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Sample records for error prone pcr

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

    PubMed

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

    2011-07-01

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

  2. [Directed evolution of lipase of Bacillus pumilus YZ02 by error-prone PCR].

    PubMed

    Huang, Ying; Cai, Yong; Yang, Jiangke; Yan, Yunjun

    2008-03-01

    Random mutagenesis on Bacillus pumilus lipase YZ02 gene was conducted by using error-prone PCR strategy. Through two cycles of directed evolution, two optimum mutants BpL1-7 and BpL2-1369 with lipase activity improved 2 folds and 6 folds respectively were screened. The sequence of BpL2-1369 lipase gene showed that four nucleotides substitution, T61C, C147T, A334G and T371A have occurred, and three of them caused amino acid changes. Thus, amine acid Ser21 was changed into Pro21, Arg112 to Gly112, and Leu124 to His124. According to the 3D structure of Bacillus pumilus lipase mimicked by SWISS-MODEL Repository, three mutated amino acids were located at the third amino acid of the first alpha-helix, the turn between the fourth and fifth beta fold, and the first amino acid of the fifth beta fold, respectively. The BpL and BpL2-1369 genes were ligated into pET28a vector, and transferred into E. coli BL21 (DE3). After induced by IPTG the lipases were purified and characterized. The results showed that the specific activity of the evolved lipase was 1.31-fold than that of the wild lipase, and the Km decreased from 8.24 mmol/L to 7.17 mmol/L. The pH stability of the evolved lipase was better than wild lipase when pH>8.0. PMID:18589821

  3. Thermostable DNA ligase-mediated PCR production of circular plasmid (PPCP) and its application in directed evolution via in situ error-prone PCR.

    PubMed

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

    2013-08-01

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

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

    PubMed Central

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

    2013-01-01

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

  5. Error-prone signalling.

    PubMed

    Johnstone, R A; Grafen, A

    1992-06-22

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

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

    PubMed

    Lin, Ling; Fu, Chenggen; Huang, Weiqian

    2016-05-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Goomber, Shelly; Kumar, Arbind; Kaur, Jagdeep

    2016-01-15

    Cold adapted enzymes have applications in detergent, textile, food, bioremediation and biotechnology processes. Bacillus lipases are 'generally recognized as safe' (GRAS) and hence are industrially attractive. Bacillus lipase of 1.4 subfamily are of lowest molecular weight and are reversibly unfolded due to absence of disulphide bonds. Therefore these are largely used to study energetic of protein stability that represents unfolding of native protein to fully unfolded state. In present study, metagenomically isolated Bacillus LipJ was laboratory evolved for cold adaptation by error Prone PCR. Library of variants were screened for high relative activity at low temperature of 10C compared to native protein LipJ. Point mutant sequenced as Phe19?Leu was determined to be active at cold and was selected for extensive biochemical, biophysical characterization. Variant F19L showed its maximum activity at 10C where parent protein LipJ had 20% relative activity. Psychrophilic nature of F19L was established with about 50% relative active at 5C where native protein was frozen to act. Variant F19L showed no activity at temperature 40C and above, establishing its thermolabile nature. Thermostability studies determined mutant to be unstable above 20C and three fold decrease in its half life at 30C compared to native protein. Far UV-CD and intrinsic fluorescence study demonstrated unstable tertiary structure of point variant F19L leading to its unfolding at low temperature of 20C. Cold adaptation of mutant F19L is accompanied with increased specific activity. Mutant was catalytically more efficient with 1.3 fold increase in kcat. Homologue structure modelling predicted disruption of intersecondary hydrophobic core formed by aromatic ring of Phe19 with non polar residues placed at ?3, ?4, ?5, ?6, ?F. Increased local flexibility of variant F19L explains molecular basis of its psychrophilic nature. PMID:26456196

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2003-07-01

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

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

    PubMed

    Rodgers, Kasey; McVey, Mitch

    2016-01-01

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

  12. Inducible error-prone repair in Escherichia coli.

    PubMed Central

    Sedgwick, S G

    1975-01-01

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

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

    PubMed Central

    Nielsen, Rasmus

    2014-01-01

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

  14. Error-prone polyploid mitosis during normal Drosophila development

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Nagy, George

    2013-01-01

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

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

    PubMed

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

    2012-03-01

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

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

    PubMed Central

    Pal, Doyel; Chen, Tingting; Khethavath, Praveen

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  19. Development of the 1984-85 Validation Selection Criteria: The Eclectic Error Prone Model.

    ERIC Educational Resources Information Center

    Advanced Technology, Inc., Reston, VA.

    The development of the error prone model (EPM) for the 1984-1985 student financial aid validation criteria for Pell Grant recipient selection is discussed, based on a comparison of the 1983-1984 EPM criteria and a newly estimated EPM. Procedures/assumptions on which the new EPM was based include: a sample of 1982-1983 Pell Grant recipients

  20. Implementation of a robust transmission system for astronomical images over error-prone links

    NASA Astrophysics Data System (ADS)

    Thienphrapa, Paul; Boussalis, Helen; Liu, Charles; Rad, Khosrow; Dong, Jane

    2006-10-01

    The James Webb Space Telescope (JWST) is expected to produce a vast amount of images that are valuable for astronomical research and education. To support research activities related to the mission, the National Aeronautical and Space Administration (NASA) has provided funds to establish the Structures Pointing and Control Engineering (SPACE) Laboratory at the California State University, Los Angeles (CSULA). One of the research activities in SPACE lab is to design and implement an effective and efficient transmission system to disseminate JWST images across networks. In on our previous research, a prioritized transmission method was proposed to provide the best quality of the transferred image based on the joint-optimization of content-based retransmission and error concealment. In this paper, the design and implementation of a robust transmission system is presented to utilize our previously proposed methods over error-prone links. The implemented system includes three parts. First, a zero-tree based error-resilient wavelet codec is used to compress the incoming astronomical image at the sender. Tree-based interleaving is adopted in packetization to increase the system's capability to combat burst losses in error-prone channels. Second, various error concealment approaches are investigated and implemented at the receiver to improve the quality of the reconstructed image. The transmission system uses UDP as the transport protocol, but with an error control module to incorporate the optimal retransmission with the delay constraint. A user-friendly graphical interface is designed to allow easy usage for users of diverse backgrounds.

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

    SciTech Connect

    Yasbin, R. E.

    1981-06-01

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

  2. The advantage of arriving first: characteristic times in finite size populations of error-prone replicators.

    PubMed

    Marn, Arturo; Tejero, Hctor; Nuo, Juan Carlos; Montero, Francisco

    2013-01-01

    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. PMID:24376656

  3. A stochastic framework for rate-distortion optimized video coding over error-prone networks.

    PubMed

    Harmanci, Oztan; Tekalp, A Murat

    2007-03-01

    This paper proposes a complete stochastic framework for RD optimal encoder design for video over error-prone networks, which applies to any motion-compensated predictive video codec. The distortion measure has been taken as the mean square error over an ensemble of channels given an estimate of the instantaneous packet loss probability. We show that 1) the optimal motion compensated prediction, in the MSE sense, requires computation of the expected value of the reference frames, and 2) calculation of the MSE (distortion measure) requires computation of the second moment of the reference frames. We propose a recursive procedure for the computation of both the expected value and second moment of the reference frames, which are together called the stochastic frame buffer. Furthermore, we propose a stochastic RD optimization method for selection of the optimal macroblock mode and motion vectors given the instantaneous packet loss probability. If available, channel feedback can also be incorporated into the proposed stochastic framework. However, the proposed framework does not require a feedback channel to exist, and when it exists, it does not have to be lossless. In the absence of any packet losses, the proposed stochastic framework reduces to the well-known deterministic RD optimization procedures. One possible application of the optimal stochastic framework would be for multicast streaming to an ensemble of receivers. Experimental results indicate that the proposed framework outperforms other available error tracking and control schemes. PMID:17357729

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

    PubMed

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

    2013-09-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-06-01

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

  7. Income Verification Pilot Project (IVPP): The Development of an Error-Prone Model for the School Meal Programs. Revised.

    ERIC Educational Resources Information Center

    Applied Management Sciences, Inc., Silver Spring, MD.

    This report describes efforts made in 1981-82 to develop an error-prone model (EPM) to help judge the extent of misreporting of income and family size on applications for government-sponsored school meal benefits. (EPM's are statistical formulas that produce scoring systems used to distinguish applications likely to result in excess benefits from

  8. Escherichia coli Rep DNA helicase and error-prone DNA polymerase IV interact physically and functionally

    PubMed Central

    Sladewski, Thomas E.; Hetrick, Kyle M.; Foster, Patricia L.

    2011-01-01

    Summary Escherichia coli DNA polymerase IV, encoded by the dinB gene, is a member of the Y family of specialized DNA polymerases. Pol IV is capable of synthesizing past DNA lesions and may help to restart stalled replication forks. However, Pol IV is error-prone, contributing to both DNA damage-induced and stress-induced (adaptive) mutations. Here we demonstrate that Pol IV interacts in vitro with Rep DNA helicase and that this interaction enhances Reps helicase activity. In addition, Pol IV polymerase activity is stimulated by interacting with Rep, and Pol IV ? clamp-binding motif appears to be required for this stimulation. However, neither Reps helicase activity nor its ability to bind DNA is required for it to stimulate Pol IVs polymerase activity. The interaction between Rep and Pol IV is biologically significant in vivo as Rep enhances Pol IVs mutagenic activity in stationary-phase cells. These data indicate a new role for Rep in contributing to Pol IV-dependent adaptive mutation. This functional interaction also provides new insight into how the cell might control or target Pol IVs mutagenic activity. PMID:21320186

  9. Development and Use of Error-Prone Models to Supplement Pre-Established Criteria (PEC) in Selecting Pell Grant Recipients for Validation.

    ERIC Educational Resources Information Center

    Advanced Technology, Inc., Reston, VA.

    The development of a number of error-prone models to select Pell Grant recipients for validation is discussed. The 1983-1984 Pell Grant validation strategy consists of a two-stage approach: selection using Pre-Established Criteria (PEC) followed by selection using Error Prone Modeling (EPM). The database used for model development consists of a

  10. Thermoadaptation-Directed Enzyme Evolution in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

    Yasbin, R.E.

    1984-12-01

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

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

    PubMed Central

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

    2010-01-01

    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 Harvards Health Professionals Follow-up Study (HPFS). PMID:20486928

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

    ERIC Educational Resources Information Center

    System Development Corp., Falls Church, VA.

    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

  14. Joining of linear plasmid DNA is reduced and error-prone in Bloom's syndrome cells.

    PubMed Central

    Rnger, T M; Kraemer, K H

    1989-01-01

    A linearized, replicating, shuttle vector plasmid, pZ189, was used to measure in vivo DNA joining ability of cells from patients with the cancer-prone, immunodeficient, chromosome breakage disorder, Bloom's syndrome (BS). The BS cell lines we studied were reported to contain reduced in vitro activity of DNA ligase I. We assessed in vivo joining ability by transfecting linear plasmids with overlapping or blunt ends (produced by EcoRI or StuI) into BS and normal fibroblast or lymphoblast host cells and measuring the amount of re-joined, replicated plasmids by their ability to transform bacteria. With plasmids having either overlapping or blunt ends we found a 1.3- to 3-fold lower (P less than 0.05) joining efficiency in BS cells than in the normal cells. The mutation frequency of the recovered plasmids was measured by screening for function of the suppressor tRNA contained in pZ189, for plasmid size, for presence of restriction sites, or by DNA sequencing. The spontaneous mutation frequency with the circular plasmid was 0.05-0.08% with both BS cell lines, values 2- to 21-fold higher (P less than 0.03) than with the normal cell lines. The mutation frequency with the linear plasmid passaged through both BS cell lines was 21-52%, values 1.4- to 5.4-fold higher (P less than 0.001) than with the normal lines. Detailed analysis of 210 recovered plasmids revealed an increase (P less than or equal to 0.001) in deletions, insertions or complex mutations at the joining sites, and in point mutations with the EcoRI cut plasmid with the BS cells in comparison to the normal cells.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2767047

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

    SciTech Connect

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

    2008-09-01

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

  16. De novo centriole formation in human cells is error-prone and does not require SAS-6 self-assembly

    PubMed Central

    Wang, Won-Jing; Acehan, Devrim; Kao, Chien-Han; Jane, Wann-Neng; Uryu, Kunihiro; Tsou, Meng-Fu Bryan

    2015-01-01

    Vertebrate centrioles normally propagate through duplication, but in the absence of preexisting centrioles, de novo synthesis can occur. Consistently, centriole formation is thought to strictly rely on self-assembly, involving self-oligomerization of the centriolar protein SAS-6. Here, through reconstitution of de novo synthesis in human cells, we surprisingly found that normal looking centrioles capable of duplication and ciliation can arise in the absence of SAS-6 self-oligomerization. Moreover, whereas canonically duplicated centrioles always form correctly, de novo centrioles are prone to structural errors, even in the presence of SAS-6 self-oligomerization. These results indicate that centriole biogenesis does not strictly depend on SAS-6 self-assembly, and may require preexisting centrioles to ensure structural accuracy, fundamentally deviating from the current paradigm. DOI: http://dx.doi.org/10.7554/eLife.10586.001 PMID:26609813

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L.

    2012-10-25

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

    Saavedra, Pedro; And Others

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

  4. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways.

    PubMed Central

    Boulton, S J; Jackson, S P

    1996-01-01

    Ku, a heterodimer of polypeptides of approximately 70 kDa and 80 kDa (Ku70 and Ku80, respectively), binds avidly to DNA double-strand breaks (DSBs). Mammalian cells defective in Ku are hypersensitive to ionizing radiation due to a deficiency in DSB repair. Here, we show that the simple inactivation of the Saccharomyces cerevisiae Ku70 homologue (Yku70p), does not lead to increased radiosensitivity. However, yku70 mutations enhance the radiosensitivity of rad52 strains, which are deficient in homologous recombination. Through establishing a rapid and reproducible in vivo plasmid rejoining assay, we show that Yku70p plays a crucial role in the repair of DSBs bearing cohesive termini. Whereas this damage is repaired accurately in YKU70 backgrounds, in yku70 mutant strains terminal deletions of up to several hundred bp occur before ligation ensues. Interestingly, this error-prone DNA repair pathway utilizes short homologies between the two recombining molecules and is thus highly reminiscent of a predominant form of DSB repair that operates in vertebrates. These data therefore provide evidence for two distinct and evolutionarily conserved illegitimate recombination pathways. One of these is accurate and Yku70p-dependent, whereas the other is error-prone and Yku70-independent. Furthermore, our studies suggest that Yku70 promotes genomic stability both by promoting accurate DNA repair and by serving as a barrier to error-prone repair processes. Images PMID:8890183

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

    PubMed

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

    2011-01-01

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

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

    PubMed

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

    2007-03-27

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

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

    SciTech Connect

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

    2009-09-25

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

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

    SciTech Connect

    Kirouac, Kevin N.; Ling, Hong

    2009-06-30

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

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

    PubMed Central

    Kirouac, Kevin N; Ling, Hong

    2009-01-01

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

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

    SciTech Connect

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

    1990-07-01

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

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

    ERIC Educational Resources Information Center

    Saavedra, Pedro; Kuchak, JoAnn

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

    Grebneva, E A

    2014-01-01

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

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

    PubMed Central

    Schipler, Agnes; Iliakis, George

    2013-01-01

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

  17. Addressing PCR Biases in Environmental Microbiology Studies

    NASA Astrophysics Data System (ADS)

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

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

  18. The Concept of Accident Proneness: A Review

    PubMed Central

    Froggatt, Peter; Smiley, James A.

    1964-01-01

    The term accident proneness was coined by psychological research workers in 1926. Since then its conceptthat certain individuals are always more likely than others to sustain accidents, even though exposed to equal riskhas been questioned but seldom seriously challenged. This article describes much of the work and theory on which this concept is based, details the difficulties encountered in obtaining valid information and the interpretative errors that can arise from the examination of imperfect data, and explains why accident proneness became so readily accepted as an explanation of the facts. A recent hypothesis of accident causation, namely that a person's accident liability may vary from time to time, is outlined, and the respective abilities of this and of accident proneness to accord with data from the more reliable literature are examined. The authors conclude that the hypothesis of individual variation in liability is more realistic and in better agreement with the data than is accident proneness. PMID:14106130

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2013-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed

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

    2014-08-19

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

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

    PubMed

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

    2016-01-01

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

  4. Virtual PCR

    SciTech Connect

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

    2006-02-23

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

  5. Propensity Score Weighting with Error-Prone Covariates

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  6. Replicative mechanisms for CNV formation are error prone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated 67 breakpoint junctions of gene copy number gains in 31 unrelated subjects. We observed a strikingly high frequency of small deletions and insertions (29%) apparently originating from polymerase slippage events, in addition to frameshifts and point mutations in homonucleotide runs (1...

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

    MedlinePLUS

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

  8. Fission Yeast Rad52 Phosphorylation Restrains Error Prone Recombination Pathways

    PubMed Central

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

    2014-01-01

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

  9. Vegetation fire proneness in Europe

    NASA Astrophysics Data System (ADS)

    Pereira, Mário; Aranha, José; Amraoui, Malik

    2015-04-01

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

  10. Video Error Correction Using Steganography

    NASA Astrophysics Data System (ADS)

    Robie, David L.; Mersereau, Russell M.

    2002-12-01

    The transmission of any data is always subject to corruption due to errors, but video transmission, because of its real time nature must deal with these errors without retransmission of the corrupted data. The error can be handled using forward error correction in the encoder or error concealment techniques in the decoder. This MPEG-2 compliant codec uses data hiding to transmit error correction information and several error concealment techniques in the decoder. The decoder resynchronizes more quickly with fewer errors than traditional resynchronization techniques. It also allows for perfect recovery of differentially encoded DCT-DC components and motion vectors. This provides for a much higher quality picture in an error-prone environment while creating an almost imperceptible degradation of the picture in an error-free environment.

  11. Cyclone hazard proneness of districts of India

    NASA Astrophysics Data System (ADS)

    Mohapatra, M.

    2015-04-01

    Hazards associated with tropical cyclones (TCs) are long-duration rotatory high velocity winds, very heavy rain, and storm tide. India has a coastline of about 7516 km of which 5400 km is along the mainland. The entire coast is affected by cyclones with varying frequency and intensity. Thus classification of TC hazard proneness of the coastal districts is very essential for planning and preparedness aspects of management of TCs. So, an attempt has been made to classify TC hazard proneness of districts by adopting a hazard criteria based on frequency and intensity of cyclone, wind strength, probable maximum precipitation, and probable maximum storm surge. Ninety-six districts including 72 districts touching the coast and 24 districts not touching the coast, but lying within 100 km from the coast have been classified based on their proneness. Out of 96 districts, 12 are very highly prone, 41 are highly prone, 30 are moderately prone, and the remaining 13 districts are less prone. This classification of coastal districts based on hazard may be considered for all the required purposes including coastal zone management and planning. However, the vulnerability of the place has not been taken into consideration. Therefore, composite cyclone risk of a district, which is the product of hazard and vulnerability, needs to be assessed separately through a detailed study.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

    2014-01-01

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

  14. Ethnic and gender differences in boredom proneness

    SciTech Connect

    Gibson, G.S.; Morales,

    1996-02-01

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

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

    PubMed Central

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

    2011-01-01

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

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

    SciTech Connect

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

    2012-04-01

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

  17. Measurement error models with interactions.

    PubMed

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

    2016-04-01

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

  18. Psychosis-proneness and socially relevant reasoning.

    PubMed

    Young, Eliane; Mason, Oliver

    2007-03-30

    Reasoning biases have been suggested as having a role in the formation and maintenance of delusions, in particular when the content is personal or social. The present study investigated whether biases when making logical inferences about neutral and personally relevant statements may be seen in individuals hypothetically prone to psychosis. Sixty-one participants completed a multi-dimensional measure of psychosis-proneness (Oxford-Liverpool Inventory of Feelings and Experiences) and a conditional inference task. It was found that highly anhedonic participants made more invalid inferences both when reasoning about the consequences of others' emotions and implications for their own self-state. Impulsive Non-conformity was also associated with poor reasoning when 'deducing consequences from others emotions'. The findings suggest that individuals with impulsive and/or anhedonic traits may tend to ignore alternative information when reasoning about personally relevant emotional statements leading to poorer reasoning. PMID:17287027

  19. Supine versus prone position for percutaneous nephrolithotomy.

    PubMed

    Salvad, J A; Mendez, C E

    2015-12-01

    Percutaneous nephrolithotripsy (PCNL) is today gold standard for the management of complex urinary calculi. Over its lifespan this surgery has been subjected to multiple modifications and variants: for example, the anatomical positioning of the patient is still under controversy, especially the opposition amongst the prone and supine approaches, the two most common patient positions currently used for PCNL. Our objective was to review the literature and to discuss advantages and drawbacks from either technique. PMID:26329756

  20. Semantic expectations can induce false perceptions in hallucination-prone individuals.

    PubMed

    Vercammen, Ans; Aleman, Andr

    2010-01-01

    Recently, it has been proposed that exaggerated top-down processing may generate spontaneous perceptual output, and that this may constitute a cognitive predisposition toward hallucinations. In this experiment, we investigated whether hallucination proneness would be associated with increased auditory-verbal perceptual expectations, and at which processing level this occurs. From 351 undergraduate students screened for hallucination proneness, using the Launay-Slade Hallucination Scale (LSHS), 42 subjects were recruited for participation. Two word recognition tasks were administered, in which top-down influences on perception were manipulated through sentence context (semantic task) or auditory imagery (phonological task). Results revealed that LSHS scores were correlated with the number of semantically primed errors. Subjects with higher levels of hallucination proneness were more likely to report hearing a word that fits the sentence context, when it was not actually presented. This effect remained significant after controlling for general performance on the task. In contrast, hallucination proneness was not associated with phonologically primed errors. We conclude that aberrant top-down processing, particularly in the form of strong semantic expectations, may contribute to the experience of auditory-verbal hallucinations. PMID:18562343

  1. PCR thermocycler

    DOEpatents

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

    2003-01-01

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

  2. PCR thermocycler

    DOEpatents

    Benett, William J.; Richards, James B.

    2005-05-17

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

  3. Error Gravity and Error Hierarchies.

    ERIC Educational Resources Information Center

    McCretton, Elena; Rider, Nigel

    1993-01-01

    In a study of error hierarchy, 10 native-speaker teachers of English and 10 non-native-speaker teachers evaluated 25 sentences containing 7 types of errors. It was concluded that error hierarchies are not inherent and "universal" but reflect the evaluators' own educational training. (Contains seven references.) (Author/LB)

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

    ERIC Educational Resources Information Center

    Langhinrichsen-Rohling, Jennifer; Lamis, Dorian A.

    2008-01-01

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

  5. New fire-prone areas in Europe

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    SciTech Connect

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

    2009-12-15

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

  7. Error analysis

    SciTech Connect

    Gardner, R.H.; O'Neill, R.V.

    1981-01-01

    Error analysis is the systematic determination of uncertainties in model predictions due to all possible sources of variability. The objective of these studies in error analysis has been to investigate phenomena associated with prediction uncertainty over as broad a range of ecosystem models as possible, in order to: (1) develop guidelines that will permit the design of experiments and models which minimize prediction error; and (2) develop and test error analysis methodologies and make these available to ecosystem modelers and researchers. The approach to the study of model error has been inductive. A Monte Carlo simulation approach has been applied to a variety of individual models and general patterns that would be applicable across a broad range of ecological models looked for. The purpose of this paper is to review current progress in error analysis of ecological models.

  8. [Ketosis prone type 2 diabetes (KPD)].

    PubMed

    Concha L, Luciana; Durruty A, Pilar; Garca de Los Ros A, Manuel

    2015-09-01

    Ketosis prone type 2 diabetes (KPD) is presently a well-defined clinical entity, characterized by a debut with severe hyperglycemia and ketoacidosis similar to the presenting form of Type 1 diabetes mellitus (DM1). However, it appears in subjects with Type 2 diabetes mellitus (DM2) phenotype. This situation is caused by an acute, reversible dysfunction of the beta cell in individuals with insulin resistance. Once the acute stage subsides, patients behave as having a DM2 and do not require insulin treatment. They should be kept on a diet and oral hypoglycemic drugs due to their susceptibility to have recurrent acute ketotic decompensations. PMID:26530207

  9. Extralevator abdominoperineal resection in the prone position.

    PubMed

    Flor-Lorente, Blas; Frasson, Matteo; Montilla, Erick

    2014-03-01

    The Miles operation is every day more in the limelight. The abdominoperineal resection compared to anterior resection results in increased rate of circumferential resection margin (CRM) infiltration, increased iatrogenic tumor perforation rate and poorer quality of the mesorectum. These worse results may be caused by excessive dissection between the distal mesorectum and the plane of the levator ani and the consequent "resection waist" or "cone" effect in the specimen. A wider excision of the pelvic floor muscles, known as extraelevator abdominoperineal resection (ELAPE), would provide a "cylindrical" specimen which would hypothetically reduce the risk of tumor perforation and CRM infiltration and local recurrence rate. However, there is insufficient evidence to conclude that the ELAPE is oncologically superior compared to standard abdominoperineal resection. Independently from the surgical technique adopted, another actual point of discussion is the position of the patient during the perineal part of the operation. The position on "prone" provides excellent pelvic exposure, a top-down dissection under direct vision and is very comfortable for the operating surgeons. However, there is no clear scientific evidence of the superiority of prone ELAPE over supine ELAPE in terms of oncologic results, morbidity and mortality. The laparoscopy seems to be the best surgical approach for the abdominal part of the operation, although it has not been validated so far by large prospective studies. Prospective, controlled and randomized trials are necessary to resolve all these issues. The current interest in a more accurate and standardized perineal surgery to obtain a cylindrical specimen, undoubtedly, will improve results. PMID:24842689

  10. Error Analysis

    NASA Astrophysics Data System (ADS)

    Scherer, Philipp O. J.

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

  11. 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 ...

  12. Refractive Errors

    MedlinePLUS

    The cornea and lens of your eye helps you focus. Refractive errors are vision problems that happen when the ... or shorter), changes in the shape of the cornea, or aging of the lens. Four common refractive ...

  13. Pathogenesis of A??+ Ketosis-Prone Diabetes

    PubMed Central

    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

    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 KPDhigher glutamate but lower glutamine and citrulline concentrations, increased ?-hydroxybutyryl-carnitine, decreased isovaleryl-carnitine (a leucine catabolite), and decreased tricarboxylic acid (TCA) cycle intermediatesgenerated 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 amidenitrogen 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. PMID:23160531

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

    SciTech Connect

    Louisiana State University; Balman, Mehmet; Kosar, Tevfik

    2010-10-27

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

  15. Piezoelectric control of structures prone to instabilities

    NASA Astrophysics Data System (ADS)

    Kim, Sunjung

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

  16. Sex Determination Using PCR

    ERIC Educational Resources Information Center

    Kima, Peter E.; Rasche, Madeline E.

    2004-01-01

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

  17. Sex Determination Using PCR

    ERIC Educational Resources Information Center

    Kima, Peter E.; Rasche, Madeline E.

    2004-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-01-01

    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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2010-01-01

    Mutations in the fmt gene (encoding formyl methionine transferase) that eliminate formylation of initiator tRNA (Met-tRNAi) 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-tRNAi IF2 mutants initiated much faster than wild-type IF2, whereas with formylated fMet-tRNAi the initiation rates were similar. Moreover, the increase in initiation rates with Met-tRNAi 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-tRNAi. 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

  1. The error-prone DNA polymerase ? provides quantitative resistance to lung tumorigenesis and mutagenesis in mice.

    PubMed

    Iguchi, M; Osanai, M; Hayashi, Y; Koentgen, F; Lee, G-H

    2014-07-01

    Opposite undamaged nucleotide T, DNA polymerase ? (Pol?) preferentially incorporates G rather than A, violating the Watson-Crick rule. Although the actual biological role of Pol? remains enigmatic, we have identified its coding gene as a candidate for pulmonary adenoma resistance 2 (Par2), a mouse quantitative trait locus modulating chemically induced lung tumor susceptibility. Notably, the most tumor-sensitive Par2 allele possessed by the 129X1/SvJ mouse is associated with a loss-of-function mutation in Pol?. To determine whether the nonfunctional Pol? is responsible for the 129X1/SvJ-specific Par2 phenotype, we knocked out Pol? in a C57BL/6J mouse carrying a less tumor-sensitive Par2 allele. Disruption of the C57BL/6J Pol? conferred 129X1/SvJ-like sensitivity on the C57BL/6J Par2 locus and increased the in vivo mutation frequency in the lung, providing definitive proof that Pol? causes the Par2 effect and inhibits tumorigenesis and mutagenesis, despite its extreme replication infidelity. PMID:23955086

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

    SciTech Connect

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

    2009-09-01

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

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

    PubMed Central

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

    2016-01-01

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

  4. Children of Stressed Parents May Be Prone to Obesity

    MedlinePLUS

    ... nlm.nih.gov/medlineplus/news/fullstory_155521.html Children of Stressed Parents May Be Prone to Obesity ... 2015 WEDNESDAY, Nov. 4, 2015 (HealthDay News) -- Hispanic children are more likely to be obese if their ...

  5. Introduction to digital PCR.

    PubMed

    Bizouarn, Francisco

    2014-01-01

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

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

    PubMed

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

    2015-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    PubMed

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

    2015-01-01

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

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  10. PCR und Real-Time PCR

    NASA Astrophysics Data System (ADS)

    Konrad, Regina; Busch, Ulrich

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

  11. Transcription errors induce proteotoxic stress and shorten cellular lifespan.

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

    As larger-scale cloning projects become more prevalent, there is an increasing need for comparisons among high fidelity DNA polymerases used for PCR amplification. All polymerases marketed for PCR applications are tested for fidelity properties (i.e., error rate determination) by vendors, and numerous literature reports have addressed PCR enzyme fidelity. Nonetheless, it is often difficult to make direct comparisons among different enzymes due to numerous methodological and analytical differences from study to study. We have measured the error rates for 6 DNA polymerases commonly used in PCR applications, including 3 polymerases typically used for cloning applications requiring high fidelity. Error rate measurement values reported here were obtained by direct sequencing of cloned PCR products. The strategy employed here allows interrogation of error rate across a very large DNA sequence space, since 94 unique DNA targets were used as templates for PCR cloning. The six enzymes included in the study, Taq polymerase, AccuPrime-Taq High Fidelity, KOD Hot Start, cloned Pfu polymerase, Phusion Hot Start, and Pwo polymerase, we find the lowest error rates with Pfu, Phusion, and Pwo polymerases. Error rates are comparable for these 3 enzymes and are >10x lower than the error rate observed with Taq polymerase. Mutation spectra are reported, with the 3 high fidelity enzymes displaying broadly similar types of mutations. For these enzymes, transition mutations predominate, with little bias observed for type of transition. PMID:25197572

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    ERIC Educational Resources Information Center

    Sundberg, Norman D.; And Others

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

  15. Modifying the Type A Coronary-Prone Behavior Pattern.

    ERIC Educational Resources Information Center

    Levenkron, Jeffrey C.; And Others

    1983-01-01

    Compared three treatments for modifying Type A coronary-prone behavior pattern (TABP). Comprehensive behavior therapy (CBT), emphasizing self-control procedures, and group support (GS), encouraging change in TABP targets but without behavioral techniques, were contrasted to brief information (BI). Results with healthy male executives (N=38) showed

  16. The Social Antecedents of Anger Proneness in Young Adulthood

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  17. The Social Antecedents of Anger Proneness in Young Adulthood

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  18. Complications associated with prone positioning in elective spinal surgery

    PubMed Central

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

    2015-01-01

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

  19. Optical measurement of dimensional parameters of the breast with subjects in prone position.

    PubMed

    Roessler, Ann-Christin; Althoff, Felix; Jaeger, Florian; Kalender, Willi; Wenkel, Evelyn

    2015-07-01

    Various applications require information on breast parameters, such as breast length and volume. An optical system was designed and tested for measuring these parameters with subjects in a prone position. The study results were used for optimizing patient positioning and handling for a future breast computed tomography (BCT) system. Measurements were conducted using an optical measurement system. To test the functionality and accuracy of the system, measurements were performed using reference phantoms. Additionally, 20 women and 5 men were examined to calculate breast parameters in alternative positions and breathing states. The results of the optical measurements were compared with magnetic resonance imaging (MRI) measurements. Volume and length of the reference phantoms were determined with errors below 2%. The patient study demonstrated a mean breast volume of 530.7ml for women during normal breathing. During an exhalation state, breast volume increased significantly by 17.7ml in comparison with normal breathing. Differences with MRI measurements were found to be 3% for breast length and 9% for breast volume on average. The proposed optical measurement system was found to be suitable for measuring the dimensional parameters of the breast in a prone position and provides a tool for evaluating breast coverage for BCT. PMID:26240833

  20. Chlamydomonas (Chlorophyceae) colony PCR.

    PubMed

    Cao, Muqing; Fu, Yu; Guo, Yan; Pan, Junmin

    2009-03-01

    The ease and effectiveness of colony polymerase chain reaction (PCR) has allowed rapid amplification of DNA fragments and screening of large number of colonies of interest including transformants and mutants with genetic manipulations. Here, we evaluated colony PCR in Chlamydomonas. Individual colonies were treated with 10 mM ethylenediaminetetraacetic acid (EDTA) or Chelex-100 and the resulting clear cell lysate was used for PCR reaction. Either genomic DNA or plasmid DNA incorporated into the genome was equally amplified. We found that the Chelex method is superior to EDTA method in certain cases. This colony PCR technique will bypass the tedious process of isolating genomic DNA for PCR reaction and will make it possible for rapid amplification of genomic DNA fragments as well as rapid large-scale screening of transformants. PMID:19242652

  1. Unforced errors and error reduction in tennis

    PubMed Central

    Brody, H

    2006-01-01

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

  2. Measurement error and dietary intake.

    PubMed

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

    1998-01-01

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

  3. Real-Time PCR

    NASA Astrophysics Data System (ADS)

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

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

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

    DOE PAGESBeta

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

    2014-01-01

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

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

    PubMed Central

    Vaibhav, Atul; Mathai, Mathew; Gorman, Shaun

    2013-01-01

    Ketosis-prone type 2 diabetes mellitus also known as atypical or flatbush diabetes is being increasingly recognised worldwide. These patients are typically obese, middle-aged men with a strong family history of type 2 diabetes. The aetiology and pathophysiological mechanism is still unclear but some initial research suggests that patients with ketosis-prone type 2 diabetes have a unique predisposition to glucose desensitisation. These patients have negative autoantibodies typically associated with type 1 diabetes but have shown to have human leucocyte antigen (HLA) positivity. At initial presentation, there is an impairment of both insulin secretion and action. ? 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

  6. Reward and Affective Regulation in Depression-Prone Smokers

    PubMed Central

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

    2014-01-01

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

  7. Error significance but not error expectancy predicts error-related negativities for different error types.

    PubMed

    Maier, Martin E; Steinhauser, Marco

    2016-01-15

    Violations of outcome expectancies have been proposed to account for error-related brain activity in the medial prefrontal cortex. The present study investigated whether early error monitoring processes are sensitive only to the expectancy of errors, or whether these processes also evaluate the significance of errors. To this end, we considered the error-related negativity (Ne/ERN), an electrophysiological marker of early error monitoring, in a modified flanker task in which errors could occur because participants responded to the flankers instead of the target (flanker error) or because a response unrelated to the stimulus was given (nonflanker error). By manipulating the onset of the flankers relative to the target, we manipulated two variables: the probability (and thus the expectancy) of flanker errors and the proportion of significant attention errors among each error type. Contrary to the predictions of outcome expectancy accounts, we found that the Ne/ERN was larger for flanker errors than for nonflanker errors only in the condition in which flanker errors were particularly frequent. Consistent with the error significance account, however, Ne/ERN amplitude mirrored the estimated proportion of significant attention errors as estimated by multinomial modeling. These results provide support for the idea that early performance monitoring as reflected by the Ne/ERN involves an evaluation of error significance. PMID:26481402

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

    PubMed

    Verona, Edelyn; Bresin, Konrad

    2015-11-01

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

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

    PubMed

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

    2007-11-20

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

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

    PubMed Central

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

    2016-01-01

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

  11. An evaluation of four CTMRI co-registration techniques for radiotherapy treatment planning of prone rectal cancer patients

    PubMed Central

    Dean, C J; Sykes, J R; Cooper, R A; Hatfield, P; Carey, B; Swift, S; Bacon, S E; Thwaites, D; Sebag-Montefiore, D; Morgan, A M

    2012-01-01

    Objectives MRI is the preferred staging modality for rectal carcinoma patients. This work assesses the CTMRI co-registration accuracy of four commercial rigid-body techniques for external beam radiotherapy treatment planning for patients treated in the prone position without fiducial markers. Methods 17 patients with biopsy-proven rectal carcinoma were scanned with CT and MRI in the prone position without the use of fiducial markers. A reference co-registration was performed by consensus of a radiologist and two physicists. This was compared with two automated and two manual techniques on two separate treatment planning systems. Accuracy and reproducibility were analysed using a measure of target registration error (TRE) that was based on the average distance of the mis-registration between vertices of the clinically relevant gross tumour volume as delineated on the CT image. Results An automated technique achieved the greatest accuracy, with a TRE of 2.3 mm. Both automated techniques demonstrated perfect reproducibility and were significantly faster than their manual counterparts. There was a significant difference in TRE between registrations performed on the two planning systems, but there were no significant differences between the manual and automated techniques. Conclusion For patients with rectal cancer, MRI acquired in the prone treatment position without fiducial markers can be accurately registered with planning CT. An automated registration technique offered a fast and accurate solution with associated uncertainties within acceptable treatment planning limits. PMID:22190750

  12. Denoising PCR-amplified metagenome data

    PubMed Central

    2012-01-01

    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 Roches 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. PMID:23113967

  13. Rapid Optical Cavity PCR.

    PubMed

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

    2016-01-01

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

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

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 44 Emergency Management and Assistance 1 2013-10-01 2013-10-01 false Planning considerations for... Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations...

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Planning considerations for... Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations...

  16. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 44 Emergency Management and Assistance 1 2012-10-01 2011-10-01 true Planning considerations for... Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations...

  17. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 44 Emergency Management and Assistance 1 2012-10-01 2011-10-01 true Planning considerations for... Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.23 Planning considerations...

  18. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Planning considerations for... Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.23 Planning considerations...

  19. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 44 Emergency Management and Assistance 1 2013-10-01 2013-10-01 false Planning considerations for... Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.23 Planning considerations...

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Planning considerations for... Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.23 Planning considerations...

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

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Planning considerations for... Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations...

  2. Numerical error in groundwater flow and solute transport simulation

    NASA Astrophysics Data System (ADS)

    Woods, Juliette A.; Teubner, Michael D.; Simmons, Craig T.; Narayan, Kumar A.

    2003-06-01

    Models of groundwater flow and solute transport may be affected by numerical error, leading to quantitative and qualitative changes in behavior. In this paper we compare and combine three methods of assessing the extent of numerical error: grid refinement, mathematical analysis, and benchmark test problems. In particular, we assess the popular solute transport code SUTRA [Voss, 1984] as being a typical finite element code. Our numerical analysis suggests that SUTRA incorporates a numerical dispersion error and that its mass-lumped numerical scheme increases the numerical error. This is confirmed using a Gaussian test problem. A modified SUTRA code, in which the numerical dispersion is calculated and subtracted, produces better results. The much more challenging Elder problem [Elder, 1967; Voss and Souza, 1987] is then considered. Calculation of its numerical dispersion coefficients and numerical stability show that the Elder problem is prone to error. We confirm that Elder problem results are extremely sensitive to the simulation method used.

  3. Supine and Prone Colon Registration using Quasi-Conformal Mapping

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

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

    2014-07-15

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

  5. Boredom proneness and emotion regulation predict emotional eating.

    PubMed

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

    2015-05-01

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

  6. Microseismic study of an outburst-prone coal seam

    SciTech Connect

    MacDonald, P.; Brown, K.M.

    1984-01-01

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

  7. Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys.

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  10. QUALITY CONTROLS FOR PCR

    EPA Science Inventory

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

  11. 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...

  12. Field error lottery

    NASA Astrophysics Data System (ADS)

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

    1990-11-01

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

  13. Field error lottery

    NASA Astrophysics Data System (ADS)

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

    1991-07-01

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

  14. Field error lottery

    SciTech Connect

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

    1990-01-01

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

  15. Predicting Fault-Prone Modules: A Comparative Study

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed Central

    Neumann, Peter M.

    2008-01-01

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

  17. Errors, Error, and Text in Multidialect Setting.

    ERIC Educational Resources Information Center

    Candler, W. J.

    1979-01-01

    This article discusses the various dialects of English spoken in Liberia and analyzes the problems of Liberian students in writing compositions in English. Errors arise mainly from differences in culture and cognition, not from superficial linguistic problems. (CFM)

  18. Inborn errors of metabolism

    MedlinePLUS

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

  19. [Errors of impulse photometers].

    PubMed

    Kutev, Iu M

    1984-01-01

    Errors of pulse photometers intended for clinical biochemical studies have been analyzed. The recommendations are given how to minimize the errors and to improve metrologic parameters of pulse photometers. PMID:6503670

  20. Systematic errors in strong lens modeling

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    SciTech Connect

    Thanh, L.T.; Man, Nguyen Thi; Morris, G.E.

    1995-08-28

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

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

    SciTech Connect

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

    1998-12-01

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

  3. Programming Errors in APL.

    ERIC Educational Resources Information Center

    Kearsley, Greg P.

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

  4. Apta-PCR.

    PubMed

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

    2016-01-01

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

  5. Systematic error revisited

    SciTech Connect

    Glosup, J.G.; Axelrod, M.C.

    1996-08-05

    The American National Standards Institute (ANSI) defines systematic error as An error which remains constant over replicative measurements. It would seem from the ANSI definition that a systematic error is not really an error at all; it is merely a failure to calibrate the measurement system properly because if error is constant why not simply correct for it? Yet systematic errors undoubtedly exist, and they differ in some fundamental way from the kind of errors we call random. Early papers by Eisenhart and by Youden discussed systematic versus random error with regard to measurements in the physical sciences, but not in a fundamental way, and the distinction remains clouded by controversy. The lack of a general agreement on definitions has led to a plethora of different and often confusing methods on how to quantify the total uncertainty of a measurement that incorporates both its systematic and random errors. Some assert that systematic error should be treated by non- statistical methods. We disagree with this approach, and we provide basic definitions based on entropy concepts, and a statistical methodology for combining errors and making statements of total measurement of uncertainty. We illustrate our methods with radiometric assay data.

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

    NASA Technical Reports Server (NTRS)

    Hobbs, Alan; Williamson, Ann

    2002-01-01

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

  7. Errors Affect Hypothetical Intertemporal Food Choice in Women

    PubMed Central

    Sellitto, Manuela; di Pellegrino, Giuseppe

    2014-01-01

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

  8. Aircraft system modeling error and control error

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

  9. 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...

  10. Assessment of trichloroethylene (TCE) exposure in murine strains genetically-prone and non-prone to develop autoimmune disease.

    PubMed

    Keil, Deborah E; Peden-Adams, Margie M; Wallace, Stacy; Ruiz, Phillip; Gilkeson, Gary S

    2009-04-01

    There is increasing laboratory and epidemiologic evidence relating exposure to trichloroethylene (TCE) with autoimmune disease including scleroderma and lupus. New Zealand Black/New Zealand White (NZBWF1) and B6C3F1 mice were exposed to TCE (0, 1, 400 or 14,000 ppb) via drinking water for 27 or 30 weeks, respectively. NZBWF1 mice spontaneously develop autoimmune disease while B6C3F1 mice, a standard strain used in immunotoxicology testing, are not genetically prone to develop autoimmune disease. During the TCE exposure period, serum levels of total IgG, and autoantibodies (anti-ssDNA, -dsDNA, and -glomerular antigen [GA]) were monitored. At the termination of the study, renal pathology, natural killer (NK) cell activity, total IgG levels, autoantibody production, T-cell activation, and lymphocytic proliferative responses were evaluated. TCE did not alter NK cell activity, or T- and B-cell proliferation in either strain. Numbers of activated T-cells (CD4+/CD44+) were increased in the B6C3F1 mice but not in the NZBWF1 mice. Renal pathology, as indicated by renal score, was significantly increased in the B6C3F1, but not in the NZBWF1 mice. Serum levels of autoantibodies to dsDNA and ssDNA were increased at more time points in B6C3F1, as compared to the NZBWF1 mice. Anti-GA autoantibodies were increased by TCE treatment in early stages of the study in NZBWF1 mice, but by 23 weeks of age, control levels were comparable to those of TCE-exposed animals. Serum levels anti-GA autoantibodies in B6C3F1 were not affected by TCE exposure. Overall, these data suggest that TCE did not contribute to the progression of autoimmune disease in autoimmune-prone mice during the period of 11-36 weeks of age, but rather lead to increased expression of markers associated with autoimmune disease in a non-genetically prone mouse strain. PMID:19241258

  11. The pathophysiology of medication errors: how and where they arise.

    PubMed

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

    2009-06-01

    1. 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. 2. 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. 3. 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. 4. 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. 5. Medication error rates in hospital are higher in paediatric departments and intensive care units than elsewhere. 6. Rates of medication errors may be higher in very young or very old patients. 7. 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'. 8. 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. PMID:19594527

  12. The Error in Total Error Reduction

    PubMed Central

    Witnauer, James E.; Urcelay, Gonzalo P.; Miller, Ralph R.

    2013-01-01

    Most models of human and animal learning assume that learning is proportional to the discrepancy between a delivered outcome and the outcome predicted by all cues present during that trial (i.e., total error across a stimulus compound). This total error reduction (TER) view has been implemented in connectionist and artificial neural network models to describe the conditions under which weights between units change. Electrophysiological work has revealed that the activity of dopamine neurons is correlated with the total error signal in models of reward learning. Similar neural mechanisms presumably support fear conditioning, human contingency learning, and other types of learning. Using a computational modelling approach, we compared several TER models of associative learning to an alternative model that rejects the TER assumption in favor of local error reduction (LER), which assumes that learning about each cue is proportional to the discrepancy between the delivered outcome and the outcome predicted by that specific cue on that trial. The LER model provided a better fit to the reviewed data than the TER models. Given the superiority of the LER model with the present data sets, acceptance of TER should be tempered. PMID:23891930

  13. Error detection method

    DOEpatents

    Olson, Eric J.

    2013-06-11

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

  14. Software error detection

    NASA Technical Reports Server (NTRS)

    Buechler, W.; Tucker, A. G.

    1981-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Goodman, Myron F

    2014-09-26

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

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

    PubMed Central

    Goodman, Myron F.

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

    Hodes, C.S.

    1987-01-01

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

  1. Geographically correlated orbit error

    NASA Technical Reports Server (NTRS)

    Rosborough, G. W.

    1989-01-01

    The dominant error source in estimating the orbital position of a satellite from ground based tracking data is the modeling of the Earth's gravity field. The resulting orbit error due to gravity field model errors are predominantly long wavelength in nature. This results in an orbit error signature that is strongly correlated over distances on the size of ocean basins. Anderle and Hoskin (1977) have shown that the orbit error along a given ground track also is correlated to some degree with the orbit error along adjacent ground tracks. This cross track correlation is verified here and is found to be significant out to nearly 1000 kilometers in the case of TOPEX/POSEIDON when using the GEM-T1 gravity model. Finally, it was determined that even the orbit error at points where ascending and descending ground traces cross is somewhat correlated. The implication of these various correlations is that the orbit error due to gravity error is geographically correlated. Such correlations have direct implications when using altimetry to recover oceanographic signals.

  2. Error coding simulations

    NASA Technical Reports Server (NTRS)

    Noble, Viveca K.

    1993-01-01

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

  3. Model Error Budgets

    NASA Technical Reports Server (NTRS)

    Briggs, Hugh C.

    2008-01-01

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

  4. Cross-Cultural Differences and Similarities in Proneness to Shame: An Adaptationist and Ecological Approach

    PubMed Central

    Takemura, Kosuke; Delton, Andrew W.; Sato, Kosuke; Robertson, Theresa; Cosmides, Leda; Tooby, John

    2013-01-01

    People vary in how easily they feel ashamed, that is, in their shame proneness. According to the information threat theory of shame, variation in shame proneness should, in part, be regulated by features of a persons social ecology. On this view, shame is an emotion program that evolved to mitigate the likelihood or costs of reputation-damaging information spreading to others. In social environments where there are fewer possibilities to form new relationships (i.e., low relational mobility), there are higher costs to damaging or losing existing ones. Therefore, shame proneness toward current relationship partners should increase as perceived relational mobility decreases. In contrast, individuals with whom one has little or no relationship history are easy to replace, and so shame-proneness towards them should not be modulated by relational mobility. We tested these predictions cross-culturally by measuring relational mobility and shame proneness towards friends and strangers in Japan, the United States, and the United Kingdom. Japanese subjects were more shame-prone than their British and American counterparts. Critically, lower relational mobility was associated with greater shame proneness towards friends (but not strangers), and this relationship partially mediated the cultural differences in shame proneness. Shame proneness appears tailored to respond to relevant features of ones social ecology. PMID:22947644

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

    ERIC Educational Resources Information Center

    Shang, Yi

    2012-01-01

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

  6. Digital PCR: Principles and Applications.

    PubMed

    Kanagal-Shamanna, Rashmi

    2016-01-01

    Digital PCR is a robust PCR technique that enables precise and accurate absolute quantitation of target molecules by diluting and partitioning of the samples into numerous compartments. Automated partitioning can be attained by creating "water-in-oil" emulsion (emulsion-based digital PCR) or using a chip with microchannels (microfluidics-based digital PCR). We discuss the advantages and a wide variety of clinical applications of this technique. We describe the droplet digital RT-PCR protocol published by Jennings et al. for identification and absolute quantitation of BCR-ABL1 transcripts. PMID:26843045

  7. Error-block detection technique for mobile video transmission

    NASA Astrophysics Data System (ADS)

    Park, Dong-Seek; Kim, Jong D.; Kim, Yoon-Soo

    1997-01-01

    This paper presents an effective and simple video decoding and simple video decoding method in H.263 over noisy channels without use of any kind of feedback information. We address that through the computer simulations the negotiable options of H.263 are of not use for error-robustness against error-prone channel, and propose one of easy error detection/correction methods. The key idea is that sacrifice of coding efficiency by restricting some functionalities of H.263 reduces the number of a set of possible administrative information, which allows a decoder to easily check whether or not the desirable syntax has been obtained and to try syntax correction. Applying this method, for example, syntax errors such as 'MCBPC' errors can be easily detected and corrected, which are crucial for removing visually annoying 'green/pink' block artifacts completely. Since the proposed method is completely H/263-compatible, the decoder is very good at finding H.263 syntax errors caused by channel errors. The channel model we have chosen was DECT2 with bit- error-rate of 2.1 X 10-3.

  8. Everyday Scale Errors

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  9. Refractive error blindness.

    PubMed Central

    Dandona, R.; Dandona, L.

    2001-01-01

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

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

    PubMed

    Padrao, Gonalo; Mallorqu, Aida; Cucurell, David; Rodriguez-Fornells, Antoni

    2015-12-01

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

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

    PubMed

    Kebschull, Justus M; Zador, Anthony M

    2015-12-01

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

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

    PubMed Central

    Kebschull, Justus M.; Zador, Anthony M.

    2015-01-01

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

  13. Investigation on reference value error in multivariate calibration

    NASA Astrophysics Data System (ADS)

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

    2008-10-01

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

  14. Disgust proneness and associated neural substrates in obesity.

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2010-11-01

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

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

    PubMed

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

    2015-12-01

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

  18. Development of Korean Smartphone Addiction Proneness Scale for Youth

    PubMed Central

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

    2014-01-01

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

  19. Male predominance in ketosis-prone diabetes mellitus

    PubMed Central

    WANG, XIAOHAO; TAN, HUIWEN

    2015-01-01

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

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

    ERIC Educational Resources Information Center

    Counts, Robert M.; Reid, Kelly

    1986-01-01

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

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

    ERIC Educational Resources Information Center

    Gerdes, Eugenia Proctor; Sidler, John P.

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

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    Cassel, Russell N.; Cassel, Susie L.

    1984-01-01

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

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

    ERIC Educational Resources Information Center

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

    2014-01-01

    In this short-term longitudinal study, we systematically examined the distinctiveness of guilt- and shame-proneness in early adolescents (N = 395, mean age = 11.8 years) in terms of differential relations with peer reported prosocial behavior, withdrawal, and aggression. Results from structural equation modeling indicated that guilt-proneness

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

    ERIC Educational Resources Information Center

    Marini, David C.

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

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

    ERIC Educational Resources Information Center

    Cassel, Russell N.; Cassel, Susie L.

    1984-01-01

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

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

    ERIC Educational Resources Information Center

    McCaulay, Marci; And Others

    1988-01-01

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

  8. Uncorrected refractive errors

    PubMed Central

    Naidoo, Kovin S; Jaggernath, Jyoti

    2012-01-01

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

  9. Error correction of microchip synthesized genes using Surveyor nuclease

    PubMed Central

    Saaem, Ishtiaq; Ma, Siying; Quan, Jiayuan; Tian, Jingdong

    2012-01-01

    The development of economical and high-throughput gene synthesis technology has been hampered by the high occurrence of errors in the synthesized products, which requires expensive labor and time to correct. Here, we describe an error correction reaction (ECR), which employs Surveyor, a mismatch-specific DNA endonuclease, to remove errors from synthetic genes. In ECR reactions, errors are revealed as mismatches by re-annealing of the synthetic gene products. Mismatches are recognized and excised by a combination of mismatch-specific endonuclease and 3??5? exonuclease activities in the reaction mixture. Finally, overlap extension polymerase chain reaction (OE-PCR) re-assembles the resulting fragments into intact genes. The process can be iterated for increased fidelity. With two iterations, we were able to reduce errors in synthetic genes by >16-fold, yielding a final error rate of ?1 in 8700?bp. PMID:22127863

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

    PubMed

    Flannery, Alexander H; Parli, Sara E

    2016-01-01

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

  11. Error Prevention Aid

    NASA Technical Reports Server (NTRS)

    1987-01-01

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

  12. Surprise beyond prediction error

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  14. Digital droplet PCR on disk.

    PubMed

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

    2015-12-15

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

  15. Diagnostic Errors Study Findings

    MedlinePLUS

    ... The study, partially funded by the Agency for Healthcare Research and Quality (AHRQ), estimates that approximately 12 million adults in the United States could experience an outpatient diagnostic error each year. ...

  16. Error mode prediction.

    PubMed

    Hollnagel, E; Kaarstad, M; Lee, H C

    1999-11-01

    The study of accidents ('human errors') has been dominated by efforts to develop 'error' taxonomies and 'error' models that enable the retrospective identification of likely causes. In the field of Human Reliability Analysis (HRA) there is, however, a significant practical need for methods that can predict the occurrence of erroneous actions--qualitatively and quantitatively. The present experiment tested an approach for qualitative performance prediction based on the Cognitive Reliability and Error Analysis Method (CREAM). Predictions of possible erroneous actions were made for operators using different types of alarm systems. The data were collected as part of a large-scale experiment using professional nuclear power plant operators in a full scope simulator. The analysis showed that the predictions were correct in more than 70% of the cases, and also that the coverage of the predictions depended critically on the comprehensiveness of the preceding task analysis. PMID:10582035

  17. Help prevent hospital errors

    MedlinePLUS

    ... Vogus TJ. Reducing hospital errors: interventions that build safety culture. Annu Rev Public Health . 2013;34:373-396. The Joint Commission. Hospital: 2014 National Patient Safety Goals. Available at: www.jointcommission.org/hap_2014_ ...

  18. The Surveillance Error Grid

    PubMed Central

    Lias, Courtney; Vigersky, Robert; Clarke, William; Parkes, Joan Lee; Sacks, David B.; Kirkman, M. Sue; Kovatchev, Boris

    2014-01-01

    Introduction: Currently used error grids for assessing clinical accuracy of blood glucose monitors are based on out-of-date medical practices. Error grids have not been widely embraced by regulatory agencies for clearance of monitors, but this type of tool could be useful for surveillance of the performance of cleared products. Diabetes Technology Society together with representatives from the Food and Drug Administration, the American Diabetes Association, the Endocrine Society, and the Association for the Advancement of Medical Instrumentation, and representatives of academia, industry, and government, have developed a new error grid, called the surveillance error grid (SEG) as a tool to assess the degree of clinical risk from inaccurate blood glucose (BG) monitors. Methods: A total of 206 diabetes clinicians were surveyed about the clinical risk of errors of measured BG levels by a monitor. The impact of such errors on 4 patient scenarios was surveyed. Each monitor/reference data pair was scored and color-coded on a graph per its average risk rating. Using modeled data representative of the accuracy of contemporary meters, the relationships between clinical risk and monitor error were calculated for the Clarke error grid (CEG), Parkes error grid (PEG), and SEG. Results: SEG action boundaries were consistent across scenarios, regardless of whether the patient was type 1 or type 2 or using insulin or not. No significant differences were noted between responses of adult/pediatric or 4 types of clinicians. Although small specific differences in risk boundaries between US and non-US clinicians were noted, the panel felt they did not justify separate grids for these 2 types of clinicians. The data points of the SEG were classified in 15 zones according to their assigned level of risk, which allowed for comparisons with the classic CEG and PEG. Modeled glucose monitor data with realistic self-monitoring of blood glucose errors derived from meter testing experiments plotted on the SEG when compared to the data plotted on the CEG and PEG produced risk estimates that were more granular and reflective of a continuously increasing risk scale. Discussion: The SEG is a modern metric for clinical risk assessments of BG monitor errors that assigns a unique risk score to each monitor data point when compared to a reference value. The SEG allows the clinical accuracy of a BG monitor to be portrayed in many ways, including as the percentages of data points falling into custom-defined risk zones. For modeled data the SEG, compared with the CEG and PEG, allows greater precision for quantifying risk, especially when the risks are low. This tool will be useful to allow regulators and manufacturers to monitor and evaluate glucose monitor performance in their surveillance programs. PMID:25562886

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

    PubMed

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

    2013-10-01

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

  20. Quantum Error Correction

    NASA Astrophysics Data System (ADS)

    Lidar, Daniel A.; Brun, Todd A.

    2013-09-01

    Prologue; Preface; Part I. Background: 1. Introduction to decoherence and noise in open quantum systems Daniel Lidar and Todd Brun; 2. Introduction to quantum error correction Dave Bacon; 3. Introduction to decoherence-free subspaces and noiseless subsystems Daniel Lidar; 4. Introduction to quantum dynamical decoupling Lorenza Viola; 5. Introduction to quantum fault tolerance Panos Aliferis; Part II. Generalized Approaches to Quantum Error Correction: 6. Operator quantum error correction David Kribs and David Poulin; 7. Entanglement-assisted quantum error-correcting codes Todd Brun and Min-Hsiu Hsieh; 8. Continuous-time quantum error correction Ognyan Oreshkov; Part III. Advanced Quantum Codes: 9. Quantum convolutional codes Mark Wilde; 10. Non-additive quantum codes Markus Grassl and Martin Rtteler; 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 Rtteler 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 Hctor Bombn; 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.

  1. Evidence, errors, and ethics.

    PubMed

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

    2014-01-01

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

  2. Alcohol and error processing.

    PubMed

    Holroyd, Clay B; Yeung, Nick

    2003-08-01

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

  3. Thermodynamics of Error Correction

    NASA Astrophysics Data System (ADS)

    Sartori, Pablo; Pigolotti, Simone

    2015-10-01

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

  4. Predicted Errors In Children's Early Sentence Comprehension

    PubMed Central

    Gertner, Yael; Fisher, Cynthia

    2012-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

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

  6. Human error in aviation operations

    NASA Technical Reports Server (NTRS)

    Nagel, David C.

    1988-01-01

    The role of human error in commercial and general aviation accidents and the techniques used to evaluate it are reviewed from a human-factors perspective. Topics addressed include the general decline in accidents per million departures since the 1960s, the increase in the proportion of accidents due to human error, methods for studying error, theoretical error models, and the design of error-resistant systems. Consideration is given to information acquisition and processing errors, visually guided flight, disorientation, instrument-assisted guidance, communication errors, decision errors, debiasing, and action errors.

  7. Emulsion PCR: Techniques and Applications.

    PubMed

    Kanagal-Shamanna, Rashmi

    2016-01-01

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

  8. Errata: Papers in Error Analysis.

    ERIC Educational Resources Information Center

    Svartvik, Jan, Ed.

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

  9. Errata: Papers in Error Analysis.

    ERIC Educational Resources Information Center

    Svartvik, Jan, Ed.

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

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

    SciTech Connect

    Varga, Zoltan; Hideghety, Katalin; Mezo, Tamas; Nikolenyi, Aliz; Thurzo, Laszlo; Kahan, Zsuzsanna

    2009-09-01

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

  11. Smoothing error pitfalls

    NASA Astrophysics Data System (ADS)

    von Clarmann, T.

    2014-09-01

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

  12. Compact disk error measurements

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

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

    PubMed

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

    2006-03-31

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

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

    PubMed

    Garca-Talavera, M; Garca-Prez, A; Rey, C; Ramos, L

    2013-09-01

    Identifying radon-prone areas is key to policies on the control of this environmental carcinogen. In the current paper, we present the methodology followed to delineate radon-prone areas in Spain. It combines information from indoor radon measurements with ?-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

  15. A trait-interpersonal analysis of suicide proneness among lesbian, gay, and bisexual community members.

    PubMed

    Cramer, Robert J; Stroud, Caroline H; Fraser, Theresa; Graham, James

    2014-12-01

    Suicide remains a concerning issue for lesbian, gay, and bisexual (LGB) persons. The integrated effects of five-factor model personality traits and interpersonal-psychological theory of suicide (IPTS) constructs on suicide proneness in a community sample of 336 LGB adults were examined. Results supported a model inclusive of all five-factor model domains predicting IPTS constructs leading to suicide proneness. Effects of neuroticism and extraversion were both mediated by perceived burdensomeness and thwarted belongingness. Thwarted belongingness mediated the effect of agreeableness on suicide proneness. Identified mediation pathways build on existing trait-interpersonal theory and may inform clinical services for sexual minority persons. PMID:24702204

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

    PubMed

    Fotos, Joseph S; Tulchinsky, Mark

    2015-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Woolley, S. I.

    1993-01-01

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

  18. An individual differences approach to multiple-target search errors: Errors correlate with attentional deficits.

    PubMed

    Adamo, Stephen; Cain, Matthew; Mitroff, Stephen

    2015-09-01

    Multiple-target visual searches, where more than one target can be present within a single search array, are especially error-prone such that a second target is more likely to be missed after a first target has been detected. This is a serious concern for many critical searches (e.g., radiology, baggage screening) and also raises interesting theoretical questions. Increasingly, evidence supports a resource depletion account of these errors-a first target consumes attentional resources leaving less available to process additional targets. The current study tested this account by comparing 60 participants' multiple-target search performance to two other attention-demanding tasks: attentional blink (AB) and vigilance. The multiple-target search task had 1 or 2 targets per trial intermixed with distractors, and participants clicked on each target they found. The AB task presented two targets (letters) 100-800ms apart in a rapid serial visual presentation (RSVP) stream of distractors (numbers), and participants reported which targets they saw. The vigilance task presented targets (the letter O) in a RSVP stream with distractors (forward or backwards letter Ds) on top of a noise mask, and participants were to indicate every time the target appeared. Second target accuracy in the multiple-target search task significantly correlated with (1) a measure of how long it took second target accuracy in an AB task to recover from the blink, and (2) sensitivity (d') in the vigilance task. Participants who took longer to recover from an AB and who were less vigilant had more second-target misses in a multiple-target search task. Taken together, these results support a resource depletion account of multiple-target search errors in that they highlight an attentional underpinning; errors in AB and vigilance tasks are believed to reflect a deficit in attentional resources and the magnitude of these deficits significantly related to the magnitude of the multiple-target search errors. Meeting abstract presented at VSS 2015. PMID:26327060

  19. Decomposing model systematic error

    NASA Astrophysics Data System (ADS)

    Keenlyside, Noel; Shen, Mao-Lin

    2014-05-01

    Seasonal forecasts made with a single model are generally overconfident. The standard approach to improve forecast reliability is to account for structural uncertainties through a multi-model ensemble (i.e., an ensemble of opportunity). Here we analyse a multi-model set of seasonal forecasts available through ENSEMBLES and DEMETER EU projects. We partition forecast uncertainties into initial value and structural uncertainties, as function of lead-time and region. Statistical analysis is used to investigate sources of initial condition uncertainty, and which regions and variables lead to the largest forecast error. Similar analysis is then performed to identify common elements of model error. Results of this analysis will be used to discuss possibilities to reduce forecast uncertainty and improve models. In particular, better understanding of error growth will be useful for the design of interactive multi-model ensembles.

  20. Error Free Software

    NASA Technical Reports Server (NTRS)

    1985-01-01

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

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

    PubMed

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

    2010-09-01

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

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

    PubMed

    Flynn, Francis J; Schaumberg, Rebecca L

    2012-01-01

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

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

    EPA Science Inventory

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

  4. The Physically Active Less Prone to Post-Heart Attack Depression

    MedlinePLUS

    ... Physically Active Less Prone to Post-Heart Attack Depression Research underscores link between physical activity and mental ... the event have a lower risk of developing depression, according to a new study. Researchers looked at ...

  5. Young Writers' Error Tendency.

    ERIC Educational Resources Information Center

    Mazur, Chet

    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

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

    PubMed

    Wiltermuth, Scott S; Cohen, Taya R

    2014-11-01

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

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

    PubMed Central

    2013-01-01

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

  8. A simple, universal, efficient PCR-based gene synthesis method: sequential OE-PCR gene synthesis.

    PubMed

    Zhang, Pingping; Ding, Yingying; Liao, Wenting; Chen, Qiuli; Zhang, Huaqun; Qi, Peipei; He, Ting; Wang, Jinhong; Deng, Songhua; Pan, Tianyue; Ren, Hao; Pan, Wei

    2013-07-25

    Herein we present a simple, universal, efficient gene synthesis method based on sequential overlap extension polymerase chain reactions (OE-PCRs). This method involves four key steps: (i) the design of paired complementary 54-mer oligonucleotides with 18 bp overlaps, (ii) the utilisation of sequential OE-PCR to synthesise full-length genes, (iii) the cloning and sequencing of four positive T-clones of the synthesised genes and (iv) the resynthesis of target genes by OE-PCR with correct templates. Mispriming and secondary structure were found to be the principal obstacles preventing successful gene synthesis and were easily identified and solved in this method. Compensating for the disadvantages of being laborious and time-consuming, this method has many attractive advantages, such as the ability to guarantee successful gene synthesis in most cases and good allowance for Taq polymerase, oligonucleotides, PCR conditions and a high error rate. Thus, this method provides an alternative tool for individual gene synthesis without strict needs of the high-specialised experience. PMID:23597923

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  10. Inborn Errors of Metabolism.

    PubMed

    Ezgu, Fatih

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Mizuno, Osamu; Kikuno, Tohru

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

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

    PubMed Central

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

    2007-01-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  15. Enhanced Named Entity Extraction via Error-Driven Aggregation

    SciTech Connect

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

    2010-02-22

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

  16. Control by model error estimation

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

  17. Automatic Error Analysis Using Intervals

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  18. Automatic Error Analysis Using Intervals

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  19. Imagery of Errors in Typing

    ERIC Educational Resources Information Center

    Rieger, Martina; Martinez, Fanny; Wenke, Dorit

    2011-01-01

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

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

    PubMed

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

    2015-01-01

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

  1. Intraoperative visualization and assessment of electromagnetic tracking error

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  2. Modular error embedding

    DOEpatents

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

    1999-01-01

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

  3. [Translation errors in ophthalmology].

    PubMed

    Franko Zeitz, P; Petersen, W

    2013-03-01

    As global networks are built up, interlingual communication in ophthalmology becomes more and more important. Similar to any other specialised discipline, this raises the dilemma that on one hand precision is mandatory for an exact translation, but on the other hand translators often do not have the scientific and physicians the linguistic knowledge to fulfill this need. Furthermore, even within one language ophthalmological terminology is partially ill defined, and this problem multiplies when translating it into various other languages. However, translation errors can have serious consequences, particularly in medical disciplines. This case study casuistically demonstrates the most common basic mechanisms for translation errors in ophthalmology and shows a potential approach for solution. PMID:23070849

  4. Error-Free Software

    NASA Technical Reports Server (NTRS)

    1989-01-01

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

  5. Error-correction coding

    NASA Technical Reports Server (NTRS)

    Hinds, Erold W. (Principal Investigator)

    1996-01-01

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

  6. Inborn errors of metabolism.

    PubMed

    El-Hattab, Ayman W

    2015-06-01

    Inborn errors of metabolism (IEM) are individually rare but collectively common. Approximately 25% of IEMs can have manifestations in the neonatal period. Neonates with IEM are usually healthy at birth; however, in hours to days after birth they can develop nonspecific signs that are common to several other neonatal conditions. Therefore, maintaining a high index of suspicion is extremely important for early diagnosis and the institution of appropriate therapy, which are mandatory to prevent death and ameliorate complications from many IEMs. PMID:26042912

  7. Memory efficient error diffusion

    NASA Astrophysics Data System (ADS)

    Chang, Ti-chiun; Allebach, Jan P.

    2003-01-01

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

  8. Human Error In Complex Systems

    NASA Technical Reports Server (NTRS)

    Morris, Nancy M.; Rouse, William B.

    1991-01-01

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

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

    PubMed

    Kim, Sehee; Li, Yi; Spiegelman, Donna

    2016-01-01

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

  10. Constrained in-loop filtering for error resiliency in high efficiency video coding

    NASA Astrophysics Data System (ADS)

    Lee, Jinho; Kim, Hui Yong; Lim, Sung-Chang; Choi, Jin Soo

    2013-07-01

    In error-prone environments, packets could be lost during the transmission of compressed video bitstream, and corrupted errors by the lost packets could be propagated until it meets a refresh point. To defect the error propagation, constrained intra-prediction in high efficiency video coding (HEVC) performs intra-prediction using only neighboring intra-coded samples. However, the errors could be propagated to intra-coded blocks by an in-loop filtering process, since the in-loop filtering is performed regardless of the prediction modes of blocks, even though constrained intra-prediction is used. In this paper, a constrained in-loop filtering is proposed to protect intra-coded samples from error propagation by adaptively applying filters depending on the prediction modes of reconstructed blocks. Simulation results show that the proposed method alleviates the distortion of the decoded pictures and thereby improves both subjective and objective quality compared with the HEVC standard.

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

    PubMed

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

    2011-01-01

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

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

    PubMed Central

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

    2013-01-01

    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. PMID:24293766

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

    SciTech Connect

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

    2012-07-01

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

  14. Droplet-based micro oscillating-flow PCR chip

    NASA Astrophysics Data System (ADS)

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

    2005-08-01

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

  15. Nanoliter high throughput quantitative PCR

    PubMed Central

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

    2006-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2011-01-01

    This study of 550 jail inmates (379 male and 171 female) held on felony charges examines the reliability and validity of the Test of Self Conscious Affect –Socially Deviant Version (TOSCA-SD; Hanson & Tangney, 1996) as a measure of offenders’ proneness to shame and proneness to guilt. Discriminant validity (e.g., vis-à-vis self-esteem, negative affect, social desirability/impression management) and convergent validity (e.g., vis-à-vis correlations with empathy, externalization of blame, anger, psychological symptoms, and substance use problems) was supported, paralleling results from community samples. Further, proneness to shame and guilt were differentially related to widely used risk measures from the field of criminal justice (e.g., criminal history, psychopathy, violence risk, antisocial personality). Guilt-proneness appears to be a protective factor, whereas there was no evidence that shame-proneness serves an inhibitory function. Subsequent analyses indicate these findings generalize quite well across gender and race. Implications for intervention and sentencing practices are discussed. PMID:21743757

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Catron, T; Rosu, M; Weiss, E

    2014-06-01

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

  20. Methylation-Specific PCR Unraveled

    PubMed Central

    Derks, Sarah; Lentjes, Marjolein H. F. M.; Hellebrekers, Debby M. E. I.; de Brune, Adriaan P.; Herman, James G.; van Engeland, Manon

    2004-01-01

    Methylation?specific PCR (MSP) is a simple, quick and cost?effective method to analyze the DNA methylation status of virtually any group of CpG sites within a CpG island. The technique comprises two parts: (1) sodium bisulfite conversion of unmethylated cytosine's to uracil under conditions whereby methylated cytosines remains unchanged and (2) detection of the bisulfite induced sequence differences by PCR using specific primer sets for both unmethylated and methylated DNA. This review discusses the critical parameters of MSP and presents an overview of the available MSP variants and the (clinical) applications. PMID:15623939

  1. Long-term correction of inhibitor-prone hemophilia B dogs treated with liver-directed AAV2-mediated factor IX gene therapy.

    PubMed

    Niemeyer, Glenn P; Herzog, Roland W; Mount, Jane; Arruda, Valder R; Tillson, D Michael; Hathcock, John; van Ginkel, Frederik W; High, Katherine A; Lothrop, Clinton D

    2009-01-22

    Preclinical studies and initial clinical trials have documented the feasibility of adenoassociated virus (AAV)-mediated gene therapy for hemophilia B. In an 8-year study, inhibitor-prone hemophilia B dogs (n = 2) treated with liver-directed AAV2 factor IX (FIX) gene therapy did not have a single bleed requiring FIX replacement, whereas dogs undergoing muscle-directed gene therapy (n = 3) had a bleed frequency similar to untreated FIX-deficient dogs. Coagulation tests (whole blood clotting time [WBCT], activated clotting time [ACT], and activated partial thromboplastin time [aPTT]) have remained at the upper limits of the normal ranges in the 2 dogs that received liver-directed gene therapy. The FIX activity has remained stable between 4% and 10% in both liver-treated dogs, but is undetectable in the dogs undergoing muscle-directed gene transfer. Integration site analysis by linear amplification-mediated polymerase chain reaction (LAM-PCR) suggested the vector sequences have persisted predominantly in extrachromosomal form. Complete blood count (CBC), serum chemistries, bile acid profile, hepatic magnetic resonance imaging (MRI) and computed tomography (CT) scans, and liver biopsy were normal with no evidence for tumor formation. AAV-mediated liver-directed gene therapy corrected the hemophilia phenotype without toxicity or inhibitor development in the inhibitor-prone null mutation dogs for more than 8 years. PMID:18957684

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

    NASA Astrophysics Data System (ADS)

    Materna, K.; Herring, T.

    2014-12-01

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

  3. Speech Errors, Error Correction, and the Construction of Discourse.

    ERIC Educational Resources Information Center

    Linde, Charlotte

    Speech errors have been used in the construction of production models of the phonological and semantic components of language, and for a model of interactional processes. Errors also provide insight into how speakers plan discourse and syntactic structure,. Different types of discourse exhibit different types of error. The present data are taken

  4. Forward Error Correction

    NASA Astrophysics Data System (ADS)

    Mizuochi, Takashi

    In this chapter, forward error correction (FEC) techniques for optical communications are described. In Sect. 17.1, the basic concepts of FEC and its terminology are explained. The various FECs developed to date for optical communications are classified as belonging to three generations. In Sect. 17.2, the first-generation FEC represented by RS(255,239) is described. The second-generation FECs are explained in Sect. 17.3, where recently developed concatenated codes are discussed. In Sect. 17.4, the third-generation FECs, which are more powerful FECs based on soft-decision decoding, are analyzed in detail. A block turbo code and low-density parity-check (LDPC) codes showing a record NCG of around 10 dB are discussed in detail. In Sect. 17.5, we compare each generation of FEC with the Shannon limit. The ultimate NCG is discussed as a function of code rate. FEC error count and its application are discussed in Sect. 17.6.

  5. Errors in CT colonography.

    PubMed

    Trilisky, Igor; Ward, Emily; Dachman, Abraham H

    2015-10-01

    CT colonography (CTC) is a colorectal cancer screening modality which is becoming more widely implemented and has shown polyp detection rates comparable to those of optical colonoscopy. CTC has the potential to improve population screening rates due to its minimal invasiveness, no sedation requirement, potential for reduced cathartic examination, faster patient throughput, and cost-effectiveness. Proper implementation of a CTC screening program requires careful attention to numerous factors, including patient preparation prior to the examination, the technical aspects of image acquisition, and post-processing of the acquired data. A CTC workstation with dedicated software is required with integrated CTC-specific display features. Many workstations include computer-aided detection software which is designed to decrease errors of detection by detecting and displaying polyp-candidates to the reader for evaluation. There are several pitfalls which may result in false-negative and false-positive reader interpretation. We present an overview of the potential errors in CTC and a systematic approach to avoid them. PMID:26164603

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2011-08-01

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

  8. Muscle relaxant or prone position, which one unfastened the entrapped epidural catheter?

    PubMed

    Zanjani, Amir Poya; Mirzashahi, Babak; Emami, Ali; Hassani, Motahareh

    2015-01-01

    Some nonsurgical steps have been introduced to remove an entrapped catheter. But occasionally, the majority of them fail, and we are forced to extract the catheter through an invasive procedure. This article depicts our team's experience on the issue. When we found that the inserted epidural catheter was entrapped, we performed all recommended noninvasive maneuvers to release the catheter, but no progress was achieved. Therefore, after obtaining informed consent, we induced anesthesia and changed her to a prone position to explore her back. The intact catheter was removed easily in this stage. The authors believe, in this process, it would have been better if they had tried pulling the catheter in a prone position as a preliminary step. Furthermore, pulling the catheter in a prone position after injecting a muscle relaxant appeared to be more effective and saved the patient from the scheduled surgery. PMID:26240556

  9. [A case of ventilation disorder and poor oxygenation after changing position from prone to supine].

    PubMed

    Yamaguchi, Satoshi; Hirakawa, Kei; Kitamura, Jiro

    2013-01-01

    A 68-year-old obese woman (BMI 35) underwent posterior lumbar interbody fusion in prone position. Immediately after changing position postoperatively from prone to supine, severe ventilation disorder and poor oxygenation occured. Chest X-ray showed severe atelectasis. Poor oxygenation was suspected to be the result of the atelectasis by the pressure of massive abdominal fatty tissue to the diaphragm. Ventilation disorder was suspected of the bronchospasm associated with inadequate anesthesia. We ventilated her manually with a bag in Fowler position for twenty minutes, and then mechanically by pressure controlled ventilation. She recovered gradually. It is concluded that in obese patients undergoing operation in prone position, changing position should be done very carefully during adequate anesthesia, understanding respiratory physiology in positioning and considering the effect of the abdominal fatty tissue to the diaphragm. PMID:23431901

  10. Skylab water balance error analysis

    NASA Technical Reports Server (NTRS)

    Leonard, J. I.

    1977-01-01

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

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

    PubMed Central

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

    2008-01-01

    Study Objectives: To determine the effects of sleeping position on development of circulatory control in infants over the first 6 months of postnatal age (PNA). Design: Effects of sleeping position, sleep state and PNA on beat-beat heart rate (HR) and mean arterial pressure (MAP) responses to a head-up tilt (HUT) were assessed during sleep in infants at 24 wks, 23 mo and 56 mo PNA. Measurements: Daytime polysomnography was performed on 20 full-term infants (12 F/8 M) and MAP was recorded continuously and noninvasively (Finometer). HUTs of 15 were performed during active sleep (AS) and quiet sleep (QS) in both the prone and supine sleeping positions. MAP and HR data were expressed as the percentage change from baseline, and responses were divided into initial, middle and late phases. Results: In the supine position HUT usually resulted in an initial increase (P < 0.05) in HR and MAP, followed by decreases (P < 0.05) in HR and MAP in the middle phase; subsequently HR and MAP returned to baseline in the late phase. By contrast, in the prone position the initial HUT-induced rises in HR and MAP were usually absent, and at 23 mo MAP actually decreased (P < 0.05); subsequently HR but not MAP returned to baseline. At 23 mo, MAP was lower (P < 0.05) in prone than supine sleeping throughout the HUT. Conclusions: Prone sleeping alters MAP responses to a HUT during QS at 23 mo PNA. Decreased autonomic responsiveness may contribute to the increased risk for SIDS of infants sleeping in the prone position. Citation: Yiallourou SR, Walker AM; Horne RSC. Prone sleeping impairs circulatory control during sleep in healthy term infants: implications for SIDS. SLEEP 2008;31(8):1139-1146. PMID:18714786

  12. Error threshold for topological color codes on Union Jack lattices

    NASA Astrophysics Data System (ADS)

    Katzgraber, Helmut G.; Andrist, Ruben S.; Bombin, Hector; Martin-Delgado, Miguel Angel

    2010-03-01

    Sensitivity to noise makes most of the current quantum computing schemes prone to error and nonscalable, allowing only for very small proof of principle devices. Topologically-protected quantum computing aimes to solve this problem by encoding quantum bits and gates in topological properties of the hardware medium that are immune to noise that does not impact the entire medium at once. There are different approaches to achieve topological protection. While traditional approaches use quasiparticle braidings, topological color codes use string-net condensates in 3-colexes. We study the error threshold of topological color codes on Union Jack lattices that allow for the implementation of the whole Clifford group of quantum gates. After mapping the error-correction process onto a statistical mechanical random 3-body Ising model on a Union Jack lattice, we compute its phase diagram in the temperature-disorder plane using Monte Carlo simulations. Our results show that topological color codes on Union Jack lattices have similar error stability than color codes on triangular lattices, as well as the Kitaev toric code.

  13. IPTV multicast with peer-assisted lossy error control

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

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

    USGS Publications Warehouse

    Meyer, Robert W.; Bowers, James C.

    2002-01-01

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

  15. Chin Necrosis as a Consequence of Prone Positioning in the Intensive Care Unit

    PubMed Central

    Bunker, Daniel Lee John; Thomson, Michael

    2015-01-01

    Pressure necrosis of the skin is a rarely reported avoidable complication of prone positioning that can be minimised by active collaboration between care teams. We report a case of pressure necrosis of the chin after prone ventilation in the intensive care setting. Such injuries pose a risk of infection, possible need for surgical intervention, and increased costs to the health care system. Pressure necrosis injuries should be diligently guarded against by the careful selection of support devices, frequent turning, and rigorous skin care to minimise extended external compression, particularly on the face and bony prominences. PMID:25810723

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

    PubMed

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

    2010-08-01

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

  17. Uncertainty quantification and error analysis

    SciTech Connect

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

    2010-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  20. [Diagnostic errors in angiomas].

    PubMed

    Kmpfer, R; Hundeiker, M

    1977-11-01

    A comparison of clinical statements and histologic findings reveals a lower diagnostic success in angiomas, compared with other benign tumours. Cavernous forms of angiomas are very often not discerned. Capillary angiomas are misdiagnosed as cavernous ones, and teleangiectatic nevi as angiomas. Mistakes and their incidences are pointing not at real difficulties of differentialdiagnosis, but at wrong information of physicians as to the cause of errors. According to this supposition, a great part of textbooks in different medical disciplines offer no correct representation of this object. Our results reveal problems concerning the representation of some aspects of skin diseases outside of Dermatology. The diagnosis of angiomas, with special regard to the therapeutic consequences of the fundamental distinction of angiomas from angiectatic nevi by proliferation of endothelial cells, and of cavernous from capillary angiomas by vascular structure imitating arteries or veins, demands more attention in medical education. PMID:930226

  1. Errors inducing radiation overdoses.

    PubMed

    Grammaticos, Philip C

    2013-01-01

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

  2. Vicarious trial and error.

    PubMed

    Redish, A David

    2016-02-19

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

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

    PubMed Central

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

    2011-01-01

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

  4. Rapid mapping of volumetric errors

    SciTech Connect

    Krulewich, D.; Hale, L.; Yordy, D.

    1995-09-13

    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 and the current state of the machine; (2) acquiring error data based on length measurements throughout the work volume; and (3) optimizing the model to the particular machine.

  5. Register file soft error recovery

    DOEpatents

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

    2013-10-15

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

  6. Realization of quantum error correction.

    PubMed

    Chiaverini, J; Leibfried, D; Schaetz, T; Barrett, M D; Blakestad, R B; Britton, J; Itano, W M; Jost, J D; Knill, E; Langer, C; Ozeri, R; Wineland, D J

    2004-12-01

    Scalable quantum computation and communication require error control to protect quantum information against unavoidable noise. Quantum error correction protects information stored in two-level quantum systems (qubits) by rectifying errors with operations conditioned on the measurement outcomes. Error-correction protocols have been implemented in nuclear magnetic resonance experiments, but the inherent limitations of this technique prevent its application to quantum information processing. Here we experimentally demonstrate quantum error correction using three beryllium atomic-ion qubits confined to a linear, multi-zone trap. An encoded one-qubit state is protected against spin-flip errors by means of a three-qubit quantum error-correcting code. A primary ion qubit is prepared in an initial state, which is then encoded into an entangled state of three physical qubits (the primary and two ancilla qubits). Errors are induced simultaneously in all qubits at various rates. The encoded state is decoded back to the primary ion one-qubit state, making error information available on the ancilla ions, which are separated from the primary ion and measured. Finally, the primary qubit state is corrected on the basis of the ancillae measurement outcome. We verify error correction by comparing the corrected final state to the uncorrected state and to the initial state. In principle, the approach enables a quantum state to be maintained by means of repeated error correction, an important step towards scalable fault-tolerant quantum computation using trapped ions. PMID:15577904

  7. Elementary and Middle School Students' Perceptions of Violence-Prone School Subcontexts.

    ERIC Educational Resources Information Center

    Astor, Ron Avi; Meyer, Heather Ann; Pitner, Ronald O.

    2001-01-01

    Examined student views regarding violence-prone subcontexts in their schools, contrasting elementary and middle schools, grade levels, and different public locations at school. Found organization and social dynamics of the middle school likely influenced students' perceptions, and students in different grades within elementary and middle schools

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

    PubMed

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

    2013-12-30

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

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

    PubMed Central

    Lockhart, Thurmon E.; Liu, Jian

    2010-01-01

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

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    ERIC Educational Resources Information Center

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

    2014-01-01

    In this short-term longitudinal study, we systematically examined the distinctiveness of guilt- and shame-proneness in early adolescents (N = 395, mean age = 11.8 years) in terms of differential relations with peer reported prosocial behavior, withdrawal, and aggression. Results from structural equation modeling indicated that guilt-proneness…

  12. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND...

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    ERIC Educational Resources Information Center

    Adegoke, Benson Adesina

    2011-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

    Wedge, Robert F.

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

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

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

    USGS Publications Warehouse

    Lamke, Robert D.; Jones, Stanley H.

    1980-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...) Permit only that development of flood-prone areas which (i) is appropriate in light of the probability of... safety; (2) Diversion of development to areas safe from flooding in light of the need to reduce flood damages and in light of the need to prevent environmentally incompatible flood plain use; (3)...

  4. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...) Permit only that development of flood-prone areas which (i) is appropriate in light of the probability of... safety; (2) Diversion of development to areas safe from flooding in light of the need to reduce flood damages and in light of the need to prevent environmentally incompatible flood plain use; (3)...

  5. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...) Permit only that development of flood-prone areas which (i) is appropriate in light of the probability of... safety; (2) Diversion of development to areas safe from flooding in light of the need to reduce flood damages and in light of the need to prevent environmentally incompatible flood plain use; (3)...

  6. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Planning considerations for flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND...

  7. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...) Permit only that development of flood-prone areas which (i) is appropriate in light of the probability of... safety; (2) Diversion of development to areas safe from flooding in light of the need to reduce flood damages and in light of the need to prevent environmentally incompatible flood plain use; (3)...

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

    ERIC Educational Resources Information Center

    Comer, David W.; And Others

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

  9. Long-range PCR with a DNA polymerase fusion.

    PubMed

    Hogrefe, Holly H; Borns, Michael C

    2011-01-01

    Proofreading DNA polymerase fusions offer several advantages for long-range PCR, including faster run times and higher fidelity compared with Taq-based enzymes. However, their use so far has been limited to amplification of small to mid-range targets. In this article, we present a modified protocol for using a DNA polymerase fusion to amplify genomic targets exceeding 20 kb in length. This procedure overcomes several limitations of Taq blends, which up until recently, were the only option for long-range PCR. With a proofreading DNA polymerase fusion, high-molecular-weight amplicon can be generated and analyzed in a single day, and a significant proportion is expected to be error-free. PMID:20967598

  10. Contour Error Map Algorithm

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

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

    SciTech Connect

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

    2010-05-01

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

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

    PubMed Central

    Nilsson, Michael; Attia, John; Ejnell, Hasse

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  14. What is a prescribing error?

    PubMed Central

    Dean, B; Barber, N; Schachter, M

    2000-01-01

    N Barber, professor of the practice of pharmacy M Schachter, senior lecturer and honorary consultant physician ObjectiveTo develop a practitioner led definition of a prescribing error for use in quantitative studies of their incidence. DesignTwo stage Delphi technique. SubjectsA panel of 34 UK judges, which included physicians, surgeons, pharmacists, nurses and risk managers. Main outcome measuresThe extent to which judges agreed with a general definition of a prescribing error, and the extent to which they agreed that each of 42 scenarios represented a prescribing error. ResultsResponses were obtained from 30 (88%) of 34 judges in the first Delphi round, and from 26 (87%) of 30 in the second round. The general definition of a prescribing error was accepted. The panel reached consensus that 24 of the 42 scenarios should be included as prescribing errors and that five should be excluded. In general, transcription errors, failure to communicate essential information, and the use of drugs or doses inappropriate for the individual patient were considered prescribing errors; deviations from policies or guidelines were not. ConclusionsHealth care professionals are in broad agreement about the types of events that should be included and excluded as prescribing errors. A general definition of a prescribing error has been developed, together with more detailed guidance regarding the types of events that should be included. This definition allows the comparison of prescribing error rates among different prescribing systems and different hospitals, and is suitable for use in both research and clinical governance initiatives. (Quality in Health Care 2000;9:232237) Key Words: prescribing errors; medication errors; definition of error PMID:11101708

  15. Sepsis: Medical errors in Poland.

    PubMed

    Rorat, Marta; Jurek, Tomasz

    2016-01-01

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

  16. Violating body movement semantics: Neural signatures of self-generated and external-generated errors.

    PubMed

    Padrao, Gonalo; Gonzalez-Franco, Mar; Sanchez-Vives, Maria V; Slater, Mel; Rodriguez-Fornells, Antoni

    2016-01-01

    How do we recognize ourselves as the agents of our actions? Do we use the same error detection mechanisms to monitor self-generated vs. externally imposed actions? Using event-related brain potentials (ERPs), we identified two different error-monitoring loops involved in providing a coherent sense of the agency of our actions. In the first ERP experiment, the participants were embodied in a virtual body (avatar) while performing an error-prone fast reaction time task. Crucially, in certain trials, participants were deceived regarding their own actions, i.e., the avatar movement did not match the participant's movement. Self-generated real errors and false (avatar) errors showed very different ERP signatures and with different processing latencies: while real errors showed a classical frontal-central error-related negativity (Ne/ERN), peaking 100ms after error commission, false errors elicited a larger and delayed parietal negative component (at about 350-400ms). The violation of the sense of agency elicited by false avatar errors showed a strong similarity to ERP signatures related to semantic or conceptual violations (N400 component). In a follow-up ERP control experiment, a subset of the same participants merely acted as observers of the avatar correct and error movements. This experimental situation did not elicit the N400 component associated with agency violation. Thus, the results show a clear neural dissociation between internal and external error-monitoring loops responsible for distinguishing our self-generated errors from those imposed externally, opening new avenues for the study of the mental processes underlying the integration of internal and sensory feedback information while being actors of our own actions. PMID:26282856

  17. Medical errors: overcoming the challenges.

    PubMed

    Kalra, Jawahar

    2004-12-01

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

  18. Random errors in egocentric networks

    PubMed Central

    Almquist, Zack W.

    2013-01-01

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

  19. The Influence of Counselor Trainee Anger-Proneness and Anger Discomfort on Reactions to an Angry Client.

    ERIC Educational Resources Information Center

    Sharkin, Bruce S.; Gelso, Charles J.

    1993-01-01

    Explored relationship between counselor trainee anger-proneness and anger discomfort and trainees' reactions to angry client. Thirty-eight trainees viewed and gave reactions to videotape of angry client-actress. Trainee anger-proneness and anger discomfort scores were positively and significantly related to discomfort with and anger toward the

  20. Numerical Error Estimation with UQ

    NASA Astrophysics Data System (ADS)

    Ackmann, Jan; Korn, Peter; Marotzke, Jochem

    2014-05-01

    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

  1. A theory of human error

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

    Human error, a significant contributing factor in a very high proportion of civil transport, general aviation, and rotorcraft accidents is investigated. Correction of the sources of human error requires that one attempt to reconstruct underlying and contributing causes of error from the circumstantial causes cited in official investigative reports. A validated analytical theory of the input-output behavior of human operators involving manual control, communication, supervisory, and monitoring tasks which are relevant to aviation operations is presented. This theory of behavior, both appropriate and inappropriate, provides an insightful basis for investigating, classifying, and quantifying the needed cause-effect relationships governing propagation of human error.

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  4. 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...

  5. Identification and Estimation of Nonlinear Models Using Two Samples with Nonclassical Measurement Errors

    PubMed Central

    Carroll, Raymond J.; Chen, Xiaohong; Hu, Yingyao

    2010-01-01

    This paper considers identification and estimation of a general nonlinear Errors-in-Variables (EIV) model using two samples. Both samples consist of a dependent variable, some error-free covariates, and an error-prone covariate, for which the measurement error has unknown distribution and could be arbitrarily correlated with the latent true values; and neither sample contains an accurate measurement of the corresponding true variable. We assume that the regression model of interest the conditional distribution of the dependent variable given the latent true covariate and the error-free covariates is the same in both samples, but the distributions of the latent true covariates vary with observed error-free discrete covariates. We first show that the general latent nonlinear model is nonparametrically identified using the two samples when both could have nonclassical errors, without either instrumental variables or independence between the two samples. When the two samples are independent and the nonlinear regression model is parameterized, we propose sieve Quasi Maximum Likelihood Estimation (Q-MLE) for the parameter of interest, and establish its root-n consistency and asymptotic normality under possible misspecification, and its semiparametric efficiency under correct specification, with easily estimated standard errors. A Monte Carlo simulation and a data application are presented to show the power of the approach. PMID:20495685

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

    PubMed

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

    2013-10-01

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

  7. Error studies for SNS Linac. Part 1: Transverse errors

    SciTech Connect

    Crandall, K.R.

    1998-12-31

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

  8. Statistical methods for efficiency adjusted real-time PCR quantification.

    PubMed

    Yuan, Joshua S; Wang, Donglin; Stewart, C Neal

    2008-01-01

    The statistical treatment for hypothesis testing using real-time PCR data is a challenge for quantification of gene expression. One has to consider two key factors in precise statistical analysis of real-time PCR data: a well-defined statistical model and the integration of amplification efficiency (AE) into the model. Previous publications in real-time PCR data analysis often fall short in integrating the AE into the model. Novel, user-friendly, and universal AE-integrated statistical methods were developed for real-time PCR data analysis with four goals. First, we addressed the definition of AE, introduced the concept of efficiency-adjusted Delta Delta Ct, and developed a general mathematical method for its calculation. Second, we developed several linear combination approaches for the estimation of efficiency adjusted Delta Delta Ct and statistical significance for hypothesis testing based on different mathematical formulae and experimental designs. Statistical methods were also adopted to estimate the AE and its equivalence among the samples. A weighted Delta Delta Ct method was introduced to analyze the data with multiple internal controls. Third, we implemented the linear models with SAS programs and analyzed a set of data for each model. In order to allow other researchers to use and compare different approaches, SAS programs are included in the Supporting Information. Fourth, the results from analysis of different statistical models were compared and discussed. Our results underline the differences between the efficiency adjusted Delta Delta Ct methods and previously published methods, thereby better identifying and controlling the source of errors introduced by real-time PCR data analysis. PMID:18074404

  9. Error coding simulations in C

    NASA Technical Reports Server (NTRS)

    Noble, Viveca K.

    1994-01-01

    When data is transmitted through a noisy channel, errors are produced within the data rendering it indecipherable. Through the use of error control coding techniques, the bit error rate can be reduced to any desired level without sacrificing the transmission data rate. The Astrionics Laboratory at Marshall Space Flight Center has decided to use a modular, end-to-end telemetry data simulator to simulate the transmission of data from flight to ground and various methods of error control. The simulator includes modules for random data generation, data compression, Consultative Committee for Space Data Systems (CCSDS) transfer frame formation, error correction/detection, error generation and error statistics. The simulator utilizes a concatenated coding scheme which includes CCSDS standard (255,223) Reed-Solomon (RS) code over GF(2(exp 8)) with interleave depth of 5 as the outermost code, (7, 1/2) convolutional code as an inner code and CCSDS recommended (n, n-16) cyclic redundancy check (CRC) code as the innermost code, where n is the number of information bits plus 16 parity bits. The received signal-to-noise for a desired bit error rate is greatly reduced through the use of forward error correction techniques. Even greater coding gain is provided through the use of a concatenated coding scheme. Interleaving/deinterleaving is necessary to randomize burst errors which may appear at the input of the RS decoder. The burst correction capability length is increased in proportion to the interleave depth. The modular nature of the simulator allows for inclusion or exclusion of modules as needed. This paper describes the development and operation of the simulator, the verification of a C-language Reed-Solomon code, and the possibility of using Comdisco SPW(tm) as a tool for determining optimal error control schemes.

  10. Clinical applications using digital PCR.

    PubMed

    Bizouarn, Francisco

    2014-01-01

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

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

    PubMed

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

    2014-12-01

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

  12. Dual Processing and Diagnostic Errors

    ERIC Educational Resources Information Center

    Norman, Geoff

    2009-01-01

    In this paper, I review evidence from two theories in psychology relevant to diagnosis and diagnostic errors. "Dual Process" theories of thinking, frequently mentioned with respect to diagnostic error, propose that categorization decisions can be made with either a fast, unconscious, contextual process called System 1 or a slow, analytical,…

  13. Explaining Errors in Children's Questions

    ERIC Educational Resources Information Center

    Rowland, Caroline F.

    2007-01-01

    The ability to explain the occurrence of errors in children's speech is an essential component of successful theories of language acquisition. The present study tested some generativist and constructivist predictions about error on the questions produced by ten English-learning children between 2 and 5 years of age. The analyses demonstrated that,

  14. Operational Interventions to Maintenance Error

    NASA Technical Reports Server (NTRS)

    Kanki, Barbara G.; Walter, Diane; Dulchinos, VIcki

    1997-01-01

    A significant proportion of aviation accidents and incidents are known to be tied to human error. However, research of flight operational errors has shown that so-called pilot error often involves a variety of human factors issues and not a simple lack of individual technical skills. In aircraft maintenance operations, there is similar concern that maintenance errors which may lead to incidents and accidents are related to a large variety of human factors issues. Although maintenance error data and research are limited, industry initiatives involving human factors training in maintenance have become increasingly accepted as one type of maintenance error intervention. Conscientious efforts have been made in re-inventing the team7 concept for maintenance operations and in tailoring programs to fit the needs of technical opeRAtions. Nevertheless, there remains a dual challenge: 1) to develop human factors interventions which are directly supported by reliable human error data, and 2) to integrate human factors concepts into the procedures and practices of everyday technical tasks. In this paper, we describe several varieties of human factors interventions and focus on two specific alternatives which target problems related to procedures and practices; namely, 1) structured on-the-job training and 2) procedure re-design. We hope to demonstrate that the key to leveraging the impact of these solutions comes from focused interventions; that is, interventions which are derived from a clear understanding of specific maintenance errors, their operational context and human factors components.

  15. Quantifying error distributions in crowding.

    PubMed

    Hanus, Deborah; Vul, Edward

    2013-01-01

    When multiple objects are in close proximity, observers have difficulty identifying them individually. Two classes of theories aim to account for this crowding phenomenon: spatial pooling and spatial substitution. Variations of these accounts predict different patterns of errors in crowded displays. Here we aim to characterize the kinds of errors that people make during crowding by comparing a number of error models across three experiments in which we manipulate flanker spacing, display eccentricity, and precueing duration. We find that both spatial intrusions and individual letter confusions play a considerable role in errors. Moreover, we find no evidence that a nave pooling model that predicts errors based on a nonadditive combination of target and flankers explains errors better than an independent intrusion model (indeed, in our data, an independent intrusion model is slightly, but significantly, better). Finally, we find that manipulating trial difficulty in any way (spacing, eccentricity, or precueing) produces homogenous changes in error distributions. Together, these results provide quantitative baselines for predictive models of crowding errors, suggest that pooling and spatial substitution models are difficult to tease apart, and imply that manipulations of crowding all influence a common mechanism that impacts subject performance. PMID:23525133

  16. Barriers to Medical Error Reporting

    PubMed Central

    Poorolajal, Jalal; Rezaie, Shirin; Aghighi, Negar

    2015-01-01

    Background: This study was conducted to explore the prevalence of medical error underreporting and associated barriers. Methods: This cross-sectional study was performed from September to December 2012. Five hospitals, affiliated with Hamadan University of Medical Sciences, in Hamedan, Iran were investigated. A self-administered questionnaire was used for data collection. Participants consisted of physicians, nurses, midwives, residents, interns, and staffs of radiology and laboratory departments. Results: Overall, 50.26% of subjects had committed but not reported medical errors. The main reasons mentioned for underreporting were lack of effective medical error reporting system (60.0%), lack of proper reporting form (51.8%), lack of peer supporting a person who has committed an error (56.0%), and lack of personal attention to the importance of medical errors (62.9%). The rate of committing medical errors was higher in men (71.4%), age of 5040 years (67.6%), less-experienced personnel (58.7%), educational level of MSc (87.5%), and staff of radiology department (88.9%). Conclusions: This study outlined the main barriers to reporting medical errors and associated factors that may be helpful for healthcare organizations in improving medical error reporting as an essential component for patient safety enhancement. PMID:26605018

  17. Dual Processing and Diagnostic Errors

    ERIC Educational Resources Information Center

    Norman, Geoff

    2009-01-01

    In this paper, I review evidence from two theories in psychology relevant to diagnosis and diagnostic errors. "Dual Process" theories of thinking, frequently mentioned with respect to diagnostic error, propose that categorization decisions can be made with either a fast, unconscious, contextual process called System 1 or a slow, analytical,

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

    ERIC Educational Resources Information Center

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

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

  20. Quantization of accumulated diffused errors in error diffusion

    NASA Astrophysics Data System (ADS)

    Chang, Ti-chiun; Allebach, Jan P.

    2005-01-01

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

  1. Quantization of accumulated diffused errors in error diffusion

    NASA Astrophysics Data System (ADS)

    Chang, Ti-chiun; Allebach, Jan P.

    2004-12-01

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

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

    PubMed Central

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

    2006-01-01

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

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

    PubMed

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

    2015-11-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

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

    PubMed

    Hernando, D; Srnmo, L; Sandberg, F; Laguna, P; Llamedo, M; Bailn, R

    2015-12-01

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

  6. Tension Pneumothorax During Surgery for Thoracic Spine Stabilization in Prone Position

    PubMed Central

    Mathew, Paul S.; Kurnutala, Lakshmi N.; Soghomonyan, Suren; Bergese, Sergio D.

    2014-01-01

    The intraoperative progression of a simple or occult pneumothorax into a tension pneumothorax can be a devastating clinical scenario. Routine use of prophylactic thoracostomy prior to anesthesia and initiation of controlled ventilation in patients with simple or occult pneumothorax remains controversial. We report the case of a 75-year-old trauma patient with an insignificant pneumothorax on the right who developed an intraoperative tension pneumothorax on the left side while undergoing thoracic spine stabilization surgery in the prone position. Management of an intraoperative tension pneumothorax requires prompt recognition and treatment; however, the prone position presents an additional challenge of readily accessing the standard anatomic sites for pleural puncture and air drainage. PMID:26425610

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

    SciTech Connect

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

    1989-03-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

  10. Human error in recreational boating.

    PubMed

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

    2007-03-01

    Each year over 600 people die and more than 4000 are reported injured in recreational boating accidents. As with most other accidents, human error is the major contributor. U.S. Coast Guard reports of 3358 accidents were analyzed to identify errors in each of the boat types by which statistics are compiled: auxiliary (motor) sailboats, cabin motorboats, canoes and kayaks, house boats, personal watercraft, open motorboats, pontoon boats, row boats, sail-only boats. The individual errors were grouped into categories on the basis of similarities in the behavior involved. Those presented here are the categories accounting for at least 5% of all errors when summed across boat types. The most revealing and significant finding is the extent to which the errors vary across types. Since boating is carried out with one or two types of boats for long periods of time, effective accident prevention measures, including safety instruction, need to be geared to individual boat types. PMID:17049472

  11. Direct in situ rt-PCR.

    PubMed

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

    2011-01-01

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

  12. Exceptional error minimization in putative primordial genetic codes

    PubMed Central

    2009-01-01

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

  13. Paediatric Intravenous Splint: A Cause of Pressure Injury during Neurosurgery in Prone Position.

    PubMed

    Haldar, Rudrashish; Kaushal, Ashutosh; Srivastava, Shashi; Singh, Prabhat K

    2016-01-01

    Splint application avoids unwanted movement of limbs and kinking of intravenous catheters in infants, allowing free flow of intravenous fluids. However, if placed in contact with dependent surfaces during prone surgeries, they have the propensity to cause inadvertent pressure injuries. This occurs due to the weight of the limb and continuous friction and is augmented by a rise in the local temperature and perspiration. We wish to share our experience of such an unintentional injury caused by a paediatric intravenous splint. PMID:26575479

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

    Stegman, Lauren D.; Beal, Katherine P.; Hunt, Margie A.; Fornier, Monica N.; McCormick, Beryl . E-mail: mccormib@mskcc.org

    2007-05-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2006-10-23

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

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

    PubMed

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

    2015-10-01

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

  20. Plasma catecholamine response to postural stimulation in normotensive and dialysis hypotension-prone uremic patients.

    PubMed

    Cannella, G; Picotti, G B; Movilli, E; Cancarini, G; De Marinis, S; Galva, M D; Maiorca, R

    1981-01-01

    The neurosympathetic responsiveness of two groups of uremics, each group treated for the same mean time by dialysis, categorized as normotensive, mean age 28.3 +/- (SE) 3 years, or dialysis hypotension-prone, mean age 49.6 +/- 5 years, was studied by determining plasma norepinephrine and epinephrine before and after postural activation of the sympathetic reflex arc. The study was performed on an interdialysis day and repeated 20 min before and after a regular dialysis on the following day. Standing caused norepinephrine to rise significantly in both the normotensive and the hypotension-prone groups and to a similar extent as in a control nonuremic group. Blood pressure did not change and the heart rate increased significantly. Plasma norepinephrine before dialysis 24 h later behaved in the same way, but both blood pressure and heart rate were unchanged. After dialysis, in spite of the usual increase in norepinephrine after standing, patients in the hypotension-prone group became hypotensive. These results suggest that there is a normal sympathetic responsiveness in uremics whatever their propensity for intradialysis hypotension. Moreover, dialysis does not seem to have an acute effect on the neurosympathetic response to a hypotensive stimulus. Dialysis-dependent hypotension, which appears to be more frequent in older subjects, probably reflects an impairment of the vasoconstrictor response of the vascular wall acutely induced by dialysis itself. PMID:7266717

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Chan, Raymond C K; Shi, Hai-song; Geng, Fu-lei; Liu, Wen-hua; Yan, Chao; Wang, Yi; Gooding, Diane C

    2015-07-30

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-09-01

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

  5. 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

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

    2014-07-01

    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 = 204 - ?). 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

  6. Child anger proneness moderates associations between child-mother attachment security and child behavior with mothers at 33 months.

    PubMed

    McElwain, Nancy L; Holland, Ashley S; Engle, Jennifer M; Wong, Maria S

    2012-02-01

    Child-mother attachment security, assessed via a modified Strange Situation procedure (Cassidy & Marvin, with the MacArthur Attachment Working Group, 1992), and parent-reported child proneness to anger were examined as correlates of observed child behavior toward mothers during a series of interactive tasks (N = 120, 60 girls). Controlling for maternal sensitivity and child gender and expressive language ability, greater attachment security, and lower levels of anger proneness were related to more child responsiveness to maternal requests and suggestions during play and snack sessions. As hypothesized, anger proneness also moderated several security-behavior associations. Greater attachment security was related to (a) more committed compliance during clean-up and snack-delay tasks for children high on anger proneness, (b) more self-assertiveness during play and snack for children moderate or high on anger proneness, and (c) more help-seeking during play and snack for children moderate or low on anger proneness. Findings further our understanding of the behavioral correlates of child-mother attachment security assessed during late toddlerhood via the Cassidy-Marvin system and underscore child anger proneness as a moderator of attachment-related differences in child behavior during this developmental period. PMID:22182337

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Astrophysics Data System (ADS)

    Busch, Paul

    2014-09-01

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

  9. [Medication errors: who is responsible?].

    PubMed

    Rosa, Mrio Borges; Perini, Edson

    2003-01-01

    New diagnostic and therapeutic technologies are used with growing frequency, improving the quality of medical assistance and increasing life expectancy. Health care, however, is becoming progressively more expensive and complex. Adverse events related to medical assistance, particularly errors, are becoming public, being debated and judged in courts. Given their training, health workers are not prepared to deal with errors, which are associated with shame, fear and punishment. The approach to errors in the health system is usually individualistic, considering such events as acts of insecurity performed by careless, non-motivated and ill-trained persons. The tendency is to hide errors when they occur, with the result that an important learning opportunity is lost. There is another way to deal with errors, a systemic view that has obtained positive results in sectors such as aviation, anesthesiology and unit-dose drug distribution systems. These systems have varied degrees of safety and should take into account human limitations when designed and applied. A change in paradigm is needed when dealing with drugs, as it is not enough for a drug to have quality assurance, but the complete process of drug use should be safe. Medication errors, avoidable by definition, are at present a serious public health issue, leading to loss of lives and significant financial losses. A systemic approach to medication errors may disclose failures in the process as a whole, and improvements can be implemented to reduce their occurrence. PMID:14666362

  10. Error compensation for thermally induced errors on a machine tool

    SciTech Connect

    Krulewich, D.A.

    1996-11-08

    Heat flow from internal and external sources and the environment create machine deformations, resulting in positioning errors between the tool and workpiece. There is no industrially accepted method for thermal error compensation. A simple model has been selected that linearly relates discrete temperature measurements to the deflection. The biggest problem is how to locate the temperature sensors and to determine the number of required temperature sensors. This research develops a method to determine the number and location of temperature measurements.

  11. [Considerations for normalisation of RT-qPCR in oncology].

    PubMed

    Ho-Pun-Cheung, A; Cellier, D; Lopez-Crapez, E

    2008-01-01

    Gene expression analysis has many applications in the management of cancer, including diagnosis, prognosis, and therapeutic care. In this context, the reverse transcription quantitative polymerase chain reaction (RT-qPCR) has become the "gold standard" for mRNA quantification. However, this technique involves several critical steps such as RNA extraction, cDNA synthesis, quantitative PCR, and analysis, which all can be source of variation. To obtain biologically meaningful results, data normalisation is required to correct sample-to-sample variations that may be introduced during this multistage process. Normalisation can be carried out against a housekeeping gene, total RNA mass, or cell number. Careful choice of the normalization method is crucial, as any variation in the reference will introduce errors in the quantification of mRNA transcripts. By reviewing the different methods available and their related problems, the aim of this article is to provide recommendations for the set up of an appropriate normalisation strategy for RT-qPCR data in oncology. PMID:18390422

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Deeg, H. J.

    2015-06-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    MacKay, Donald G; Johnson, Laura W

    2013-11-01

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

  18. Understanding the effects of leakage in superconducting quantum-error-detection circuits

    NASA Astrophysics Data System (ADS)

    Ghosh, Joydip; Fowler, Austin G.; Martinis, John M.; Geller, Michael R.

    2013-12-01

    The majority of quantum-error-detection and correction protocols assume that the population in a qubit does not leak outside of its computational subspace. For many existing approaches, however, the physical qubits do possess more than two energy levels and consequently are prone to such leakage events. Analyzing the effects of leakage is therefore essential to devise optimal protocols for quantum gates, measurement, and error correction. In this article, we present a detailed study of leakage in a two-qubit superconducting stabilizer measurement circuit. We simulate the repeated ancilla-assisted measurement of a single ?z operator for a data qubit, record the outcome at the end of each measurement cycle, and explore the signature of leakage events in the obtained readout statistics. An analytic model is also developed that closely approximates the results of our numerical simulations. We find that leakage leads to destructive features in the quantum-error-detection scheme, making additional hardware and software protocols necessary.

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

    SciTech Connect

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

    2010-03-24

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

  20. Error bounds in cascading regressions

    USGS Publications Warehouse

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

    1985-01-01

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

  1. Stochastic Models of Human Errors

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

    Humans play an important role in the overall reliability of engineering systems. More often accidents and systems failure are traced to human errors. Therefore, in order to have meaningful system risk analysis, the reliability of the human element must be taken into consideration. Describing the human error process by mathematical models is a key to analyzing contributing factors. Therefore, the objective of this research effort is to establish stochastic models substantiated by sound theoretic foundation to address the occurrence of human errors in the processing of the space shuttle.

  2. Differential expression of candidate virus receptors in human T lymphocytes prone or resistant to infection with patient-derived hepatitis C virus.

    PubMed

    Sarhan, Mohammed A; Chen, Annie Y; Michalak, Tomasz I

    2013-01-01

    Accumulated evidence implies that hepatitis C virus (HCV) infects not only the liver but also the immune system. A lymphocyte-specific CD5 molecule was recently identified as essential for infection of T cells with native, patient-derived HCV. To assess whether the proposed hepatocyte receptors may also contribute to HCV lymphotropism, expression of scavenger receptor-class B type 1 (SR-B1), claudin-1 (CLDN-1), claudin-6 (CLDN-6), occludin (OCLN), CD5 and CD81 was examined by real-time RT-PCR and the respective proteins quantified by immunoblotting in HCV-prone and resistant T cell lines, peripheral blood mononuclear cells (PBMC), primary T cells and their subsets, and compared to hepatoma Huh7.5 and HepG2 cells. SR-B1 protein was found in T and hepatoma cell lines but not in PBMC or primary T lymphocytes, CLDN-1 in HCV-resistant PM1 T cell line and hepatoma cells only, while CLDN-6 equally in the cells investigated. OCLN protein occurred in HCV-susceptible Molt4 and Jurkat T cells and its traces in primary T cells, but not in PBMC. CD5 was displayed by HCV-prone T cell lines, primary T cells and PBMC, but not by non-susceptible T and hepatoma cell lines, while CD81 in all cell types except HepG2. Knocking-down OCLN in virus-prone T cell line inhibited HCV infection, while de novo infection downregulated OCLN and CD81, and upregulated CD5 without modifying SR-B1 expression. Overall, while no association between SR-B1, CLDN-1 or CLDN-6 and the susceptibility to HCV was found, CD5 and CD81 expression coincided with virus lymphotropism and that of OCLN with permissiveness of T cell lines but unlikely primary T cells. This study narrowed the range of factors potentially utilized by HCV to infect T lymphocytes amongst those uncovered using laboratory HCV and Huh7.5 cells. Together with the demonstrated role for CD5 in HCV lymphotropism, the findings indicate that virus utilizes different molecules to enter hepatocytes and lymphocytes. PMID:23626783

  3. Differential Expression of Candidate Virus Receptors in Human T Lymphocytes Prone or Resistant to Infection with Patient-Derived Hepatitis C Virus

    PubMed Central

    Sarhan, Mohammed A.; Chen, Annie Y.; Michalak, Tomasz I.

    2013-01-01

    Accumulated evidence implies that hepatitis C virus (HCV) infects not only the liver but also the immune system. A lymphocyte-specific CD5 molecule was recently identified as essential for infection of T cells with native, patient-derived HCV. To assess whether the proposed hepatocyte receptors may also contribute to HCV lymphotropism, expression of scavenger receptor-class B type 1 (SR-B1), claudin-1 (CLDN-1), claudin-6 (CLDN-6), occludin (OCLN), CD5 and CD81 was examined by real-time RT-PCR and the respective proteins quantified by immunoblotting in HCV-prone and resistant T cell lines, peripheral blood mononuclear cells (PBMC), primary T cells and their subsets, and compared to hepatoma Huh7.5 and HepG2 cells. SR-B1 protein was found in T and hepatoma cell lines but not in PBMC or primary T lymphocytes, CLDN-1 in HCV-resistant PM1 T cell line and hepatoma cells only, while CLDN-6 equally in the cells investigated. OCLN protein occurred in HCV-susceptible Molt4 and Jurkat T cells and its traces in primary T cells, but not in PBMC. CD5 was displayed by HCV-prone T cell lines, primary T cells and PBMC, but not by non-susceptible T and hepatoma cell lines, while CD81 in all cell types except HepG2. Knocking-down OCLN in virus-prone T cell line inhibited HCV infection, while de novo infection downregulated OCLN and CD81, and upregulated CD5 without modifying SR-B1 expression. Overall, while no association between SR-B1, CLDN-1 or CLDN-6 and the susceptibility to HCV was found, CD5 and CD81 expression coincided with virus lymphotropism and that of OCLN with permissiveness of T cell lines but unlikely primary T cells. This study narrowed the range of factors potentially utilized by HCV to infect T lymphocytes amongst those uncovered using laboratory HCV and Huh7.5 cells. Together with the demonstrated role for CD5 in HCV lymphotropism, the findings indicate that virus utilizes different molecules to enter hepatocytes and lymphocytes. PMID:23626783

  4. Multiplexed Primer Prediction for PCR

    SciTech Connect

    2007-07-23

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

  5. Multiplexed Primer Prediction for PCR

    Energy Science and Technology Software Center (ESTSC)

    2007-07-23

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    Physically based models provide insights into key hydrologic processes but are associated with uncertainties due to deficiencies in forcing data, model parameters, and model structure. Forcing uncertainty is enhanced in snow-affected catchments, where weather stations are scarce and prone to measurement errors, and meteorological variables exhibit high variability. Hence, there is limited understanding of how forcing error characteristics affect simulations of cold region hydrology and which error characteristics are most important. Here we employ global sensitivity analysis to explore how (1) different error types (i.e., bias, random errors), (2) different error probability distributions, and (3) different error magnitudes influence physically based simulations of four snow variables (snow water equivalent, ablation rates, snow disappearance, and sublimation). We use the Sobol' global sensitivity analysis, which is typically used for model parameters but adapted here for testing model sensitivity to coexisting errors in all forcings. We quantify the Utah Energy Balance model's sensitivity to forcing errors with 1 840 000 Monte Carlo simulations across four sites and five different scenarios. Model outputs were (1) consistently more sensitive to forcing biases than random errors, (2) generally less sensitive to forcing error distributions, and (3) critically sensitive to different forcings depending on the relative magnitude of errors. For typical error magnitudes found in areas with drifting snow, precipitation bias was the most important factor for snow water equivalent, ablation rates, and snow disappearance timing, but other forcings had a more dominant impact when precipitation uncertainty was due solely to gauge undercatch. Additionally, the relative importance of forcing errors depended on the model output of interest. Sensitivity analysis can reveal which forcing error characteristics matter most for hydrologic modeling.

  7. Quantile Regression With Measurement Error

    PubMed Central

    Wei, Ying; Carroll, Raymond J.

    2010-01-01

    Regression quantiles can be substantially biased when the covariates are measured with error. In this paper we propose a new method that produces consistent linear quantile estimation in the presence of covariate measurement error. The method corrects the measurement error induced bias by constructing joint estimating equations that simultaneously hold for all the quantile levels. An iterative EM-type estimation algorithm to obtain the solutions to such joint estimation equations is provided. The finite sample performance of the proposed method is investigated in a simulation study, and compared to the standard regression calibration approach. Finally, we apply our methodology to part of the National Collaborative Perinatal Project growth data, a longitudinal study with an unusual measurement error structure. PMID:20305802

  8. Human errors and measurement uncertainty

    NASA Astrophysics Data System (ADS)

    Kuselman, Ilya; Pennecchi, Francesca

    2015-04-01

    Evaluating the residual risk of human errors in a measurement and testing laboratory, remaining after the error reduction by the laboratory quality system, and quantifying the consequences of this risk for the quality of the measurement/test results are discussed based on expert judgments and Monte Carlo simulations. A procedure for evaluation of the contribution of the residual risk to the measurement uncertainty budget is proposed. Examples are provided using earlier published sets of expert judgments on human errors in pH measurement of groundwater, elemental analysis of geological samples by inductively coupled plasma mass spectrometry, and multi-residue analysis of pesticides in fruits and vegetables. The human error contribution to the measurement uncertainty budget in the examples was not negligible, yet also not dominant. This was assessed as a good risk management result.

  9. Prospective errors determine motor learning

    PubMed Central

    Takiyama, Ken; Hirashima, Masaya; Nozaki, Daichi

    2015-01-01

    Diverse features of motor learning have been reported by numerous studies, but no single theoretical framework concurrently accounts for these features. Here, we propose a model for motor learning to explain these features in a unified way by extending a motor primitive framework. The model assumes that the recruitment pattern of motor primitives is determined by the predicted movement error of an upcoming movement (prospective error). To validate this idea, we perform a behavioural experiment to examine the models novel prediction: after experiencing an environment in which the movement error is more easily predictable, subsequent motor learning should become faster. The experimental results support our prediction, suggesting that the prospective error might be encoded in the motor primitives. Furthermore, we demonstrate that this model has a strong explanatory power to reproduce a wide variety of motor-learning-related phenomena that have been separately explained by different computational models. PMID:25635628

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

    PubMed Central

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

    2016-01-01

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

  11. Iatrogenic error and physician responsibility.

    PubMed

    Sandroni, S

    2001-03-01

    The recent report on iatrogenic errors highlighted the scope of the problem and suggested solutions including a national agency to oversee error reporting. This may or may not occur; in the meantime physicians are not relieved of their responsibility to respond to the issue of patient safety. Reasons for the slow response to date are discussed and suggestions for the future are offered. PMID:11291568

  12. Multiplex nested PCR for Brazilian Alphavirus diagnosis.

    PubMed

    Bronzoni, Roberta V M; Moreli, Marcos L; Cruz, Ana Ceclia R; Figueiredo, Luiz Tadeu M

    2004-08-01

    A reverse-transcriptase PCR (RT-PCR) and a multiplex nested PCR were developed for the rapid detection and identification of 14 Brazilian alphaviruses. Using Alphavirus genus-specific primers in a RT-PCR, we obtained amplified products of 434 bp. Species-specific primers were selected and simultaneously tested in a multiplex nested PCR. The nested PCR increased the test sensitivity 1000-fold and was capable of identifying Brazilian Alphavirus showing the expected bands with diagnostic sizes for Venezuelan (400 bp), Eastern (124 bp), and Western (208 bp) equine encephalitis, Aura (86 bp), and Mayaro (270 bp) viruses. This strategy for diagnosis is fast, sensitive, specific and it can be used as a reliable alternative for routine Brazilian Alphavirus diagnosis. PMID:15186933

  13. Measuring verification device error rates

    SciTech Connect

    Watson, J.G.; Johnstone, I.M.; Driscoll, E.C. Jr.

    1987-07-01

    A verification device generates a Type I (II) error when it recommends to reject (accept) a valid (false) identity claim. For a given identity, the rates or probabilities of these errors quantify random variations of the device from claim to claim. These are intra-identity variations. To some degree, these rates depend on the particular identity being challenged, and there exists a distribution of error rates characterizing inter-identity variations. However, for most security system applications we only need to know averages of this distribution. These averages are called the pooled error rates. In this paper the authors present the statistical underpinnings for the measurement of pooled Type I and Type II error rates. The authors consider a conceptual experiment, ''a crate of biased coins''. This model illustrates the effects of sampling both within trials of the same individual and among trials from different individuals. Application of this simple model to verification devices yields pooled error rate estimates and confidence limits for these estimates. A sample certification procedure for verification devices is given in the appendix.

  14. The usability-error ontology.

    PubMed

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

    2013-01-01

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

  15. Memory efficient hierarchical error diffusion

    NASA Astrophysics Data System (ADS)

    He, Zhen; Fan, Zhigang

    2010-01-01

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

  16. Error image aware content restoration

    NASA Astrophysics Data System (ADS)

    Choi, Sungwoo; Lee, Moonsik; Jung, Byunghee

    2015-12-01

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

  17. Real-time PCR in microfluidic devices

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

    Pinto, Ameet J.; Raskin, Lutgarde

    2012-01-01

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

  1. Dysfunctional meta-cognitive beliefs mediate the relation between temperament traits and hallucination-proneness in non-clinical population.

    PubMed

    Gaw?da, ?ukasz; Cicho?, Ewelina; Szczepanowski, Remigiusz

    2015-10-30

    We investigated whether dysfunctional metacognitive beliefs (negative beliefs about uncontrollability and danger of thoughts) mediate the relationship between temperamental characteristics of behavior and hallucinatory-like experiences in healthy subjects (n=137). Our analyses showed that four temperamental traits (emotional reactivity, perseveration, endurance and briskness) were mediated by negative beliefs about uncontrollability and danger of thoughts in relation to hallucination proneness. Our research tentatively suggests that temperament affects hallucination proneness via metacognition. PMID:26296753

  2. Quantifying Potential Error in Painting Breast Excision Specimens

    PubMed Central

    Godden, Amy

    2013-01-01

    Aim. When excision margins are close or involved following breast conserving surgery, many surgeons will attempt to reexcise the corresponding cavity margin. Margins are ascribed to breast specimens such that six faces are identifiable to the pathologist, a process that may be prone to error at several stages. Methods. An experimental model was designed according to stated criteria in order to answer the research question. Computer software was used to measure the surface areas of experimental surfaces to compare human-painted surfaces with experimental controls. Results. The variability of the hand-painted surfaces was considerable. Thirty percent of hand-painted surfaces were 20% larger or smaller than controls. The mean area of the last surface painted was significantly larger than controls (mean 58996 pixels versus 50096 pixels, CI 1477–16324, P = 0.014). By chance, each of the six volunteers chose to paint the deep surface last. Conclusion. This study is the first to attempt to quantify the extent of human error in marking imaginary boundaries on a breast excision model and suggests that humans do not make these judgements well, raising questions about the safety of targeting single margins at reexcision. PMID:23762569

  3. Quick Analysis Method for Estimating Debris Flow Prone Area Caused by Overflow from Landslide dam

    NASA Astrophysics Data System (ADS)

    Shimizu, T.; Uchida, T.; Yamakoshi, T.; Yoshino, K.; Kisa, H.; Ishizuka, T.; Kaji, A.

    2012-04-01

    When earthquake or torrential rainfall cause deep catastrophic landslides, landslide dams can be formed in mountainous region. If water overflows from the landslide dams, large scale debris flow can occurs and possibly causes serious disasters in the downward region. Debris flow caused by the overflow from landslide dam is possible to affect the larger area than normal debris flow and flash flood. It is important for both a decision maker and resident in the area to recognize the disaster prone area as early as possible. For that reason, it is important to establish a quick analysis method for estimating debris flow prone area caused by overflow from landslide dams under the emergency situation. This situation requires the method to have both accuracy and speed for release. Nonetheless these two factors have trade-off relationship. We recently developed the quick analysis method to estimate debris flow disaster prone area caused by overflow from landslide dams. The method including the ways of efficient survey and numerical simulation programs called QUAD-L (QUick Analysis system for Debris flow caused by Landslide dam overflow). Our quick analysis system was actually applied to show the area for evacuation against debris flow caused by overflow from landslide dam formed by the 2011 Typhoon Talas which hit mainly the central region of Japan on September 2-4th, 2011. In addition to background of this application, since May 1st, 2011, Erosion and Sediment Control (SABO) Department of the Ministry of Land, Infrastructure, Transport and Tourism, Japan (MLIT) launched a new scheme using above-mentioned quick analysis method.

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

    SciTech Connect

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kreuer, Dieter; Quernheim, Ulrich

    1991-10-01

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

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

    PubMed

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

    2015-01-01

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

  7. Depression is an early disease manifestation in lupus-prone MRL/lpr mice.

    PubMed

    Gao, Hua-Xin; Campbell, Sean R; Cui, Min-Hui; Zong, Pu; Hee-Hwang, Jong; Gulinello, Maria; Putterman, Chaim

    2009-02-15

    Many lupus patients develop neuropsychiatric manifestations, including cognitive dysfunction, depression, and anxiety. However, it is not clear if neuropsychiatric lupus is a primary disease manifestation, or is secondary to non-CNS disease. We found that MRL/lpr lupus-prone mice exhibited significant depression-like behavior already at 8 weeks of age, despite normal visual working memory, locomotor coordination and social preference. Moreover, depression was significantly correlated with titers of autoantibodies against DNA, NMDA receptors and cardiolipin. Our results indicate that lupus mice develop depression and CNS dysfunction very early in the course of disease, in the absence of substantial pathology involving other target organs. PMID:19121871

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

    PubMed Central

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

    2014-01-01

    In Parkinsons 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 Parkinsons 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

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

    PubMed Central

    Froggatt, P.

    1970-01-01

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

  10. Anesthesia management of a morbidly obese patient in prone position for lumbar spine surgery

    PubMed Central

    Baxi, Vaibhavi; Budhakar, Shashank

    2010-01-01

    A morbidly obese, 45-year-old woman with a body mass index of 47 kg/m2 , presented with a prolapsed intervertebral disc of the lumbar spine for decompression and fixation. Anesthesia and surgical positioning of morbidly obese patient carries 3 main hazards, namely, morbid obesity, prone position, and airway preservation problems. Morbid obesity has its own hazards of deep vein thrombosis and pulmonary embolus. Here we describe anesthetic management, successfully dealing with the specific problems of this patient due to obesity. PMID:20890416

  11. Error-associated behaviors and error rates for robotic geology

    NASA Technical Reports Server (NTRS)

    Anderson, Robert C.; Thomas, Geb; Wagner, Jacob; Glasgow, Justin

    2004-01-01

    This study explores human error as a function of the decision-making process. One of many models for human decision-making is Rasmussen's decision ladder [9]. The decision ladder identifies the multiple tasks and states of knowledge involved in decision-making. The tasks and states of knowledge can be classified by the level of cognitive effort required to make the decision, leading to the skill, rule, and knowledge taxonomy (Rasmussen, 1987). Skill based decisions require the least cognitive effort and knowledge based decisions require the greatest cognitive effort. Errors can occur at any of the cognitive levels.

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

    PubMed Central

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

    1996-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    2015-07-15

    Purpose: Previous studies have demonstrated how imaging of the breast with patients lying prone using a supportive positioning device markedly facilitates longitudinal and/or multimodal image registration. In this contribution, the authors’ primary objective was to determine if there are differences in the standardized uptake value (SUV) derived from [{sup 18}F]fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) in breast tumors imaged in the standard supine position and in the prone position using a specialized positioning device. Methods: A custom positioning device was constructed to allow for breast scanning in the prone position. Rigid and nonrigid phantom studies evaluated differences in prone and supine PET. Clinical studies comprised 18F-FDG-PET of 34 patients with locally advanced breast cancer imaged in the prone position (with the custom support) followed by imaging in the supine position (without the support). Mean and maximum values (SUV{sub peak} and SUV{sub max}, respectively) were obtained from tumor regions-of-interest for both positions. Prone and supine SUV were linearly corrected to account for the differences in 18F-FDG uptake time. Correlation, Bland–Altman, and nonparametric analyses were performed on uptake time-corrected and uncorrected data. Results: SUV from the rigid PET breast phantom imaged in the prone position with the support device was 1.9% lower than without the support device. In the nonrigid PET breast phantom, prone SUV with the support device was 5.0% lower than supine SUV without the support device. In patients, the median (range) difference in uptake time between prone and supine scans was 16.4 min (13.4–30.9 min), which was significantly—but not completely—reduced by the linear correction method. SUV{sub peak} and SUV{sub max} from prone versus supine scans were highly correlated, with concordance correlation coefficients of 0.91 and 0.90, respectively. Prone SUV{sub peak} and SUV{sub max} were significantly lower than supine in both original and uptake time-adjusted data across a range of index times (P < < 0.0001, Wilcoxon signed rank test). Before correcting for uptake time differences, Bland–Altman analyses revealed proportional bias between prone and supine measurements (SUV{sub peak} and SUV{sub max}) that increased with higher levels of FDG uptake. After uptake time correction, this bias was significantly reduced (P < 0.01). Significant prone-supine differences, with regard to the spatial distribution of lesions relative to isocenter, were observed between the two scan positions, but this was poorly correlated with the residual (uptake time-corrected) prone-supine SUV{sub peak} difference (P = 0.78). Conclusions: Quantitative 18F-FDG-PET/CT of the breast in the prone position is not deleteriously affected by the support device but yields SUV that is consistently lower than those obtained in the standard supine position. SUV differences between scans arising from FDG uptake time differences can be substantially reduced, but not removed entirely, with the current correction method. SUV from the two scan orientations is quantitatively different and should not be assumed equivalent or interchangeable within the same subject. These findings have clinical relevance in that they underscore the importance of patient positioning while scanning as a clinical variable that must be accounted for with longitudinal PET measurement, for example, in the assessment of treatment response.

  15. A comparison of errorless and errorful therapies for dysgraphia after stroke.

    PubMed

    Thiel, Lindsey; Conroy, Paul

    2014-01-01

    Despite the increasing significance of written communication, there is limited research into spelling therapy for adults with acquired dysgraphia. Existing studies have typically measured spelling accuracy as an outcome, although speed may also be important for functional writing. As spelling is relatively slow, effortful and prone to errors in people with dysgraphia, minimising errors within therapy could be a factor in therapy success. This within-participant case-series study investigated whether errorless and errorful therapies would differ in their effects on spelling speed and accuracy for four participants with acquired dysgraphia. Matched sets of words were treated with errorless or errorful therapy or left untreated. Results were collated one week and five weeks after therapy. Both therapy approaches were successful in improving spelling accuracy. For three participants, equivalent gains were demonstrated following errorless and errorful therapy. One participant made significantly greater improvements in spelling accuracy following errorless therapy. The effects were maintained five weeks later. There was no significant difference in post-therapy spelling speed between the two therapy conditions. The results of this study suggest that both errorful and errorless therapies can be effective methods with which to treat spelling in adults with acquired dysgraphia. PMID:24517315

  16. Testing for Genetically Modified Foods Using PCR

    ERIC Educational Resources Information Center

    Taylor, Ann; Sajan, Samin

    2005-01-01

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

  17. Testing for Genetically Modified Foods Using PCR

    ERIC Educational Resources Information Center

    Taylor, Ann; Sajan, Samin

    2005-01-01

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

  18. Error Field Correction in ITER

    SciTech Connect

    Park, Jong-kyu; Boozer, Allen H.; Menard, Jonathan E.; Schaffer, Michael J.

    2008-05-22

    A new method for correcting magnetic field errors in the ITER tokamak is developed using the Ideal Perturbed Equilibrium Code (IPEC). The dominant external magnetic field for driving islands is shown to be localized to the outboard midplane for three ITER equilibria that represent the projected range of operational scenarios. The coupling matrices between the poloidal harmonics of the external magnetic perturbations and the resonant fields on the rational surfaces that drive islands are combined for different equilibria and used to determine an ordered list of the dominant errors in the external magnetic field. It is found that efficient and robust error field correction is possible with a fixed setting of the correction currents relative to the currents in the main coils across the range of ITER operating scenarios that was considered.

  19. Constraint checking during error recovery

    NASA Technical Reports Server (NTRS)

    Lutz, Robyn R.; Wong, Johnny S. K.

    1993-01-01

    The system-level software onboard a spacecraft is responsible for recovery from communication, power, thermal, and computer-health anomalies that may occur. The recovery must occur without disrupting any critical scientific or engineering activity that is executing at the time of the error. Thus, the error-recovery software may have to execute concurrently with the ongoing acquisition of scientific data or with spacecraft maneuvers. This work provides a technique by which the rules that constrain the concurrent execution of these processes can be modeled in a graph. An algorithm is described that uses this model to validate that the constraints hold for all concurrent executions of the error-recovery software with the software that controls the science and engineering activities of the spacecraft. The results are applicable to a variety of control systems with critical constraints on the timing and ordering of the events they control.

  20. Spacecraft and propulsion technician error

    NASA Astrophysics Data System (ADS)

    Schultz, Daniel Clyde

    Commercial aviation and commercial space similarly launch, fly, and land passenger vehicles. Unlike aviation, the U.S. government has not established maintenance policies for commercial space. This study conducted a mixed methods review of 610 U.S. space launches from 1984 through 2011, which included 31 failures. An analysis of the failure causal factors showed that human error accounted for 76% of those failures, which included workmanship error accounting for 29% of the failures. With the imminent future of commercial space travel, the increased potential for the loss of human life demands that changes be made to the standardized procedures, training, and certification to reduce human error and failure rates. Several recommendations were made by this study to the FAA's Office of Commercial Space Transportation, space launch vehicle operators, and maintenance technician schools in an effort to increase the safety of the space transportation passengers.

  1. Motion errors and compensation possibilities

    NASA Astrophysics Data System (ADS)

    Hounam, David

    1992-08-01

    The synthetic aperture radar (SAR) technique relies on knowledge of the relative motion between the sensor and the target. If the flight path of the sensor is not accurately known or the SAR processor is limited in its ability to take the flight data into account, the SAR image will be degraded. Motion errors are particularly critical for SAR sensors on small, low-flying aircraft, due to turbulence, and where high spatial resolution is required. The lecture discusses the effects of motion errors on image quality and the requirements on the sensor and processor to compensate for motion errors. The DLR airborne sensor, E-SAR, and associated image processor will be used as examples. Techniques using a priori knowledge of the flight path from independent sensors, e.g., inertial navigation systems (INS), and by extracting the flight data from the SAR data, e.g., autofocus and reflectivity displacement method (RDM), are treated.

  2. Error analysis using organizational simulation.

    PubMed Central

    Fridsma, D. B.

    2000-01-01

    Organizational simulations have been used by project organizations in civil and aerospace industries to identify work processes and organizational structures that are likely to fail under certain conditions. Using a simulation system based on Galbraith's information-processing theory and Simon's notion of bounded-rationality, we retrospectively modeled a chemotherapy administration error that occurred in a hospital setting. Our simulation suggested that when there is a high rate of unexpected events, the oncology fellow was differentially backlogged with work when compared with other organizational members. Alternative scenarios suggested that providing more knowledge resources to the oncology fellow improved her performance more effectively than adding additional staff to the organization. Although it is not possible to know whether this might have prevented the error, organizational simulation may be an effective tool to prospectively evaluate organizational "weak links", and explore alternative scenarios to correct potential organizational problems before they generate errors. PMID:11079885

  3. Genetic analysis with nanoPCR.

    PubMed

    Pan, Dun; Mi, Lijuan; Huang, Qing; Hu, Jun; Fan, Chunhai

    2012-10-01

    Polymerase chain reaction (PCR) has become a standard and important molecular biological technique with numerous applications in genetic analysis, forensics and in vitro diagnostics. Since its invention in the 1980s, there has been dramatic performance improvement arising from long-lasting efforts to optimize amplification conditions in both academic studies and commercial applications. More recently, a range of nanometer-sized materials including metal nanoparticles, semiconductor quantum dots, carbon nanomaterials and polymer nanoparticles, have shown unique effects in tuning amplification processes of PCR. It is proposed that these artificial nanomaterials mimic protein components in the natural DNA replication machinery in vivo. These so-called nanomaterials-assisted PCR (nanoPCR) strategies shed new light on powerful PCR with unprecedented sensitivity, selectivity and extension rate. In this review, we aim to summarize recent progress in this direction and discuss possible mechanisms for such performance improvement and potential applications in genetic analysis (particularly gene typing and haplotyping) and diagnostics. PMID:22907590

  4. 20 Tips to Help Prevent Medical Errors

    MedlinePLUS

    ... Prevent Medical Errors 20 Tips to Help Prevent Medical Errors: Patient Fact Sheet This information is for ... current information. Select to Download PDF (295 KB). Medical errors can occur anywhere in the health care ...

  5. SU-E-J-227: Breathing Pattern Consistency and Reproducibility: Comparative Analysis for Supine and Prone Body Positioning

    SciTech Connect

    Laugeman, E; Weiss, E; Chen, S; Hugo, G; Rosu, M

    2014-06-01

    Purpose: Evaluate and compare the cycle-to-cycle consistency of breathing patterns and their reproducibility over the course of treatment, for supine and prone positioning. Methods: Respiratory traces from 25 patients were recorded for sequential supine/prone 4DCT scans acquired prior to treatment, and during the course of the treatment (weekly or bi-weekly). For each breathing cycle, the average(AVE), end-of-exhale(EoE) and end-of-inhale( EoI) locations were identified using in-house developed software. In addition, the mean values and variations for the above quantities were computed for each breathing trace. F-tests were used to compare the cycle-to-cycle consistency of all pairs of sequential supine and prone scans. Analysis of variances was also performed using population means for AVE, EoE and EoI to quantify differences between the reproducibility of prone and supine respiration traces over the treatment course. Results: Consistency: Cycle-to-cycle variations are less in prone than supine in the pre-treatment and during-treatment scans for AVE, EoE and EoI points, for the majority of patients (differences significant at p<0.05). The few cases where the respiratory pattern had more variability in prone appeared to be random events. Reproducibility: The reproducibility of breathing patterns (supine and prone) improved as treatment progressed, perhaps due to patients becoming more comfortable with the procedure. However, variability in supine position continued to remain significantly larger than in prone (p<0.05), as indicated by the variance analysis of population means for the pretreatment and subsequent during-treatment scans. Conclusions: Prone positioning stabilizes breathing patterns in most subjects investigated in this study. Importantly, a parallel analysis of the same group of patients revealed a tendency towards increasing motion amplitude of tumor targets in prone position regardless of their size or location; thus, the choice for body positioning during radiation therapy will have to consider the clinical relevance of the two opposing trends - breathing consistency and motion amplitude.

  6. Acute exacerbations of asthma: epidemiology, biology and the exacerbation-prone phenotype.

    PubMed

    Dougherty, R H; Fahy, J V

    2009-02-01

    Asthma is a highly prevalent chronic respiratory disease affecting 300 million people world-wide. A significant fraction of the cost and morbidity of asthma derives from acute care for asthma exacerbations. In the United States alone, there are approximately 15 million outpatient visits, 2 million emergency room visits, and 500,000 hospitalizations each year for management of acute asthma. Common respiratory viruses, especially rhinoviruses, cause the majority of exacerbations in children and adults. Infection of airway epithelial cells with rhinovirus causes the release of pro-inflammatory cytokines and chemokines, as well as recruitment of inflammatory cells, particularly neutrophils, lymphocytes, and eosinophils. The host response to viral infection is likely to influence susceptibility to asthma exacerbation. Having had at least one exacerbation is an important risk factor for recurrent exacerbations suggesting an 'exacerbation-prone' subset of asthmatics. Factors underlying the 'exacerbation-prone' phenotype are incompletely understood but include extrinsic factors: cigarette smoking, medication non-compliance, psychosocial factors, and co-morbidities such as gastroesophageal reflux disease, rhinosinusitis, obesity, and intolerance to non-steroidal anti-inflammatory medications; as well as intrinsic factors such as deficient epithelial cell production of the anti-viral type I interferons (IFN-alpha and IFN-beta). A better understanding of the biologic mechanisms of host susceptibility to recurrent exacerbations will be important for developing more effective preventions and treatments aimed at reducing the significant cost and morbidity associated with this important global health problem. PMID:19187331

  7. Prone breast tumor imaging using vertical axis-of-rotation (VAOR) SPECT systems: An initial study

    SciTech Connect

    Wang, Huili; Scarfone, C.; Greer, K.L.; Coleman, R.E.

    1996-12-31

    We propose the use of a single photon emission computed tomography (SPECT) system equipped with multiple cameras revolving around a vertical axis-of-rotation (VAOR) to image tumors in a prone-dependent breast. This innovative breast imaging approach has the advantages of a small attenuation volume between breast lesions and gamma detector as well as a minimal radius-of-rotation compared to conventional (horizontal axis-of-rotation) breast SPECT. Small attenuation volume results in improved detected counts and minimal radius-of-rotation leads to increased collimator resolution. Because of no VAOR SPECT system currently available, we conducted our experiments on a conventional SPECT system using an isolated breast phantom to investigate the proposed VAOR breast SPECT. Our experimental setup simulated a VAOR SPECT study with a prone-dependent breast in the camera`s field-of-view. The results of our experiment indicate that VAOR breast SPECT with Trionix LESR parallel hole collimator is capable of detecting a breast lesion with a diameter of 10 mm and a lesion-to-background concentration ratio of 6 to 1. The results also demonstrate that VAOR breast SPECT provides improved lesion visualization over planar scintimammography and conventional breast SPECT.

  8. Gene expression profiling of white adipose tissue reveals paternal transmission of proneness to obesity

    PubMed Central

    Morita, Sumiyo; Nakabayashi, Kazuhiko; Kawai, Tomoko; Hayashi, Keiko; Horii, Takuro; Kimura, Mika; Kamei, Yasutomi; Ogawa, Yoshihiro; Hata, Kenichiro; Hatada, Izuho

    2016-01-01

    Previously, we found that C57BL/6J (B6) mice are more prone to develop obesity than PWK mice. In addition, we analyzed reciprocal crosses between these mice and found that (PWK × B6) F1 mice, which have B6 fathers, are more likely to develop dietary obesity than (B6 × PWK) F1 mice, which have B6 mothers. These results suggested that diet-induced obesity is paternally transmitted. In this study, we performed transcriptome analysis of adipose tissues of B6, PWK, (PWK × B6) F1, and (B6 × PWK) F1 mice using next-generation sequencing. We found that paternal transmission of diet-induced obesity was correlated with genes involved in adipose tissue inflammation, metal ion transport, and cilia. Furthermore, we analyzed the imprinted genes expressed in white adipose tissue (WAT) and obesity. Expression of paternally expressed imprinted genes (PEGs) was negatively correlated with body weight, whereas expression of maternally expressed imprinted genes (MEGs) was positively correlated. In the obesity-prone B6 mice, expression of PEGs was down-regulated by a high-fat diet, suggesting that abnormally low expression of PEGs contributes to high-fat diet-induced obesity in B6 mice. In addition, using single-nucleotide polymorphisms that differ between B6 and PWK, we identified candidate imprinted genes in WAT. PMID:26868178

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

    PubMed Central

    2014-01-01

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

  10. Risk Perception in Flood-Prone Lands of Costa Brava, Spain

    NASA Astrophysics Data System (ADS)

    Serra Llobet, A.; Kondolf, G. M.

    2009-12-01

    How well residents of flood-prone lands understand the risks of flooding is a question with profound implications for public policies to manage flood risk and land use on floodplains. Surveys of 300 residents of rapidly urbanizing floodplains in three coastal cities (100-135 km north of Barcelona), supplanted by interviews with public officials and government agency staff, indicate that most residents underestimate the probability and extent of flooding, unless they have experienced a flood within the previous three years. However, most dwelling units are now in multistory buildings, so residents of upper stories are vertically removed from floodwaters. Moreover, unlike the poor fishermen who formerly inhabited villages along this coast and who were devastated by periodic floods, the new inhabitants are mostly affluent and well-insured, so they can recover quickly from flood damage. Thus, while exposure to flooding has increased through urbanization of flood-prone lands, resistance to flooding has increased due to multistory buildings and sump pumps in lower floors, and resilience is much greater thanks to the financial resources of new residents.

  11. A Consensus Method for the Prediction of Aggregation-Prone Peptides in Globular Proteins

    PubMed Central

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

    2013-01-01

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

  12. Too Little Oxygen: Ventilation, Prone Positioning, and Extracorporeal Membrane Oxygenation for Severe Hypoxemia.

    PubMed

    Park, Pauline K

    2016-02-01

    Severe hypoxemia is associated with untoward outcomes in acute respiratory distress syndrome patients. Nevertheless, in and of itself, correction of hypoxemia is not an adequate surrogate outcome for mortality and clear evidence-based targets for correction of hypoxemia remain to be determined. At present, clinical management is directed toward achieving sufficient oxygenation while minimizing toxicity of ventilator-induced lung injury. The gold standard remains lung-protective mechanical ventilation, using lower-tidal volumes and pressure-limited ventilator titration. Notable progress in care includes further refinements in mechanical ventilation, consideration of salutatory effects of early prone positioning and neuromuscular blockade, and exploration of adjunctive extrapulmonary support with extracorporeal membrane oxygenation. This review focuses on three specific aspects: the evolving trend toward open lung ventilation, tempered by the recent cautionary experience with high-frequency oscillation ventilation; the evolution of prone positioning as a treatment for the most hypoxemic patients; and the continued future promise of extracorporeal support as a true rescue therapy. PMID:26820269

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

    PubMed Central

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

    2014-01-01

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

  14. A bifactor model of disgust proneness: examination of the Disgust Emotion Scale.

    PubMed

    Olatunji, Bunmi O; Ebesutani, Chad; Reise, Steven P

    2015-04-01

    The current research evaluated a bifactor model for the Disgust Emotion Scale (DES) in three samples: N = 1,318 nonclinical participants, N = 152 clinic-referred patients, and N = 352 nonclinical participants. The primary goals were to (a) use bifactor modeling to examine the latent structure of the DES and in turn (b) evaluate whether the DES should be scored as a unidimensional scale or whether subscales should also be interpreted. Results suggested that a bifactor model fit the DES data well and that all DES items were strongly influenced by a general disgust proneness dimension and by five content dimensions. Moreover, model-based reliability analyses suggested that scoring a general disgust dimension is justified despite the confirmed multidimensional structure. However, subscales were found to be unreliable after controlling for the general disgust factor with the potential exception of the Mutilation/Death and Animals subscale. Subsequent analysis also showed that only the general disgust factor robustly predicted an obsessive-compulsive disorder symptom latent factor-a clinical condition closely related to disgust proneness; latent variables representing DES domains displayed weak relations with an obsessive-compulsive disorder factor above and beyond the general disgust factor. Implications for better understanding the structure of DES responses and its use in clinical research are discussed. PMID:25006025

  15. Clearance of senescent hepatocytes in a neoplastic-prone microenvironment delays the emergence of hepatocellular carcinoma.

    PubMed

    Marongiu, Fabio; Serra, Maria Paola; Sini, Marcella; Angius, Fabrizio; Laconi, Ezio

    2014-01-01

    Increasing evidence indicates that carcinogenesis is dependent on the tissue context in which it occurs, implying that the latter can be a target for preventive or therapeutic strategies. We tested the possibility that re-normalizing a senescent, neoplastic-prone tissue microenvironment would exert a modulatory effect on the emergence of neoplastic disease. Rats were exposed to a protocol for the induction of hepatocellular carcinoma (HCC). Using an orthotopic and syngeneic system for cell transplantation, one group of animal was then delivered 8 million normal hepatocytes, via the portal circulation. Hepatocytes transplantation resulted in a prominent decrease in the incidence of both pre-neoplastic and neoplastic lesions. At the end of 1 year 50% of control animals presented with HCC, while no HCC were observed in the transplanted group. Extensive hepatocyte senescence was induced by the carcinogenic protocol in the host liver; however, senescent cells were largely cleared following infusion of normal hepatocytes. Furthermore, levels of Il-6 increased in rats exposed to the carcinogenic protocol, while they returned to near control values in the group receiving hepatocyte transplantation. These results support the concept that strategies aimed at normalizing a neoplastic-prone tissue landscape can modulate progression of neoplastic disease. PMID:24464501

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

    SciTech Connect

    Lee, Minjung; Shin, Jaekyoon

    2011-09-16

    Highlights: {yields} The mitochondrion contains its own protein quality control system. {yields} p62 localizes within the mitochondria and forms mega-dalton sized complexes. {yields} p62 interacts with oxidation-prone proteins and the proteins of quality control. {yields} In vitro delivery of p62 improves mitochondrial functions. {yields} p62 is implicated as a participant in mitochondrial protein quality control. -- Abstract: As the mitochondrion is vulnerable to oxidative stress, cells have evolved several strategies to maintain mitochondrial integrity, including mitochondrial protein quality control mechanisms and autophagic removal of damaged mitochondria. Involvement of an autophagy adaptor, Sqstm1/p62, in the latter process has been recently described. In the present study, we provide evidence that a portion of p62 directly localizes within the mitochondria and supports stable electron transport by forming heterogeneous protein complexes. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) of mitochondrial proteins co-purified with p62 revealed that p62 interacts with several oxidation-prone proteins, including a few components of the electron transport chain complexes, as well as multiple chaperone molecules and redox regulatory enzymes. Accordingly, p62-deficient mitochondria exhibited compromised electron transport, and the compromised function was partially restored by in vitro delivery of p62. These results suggest that p62 plays an additional role in maintaining mitochondrial integrity at the vicinity of target machineries through its function in relation to protein quality control.

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

    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.

  18. Tolerability and cosmetic acceptability of a body wash in atopic dermatitis-prone subjects.

    PubMed

    Brandt, Staci; Meckfessel, Matthew H; Lio, Peter A

    2014-09-01

    Atopic dermatitis is a common skin disease characterized by eczematous eruptions and impaired skin barrier function. Patients, as well as their families, frequently report reductions in quality of life. Pruritus, lack of sleep, and impaired social functioning all contribute to this reduction. A skincare regimen of gentle cleansing and daily moisturization is integral to managing atopic dermatitis. While there are a multitude of reports supporting the use of moisturizers, there is a paucity regarding the use of cleansers, especially cleansers formulated with ingredients known to improve skin hydration. A clinical study was conducted to assess the tolerability and cosmetic acceptability of a body wash formulated with the filaggrin break-down products arginine and pyrrolidone carboxylic acid in subjects with atopic dermatitis-prone skin (Cetaphil RestoraDerm Body Wash). The results of this study indicate that Cetaphil RestoraDerm Body Wash was well tolerated, reduced itch, improved quality of life, and was well-liked by subjects with atopic dermatitis-prone skin. PMID:25226012

  19. Gene expression profiling of white adipose tissue reveals paternal transmission of proneness to obesity.

    PubMed

    Morita, Sumiyo; Nakabayashi, Kazuhiko; Kawai, Tomoko; Hayashi, Keiko; Horii, Takuro; Kimura, Mika; Kamei, Yasutomi; Ogawa, Yoshihiro; Hata, Kenichiro; Hatada, Izuho

    2016-01-01

    Previously, we found that C57BL/6J (B6) mice are more prone to develop obesity than PWK mice. In addition, we analyzed reciprocal crosses between these mice and found that (PWK × B6) F1 mice, which have B6 fathers, are more likely to develop dietary obesity than (B6 × PWK) F1 mice, which have B6 mothers. These results suggested that diet-induced obesity is paternally transmitted. In this study, we performed transcriptome analysis of adipose tissues of B6, PWK, (PWK × B6) F1, and (B6 × PWK) F1 mice using next-generation sequencing. We found that paternal transmission of diet-induced obesity was correlated with genes involved in adipose tissue inflammation, metal ion transport, and cilia. Furthermore, we analyzed the imprinted genes expressed in white adipose tissue (WAT) and obesity. Expression of paternally expressed imprinted genes (PEGs) was negatively correlated with body weight, whereas expression of maternally expressed imprinted genes (MEGs) was positively correlated. In the obesity-prone B6 mice, expression of PEGs was down-regulated by a high-fat diet, suggesting that abnormally low expression of PEGs contributes to high-fat diet-induced obesity in B6 mice. In addition, using single-nucleotide polymorphisms that differ between B6 and PWK, we identified candidate imprinted genes in WAT. PMID:26868178

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

    NASA Technical Reports Server (NTRS)

    Allen, L. H., Jr. (Principal Investigator)

    1983-01-01

    Pairs of HCMM day-night thermal infrared (IR) data were selected during the 1978-79 winter to examine patterns of surface temperature and thermal inertia (TI) of peninsular Florida. The GOES and NOAA-6 thermal IR, as well as National Climatic Center temperatures and rainfall, were also used. The HCMM apparent thermal inertia (ATI) images closely corresponded to the general soil map of Florida, based on soil drainage classes. Areas with low ATI overlay well-drained soils, such as deep sands and drained organic soils, whereas with high ATI overlay areas with wetlands and bodies of water. The HCMM ATI images also corresponded well with GOES-detected winter nocturnal cold-prone areas. Use of HCMM data with Carlson's energy balance model showed both high moisture availability (MA) and high thermal inertia (TI) of wetland-type surfaces and low MA and low TI of upland, well-drained soils. Since soil areas with low TI develop higher temperatures during the day, then antecedent patterns of highest maximum daytime surface temperature can also be used to predict nocturnal cold-prone areas in Florida.

  1. Detection of individuals prone to develop hypertension in their future life.

    PubMed

    Pramanik, T; Regmi, P; Shrestha, P

    2008-03-01

    Hypertension is a global burning health problem. Early detection of proneness to hypertension may help an individual to lead a healthy life by altering the life style (by diet restriction, exercise etc.). Subjects at high risk of future hypertension e.g. the persons of hypertensive family and/or having high resting heart rate etc. show blood pressure hyper-responsiveness to stress. Elevated blood pressure due to sympathetic stimulation prevailed longer time in susceptible persons. In the present study sympathetic stimulation exerted through cold pressor test (hand immersion up to the wrist in 4 degrees C water) resulted in elevation of blood pressure and heart rate in all young male normotensive individuals (age 18-35 years, n=72). Nevertheless, blood pressure and heart rate returned to baseline, following 5 minutes of withdrawal of the stressor, in case of volunteers from normotensive families. On the other hand, the subjects whose parents, either or both were reported to be hypertensive showed elevated diastolic blood pressure even after 5 minutes of withdrawal of the said stressor- indicating that the autonomic nervous system in them was not competent enough for lowering the diastolic pressure quickly to baseline as observed in the volunteers from the normotensive families. The present study revealed that the young subjects who showed greater and prolonged responsiveness to diastolic blood pressure due to sympathetic stimulation through cold pressor test are prone to develop hypertension in future. PMID:18700629

  2. Clearance of senescent hepatocytes in a neoplastic-prone microenvironment delays the emergence of hepatocellular carcinoma

    PubMed Central

    Sini, Marcella; Angius, Fabrizio; Laconi, Ezio

    2014-01-01

    Increasing evidence indicates that carcinogenesis is dependent on the tissue context in which it occurs, implying that the latter can be a target for preventive or therapeutic strategies. We tested the possibility that re-normalizing a senescent, neoplastic-prone tissue microenvironment would exert a modulatory effect on the emergence of neoplastic disease. Rats were exposed to a protocol for the induction of hepatocellular carcinoma (HCC). Using an orthotopic and syngeneic system for cell transplantation, one group of animal was then delivered 8 million normal hepatocytes, via the portal circulation. Hepatocytes transplantation resulted in a prominent decrease in the incidence of both pre-neoplastic and neoplastic lesions. At the end of 1 year 50% of control animals presented with HCC, while no HCC were observed in the transplanted group. Extensive hepatocyte senescence was induced by the carcinogenic protocol in the host liver; however, senescent cells were largely cleared following infusion of normal hepatocytes. Furthermore, levels of Il-6 increased in rats exposed to the carcinogenic protocol, while they returned to near control values in the group receiving hepatocyte transplantation. These results support the concept that strategies aimed at normalizing a neoplastic-prone tissue landscape can modulate progression of neoplastic disease. PMID:24464501

  3. Automatic-repeat-request error control schemes

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

    Error detection incorporated with automatic-repeat-request (ARQ) is widely used for error control in data communication systems. This method of error control is simple and provides high system reliability. If a properly chosen code is used for error detection, virtually error-free data transmission can be attained. Various types of ARQ and hybrid ARQ schemes, and error detection using linear block codes are surveyed.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  5. Digital stereo photogrammetry for grain-scale monitoring of fluvial surfaces: Error evaluation and workflow optimisation

    NASA Astrophysics Data System (ADS)

    Bertin, Stephane; Friedrich, Heide; Delmas, Patrice; Chan, Edwin; Gimel'farb, Georgy

    2015-03-01

    Grain-scale monitoring of fluvial morphology is important for the evaluation of river system dynamics. Significant progress in remote sensing and computer performance allows rapid high-resolution data acquisition, however, applications in fluvial environments remain challenging. Even in a controlled environment, such as a laboratory, the extensive acquisition workflow is prone to the propagation of errors in digital elevation models (DEMs). This is valid for both of the common surface recording techniques: digital stereo photogrammetry and terrestrial laser scanning (TLS). The optimisation of the acquisition process, an effective way to reduce the occurrence of errors, is generally limited by the use of commercial software. Therefore, the removal of evident blunders during post processing is regarded as standard practice, although this may introduce new errors. This paper presents a detailed evaluation of a digital stereo-photogrammetric workflow developed for fluvial hydraulic applications. The introduced workflow is user-friendly and can be adapted to various close-range measurements: imagery is acquired with two Nikon D5100 cameras and processed using non-proprietary "on-the-job" calibration and dense scanline-based stereo matching algorithms. Novel ground truth evaluation studies were designed to identify the DEM errors, which resulted from a combination of calibration errors, inaccurate image rectifications and stereo-matching errors. To ensure optimum DEM quality, we show that systematic DEM errors must be minimised by ensuring a good distribution of control points throughout the image format during calibration. DEM quality is then largely dependent on the imagery utilised. We evaluated the open access multi-scale Retinex algorithm to facilitate the stereo matching, and quantified its influence on DEM quality. Occlusions, inherent to any roughness element, are still a major limiting factor to DEM accuracy. We show that a careful selection of the camera-to-object and baseline distance reduces errors in occluded areas and that realistic ground truths help to quantify those errors.

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

    PubMed

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

    2016-02-01

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

  7. Management of human error by design

    NASA Technical Reports Server (NTRS)

    Wiener, Earl

    1988-01-01

    Design-induced errors and error prevention as well as the concept of lines of defense against human error are discussed. The concept of human error prevention, whose main focus has been on hardware, is extended to other features of the human-machine interface vulnerable to design-induced errors. In particular, it is pointed out that human factors and human error prevention should be part of the process of transport certification. Also, the concept of error tolerant systems is considered as a last line of defense against error.

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

    SciTech Connect

    Chino, Junzo P. Marks, Lawrence B.

    2008-03-01

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

  9. Theory of Test Translation Error

    ERIC Educational Resources Information Center

    Solano-Flores, Guillermo; Backhoff, Eduardo; Contreras-Nino, Luis Angel

    2009-01-01

    In this article, we present a theory of test translation whose intent is to provide the conceptual foundation for effective, systematic work in the process of test translation and test translation review. According to the theory, translation error is multidimensional; it is not simply the consequence of defective translation but an inevitable fact

  10. Reduced discretization error in HZETRN

    SciTech Connect

    Slaba, Tony C.; Blattnig, Steve R.; Tweed, John

    2013-02-01

    The deterministic particle transport code HZETRN is an efficient analysis tool for studying the effects of space radiation on humans, electronics, and shielding materials. In a previous work, numerical methods in the code were reviewed, and new methods were developed that further improved efficiency and reduced overall discretization error. It was also shown that the remaining discretization error could be attributed to low energy light ions (A < 4) with residual ranges smaller than the physical step-size taken by the code. Accurately resolving the spectrum of low energy light particles is important in assessing risk associated with astronaut radiation exposure. In this work, modifications to the light particle transport formalism are presented that accurately resolve the spectrum of low energy light ion target fragments. The modified formalism is shown to significantly reduce overall discretization error and allows a physical approximation to be removed. For typical step-sizes and energy grids used in HZETRN, discretization errors for the revised light particle transport algorithms are shown to be less than 4% for aluminum and water shielding thicknesses as large as 100 g/cm{sup 2} exposed to both solar particle event and galactic cosmic ray environments.

  11. Typical errors of ESP users

    NASA Astrophysics Data System (ADS)

    Eremina, Svetlana V.; Korneva, Anna A.

    2004-07-01

    The paper presents analysis of the errors made by ESP (English for specific purposes) users which have been considered as typical. They occur as a result of misuse of resources of English grammar and tend to resist. Their origin and places of occurrence have also been discussed.

  12. Having Fun with Error Analysis

    ERIC Educational Resources Information Center

    Siegel, Peter

    2007-01-01

    We present a fun activity that can be used to introduce students to error analysis: the M&M game. Students are told to estimate the number of individual candies plus uncertainty in a bag of M&M's. The winner is the group whose estimate brackets the actual number with the smallest uncertainty. The exercise produces enthusiastic discussions and

  13. Amplify Errors to Minimize Them

    ERIC Educational Resources Information Center

    Stewart, Maria Shine

    2009-01-01

    In this article, the author offers her experience of modeling mistakes and writing spontaneously in the computer classroom to get students' attention and elicit their editorial response. She describes how she taught her class about major sentence errors--comma splices, run-ons, and fragments--through her Sentence Meditation exercise, a rendition…

  14. Error Processing in Huntington's Disease

    PubMed Central

    Andrich, Jürgen; Gold, Ralf; Falkenstein, Michael

    2006-01-01

    Background Huntington's disease (HD) is a genetic disorder expressed by a degeneration of the basal ganglia inter alia accompanied with dopaminergic alterations. These dopaminergic alterations are related to genetic factors i.e., CAG-repeat expansion. The error (related) negativity (Ne/ERN), a cognitive event-related potential related to performance monitoring, is generated in the anterior cingulate cortex (ACC) and supposed to depend on the dopaminergic system. The Ne is reduced in Parkinson's Disease (PD). Due to a dopaminergic deficit in HD, a reduction of the Ne is also likely. Furthermore it is assumed that movement dysfunction emerges as a consequence of dysfunctional error-feedback processing. Since dopaminergic alterations are related to the CAG-repeat, a Ne reduction may furthermore also be related to the genetic disease load. Methodology/Principle Findings We assessed the error negativity (Ne) in a speeded reaction task under consideration of the underlying genetic abnormalities. HD patients showed a specific reduction in the Ne, which suggests impaired error processing in these patients. Furthermore, the Ne was closely related to CAG-repeat expansion. Conclusions/Significance The reduction of the Ne is likely to be an effect of the dopaminergic pathology. The result resembles findings in Parkinson's Disease. As such the Ne might be a measure for the integrity of striatal dopaminergic output function. The relation to the CAG-repeat expansion indicates that the Ne could serve as a gene-associated “cognitive” biomarker in HD. PMID:17183717

  15. Amplify Errors to Minimize Them

    ERIC Educational Resources Information Center

    Stewart, Maria Shine

    2009-01-01

    In this article, the author offers her experience of modeling mistakes and writing spontaneously in the computer classroom to get students' attention and elicit their editorial response. She describes how she taught her class about major sentence errors--comma splices, run-ons, and fragments--through her Sentence Meditation exercise, a rendition

  16. Motion compensated shape error concealment.

    PubMed

    Schuster, Guido M; Katsaggelos, Aggelos K

    2006-02-01

    The introduction of Video Objects (VOs) is one of the innovations of MPEG-4. The alpha-plane of a VO defines its shape at a given instance in time and hence determines the boundary of its texture. In packet-based networks, shape, motion, and texture are subject to loss. While there has been considerable attention paid to the concealment of texture and motion errors, little has been done in the field of shape error concealment. In this paper we propose a post-processing shape error concealment technique that uses the motion compensated boundary information of the previously received alpha-plane. The proposed approach is based on matching received boundary segments in the current frame to the boundary in the previous frame. This matching is achieved by finding a maximally smooth motion vector field. After the current boundary segments are matched to the previous boundary, the missing boundary pieces are reconstructed by motion compensation. Experimental results demonstrating the performance of the proposed motion compensated shape error concealment method, and comparing it with the previously proposed weighted side matching method are presented. PMID:16479820

  17. Multichannel error correction code decoder

    NASA Technical Reports Server (NTRS)

    Wagner, Paul K.; Ivancic, William D.

    1993-01-01

    A brief overview of a processing satellite for a mesh very-small-aperture (VSAT) communications network is provided. The multichannel error correction code (ECC) decoder system, the uplink signal generation and link simulation equipment, and the time-shared decoder are described. The testing is discussed. Applications of the time-shared decoder are recommended.

  18. Chip PCR. I. Surface passivation of microfabricated silicon-glass chips for PCR.

    PubMed Central

    Shoffner, M A; Cheng, J; Hvichia, G E; Kricka, L J; Wilding, P

    1996-01-01

    The microreaction volumes of PCR chips (a microfabricated silicon chip bonded to a piece of flat glass to form a PCR reaction chamber) create a relatively high surface to volume ratio that increases the significance of the surface chemistry in the polymerase chain reaction (PCR). We investigated several surface passivations in an attempt to identify 'PCR friendly' surfaces and used those surfaces to obtain amplifications comparable with those obtained in conventional PCR amplification systems using polyethylene tubes. Surface passivations by a silanization procedure followed by a coating of a selected protein or polynucleotide and the deposition of a nitride or oxide layer onto the silicon surface were investigated. Native silicon was found to be an inhibitor of PCR and amplification in an untreated PCR chip (i.e. native slicon) had a high failure rate. A silicon nitride (Si(3)N(4) reaction surface also resulted in consistent inhibition of PCR. Passivating the PCR chip using a silanizing agent followed by a polymer treatment resulted in good amplification. However, amplification yields were inconsistent and were not always comparable with PCR in a conventional tube. An oxidized silicon (SiO(2) surface gave consistent amplifications comparable with reactions performed in a conventional PCR tube. PMID:8628665

  19. Online exercise for the design and simulation of PCR and PCR-RFLP experiments

    PubMed Central

    2013-01-01

    Background Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes, compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions The exercise is freely available at http://insilico.ehu.es/edu. PMID:24314313

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

    NASA Astrophysics Data System (ADS)

    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

    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

  1. Real-time PCR detection chemistry.

    PubMed

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

    2015-01-15

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

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

    USGS Publications Warehouse

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

    2005-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Cheung, David J.

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

  4. Detection and screening of chromosomal rearrangements in uterine leiomyomas by long-distance inverse PCR.

    PubMed

    Pradhan, Barun; Sarvilinna, Nanna; Matilainen, Juha; Aska, Elli; Sjberg, Jari; Kauppi, Liisa

    2016-03-01

    Genome instability is a hallmark of many tumors and recently, next-generation sequencing methods have enabled analyses of tumor genomes at an unprecedented level. Studying rearrangement-prone chromosomal regions (putative "breakpoint hotspots") in detail, however, necessitates molecular assays that can detect de novo DNA fusions arising from these hotspots. Here we demonstrate the utility of a long-distance inverse PCR-based method for the detection and screening of de novo DNA rearrangements in uterine leiomyomas, one of the most common types of human neoplasm. This assay allows in principle any genomic region suspected of instability to be queried for DNA rearrangements originating there. No prior knowledge of the identity of the fusion partner chromosome is needed. We used this method to screen uterine leiomyomas for rearrangements at genomic locations known to be rearrangement-prone in this tumor type: upstream HMGA2 and within RAD51B. We identified a novel DNA rearrangement upstream of HMGA2 that had gone undetected in an earlier whole-genome sequencing study. In more than 30 additional uterine leiomyoma samples, not analyzed by whole-genome sequencing previously, no rearrangements were observed within the 1,107 bp and 1,996 bp assayed in the RAD51B and HMGA2 rearrangement hotspots. Our findings show that long-distance inverse PCR is a robust, sensitive, and cost-effective method for the detection and screening of DNA rearrangements from solid tumors that should be useful for many diagnostic applications. 2015 Wiley Periodicals, Inc. PMID:26608380

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

    PubMed Central

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

    2014-01-01

    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. PMID:24980910

  6. Space Saving Statistics: An Introduction to Constant Error, Variable Error, and Absolute Error.

    ERIC Educational Resources Information Center

    Guth, David

    1990-01-01

    Article discusses research on orientation and mobility (O&M) for individuals with visual impairments, examining constant, variable, and absolute error (descriptive statistics that quantify fundamentally different characteristics of distributions of spatially directed behavior). It illustrates the statistics with examples, noting their application

  7. qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

    SciTech Connect

    Jackson, Christopher B.; Gallati, Sabina; Schaller, Andre

    2012-07-06

    Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two genomes is demonstrated and which evaluates systematically the impact of DNA degradation on quantification of mtDNA copy number.

  8. Using Block-local Atomicity to Detect Stale-value Concurrency Errors

    NASA Technical Reports Server (NTRS)

    Artho, Cyrille; Havelund, Klaus; Biere, Armin

    2004-01-01

    Data races do not cover all kinds of concurrency errors. This paper presents a data-flow-based technique to find stale-value errors, which are not found by low-level and high-level data race algorithms. Stale values denote copies of shared data where the copy is no longer synchronized. The algorithm to detect such values works as a consistency check that does not require any assumptions or annotations of the program. It has been implemented as a static analysis in JNuke. The analysis is sound and requires only a single execution trace if implemented as a run-time checking algorithm. Being based on an analysis of Java bytecode, it encompasses the full program semantics, including arbitrarily complex expressions. Related techniques are more complex and more prone to over-reporting.

  9. The Sources of Error in Spanish Writing.

    ERIC Educational Resources Information Center

    Justicia, Fernando; Defior, Sylvia; Pelegrina, Santiago; Martos, Francisco J.

    1999-01-01

    Determines the pattern of errors in Spanish spelling. Analyzes and proposes a classification system for the errors made by children in the initial stages of the acquisition of spelling skills. Finds the diverse forms of only 20 Spanish words produces 36% of the spelling errors in Spanish; and substitution is the most frequent type of error. (RS)

  10. Discretization vs. Rounding Error in Euler's Method

    ERIC Educational Resources Information Center

    Borges, Carlos F.

    2011-01-01

    Euler's method for solving initial value problems is an excellent vehicle for observing the relationship between discretization error and rounding error in numerical computation. Reductions in stepsize, in order to decrease discretization error, necessarily increase the number of steps and so introduce additional rounding error. The problem is…

  11. Discretization vs. Rounding Error in Euler's Method

    ERIC Educational Resources Information Center

    Borges, Carlos F.

    2011-01-01

    Euler's method for solving initial value problems is an excellent vehicle for observing the relationship between discretization error and rounding error in numerical computation. Reductions in stepsize, in order to decrease discretization error, necessarily increase the number of steps and so introduce additional rounding error. The problem is

  12. Error-Related Psychophysiology and Negative Affect

    ERIC Educational Resources Information Center

    Hajcak, G.; McDonald, N.; Simons, R.F.

    2004-01-01

    The error-related negativity (ERN/Ne) and error positivity (Pe) have been associated with error detection and response monitoring. More recently, heart rate (HR) and skin conductance (SC) have also been shown to be sensitive to the internal detection of errors. An enhanced ERN has consistently been observed in anxious subjects and there is some

  13. Reducing Error in Mail Surveys. ERIC Digest.

    ERIC Educational Resources Information Center

    Cui, Weiwei

    This Digest describes four types of errors in mail surveys and summarizes the ways they can be reduced. Any one of these sources of error can make survey results unacceptable. Sampling error is examined through inferential statistics applied to sample survey results. In general, increasing sample size will decrease sampling error when simple

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

    PubMed

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

    2002-03-01

    The effects of aniracetam, a cognition enhancer, on extracellular levels of glutamate (Glu), gamma-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, whereas no difference in GABA and NOx was noted. Aniracetam (100 mg/kg, p.o.) significantly increased the area under the curve of Glu levels in the PFC, but not in the AMG, of SHRSP. Aniracetam failed to exert any remarkable effects on GABA or NOx levels in either brain region. Our findings suggest that aniracetam enhances cortical glutamatergic release, which may be the mechanism involved in the ameliorating effects of aniracetam on various neuronal dysfunctions. PMID:11852174

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

    SciTech Connect

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

    2014-04-01

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

  16. Coronary artery bypass graft: why is the saphenous vein prone to intimal hyperplasia?

    PubMed

    Sur, Swastika; Sugimoto, Jeffrey T; Agrawal, Devendra K

    2014-07-01

    Proliferation and migration of smooth muscle cells and the resultant intimal hyperplasia cause coronary artery bypass graft failure. Both internal mammary artery and saphenous vein are the most commonly used bypass conduits. Although an internal mammary artery graft is immune to restenosis, a saphenous vein graft is prone to develop restenosis. We found significantly higher activity of phosphatase and tensin homolog (PTEN) in the smooth muscle cells of the internal mammary artery than in the saphenous vein. In this article, we critically review the pathophysiology of vein-graft failure with detailed discussion of the involvement of various factors, including PTEN, matrix metalloproteinases, and tissue inhibitor of metalloproteinases, in uncontrolled proliferation and migration of smooth muscle cells towards the lumen, and invasion of the graft conduit. We identified potential target sites that could be useful in preventing and (or) reversing unwanted consequences following coronary artery bypass graft using saphenous vein. PMID:24933515

  17. InSAR imaging of volcanic deformation over cloud-prone areas - Aleutian islands

    USGS Publications Warehouse

    Lu, Zhong

    2007-01-01

    Interferometric synthetic aperture radar (INSAR) is capable of measuring ground-surface deformation with centimeter-tosubcentimeter precision and spatial resolution of tens-of meters over a relatively large region. With its global coverage and all-weather imaging capability, INSAR is an important technique for measuring ground-surface deformation of volcanoes over cloud-prone and rainy regions such as the Aleutian Islands, where only less than 5 percent of optical imagery is usable due to inclement weather conditions. The spatial distribution of surface deformation data, derived from INSAR images, enables the construction of detailed mechanical models to enhance the study of magmatic processes. This paper reviews the basics of INSAR for volcanic deformation mapping and the INSAR studies of ten Aleutian volcanoes associated with both eruptive and noneruptive activity. These studies demonstrate that all-weather INSAR imaging can improve our understanding of how the Aleutian volcanoes work and enhance our capability to predict future eruptions and associated hazards.

  18. Detection of potential microbial antigens by immuno-PCR (PCR-amplified immunoassay).

    PubMed

    Mehta, Promod K; Raj, Ankush; Singh, Netra Pal; Khuller, Gopal K

    2014-05-01

    Immuno-PCR (PCR-amplified immunoassay; I-PCR) is a novel ultrasensitive method combining the versatility of ELISA with the sensitivity of nucleic acid amplification of PCR. The enormous exponential amplification power of PCR in an I-PCR assay leads to at least a 10(2)-10(4)-fold increase in sensitivity compared with an analogous ELISA. I-PCR has been used to detect many biological molecules such as proto-oncogenes, toxins, cytokines, hormones, and biomarkers for autoimmune and Alzheimer's diseases, as well as microbial antigens and antibodies, and it can be adapted as a novel diagnostic tool for various infectious and non-infectious diseases. Quantitative real-time I-PCR has the potential to become the most analytically sensitive method for the detection of proteins. The sensitivity and specificity of a real-time I-PCR assay can be enhanced further with the use of magnetic beads and nanoparticles. This review is primarily focused on the detection of potential viral, bacterial and parasitic antigens by I-PCR assay, thus enabling their application for immunological research and for early diagnosis of infectious diseases. PMID:24568881

  19. Foraging errors play a role in resource exploration by bumble bees (Bombus terrrestris).

    PubMed

    Evans, Lisa J; Raine, Nigel E

    2014-06-01

    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

  20. Determining relative error bounds for the CVBEM

    USGS Publications Warehouse

    Hromadka, T.V., II

    1985-01-01

    The Complex Variable Boundary Element Methods provides a measure of relative error which can be utilized to subsequently reduce the error or provide information for further modeling analysis. By maximizing the relative error norm on each boundary element, a bound on the total relative error for each boundary element can be evaluated. This bound can be utilized to test CVBEM convergence, to analyze the effects of additional boundary nodal points in reducing the modeling error, and to evaluate the sensitivity of resulting modeling error within a boundary element from the error produced in another boundary element as a function of geometric distance. ?? 1985.