk L. Smits; Rudy A. Hartskeerl

1995-01-01

249

Improving MIMO-OFDM decision-directed channel estimation by utilizing error-correcting codes  

Microsoft Academic Search

In this paper a decision-directed Multiple-Input Multiple-Output (MIMO) channel tracking algorithm is enhanced to raise the channel estimate accuracy. While DDCE is prone to error propagation the enhancement employs channel decoding in the tracking process. Therefore, a quantized block of symbols is checked on consistency via the channel decoder, possibly corrected and then used. This yields a more robust tracking

P. Beinschob; M. Lieberei; U. Zölzer

2009-01-01

250

Enhanced analysis of real-time PCR data by using a variable efficiency model: FPK-PCR  

PubMed Central

Current methodology in real-time Polymerase chain reaction (PCR) analysis performs well provided PCR efficiency remains constant over reactions. Yet, small changes in efficiency can lead to large quantification errors. Particularly in biological samples, the possible presence of inhibitors forms a challenge. We present a new approach to single reaction efficiency calculation, called Full Process Kinetics-PCR (FPK-PCR). It combines a kinetically more realistic model with flexible adaptation to the full range of data. By reconstructing the entire chain of cycle efficiencies, rather than restricting the focus on a ‘window of application’, one extracts additional information and loses a level of arbitrariness. The maximal efficiency estimates returned by the model are comparable in accuracy and precision to both the golden standard of serial dilution and other single reaction efficiency methods. The cycle-to-cycle changes in efficiency, as described by the FPK-PCR procedure, stay considerably closer to the data than those from other S-shaped models. The assessment of individual cycle efficiencies returns more information than other single efficiency methods. It allows in-depth interpretation of real-time PCR data and reconstruction of the fluorescence data, providing quality control. Finally, by implementing a global efficiency model, reproducibility is improved as the selection of a window of application is avoided.

Lievens, Antoon; Van Aelst, S.; Van den Bulcke, M.; Goetghebeur, E.

2012-01-01

251

Directional genome walking using PCR.  

PubMed

We describe here a PCR-based "directional genome walking" protocol. The basic procedure for the amplification consists of two rounds of PCR. A primary PCR was performed, on the genomic DNA using a biotinylated primer specific to a known sequence in the genome along with four universal walker primers that were designed with partial degeneracy. The biotinylated primary PCR products were immobilized on streptavidin-linked paramagnetic beads. This step removed all nonspecific amplification products, and the purified template was used for the second PCR using a nested primer and the walker primer-2 to increase specificity. This technique is potentially useful for cloning promoter regions and has been successfully used to isolate 5'-flanking genomic regions of many cDNA clones previously isolated by us. PMID:12398192

Mishra, R N; Singla-Pareek, S L; Nair, S; Sopory, S K; Reddy, M K

2002-10-01

252

Errors and ozone measurement  

NASA Technical Reports Server (NTRS)

It is held that Mimm's (1993) comparison of hand-held TOPS instrument data with the Nimbus 7 satellite's Total Ozone Mapping Spectrometer's (TOMS) ozone data was intrinsically flawed, in that the TOMS data were preliminary and therefore unsuited for quantitative analysis. It is noted that the TOMS calibration was in error.

Mcpeters, Richard D.; Gleason, James F.

1993-01-01

253

Young Writers' Error Tendency.  

ERIC Educational Resources Information Center

Six pupils were selected at random from each of grades one through eight in a single school and were asked to write a rough draft of any length on any topic of interest to them. The 48 resulting essays were analyzed for errors in punctuation and sentence structure. Results indicated that elementary school children have difficulty in placing…

Mazur, Chet

254

Laboratory 0: Error Analysis  

NSDL National Science Digital Library

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

Virtual Labs, Real Data (Cornell University)

2011-01-19

255

Floating point error analysis  

Microsoft Academic Search

In many floating point calculations it is important to arrange the sequence of calculations such that significant digits are not deleted by intermediate rounding of the numbers. The danger that gross errors may be introduced is always present in floating point calculations, since the number of digits carried in each number is restricted in normal operation by the design of

R. C. Nickerson

1959-01-01

256

Orwell's Instructive Errors  

ERIC Educational Resources Information Center

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…

Julian, Liam

2009-01-01

257

Evolution and obesity: resistance of obese-prone rats to a challenge of food restriction and wheel running.  

PubMed

The adaptive hypothesis that an obese-prone genotype confers a fitness advantage when challenged with food restriction and food-related locomotion was tested using a rat model. Juvenile (35-40 days) and adolescent (45-50 days) JCR:LA-cp rats, obese prone (cp/cp) and lean prone (+/?), were exposed to 1.5 h daily meals and 22.5 h of voluntary wheel running, a procedure that normally leads to self-starvation. Genotype had a dramatic effect on survival of rats when exposed to the challenge of food restriction and wheel running. Although similar in initial body weight, obese-prone juveniles survived twice as long, and ran three times as far, as their lean-prone counterparts. Biochemical measures indicated that young obese-prone animals maintained blood glucose and fat mass, whereas lean-prone rats depleted these energy reserves. Corticosterone concentration indicated that obese-prone juveniles exhibited a lower stress response to the survival challenge than lean-prone rats, possibly due to lower energy demands and greater energy reserves. Collectively, the findings support the hypothesis that an obese-prone genotype provides a fitness advantage when food supply is inadequate, but is deleterious during periods of food surfeit, such as the energy-rich food environment of prosperous and developing societies worldwide. PMID:20065962

Pierce, W D; Diane, A; Heth, C D; Russell, J C; Proctor, S D

2010-03-01

258

Cognitive correlates of boredom proneness: the role of private self-consciousness and absorption.  

PubMed

The contributions of private self-consciousness and absorption in explaining boredom proneness were investigated. University students enrolled at a public university in the southeastern United States completed a packet containing the Boredom Proneness Scale (BPS; R. Farmer & N. D. Sundberg, 1986), the Self-Consciousness Scale (SCS; A. Fenigstein, M. F. Scheier, & A. H. Buss, 1975), the Tellegen Absorption Scale (TAS; A. Tellegen & G. Atkinson, 1974), the Need for Cognition Scale (NCS; J. T. Cacioppo, R. E. Petty, & C. F. Kao, 1984), and a demographic questionnaire. Scores on the Boredom Proneness subscale, Internal Stimulation, which indicates the difficulty in keeping oneself interested and entertained, were significantly lower for individuals high in absorption (a measure of attention). Individuals high in positive self-awareness, representing awareness of one's internal states, reported lower overall boredom. Individuals high in negative self-awareness, which focuses on evaluation and judgment, reported increased total boredom proneness scores. Implications of these findings for the treatment of boredom proneness and future research are discussed. PMID:9857501

Seib, H M; Vodanovich, S J

1998-11-01

259

The prone position results in smaller ventilation defects during bronchoconstriction in asthma  

PubMed Central

The effect of body posture on regional ventilation during bronchoconstriction is unknown. In five subjects with asthma, we measured spirometry, low-frequency (0.15-Hz) lung elastance, and resistance and regional ventilation by intravenous 13NN-saline positron emission tomography before and after nebulized methacholine. The subjects were imaged prone on 1 day and supine on another, but on both days the methacholine was delivered while prone. From the residual 13NN after washout, ventilation defective areas were defined, and their location, volume, ventilation, and fractional gas content relative to the rest of the lung were calculated. Independent of posture, all subjects developed ventilation defective areas. Although ventilation within these areas was similarly reduced in both postures, their volume was smaller in prone than supine (25 vs. 41%, P < 0.05). The geometric center of the ventilation defective areas was gravitationally dependent relative to that of the lung in both postures. Mean lung fractional gas content was greater in the prone position before methacholine and did not increase as much as in the supine position after methacholine. In the prone position at baseline, areas that became ventilation defects had lower gas content than the rest of the lung. In both positions at baseline, there was a gradient of gas content in the vertical direction. In asthma, the size and location of ventilation defects is affected by body position and likely affected by small differences in lung expansion during bronchoconstriction.

Harris, R. Scott; Winkler, Tilo; Musch, Guido; Vidal Melo, Marcos F.; Schroeder, Tobias; Tgavalekos, Nora; Venegas, Jose G.

2009-01-01

260

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

PubMed Central

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.

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

2011-01-01

261

Rapid mapping of volumetric errors  

Microsoft Academic Search

This paper describes a relatively inexpensive, fast, and easy to execute approach to mapping the volumetric errors of a machine tool, coordinate measuring machine, or robot. An error map is used to characterize a machine or to improve its accuracy by compensating for the systematic errors. The method consists of three steps: (1) modeling the relationship between the volumetric error

D. Krulewich; L. Hale; D. Yordy

1995-01-01

262

Error Analysis: Procedures and Guidelines.  

ERIC Educational Resources Information Center

Error analysis is proposed as a means to supplement diagnostic techniques with exceptional children. A purpose and definition of error analysis are provided. Also, procedures to use error analysis are explained along with basic guidelines to prevent abuse of error analytic techniques. (Author/CL)

Carpentar, Dale

1982-01-01

263

Imagery of Errors in Typing  

ERIC Educational Resources Information Center

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…

Rieger, Martina; Martinez, Fanny; Wenke, Dorit

2011-01-01

264

Automatic Error Analysis Using Intervals  

ERIC Educational Resources Information Center

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…

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

2012-01-01

265

Control by model error estimation  

NASA Technical Reports Server (NTRS)

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).

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

1976-01-01

266

The Role of Depression, Shame-Proneness, and Guilt-Proneness in Predicting Criticism of Relatives Towards People With Bipolar Disorder  

PubMed Central

Expressed emotion (EE) has been associated with poor patient outcomes in many different psychiatric disorders. Given its robust association with relapse, EE has become a major target of family psychoeducational interventions. Most psychoeducational interventions to date have failed to change EE levels among families of those with bipolar disorder. Better intervention strategies, then, may depend on an increased understanding of the predictors of EE. Although EE has traditionally included many facets, criticism appears to be the most robust predictor of outcome within bipolar disorder. The present study tested three primary predictors of criticism among family members of people with bipolar disorder: shame-proneness, guilt-proneness, and depression. Depressive symptoms were significantly associated with EE. Discussion focuses on limitations and implications of the study and suggestions for future research.

McMurrich, Stephanie L.; Johnson, Sheri L.

2010-01-01

267

Error-resilient video coding using long-term memory motion-compensated prediction over feedback channel  

NASA Astrophysics Data System (ADS)

The MC-DCT based video coding has been generally used for its efficiency and easy implementation, but it is very vulnerable in error-prone environments. In this paper, we present an error-resilient video coding using multiple reference frame, based on the long-term memory motion compensated prediction (LTMP), and an error concealment technique associated with the proposed technique. The rate- distortion optimization of the LTMP is extended in order to yield the improved error-resilience and error concealment capabilities. Also, the proposed algorithm confines effectively the temporal error propagation using the negative acknowledgement in feedback channel, in which the corrupted area by channel errors as well as the propagated is estimated and removed from the search region for the motion compensation. Thus, the proposed algorithm yields the similar performance to the forced intra update (FIU) method in terms of the PSNR, but avoids the abrupt increase in the bitrate, resulting in more efficient network utilization than the FIU. By the computer simulations, we shall demonstrate that the proposed technique provides an acceptable performance both subjectively and objectively in error-prone environments, as compared with the H.263 and LTMP, with or without the feedback messages.

Jung, Han S.; Kim, Rin-Chul; Lee, Sang U.

2000-05-01

268

Flexible bronchoscopy during mechanical ventilation in the prone position to treat acute lung injury.  

PubMed

In patients with severe acute lung injury (ALI) or acute respiratory distress syndrome (ARDS) the prone position has been shown to improve survival of patients who are severely hypoxemic with an arterial oxygen tension to inspiratory oxygen fraction ratio (PaO(2)/FiO(2))<100. In those patients tracheobronchial toilette is crucial in preventing or treating airways obstructed by secretions and deterioration of oxygenation. Flexible fiberoptic bronchoscopy is widely recognized as an effective technique to perform bronchial toilette in the intensive care unit (ICU). Flexible bronchoscopy performed during prone mechanical ventilation in two cardiosurgical patients who developed ALI after complex surgery, proved feasible and safe and helped to avoid undesirable earlier cessation of prone mechanical ventilation. However decision making about bronchoscopy in severe hypoxia should be even more cautious than in the supine patient, as dangerous delay in resuscitation manoeuvres due to postponed switching the patient to the supine position should always be prevented. PMID:22868006

Guarracino, F; Bertini, P; Bortolotti, U; Stefani, M; Ambrosino, N

2013-01-01

269

[The prone position as an indicator of deviated motor development during the first year of life].  

PubMed

The adequate control and alignment of a baby in the prone position during the first year of life is a basic necessary milestone for a normal, neuromotor development. In this study the prone position was registered in 246 babies with a previous pediatric evaluation, three options could be made: normal retarded or altered. The Milani Comparetti neuromotor evaluation was also realized for each baby at the same time with the same classification options. Both results were compared. A sensitivity and specificity = 1.0 were found for the prone position registered. This test is fast and simple, so it is recommended at a first attention level in high risk population for neuromotor disability. PMID:2481459

Benavides-González, H M; Ibarra-Reyes, M D; Jiménez-Pérez, L; Aranda-Valdez, R M; Bravo-Cabrera, Z; Venta-Sobero, J A; Pinzón-Godinez, D; Fernández-Carrocera, L A

1989-09-01

270

Registration of prone and supine colons in the presence of topological changes  

NASA Astrophysics Data System (ADS)

CT colonography is a minimally-invasive screening technique for colorectal polyps in which X-ray CT images of the distended colon are acquired, usually in the prone and supine positions. Registration of segmented colons from both images will be useful for computer-assisted polyp detection. We have previously presented algorithms for registration of the prone and supine colon when both are well distended and there is a single connected lumen. However due to inadequate bowel preparation or peristalsis there may be collapsed segments in one or both of the colons resulting in a topological change in the images. Such changes make deformable registrations of the colons difficult, and at present there are no registration algorithms which can accommodate them. In this paper we present an algorithm which can perform volume registration of prone/supine colon images in the presence of a topological change.

Suh, Jung W.; Wyatt, Christopher L.

2008-04-01

271

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

PubMed Central

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.

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

2012-01-01

272

Modular error embedding  

DOEpatents

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.

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

1999-01-01

273

Bolstered error estimation  

Microsoft Academic Search

Abstract: We proposeagT"kxdmethodfor error estimation that displays low varianceandgcedIIIT low bias as well. This methodis based on"bolsteringtheorig#G" empirical distribution of the data. It has a directgrectdIk interpretation and can beeasily appliedto any classi#cation rule andany number of classes. This methodcan be usedto improve the performance ofanyerror-countingestimation method, such as resubstitution and all cross-validation estimators, particularly in small-samplesettingsWe ...

Ulisses Braga-neto; Edward R. Dougherty

2004-01-01

274

Effects of supine, prone, and lateral positions on cardiovascular and renal variables in humans.  

PubMed

The hypothesis was tested that changing the direction of the transverse gravitational stress in horizontal humans modulates cardiovascular and renal variables. On different study days, 14 healthy males were placed for 6 h in either the horizontal supine or prone position following 3 h of being supine. Eight of the subjects were in addition investigated in the horizontal left lateral position. Compared with supine, the prone position slightly increased free water clearance (349 +/- 38 vs. 447 +/- 39 ml/6 h, P = 0.05) and urine output (1,387 +/- 55 vs. 1,533 +/- 52 ml/6 h, P = 0.06) with no statistically significant effect on renal sodium excretion (69 +/- 3 vs. 76 +/- 5 mmol/6 h, P = 0.21). Mean arterial pressure and left atrial diameter were similar comparing effects of supine with prone. The prone position induced an increase in heart rate (54 +/- 2 to 58 +/- 2 beats/min, P < 0.05), total peripheral vascular resistance (13 +/- 1 to 16 +/- 1 mmHg. min(-1). l(-1), P < 0.05), forearm venous plasma concentration of norepinephrine (97 +/- 9 to 123 +/- 16 pg/ml, P < 0.05), and atrial natriuretic peptide (49 +/- 4 to 79 +/- 12 pg/ml, P < 0.05), whereas stroke volume decreased (122 +/- 5 to 102 +/- 3 ml, P < 0.05, n = 6). The left lateral position had no effect on renal variables, whereas left atrial diameter increased (32 +/- 1 to 35 +/- 1 mm, P < 0.05) and mean arterial pressure decreased (90 +/- 2 to mean value of 85 +/- 2 mmHg, P < 0.05). In conclusion, the prone position reduced stroke volume and increased sympathetic nervous activity, possibly because of mechanical compression of the thorax with slight impediment of arterial filling. The mechanisms of the slightly augmented urine output in prone position require further experimentation. PMID:12069943

Pump, Bettina; Talleruphuus, Ulrik; Christensen, Niels Juel; Warberg, Jørgen; Norsk, Peter

2002-07-01

275

Nature of Human Error  

PubMed Central

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.

Cuschieri, Alfred

2006-01-01

276

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

PubMed Central

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

2013-01-01

277

[Prone position for the treatment of acute respiratory distress syndrome: a review of current literature].  

PubMed

Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) have high incidence and mortality rates. Most of the recently introduced treatments have failed to improve the prognosis of patients with ALI or ARDS or to reduce mortality. Several studies have shown improved oxygenation in the prone position during mechanical ventilation in patients with ARDS. However, current evidence strongly suggests that placing ARDS patients in prone position does not improve survival or reduce the duration of mechanical ventilation. Therefore, though in clinical practice this position may improve refractory hypoxemia in patients with ARDS, there is no evidence to support its systematic use. PMID:19403223

Martínez, Oscar; Nin, Nicolás; Esteban, Andrés

2009-06-01

278

IPTV multicast with peer-assisted lossy error control  

NASA Astrophysics Data System (ADS)

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.

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

2010-07-01

279

Observation errors in early historical upper-air observations  

NASA Astrophysics Data System (ADS)

Upper-air observations are a fundamental data source for global atmospheric data products, but uncertainties, particularly in the early years, are not well known. Most of the early observations, which have now been digitized, are prone to a large variety of undocumented uncertainties (errors) that need to be quantified, e.g., for their assimilation in reanalysis projects. We apply a novel approach to estimate errors in upper-air temperature, geopotential height, and wind observations from the Comprehensive Historical Upper-Air Network for the time period from 1923 to 1966. We distinguish between random errors, biases, and a term that quantifies the representativity of the observations. The method is based on a comparison of neighboring observations and is hence independent of metadata, making it applicable to a wide scope of observational data sets. The estimated mean random errors for all observations within the study period are 1.5 K for air temperature, 1.3 hPa for pressure, 3.0 ms-1for wind speed, and 21.4° for wind direction. The estimates are compared to results of previous studies and analyzed with respect to their spatial and temporal variability.

Wartenburger, R.; Brönnimann, S.; Stickler, A.

2013-11-01

280

FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis.  

PubMed

This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a program to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, and linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with CG or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyzes sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and online version at http://primerdigital.com/tools/pcr.html . PMID:24395370

Kalendar, Ruslan; Lee, David; Schulman, Alan H

2014-01-01

281

Is homologous recombination really an error-free process?  

PubMed Central

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.

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

2014-01-01

282

Sequetyping: Serotyping Streptococcus pneumoniae by a Single PCR Sequencing Strategy  

PubMed Central

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.

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

2012-01-01

283

Error propagation properties for ICBM  

NASA Astrophysics Data System (ADS)

This paper describes the error propagation properties of IGS (Inertial Guidance System) for ICBM. The transition matrix analytic solution of IGS is derived. By means of the Regression Analysis technique, the perturbance model is set up. Based upon this, the analytic solutions of impact position error is obtained. Using the analytic solution, the error analysis of IGS can be complete without integrating differential equations. For calculating impact position error, it is only necessary to determine the perturbance parameters and error propagation parameters by means of the algebraic method. Finally, the numerical results calculated for 42 trajectories show that the maximum error due to the analytic solution is less than 10 meters.

Chen, G.

1984-07-01

284

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

PubMed

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

Liu, Xiaoming

2012-08-01

285

Soft error recovery during operation of the compact muon solenoid experiment  

NASA Astrophysics Data System (ADS)

In high energy physics experiments, the electronics located near the interaction region are prone to soft errors as a result of radiation coming from the collisions. Depending on the type of error, the scope of its impact on data collection can range from being hardly noticeable to being completely debilitating. In this paper, we define the mechanism used by the Compact Muon Solenoid (CMS) experiment to pause the data collection machine in order to allow subsystems to recover from soft errors. An attractive feature of this mechanism is that it is general enough to facilitate the recovery from any well-defined error, not only those caused by radiation. We show the effectiveness of this method to maximize the data collection efficiency of CMS.

Rakness, G.

2013-02-01

286

Estimating Prediction Error: Cross-Validation vs. Accumulated Prediction Error  

Microsoft Academic Search

We study the validation of prediction rules such as regression models and classification algorithms through two out-of-sample strategies, cross-validation and accumulated prediction error. We use the framework of Efron (1983) where measures of prediction errors are defined as sample averages of expected errors and show through exact finite sample calculations that cross-validation and accumulated prediction error yield different smoothing parameter

Jenny Häggström; Xavier de Luna

2010-01-01

287

A Posteriori Control of Modeling Errors and Discretization Errors  

Microsoft Academic Search

Abstract: We investigate the concept of dual-weighted residuals for measuring model errorsin the numerical solution of nonlinear partial dierential equations. The method isrst derivedin the case where only model errors arise and then extended to handle simultaneously model anddiscretization errors. We next present an adaptive model\\/mesh renement procedure where bothsources of errors are equilibrated. Various test cases involving Poisson equations

Malte Braack; Alexandre Ern

2003-01-01

288

An updated study-level meta-analysis of randomised controlled trials on proning in ARDS and acute lung injury  

PubMed Central

Introduction In patients with acute lung injury (ALI) and/or acute respiratory distress syndrome (ARDS), recent randomised controlled trials (RCTs) showed a consistent trend of mortality reduction with prone ventilation. We updated a meta-analysis on this topic. Methods RCTs that compared ventilation of adult patients with ALI/ARDS in prone versus supine position were included in this study-level meta-analysis. Analysis was made by a random-effects model. The effect size on intensive care unit (ICU) mortality was computed in the overall included studies and in two subgroups of studies: those that included all ALI or hypoxemic patients, and those that restricted inclusion to only ARDS patients. A relationship between studies' effect size and daily prone duration was sought with meta-regression. We also computed the effects of prone positioning on major adverse airway complications. Results Seven RCTs (including 1,675 adult patients, of whom 862 were ventilated in the prone position) were included. The four most recent trials included only ARDS patients, and also applied the longest proning durations and used lung-protective ventilation. The effects of prone positioning differed according to the type of study. Overall, prone ventilation did not reduce ICU mortality (odds ratio = 0.91, 95% confidence interval = 0.75 to 1.2; P = 0.39), but it significantly reduced the ICU mortality in the four recent studies that enrolled only patients with ARDS (odds ratio = 0.71; 95% confidence interval = 0.5 to 0.99; P = 0.048; number needed to treat = 11). Meta-regression on all studies disclosed only a trend to explain effect variation by prone duration (P = 0.06). Prone positioning was not associated with a statistical increase in major airway complications. Conclusions Long duration of ventilation in prone position significantly reduces ICU mortality when only ARDS patients are considered.

2011-01-01

289

ECG Segmentation and P-Wave Feature Extraction: Application to Patients Prone to Atrial Fibrillation.  

National Technical Information Service (NTIS)

This paper presents an automatic analysis method of the P-wave, based on lead II of a 12 lead standard ECG, which will be applied to the detection of patients prone to atrial fibrillation (AF), one of the most frequent arrhythmias. It focuses first on the...

R. Lepage J. Boucher J. Blanc J. Cornilly

2001-01-01

290

Pathogenesis of vascular dementia in stroke-prone spontaneously hypertensive rats  

Microsoft Academic Search

Stroke-prone spontaneously hypertensive rats (SHRSP) are the best model for essential hypertension and stroke. In this study, one investigated whether SHRSP might be a useful animal model for vascular dementia. An impairment of learning-memory function was found in SHRSP. A disturbance in circadian rhythm after stroke in SHRSP was clarified. Desynchronization of light and dark alternation cycles and abnormal rhythm

Shinichi Kimura; Hideya Saito; Masaru Minami; Hiroko Togashi; Nishio Nakamura; Masahiro Nemoto; Hasan S. Parvez

2000-01-01

291

Objective characterisation of fire regimes for science-based management of fire-prone landscapes  

Microsoft Academic Search

In fire-prone landscapes many of the ecosystem properties that land managers aim to maintain or enhance are closely linked to the incidence and patterning of fire, particularly of fire intensity, extent, season, and frequency of burning. Characteristic combinations of these attributes are often referred to as fire regimes. The term fire regime is mostly used as a qualitative descriptor rather

Matthias Boer; Rohan Sadler; Pauline Grierson

292

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

Microsoft Academic Search

Background: Individuals who are less invested in their bodies, experiencing symptoms of depression, and consuming alcohol are at increased risk for engaging in suicidal behaviors. Aims: This study examined the relationships among three risk factors – body investment, depression, and alcohol use – and suicide proneness as measured by the Life Attitudes Schedule – Short Form (LAS-SF) in college students

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

2010-01-01

293

Homes in Wildfire-Prone Areas: An Empirical Analysis of Wildfire Suppression Costs and Climate Change  

Microsoft Academic Search

This paper empirically estimates the budgetary cost of wildfire suppression and assesses how development in wildfire-prone areas and climate change may affect future suppression costs. Given reasonable assumptions for development and warming trends, our statistical model predicts expenses devoted to protecting homes from wildfires in Montana will more than double by 2025. Our analysis uses daily data from 18 large

Patricia H. Gude; J. Anthony CooksonB; Mark C. GreenwoodC; Mark HaggertyA

294

Use of the Prone Position in the MRI Evaluation of Spinal Cord Retethering  

Microsoft Academic Search

In order to determine the impact of magnetic resonance imaging (MRI) in the management of spinal cord retethering, we retrospectively reviewed case and imaging records of 51 patients who underwent MRI examination in supine and prone positions. Group 1 included 8 control patients without cord tethering. They exhibited a normal level of the conus medullaris with normal surrounding subarachnoid space,

Olivier Vernet; Augustin M. O’Gorman; Jean-Pierre Farmer; Maeve McPhillips; José L. Montes

1996-01-01

295

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

USGS Publications Warehouse

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)

Lamke, Robert D.; Jones, Stanley H.

1980-01-01

296

Nerve cell injury in the brain of stroke-prone spontaneously hypertensive rats  

Microsoft Academic Search

The brain lesions in stroke-prone spontaneously hypertensive rats (SHRSP) are characterized by multifocal microvascular and spongy-cystic parenchymal alterations particularly in the gray matter. An essential feature of the lesions is the presence of edema with massive extravasation of plasma constituents as evidenced by specific gravity measurements, Evans blue technique and immunohistochemistry. The nerve cell injury occurring in the brain lesions

K. Fredrikssonl; H. Kalimo; C. Nordborg; B. B. Johansson; Y. Olsson

1988-01-01

297

SIDS risk factors and factors associated with prone sleeping in Sweden  

Microsoft Academic Search

Objective: To compare the current prevalence of risk factors for sudden infant death syndrome (SIDS) in Sweden with a decade earlier, and assess factors associated with prone sleeping.Methods: The results of a cohort study (Infants of Western Sweden) and a population based case-control study (Nordic Epidemiological SIDS Study) were examined. Subjects were 5600 healthy 6 month old infants born in

B Alm; P Mo?llborg; L Erdes; R Pettersson; N A?berg; G Norvenius; G Wennergren

2006-01-01

298

Biomechanical simulations of scoliotic spine correction due to prone position and anaesthesia prior to surgical instrumentation  

Microsoft Academic Search

BackgroundThe positioning of patients during scoliosis surgery has been shown to affect the scoliosis curve, yet positioning has not been exploited to help improve surgical outcome from a biomechanics point of view. Biomechanical models have been used to study other aspects of scoliosis. The goal of this study is to simulate the specific influence of the prone operative position and

Kajsa Duke; Carl-Eric Aubin; Jean Dansereau; Hubert Labelle

2005-01-01

299

Variations in cardiac noradrenaline content during sodium loading in hypertension prone and resistant rats  

Microsoft Academic Search

Summary The cardiac catecholamine content of Sabra rats and their 2 genetically derived substrains, hypertension prone and resistant rats, was studied by high pressure liquid chromatography and electrochemical detection. Both in the control period and after sodium and DOCA administration the cardiac noradrenaline level is higher in hypertension resistant rats than in Sabra rats, and also higher than in hypertension

K. H. Le Quan-Bui; Marie-Aude Devynck; Marie-Gabrielle Pernollet; D. Ben-Ishay; P. Meyer

1981-01-01

300

Prone position as prevention of lung injury in comatose patients: a prospective, randomized, controlled study  

Microsoft Academic Search

Objective: Comatose patients frequently exhibit pulmonary function worsening, especially in cases of pulmonary infection. It appears to have a deleterious effect on neurologic outcome. We therefore conducted a randomized trial to determine whether daily prone positioning would prevent lung worsening in these patients. Design: Prospective, randomized, controlled study. Setting: Sixteen-bed intensive care unit. Patients: Fifty-one patients who required invasive mechanical

Pascal Beuret; Marie-Jose Carton; Karim Nourdine; Mahmoud Kaaki; Gerard Tramoni; Jean-Claude Ducreux

2002-01-01

301

The Dynamics of Visual Reweighting in Healthy and Fall-Prone Older Adults  

Microsoft Academic Search

Multisensory reweighting (MSR) is an adaptive process that prioritizes the visual, vestibular, and somatosensory inputs to provide the most reliable information for postural stability when environmental conditions change. This process is thought to degrade with increasing age and to be particularly deficient in fall-prone versus healthy older adults. In the present study, the authors investigate the dynamics of sensory reweighting,

John J. Jeka; Leslie K. Allison; Tim Kiemel

2010-01-01

302

Aniracetam enhances glutamatergic transmission in the prefrontal cortex of stroke-prone spontaneously hypertensive rats  

Microsoft Academic Search

The effects of aniracetam, a cognition enhancer, on extracellular levels of glutamate (Glu), ?-aminobutyric acid (GABA) and nitric oxide metabolites (NOx) were examined in the prefrontal cortex (PFC) and the basolateral amygdala (AMG) in stroke-prone spontaneously hypertensive rats (SHRSP) using in vivo microdialysis. Basal release of Glu, was lower in the AMG of SHRSP than in normotensive Wistar Kyoto rats,

Hiroko Togashi; Kazuo Nakamura; Machiko Matsumoto; Ken-ichi Ueno; Satoshi Ohashi; Hideya Saito; Mitsuhiro Yoshioka

2002-01-01

303

Aggregate-prone proteins with polyglutamine and polyalanine expansions are degraded by autophagy  

Microsoft Academic Search

Protein conformational disorders (PCDs), such as Alzheimer's disease, Huntington's disease (HD), Parkinson's disease and oculopharyngeal muscular dystrophy, are associated with proteins that misfold and aggregate. Here we have used exon 1 of the HD gene with expanded polyglutamine (poly(Q)) repeats and enhanced green fluorescent protein tagged to 19 alanines as models for aggregate-prone proteins, to investigate the pathways mediating their

Brinda Ravikumar; Rainer Duden; David C. Rubinsztein

2002-01-01

304

Error and Error Mitigation in Low-Coverage Genome Assemblies  

PubMed Central

The recent release of twenty-two new genome sequences has dramatically increased the data available for mammalian comparative genomics, but twenty of these new sequences are currently limited to ?2× coverage. Here we examine the extent of sequencing error in these 2× assemblies, and its potential impact in downstream analyses. By comparing 2× assemblies with high-quality sequences from the ENCODE regions, we estimate the rate of sequencing error to be 1–4 errors per kilobase. While this error rate is fairly modest, sequencing error can still have surprising effects. For example, an apparent lineage-specific insertion in a coding region is more likely to reflect sequencing error than a true biological event, and the length distribution of coding indels is strongly distorted by error. We find that most errors are contributed by a small fraction of bases with low quality scores, in particular, by the ends of reads in regions of single-read coverage in the assembly. We explore several approaches for automatic sequencing error mitigation (SEM), making use of the localized nature of sequencing error, the fact that it is well predicted by quality scores, and information about errors that comes from comparisons across species. Our automatic methods for error mitigation cannot replace the need for additional sequencing, but they do allow substantial fractions of errors to be masked or eliminated at the cost of modest amounts of over-correction, and they can reduce the impact of error in downstream phylogenomic analyses. Our error-mitigated alignments are available for download.

Hubisz, Melissa J.; Lin, Michael F.; Kellis, Manolis; Siepel, Adam

2011-01-01

305

Skylab water balance error analysis  

NASA Technical Reports Server (NTRS)

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.

Leonard, J. I.

1977-01-01

306

Multiple Regression with Stationary Errors.  

National Technical Information Service (NTIS)

A practical computing technique is presented for the joint estimation of regression coefficients and the error spectrum in regression problems with stationary errors. In problems where unweighted least squares is not efficient, the procedure gives an esti...

D. B. Duncan R. H. Jones

1966-01-01

307

Angle interferometer cross axis errors.  

National Technical Information Service (NTIS)

The authors have found what appears to be a previously unreported error in the measurement of surface plate flatness and the measurement of angular displacement errors in rotary tables using angle interferometers.

J. B. Bryan D. L. Carter S. L. Thompson

1993-01-01

308

Standard Errors for Matrix Correlations.  

ERIC Educational Resources Information Center

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)

Ogasawara, Haruhiko

1999-01-01

309

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

SciTech Connect

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.

Wilder, Richard B.; Chittenden, Lucy; Mesa, Albert V.; Bunyapanasarn, Jane; Agustin, Jeff; Lizarde, Jessica; Ravera, John; Tokita, Kenneth M. [Cancer Center of Irvine, 16100 Sand Canyon Ave., Ste. 130, Irvine, CA 92618 (United States)

2010-05-01

310

Radiation dose to the nodal regions during prone versus supine breast irradiation  

PubMed Central

Background Prone positioning for breast radiotherapy is preferable when the aim is a reduction of the dose to the ipsilateral lung or the heart in certain left-sided cases. Materials and methods In 100 breast cancer cases awaiting postoperative whole-breast radiotherapy, conformal radiotherapy plans were prospectively generated in both prone and supine positions. The axillary nodal region (levels I–III) and internal mammary (IM) lymph-node region in the upper three intercostal spaces were retrospectively contoured. The mean doses to the nodal regions and the volume receiving 25 Gy (V25Gy), V45Gy, and V47.5Gy were compared between the two treatment positions. Results In most cases, the doses to axillary levels I–III and the IM lymph nodes were inadequate, regardless of the treatment position. The nodal doses were significantly lower in the prone than in the supine position. The radiation doses to levels II–III and IM nodes were especially low. The V45Gy and V47.5Gy of the level I axillary lymph nodes were 54.6% and 40.2%, respectively, in the supine, and 3.0% and 1.7%, respectively, in the prone position. In the supine position, only 17 patients (17%) received a mean dose of 45 Gy to the axillary level I nodes. Conclusion The radiation dose to the axillary and IM lymph nodes during breast radiotherapy is therapeutically insufficient in most cases, and is significantly lower in the prone position than in the supine position.

Csenki, Melinda; Ujhidy, Dora; Cserhati, Adrienn; Kahan, Zsuzsanna; Varga, Zoltan

2014-01-01

311

Perceived threat mediates the relationship between psychosis proneness and aggressive behavior  

PubMed Central

Psychotic symptoms are associated with aggressive tendencies, but this relationship is both complex and imperfect. In contrast to psychotic disorders, little is known about aggressive behavior and sub-clinical psychotic symptoms (e.g., “psychosis proneness”), which are relatively common in the general population. Threat/control-override (TCO), which is the propensity to overestimate the likelihood that an outside agent will (1) inflict harm (threat) or (2) control one’s behaviors (control-override), has been associated with aggression in both psychiatric and community samples. The purpose of this study was to determine if psychosis proneness is related to aggression, and if one or both aspects of TCO mediate this relationship. We hypothesized that the propensity to overestimate threat would mediate this relationship, but control-override would not. Sixty men and sixty women (mean age = 20.00 years, sd = 3.00) with no history of psychotic disorder completed measures assessing psychosis proneness, threat control/override, aggressive history, aggressive ideation, and aggressive behavior. Three structural equation models were tested: (1) Threat and control-override modeled as separate mediating variables, (2) TCO as a unitary mediating latent construct, and (3) TCO considered as part of a psychosis-proneness latent variable. Results indicated that psychosis proneness is positively related to aggression and that the best model fit was obtained when threat and control-override were modeled as separate variables, with mediation through threat alone. The utility of TCO for explaining the relation between psychosis spectrum symptoms and aggression is discussed.

Fanning, Jennifer Renee; Berman, Mitchell Eric; Mohn, Richard Samuel; McCloskey, Michael Sean

2010-01-01

312

Simultaneous irradiation of the breast and regional lymph nodes in prone position using helical tomotherapy  

PubMed Central

Objective We investigated dosimetric advantages of using helical tomotherapy to simultaneously irradiate the breast and regional lymph nodes for patients positioned prone, and compared tomotherapy plan qualities for the prone position with those previously published for the supine position. Methods Tomotherapy plans for 11 patients (5 left breast, 6 right) simulated with the involved breast suspended downward were generated. Each target (ipsilateral breast and supraclavicular, axillary and internal mammary chain nodes) was to receive 45 Gy. Results For targets, V40.5?99.9% and V42.8?99.5% for all patients, where V40.5 and V42.8 denote the relative target volume receiving at least 40.5 and 42.8 Gy, respectively. The targets' maximum dose was, on average, approximately 49.5 Gy. The mean doses to the contralateral lung and heart were lower for right-breast cases (2.8 Gy lung, 2.7 Gy heart) than for left-breast cases (3.8 Gy lung, 8.7 Gy heart). Mean organ doses to the ipsilateral lung (9.3 Gy) and contralateral breast (2.3 Gy) from the prone breast tomotherapy plans were similar to those reported for conventional radiotherapy techniques. For the left breast with regional nodes, tomotherapy plans for prone-positioned patients yielded lower mean doses to the contralateral breast and heart than previously reported data for tomotherapy plans for supine-positioned patients. Conclusion Helical tomotherapy with prone breast positioning can simultaneously cover the breast and regional nodes with acceptable uniformity and can provide reduced mean dose to proximal organs at risk compared with tomotherapy with supine position. The similarity of plan quality to existing data for conventional breast radiotherapy indicates that this planning approach is appropriate, and that the risk of secondary tumour formation should not be significantly greater.

Kainz, K; White, J; Chen, G-P; Hermand, J; England, M; Li, X A

2012-01-01

313

Investigation of Helical Tomotherapy for Partial-Breast Irradiation of Prone-Positioned Patients  

SciTech Connect

Purpose: To investigate whether helical tomotherapy can provide conformal, uniform target-dose coverage for partial-breast irradiation (PBI) of patients positioned prone while achieving organ-at-risk sparing compliant with National Surgical Adjuvant Breast and Bowel Project (NSABP) B-39/Radiation Therapy Oncology Group (RTOG) 0413 guidelines; and to report our initial experience with the delivery of prone-breast PBI treatments using tomotherapy. Methods and Materials: For our pilot study, we generated helical tomotherapy plans upon the images of 10 prone-positioned patients previously treated using conventional techniques. We also generated plans for 4 left-breast prone-positioned PBI patients who were treated using helical tomotherapy, and recalculated the planned sinograms upon the pretreatment megavoltage computed tomographic images. Of the planning target volume (PTV), 95% was prescribed to receive 38.5 Gy, administered twice daily for 5 days. Results: For our pilot study, on average the maximum point dose to the PTV was 41.3 Gy, and 99% or more of the PTV received 90% or more of the prescribed dose. RTOG 0413 dose-volume histogram objectives were fulfilled for all organs at risk except the contralateral breast, which received a maximum point dose as high as 3.2 Gy in 1 case. For the prospective prone-positioned tomotherapy PBI plans, all objectives were met except the contralateral-breast maximum dose, which was 3.7 Gy on average. Dose calculation using the planned sinogram upon the pretreatment megavoltage computed tomographic images indicated consistency with the planned dose distributions. Conclusions: Helical tomotherapy can provide conformal and uniform target-dose coverage simultaneous with adequate sparing of critical structures; in this study only the contralateral breast dose exceeded RTOG 0413 guidelines. Dosimetric results for our 4 prospective patient cases were consistent with those for our 10-case pilot study.

Kainz, Kristofer [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States)], E-mail: kkainz@mcw.edu; White, Julia; Herman, Joann; Li, X. Allen [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States)

2009-05-01

314

Approaches to Quantum Error Correction  

Microsoft Academic Search

In a ground breaking discovery in 1994, Shor has shown that quantum computers, if built, can factor numbers efficiently. Since\\u000a then quantum computing has become a burgeoning field of research, attracting theoreticians and experimentalists alike, and\\u000a regrouping researchers from fields like computer science, physics, mathematics and engineering. Quantum information is very\\u000a fragile and prone to decoherence. Yet by the middle

Julia Kempe

2006-01-01

315

Interactive Histogram with Error Graph  

NSDL National Science Digital Library

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

Siegrist, Kyle

316

MOPITT V4 processing error  

MOPITT V4 processing error Version 4 The MOPITT/NCAR team discovered a data processing error that affects all V4 products previously generated for the period between ... the NASA ASDC. Details regarding the cause of the processing error and its effect on the MOPITT products are available on  News and Status ...

2013-08-06

317

Error Bounds for Interpolative Approximations.  

ERIC Educational Resources Information Center

Elementary error estimation in the approximation of functions by polynomials as a computational assignment, error-bounding functions and error bounds, and the choice of interpolation points are discussed. Precalculus and computer instruction are used on some of the calculations. (KR)

Gal-Ezer, J.; Zwas, G.

1990-01-01

318

Safety Stock and Forecast Error  

Microsoft Academic Search

This paper shows how the need for safety stock increases when the forecast error increases - and conversely -- how the ne ed for safety stock decreases when the forecast error decreases. A way to measure the change in safety stock with forecast error changes is presented. The paper also shows how much safety stock is needed relative to the

Nick T. Thomopoulos

319

Dietary ?-carotene regulates interleukin-1?-induced expression of apolipoprotein E in astrocytes isolated from stroke-prone spontaneously hypertensive rats.  

PubMed

Stroke-prone spontaneously hypertensive rats (SHRSP) have an abnormality in cholesterol synthesis, but the pathological relevance of this to stroke and related neuronal disorders is not yet clear. The induction of astrocyte-derived cholesterol transportation to neurons by apolipoprotein E (apoE) promotes neuronal repair after brain injuries such as stroke. Such repair is reduced by interleukin-1 beta (IL-1?) and stroke conditions. Furthermore, fibroblast growth factor 1 (FGF1) regulates the production of apoE-cholesterol-rich high density lipoproteins (HDL) and induces gliosis of astrocytes. On the other hand, high levels of plasma carotenoids reduce the risk of ischemic stroke. Thus, we investigated the expression of apoE in primary astrocytes that had been treated with IL-1? or ?-carotene. In addition, we compared the expression levels of Apoe genes in astrocytes from SHRSP/Izm and normal control rats, Wistar-Kyoto rats (WKY/Izm) following hypoxia/reoxygenation (H/R). The expression levels of genes and proteins were investigated by RT-PCR, Western blotting (WB), and immunofluorescence analysis. IL-1? decreased the expression levels of the Apoe gene. Conversely, ?-carotene significantly enhanced the expression levels of genes related to cholesterol regulation, including Abca1, Abcg1, Hmgcr as well as Apoe. During H/R, the gene expression levels of Apoe were decreased in the SHRSP/Izm rats in comparison with the WKY/Izm rats. These results suggest that IL-1? decreases Apoe expression levels, whereas ?-carotene strongly elevates Apoe levels and inhibits FGF1-mediated gliosis of astrocytes. Furthermore, under hypoxic stress, astrocytes isolated from SHRSP/Izm rats displayed altered regulation of Apoe compared with those from WKY/Izm rats. PMID:23147682

Yamagata, Kazuo; Nakayama, Chika; Suzuki, Koichi

2013-01-01

320

Maternal milk, but not formula, regulates the immune response to beta-lactoglobulin in allergy-prone rat pups.  

PubMed

Controversy exists regarding the timing of the introduction of allergic foods into the diet. We investigated the immune response of rat pups exposed to beta-lactoglobulin (BLG), one of the main allergenic proteins in cow milk. Brown Norway allergy-prone rats were allocated into groups: dam-reared and unchallenged (DR), DR challenged with BLG via gavage (11 mg/d), or rats fed via gastric cannula a formula containing BLG (11 mg/d). BLG was given from d 4 of life. Rats were killed at d 10, 14, or 21. Sera were assayed for total IgE, BLG-specific IgG1, and rat mucosal mast cell protease II (RMCPII; indicator of mucosal mast cell degranulation). Ileum was assessed for cytokine mRNA. Mesenteric lymph nodes (MLN) were assessed for forkhead boxP3 (Foxp3) and chemokine (C-C motif) receptor 7 (CCR7) expression by real-time PCR and immunostained for Foxp3(+) CD4(+) regulatory cells. Formula feeding compared with dam-rearing with or without oral BLG challenge resulted in significantly greater serum IgE, BLG-specific IgG1, RMCPII, and intestinal mast cells but reduced MLN Foxp3(+) cells, Foxp3, and CCR7 expression and ileal cytokines, interleukin (IL)-4, IL-10, and interferon-gamma (P < 0.05). Importantly, giving BLG in the presence of maternal milk resulted in an immune response profile similar to that of unchallenged DR rats but with greater Foxp3 and CCR7 mRNA expression and CD4(+) Foxp3(+) cells (P < 0.05). We conclude that introducing an allergenic food with breast milk reduces immunological indicators of an allergic response, whereas introduction during formula feeding generates an allergic response. PMID:19759244

Tooley, Katie L; El-Merhibi, Adaweyah; Cummins, Adrian G; Grose, Randall H; Lymn, Kerry A; DeNichilo, Mark; Penttila, Irmeli A

2009-11-01

321

Mask error enhancement factor  

NASA Astrophysics Data System (ADS)

Optical lithography at the limit of resolution is a highly non-linear pattern transfer process. One consequence of this is an apparent magnification of mask errors. The paper first demonstrates early experimental evidence of this effect. Then it assesses the influence of pattern geometry, of the lithography tool setup, and of different optical enhancement techniques on the MEEF using primarily simulation data. The correspondence of MEEF as an effect of mask linewidth variations to the increased printability of mask defects is illustrated. Strategies to minimize the MEEF--like alternating phase shift masks--are presented. Because the MEEF describes conveniently the concerted action of all components on the whole lithographic pattern transfer process, it is proposed to use the MEEF as a new yardstick to characterize the degree of difficulty of a given lithographic process.

Maurer, Wilhelm

2000-02-01

322

Quantification bias caused by plasmid DNA conformation in quantitative real-time PCR assay.  

PubMed

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

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

2011-01-01

323

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

PubMed Central

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.

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

2011-01-01

324

Mal-Adaptation of Event-Related EEG Responses Preceding Performance Errors  

PubMed Central

Recent EEG and fMRI evidence suggests that behavioral errors are foreshadowed by systematic changes in brain activity preceding the outcome by seconds. In order to further characterize this type of error precursor activity, we investigated single-trial event-related EEG activity from 70 participants performing a modified Eriksen flanker task, in particular focusing on the trial-by-trial dynamics of a fronto-central independent component that previously has been associated with error and feedback processing. The stimulus-locked peaks in the N2 and P3 latency range in the event-related averages showed expected compatibility and error-related modulations. In addition, a small pre-stimulus negative slow wave was present at erroneous trials. Significant error-preceding activity was found in local stimulus sequences with decreased conflict in the form of less negativity at the N2 latency (310–350?ms) accumulating across five trials before errors; concomitantly response times were speeding across trials. These results illustrate that error-preceding activity in event-related EEG is associated with the performance monitoring system and we conclude that the dynamics of performance monitoring contribute to the generation of error-prone states in addition to the more remote and indirect effects in ongoing activity such as posterior alpha power in EEG and default mode drifts in fMRI.

Eichele, Heike; Juvodden, Hilde T.; Ullsperger, Markus; Eichele, Tom

2010-01-01

325

Error negativity and response control.  

PubMed

Error trials are associated with faster responses than correct trials in simple discrimination tasks suggesting that errors result from impulsive responding. We investigated the relationship between error negativity (Ne/ERN), an event-related potential associated with error detection, and two behavioral indices of response control: response time (RT) differences between incorrect and correct trials (an index of impulsivity) and percentage of errors. Response-locked ERPs were collected from 17 young adults during a visual flanker task. Consistent with previous findings, participants were significantly faster on error trials. However, participants who exhibited larger Ne/ERN peak amplitudes had significantly smaller RT differences, suggesting a more controlled response strategy. Furthermore, Ne/ERN latencies were positively associated with percentage of errors. These findings are consistent with the view that the Ne/ERN reflects the activity of a monitoring system that is closely linked to remedial systems responsible for individual differences in response control or impulsive behavior. PMID:12212669

Pailing, Patricia E; Segalowitz, Sidney J; Dywan, Jane; Davies, Patricia L

2002-03-01

326

Error awareness and antisaccade performance.  

PubMed

In the antisaccade task, healthy participants often make errors by saccading towards the sudden onset target, despite instructions to saccade to the mirror image location. One interesting and relatively unexplored feature of antisaccade performance is that participants are typically unaware of a large proportion of the errors they make. Across two experiments, we explored the extent to which error awareness is altered by manipulations known to affect antisaccade error rate. In experiment 1, participants performed the antisaccade task under standard instructions, instructions to respond as quickly as possible or instructions to delay responding. Delay instructions significantly reduced antisaccade error rate compared to the other instructions, but this reduction was driven by a decrease only in the number of errors that participants were aware of-the number of errors of which participants were unaware remained constant across instruction condition. In experiment 2, participants performed antisaccades alone, or concurrently with two different distractor tasks-spatial tapping and random number generation task. Both the dual task conditions increased the number of errors of which participants were aware, but again, unaware error rates remained unchanged. These results are discussed in the light of recent models of antisaccade performance and the role of conscious awareness in error correction. PMID:21735247

Taylor, A J G; Hutton, S B

2011-08-01

327

Telomere measurement by quantitative PCR  

Microsoft Academic Search

It has long been presumed impossible to measure telomeres in vertebrate DNA by PCR amplification with oligonucleotide primers designed to hybridize to the TTAGGG and CCCTAA repeats, because only primer dimer-derived products are expected. Here we present a primer pair that eliminates this problem, allowing simple and rapid measurement of telomeres in a closed tube, fluorescence-based assay. This assay will

Richard M. Cawthon

2002-01-01

328

Gut microbiome in sudden infant death syndrome (SIDS) differs from that in healthy comparison babies and offers an explanation for the risk factor of prone position.  

PubMed

The role of bacteria in the causation of sudden infant death syndrome (SIDS) is gaining acceptance. Mainstream research favouring respiratory compromise has failed to provide a plausible pathogenetic mechanism despite many years of investigation and thousands of research papers. Bacterial colonisation of the colon of the human infant is influenced by many factors including age, mode of delivery, diet, environment, and antibiotic exposure. The gut microbiome influences development of the immune system. The gut microflora could be important in protection against the bacteria and/or their toxins purportedly involved in SIDS pathogenesis. The aim was to perform a preliminary investigation of the gut microflora in sudden infant death syndrome (SIDS) compared with live comparison babies. The intestinal contents from 52 SIDS, and 102 faecal samples from age-matched live comparison infants were screened by PCR to target 16s RNA genes of Clostridium innocuum, Cl. Perfringens, Cl. difficile, Bacteroides thetaiotaomicron and Staphylococcus aureus. Gut colonisation of the babies with these bacteria was analysed in relation to age, gender and type of feeding; and for SIDS babies sleeping position. Cl. difficile, Cl. innocuum and B. thetaiotaomicron were significantly associated with SIDS with 25%, 46% and 30% of cases PCR positive for these respective bacteria compared with only 6%, 23% and 8.8% respectively in the comparison group. SIDS babies had dual colonisation by both Cl. perfringens and Cl. difficile significantly more often than comparison babies and also with triple colonisation by Cl. perfringens, Cl. difficile and Cl. innocuum. SIDS babies were more often colonised by S. aureus than comparison babies. In addition, SIDS babies found prone were significantly more likely to be colonised by S. aureus than for other positions recorded (OR = ?; CI = 2·04 - ?). No significant differences between breast and bottle-fed SIDS babies was observed in regard to each clostridial bacterium, or S. aureus, however Cl. innocuum was found to be significantly associated with formula feeding in the comparison cohort. Comparison of breast and formula feeding of SIDS babies with live comparison babies revealed significant differences with regards to some of the clostridial bacteria. Age-specific differences in gut bacterial microbiome were observed in both SIDS and comparison healthy babies. This study gives an insight into differences in the gut bacterial microbiome of SIDS babies compared with healthy babies. These differences could be important in contributing to a baby's susceptibility to infection and therefore to SIDS. The association of S. aureus colonisation with prone sleep position supports the hypothesis that prone sleep position could increase the risk of ingestion/inhalation of bacteria contaminating the sleeping surface and could account for the increased risk of SIDS in babies who are put to sleep prone. The study provides impetus for broader studies into the gut microbiome of babies and could lead to effective approaches to SIDS prevention. PMID:24951305

Highet, Amanda R; Berry, Anne M; Bettelheim, Karl A; Goldwater, Paul N

2014-07-01

329

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

SciTech Connect

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.

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

1989-03-01

330

Update on diagnosis, pathogenesis and management of ketosis-prone Type 2 diabetes mellitus  

PubMed Central

SUMMARY Diabetic ketoacidosis (DKA) has been considered a key clinical feature of Type 1 diabetes mellitus; however, increasing evidence indicates that DKA is also a common feature of Type 2 diabetes (T2DM). Many cases of DKA develop under stressful conditions such as trauma or infection but an increasing number of cases without precipitating cause have been reported in children and adults with T2DM. Such patients present with severe hyperglycemia and ketosis as in Type 1 diabetes mellitus but can discontinue insulin after a few months and maintain acceptable glycemic control on diet or oral agents. This subtype of diabetes has been referred to as ketosis-prone T2DM. In this article, we reviewed the literature on ketosis-prone T2DM and summarized the epidemiology, putative pathophysiology and approaches to management.

Smiley, Dawn; Chandra, Prakash; Umpierrez, Guillermo E

2011-01-01

331

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

PubMed Central

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.

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

332

Design of Low Power & Reliable Networks on Chip Through Joint Crosstalk Avoidance and Multiple Error Correction Coding  

Microsoft Academic Search

Network on Chip (NoC) is an enabling methodology of integrating a very high number of intellectual property (IP) blocks in\\u000a a single System on Chip (SoC). A major challenge that NoC design is expected to face is the intrinsic unreliability of the\\u000a interconnect infrastructure under technology limitations. Research must address the combination of new device-level defects\\u000a or error-prone technologies within

Amlan Ganguly; Partha Pratim Pande; Benjamin Belzer; Cristian Grecu

2008-01-01

333

Medical errors: overcoming the challenges.  

PubMed

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

Kalra, Jawahar

2004-12-01

334

Local housing price index analysis in wind-disaster-prone areas  

Microsoft Academic Search

This study examines the effect of severe wind events on the mean and variance of housing price indices of six metropolitan\\u000a statistical areas (MSA) that are vulnerable to hurricanes and\\/or tornadoes. The research focuses on three areas that experienced\\u000a significant tornado activity (Fort Worth-Arlington, Nashville, and Oklahoma City) and three hurricane-prone areas (Corpus\\u000a Christi, Miami, and Wilmington, NC). An econometric

Bradley T. Ewing; Jamie B. Kruse; Yongsheng Wang

2007-01-01

335

Low Dose Poly I:C Prevents Diabetes in the Diabetes Prone BB Rat  

Microsoft Academic Search

Poly I:C, an inducer of IFN-? and other cytokines, has been used to study the development of diabetes in both the BioBreeding (BB) diabetes prone rat and non-obese diabetic (NOD) mouse animal models of insulin-dependent diabetes mellitus (IDDM). Surprisingly, poly I:C accelerates the disease in the BB rat while inhibiting it in the NOD mouse. Since cytokines can have dose

Douglas O Sobel; Deepshika Goyal; Behrouz Ahvazi; Ji-Won Yoon; Young Hwa Chung; Adam Bagg; David M Harlan

1998-01-01

336

Shame Aversion and Shame-Proneness in Cluster C Personality Disorders  

Microsoft Academic Search

The associations between shame and Cluster C personality disorders (PDs) were examined in 237 undergraduates, 35 of whom met at least subthreshold criteria for Cluster C PDs assessed using the Personality Disorder Interview–IV. Shame-proneness (the propensity to experience shame across many situations) was measured using the Test of Self-Conscious Affect–3, and shame aversion (the tendency to perceive shame as especially

Michelle Schoenleber; Howard Berenbaum

2010-01-01

337

Comparison of Outlier Detection Methods in Fault-Prone Module Detection  

Microsoft Academic Search

The goal of this paper is to improve the prediction performance of fault-proneness models by removing outliers from a dataset used for model construction. We experimentally eval- uated the effect of four outlier removal methods; Mahalanobis Outlier Analysis (MOA) and Local Outlier Factor Method (LOFM) which are well-known outlier detection methods for a single sample, and Rule-Based Modeling (RBM) suitable

Shinsuke Matsumoto; Yasutaka Kamei; Akito Monden; Ken-ichi Matsumoto

2008-01-01

338

Mild ischemia produces hippocampal neuronal death in stroke-prone spontaneously hypertensive rats  

Microsoft Academic Search

The blood flow in the hippocampus of stroke-prone spontaneously hypertensive rats (SHRSPs) and Wistar Kyoto (WKY) rats during occlusion of the carotid arteries was examined because it has been previously found that 2-vessel occlusion (2-VO) induces delayed neuronal death (DND) in the pyramidal cells of the CA1 hippocampal area in SHRSPs but not in WKY rats. DND was also examined

Hidekazu Kinugawa; Yasuko Sakurai-Yamashita; Masami Niwa

2008-01-01

339

Enalapril Prevents Imminent and Reduces Manifest Cerebral Edema in Stroke-Prone Hypertensive Rats  

Microsoft Academic Search

Background and Purpose—Stroke-prone spontaneously hypertensive rats (SHRSP), subjected to high NaCl intake, show severe hypertension, organ damage, and early death. Preventive treatment with an angiotensin-converting enzyme (ACE) inhibitor is known to reduce mortality. Previously we found that proteinuria always precedes cerebral edema in SHRSP. Hence, in this study ACE inhibition was started later, ie, directly after manifestation of either proteinuria

Erwin L. A. Blezer; Klaas Nicolay; P. R. Dop Bar; Roel Goldschmeding; Gerard H. Jansen; Hein A. Koomans; Jaap A. Joles

340

Use of new methods of compaction for soils prone to slump-type settlement  

SciTech Connect

The results of compaction of soils classed as type II in terms of proneness to slump-type settlement with the use of new procedures calling for the tamping out of soil cushions by a tampers weighing 5 and 11.8 tons, including tamping with wetting and sectioning of the wetted mass, made it possible to shorten considerably the time required to prepare the beds and construct buildings on a military post Budennovsk.

Bagdasarov, Yu.A.; Fingerov, S.L.

1995-03-01

341

Genetic and Environmental Influences on the Relationship between Flow Proneness, Locus of Control and Behavioral Inhibition  

PubMed Central

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.

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

2012-01-01

342

Sexual Attraction Status and Adolescent Suicide Proneness: The Roles of Hopelessness, Depression, and Social Support  

Microsoft Academic Search

This study explored the relationship between sexual attraction status (same-sex, both-sex, and opposite-sex) and suicidal behavior in a diverse sample of adolescents (N = 1,533 youth). Adolescents with attractions to both sexes reported greater suicide proneness, recent and lifetime suicidal ideation, and past suicide attempts than those with exclusively opposite-sex attractions; individuals reporting same-sex attractions generally demonstrated moderate elevations on

Jennifer Langhinrichsen-Rohling; Dorian A. Lamis; Patrick S. Malone

2010-01-01

343

New advances in identifying genetic anomalies in stroke-prone probands  

Microsoft Academic Search

The past several years have been marked by significant progress in identifying genetic anomalies in stroke-prone probands.\\u000a These advances have occurred in both highly penetrant single-gene disorders and in common stroke, which is influenced by risk\\/susceptibility\\u000a genes. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) can be challenging\\u000a to diagnose because of the wide range of notch 3

James F. Meschia; Bradford B. Worrall

2004-01-01

344

New advances in identifying genetic anomalies in stroke-prone probands  

Microsoft Academic Search

The past several years have been marked by significant progress in identifying genetic anomalies in stroke-prone probands.\\u000a These advances have occurred in both highly penetrant single-gene disorders and in common stroke, which is influenced by risk\\/susceptibility\\u000a genes. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) can be challenging\\u000a to diagnose because of the wide range of notch 3

James F. Meschia; Bradford B. Worrall

2003-01-01

345

Fault-prone module detection using large-scale text features based on spam filtering  

Microsoft Academic Search

This paper proposes an approach using large-scale text features for fault-prone module detection inspired by spam filtering.\\u000a The number of every text feature in the source code of a module is counted and used as data for training detection models.\\u000a In this paper, we prepared a naive Bayes classifier and a logistic regression model as detection models. To show the

Hideaki Hata; Osamu Mizuno; Tohru Kikuno

2010-01-01

346

Health Departments Do It Better: Prenatal Care Site and Prone Infant Sleep Position  

Microsoft Academic Search

Objectives: Reduction of prone infant sleep position has been the main public health effort to reduce the incidence of Sudden Infant Death Syndrome (SIDS). Methods: Oregon Pregnancy Risk Assessment Monitoring System (PRAMS) surveys a stratified random sample of women after a live birth. In 1998–1999, 1867 women completed the survey (64.0% unweighted response; 73.5% weighted response). Results: Overall, 9.2% of

Martin B. Lahr; Kenneth D. Rosenberg; Jodi A. Lapidus

2005-01-01

347

Lupeol supplementation improves blood pressure and lipid metabolism parameters in stroke-prone spontaneously hypertensive rats.  

PubMed

Supplementation with lupeol (0.67 g·kg(-1)) of the AIN-93M-based diet fed for 7 weeks to stroke-prone spontaneously hypertensive rats caused significantly decreased blood pressure as compared with a control group. Urinary 8-hydroxy-2'-deoxyguanosine was significantly lower in the lupeol group. Finally, lupeol suppressed the hepatic mRNA expression levels of the genes involved in triglyceride and cholesterol synthesis. PMID:22232260

Ardiansyah; Yamaguchi, Eri; Shirakawa, Hitoshi; Hata, Keishi; Hiwatashi, Kazuyuki; Ohinata, Kousaku; Goto, Tomoko; Komai, Michio

2012-01-01

348

Kinetics of thermal aging and its effect on the proneness of hull steels to brittle failure  

Microsoft Academic Search

1.The hull steels 10GN2MFA and 15Kh2NMFA-A have little proneness to aging) this is in keeping with the requirements that modern shell materials have to fulfill.2.The activation energy of the process of thermal aging (Q=70–80 kJ\\/mole) is close to the activation energy of diffusion of carbon in ferrite. The magnitude of the activation energy, and also the nature of the change

A. A. Astaf'ev; V. A. Yukhanov; A. D. Shur

1988-01-01

349

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

SciTech Connect

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

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

2010-06-01

350

Error modeling in stereo navigation  

Microsoft Academic Search

In stereo navigation, a mobile robot estimates its position by tracking landmarks with on-board cameras. Previous systems for stereo navigation have suffered from poor accuracy, in part because they relied on scalar models of measurement error in triangulation. Using three-dimensional (3D) Gaussian distributions to model triangulation error is shown to lead to much better performance. How to compute the error

L. Matthies; S. A. Shafer

1987-01-01

351

Exceptional error minimization in putative primordial genetic codes  

PubMed Central

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.

2009-01-01

352

Structure errors in system identification  

NASA Technical Reports Server (NTRS)

An approach to system identification is presented which explicitly takes structure errors into account and hence provides a systematic way for answering questions concerning the magnitude of estimated parameter errors resulting from structural errors. It is indicated that, from this point of view, it is possible to define near equivalence between process and model and to obtain meaningful theoretical results on solution error system identification. It remains to apply these results to large realistic problems such as those involving models of complex man machine systems.

Bekey, G. A.; Hadaegh, F. Y.

1984-01-01

353

A theory of human error  

NASA Technical Reports Server (NTRS)

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.

Mcruer, D. T.; Clement, W. F.; Allen, R. W.

1980-01-01

354

Zonal Error Propagation for JMAPS  

NASA Astrophysics Data System (ADS)

Propagation of accidental zonal errors of parallax is analyzed for J-MAPS. A method based on orthogonal spherical functions and a simplified setup of observational grid equations is proposed. Using this method, a full-scale simulation can be performed for a limited number of large-scale zonal errors, including the zero-point error, on a regular personal computer. Covariances of parallax zonal errors and their dependence on the density of grid quasars, the density and overlap of grid stars, the observing scenario, etc., can be investigated by this technique and the accompanying Matlab software.

Hennessy, Gregory S.; Makarov, V.

2009-12-01

355

Retransmission error control with memory  

NASA Technical Reports Server (NTRS)

In this paper, an error control technique that is a basic improvement over automatic-repeat-request ARQ is presented. Erroneously received blocks in an ARQ system are used for error control. The technique is termed ARQ-with-memory (MRQ). The general MRQ system is described, and simple upper and lower bounds are derived on the throughput achievable by MRQ. The performance of MRQ with respect to throughput, message delay and probability of error is compared to that of ARQ by simulating both systems using error data from a VHF satellite channel being operated in the ALOHA packet broadcasting mode.

Sindhu, P. S.

1977-01-01

356

Numerical Error Estimation with UQ  

NASA Astrophysics Data System (ADS)

Ocean models are still in need of means to quantify model errors, which are inevitably made when running numerical experiments. The total model error can formally be decomposed into two parts, the formulation error and the discretization error. The formulation error arises from the continuous formulation of the model not fully describing the studied physical process. The discretization error arises from having to solve a discretized model instead of the continuously formulated model. Our work on error estimation is concerned with the discretization error. Given a solution of a discretized model, our general problem statement is to find a way to quantify the uncertainties due to discretization in physical quantities of interest (diagnostics), which are frequently used in Geophysical Fluid Dynamics. The approach we use to tackle this problem is called the "Goal Error Ensemble method". The basic idea of the Goal Error Ensemble method is that errors in diagnostics can be translated into a weighted sum of local model errors, which makes it conceptually based on the Dual Weighted Residual method from Computational Fluid Dynamics. In contrast to the Dual Weighted Residual method these local model errors are not considered deterministically but interpreted as local model uncertainty and described stochastically by a random process. The parameters for the random process are tuned with high-resolution near-initial model information. However, the original Goal Error Ensemble method, introduced in [1], was successfully evaluated only in the case of inviscid flows without lateral boundaries in a shallow-water framework and is hence only of limited use in a numerical ocean model. Our work consists in extending the method to bounded, viscous flows in a shallow-water framework. As our numerical model, we use the ICON-Shallow-Water model. In viscous flows our high-resolution information is dependent on the viscosity parameter, making our uncertainty measures viscosity-dependent. We will show that we can choose a sensible parameter by using the Reynolds-number as a criteria. Another topic, we will discuss is the choice of the underlying distribution of the random process. This is especially of importance in the scope of lateral boundaries. We will present resulting error estimates for different height- and velocity-based diagnostics applied to the Munk gyre experiment. References [1] F. RAUSER: Error Estimation in Geophysical Fluid Dynamics through Learning; PhD Thesis, IMPRS-ESM, Hamburg, 2010 [2] F. RAUSER, J. MAROTZKE, P. KORN: Ensemble-type numerical uncertainty quantification from single model integrations; SIAM/ASA Journal on Uncertainty Quantification, submitted

Ackmann, Jan; Korn, Peter; Marotzke, Jochem

2014-05-01

357

Errors and error correction in automatic speech recognition systems  

Microsoft Academic Search

Errors, whether created by the user, the recognizer, or inadequate systems design, are an important consideration in the more widespread and successful use of automatic speech recognition (ASR). An experiment is described in which recognition errors are studied under different types of feedback. Subjects entered data verbally to a microcomputer according to four experimental conditions: namely, orthogonal combinations of spoken

J. M. NOYES; C. R. FRANKISH

1994-01-01

358

Thermal error modelling for real-time error compensation  

Microsoft Academic Search

A modelling strategy for the prediction of both the scalar and the position-dependent thermal error components is presented. Two types of empirical modelling method based on the multiple regression analysis (MRA) and the artificial neural network (ANN) have been proposed for the real-time prediction of thermal errors with multiple temperature measurements. Both approaches have a systematic and computerised algorithm to

J. S. Chen; J. Yuan; J. Ni

1996-01-01

359

Prone ventilation in a United States Marine with acute respiratory distress syndrome and an open abdominal injury.  

PubMed

A United States Marine with an open abdominal injury from a single gunshot wound to the chest and abdomen was placed in the prone position after suffering from acute respiratory distress syndrome (ARDS). Prone ventilation in traumatic injuries involving an open abdomen has been rarely reported or attempted because of the potentially fatal complication of bowel dehiscence. Improvement of gas exchange in patients with ARDS has been shown to occur with prone ventilation when conventional modes of ventilation have failed. The patient benefited from a sustained improvement in oxygenation hours after return to the supine position allowing for his rapid transport to a higher echelon of care and definitive management. PMID:19434044

Guerrero, Melanie; Cannizzo, Francis; Falta, Edward; Berndt, George

2009-06-01

360

A posteriori error estimator and error control for contact problems  

NASA Astrophysics Data System (ADS)

In this paper, we consider two error estimators for one-body contact problems. The first error estimator is defined in terms of H( div ) -conforming stress approximations and equilibrated fluxes while the second is a standard edge-based residual error estimator without any modification with respect to the contact. We show reliability and efficiency for both estimators. Moreover, the error is bounded by the first estimator with a constant one plus a higher order data oscillation term plus a term arising from the contact that is shown numerically to be of higher order. The second estimator is used in a control-based AFEM refinement strategy, and the decay of the error in the energy is shown. Several numerical tests demonstrate the performance of both estimators.

Weiss, Alexander; Wohlmuth, Barbara I.

2009-09-01

361

Error studies for SNS Linac. Part 1: Transverse errors  

SciTech Connect

The SNS linac consist of a radio-frequency quadrupole (RFQ), a drift-tube linac (DTL), a coupled-cavity drift-tube linac (CCDTL) and a coupled-cavity linac (CCL). The RFQ and DTL are operated at 402.5 MHz; the CCDTL and CCL are operated at 805 MHz. Between the RFQ and DTL is a medium-energy beam-transport system (MEBT). This error study is concerned with the DTL, CCDTL and CCL, and each will be analyzed separately. In fact, the CCL is divided into two sections, and each of these will be analyzed separately. The types of errors considered here are those that affect the transverse characteristics of the beam. The errors that cause the beam center to be displaced from the linac axis are quad displacements and quad tilts. The errors that cause mismatches are quad gradient errors and quad rotations (roll).

Crandall, K.R. [TechSource, Inc. (United States)

1998-12-31

362

Muscle Activation and Movement Patterns During Prone Hip Extension Exercise in Women  

PubMed Central

Context: The consistency of muscle activation order during prone hip extension has been debated. Objective: To investigate whether women use a consistent and distinguishable muscle activation order when extending the hip while prone and to explore the effects of verbal cues on muscle activation and movement. Design: Single-session, repeated-measures design. Setting: University laboratory. Patients or Other Participants: Eleven healthy women (age ?=? 27.7 ± 6.2 years [range, 22–37 years]). Intervention(s): We tested the participants under 3 conditions: no cues, cues to contract the gluteal muscles, and cues to contract the hamstrings muscles. Main Outcome Measure(s): We measured hip and knee angle and electromyographic data from the gluteus maximus, medial hamstrings, and lateral hamstrings while participants performed prone hip extension from 30° of hip flexion to neutral. Results: When not given cues, participants used the consistent and distinguishable muscle activation order of medial hamstrings, followed by lateral hamstrings, then gluteus maximus (195.5 ± 74.9, 100.2 ± 70.3, and 11.5 ± 81.9 milliseconds preceding start of movement, respectively). Compared with the no-cues condition, the gluteal-cues condition resulted in nearly simultaneous onset of medial hamstrings, lateral hamstrings, and gluteus maximus (131.3 ± 84.0, 38.8 ± 96.9, and 45.1 ± 93.4 milliseconds, respectively) (P > .059); decreased activation of the medial hamstrings (P < .03) and lateral hamstrings (P < .024) around the initiation of movement; increased activation of gluteus maximus throughout the movement (P < .001); and decreased knee flexion (P ?=? .002). Compared with the no-cues condition, the hamstrings-cues condition resulted in decreased activation of the medial hamstrings just after the initiation of movement (P ?=? .028) and throughout the movement (P ?=? .034) and resulted in decreased knee flexion (P ?=? .003). Conclusions: Our results support the contention that the muscle activation order during prone hip extension is consistent in healthy women and demonstrates that muscle timing and activation amplitude and movement can be modified with verbal cues. This information is important for clinicians using prone hip extension as either an evaluation tool or a rehabilitation exercise.

Lewis, Cara L; Sahrmann, Shirley A

2009-01-01

363

Accuracy in Copy Number Calling by qPCR and PRT: A Matter of DNA  

PubMed Central

The possible implication of copy number variation (CNV) in the genetic susceptibility to human disease needs to be assessed using robust methods that can be applied at a population scale. In this report, we analyze the performance of the two major techniques, quantitative PCR (qPCR) and paralog ratio test (PRT), and investigate the influence of input DNA amount and template integrity on the reliability of both methods. Analysis of three genes (PRELID1, SYNPO and DEFB4) in a large sample set showed that both methods are prone to false copy number assignments if sufficient attention is not paid to DNA concentration and quality. Accurate normalization of samples is essential for reproducible qPCR because it avoids the effect of differential amplification efficiencies between target and control assays, whereas PRT is generally more sensitive to template degradation due to the fact that longer amplicons are usually needed to optimize sensitivity and specificity of paralog sequence PCR. The use of normalized, high quality genomic DNA yields comparable results with both methods.

Fernandez-Jimenez, Nora; Castellanos-Rubio, Ainara; Plaza-Izurieta, Leticia; Gutierrez, Galder; Irastorza, Inaki; Castano, Luis; Vitoria, Juan Carlos; Bilbao, Jose Ramon

2011-01-01

364

Development of a multiplex quantitative fluorescent PCR assay for identification of rearrangements in the AZFb and AZFc regions.  

PubMed

The azoospermia factor b (AZFb) and azoospermia factor c (AZFc) regions in the human Y chromosome consist of five palindromes constructed from six distinct families of amplicons and are prone to rearrangement. Partial deletion and duplication in the region can cause azoospermia or oligozoospermia and male infertility. The aim of the study was to establish a quantitative fluorescent PCR (QF-PCR) assay to classify AZFb and AZFc rearrangements. A single pair of fluorescent primers was designed to amplify simultaneously the amplicon in AZFc and the length-variant homologous sequences outside of the region as control. Since the copy number of the control sequences is fixed in the human genome, dosage of the target could be easily obtained through comparing the height of the fluorescent peaks between the target and the control after amplification with limited PCR cycles. Most types of rearrangements in AZFb and AZFc regions could be classified with QF-PCR containing four such primer pairs. Eleven types of rearrangement in AZFb and AZFc regions were well discriminated with QF-PCR. In conclusion, QF-PCR is a simple and reliable method to detect rearrangements in AZFb and AZFc. PMID:18445645

Zhang, Jun; Li, Pei-qiong; Yu, Qi-hong; Chen, Hua-yun; Li, Juan; He, Yun-shao

2008-06-01

365

Comparative Study of Hemodynamics Electrolyte and Metabolic Changes During Prone and Complete Supine Percutaneous Nephrolithotomy  

PubMed Central

Background Nowadays Percutaneous Nephrolithotomy (PCNL) is performed in prone and supine positions. Physiologic solutions should be used to irrigate during PCNL. Irrigation can cause hemodynamic, electrolyte and acid-base changes during PCNL. Objectives The current study aimed to compare the electrolyte, hemodynamic and metabolic changes of prone and complete supine PCNL. Patients and Methods It was a randomized clinical trial study on 40 ASA class I and II patients. Twenty of patients underwent prone PCNL (Group A) and the other twenty underwent complete supine PCNL (Group B). The two groups received the same premedication and induction of anesthesia. Blood pressure (systolic, diastolic and mean) and pulse rate were recorded before, during and after anesthesia and Hb, Hct, BUN, Cr, Na, and K were also measured before and after operation in the two groups. The volume of irrigation fluid, total effluent fluid (the fluid in the bucket and the gazes) and volume of absorbed fluid were measured. Results There were no significant differences in Na, K, BUN, Cr, Hb and Hct between the two groups. Absorption volume was significantly different between the two groups (335 ± 121.28 mL in group A and 159.45 ± 73.81 mL in group B, respectively) (P = 0.0001). The mean anesthesia time was significantly different between the two groups (P = 0.012). There was a significant difference in bleeding volume between supine and prone PCNL (270.4 ± 229.14 in group A and 594.2 ± 290 in group B, respectively) (P = 0.0001). Mean systolic blood pressure during operation and recovery was 120.2 ± 10.9 and 140.7 ± 25.1 in group B, and 113.4 ± 6.4 and 126.2 ± 12.7 in group A, respectively. Systolic blood pressure between the two groups during operation and recovery was significantly different (P = 0.027 and P = 0.022, respectively). Mean diastolic blood pressure in supine group during operation and recovery was 80.53 ± 7.57 and 95.75 ± 17.48, and 73.95 ± 3.94 and 83.4 ± 12.54 in prone group, respectively. Diastolic blood pressure was significantly different between the two groups. It was 80.55 ± 7.57 and 95.75 ± 17.48, respectively during operation and recoveryin the supine group and 73.95 ± 3.94 and 83.4 ± 12.54 in the prone group, respectively (P = 0.001 and P = 0.014, respectively), but there was no significant difference between the pulse rate mean value of the two groups. Conclusions The electrolyte and metabolic changes were not significantly different between the two groups, and although fluid absorption in prone group was more than that of the complete supine group, there was no significant difference between the two groups. Considering advantages of complete supine PCNL such as less hemodynamic changes (less hypotension, less fluid absorption and less duration of operation) this kind of PCNL was recommended.

Khoshrang, Hosein; Falahatkar, Siavash; Ilat, Sara; Akbar, Manzar Hossein; Shakiba, Maryam; Farzan, Alireza; Herfeh, Nadia Rastjou; Allahkhah, Aliakbar

2012-01-01

366

Eliminating US hospital medical errors  

Microsoft Academic Search

Purpose – Healthcare costs in the USA have continued to rise steadily since the 1980s. Medical errors are one of the major causes of deaths and injuries of thousands of patients every year, contributing to soaring healthcare costs. The purpose of this study is to examine what has been done to deal with the medical-error problem in the last two

Sameer Kumar; Marc Steinebach

2008-01-01

367

Rapid mapping of volumetric errors.  

National Technical Information Service (NTIS)

This paper describes a relatively inexpensive, fast, and easy to execute approach to mapping the volumetric errors of a machine tool, coordinate measuring machine, or robot. An error map is used to characterize a machine or to improve its accuracy by comp...

D. Krulewich L. Hale D. Yordy

1995-01-01

368

Numerical Errors: Reliable Numerical Simulations.  

National Technical Information Service (NTIS)

Understanding numerical errors in long calculations is a very subtle science and is critical to understanding the reliability of the final answer. We will carefully examine the accumulation of numerical errors over time and discuss how these can lead to r...

L. Jameson

2001-01-01

369

Dual Processing and Diagnostic Errors  

ERIC Educational Resources Information Center

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,…

Norman, Geoff

2009-01-01

370

Error Correction, Revision, and Learning  

ERIC Educational Resources Information Center

Previous research has shown that corrective feedback on an assignment helps learners reduce their errors on that assignment during the revision process. Does this finding constitute evidence that learning resulted from the feedback? Differing answers play an important role in the ongoing debate over the effectiveness of error correction,…

Truscott, John; Hsu, Angela Yi-ping

2008-01-01

371

Explaining Errors in Children's Questions  

ERIC Educational Resources Information Center

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,…

Rowland, Caroline F.

2007-01-01

372

Human error in recreational boating.  

PubMed

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

McKnight, A James; Becker, Wayne W; Pettit, Anthony J; McKnight, A Scott

2007-03-01

373

Angle interferometer cross axis errors  

SciTech Connect

Angle interferometers are commonly used to measure surface plate flatness. An error can exist when the centerline of the double comer cube mirror assembly is not square to the surface plate and the guide bar for the mirror sled is curved. Typical errors can be one to two microns per meter. A similar error can exist in the calibration of rotary tables when the centerline of the double comer cube mirror assembly is not square to the axes of rotation of the angle calibrator and the calibrator axis is not parallel to the rotary table axis. Commercial double comer cube assemblies typically have non-parallelism errors of ten milli-radians between their centerlines and their sides and similar values for non-squareness between their centerlines and end surfaces. The authors have developed a simple method for measuring these errors and correcting them by remachining the reference surfaces.

Bryan, J.B.; Carter, D.L.; Thompson, S.L.

1994-01-01

374

Same-session endourological removal of upper and impacted lower urinary tract stones with the aid of prone flexible cystoscopy.  

PubMed

Calculi were removed from the upper urinary tracts and the distal ureter in single sessions in 2 patients with the aid of prone flexible cystoscopy and a through-and-through stone basket. PMID:3599194

Eshghi, M; Addonizio, J C

1987-07-01

375

Investigation of the Causes of the Coronary-Prone (Type A) Behavior Pattern and Coronary Heart Disease.  

National Technical Information Service (NTIS)

This study investigates the relationships between the coronary-prone (Type A) behavior pattern, coronary heart disease (CHD), and stress. Behavioral and organizational data were obtained from 204 respondents; physiological data were obtained from 184 resp...

M. S. Kalna

1983-01-01

376

An Assessment of the Relationship between the Coronary-Prone (Type A) Behavior Pattern, Stress, and Coronary Heart Disease.  

National Technical Information Service (NTIS)

This cross-sectional study examines the relationships between the coronary-prone (Tpe A) behavior pattern, stress, and coronary heart disease (CHD). Past research indicates that Type A behavior is related to both CHD and stress. Behavioral and organizatio...

T. J. McDonald

1982-01-01

377

A hybrid fem-based method for aligning prone and supine images for image guided breast surgery  

Microsoft Academic Search

In breast conserving surgery clinicians may benefit from information from preoperative images (e.g. high quality dynamic contrast enhanced magnetic resonant image obtained in the prone position), by registering them to the supine patient on the operating table in the theatre. Due to large deformation involved between prone and supine, either non-rigid intensity-based mage registration methods or biomechanical model based methods

Lianghao Han; John Hipwell; Thomy Mertzanidou; Tim Carter; Marc Modat; Sebastien Ourselin; David Hawkes

2011-01-01

378

Real-time PCR in virology  

Microsoft Academic Search

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

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

2002-01-01

379

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...

380

Stochastic Models of Human Errors  

NASA Technical Reports Server (NTRS)

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.

Elshamy, Maged; Elliott, Dawn M. (Technical Monitor)

2002-01-01

381

Mars gravitational field estimation error  

NASA Technical Reports Server (NTRS)

The error covariance matrices associated with a weighted least-squares differential correction process have been analyzed for accuracy in determining the gravitational coefficients through degree and order five in the Mars gravitational potential junction. The results are presented in terms of standard deviations for the assumed estimated parameters. The covariance matrices were calculated by assuming Doppler tracking data from a Mars orbiter, a priori statistics for the estimated parameters, and model error uncertainties for tracking-station locations, the Mars ephemeris, the astronomical unit, the Mars gravitational constant (G sub M), and the gravitational coefficients of degrees six and seven. Model errors were treated by using the concept of consider parameters.

Compton, H. R.; Daniels, E. F.

1972-01-01

382

Error bounds in cascading regressions  

USGS Publications Warehouse

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.

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

1985-01-01

383

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

SciTech Connect

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.

Croog, Victoria J.; Wu, Abraham J.; McCormick, Beryl [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Beal, Kathryn P. [Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (United States)], E-mail: bealk@mskcc.org

2009-01-01

384

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

ERIC Educational Resources Information Center

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…

Thornton, Brenda; Basu, Chhandak

2011-01-01

385

Protective effects of CD832 on organ damage in stroke-prone spontaneously hypertensive rats  

Microsoft Academic Search

Effects of a newly developed Ca2+ channel antagonist, (4R)-(?)-2-(nicotinoylamino)ethyl 3 nitrooxypropyl 1,4-dihydro-2,6-dimethyl-4-(3-nitrophenyl) 3,5-pyridine-dicarboxylate (CD-832), on hypertensive complications in stroke-prone spontaneously hypertensive rats (SHRSPs) were compared with effects of diltiazem. We examined changes in histological and hematological parameters in SHRSPs given the following treatments at 8 to 20 weeks of age: (a) CD-832; (b) diltiazem; (c) no treatment. CD-832 and diltiazem

Teisuke Takahashi; Satomi Tanikawa; Kenzo Takahashi

1997-01-01

386

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

PubMed

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

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

2014-05-01

387

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

PubMed Central

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.

Froggatt, P.

1970-01-01

388

Clinical applications using digital PCR.  

PubMed

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

Bizouarn, Francisco

2014-01-01

389

Label-free microelectronic PCR quantification.  

PubMed

We present a robust and simple method for direct, label-free PCR product quantification using an integrated microelectronic sensor. The field-effect sensor can sequentially detect the intrinsic charge of multiple unprocessed PCR products and does not require sample processing or additional reagents in the PCR mixture. The sensor measures nucleic acid concentration in the PCR relevant range and specifically detects the PCR products over reagents such as Taq polymerase and nucleotide monomers. The sensor can monitor the product concentration at various stages of PCR and can generate a readout that resembles that of a real-time fluorescent measurement using an intercalating dye but without its potential inhibition artifacts. The device is mass-produced using standard semiconductor processes, can be reused for months, and integrates all sensing components directly on-chip. As such, our approach establishes a foundation for the direct integration of PCR-based in vitro biotechnologies with microelectronics. PMID:16615760

Hou, Chih-Sheng Johnson; Milovic, Nebojsa; Godin, Michel; Russo, Peter R; Chakrabarti, Raj; Manalis, Scott R

2006-04-15

390

Static Detection of Disassembly Errors  

SciTech Connect

Static disassembly is a crucial ?rst step in reverse engineering executable ?les, 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.

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

2009-10-13

391

Error-correcting microarray design.  

PubMed

We describe a microarray design based on the concept of error-correcting codes from digital communication theory. Currently, microarrays are unable to efficiently deal with "drop-outs," when one or more spots on the array are corrupted. The resulting information loss may lead to decoding errors in which no quantitation of expression can be extracted for the corresponding genes. This issue is expected to become increasingly problematic as the number of spots on microarrays expands to accommodate the entire genome. The error-correcting approach employs multiplexing (encoding) of more than one gene onto each spot to efficiently provide robustness to drop-outs in the array. Decoding then allows fault-tolerant recovery of the expression information from individual genes. The error-correcting method is general and may have important implications for future array designs in research and diagnostics. PMID:12620393

Khan, Arshad H; Ossadtchi, Alex; Leahy, Richard M; Smith, Desmond J

2003-02-01

392

Detecting Reference Errors Before Publication.  

National Technical Information Service (NTIS)

When conducting research, the author has become increasingly frustrated by citation and quotation errors. In a recently published book chapter, its author summarized a research study but cited a paper from a completely different study. This same author ma...

M. J. De Jong

2003-01-01

393

Guiding Intellect for Occlusal Errors  

PubMed Central

Purpose: The purpose of the study is to quantify occlusal errors seen, during the processing of complete denture. Material and Methods: Maxillary and mandibular complete dentures were fabricated for 30 subjects. Anterior and posterior markings were made on articulator and the distance was measured from these points before and after processing of complete dentures. Occlusal errors following processing of complete dentures was determined by subjecting the values obtained to statistical analysis using paired t-test. Results: The results indicated the existence of discrepant amount of occlusal errors following processing of complete denture and statistical test applied was paired t-test, p-values obtained are, p=0.00 anterior reference markings and p=0.006 for posterior reference markings (p ? 0.001 highly significant). Conclusion: The processing errors are inevitable. Hence for patient comfort, laboratory remounting is an important procedure that needs to be followed as a regular step after processing of each and every denture.

Patel, Mansi; A.A., Ponnanna; Tripathi, Gaurav

2013-01-01

394

A simple ABO genotyping by PCR using sequence-specific primers with mismatched nucleotides.  

PubMed

In forensics, the specific ABO blood group is often determined by analyzing the ABO gene. Among various methods used, PCR employing sequence-specific primers (PCR-SSP) is simpler than other methods for ABO typing. When performing the PCR-SSP, the pseudo-positive signals often lead to errors in ABO typing. We introduced mismatched nucleotides at the second and the third positions from the 3'-end of the primers for the PCR-SSP method and examined whether reliable typing could be achieved by suppressing pseudo-positive signals. Genomic DNA was extracted from nail clippings of 27 volunteers, and the ABO gene was examined with PCR-SSP employing primers with and without mismatched nucleotides. The ABO blood group of the nail clippings was also analyzed serologically, and these results were compared with those obtained using PCR-SSP. When mismatched primers were employed for amplification, the results of the ABO typing matched with those obtained by the serological method. When primers without mismatched nucleotides were used for PCR-SSP, pseudo-positive signals were observed. Thus our method may be used for achieving more reliable ABO typing. PMID:24656782

Taki, Takashi; Kibayashi, Kazuhiko

2014-05-01

395

qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data  

Microsoft Academic Search

Although quantitative PCR (qPCR) is becoming the method of choice for expression profiling of selected genes, accurate and\\u000a straightforward processing of the raw measurements remains a major hurdle. Here we outline advanced and universally applicable\\u000a models for relative quantification and inter-run calibration with proper error propagation along the entire calculation track.\\u000a These models and algorithms are implemented in qBase, a

Jan Hellemans; Geert Mortier; Anne De Paepe; Frank Speleman; Jo Vandesompele

2007-01-01

396

Relative-Error-Covariance Algorithms  

NASA Technical Reports Server (NTRS)

Two algorithms compute error covariance of difference between optimal estimates, based on data acquired during overlapping or disjoint intervals, of state of discrete linear system. Provides quantitative measure of mutual consistency or inconsistency of estimates of states. Relative-error-covariance concept applied, to determine degree of correlation between trajectories calculated from two overlapping sets of measurements and construct real-time test of consistency of state estimates based upon recently acquired data.

Bierman, Gerald J.; Wolff, Peter J.

1991-01-01

397

Color error-diffusion halftoning  

Microsoft Academic Search

Grayscale halftoning converts a continuous-tone image (e.g., 8 bits per pixel) to a lower resolution (e.g., 1 bit per pixel) for printing or display. Grayscale halftoning by error diffusion uses feedback to shape the quantization noise into high frequencies where the human visual system (HVS) is least sensitive. In color halftoning, the application of grayscale error-diffusion methods to the individual

Niranjan Damera-Venkata; Brian L. Evans; Vishal Monga

2003-01-01

398

Range from focus-error  

Microsoft Academic Search

We derive theoretically and demonstrate experimentally an approach to range-from-focus with an important improvement over all previous methods. Previous methods rely on subjective measures of sharpness to focus a selected locale of the image. Our method uses measured physical features of the optical signal to generate an objective focus-error distance map. To compute range-from-focus-error distance it is not necessary to

M. W. Siegel; M. L. Leary

399

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

NASA Astrophysics Data System (ADS)

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.

Kreuer, Dieter; Quernheim, Ulrich

1991-10-01

400

Quantum error correction for beginners  

NASA Astrophysics Data System (ADS)

Quantum error correction (QEC) and fault-tolerant quantum computation represent one of the most vital theoretical aspects of quantum information processing. It was well known from the early developments of this exciting field that the fragility of coherent quantum systems would be a catastrophic obstacle to the development of large-scale quantum computers. The introduction of quantum error correction in 1995 showed that active techniques could be employed to mitigate this fatal problem. However, quantum error correction and fault-tolerant computation is now a much larger field and many new codes, techniques, and methodologies have been developed to implement error correction for large-scale quantum algorithms. In response, we have attempted to summarize the basic aspects of quantum error correction and fault-tolerance, not as a detailed guide, but rather as a basic introduction. The development in this area has been so pronounced that many in the field of quantum information, specifically researchers who are new to quantum information or people focused on the many other important issues in quantum computation, have found it difficult to keep up with the general formalisms and methodologies employed in this area. Rather than introducing these concepts from a rigorous mathematical and computer science framework, we instead examine error correction and fault-tolerance largely through detailed examples, which are more relevant to experimentalists today and in the near future.

Devitt, Simon J.; Munro, William J.; Nemoto, Kae

2013-07-01

401

The usability-error ontology.  

PubMed

Clinical Systems have become standard partners with clinicians in the care of patients. As these systems become integral parts of the clinical workflow, they have the potential to help improve patient outcomes, however they have also in some cases have led to adverse events and has resulted in patients coming to harm. Often the root cause analysis of these adverse events can be traced back to Usability Errors in the Health Information Technology (HIT) or its interaction with users. Interoperability of the documentation of HIT related Usability Errors in a consistent fashion can improve our ability to do systematic reviews and meta-analyses. In an effort to support improved and more interoperable data capture regarding Usability Errors, we have created the Usability Error Ontology (UEO) as a classification method for representing knowledge regarding Usability Errors. We expect the UEO will grow over time to support an increasing number of HIT system types. In this manuscript, we present this Ontology of Usability Error Types and specifically address Computerized Physician Order Entry (CPOE), Electronic Health Records (EHR) and Revenue Cycle HIT systems. PMID:23941937

Elkin, Peter L; Beuscart-Zephir, Marie-Catherine; Pelayo, Sylvia; Patel, Vimla; Nøhr, Christian

2013-01-01

402

Multiplex real-time PCR (MRT-PCR) for diarrheagenic.  

PubMed

Diarrheagenic Escherichia coli strains are important causes of diarrhea in children from the developing world and are now being recognized as emerging enteropathogens in the developed world. Current methods of detection are too expensive and labor-intensive for routine detection of these organisms to be practical. We developed a real-time fluorescence-based multiplex PCR for the detection of all six of the currently recognized classes of diarrheagenic E. coli. The primers were designed to specifically amplify eight different virulence genes in the same reaction: aggR for enteroaggregative E. coli (EAEC), stIa/stIb and lt for enterotoxigenic E. coli (ETEC), eaeA for enteropathogenic E. coli (EPEC), stx1 and stx2 for Shiga toxin-producing E. coli (STEC), ipaH for enteroinvasive E. coli (EIEC), and daaD for diffusely adherent E. coli (DAEC). PMID:23104299

Barletta, Francesca; Ochoa, Theresa J; Cleary, Thomas G

2013-01-01

403

An Analysis of Muscle Activities of Healthy Women during Pilates Exercises in a Prone Position.  

PubMed

[Purpose] This study analyzed the activities of the back and hip muscles during Pilates exercises conducted in a prone position. [Subjects] The subjects were 18 healthy women volunteers who had practiced at a Pilates center for more than three months. [Methods] The subjects performed three Pilates exercises. To examine muscle activity during the exercises, 8-channel surface electromyography (Noraxon USA, Inc., Scottsdale, AZ) was used. The surface electrodes were attached to the bilateral latissimus dorsi muscle, multifidus muscle, gluteus maximus, and semitendinous muscle. Three Pilates back exercises were compared: (1) double leg kick (DLK), (2) swimming (SW), and (3) leg beat (LB). Electrical muscle activation was normalized to maximal voluntary isometric contraction. Repeated measures analysis of variance was performed to assess the differences in activation levels among the exercises. [Results] The activity of the multifidus muscle was significantly high for the SW (52.3±11.0, 50.9±9.8) and LB exercises(51.8±12.8, 48.3±13.9) and the activity of the semitendinosus muscle was higher for the LB exercise (49.2±8.7, 52.9±9.3) than for the DLK and SW exercises. [Conclusion] These results may provide basic material for when Pilates exercises are performed in a prone position and may be useful information on clinical Pilates for rehabilitation programs. PMID:24567680

Kim, Bo-In; Jung, Ju-Hyeon; Shim, Jemyung; Kwon, Hae-Yeon; Kim, Haroo

2014-01-01

404

Acute Exacerbations of Asthma: Epidemiology, Biology and the Exacerbation-Prone Phenotype  

PubMed Central

Asthma is a highly prevalent chronic respiratory disease affecting 300 million people worldwide. 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 15.0 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 for the “exacerbation-prone” phenotype are incompletely understood but include extrinsic factors: cigarette smoking, medication noncompliance, 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-? and IFN-?). 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.

Dougherty, RH; Fahy, John V

2009-01-01

405

Xenobiotic acceleration of idiopathic systemic autoimmunity in lupus-prone bxsb mice.  

PubMed Central

The diverse genetic backgrounds of lupus-prone murine models, which produce both quantitative and qualitative differences in disease expression, may be a valuable resource for studying the influence of environmental exposure on autoimmune disease in sensitive populations. We tested this premise by exposing autoimmune-prone BXSB and the nonautoimmune C57BL/6 mice to the heavy metal mercury. Although both strains express a nonsusceptible H-2 haplotype, exposure to mercury accelerated systemic autoimmunity in both male and female BXSB mice, whereas the C57BL/6 mice were resistant. The subclasses of antichromatin antibodies elicited in BXSB mice by mercury exposure were more consistent with the predominant Th1-type response of idiopathic disease than with the Th2-type response found in mercury-induced autoimmunity (HgIA). The appearance and magnitude of both humoral and cellular features of systemic autoimmunity correlated with the mercury dose. Furthermore, environmentally relevant tissue levels of mercury were associated with exacerbated systemic autoimmunity. These studies demonstrate that xenobiotic exposure can accelerate spontaneous systemic autoimmunity, and they support the possibility that low-level xenobiotic exposure enhances susceptibility to systemic autoimmunity in genetically susceptible individuals.

Pollard, K M; Pearson, D L; Hultman, P; Deane, T N; Lindh, U; Kono, D H

2001-01-01

406

Efficacy of hemocontrol biofeedback system in intradialytic hypotension-prone hemodialysis patients.  

PubMed

We conducted a study to determine whether the hemocontrol biofeedback system (HBS) can improve intradialytic hypotension (IDH) in hypotension-prone hemodialysis (HD) patients compared with conventional HD. In this multicenter prospective crossover study, 60 hypotension-prone patients were serially treated by conventional HD for 8 weeks (period A), by HD with hemoscan blood volume monitoring for 2 weeks (period B0), and by HBS HD for 8 weeks (period B1). The number of sessions complicated by symptomatic IDH during 24 HD sessions (14.9±5.8 sessions, 62.1% in period A vs 9.2±7.2 sessions, 38.4% in period B1, P<0.001) and the number of IDH-related nursing interventions in a session (0.96±0.66 in period A vs 0.56±0.54 in period B1, P<0.001) significantly decreased in period B1 than in period A. Recovery time from fatigue after dialysis was significantly shorter in period B1 than in period A. The patients with higher post-dialysis blood pressure, lower difference between pre- and post-dialysis blood pressure, less frequent IDH, and higher pre- and post-dialysis body weight in period A responded better to HBS in period B1 in regard to the reduction of IDH. In conclusion, HBS may improve the patient tolerability to HD by reducing the IDH frequency and promoting faster recovery from fatigue after dialysis. PMID:24932082

Gil, Hyo-Wook; Bang, Kitae; Lee, So Young; Han, Byoung Geun; Kim, Jin Kuk; Kim, Young Ok; Song, Ho Cheol; Kwon, Young Joo; Kim, Yong-Soo

2014-06-01

407

Automated matching of supine and prone colonic polyps based on PCA and SVMs  

NASA Astrophysics Data System (ADS)

Computed tomographic colonography (CTC) is a feasible and minimally invasive method for the detection of colorectal polyps and cancer screening. In current practice, a patient will be scanned twice during the CTC examination - once supine and once prone. In order to assist the radiologists in evaluating colon polyp candidates in both scans, we expect the computer aided detection (CAD) system can provide not only the locations of suspicious polyps, but also the possible matched pairs of polyps in two scans. In this paper, we propose a new automated matching method based on the extracted features of polyps by using principal component analysis (PCA) and Support Vector Machines (SVMs). Our dataset comes from the 104 CT scans of 52 patients with supine and prone positions collected from three medical centers. From it we constructed two groups of matched polyp candidates according to the size of true polyps: group A contains 12 true polyp pairs (> 9 mm) and 454 false pairs; group B contains 24 true polyp pairs (6-9 mm) and 514 false pairs. By using PCA, we reduced the dimensions of original data (with 157 attributes) to 30 dimensions. We did leave-one-patient-out test on the two groups of data. ROC analysis shows that it is easier to match bigger polyps than that of smaller polyps. On group A data, when false alarm probability is 0.18, the sensitivity of SVM achieves 0.83 which shows that automated matching of polyp candidates is practicable for clinical applications.

Wang, Shijun; Van Uitert, Robert L.; Summers, Ronald M.

2008-04-01

408

Triage of oxidation-prone proteins by Sqstm1/p62 within the mitochondria  

SciTech Connect

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.

Lee, Minjung [Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine and Samsung Biomedical Research Institute, Suwon-Si, Kyonggi-Do (Korea, Republic of)] [Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine and Samsung Biomedical Research Institute, Suwon-Si, Kyonggi-Do (Korea, Republic of); Shin, Jaekyoon, E-mail: jkshin@med.skku.ac.kr [Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine and Samsung Biomedical Research Institute, Suwon-Si, Kyonggi-Do (Korea, Republic of)] [Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine and Samsung Biomedical Research Institute, Suwon-Si, Kyonggi-Do (Korea, Republic of)

2011-09-16

409

Aggregation-Prone Proteins Modulate Huntingtin Inclusion Body Formation in Yeast  

PubMed Central

Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a polyglutamine expansion in the huntingtin (HTT) protein. The expression of mutant HTT in the baker’s yeast Saccharomyces cerevisiae recapitulates many of the cellular phenotypes observed in mammalian HD models. Mutant HTT aggregation and toxicity in yeast is influenced by the presence of the Rnq1p and Sup35p prions, as well as other glutamine/asparagine-rich aggregation-prone proteins. Here we investigated the ability of a subset of these proteins to modulate mutant HTT aggregation and to substitute for the prion form of Rnq1p. We find that overexpression of either the putative prion Ybr016wp or the Sup35p prion restores aggregation of mutant HTT in yeast cells lacking the Rnq1p prion. These results indicate that an interchangeable suite of aggregation-prone proteins regulates mutant HTT aggregation dynamics in yeast, which may have implications for mutant HTT aggregation in human cells.

Kantcheva, Ralitsa B.; Mason, Robert; Giorgini, Flaviano

2014-01-01

410

Use of thermal inertia determined by HCMM to predict nocturnal cold prone areas in Florida  

NASA Technical Reports Server (NTRS)

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.

Allen, L. H., Jr. (principal investigator)

1983-01-01

411

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

PubMed Central

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

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

2014-01-01

412

Aggregation-prone proteins modulate huntingtin inclusion body formation in yeast.  

PubMed

Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a polyglutamine expansion in the huntingtin (HTT) protein. The expression of mutant HTT in the baker's yeast Saccharomyces cerevisiae recapitulates many of the cellular phenotypes observed in mammalian HD models. Mutant HTT aggregation and toxicity in yeast is influenced by the presence of the Rnq1p and Sup35p prions, as well as other glutamine/asparagine-rich aggregation-prone proteins. Here we investigated the ability of a subset of these proteins to modulate mutant HTT aggregation and to substitute for the prion form of Rnq1p. We find that overexpression of either the putative prion Ybr016wp or the Sup35p prion restores aggregation of mutant HTT in yeast cells lacking the Rnq1p prion. These results indicate that an interchangeable suite of aggregation-prone proteins regulates mutant HTT aggregation dynamics in yeast, which may have implications for mutant HTT aggregation in human cells. PMID:24804153

Kantcheva, Ralitsa B; Mason, Robert; Giorgini, Flaviano

2014-01-01

413

Rock fragments and soil physical properties in the fire-prone Portuguese schist region  

NASA Astrophysics Data System (ADS)

Fires often occur on shallow or stony soils. In Portugal for instance, one of the most fire-prone countries in Europe, 51% of the fires between 1990 and 2008 occurred on shallow soils ( 2300 topsoil samples collected at 13 sites in the Portuguese schist region in north-central Portugal. Soil physical properties assessed include soil water retention, saturated hydraulic conductivity, soil water repellency, bulk density and soil organic matter content. I will additionally show how surface rock fragments, and rock fragments incorporated into the soil, affect soil temperatures during fire. The particle density of these rock fragments was determined at 2.36 g cm-3 (for particles 2-20 mm), indicating that use of the common value of 2.65 g cm-3 to calculate rock fragment volume from their weight may lead to underestimation of the volume of rock fragments in the soil, and an associated underestimation of the bulk density of the fine earth fraction. The differences and commonalities between sites will be highlighted, and the impacts of rock fragments on fire impact and soil hydrology in fire-prone environments discussed.

Stoof, Cathelijne R.

2014-05-01

414

Identification of error sources in shock data  

Microsoft Academic Search

Instrumentation error sources are frequently encountered during the measurement of mechanical shock transients. This paper investigates the effects of two common errors: zero shifts and noise spikes. Non-trivial frequency domain manifestations of these errors are noted. Effective methods of identifying these errors are introduced and demonstrated. The significance of the problem is founded on the implications which these errors have

Thomas J. Baca; R. Glenn Bell

1988-01-01

415

Error Statistics for Normal Random Variables.  

National Technical Information Service (NTIS)

Four commonly used error statistics (the root mean square error, the geometric mean error, the mean radial error, and the spherical (or circular) error probable) are surveyed and compared in two and three dimensions. Exact or approximate closed-form expre...

D. R. Childs D. M. Coffey S. P. Travis

1975-01-01

416

Execution error recovery for planning systems  

Microsoft Academic Search

A system is presented that is capable of handling failures during execution. The error recovery process consists of error detection, error identification and plan repair. The problem of error identification has been solved by using the condition-oriented approach, which is the central theme of this study. Error classification is necessary for accurate modification of a failing plan. The classification process

K. H. Chang; M. Edhala

1988-01-01

417

Simulation of error sources in digital channels  

Microsoft Academic Search

A general approach to error-source simulation in digital channels is discussed. It is shown that the stochastic sequential machine (SSM) model is general enough to describe error-source statistics in digital communication channels. The SSM model is capable of describing both the correlation between errors in a channel (bursts of errors) and the correlation between errors in different channels (crosstalk). Physical

WILLIAM TURIN

1988-01-01

418

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

419

High-throughput real-time PCR.  

PubMed

Real-time PCR is presently the gold standard of gene expression quantification. Configuration of real-time PCR instruments with 384-well reaction blocks, enables the instrument to be used essentially as a low-density array. While PCR will never rival the throughput of microchip arrays, in situations where one is interested in assaying several hundreds of genes, high throughput, real-time PCR is an excellent alternative to microchip arrays. By combining SYBR green detection and 5 microL reaction volume, the associated costs of high-throughput real-time PCR are comparable to microarrays. Described here is a complete protocol to perform real-time PCR in a 384-well configuration. Examples are provided to access numerous PCR primer sequences that may be used for high-throughput real-time PCR. Methods of analysis are described to present real-time PCR data as heat maps and clustered similar to the presentation of cDNA microarray data. An example is provided to profile the expression of over 200 microRNA precursors using high-throughput real-time PCR. PMID:18695961

Schmittgen, Thomas D; Lee, Eun Joo; Jiang, Jinmai

2008-01-01

420

Error-Prone Translesion DNA Synthesis by Escherichia coli DNA Polymerase IV (DinB) on Templates Containing 1,2-dihydro-2-oxoadenine.  

PubMed

Escherichia coli DNA polymerase IV (Pol IV) is involved in bypass replication of damaged bases in DNA. Reactive oxygen species (ROS) are generated continuously during normal metabolism and as a result of exogenous stress such as ionizing radiation. ROS induce various kinds of base damage in DNA. It is important to examine whether Pol IV is able to bypass oxidatively damaged bases. In this study, recombinant Pol IV was incubated with oligonucleotides containing thymine glycol (dTg), 5-formyluracil (5-fodU), 5-hydroxymethyluracil (5-hmdU), 7,8-dihydro-8-oxoguanine (8-oxodG) and 1,2-dihydro-2-oxoadenine (2-oxodA). Primer extension assays revealed that Pol IV preferred to insert dATP opposite 5-fodU and 5-hmdU, while it inefficiently inserted nucleotides opposite dTg. Pol IV inserted dCTP and dATP opposite 8-oxodG, while the ability was low. It inserted dCTP more effectively than dTTP opposite 2-oxodA. Pol IV's ability to bypass these lesions decreased in the order: 2-oxodA > 5-fodU~5-hmdU > 8-oxodG > dTg. The fact that Pol IV preferred to insert dCTP opposite 2-oxodA suggests the mutagenic potential of 2-oxodA leading to A:T?G:C transitions. Hydrogen peroxide caused an ~2-fold increase in A:T?G:C mutations in E. coli, while the increase was significantly greater in E. coli overexpressing Pol IV. These results indicate that Pol IV may be involved in ROS-enhanced A:T?G:C mutations. PMID:20976264

Hori, Masaki; Yonekura, Shin-Ichiro; Nohmi, Takehiko; Gruz, Petr; Sugiyama, Hiroshi; Yonei, Shuji; Zhang-Akiyama, Qiu-Mei

2010-01-01

421

Application of reverse transcription-PCR and real-time PCR in nanotoxicity research.  

PubMed

Reverse transcription-polymerase chain reaction (RT-PCR) is a relatively simple and inexpensive technique to determine the expression level of target genes and is widely used in biomedical science research including nanotoxicology studies for semiquantitative analysis. Real-time PCR allows for the detection of PCR amplification in the exponential growth phase of the reaction and is much more quantitative than traditional RT-PCR. Although a number of kits and reagents for RT-PCR and real-time PCR are commercially available, the basic principles are the same. Here, we describe the procedures for total RNA isolation by using TRI Reagent, for reverse transcription (RT) by M-MLV reverse transcriptase, and for PCR by GoTaq(®) DNA Polymerase. And real-time PCR will be performed on an iQ5 multicolor real-time PCR detection system by using iQ™ SYBR Green Supermix. PMID:22975959

Mo, Yiqun; Wan, Rong; Zhang, Qunwei

2012-01-01

422

Sensitivity to prediction error in reach adaptation  

PubMed Central

It has been proposed that the brain predicts the sensory consequences of a movement and compares it to the actual sensory feedback. When the two differ, an error signal is formed, driving adaptation. How does an error in one trial alter performance in the subsequent trial? Here we show that the sensitivity to error is not constant but declines as a function of error magnitude. That is, one learns relatively less from large errors compared with small errors. We performed an experiment in which humans made reaching movements and randomly experienced an error in both their visual and proprioceptive feedback. Proprioceptive errors were created with force fields, and visual errors were formed by perturbing the cursor trajectory to create a visual error that was smaller, the same size, or larger than the proprioceptive error. We measured single-trial adaptation and calculated sensitivity to error, i.e., the ratio of the trial-to-trial change in motor commands to error size. We found that for both sensory modalities sensitivity decreased with increasing error size. A reanalysis of a number of previously published psychophysical results also exhibited this feature. Finally, we asked how the brain might encode sensitivity to error. We reanalyzed previously published probabilities of cerebellar complex spikes (CSs) and found that this probability declined with increasing error size. From this we posit that a CS may be representative of the sensitivity to error, and not error itself, a hypothesis that may explain conflicting reports about CSs and their relationship to error.

Haith, Adrian M.; Harran, Michelle D.; Shadmehr, Reza

2012-01-01

423

PCR diagnostics and monitoring of adenoviral infections in hematopoietic stem cell transplantation recipients  

PubMed Central

After stem cell transplantation, human patients are prone to life-threatening opportunistic infections with a plethora of microorganisms. We report a retrospective study on 116 patients (98 children, 18 adults) who were transplanted in a pediatric bone marrow transplantation unit. Blood, urine and stool samples were collected and monitored for adenovirus (AdV) DNA using polymerase chain reaction (PCR) and real-time PCR (RT-PCR) on a regular basis. AdV DNA was detected in 52 (44.8%) patients, with mortality reaching 19% in this subgroup. Variables associated with adenovirus infection were transplantations from matched unrelated donors and older age of the recipient. An increased seasonal occurrence of adenoviral infections was observed in autumn and winter. Analysis of immune reconstitution showed a higher incidence of AdV infections during periods of low T-lymphocyte count. This study also showed a strong interaction between co-infections of AdV and BK polyomavirus in patients undergoing hematopoietic stem cell transplantations.

Ussowicz, Marek; Rybka, Blanka; Wendycz-Domalewska, Danuta; Ryczan, Renata; Gorczynska, Ewa; Kalwak, Krzysztof; Wozniak, Mieczyslaw

2010-01-01

424

Shot through with voices: Dissociation mediates the relationship between varieties of inner speech and auditory hallucination proneness  

PubMed Central

Inner speech is a commonly experienced but poorly understood phenomenon. The Varieties of Inner Speech Questionnaire (VISQ; McCarthy-Jones & Fernyhough, 2011) assesses four characteristics of inner speech: dialogicality, evaluative/motivational content, condensation, and the presence of other people. Prior findings have linked anxiety and proneness to auditory hallucinations (AH) to these types of inner speech. This study extends that work by examining how inner speech relates to self-esteem and dissociation, and their combined impact upon AH-proneness. 156 students completed the VISQ and measures of self-esteem, dissociation and AH-proneness. Correlational analyses indicated that evaluative inner speech and other people in inner speech were associated with lower self-esteem and greater frequency of dissociative experiences. Dissociation and VISQ scores, but not self-esteem, predicted AH-proneness. Structural equation modelling supported a mediating role for dissociation between specific components of inner speech (evaluative and other people) and AH-proneness. Implications for the development of “hearing voices” are discussed.

Alderson-Day, Ben; McCarthy-Jones, Simon; Bedford, Sarah; Collins, Hannah; Dunne, Holly; Rooke, Chloe; Fernyhough, Charles

2014-01-01

425

A preliminary investigation on the relationship between color-word Stroop task performance and delusion-proneness in nonpsychiatric adults.  

PubMed

The current study examined whether there is a relationship between the dimension of delusion-proneness and performance on the color-word Stroop task. As dysfunction in the anterior cingulate cortex (ACC) has been related to both Stroop task performance and the presence of delusions in various psychiatric populations, we hypothesized that impaired Stroop performance would relate to increased delusion-proneness in a nonpsychiatric sample. A total of 36 college students, representing a wide range of scores on a measure of delusion-proneness (Peters et al. Delusions Inventory-PDI-21), completed a computerized version of the classic color-word Stroop task. Results revealed a statistically significant positive correlation between the PDI-21 score and the Stroop effect. The pattern of results suggests that reduced efficiency of Stroop performance is related to increasing levels of delusion-proneness. This study appears to be the first to report this relationship across a continuum of delusion-proneness in a nonpsychiatric sample. This finding contributes to the cognitive neurobiological understanding of delusions and adds further support for the dimensional construct of propensity for delusions. PMID:19913920

Orem, Diana M; Bedwell, Jeffrey S

2010-01-30

426

42 CFR 1005.23 - Harmless error.  

Code of Federal Regulations, 2013 CFR

... 2013-10-01 2013-10-01 false Harmless error. 1005.23 Section 1005.23 Public Health ...MONEY PENALTIES AND ASSESSMENTS § 1005.23 Harmless error. No error in either the admission or the exclusion of...

2013-10-01

427

42 CFR 3.552 - Harmless error.  

Code of Federal Regulations, 2012 CFR

...DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL PROVISIONS PATIENT SAFETY ORGANIZATIONS AND PATIENT SAFETY WORK PRODUCT Enforcement Program § 3.552 Harmless error. No error in either the admission or the exclusion of evidence, and no error or...

2012-10-01

428

Delineation of flood-prone areas and the identification of residential hotspots for two African cities  

NASA Astrophysics Data System (ADS)

This work employs two GIS-based frameworks for identifying the urban residential hot spots. This is done by overlaying a map of potentially flood prone areas (the topographic wetness index, TWI) and a map of urban morphology types (UMT) classified as residential. The topographic wetness index (TWI, Qin et al. 2011) allows for the delineation of a portion of a hydrographic basin potentially exposed to flood inundation by identifying all the areas characterized by a topographic index that exceeds a given threshold. The urban morphological types (Pauleit and Duhme 2000, Gill et al. 2008, Cavan et al. 2012) form the foundation of a classification scheme which brings together facets of urban form and function. The application of the UMTs allows the delineation of geographical units. The distinction of UMTs at a 'meso'-scale (i.e. between the city level and that of the individual units) makes a suitable basis for the spatial analysis of cities. The TWI threshold value depends on the resolution of the digital elevation model (DEM), topology of the hydrographic basin (i.e. urban, peri-urban or rural) and the constructed infrastructure (Manfreda et al. 2011). This threshold value is usually calibrated based on the results of detailed delineation of the inundation profile for selected zones. In this study, the TWI threshold is calibrated based on the calculated inundation profiles for various return periods for selected zones within the basin through a Bayesian framework. The Bayesian framework enables the probabilistic characterization of the threshold value by calculating the complementary probability of false delineation of flood prone zones as a function of various threshold values. For a given return period, the probability of false delineation is calculated as the sum of the probability of indicating a zone flood prone which is not indicated as such by the inundation profile and the probability that a zone is indicated as not flood prone but indicated as flood prone by the inundation profile. Applying the above-mentioned procedure, taking into account all available information on the inundation profiles for various zones within the basin, leads to a probability distribution for the TWI threshold value. In the next step, the urban residential hot spots to flooding are delineated in the GIS environment by overlaying the map of TWI and the UMT units classified as residential for various percentiles of the TWI threshold. Differences in exposure characteristics can be assessed for a range of different residential types, including for example between condominium/multi-storey, single storey stone/concrete and areas predominantly associated with mud/wood construction. For each percentile value considered, the delineated flood-prone residential areas and the number of people potentially affected to flooding are calculated. Moreover, the potential dependence of the estimated threshold percentiles on the flooding return period is investigated. As a demonstration, the urban residential hotspots to flooding are delineated for 16th, 50th and 84th percentiles of the TWI value for the cities of Dar es Salaam and Addis Ababa. References Qin C.Z., Zhu A.X., Pei T., Li B.L., Scholten T., Behrens T., Zhou C.H.. An approach to computing topographic wetness index based on maximum downslope gradient. Precision Agric, 12:32-43, DOI 10.1007/s11119-009-9152-y, 2011. Manfreda S., Di Leo M., Sole A. Detection of Flood-Prone Areas Using Digital Elevation Models. Journal of Hydrologic Engineering, 16 (10):781-790, 2011. Pauleit, S. and Duhme, F. (2000). Assessing the environmental performance of land cover types for urban planning. Landscape and Urban Planning, 52 (1): 1-20. Gill, S.E., Handley, J.F., Ennos, A.R. Pauleit, S., Theuray, N., and Lindley, S.J. (2008). Characterising the urban environment of UK cities and towns: a template for landscape planning in a changing climate. Landscape and Urban Planning, 87: 210-222. Cavan, G., Lindley, S., Yeshitela, K., Nebebe, A., Woldegerima, T., Shemdoe, R., Kibassa, D., Pauleit, S., Renner, R., Printz, A., Buc

De Risi, Raffaele; Jalayer, Fatemeh; De Paola, Francesco; Iervolino, Iunio; Giugni, Maurizio; Topa, Maria Elena; Yonas, Nebyou; Nebebe, Alemu; Woldegerima, Tekle; Yeshitela, Kumelachew; Kibassa, Deusdedit; Shemdoe, Riziki; Cavan, Gina; Lindley, Sarah; Renner, Florian; Printz, Andreas

2013-04-01

429

Automatic-repeat-request error control schemes  

NASA Technical Reports Server (NTRS)

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.

Lin, S.; Costello, D. J., Jr.; Miller, M. J.

1983-01-01

430

Bit error rate in NAND Flash memories  

Microsoft Academic Search

NAND flash memories have bit errors that are corrected by error-correction codes (ECC). We present raw error data from multi-level-cell devices from four manufacturers, identify the root-cause mechanisms, and estimate the resulting uncorrectable bit error rates (UBER). Write, retention, and read-disturb errors all contribute. Accurately estimating the UBER requires care in characterization to include all write errors, which are highly

Neal Mielke; Todd Marquart; Ning Wu; Jeff Kessenich; Hanmant Belgal; Eric Schares; Falgun Trivedi; Evan Goodness; Leland R. Nevill

2008-01-01

431

Synthetic aperture interferometry: error analysis  

SciTech Connect

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)].APOPAI0003-693510.1364/AO.42.000701 A method to measure steep aspherics using the SAI technique has been previously reported [Appl. Opt.47, 1705 (2008)].APOPAI0003-693510.1364/AO.47.001705 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.

Biswas, Amiya; Coupland, Jeremy

2010-07-10

432

Spacecraft and propulsion technician error  

NASA Astrophysics Data System (ADS)

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.

Schultz, Daniel Clyde

433

Error in statistical tests of error in statistical tests  

Microsoft Academic Search

BACKGROUND: A recent paper found that terminal digits of statistical values in Nature deviated significantly from an equiprobable distribution, indicating errors or inconsistencies in rounding. This finding, as well as the discovery that a large percentage of p values were inconsistent with reported test statistics, led to a great deal of concern in the popular press and scientific community. The

Monwhea Jeng

2006-01-01

434

Crediting errors: Credit, liquidity, performance and The Comedy of Errors  

Microsoft Academic Search

The spectre of the market is a predictable end of teleological economic criticism, which promotes a play like TheComedy of Errors for anticipating and neatly illustrating the bewildering liquidity of the capitalist market. But looking to its pre-classical source and not only to a putative future, the play seems to reject cash liquidity – a striking choice given the much

Colette Gordon

2010-01-01

435

Real-time PCR in microfluidic devices  

NASA Astrophysics Data System (ADS)

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.

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

2014-03-01

436

DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity.  

PubMed

DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability. PMID:24473148

Gonzalez-Huici, Victor; Szakal, Barnabas; Urulangodi, Madhusoodanan; Psakhye, Ivan; Castellucci, Federica; Menolfi, Demis; Rajakumara, Eerappa; Fumasoni, Marco; Bermejo, Rodrigo; Jentsch, Stefan; Branzei, Dana

2014-02-18

437

Foraging errors play a role in resource exploration by bumble bees (Bombus terrrestris).  

PubMed

If the cognitive performance of animals reflects their particular ecological requirements, how can we explain appreciable variation in learning ability amongst closely related individuals (e.g. foraging workers within a bumble bee colony)? One possibility is that apparent 'errors' in a learning task actually represent an alternative foraging strategy. In this study we investigate the potential relationship between foraging 'errors' and foraging success among bumble bee (Bombus terrestris) workers. Individual foragers were trained to choose yellow, rewarded flowers and ignore blue, unrewarded flowers. We recorded the number of errors (visits to unrewarded flowers) each bee made during training, then tested them to determine how quickly they discovered a more profitable food source (either familiar blue flowers, or novel green flowers). We found that error prone bees discovered the novel food source significantly faster than accurate bees. Furthermore, we demonstrate that the time taken to discover the novel, more profitable, food source is positively correlated with foraging success. These results suggest that foraging errors are part of an 'exploration' foraging strategy, which could be advantageous in changeable foraging environments. This could explain the observed variation in learning performance amongst foragers within social insect colonies. PMID:24838937

Evans, Lisa J; Raine, Nigel E

2014-06-01

438

The Rad5 helicase activity is dispensable for error-free DNA post-replication repair.  

PubMed

DNA post-replication repair (PRR) functions to bypass replication-blocking lesions and is subdivided into two parallel pathways: error-prone translesion DNA synthesis and error-free PRR. While both pathways are dependent on the ubiquitination of PCNA, error-free PRR utilizes noncanonical K63-linked polyubiquitinated PCNA to signal lesion bypass through template switch, a process thought to be dependent on Mms2-Ubc13 and a RING finger motif of the Rad5 ubiquitin ligase. Previous in vitro studies demonstrated the ability of Rad5 to promote replication fork regression, a function dependent on its helicase activity. To investigate the genetic and mechanistic relationship between fork regression in vitro and template switch in vivo, we created and characterized site-specific mutations defective in the Rad5 RING or helicase activity. Our results indicate that both the Rad5 ubiquitin ligase and the helicase activities are exclusively involved in the same error-free PRR pathway. Surprisingly, the Rad5 helicase mutation abolishes its physical interaction with Ubc13 and the K63-linked PCNA polyubiquitin chain assembly. Indeed, physical fusions of Rad5 with Ubc13 bypass the requirement for either the helicase or the RING finger domain. Since the helicase domain overlaps with the SWI/SNF chromatin-remodelling domain, our findings suggest a structural role of this domain and that the Rad5 helicase activity is dispensable for error-free lesion bypass. PMID:24674630

Ball, Lindsay G; Xu, Xin; Blackwell, Susan; Hanna, Michelle D; Lambrecht, Amanda D; Xiao, Wei

2014-04-01

439

Program Analyzes Errors In STAGS  

NASA Technical Reports Server (NTRS)

EAC computer program designed for analysis of errors in results of STAGS computer program (COSMIC Program HQN-10967). Requires input data for geometry of plate, properties of material, and set of boundary conditions. These input data come from STAGS code. (The specific link between input and output data from STAGS and input data for EAC is POSTP, postprocessor program in STAGS processors.) EAC computes continuous solution from discrete results of STAGS in order to estimate error of results of STAGS. Written in FORTRAN 77.

Thurston, Gaylen A.; Bains, Nancy Jane C.

1991-01-01

440

Correction of errors in tandem mass spectrum extraction enhances phosphopeptide identification.  

PubMed

The tandem mass spectrum extraction of phosphopeptides is more difficult and error-prone than that of unmodified peptides due to their lower abundance, lower ionization efficiency, the cofragmentation with other high-abundance peptides, and the use of MS(3) on MS(2) fragments with neutral losses. However, there are still no established methods to evaluate its correctness. Here we propose to identify and correct these errors via the combinatorial use of multiple spectrum extraction tools. We evaluated five free and two commercial extraction tools using Mascot and phosphoproteomics raw data from LTQ FT Ultra, in which RawXtract 1.9.9.2 identified the highest number of unique phosphopeptides (peptide expectation value <0.05). Surprisingly, ProteoWizzard (v. 3.0.3476) extracted wrong precursor mass for most MS(3) spectra. Comparison of the top three free extraction tools showed that only 54% of the identified spectra were identified consistently from all three tools, indicating that some errors might happen during spectrum extraction. Manual check of 258 spectra not identified from all three tools revealed 405 errors of spectrum extraction with 7.4% in selecting wrong precursor charge, 50.6% in selecting wrong precursor mass, and 42.1% in exporting MS/MS fragments. We then corrected the errors by selecting the best extracted MGF file for each spectrum among the three tools for another database search. With the errors corrected, it results in the 22.4 and 12.2% increase in spectrum matches and unique peptide identification, respectively, compared with the best single method. Correction of errors in spectrum extraction improves both the sensitivity and confidence of phosphopeptide identification. Data analysis on nonphosphopeptide spectra indicates that this strategy applies to unmodified peptides as well. The identification of errors in spectrum extraction will promote the improvement of spectrum extraction tools in future. PMID:24147958

Hao, Piliang; Ren, Yan; Tam, James P; Sze, Siu Kwan

2013-12-01

441

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

USGS Publications Warehouse

Non-invasive genetic sampling (NGS) is becoming a popular tool for population estimation. However, multiple NGS studies have demonstrated that polymerase chain reaction (PCR) genotyping errors can bias demographic estimates. These errors can be detected by comprehensive data filters such as the multiple-tubes approach, but this approach is expensive and time