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1

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

PubMed

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

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

2011-07-01

2

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

PubMed Central

TraJ is the essential activator of PY, the promoter of the F and F-like plasmid tra operon that encodes the majority of the proteins for bacterial conjugation. By combining error-prone PCR mutagenesis with a two-plasmid screen, we isolated 55 missense mutations in traJ, each affecting the ability of TraJ to activate PY. These mutations define two distinct functional clusters (amino acids [aa] 21 to 117 and aa 150 to 219). Limited proteolytic analysis of TraJ suggested that the N- and C-terminal functional clusters are two structurally distinct domains. Most TraJ mutants exhibited decreased intracellular protein levels, and the HslVU protease-chaperone pair was found to be responsible for degrading those mutants without extracytoplasmic stress-induced overexpression. In vivo cross-linking analysis of TraJ mutants indicated that the N-terminal domain is responsible for dimerization. This was confirmed by the finding that the purified N-terminal region of TraJ forms dimers in solution. The levels of dimerization and in vivo activities of TraJ mutants are well correlated, suggesting that dimerization of TraJ is required for its biological function. We propose that the regulation of TraJ dimerization and/or its susceptibility to HslVU could be a key mechanism in various signaling processes for controlling bacterial conjugation in response to physiological or environmental stimuli. PMID:22563049

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

2012-01-01

3

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

PubMed

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

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

2008-03-01

4

Estimation of the Mutation Rate during Error-prone Polymerase Chain Reaction  

E-print Network

Estimation of the Mutation Rate during Error-prone Polymerase Chain Reaction Dai Wang1 , Cheng-prone polymerase chain reaction (PCR) is widely used to introduce point mutations during in vitro evolution step of in vitro evolution is mutagenesis. Error-prone polymerase chain reaction (PCR) (Leung et al

Sun, Fengzhu - Sun, Fengzhu

5

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

PubMed Central

The HER3 receptor is implicated in the progression of various cancers as well as in resistance to several currently used drugs, and is hence a potential target for development of new therapies. We have previously generated Affibody molecules that inhibit heregulin-induced signaling of the HER3 pathways. The aim of this study was to improve the affinity of the binders to hopefully increase receptor inhibition efficacy and enable a high receptor-mediated uptake in tumors. We explored a novel strategy for affinity maturation of Affibody molecules that is based on alanine scanning followed by design of library diversification to mimic the result from an error-prone PCR reaction, but with full control over mutated positions and thus less biases. Using bacterial surface display and flow-cytometric sorting of the maturation library, the affinity for HER3 was improved more than 30-fold down to 21 pM. The affinity is among the higher that has been reported for Affibody molecules and we believe that the maturation strategy should be generally applicable for improvement of affinity proteins. The new binders also demonstrated an improved thermal stability as well as complete refolding after denaturation. Moreover, inhibition of ligand-induced proliferation of HER3-positive breast cancer cells was improved more than two orders of magnitude compared to the previously best-performing clone. Radiolabeled Affibody molecules showed specific targeting of a number of HER3-positive cell lines in vitro as well as targeting of HER3 in in vivo mouse models and represent promising candidates for future development of targeted therapies and diagnostics. PMID:23675426

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

2013-01-01

6

Efficient Symbol-Level Transmission in Error-Prone  

E-print Network

;10101010 Single Packet (Multiple Destinations) In the case of different transmission error rates, the roundEfficient Symbol-Level Transmission in Error-Prone Wireless Networks Pouya Ostovari, Jie Wu and control messages Error-prone wireless links Provide reliability ARQ Hybrid-ARQ Erasure codes

Wu, Jie

7

AIDing antibody diversity by error-prone mismatch repair  

PubMed Central

The creation of a highly diverse antibody repertoire requires the synergistic activity of a DNA mutator, known as activation-induced deaminase (AID), coupled with an error-prone repair process that recognizes the DNA mismatch catalyzed by AID. Instead of facilitating the canonical error-free response, which generally occurs throughout the genome, DNA mismatch repair (MMR) participates in an error-prone repair mode that promotes A:T mutagenesis and double-strand breaks at the immunoglobulin (Ig) genes. As such, MMR is capable of compounding the mutation frequency of AID activity as well as broadening the spectrum of base mutations; thereby increasing the efficiency of antibody maturation. We here review the current understanding of this MMR-mediated process and describe how the MMR signaling cascade downstream of AID diverges in a locus dependent manner and even within the Ig locus itself to differentially promote somatic hypermutation (SHM) and class switch recombination (CSR) in B cells. PMID:22703640

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

2012-01-01

8

Error Correction Techniques for Handwriting, Speech, and other ambiguous or error prone systems  

E-print Network

Error Correction Techniques for Handwriting, Speech, and other ambiguous or error prone systems: handwriting and speech recognition, in­ terface design, error handling 1 INTRODUCTION 1.1 Motivating the Problem Computer interfaces which support more natural hu­ man forms of communication (e.g. handwriting

Abowd, Gregory D.

9

Replicative mechanisms for CNV formation are error prone  

PubMed Central

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

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

2013-01-01

10

Random mutagenesis by error-prone pol plasmid replication in Escherichia coli.  

PubMed

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

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

2014-01-01

11

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

PubMed Central

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

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

2014-01-01

12

Error-prone polymerase activity causes multinucleotide mutations in humans  

PubMed Central

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

Nielsen, Rasmus

2014-01-01

13

Analysis and Tuning of the PROFIBUS Token Passing Protocol for Use over Error Prone Links  

Microsoft Academic Search

In this paper we investigate the properties of the PROFIBUS MAC protocol when operatedover error prone links, with error behaviour similar to e.g. wireless links. First we showthat the frame error detection method of PROFIBUS has inferior performance as comparedto standard techniques like CRC's. Then we show with a simulation approach, that theMAC protocol is very sensitive to loss or

Andreas Willig

1999-01-01

14

Mechanistic Comparison of High-Fidelity and Error-Prone DNA Polymerases and Ligases Involved in DNA Repair  

E-print Network

Mechanistic Comparison of High-Fidelity and Error-Prone DNA Polymerases and Ligases Involved in DNA for the DNA-Repairing Enzyme Pol 348 2.8. Is the Mechanism of Pol an Anomaly? 348 3. Mammalian Error-Prone DNA Polymerases 349 3.1. Background 349 3.2. Kinetic Mechanism of Error-Prone DNA Polymerases 349 3.3. Structures

Tsai, Ming-Daw

15

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

PubMed Central

Summary Although homologous recombination (HR) is considered an accurate form of DNA repair, genetics suggest that Escherichia coli (E. coli) translesion DNA polymerase (pol) IV (DinB) promotes error-prone recombination during stress which allows cells to overcome adverse conditions. How pol IV functions and is regulated during recombination under stress, however, is unknown. We show that pol IV is highly proficient in error-prone recombination, and is preferentially recruited to D-loops at stress-induced concentrations in vitro. Unexpectedly, we find that high-fidelity pol II switches to exonuclease mode at D-loops which is stimulated by topological stress and reduced deoxy-ribonucleotide pools observed during stationary-phase. The exonuclease activity of pol II enables it to compete with pol IV which likely suppresses error-prone recombination. These findings indicate that preferential D-loop extension by pol IV facilitates error-prone recombination and explain how pol II reduces such errors in vivo. PMID:23686288

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

2013-01-01

16

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

PubMed Central

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

Pal, Doyel; Chen, Tingting; Khethavath, Praveen

2014-01-01

17

Analysis of the PROFIBUS token passing protocol over error prone links  

Microsoft Academic Search

In this paper, the authors investigate the properties of the PROFIBUS MAC protocol when operated over error prone links, like wireless links. In order to show that the protocol is very sensible to loss of control frames (e.g. token frames), the authors evaluate three performance measures, using a simulation approach: the mean delay, the mean station outage time and the

Andreas Willig

1999-01-01

18

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

PubMed Central

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

Maity, Arnab; Apanasovich, Tatiyana V.

2011-01-01

19

Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I  

PubMed Central

We present a system for random mutagenesis in Escherichia coli for the evolution of targeted genes. To increase error rates of DNA polymerase I (Pol I) replication, we introduced point mutations in three structural domains that govern Pol I fidelity. Expression of error-prone Pol I in vivo results in strong mutagenesis of a target sequence encoded in a Pol I-dependent plasmid (8.1 × 10–4 mutations per bp, an 80,000-fold increase), with a preference for plasmid relative to chromosome sequence. Mutagenesis is maximal in cultures maintained at stationary phase. Mutations are evenly distributed and show a variety of base pair substitutions, predominantly transitions. Mutagenesis extends at least 3 kb beyond the 400–500 nt reportedly synthesized by Pol I. We demonstrate that our error-prone Pol I can be used to generate enzymes with distinct properties by generating TEM-1 ?-lactamase mutants able to hydrolyze a third-generation lactam antibiotic, aztreonam. Three different mutations contribute to aztreonam resistance. Two are found in the extended-spectrum ?-lactamases most frequently identified in clinical isolates, and the third (G276R) has not been previously described. Our system of targeted mutagenesis in E. coli should have an impact on enzyme-based applications in areas such as synthetic chemistry, gene therapy, and molecular biology. Given the structural conservation between polymerases, this work should also provide a reference for altering the fidelity of other polymerases. PMID:12909725

Camps, Manel; Naukkarinen, Jussi; Johnson, Ben P.; Loeb, Lawrence A.

2003-01-01

20

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

PubMed Central

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

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

2014-01-01

21

Error-prone mammalian female meiosis from silencing the spindle assembly checkpoint without normal interkinetochore tension.  

PubMed

It is well established that chromosome segregation in female meiosis I (MI) is error-prone. The acentrosomal meiotic spindle poles do not have centrioles and are not anchored to the cortex via astral microtubules. By Cre recombinase-mediated removal in oocytes of the microtubule binding site of nuclear mitotic apparatus protein (NuMA), which is implicated in anchoring microtubules at poles, we determine that without functional NuMA, microtubules lose connection to MI spindle poles, resulting in highly disorganized early spindle assembly. Subsequently, very long spindles form with hyperfocused poles. The kinetochores of homologs make attachments to microtubules in these spindles but with reduced tension between them and accompanied by alignment defects. Despite this, the spindle assembly checkpoint is normally silenced and the advance to anaphase I and first polar body extrusion takes place without delay. Females without functional NuMA in oocytes are sterile, producing aneuploid eggs with altered chromosome number. These findings establish that in mammalian MI, the spindle assembly checkpoint is unable to sustain meiotic arrest in the presence of one or few misaligned and/or misattached kinetochores with reduced interkinetochore tension, thereby offering an explanation for why MI in mammals is so error-prone. PMID:22552228

Kolano, Agnieszka; Brunet, Stéphane; Silk, Alain D; Cleveland, Don W; Verlhac, Marie-Hélène

2012-07-01

22

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

PubMed Central

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

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

2014-01-01

23

Error-prone and error-restrictive mutations affecting ribosomal protein S12.  

PubMed

Ribosomal protein S12 plays a pivotal role in decoding functions on the ribosome. X-ray crystallographic analyses of ribosomal complexes have revealed that S12 is involved in the inspection of codon-anticodon pairings in the ribosomal A site, as well as in the succeeding domain rearrangements of the 30S subunit that are essential for accommodation of aminoacyl-tRNA. A role for S12 in tRNA selection is also well supported by classical genetic analyses; mutations affecting S12 are readily isolated in bacteria and organelles, since specific alterations in S12 confer resistance to the error-inducing antibiotic streptomycin, and the ribosomes from many such streptomycin-resistant S12 mutants display decreased levels of miscoding. However, substitutions that confer resistance to streptomycin likely represent a very distinct class of all possible S12 mutants. Until recently, the technical difficulties in generating random, unselectable mutations in essential genes in complex operons have generally precluded the analysis of other classes of S12 alterations. Using a recombineering approach, we have targeted the Escherichia coli rpsL gene, encoding S12, for random mutagenesis and screened the resulting mutants for effects on decoding fidelity. We have recovered over 40 different substitutions located throughout the S12 protein that alter the accuracy of translation without substantially affecting the sensitivity to streptomycin. Moreover, this collection includes mutants that promote miscoding, as well as those that restrict decoding errors. These results affirm the importance of S12 in decoding processes and indicate that alterations in this essential protein can have diverse effects on the accuracy of decoding. PMID:21575643

Agarwal, Deepali; Gregory, Steven T; O'Connor, Michael

2011-07-01

24

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

PubMed Central

We study the evolution of a finite size population formed by mutationally isolated lineages of error-prone replicators in a two-peak fitness landscape. Computer simulations are performed to gain a stochastic description of the system dynamics. More specifically, for different population sizes, we compute the probability of each lineage being selected in terms of their mutation rates and the amplification factors of the fittest phenotypes. We interpret the results as the compromise between the characteristic time a lineage takes to reach its fittest phenotype by crossing the neutral valley and the selective value of the sequences that form the lineages. A main conclusion is drawn: for finite population sizes, the survival probability of the lineage that arrives first to the fittest phenotype rises significantly. PMID:24376656

Marín, Arturo; Tejero, Héctor; Nuño, Juan Carlos; Montero, Francisco

2013-01-01

25

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

SciTech Connect

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

Yasbin, R. E.

1981-06-01

26

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

PubMed

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

Marín, Arturo; Tejero, Héctor; Nuño, Juan Carlos; Montero, Francisco

2013-01-01

27

Polyphosphate kinase regulates error-prone replication by DNA polymerase IV in Escherichia coli  

PubMed Central

Summary The ppk gene encodes polyphosphate kinase (Ppk), an enzyme that catalyses the polymerization of inorganic phosphate into long chains of polyphosphate (polyP). An insertion mutation in ppk causes a decrease in adaptive mutation in Escherichia coli strain FC40. Adaptive mutation in FC40 mostly results from error-prone DNA polymerase IV (Pol IV), encoded by dinB; most of the antimutagenic phenotype of the ppk mutant disappears in a dinB mutant strain. In addition, the ppk mutant causes a decrease in growth-dependent mutations produced by overexpressing Pol IV. However, the amount of Pol IV protein is unchanged in the ppk mutant strain, indicating that the activity or fidelity of Pol IV is altered. Adaptive mutation is inhibited both by the absence of Ppk, which results in low amounts of polyP, and by overproduction of Ppk, which results in high amounts of polyP, suggesting that an optimal level of polyP is necessary. Taken together, these results suggest a novel mechanism involving polyP that directly or indirectly regulates DNA polymerase activity or fidelity. PMID:16045619

Stumpf, Jeffrey D.; Foster, Patricia L.

2005-01-01

28

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

E-print Network

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

Tsai, Ming-Daw

29

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

Microsoft Academic Search

In this undergraduate laboratory experiment we measure the centripetal force acting on a bob in uniform circular motion. As the experiment was originally designed, it consistently yielded large errors due to a subtle twist of the bob as the mass was increased incrementally. This error is due to the fact that the center of mass changes relative position as the

Peter Ronhovde; Rudy Sirochman

2003-01-01

30

Enhancing thermostability of Escherichia coli phytase AppA2 by error-prone PCR  

Microsoft Academic Search

Phytases are used to improve phosphorus nutrition of food animals and reduce their phosphorus excretion to the environment.\\u000a Due to favorable properties, Escherichia coli AppA2 phytase is of particular interest for biotechnological applications. Directed evolution was applied in the present\\u000a study to improve AppA2 phytase thermostability for lowering its heat inactivation during feed pelleting (60–80°C). After a\\u000a mutant library of

Moon-Soo Kim; Xin Gen Lei

2008-01-01

31

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

SciTech Connect

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.

Tan, W.-M. [Division of Cellular and Molecular Research, National Cancer Centre (Singapore); Paterson, Malcolm C. [Division of Cellular and Molecular Research, National Cancer Centre (Singapore); Division of Research, Singapore General Hospital (Singapore); Koo, Ghee Chong [Division of Cellular and Molecular Research, National Cancer Centre (Singapore); Li Huihua [Division of Clinical Trials and Epidemiology, National Cancer Centre (Singapore); Price, Allan [Division of Oncology, University of Edinburgh, Western General Hospital (Singapore); Loong, Susan L.E. [Division of Cellular and Molecular Research, National Cancer Centre (Singapore); Department of Radiation Oncology, National Cancer Centre (Singapore)], E-mail: trdlle@nccs.com.sg

2008-09-01

32

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

PubMed Central

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

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

33

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

NASA Astrophysics Data System (ADS)

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

Ronhovde, Peter; Sirochman, Rudy

2003-02-01

34

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

SciTech Connect

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

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

2012-10-25

35

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

PubMed Central

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

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

2015-01-01

36

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

ERIC Educational Resources Information Center

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

Saavedra, Pedro; And Others

37

Error-prone replication bypass of the primary aflatoxin B1 DNA adduct, AFB1-N7-Gua.  

PubMed

Hepatocellular carcinomas (HCCs) are the third leading cause of cancer deaths worldwide. The highest rates of early onset HCCs occur in geographical regions with high aflatoxin B1 (AFB1) exposure, concomitant with hepatitis B infection. Although the carcinogenic basis of AFB1 has been ascribed to its mutagenic effects, the mutagenic property of the primary AFB1-DNA adduct, AFB1-N7-Gua, in mammalian cells has not been studied extensively. Taking advantage of the ability to create vectors containing a site-specific DNA adduct, the mutagenic potential was determined in primate cells. This adduct was highly mutagenic following replication in COS-7 cells, with a mutation frequency of 45%. The spectrum of mutations was predominantly G to T base substitutions, a result that is consistent with previous mutation data derived from aflatoxin-associated HCCs. To assess which DNA polymerases (pol) might contribute to the mutational outcome, in vitro replication studies were performed. Unexpectedly, replicative pol ? and the error-prone translesion synthesis pol ? were able to accurately bypass AFB1-N7-Gua. In contrast, replication bypass using pol ? was shown to occur with low fidelity and could account for the commonly detected G to T transversions. PMID:24838242

Lin, Ying-Chih; Li, Liang; Makarova, Alena V; Burgers, Peter M; Stone, Michael P; Lloyd, R Stephen

2014-06-27

38

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

PubMed Central

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

Boulton, S J; Jackson, S P

1996-01-01

39

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

SciTech Connect

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.

Kirouac, Kevin N.; Ling, Hong; (UWO)

2009-06-30

40

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

SciTech Connect

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.

Hays, J.B.; Ackerman, E.J.; Pang, Q.S. (Oregon State Univ., Corvallis (USA))

1990-07-01

41

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

PubMed Central

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

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

2014-01-01

42

Error-prone processing of apurinic/apyrimidinic (AP) sites by PolX underlies a novel mechanism that promotes adaptive mutagenesis in Bacillus subtilis.  

PubMed

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

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

2014-08-15

43

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

PubMed Central

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

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

2014-01-01

44

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

PubMed

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

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

2015-01-01

45

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

PubMed Central

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

Schipler, Agnes; Iliakis, George

2013-01-01

46

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

PubMed Central

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

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

2008-01-01

47

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

PubMed

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

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

2008-09-15

48

Upscaled CTAB-based DNA extraction and real-time PCR assays for Fusarium culmorum and F. graminearum DNA in plant material with reduced sampling error.  

PubMed

Fusarium graminearum Schwabe (Gibberella zeae Schwein. Petch.) and F. culmorum W.G. Smith are major mycotoxin producers in small-grain cereals afflicted with Fusarium head blight (FHB). Real-time PCR (qPCR) is the method of choice for species-specific, quantitative estimation of fungal biomass in plant tissue. We demonstrated that increasing the amount of plant material used for DNA extraction to 0.5-1.0 g considerably reduced sampling error and improved the reproducibility of DNA yield. The costs of DNA extraction at different scales and with different methods (commercial kits versus cetyltrimethylammonium bromide-based protocol) and qPCR systems (doubly labeled hybridization probes versus SYBR Green) were compared. A cost-effective protocol for the quantification of F. graminearum and F. culmorum DNA in wheat grain and maize stalk debris based on DNA extraction from 0.5-1.0 g material and real-time PCR with SYBR Green fluorescence detection was developed. PMID:19330077

Brandfass, Christoph; Karlovsky, Petr

2008-11-01

49

Single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity  

Microsoft Academic Search

Conservation genetic studies often employ DNA extracts from museum specimens for comparisons with extant populations to monitor\\u000a temporal changes in genetic diversity. Here, we report on artifact base changes in mitochondrial DNA sequences amplified from\\u000a relatively recent (? 35 years) museum specimens of indigobirds (Vidua spp.). Single base errors were confirmed by replicate sequencing and included both double peaks and artifact substitutions

Kristina M. Sefc; Robert B. Payne; Michael D. Sorenson

2007-01-01

50

Injury proneness and personality.  

PubMed

The aim of this research was to investigate some personality factors among groups of 43 physically injured inpatients and 43 non-injured hospital-based controls. The participants completed the Eysenck Personality Questionnaire (EPQ) and the Coping Styles Questionnaire (CSQ). Logistic regression was used to compare the two groups on six psychological risk factors. The univariate regression models suggested three possible risk factors: extraversion, sensitization, and avoidance coping style. The multivariate regression model supported only extraversion and sensitization of emotion. Next, patients in the experimental group were questioned about whether they had considered preventive measures before the accident and whether they felt responsible for their injuries. Correlation analysis showed that introverted subjects felt more responsible for the sustained injuries than their extraverted counterparts. Sensitizers and subjects who scored high on psychoticism, neuroticism, and emotional coping had not considered preventive measures as often as others. Finally, the principal component analysis of risk factors was used to extract two correlates of injury-prone behaviour: extraversion and sensitized avoidance. It was concluded that psychological factors play an important role in predicting injury that is significant enough to require inpatient treatment. Two potential mechanisms of psychological impact have been suggested, notably distraction in extraverted subjects and overestimation in sensitizing avoiders. PMID:11827609

Marusic, A; Musek, J; Gudjonsson, G

2001-01-01

51

Virtual PCR  

SciTech Connect

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).

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

2006-02-23

52

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

MedlinePLUS

... been misinterpreted as “discontinued” when followed by a list of discharge medications Use “discharge” and “discontinue” IJ ... abbreviations are included on The Joint Commission’s “minimum list” of dangerous abbreviations, acronyms, and symbols that must ...

53

Error-prone translesion synthesis mediates acquired chemoresistance  

E-print Network

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

Xie, Kun

54

Propensity Score Weighting with Error-Prone Covariates  

ERIC Educational Resources Information Center

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

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

2011-01-01

55

Fission Yeast Rad52 Phosphorylation Restrains Error Prone Recombination Pathways  

PubMed Central

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

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

2014-01-01

56

Fantasy Proneness: Hypnosis, Developmental Antecedents, and Psychopathology  

Microsoft Academic Search

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

Steven Jay Lynn; Judith W. Rhue

1988-01-01

57

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

PubMed Central

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

2014-01-01

58

Ethnic and gender differences in boredom proneness  

SciTech Connect

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.

Gibson, G.S.; Morales,

1996-02-01

59

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

SciTech Connect

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

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

2012-04-01

60

The Detection of Fault-Prone Programs  

Microsoft Academic Search

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

John C. Munson; Taghi M. Khoshgoftaar

1992-01-01

61

PCR thermocycler  

DOEpatents

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

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

2003-01-01

62

PCR thermocycler  

DOEpatents

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

Benett, William J.; Richards, James B.

2005-05-17

63

Medication administration errors in adult patients in the ICU  

Microsoft Academic Search

Objective: To quantify the incidence and specify the types of medication administration errors from a list of error-prone medications and to determine if patient harm resulted from these errors. Design: An observational evaluation. Setting: Five intensive care units (ICUs) in the United States. Patients and participants: Eight hundred fifty-one patients who were at least 18 years of age and admitted

Andrea D. Calabrese; Brian L. Erstad; Katherine Brandl; Jeffrey F. Barletta; Sandra L. Kane; Deb S. Sherman

2001-01-01

64

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

Code of Federal Regulations, 2011 CFR

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

2011-10-01

65

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

Code of Federal Regulations, 2010 CFR

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

2010-10-01

66

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

Code of Federal Regulations, 2011 CFR

...AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.22 Planning considerations for flood-prone areas. (a) The flood plain management...

2011-10-01

67

Genome sequencing accuracy by RCA-seq versus long PCR template cloning and sequencing in identification of human papillomavirus type 58  

PubMed Central

Background Genome variations in human papillomaviruses (HPVs) are common and have been widely investigated in the past two decades. HPV genotyping depends on the finding of the viral genome variations in the L1 ORF. Other parts of the viral genome variations have also been implicated as a possible genetic factor in viral pathogenesis and/or oncogenicity. Results In this study, the HPV58 genome in cervical lesions was completely sequenced both by rolling-circle amplification of total cell DNA and deep sequencing (RCA-seq) and by long PCR template cloning and sequencing. By comparison of three HPV58 genome sequences decoded from three clinical samples to reference HPV-58, we demonstrated that RCA-seq is much more accurate than long-PCR template cloning and sequencing in decoding HPV58 genome. Three HPV58 genomes decoded by RCA-seq displayed a total of 52 nucleotide substitutions from reference HPV58, which could be verified by long PCR template cloning and sequencing. However, the long PCR template cloning and sequencing led to additional nucleotide substitutions, insertions, and deletions from an authentic HPV58 genome in a clinical sample, which vary from one cloned sequence to another. Because the inherited error-prone nature of Tgo DNA polymerase used in preparation of the long PCR templates of HPV58 genome from the clinical samples, the measurable error rate in incorporation of nucleotide into an elongating DNA template was about 0.149% ±0.038% in our studies. Conclusions Since PCR template cloning and sequencing is widely used in identification of single nucleotide polymorphism (SNP), our data indicate that a serious caution should be taken in finding of true SNPs in various genetic studies. PMID:24410913

2014-01-01

68

Single-molecule PCR: an artifact-free PCR approach for the analysis of somatic mutations.  

PubMed

A critical review of the clone-by-clone approach to the analysis of complex spectra of somatic mutations is presented. The study of a priori unknown somatic mutations requires painstaking analysis of complex mixtures of multiple mutant and non-mutant DNA molecules. If mutant fractions are sufficiently high, these mixtures can be dissected by the cloning of individual DNA molecules and scanning of the individual clones for mutations (e.g., by sequencing). Currently, the majority of such cloning is performed using PCR fragments. However, post-PCR cloning may result in various PCR artifacts - PCR errors and jumping PCR - and preferential amplification of certain mutations. This review argues that single-molecule PCR is a simple alternative that promises to evade the disadvantages inherent to post-PCR cloning and enhance mutational analysis in the future. PMID:16149882

Kraytsberg, Yevgenya; Khrapko, Konstantin

2005-09-01

69

Patient evaluation of prone carts used in spinal cord injury.  

PubMed

Prone carts are used for mobility by individuals with spinal cord injury who cannot use a wheelchair due to the risk of aggravating existing pressure ulcers. A prone cart is a flat/horizontal cart with a fixed height, propelled by the user while laying in a prone position. Patients reported that prolonged use of a prone cart resulted in chronic neck, shoulder and back pain. Additionally the existing prone carts lack user accessible angle adjustability, chest support area, as well as a storage, eating or working area. An interdisciplinary research team collaborated to address these concerns. Three prone carts were evaluated: E&J, Gendron, and a newly developed prototype, MIAD/PVA. Questionnaires were administered to caregivers and patients regarding usage and effectiveness of the prone carts as well as the features of an ideal cart. This data led to the design and refinement of a prototype prone cart which was tested on 20 patients and 19 caregivers at the SCI Centers of the Milwaukee and Tampa VAMC's from 1994-1995. The new prone cart enables the user to lie at an angle rather than laying flat. This position has been found to relieve back and neck pressure. With an hydraulic system, the the user can adjust both the front and rear angles of the cart to achieve desired comfort. In addition, a front deck provides an eating and working area. This study resulted in research-based information and criteria for the design of new prone carts. Findings of this pilot study will be incorporated in a development merit review proposal to the VA Rehabilitation Research & Development service for the design of a new manual and motorized prone cart. The researchers are collaborating with Ortho-Kinetics Inc. to promote ease in manufacturing. PMID:8900708

Nelson, A; Malassigné, P; Cors, M; Amerson, T L; Bonifay, R; Schnurr, E

1996-06-01

70

[Medical device use errors].  

PubMed

Medical devices define our everyday patient treatment processes. But despite the beneficial effect, every use can also lead to damages. Use errors are thus often explained by human failure. But human errors can never be completely extinct, especially in such complex work processes like those in medicine that often involve time pressure. Therefore we need error-tolerant work systems in which potential problems are identified and solved as early as possible. In this context human engineering uses the TOP principle: technological before organisational and then person-related solutions. But especially in everyday medical work we realise that error-prone usability concepts can often only be counterbalanced by organisational or person-related measures. Thus human failure is pre-programmed. In addition, many medical work places represent a somewhat chaotic accumulation of individual devices with totally different user interaction concepts. There is not only a lack of holistic work place concepts, but of holistic process and system concepts as well. However, this can only be achieved through the co-operation of producers, healthcare providers and clinical users, by systematically analyzing and iteratively optimizing the underlying treatment processes from both a technological and organizational perspective. What we need is a joint platform like medilab V of the TU Berlin, in which the entire medical treatment chain can be simulated in order to discuss, experiment and model--a key to a safe and efficient healthcare system of the future. PMID:19213452

Friesdorf, Wolfgang; Marsolek, Ingo

2008-01-01

71

FANTASY PRONENESS AND OTHER PSYCHOLOGICAL CORRELATES OF UFO EXPERIENCE  

Microsoft Academic Search

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

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

72

Parent Proneness to Shame and the Use of Psychological Control  

ERIC Educational Resources Information Center

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

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

2007-01-01

73

Pathogenesis of A??+ Ketosis-Prone Diabetes  

PubMed Central

A??+ ketosis-prone diabetes (KPD) is an emerging syndrome of obesity, unprovoked ketoacidosis, reversible ?-cell dysfunction, and near-normoglycemic remission. We combined metabolomics with targeted kinetic measurements to investigate its pathophysiology. Fasting plasma fatty acids, acylcarnitines, and amino acids were quantified in 20 KPD patients compared with 19 nondiabetic control subjects. Unique signatures in KPD—higher glutamate but lower glutamine and citrulline concentrations, increased ?-hydroxybutyryl-carnitine, decreased isovaleryl-carnitine (a leucine catabolite), and decreased tricarboxylic acid (TCA) cycle intermediates—generated hypotheses that were tested through stable isotope/mass spectrometry protocols in nine new-onset, stable KPD patients compared with seven nondiabetic control subjects. Free fatty acid flux and acetyl CoA flux and oxidation were similar, but KPD had slower acetyl CoA conversion to ?-hydroxybutyrate; higher fasting ?-hydroxybutyrate concentration; slower ?-hydroxybutyrate oxidation; faster leucine oxidative decarboxylation; accelerated glutamine conversion to glutamate without increase in glutamate carbon oxidation; and slower citrulline flux, with diminished glutamine amide–nitrogen transfer to citrulline. The confluence of metabolomic and kinetic data indicate a distinctive pathogenic sequence: impaired ketone oxidation and fatty acid utilization for energy, leading to accelerated leucine catabolism and transamination of ?-ketoglutarate to glutamate, with impaired TCA anaplerosis of glutamate carbon. They highlight a novel process of defective energy production and ketosis in A??+ KPD. PMID:23160531

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

74

Sex Determination Using PCR  

ERIC Educational Resources Information Center

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…

Kima, Peter E.; Rasche, Madeline E.

2004-01-01

75

Refractive Errors  

MedlinePLUS

... and lens of your eye helps you focus. Refractive errors are vision problems that happen when the shape ... cornea, or aging of the lens. Four common refractive errors are Myopia, or nearsightedness - clear vision close up ...

76

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

PubMed

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

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

2015-04-01

77

Hemodynamic evaluation of the prone position by transesophageal echocardiography  

Microsoft Academic Search

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

Shigeyoshi Toyota; Yoshikiyo Amaki

1998-01-01

78

DEM-based Approaches for the Identification of Flood Prone Areas  

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

79

Three-dimensional conformal breast irradiation in the prone position.  

PubMed

The prone position can be used for the planning of adjuvant radiotherapy after conservative breast surgery in order to deliver less irradiation to lung and cardiac tissue. In the present study, we compared the results of three-dimensional conformal radiotherapy planning for five patients irradiated in the supine and prone position. Tumor stage was T1N0M0 in four patients and T1N1M0 in one. All patients had been previously submitted to conservative breast surgery. Breast size was large in three patients and moderate in the other two. Irradiation in the prone position was performed using an immobilization foam pad with a hole cut into it to accommodate the breast so that it would hang down away from the chest wall. Dose-volume histograms showed that mean irradiation doses reaching the ipsilateral lung were 8.3+/-3.6 Gy with the patient in the supine position and 1.4+/-1.0 Gy with the patient in the prone position (P = 0.043). The values for the contralateral lung were 1.3+/-0.7 and 0.3+/-0.1 Gy (P = 0.043) and the values for cardiac tissue were 4.6+/-1.6 and 3.0+/-1.7 Gy (P = 0.079), respectively. Thus, the dose-volume histograms demonstrated that lung tissue irradiation was significantly lower with the patient in the prone position than in the supine position. Large-breasted women appeared to benefit most from irradiation in the prone position. Prone position breast irradiation appears to be a simple and effective alternative to the conventional supine position for patients with large breasts, since they are subjected to lower pulmonary doses which may cause less pulmonary side effects in the future. PMID:14502379

Kurtman, C; Nalça Andrieu, M; Hiçsönmez, A; Celebio?lu, B

2003-10-01

80

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

SciTech Connect

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.

Louisiana State University; Balman, Mehmet; Kosar, Tevfik

2010-10-27

81

Estrogen-Related Abnormalities in Glomerulosclerosis-Prone Mice  

PubMed Central

The development and progression of glomerulosclerosis (GS) is determined by the genetic background. The incidence of end-stage renal disease is increased in postmenopausal women, suggesting that estrogen deficiency may play a role in the accumulation of extracellular matrix by mesangial cells (MCs), which are primarily responsible for the synthesis and degradation of this matrix. Using mouse models that are prone or resistant to the development of GS, we compared the expression of estrogen receptor (ER)-? and ER-? subtypes in GS-prone and GS-resistant glomeruli and isolated MCs, and examined the effects of estrogens on ER, collagen, and matrix metalloproteinase (MMP) expression in MCs. Glomeruli and MCs from GS-prone mice had decreased expression of ER-? and ER-? subtypes and ER transcriptional activity was also decreased in their MCs. Importantly, although 17?-estradiol treatment resulted in decreased collagen accumulation and increased MMP-9 expression and activity in MCs from GS-resistant mice, there was, paradoxically, no effect on collagen accumulation and decreased MMP-9 expression and activity in MCs from GS-prone mice. Thus, GS susceptibility is associated with diminished ER expression in MCs. The renal protective effects of estrogens, including decreased collagen accumulation and increased MMP-9 expression, seem to be blunted in GS-prone MCs. PMID:12000739

Potier, Mylène; Karl, Michael; Zheng, Feng; Elliot, Sharon J.; Striker, Gary E.; Striker, Liliane J.

2002-01-01

82

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

PubMed

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

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

2014-07-01

83

Policing of adult honey bees with activated ovaries is error prone  

Microsoft Academic Search

Summary. Individually-marked day-old anarchistic (from a line where workers lay eggs at high frequency) and wild-type worker honey bees (Apis mellifera) were introduced to queenless sections of anarchistic or wildtype host colonies housed in observation hives. After 14 days, some introduced workers had activated ovaries, and we then removed the screens separating the queenless from the queenright sections of the

J. R. Dampney; A. B. Barron; B. P. Oldroyd

2002-01-01

84

Inducible error-prone repair in Bacillus subtilis. Progress report, May 1, 1985-April 30, 1986  

SciTech Connect

DNA damage-inducible star operon fusions were generated in B. subtilis by transpositional mutagenesis. These fusion isolates produce increased beta-galactosidase when exposed to mitomycin C, uv radiation, or ethyl methanesulfonate, indicating that the lacZ structural gene had inserted into host transcriptional units that are induced by a variety of DNA damaging agents. One of the fusion strains was DNA-repair deficient and phenotypically resembled a uv-sensitive excision-repair deficient mutant of B. subtilis. Induction of beta-galactosidase also occurred in the competent subpopulation of each of the din fusion strains, independent of exposure to DNA-damaging agents. Both the DNA-damage-inducible and competence-inducible components of beta-galactosidase expression were abolished by the recE4 mutation, which inhibits SOS-like (SOB) induction but does not interfere with the development of the competent state. The results indicate that gene expression is stimulated at specific loci within the B. subtilis chromosome both by DNA-damaging agents and by the development of competence and this response is under the control of the SOB regulon. Furthermore, they demonstrated that at the molecular level SOB induction and the development of competence are interrelated cellular events.

Yasbin, R.E.

1986-06-01

85

Ring stability of the PROFIBUS token-passing protocol over error-prone links  

Microsoft Academic Search

The PROFIBUS is a well-known and widely used fieldbus. On the medium access control layer, it employs a token-passing protocol where all active stations form a logical ring on top of a broadcast medium. This protocol is designed to deliver real-time data transmission services in harsh industrial environments. A necessary prerequisite for timeliness and quality of service is the ring

Andreas Willig; Adam Wolisz

2001-01-01

86

The physiological impact of upper limb position in prone restraint.  

PubMed

Deaths occurring during and/or in close proximity to physical restraint have been attributed to positional asphyxia. This study investigated the physiological impact of three recognized prone-restraint positions with participants remaining passive. Position 3 (P3) the supported prone position (SPP) was designed to reduce the extent of pressure on the anterior chest wall (PAC) by bringing the upper limbs underneath the shoulder joint whereas for the other two positions (P1 and P2) the arms were abducted from the torso. Twenty-five adults participated. Forced vital capacity (FVC), expiratory volume in one second (FEV1), heart rate (HR) and oxygen saturations (SpO2) were taken three times in an upright seated position (baseline) and in each prone position. Mean PAC was measured at 102.6 (±24.3) and 101.4 (±24.4)?mmHg for P1 and P2, respectively; however, in the SPP (P3) the mean PAC pressure reduced to 72.7 (±16.9)?mmHg. All three prone-restraint positions reduced FVC and FEV1 compared with baseline (P?prone-restraint positions and HR and SpO2 were unaffected. In summary, all prone-restraint positions restrict respiratory function but the risk associated with the position reduces as the PAC reduces. PMID:22969148

Barnett, Richard; Hanson, Paul; Stirling, Chris; Pandyan, Anand D

2013-07-01

87

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 ...

88

Pattern recognition of earthquake prone area in North China  

E-print Network

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

Gu, Ji-Min

1989-01-01

89

PCR Project: Making PCR (Polymerase Chain Reaction)  

NSDL National Science Digital Library

Paul Rabinow, professor of Anthropology at the University of California Berkeley; Suzanne Calpestri, Head of the George and Mary Foster Anthropology Library at UC Berkeley; and Soren Germer, a recent PhD from the UC Berkeley Anthropology Department, developed this site with a grant from the Alfred P. Sloan Foundation's Science and Technology in the Making (STIM) initiative. STIM encourages "use [of] an innovative approach to investigating and documenting recent/contemporary events in science and technology." Making PCR does this by furnishing over thirty "foundational papers" on the topic, in three major subject categories (foundations, applications, and technological variations of the basics). In addition, users can access Cetus' 1989 39 page PCR bibliography. These full texts are available as page images and come from several different scholarly journals. Interested users can submit their thoughts about the past and future of PCR through interactive discussion forums.

90

Distributed Computing in Fault-Prone Dynamic Networks Philipp Brandes  

E-print Network

Distributed Computing in Fault-Prone Dynamic Networks Philipp Brandes Computer Engineering & Department of Computer Science University of Paderborn fmadh@upb.de ABSTRACT Dynamics in networks is caused and Networks Lab (TIK) ETH Zurich pbrandes@ethz.ch Friedhelm Meyer auf der Heide Heinz Nixdorf Institute

91

Complications associated with prone positioning in elective spinal surgery  

PubMed Central

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.

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

2015-01-01

92

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...

93

The Social Antecedents of Anger Proneness in Young Adulthood  

ERIC Educational Resources Information Center

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

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

2007-01-01

94

A syntax-preserving error resilience tool for JPEG 2000 based on error correcting arithmetic coding.  

PubMed

JPEG 2000 is the novel ISO standard for image and video coding. Besides its improved coding efficiency, it also provides a few error resilience tools in order to limit the effect of errors in the codestream, which can occur when the compressed image or video data are transmitted over an error-prone channel, as typically occurs in wireless communication scenarios. However, for very harsh channels, these tools often do not provide an adequate degree of error protection. In this paper, we propose a novel error-resilience tool for JPEG 2000, based on the concept of ternary arithmetic coders employing a forbidden symbol. Such coders introduce a controlled degree of redundancy during the encoding process, which can be exploited at the decoder side in order to detect and correct errors. We propose a maximum likelihood and a maximum a posteriori context-based decoder, specifically tailored to the JPEG 2000 arithmetic coder, which are able to carry out both hard and soft decoding of a corrupted code-stream. The proposed decoder extends the JPEG 2000 capabilities in error-prone scenarios, without violating the standard syntax. Extensive simulations on video sequences show that the proposed decoders largely outperform the standard in terms of PSNR and visual quality. PMID:16579370

Grangetto, Marco; Magli, Enrico; Olmo, Gabriella

2006-04-01

95

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

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

96

''I'm Sitting Here Feeling Aphasic!'' A Study of Recurrent Perseverative Errors Elicited in Unimpaired Speakers  

ERIC Educational Resources Information Center

In this study, the recurrent perseverative errors produced by 44 speakers without impairment were examined in picture naming and reading aloud tasks under a fast response deadline. The proportion of perseverative relative to non-perseverative errors was greater in picture naming, the more error-prone task, than in reading aloud. Additionally,…

Moses, Melanie S.; Nickels, Lyndsey A.; Sheard, Christine

2004-01-01

97

Ultrasound-guided central venous catheterization in prone position  

PubMed Central

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

Sofi, Khalid; Arab, Samer

2010-01-01

98

Identifying crash-prone locations with quantile regression.  

PubMed

Identifying locations that exhibit the greatest potential for safety improvements is becoming more and more important because of competing needs and a tightening safety improvement budget. Current crash modeling practices mainly target changes at the mean level. However, crash data often have skewed distributions and exhibit substantial heterogeneity. Changes at mean level do not adequately represent patterns present in the data. This study employs a regression technique known as the quantile regression. Quantile regression offers the flexibility of estimating trends at different quantiles. It is particularly useful for summarizing data with heterogeneity. Here, we consider its application for identifying intersections with severe safety issues. Several classic approaches for determining risk-prone intersections are also compared. Our findings suggest that relative to other methods, quantile regression yields a sensible and much more refined subset of risk-prone locations. PMID:20728599

Qin, Xiao; Ng, Marie; Reyes, Perla E

2010-11-01

99

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

PubMed

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

Vaibhav, Atul; Mathai, Mathew; Gorman, Shaun

2013-01-01

100

Quantitative PCR Protocol  

NSDL National Science Digital Library

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

The Jackson Laboratory (The Jackson Laboratory)

2012-01-06

101

Supine and prone colon registration using quasi-conformal mapping.  

PubMed

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

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

2010-01-01

102

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

Code of Federal Regulations, 2012 CFR

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

2012-10-01

103

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

Code of Federal Regulations, 2014 CFR

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

2014-10-01

104

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

Code of Federal Regulations, 2013 CFR

...2013-10-01 false Planning considerations for flood-prone areas. 60.22 Section 60...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT... Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

2013-10-01

105

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

Code of Federal Regulations, 2012 CFR

...2011-10-01 true Planning considerations for flood-prone areas. 60.22 Section 60...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT... Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

2012-10-01

106

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

Code of Federal Regulations, 2013 CFR

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

2013-10-01

107

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

Code of Federal Regulations, 2014 CFR

...2014-10-01 false Planning considerations for flood-prone areas. 60.22 Section 60...INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT... Additional Considerations in Managing Flood-Prone, Mudslide (i.e.,...

2014-10-01

108

Using Software Engineering Technology to Reduce Medical Errors Lori A. Clarke  

E-print Network

of Nursing and the Baystate Medical Center, we are undertaking in-depth case studies on error-prone and life-criticalUsing Software Engineering Technology to Reduce Medical Errors Lori A. Clarke Department Safety Project, we are investigating the use of software engineering technologies to model, evaluate

Taufer, Michela

109

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

ERIC Educational Resources Information Center

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

Calamari, Elena; Pini, Mauro

2003-01-01

110

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

PubMed Central

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

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

2015-01-01

111

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

SciTech Connect

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.

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

1995-08-28

112

The pathophysiology of medication errors: how and where they arise  

PubMed Central

Errors arise when an action is intended but not performed; errors that arise from poor planning or inadequate knowledge are characterized as mistakes; those that arise from imperfect execution of well-formulated plans are called slips when an erroneous act is committed and lapses when a correct act is omitted. Some tasks are intrinsically prone to error. Examples are tasks that are unfamiliar to the operator or performed under pressure. Tasks that require the calculation of a dosage or dilution are especially susceptible to error. The tasks of prescribing, preparation, and administration of medicines are complex, and are carried out within a complex system; errors can occur at each of many steps and the error rate for the overall process is therefore high. The error rate increases when health-care professionals are inexperienced, inattentive, rushed, distracted, fatigued, or depressed; orthopaedic surgeons and nurses may be more likely than other health-care professionals to make medication errors. Medication error rates in hospital are higher in paediatric departments and intensive care units than elsewhere. Rates of medication errors may be higher in very young or very old patients. Intravenous antibiotics are the drugs most commonly involved in medication errors in hospital; antiplatelet agents, diuretics, and non-steroidal anti-inflammatory drugs are most likely to account for ‘preventable admissions’. Computers effectively reduce the rates of easily counted errors. It is not clear whether they can save lives lost through rare but dangerous errors in the medication process. PMID:19594527

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

2009-01-01

113

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...

114

Human factors and medication errors: a case study.  

PubMed

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

Gluyas, Heather; Morrison, Paul

2014-12-15

115

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...

116

Quantitative electroencephalography as a biomarker for proneness toward developing psychosis.  

PubMed

The fully dimensional approach to the relationship between schizotypal personality traits and schizophrenia describes schizotypy as a continuum throughout the general population ranging from low schizotypy (LoS) and psychological health to high schizotypy (HiS) and psychosis-proneness. However, no biological markers have yet been discovered that reliably quantify an individual's degree of schizotypy and/or psychosis. This study aimed to evaluate quantitative electroencephalographic (qEEG) measures of power spectra as potential biomarkers of the proneness towards the development of psychosis in schizotypal individuals. The resting-state oscillatory brain dynamics under eyes-closed condition from 16 LoS and 16 HiS individuals were analysed for qEEG measures of background rhythm frequency, relative power in ?, ?, low-?, high-?, low-?, high-? and low-? frequency bands, and the high-temporal cross-correlation of power spectra between low- and high-frequency bands observed by averaging signals from whole-head EEG electrodes. HiS individuals at rest locked the thalamocortical loop in the low-? band at a lower-frequency oscillation and displayed an abnormally high level of neural synchronisation. In addition, the high-? band was found to be positively correlated with both the high-? and low-? bands unlike LoS individuals, indicating widespread thalamocortical resonance in HiS individuals. The increase of regional alpha oscillations in HiS individuals suggests abnormal high-level attention, whereas the pattern of correlation between frequency bands resembles the thalamocortical dysrhythmia phenomenon which underlies the symptomatology of a variety of neuropsychiatric disorders including schizophrenia. These qEEG biomarkers may aid clinicians in identifying HiS individuals with a high-risk of developing psychosis. PMID:24508484

Fuggetta, Giorgio; Bennett, Matthew A; Duke, Philip A; Young, Andrew M J

2014-03-01

117

Shame-Proneness as a Diathesis for Dissociation in Women with Histories of Childhood Sexual Abuse  

Microsoft Academic Search

This study examined whether shame-proneness is associated with dissociation among abused women. Participants were 99 hospitalized women with and without reported histories of childhood sexual abuse. Hypotheses were that childhood sexual abuse and shame-proneness would each be associated with dissociation, and that the relationship between sexual abuse and dissociation would be greater among women with higher shame-proneness. Multiple regression analysis

Jean A. Talbot; Nancy L. Talbot; Xin Tu

2004-01-01

118

Topological quantum computing with a very noisy network and local error rates approaching one percent  

PubMed Central

A scalable quantum computer could be built by networking together many simple processor cells, thus avoiding the need to create a single complex structure. The difficulty is that realistic quantum links are very error prone. A solution is for cells to repeatedly communicate with each other and so purify any imperfections; however prior studies suggest that the cells themselves must then have prohibitively low internal error rates. Here we describe a method by which even error-prone cells can perform purification: groups of cells generate shared resource states, which then enable stabilization of topologically encoded data. Given a realistically noisy network (?10% error rate) we find that our protocol can succeed provided that intra-cell error rates for initialisation, state manipulation and measurement are below 0.82%. This level of fidelity is already achievable in several laboratory systems. PMID:23612297

Nickerson, Naomi H.; Li, Ying; Benjamin, Simon C.

2013-01-01

119

Topological quantum computing with a very noisy network and local error rates approaching one percent  

E-print Network

A scalable quantum computer could be built by networking together many simple processor cells, thus avoiding the need to create a single complex structure. The difficulty is that realistic quantum links are very error prone. A solution is for cells to repeatedly communicate with each other and so 'purify' any imperfections; however prior studies suggest that the cells themselves must then have prohibitively low internal error rates. Here we describe a method by which even error-prone cells can perform purification: groups of cells generate shared resource states, which then enable stabilization of topologically encoded data. Given a realistically noisy network (>=10% error rate) we find that our protocol can succeed provided that intra-cell error rates for initialisation, state manipulation and measurement are below 0.82%. This level of fidelity is already achievable in several laboratory systems.

Naomi H. Nickerson; Ying Li; Simon C. Benjamin

2013-04-25

120

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

PubMed

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

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

2014-03-01

121

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

PubMed

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

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

2014-05-01

122

Help prevent hospital errors  

MedlinePLUS

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

123

Cognitive Correlates of Boredom Proneness: The Role of Private Self-Consciousness and Absorption  

Microsoft Academic Search

The contributions of private self-consciousness and absorption in explaining boredom proneness were investigated. University students enrolled at a public university in the southeastern United States completed a packet containing the Boredom Proneness Scale (BPS; R. Farmer & N. D. Sundberg, 1986), the Self-Consciousness Scale (SCS; A. Fenigstein, M. F. Scheier, & A. H. Buss, 1975), the Tellegen Absorption Scale (TAS;

Hope M. Seib; Stephen J. Vodanovich

1998-01-01

124

The carbon accounting consequences of two possible options for a given fire-prone  

E-print Network

The carbon accounting consequences of two possible options for a given fire-prone forest stand in Fire-Prone Forests As trees grow, they sequester carbon from the atmosphere, some of which is converted. However, on lands that are currently forested, increasing the climate mitigation benefit is more

North, Malcolm

125

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

ERIC Educational Resources Information Center

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

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

2011-01-01

126

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

ERIC Educational Resources Information Center

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

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

2014-01-01

127

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

ERIC Educational Resources Information Center

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.…

Counts, Robert M.; Reid, Kelly

1986-01-01

128

Dependence-Proneness as a Criterion for the Grouping of Students in the Chemistry Laboratory.  

ERIC Educational Resources Information Center

The purpose of the study was to determine the relationship between a personality trait, dependence-proneness, and performance in the high school chemistry laboratory; to arrange laboratory groupings based on the pupil trait of dependence-proneness and to determine if these groupings affect laboratory performance; and to include and test other…

Lefkowitz, Arnold Nathan

129

Development of Korean Smartphone addiction proneness scale for youth.  

PubMed

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

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

2014-01-01

130

How do eubacterial organisms manage aggregation-prone proteome?  

PubMed Central

Eubacterial genomes vary considerably in their nucleotide composition. The percentage of genetic material constituted by guanosine and cytosine (GC) nucleotides ranges from 20% to 70%.  It has been posited that GC-poor organisms are more dependent on protein folding machinery. Previous studies have ascribed this to the accumulation of mildly deleterious mutations in these organisms due to population bottlenecks. This phenomenon has been supported by protein folding simulations, which showed that proteins encoded by GC-poor organisms are more prone to aggregation than proteins encoded by GC-rich organisms. To test this proposition using a genome-wide approach, we classified different eubacterial proteomes in terms of their aggregation propensity and chaperone-dependence using multiple machine learning models. In contrast to the expected decrease in protein aggregation with an increase in GC richness, we found that the aggregation propensity of proteomes increases with GC content. A similar and even more significant correlation was obtained with the GroEL-dependence of proteomes: GC-poor proteomes have evolved to be less dependent on GroEL than GC-rich proteomes. We thus propose that a decrease in eubacterial GC content may have been selected in organisms facing proteostasis problems. PMID:25339987

Das Roy, Rishi; Bhardwaj, Manju; Bhatnagar, Vasudha; Chakraborty, Kausik; Dash, Debasis

2014-01-01

131

Development of Korean Smartphone Addiction Proneness Scale for Youth  

PubMed Central

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

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

2014-01-01

132

Psychosis-proneness correlates with expression levels of dopaminergic genes.  

PubMed

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

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

2014-06-01

133

When soft controls get slippery: User interfaces and human error  

SciTech Connect

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

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

1998-12-01

134

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

SciTech Connect

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

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

2010-09-01

135

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

PubMed Central

Objective To describe the effects of prone positioning on airway management, mechanical ventilation, enteral nutrition, pain and sedation management and staff utilization in infants and children with acute lung injury (ALI). Design Secondary analysis of data collected in a multi-center, randomized, controlled clinical trial of supine versus prone positioning. Patients and Setting 102 pediatric patients (51 prone and 51 supine) with ALI from seven pediatric intensive care units located in the Untied States. Interventions Patients randomized to the supine group remained supine. Patients randomized to the prone group were positioned prone per protocol during the acute phase of their illness for a maximum of 7 days. Both groups were managed using ventilator and sedation protocols and nutrition and skin care guidelines. Measurements Airway management and mechanical ventilatory parameters pre and post repositioning, enteral nutrition management, pain and sedation management, staff utilization, and adverse event data collected for up to 28 days after enrollment. Main Results There were a total of 202 supine-prone-supine cycles. There were no differences in the incidence of endotracheal tube leak between the two groups (p=0.30). Per protocol, 95% of patients remained connected to the ventilator during repositioning. The inadvertent extubation rate was 0.85 for the prone group and 1.03 for the supine group per 100 ventilator days (p=1.00). There were no significant differences in the initiation of trophic (p=0.24), advancing (p=0.82) or full enteral feeds (p=0.80) between the prone and supine groups and in the average pain (p=0.81) and sedation (p=0.18) scores over the acute phase and in the amount of comfort medications received between the two groups. (p=.91). There were no critical events during a turn procedure. While prone, two patients experienced an obstructed ETT. One patient, supported on HFOV, experienced persistent hypercapnea when prone and was withdrawn from the study. The occurrence of pressure ulcers was similar between the two groups (p=0.71). Compared to the supine group, more staff (p ?0.001) and more time were necessary to reposition patients in the prone group. Conclusions Our data show that prone positioning can be safely performed in critically ill pediatric patients and that these patients can be safely managed while in the prone position for prolonged periods of time. PMID:16885792

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

2006-01-01

136

Medication errors in children.  

PubMed

Medication errors commonly involve children, with dosing errors being the most common. Medication errors are more frequent among the most sick patients who have urgent and complex medical conditions. Physicians who are less experienced, tired, depressed, and burnt out make more errors. The systems approach views every medical error as a system failure. The focus is on how to change the system in order to prevent errors. Adopting the systems approach will enhance patients' safety. Strategies that have been found to be effective in reducing medication errors include the use of computerized physician order entry systems, pre-printed order forms, color-coded systems, and involving pharmacists in clinical care. PMID:19127955

Kozer, Eran

2009-01-01

137

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

NASA Technical Reports Server (NTRS)

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

Hobbs, Alan; Williamson, Ann

2002-01-01

138

Errors Affect Hypothetical Intertemporal Food Choice in Women  

PubMed Central

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

Sellitto, Manuela; di Pellegrino, Giuseppe

2014-01-01

139

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

PubMed Central

Background & objectives: Mycoplasma pneumoniae is the most important and common cause of community-acquired pneumonia (CAP). The conventional detection methods (culture and serology) lack sensitivity. PCR offers a better approach for rapid detection but is prone to carry over contamination during manipulation of amplification products. Quantitative real-time PCR (qRT-PCR) method offers an attractive alternative detection method. In the present study, qRT-PCR, PCR and serology methods were used to detect M. pneumoniae infection in cases of pneumonias and findings compared. Methods: A total of 134 samples consisting of blood (for serology) and respiratory secretions (for PCR and qRT-PCR) from 134 patients were collected. The blood samples were tested for IgG, IgM and IgA using commercially available kits. For standardization of PCR of M. pneumoniae P1 gene was cloned in pGEMTEasy vector. Specific primers and reporter sequence were designed and procured for this fragment. The qRT-PCR assay was performed to prepare the standard curve for M. pneumoniae positive control DNA template and detection in patient samples. Results: Of the 134 patients, 26 (19%) were positive for antibodies against M. pneumoniae. IgG was positive in 14.92 per cent (20) cases, IgM in 4.47 per cent (6) and IgA was positive in 5.22 per cent (7) cases. In the qRT-PCR assay 19 per cent (26) samples were positive. Of the 26 qRT-PCR positive samples, nine could be detected by serology. PCR was positive for 25 samples. An extra sample negative by PCR was detected by qRT-PCR. Thus, real-time PCR assay, PCR and serology in combination could detect M. pneumoniae infection in 43 patients. Interpretation & conclusions: The study shows that 17 patients were detected by serology alone, 17 were detected by qRT-PCR only and nine patients were positive by both serology and real-time PCR. Of the 134 samples tested, 25 were positive by conventional PCR, but qRT-PCR could detect one more sample that was negative by PCR and serology. These results suggest that a combination of two or three methods may be required for reliable identification of CAP due to M. pneumoniae. PMID:24056602

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

2013-01-01

140

Reducing errors in radiology.  

PubMed

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

Brusin, Joyce Helena

2014-01-01

141

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

NASA Technical Reports Server (NTRS)

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.

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

2000-01-01

142

Quantitative Real-Time PCR  

Microsoft Academic Search

Unlike classical end-point analysis PCR, real-time PCR provides the data required for quantification of the target nucleic acid. The results can be expressed in absolute terms by reference to external quantified standards or in relative terms compared to another target sequence present within the sample. Absolute quantification requires that the efficiency of the amplification reaction is the same in all

N. A. Saunders

143

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

SciTech Connect

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.

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

2009-09-01

144

Suicide proneness in American and Japanese college students: associations with suicide acceptability and emotional expressivity.  

PubMed

This study considered whether suicide acceptability and emotional expressivity were associated with suicide proneness in American and Japanese women and men. Participants included 417 (283 women, 134 men) American and 396 (243 women, 150 men) Japanese college students. Regression models indicated that suicide acceptability predicted unique variance in suicide proneness for both American and Japanese women and men. However, emotional expressivity contributed to understanding the suicide proneness of American college students only. Culturally appropriate prevention and intervention implications associated with reducing suicide acceptance and cultivating well-being and resiliency are offered. PMID:24517594

Saito, Motoko; Klibert, Jeffrey; Langhinrichsen-Rohling, Jennifer

2013-10-01

145

Prone-position thoracoscopic resection of posterior mediastinal lymph node metastasis from rectal cancer.  

PubMed

Mediastinal lymph node metastasis from colorectal cancer is rare, and barely any reports have described resection of this pathology. We report herein a successful thoracoscopic resection of mediastinal lymph node metastasis in a prone position. A 65-year-old man presented with posterior mediastinal lymph node metastasis after resection of the primary rectal cancer and metachronous hepatic metastasis. Metastatic lymph nodes were resected completely using thoracoscopic surgery in the prone position, which provided advantages of minimal invasiveness, good surgical field, and reduced ergonomic burden on the surgeon. Thoracoscopic resection in the prone position was thought to have the potential to become the standard procedure of posterior mediastinal tumors. PMID:25778039

Shirakawa, Yasuhiro; Noma, Kazuhiro; Koujima, Takeshi; Maeda, Naoaki; Tanabe, Shunsuke; Ohara, Toshiaki; Fujiwara, Toshiyoshi

2015-12-01

146

Modelling carbon emissions in mediterranean fire-prone ecosystems: errors in Translating across scales from global to landscape  

NASA Astrophysics Data System (ADS)

Wildfires are both an agent of disturbance for vegetation dynamic and biosphere/atmosphere carbon fluxes. They affect ecosystems and atmosphere both during the fire event itself (combustion) but also for decades after burning through biomass reconstruction. Fires are initially a stochastic events being part of the natural functioning of ecosystems so that the carbon released during fire events will be sequestrated by vegetation regrowth. Recent modeling studies have started to quantify these changes at the global scale using global remote sensing products. Uncertainties and discrepancies between fire products remain high in burnt surfaces estimates and in turn fire emissions to atmosphere. In addition, translating across scales in different modeling approaches rises key issues that I will develop in this talk. I will focus on the sources of uncertainties in datasets and models, with a peculiar interest on translating across scales in mixed vegetation with an example in the Mediterranean region at the regional scale where local statistics for fire counts, area burnt, and vegetation maps are available. Results on biases in burnt areas, and carbon emissions will be discussed for future needs in global remote sensing products, as part of the ESA fire-CCI project.

Mouillot, F.; Ruffault, J.; Moebius, F.

2012-04-01

147

Error-prone nonhomologous end joining repair operates in human pluripotent stem cells during late G2  

PubMed Central

Genome stability of human embryonic stem cells (hESC) is an important issue because even minor genetic alterations can negatively impact cell functionality and safety. The incorrect repair of DNA double-stranded breaks (DSBs) is the ultimate cause of the formation of chromosomal aberrations. Using G2 radiosensitivity assay, we analyzed chromosomal aberrations in pluripotent stem cells and somatic cells. The chromatid exchange aberration rates in hESCs increased manifold 2 hours after irradiation as compared with their differentiated derivatives, but the frequency of radiation-induced chromatid breaks was similar. The rate of radiation-induced chromatid exchanges in hESCs and differentiated cells exhibited a quadratic dose response, revealing two-hit mechanism of exchange formation suggesting that a non-homologous end joining (NHEJ) repair may contribute to their formation. Inhibition of DNA-PK, a key NHEJ component, by NU7026 resulted in a significant decrease in radiation-induced chromatid exchanges in hESCs but not in somatic cells. In contrast, NU7026 treatment increased the frequency of radiation-induced breaks to a similar extent in pluripotent and somatic cells. Thus, DNA-PK dependent NHEJ efficiently participates in the elimination of radiation-induced chromatid breaks during the late G2 in both cell types and DNA-PK activity leads to a high level of misrejoining specifically in pluripotent cells. PMID:21685510

Bogomazova, Alexandra N.; Lagarkova, Maria A.; Tskhovrebova, Leyla V.; Shutova, Maria V.; Kiselev, Sergey L.

2011-01-01

148

Modeling fluxes and form in landslide-prone terrain  

NASA Astrophysics Data System (ADS)

Landslides dramatically alter the Earth's surface over short timescales. The mass transfer associated with a limited number of slope failures can dominate the sediment budget of a region for decades or longer. The initiation, failure geometry, and runout of individual landslides depend on a range of factors and cannot be predicted from current models. Given these realities of landslide behavior over human timescales, it is challenging to reasonably represent these processes in landscape evolution models. Here, we evaluate the ability of two landslide models, both of which are formulated to apply at geomorphic timescales, to generate topographic patterns and sediment flux rates observed in natural landscapes. Episodic debris flow activity is ubiquitous in steep, low-order mountainous catchments and generates valley networks with low concavity. A physically-based model for debris flow incision (Stock and Dietrich, GSA Bull, 2006) proposes that incision rates depend on the frequency, volume, and velocity of debris flows as well as the density of trigger sites and the state of bedrock weathering in low-order valleys. Valley slope angles are predicted to decline with drainage area according to how these properties vary spatially. We calibrated the model for a well-studied small catchment in the Oregon Coast Range using cosmogenic radionuclide erosion rates and then analyzed the slope-area signature of low-order valleys across much of the Central Oregon Coast Range to explore spatial variations in baselevel lowering. This endeavor shows that baselevel lowering rates vary significantly due to patches of resistant bedrock, drainage reorganization, and tectonic forcing. In regions with weak sedimentary bedrock, earthflows can reduce hillslope gradients, promote gullying, and dominate sediment yield through their downslope translation. A one-dimensional, physically-based model for earthflow-prone hillslope evolution (Booth and Roering, JGR, in press) incorporates earthflow, gully, and soil creep transport and predicts that average hillslope gradient increases nonlinearly with erosion rate. We applied the model to interpret catchment adjustment in the wake of a well-characterized knickpoint in the Waipaoa River, New Zealand. The model predicts the spatial pattern of erosion rate in the catchment based on average gradients and can be further tested by characterizing the morphology of individual hillslopes. Landslide models that integrate across multiples events or episodes of landslide activity should be crafted with testable (and thus rejectable) morphologic and sediment flux constraints. Airborne lidar and erosion rates from cosmogenic radionuclides have greatly facilitated this endeavor although additional constraints are needed.

Roering, J. J.; Booth, A. M.; Stock, J. D.

2011-12-01

149

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

Code of Federal Regulations, 2011 CFR

...management criteria for flood-related erosion-prone areas. 60.5 Section 60...management criteria for flood-related erosion-prone areas. The Federal Insurance...management regulations for flood-related erosion-prone areas shall be based....

2011-10-01

150

Medication errors in children.  

PubMed

Medication error is a major source of iatrogenic injuries in children. Dosing errors are the most common type of medication errors in pediatrics. Sicker patients in intensive care units and emergency departments are more often harmed by such errors. Strategies that have been found to be effective in reducing medication errors include the use of computerized physician order entry systems, preprinted order forms, and color-coded systems. Adopting the "systems approach" to medication errors is crucial to every health system where practitioners seek to enhance patient safety. PMID:17126688

Kozer, Eran; Berkovitch, Matitiahu; Koren, Gideon

2006-12-01

151

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...

152

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

Code of Federal Regulations, 2014 CFR

... 1 2014-10-01 2014-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency...SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...

2014-10-01

153

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

Code of Federal Regulations, 2013 CFR

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

2013-10-01

154

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

Code of Federal Regulations, 2011 CFR

... 1 2011-10-01 2011-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency...SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...

2011-10-01

155

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

Code of Federal Regulations, 2012 CFR

... 1 2012-10-01 2011-10-01 true Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency...SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...

2012-10-01

156

Field error lottery  

SciTech Connect

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

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

1990-01-01

157

Comparing Errors in Medicaid Reporting across Surveys: Evidence to Date  

PubMed Central

Objective To synthesize evidence on the accuracy of Medicaid reporting across state and federal surveys. Data Sources All available validation studies. Study Design Compare results from existing research to understand variation in reporting across surveys. Data Collection Methods Synthesize all available studies validating survey reports of Medicaid coverage. Principal Findings Across all surveys, reporting some type of insurance coverage is better than reporting Medicaid specifically. Therefore, estimates of uninsurance are less biased than estimates of specific sources of coverage. The CPS stands out as being particularly inaccurate. Conclusions Measuring health insurance coverage is prone to some level of error, yet survey overstatements of uninsurance are modest in most surveys. Accounting for all forms of bias is complex. Researchers should consider adjusting estimates of Medicaid and uninsurance in surveys prone to high levels of misreporting. PMID:22816493

Call, Kathleen T; Davern, Michael E; Klerman, Jacob A; Lynch, Victoria

2013-01-01

158

Body image, self-esteem, and depression-proneness: Closing the gender gap  

Microsoft Academic Search

Gender differences in body image and related correlates have received increasing attention in recent psychological research. The purposes of the present study were to further examine gender differences in body image and its relationship to depression-proneness and self-esteem. The Body Cathexis Scale, the Depression-Proneness Inventory, the Janis-Field Feelings of Inadequacy Scale, and a background questionnaire were administered to 176 female

Marci McCaulay; Laurie Mintz; Audrey A. Glenn

1988-01-01

159

Short-term effects of prone position in critically ill patients with acute respiratory distress syndrome  

Microsoft Academic Search

.  \\u000a \\u000a Objective: Changing the position from supine to prone is an emerging strategy to improve gas exchange in patients with the acute respiratory\\u000a distress syndrome (ARDS). The aim of this study was to evaluate the acute effects on gas exchange, hemodynamics, and respiratory\\u000a system mechanics of turning critically ill patients with ARDS from supine to prone. Design: Open, prospective study.

L. Blanch; J. Mancebo; M. Perez; M. Martinez; A. Mas; A. J. Betbese; D. Joseph; J. Ballús; U. Lucangelo; E. Bak

1997-01-01

160

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

Microsoft Academic Search

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

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

2010-01-01

161

Prone position increases collapsibility of the passive pharynx in infants and small children.  

PubMed

On the basis of two observations that avoiding prone sleeping decreased incidence of sudden infant death syndrome and that obstructive sleep apnea is closely linked with the syndrome, we hypothesized that the prone position may increase upper airway collapsibility in infants and small children. Passive pharyngeal collapsibility of 19 infants and small children (10-101 weeks old) was examined in three postures: supine with face straight up, supine with neck rotated, and prone with neck rotated. The collapsibility was evaluated with the maximal distension of the most collapsible region, pharyngeal stiffness, and pharyngeal closing pressure, estimated from static pressure-area relationship of the passive pharynx. No significant changes in pharyngeal stiffness were detected; however, maximal distension was reduced in the prone position (mean +/- SD, 0.56 +/- 0.26 versus 0.44 +/- 0.20 cm(2); supine with face straight up versus prone position, p < 0.05). Pharyngeal closing pressure increased at neck rotation in the supine position (-4.5 +/- 2.4 versus -2.8 +/- 2.3 cm H(2)O; supine with face straight up versus supine with neck rotated, p < 0.05), and a further increase was observed in the prone position (-0.3 +/- 2.9 cm H(2)O, p < 0.05 versus supine with neck rotation). Pharyngeal closing pressure in the prone position was above atmospheric pressure in half of our subjects, whereas all subjects had negative pharyngeal pressure in the supine position. We conclude that the prone position increases upper airway collapsibility, although the mechanism is yet unclear. PMID:12204878

Ishikawa, Teruhiko; Isono, Shiroh; Aiba, Junko; Tanaka, Atsuko; Nishino, Takashi

2002-09-01

162

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

PubMed

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

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

163

Shame- and guilt-proneness: relationships with anxiety disorder symptoms in a clinical sample.  

PubMed

Researchers postulate that both shame and guilt are emotions important to anxiety disorders. Extant data, however, indicate that guilt-proneness shares non-significant relationships with psychopathology symptoms after controlling for shame-proneness. To further investigate the relevance of shame and guilt to the anxiety disorders domain, the current study examined associations between shame- and guilt-proneness and anxiety disorder symptoms using data from patients (N=124) with primary anxiety disorder diagnoses. Results indicated that only symptoms of social anxiety disorder (SAD) and generalized anxiety disorder (GAD) shared significant relations with shame-proneness after controlling for other types of anxiety disorder symptoms, depression symptoms, and guilt-proneness. Further, changes in shame-proneness during treatment were found to share significant relations with changes in obsessive-compulsive disorder, SAD, and GAD symptoms. The current results indicate that shame is more relevant to symptoms of the anxiety disorders domain than is guilt. The implications of these results for the conceptualization and treatment of anxiety disorders are discussed. PMID:20591613

Fergus, Thomas A; Valentiner, David P; McGrath, Patrick B; Jencius, Simon

2010-12-01

164

Design and Evaluation of a Stand-Up Motorized Prone Cart  

PubMed Central

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

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

2007-01-01

165

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

PubMed

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

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

2015-04-01

166

Digital FM double errors  

Microsoft Academic Search

This paper evaluates the double-error probability (average probability of two consecutive bit errors) in digital FM for a noncoherent limiter\\/discriminator receiver with either integrate and dump or sample and hold (S&H) bit detection. A remarkably simple relationship is found relating the S&H double-error probability to the optimum coherent CPFSK bit error probability of Osborne and Luntz (1974)

R. F. Pawula

2001-01-01

167

Sources of Model Error  

NSDL National Science Digital Library

This undergraduate meteorology tutorial from Texas A&M University describes the common sources of weather forecasting computer model error, ways to identify model error, and how to correct a forecast for some simple types of error. Model sensitivity to parameterization and topography are covered.

John Nielsen-Gammon

1996-01-01

168

Generic error probabilities  

Microsoft Academic Search

This paper presents new forms for an error probability associated, with the phase angle between two vectors perturbed by Gaussian noise. An interesting consequence of the underlying generic form is a new expression for the symbol error rate in MDPSK that is very similar to its counterpart for MPSK. The generic error probability is further shown to contain as special

R. F. Pawula

1999-01-01

169

Neuroergonomics and human error  

Microsoft Academic Search

Neuroergonomics complements traditional ergonomic approaches to understanding many aspects of human–system performance, including the analysis of human error. This paper reviews the evidence on neural signals associated with different error types, specifically the error-related negativity (ERN), a brain potential that is extracted from the scalp electroencephalogram and that is generated in a medial prefrontal brain region, the anterior cingulate cortex.

John R. Fedota; Raja Parasuraman

2010-01-01

170

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

PubMed

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

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

2014-01-01

171

Calibration of quantitative PCR assays  

Microsoft Academic Search

Quantitative real-time PCR (polymerase chain reaction) assays are increasingly used to measure quantities of nucleic acids\\u000a in samples. They may be used to provide a high-throughput alternative to more traditional biological assays. In this case,\\u000a a calibration process may be required to convert the PCR measurements onto a more relevant scale. This is most commonly undertaken\\u000a using simple linear regression.

A. M. I. Roberts; C. M. Theobald; M. McNeil

2007-01-01

172

Highly Reproducible Absolute Quantification of Mycobacterium tuberculosis Complex by Digital PCR.  

PubMed

Digital PCR (dPCR) offers absolute quantification through the limiting dilution of template nucleic acid molecules and has the potential to offer high reproducibility. However, the robustness of dPCR has yet to be evaluated using complex genomes to compare different dPCR methods and platforms. We used DNA templates from the pathogen Mycobacterium tuberculosis to evaluate the impact of template type, master mixes, primer pairs and, crucially, extraction methods on dPCR performance. Performance was compared between the chip (BioMark) and droplet (QX100) formats. In the absence of any external calibration, dPCR measurements were generally consistent within ?2-fold between different master mixes and primers. Template DNA integrity could influence dPCR performance: high molecular weight gDNA resulted in underperformance of one master mix, while restriction digestion of a low molecular weight sample also caused underestimation. Good concordance (?1.5-fold difference) was observed between chip and droplet formats. Platform precision was in agreement with predicted Poisson error based on partition number, but this was a minor component (<10%) of the total variance when extraction was included. dPCR offers a robust reproducible method for DNA measurement; however, as a predominant source of error, the process of DNA extraction will need to be controlled with suitable calibrators to maximize agreement between laboratories. PMID:25646934

Devonshire, Alison S; Honeyborne, Isobella; Gutteridge, Alice; Whale, Alexandra S; Nixon, Gavin; Wilson, Philip; Jones, Gerwyn; McHugh, Timothy D; Foy, Carole A; Huggett, Jim F

2015-04-01

173

Medical errors in neurosurgery  

PubMed Central

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

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

2014-01-01

174

Droplet-based micro oscillating-flow PCR chip  

NASA Astrophysics Data System (ADS)

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.

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

2005-08-01

175

Sequetyping: Serotyping Streptococcus pneumoniae by a Single PCR Sequencing Strategy  

PubMed Central

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

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

2012-01-01

176

Aircraft system modeling error and control error  

NASA Technical Reports Server (NTRS)

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

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

2012-01-01

177

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

PubMed

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

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

2011-07-01

178

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

PubMed Central

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

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

2011-01-01

179

Software error detection  

NASA Technical Reports Server (NTRS)

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

Buechler, W.; Tucker, A. G.

1981-01-01

180

Error detection method  

DOEpatents

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.).

Olson, Eric J.

2013-06-11

181

Science Shorts: Experimental Error  

NSDL National Science Digital Library

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

Kimberly J. Davis

2008-10-01

182

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

PubMed Central

Expressed emotion (EE) has been associated with poor patient outcomes in many different psychiatric disorders. Given its robust association with relapse, EE has become a major target of family psychoeducational interventions. Most psychoeducational interventions to date have failed to change EE levels among families of those with bipolar disorder. Better intervention strategies, then, may depend on an increased understanding of the predictors of EE. Although EE has traditionally included many facets, criticism appears to be the most robust predictor of outcome within bipolar disorder. The present study tested three primary predictors of criticism among family members of people with bipolar disorder: shame-proneness, guilt-proneness, and depression. Depressive symptoms were significantly associated with EE. Discussion focuses on limitations and implications of the study and suggestions for future research. PMID:19892077

McMurrich, Stephanie L.; Johnson, Sheri L.

2010-01-01

183

Challenge and error: Critical events and attention-related errors  

Microsoft Academic Search

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?attention-lapse: Cheyne, Solman, Carriere, & Smilek, 2009) argues that errors beget errors by generating attention lapses; resource-depleting cognitions interfering with attention to subsequent task challenges. Attention lapses lead to errors, and errors themselves

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

2011-01-01

184

Quantum error control codes  

E-print Network

valid codeword in the codespace [30]. Shor’s demonstrated the first quantum error correcting code [137]. The code encodes one qubit into nine qubits, and is able to correct for one error and detect two errors. Shortly Gottesman[58], Steane[144], and... is the added noise. Then one can use the matrix H to perform error correction and detection capabilities of the code C. s = rHT = (v+e)HT = eHT. (2.7) Based on the value of the syndrome s, one might be able to correct the received codeword r to the original...

Abdelhamid Awad Aly Ahmed, Sala

2008-10-10

185

COP Gage error budget  

SciTech Connect

The error budget for the COP Gage is based in part on similar budgets generated for two earlier LLNL projects: The Large Optics Diamond Turning Machine (Donaldson,1979), and the Dual Transducer Gage (Thompson et al, 1985). As with these previous efforts, we need to start with a set of assumptions relating to the treatment of individual error sources, the combinatorial rules by which individual errors will be incorporated into the overall budget, and those categories of errors which will be included (or excluded) in the formulation of the budget. 3 tabs.

Thompson, D.C.

1988-08-25

186

Error coding simulations  

NASA Technical Reports Server (NTRS)

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.

Noble, Viveca K.

1993-01-01

187

Prospective pilot intervention study to prevent medication errors in drugs administered to children by mouth or gastric tube: a programme for nurses, physicians and parents  

Microsoft Academic Search

BackgroundDrug administration in children is an error-prone task for nurses and parents because individual dose adjustment is often necessary, and suitable formulations for children are frequently lacking. Hence, in the absence of measures for their prevention, medication errors are likely to occur.ObjectiveTo assess the error prevalence in drug administration by mouth or gastric tube before and after implementing a programme

T. Bertsche; A. Bertsche; E. M. Krieg; N. Kunz; K. Bergmann; G. Hanke; T. Hoppe-Tichy; F. Ebinger

2010-01-01

188

Action errors, error management, and learning in organizations.  

PubMed

Every organization is confronted with errors. Most errors are corrected easily, but some may lead to negative consequences. Organizations often focus on error prevention as a single strategy for dealing with errors. Our review suggests that error prevention needs to be supplemented by error management--an approach directed at effectively dealing with errors after they have occurred, with the goal of minimizing negative and maximizing positive error consequences (examples of the latter are learning and innovations). After defining errors and related concepts, we review research on error-related processes affected by error management (error detection, damage control). Empirical evidence on positive effects of error management in individuals and organizations is then discussed, along with emotional, motivational, cognitive, and behavioral pathways of these effects. Learning from errors is central, but like other positive consequences, learning occurs under certain circumstances--one being the development of a mind-set of acceptance of human error. PMID:25251490

Frese, Michael; Keith, Nina

2015-01-01

189

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

PubMed

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

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

2013-01-01

190

The Presence of Neurological Soft Signs Along the Psychosis Proneness Continuum  

PubMed Central

Neurological soft signs have been observed in patients with schizophrenia and their relatives. However, it has not been considered whether the increased rates of neurological soft signs are related to measures of psychosis proneness in the general population. We tested this hypothesis in a group of normal volunteers (n = 28) who scored highly for positive schizotypy when assessed online and a control group (n = 33) who scored below the mean. Compared with the controls, high psychosis-prone individuals showed significantly higher Total and Other Soft Signs subscale scores on the Neurological Evaluation Scale. It appears that soft signs are also associated with psychosis proneness when measured in the general population, which suggests that soft signs are distributed along a continuum of risk for schizophrenia. PMID:16407574

Barkus, Emma; Stirling, John; Hopkins, Richard; Lewis, Shôn

2006-01-01

191

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

PubMed

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

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

2013-04-01

192

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

PubMed

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

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

2010-08-01

193

Protective effect of prone posture against hypergravity-induced arterial hypoxaemia in humans  

PubMed Central

Patients with acute respiratory distress syndrome have increased lung tissue weight and therefore an increased hydrostatic pressure gradient down the lung. Also, they have a better arterial oxygenation in prone (face down) than in supine (face up) posture. We hypothesized that this effect of the direction of gravity also existed in healthy humans, when increased hydrostatic gradients were induced by hypergravity. Ten healthy subjects were studied in a human centrifuge while exposed to 1 or 5 G in anterio-posterior (supine) or posterio-anterior (prone) direction. We measured blood gases using remote-controlled sampling and gas exchange by mass spectrometry. Hypergravity led to marked impairments of arterial oxygenation in both postures and more so in supine posture. At 5 G, the arterial oxygen saturation was 84.6 ± 1.2 % (mean ±s.e.m.) in supine and 89.7 ± 1.4 % in prone posture (P < 0.001 for supine vs. prone). Ventilation and alveolar PO2 were increased at 5 G and did not differ between postures. The alveolar-to-arterial PO2 difference increased at 5 G to 8.0 ± 0.2 kPa and 6.6 ± 0.3 kPa in supine and prone postures (P = 0.003). Arterial oxygenation was less impaired in prone during hypergravity due to a better-preserved alveolo-arterial oxygen transport. We speculate that mammals have developed a cardiopulmonary structure that favours function with the gravitational vector in the posterio-anterior direction. PMID:12598589

Rohdin, M; Petersson, J; Mure, M; Glenny, R W; Lindahl, S G E; Linnarsson, D

2003-01-01

194

Experimental investigation of observation error in anuran call surveys  

USGS Publications Warehouse

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

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

2010-01-01

195

The importance of robust error control in data compression applications  

NASA Technical Reports Server (NTRS)

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

Woolley, S. I.

1993-01-01

196

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

USGS Publications Warehouse

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.

Meyer, Robert W.; Bowers, James C.

2002-01-01

197

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

PubMed Central

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.

Bunker, Daniel Lee John; Thomson, Michael

2015-01-01

198

Refractive error blindness.  

PubMed Central

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

Dandona, R.; Dandona, L.

2001-01-01

199

Facts about Refractive Errors  

MedlinePLUS

... errors occur when the shape of the eye prevents light from focusing directly on the retina. The length of the eyeball (longer or shorter), changes in the shape of the cornea, or aging of the lens can cause refractive errors. What ...

200

Neurocryptococcosis: diagnosis by PCR method  

Microsoft Academic Search

Cryptococcus neoformans detection was optimized using PCR technique with the objective of application in the clinical laboratory diagnosis. The amplification area was ITS and 5,6S which encodes the ribosomal RNA (rRNA). A total of 72 cerebrospinal fluid (CSF) samples were used, obtained from cases with and without AIDS. The patients had cryptococcal meningitis (n = 56) and meningitis caused by

Regina Célia Paschoal; Mário Hiroyuki Hirata; Rosário Crespo Hirata; Márcia de Souza Carvalho Melhem; Amanda Latercia Tranches Dias; Claudete Rodrigues Paula

2004-01-01

201

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

202

Uncorrected refractive errors.  

PubMed

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

Naidoo, Kovin S; Jaggernath, Jyoti

2012-01-01

203

TOPO-cloning of PCR products 1. Perform PCR  

E-print Network

with Taq), allow reaction to sit at room temperature (RT) or at 4°C overnight, then add Taq and incubate the following into an eppi tube: 2 µL PCR 1 µL TOPO salt solution 0.25 µL TOPO vector 2.75 µL sterile water 3/white screening) on ice during this incubation step 4. Chill TOPO ligation reaction on ice for 5 min 5. Transform

Odorizzi, Greg

204

Error Prevention Aid  

NASA Technical Reports Server (NTRS)

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

1987-01-01

205

Surprise beyond prediction error.  

PubMed

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

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

2014-09-01

206

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

ERIC Educational Resources Information Center

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…

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

2012-01-01

207

Differentiating fall-prone and healthy adults using local dynamic stability  

PubMed Central

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

Lockhart, Thurmon E.; Liu, Jian

2010-01-01

208

Intra-patient Prone to Supine Colon Registration for Synchronized Virtual Colonoscopy  

Microsoft Academic Search

In this paper, we present an automated method for colon reg- istration. The method uses dynamic programming to align data defined on colon center-line paths, as extracted from the prone and supine scans. This data may include information such as path length and curvature as well as descriptors of the shape and size of the colon near the path. We

Delphine Nain; Steven Haker; W. Eric L. Grimson; Eric R. Cosman Jr.; William M. Wells III; Hoon Ji; Ron Kikinis; Carl-fredrik Westin

2002-01-01

209

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...

210

Premorbid proneness to distress and episodic memory impairment in Alzheimer's disease  

PubMed Central

Background: Chronic stress has been associated with impaired episodic memory, but the association of premorbidly experienced distress with memory function in Alzheimer's disease is unknown. Objective: To investigate the link between proneness to distress and Alzheimer's disease. Methods: Participants were 363 persons with clinically diagnosed Alzheimer's disease. At baseline, a knowledgeable informant rated each person's premorbid personality (that is, before dementia onset) along five dimensions, one of which was the tendency to experience psychological distress. Participants underwent structured clinical evaluations at baseline and then annually for up to four years. Each evaluation included 17 cognitive tests from which previously established measures of episodic memory, visuoconstruction, repetition, and naming were derived. Results: In a series of random effects models adjusted for age, sex, and education, premorbid distress proneness was associated with baseline impairment in episodic memory but not with impairment in other cognitive domains, or with change in any cognitive domain. No other trait was related to baseline function or rate of decline in any cognitive domain. Conclusions: The results suggest that premorbid proneness to experience psychological distress is related to level of impairment in episodic memory in persons with Alzheimer's disease, but neither distress proneness nor other personality traits are related to disease progression. PMID:14742585

Wilson, R; Fleischman, D; Myers, R; Bennett, D; Bienias, J; Gilley, D; Evans, D

2004-01-01

211

Prone Positioning Improves Pulmonary Function in Obese Patients During General Anesthesia  

Microsoft Academic Search

We investigated the effects of prone position on func- tional residual capacity (FRC), the mechanical proper- ties (compliance and resistance) of the total respiratory system, lung and chest wall, and the gas exchange in 10 anesthetized and paralyzed obese (body mass index more than 30 kg\\/m*) patients, undergoing elective sur- gery. We used the esophageal balloon technique to- gether with

Paolo Pelosi; Massimo Croci; Emiliana Calappi; Davide Mulazzi; Marco Cerisara; Paola Vercesi; Pierluigi Vicardi; Luciano Gattinoni

1996-01-01

212

Costs and benefits of fruiting to future reproduction in two dormancy-prone orchids  

Microsoft Academic Search

Summary 1 Reproduction is expected to occur at a cost to survival, growth or future reproduction. However, trade-offs in long-lived, clonal herbs have proven difficult to assess, particularly when they are prone to adult dormancy. 2 We assessed the costs of fruiting in a study of two species of lady's slipper orchid, Cypripedium candidum and C. parviflorum , growing sympatrically

RICHARD P. SHEFFERSON; ELLEN L. SIMMS

2007-01-01

213

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

ERIC Educational Resources Information Center

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

McConochie, William A.

214

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

Microsoft Academic Search

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

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

2009-01-01

215

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

Microsoft Academic Search

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

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

2010-01-01

216

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

USGS Publications Warehouse

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

Lamke, Robert D.; Jones, Stanley H.

1980-01-01

217

S 35171 exerts protective effects in spontaneously hypertensive stroke-prone rats by preserving mitochondrial function  

Microsoft Academic Search

S 35171 is one of a family of compounds that have been designed to protect mitochondrial function. We tested the hypothesis that S 35171 exerts protective effects in spontaneously hypertensive stroke-prone rats (SHRSPs), an animal model developing spontaneous brain damage preceded by proteinuria and systemic inflammation revealed by the urinary accumulation of acute-phase proteins (APPs) originating in the liver. Male

Paolo Gelosa; Cristina Banfi; Maura Brioschi; Elena Nobili; Anita Gianella; Uliano Guerrini; Alice Pignieri; Elena Tremoli; Luigi Sironi

2009-01-01

218

Personality traits and the process of store loyalty in a transactional prone context  

Microsoft Academic Search

Purpose – This study sets out to replicate Garbarino and Johnson's paper, where the effects of trust, commitment and satisfaction towards service provider loyalty were examined. However, whereby Garbarino and Johnson tested their model in a relationship prone environment, i.e. a theatre company, this study was set in a retail context where transactional customers are more likely. Personality traits as

Liliana Bove; Betty Mitzifiris

2007-01-01

219

Binge Eating Proneness Emerges During Puberty in Female Rats: A Longitudinal Study  

E-print Network

Binge Eating Proneness Emerges During Puberty in Female Rats: A Longitudinal Study Kelly L. Klump Puberty is a critical risk period for binge eating and eating disorders characterized by binge eating eating during puberty in a rat model. We predicted that there would be minimal differences in binge

Sisk, Cheryl

220

The effects of ovariectomy on binge eating proneness in adult female rats Kelly L. Klump a,  

E-print Network

The effects of ovariectomy on binge eating proneness in adult female rats Kelly L. Klump a: Binge eating Bulimia nervosa Ovariectomy Animal models Ovarian hormones Ovarian hormones are associated with binge eating in women, however findings are limited by the lack of experimental control inherent

Sisk, Cheryl

221

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

ERIC Educational Resources Information Center

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…

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

2007-01-01

222

Direct seeding and transplanting for rice production under flood-prone lowland conditions  

Microsoft Academic Search

Rice productivity in flood-prone lowlands of South and Southeast Asia is low and highly variable. Ensuring good crop stands through optimal combinations of agronomic practices is important for improving yields. Present studies investigated the effect of various stand establishment practices, including vegetative propagation, under naturally flooded conditions (0–60 cm water depth) during 1992 and 1993 at Cuttack, India. Two popular

A. R. Sharma

1995-01-01

223

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

PubMed

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

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

2011-01-01

224

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

SciTech Connect

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

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

2010-05-01

225

Perceived threat mediates the relationship between psychosis proneness and aggressive behavior  

PubMed Central

Psychotic symptoms are associated with aggressive tendencies, but this relationship is both complex and imperfect. In contrast to psychotic disorders, little is known about aggressive behavior and sub-clinical psychotic symptoms (e.g., “psychosis proneness”), which are relatively common in the general population. Threat/control-override (TCO), which is the propensity to overestimate the likelihood that an outside agent will (1) inflict harm (threat) or (2) control one’s behaviors (control-override), has been associated with aggression in both psychiatric and community samples. The purpose of this study was to determine if psychosis proneness is related to aggression, and if one or both aspects of TCO mediate this relationship. We hypothesized that the propensity to overestimate threat would mediate this relationship, but control-override would not. Sixty men and sixty women (mean age = 20.00 years, sd = 3.00) with no history of psychotic disorder completed measures assessing psychosis proneness, threat control/override, aggressive history, aggressive ideation, and aggressive behavior. Three structural equation models were tested: (1) Threat and control-override modeled as separate mediating variables, (2) TCO as a unitary mediating latent construct, and (3) TCO considered as part of a psychosis-proneness latent variable. Results indicated that psychosis proneness is positively related to aggression and that the best model fit was obtained when threat and control-override were modeled as separate variables, with mediation through threat alone. The utility of TCO for explaining the relation between psychosis spectrum symptoms and aggression is discussed. PMID:20965573

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

2010-01-01

226

Enhanced Named Entity Extraction via Error-Driven Aggregation  

SciTech Connect

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.

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

2010-02-22

227

Measurement Error Webinar Series  

Cancer.gov

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

228

Estimating Bias Error Distributions  

NASA Technical Reports Server (NTRS)

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

Liu, Tian-Shu; Finley, Tom D.

2001-01-01

229

Errors in prenatal diagnosis.  

PubMed

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

Anumba, Dilly O C

2013-08-01

230

PCR for Diagnosis of Paracoccidioidomycosis  

Microsoft Academic Search

A PCR assay based on oligonucleotide primers derived from the sequence of the gene coding for the 43,000-Da (gp43) antigen was developed to detect Paracoccidioides brasiliensis DNA in sputa. In the standard- ized conditions, it could detect 10 cells\\/ml of sputum, providing sufficient accuracy to be useful for diagnosis of paracoccidioidomycosis. Paracoccidioides brasiliensis, a thermodimorphic fungus, is the causative agent

GLAUCE M. GOMES; PATRICIA S. CISALPINO; CARLOS P. TABORDA; ZOILO P. DE CAMARGO

2000-01-01

231

Error threshold of topological color codes and random three-dimensional color gauge models  

Microsoft Academic Search

Sensitivity to noise makes most of the current quantum computing schemes prone to error and non-scalable. Topologically-protected quantum computing solves this problem and prevents decoherence effects at the hardware level by encoding quantum states and gates in topological properties of the hardware medium. Recently, a braid-less implementation using brane-net condensates in 3-colexes has been proposed that allows for the implementation

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

2010-01-01

232

Speech Errors across the Lifespan  

ERIC Educational Resources Information Center

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

Vousden, Janet I.; Maylor, Elizabeth A.

2006-01-01

233

Prone positioning decreases episodes of hypoxemia in extremely low birth weight infants (1000 grams or less) with chronic lung disease  

Microsoft Academic Search

Extremely low birth weight infants with chronic lung disease (CLD) have frequent episodes of desaturation (hypoxemia). We quantified oxygenation and episodes of hypoxemia in 55 infants (birth weight ?1000 gm) with CLD in the supine versus prone position, for 1-hour time intervals. Oxygen saturation was measured with the Nellcor N-200 pulse oximeter and a computer program. Prone positioning increased oxygen

Cindy McEvoy; Maria Elena Mendoza; Susan Bowling; Valerie Hewlett; Smeeta Sardesai; Manuel Durand

1997-01-01

234

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...

235

Real-time PCR in virology  

Microsoft Academic Search

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

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

2002-01-01

236

Error monitoring in musicians  

PubMed Central

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

Maidhof, Clemens

2013-01-01

237

GPS Satellite Multipath Range Errors  

NASA Technical Reports Server (NTRS)

Report discusses errors in range measurements in GPS system due to multipath transmissions originating at satellites. Large uncertainties in sizes of multipath errors limit precision of GPS measurements. Experiments proposed to determine systematic multipath errors under various operating conditions.

Young, Lawrence E.

1988-01-01

238

Smoothing error pitfalls  

NASA Astrophysics Data System (ADS)

The difference due to the content of a priori information between a constrained retrieval and the true atmospheric state is usually represented by 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.

von Clarmann, T.

2014-09-01

239

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

E-print Network

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

240

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

ERIC Educational Resources Information Center

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

Thornton, Brenda; Basu, Chhandak

2011-01-01

241

Subseasonal GNSS positioning errors  

NASA Astrophysics Data System (ADS)

Navigation Satellite System (GNSS) station coordinate errors over seasonal and longer time scales are known to be spatially and temporally correlated with flicker noise spectra. Overlaying this are strong annual and semiannual variations that cannot be explained by any single phenomenon. Next most prominent are harmonics of the GPS draconitic year with periods of (351.4/N) days. One explanation is that errors in the standard model for Earth orientation parameter (EOP) tidal variations near 12 and 24 h periods are absorbed into the resonant GPS orbit and daily EOP estimates, resulting mainly in draconitic and fortnightly alias signatures for 24 h product sampling. With the change in International GNSS Service (IGS) station coordinates from weekly to daily resolution in August 2012, it is now possible to study subseasonal performance. All IGS Analysis Centers (ACs) show fortnightly signals, but the resolution will not be sufficient to distinguish direct from aliased subdaily tidal error sources till two more years of data are available. Nevertheless, aliased errors from the subdaily EOP tide model are expected. All but one of the ACs that includes GLONASS data have signals at ~8 day periods, the ground repeat period for GLONASS orbits. This most likely arises from larger geographically correlated orbit errors for GLONASS. Two ACs possess unique short-period features that appear to be caused by peculiarities of their analysis strategies.

Ray, J.; Griffiths, J.; Collilieux, X.; Rebischung, P.

2013-11-01

242

Compact disk error measurements  

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

243

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

PubMed

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

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

2014-07-01

244

Experimental Quantum Error Detection  

PubMed Central

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

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

2012-01-01

245

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

NASA Technical Reports Server (NTRS)

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.

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

1975-01-01

246

Challenge and Error: Critical Events and Attention-Related Errors  

ERIC Educational Resources Information Center

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…

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

2011-01-01

247

Phenotypic expression of the systemic toxicity of cocaine in genetically epilepsy-prone rats  

Microsoft Academic Search

The purpose of the present investigation was to determine whether the sensitivity to systemic toxic effects of cocaine is altered in genetically epilepsy-prone rats (GEPRs). Moderate seizure (GEPR-3) and severe seizure (GEPR-9) rats, and the control strain, Sprague-Dawley rats, 10 weeks of age, were lightly anesthetized with halothane and nitrous oxide. Following surgical preparation and stabilization, the animals were given

Bing Shi; James E. Heavner; Charles E. Reigel; Y. James Kao; Alan D. Kaye

2000-01-01

248

Functional solubilization of aggregation-prone TRAIL protein facilitated by coexpressing with protein isoaspartate methyltranferase  

Microsoft Academic Search

TRAIL was a tumor-specific protein in development as a novel anticancer therapeutic agent. Generally, when expressed in recombinant Escherichia\\u000a coli, TRAIL protein was prone to form inclusion bodies. In this study, coexpression of human TRAIL protein and protein isoaspartate methyltranferase (PIMT) from E. coli on plasmid pBV–TRAIL–PCM in E. coli C600 was investigated to overcome the difficulties in soluble expression.

Hu Zhu; Ruo-Jun Pan; Tian-Wen Wang; Ya-Ling Shen; Dong-Zhi Wei

2006-01-01

249

A Genetic Algorithm to Configure Support Vector Machines for Predicting Fault-Prone Components  

Microsoft Academic Search

\\u000a In some studies, Support Vector Machines (SVMs) have been turned out to be promising for predicting fault-prone software components.\\u000a Nevertheless, the performance of the method depends on the setting of some parameters. To address this issue, we propose the\\u000a use of a Genetic Algorithm (GA) to search for a suitable configuration of SVMs parameters that allows us to obtain optimal

Sergio Di Martino; Filomena Ferrucci; Carmine Gravino; Federica Sarro

250

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

Microsoft Academic Search

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

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

1999-01-01

251

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

SciTech Connect

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.

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

2007-05-01

252

Vascular protective effects of selective sodium transport inhibition in stroke-prone hypertensive rats  

Microsoft Academic Search

We previously reported that mineralocorticoid receptor antagonists and amiloride markedly reduced proteinuria and vascular injury in saline-drinking stroke-prone spontaneously hypertensive rats (SHRSP). By inhibiting epithelial sodium channels (ENaC) and sodium-hydrogen exchange (NHE), these agents interfere with sodium transport in the kidney and at extrarenal sites. Presently, we examined whether benzamil (BENZ), an ENaC inhibitor with little NHE inhibitory activity, and

Reza Sepehrdad; Praveen N. Chander; Gagan Singh; Charles T. Stier

2002-01-01

253

Tamm-Horsfall protein knockout mice are more prone to urinary tract infection Rapid Communication  

Microsoft Academic Search

Tamm-Horsfall protein knockout mice are more prone to urinary tract infection.BackgroundHuman colon contains many bacteria that commonly colonize the perineum and frequently enter the urinary tract. Uropathogenic Escherichia coli are the most common cause of urinary tract infection. Type 1 fimbriated E. coli have been associated with cystitis, and P fimbriated E. coli with pyelonephritis. Factors involved in clearing bacteria

James M. Bates; HAJA MOHIDEEN RAFFI; KRISHNA PRASADAN; RANJAN MASCARENHAS; ZOLTAN LASZIK; NOBUYO MAEDA; Scott J. Hultgren; SATISH KUMAR

2004-01-01

254

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

SciTech Connect

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

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

2010-06-01

255

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

Microsoft Academic Search

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

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

2010-01-01

256

Effects of the Prone Position on Respiratory Mechanics and Gas Exchange during Acute Lung Injury  

Microsoft Academic Search

We studied 16 patients with acute lung injury receiving volume-controlled ventilation to assess the relationships between gas exchange and respiratory mechanics before, during, and after 2 h in the prone position. We measured the end-expiratory lung volume (EELV, helium dilution), the total respi- ratory system (Cst,rs), the lung (Cst,L) and the thoracoabdominal cage (Cst,w) compliances (end- inspiratory occlusion technique and

PAOLO PELOSI; DANIELA TUBIOLO; DANIELE MASCHERONI; PIERLUIGI VICARDI; STEFANIA CROTTI; FRANCO VALENZA; LUCIANO GATTINONI

1998-01-01

257

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

Microsoft Academic Search

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

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

2007-01-01

258

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

PubMed Central

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

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

2012-01-01

259

Intrinsically Disordered and Aggregation Prone Regions Underlie ?-Aggregation in S100 Proteins  

PubMed Central

S100 proteins are small dimeric calcium-binding proteins which control cell cycle, growth and differentiation via interactions with different target proteins. Intrinsic disorder is a hallmark among many signaling proteins and S100 proteins have been proposed to contain disorder-prone regions. Interestingly, some S100 proteins also form amyloids: S100A8/A9 forms fibrils in prostatic inclusions and S100A6 fibrillates in vitro and seeds SOD1 aggregation. Here we report a study designed to investigate whether ?-aggregation is a feature extensive to more members of S100 family. In silico analysis of seven human S100 proteins revealed a direct correlation between aggregation and intrinsic disorder propensity scores, suggesting a relationship between these two independent properties. Averaged position-specific analysis and structural mapping showed that disorder-prone segments are contiguous to aggregation-prone regions and that whereas disorder is prominent on the hinge and target protein-interaction regions, segments with high aggregation propensity are found in ordered regions within the dimer interface. Acidic conditions likely destabilize the seven S100 studied by decreasing the shielding of aggregation-prone regions afforded by the quaternary structure. In agreement with the in silico analysis, hydrophobic moieties become accessible as indicated by strong ANS fluorescence. ATR-FTIR spectra support a structural inter-conversion from ?-helices to intermolecular ?-sheets, and prompt ThT-binding takes place with no noticeable lag phase. Dot blot analysis using amyloid conformational antibodies denotes a high diversity of conformers; subsequent analysis by TEM shows fibrils as dominant species. Altogether, our data suggests that ?-aggregation and disorder-propensity are related properties in S100 proteins, and that the onset of aggregation is likely triggered by loss of protective tertiary and quaternary interactions. PMID:24098542

Carvalho, Sofia B.; Botelho, Hugo M.; Leal, Sónia S.; Cardoso, Isabel; Fritz, Günter; Gomes, Cláudio M.

2013-01-01

260

Lupus-Prone Mice Fail to Raise Antigen-Specific T Cell Responses to Intracellular Infection  

PubMed Central

Systemic lupus erythematosus (SLE) is characterized by multiple cellular abnormalities culminating in the production of autoantibodies and immune complexes, resulting in tissue inflammation and organ damage. Besides active disease, the main cause of morbidity and mortality in SLE patients is infections, including those from opportunistic pathogens. To understand the failure of the immune system to fend off infections in systemic autoimmunity, we infected the lupus-prone murine strains B6.lpr and BXSB with the intracellular parasite Toxoplasma gondii and survival was monitored. Furthermore, mice were sacrificed days post infection and parasite burden and cellular immune responses such as cytokine production and cell activation were assessed. Mice from both strains succumbed to infection acutely and we observed greater susceptibility to infection in older mice. Increased parasite burden and a defective antigen-specific IFN-gamma response were observed in the lupus-prone mice. Furthermore, T cell:dendritic cell co-cultures established the presence of an intrinsic T cell defect responsible for the decreased antigen-specific response. An antigen-specific defect in IFN- gamma production prevents lupus-prone mice from clearing infection effectively. This study reveals the first cellular insight into the origin of increased susceptibility to infections in SLE disease and may guide therapeutic approaches. PMID:25360768

Lieberman, Linda A.; Tsokos, George C.

2014-01-01

261

Changes in cardiac index and blood pressure on positioning children prone for scoliosis surgery.  

PubMed

In this prospective observational study we investigated the changes in cardiac index and mean arterial pressure in children when positioned prone for scoliosis correction surgery. Thirty children (ASA 1-2, aged 13-18 years) undergoing primary, idiopathic scoliosis repair were recruited. The cardiac index and mean arterial blood pressure (median (IQR [range])) were 2.7 (2.3-3.1 [1.4-3.7]) l.min(-1).m(-2) and 73 (66-80 [54-91]) mmHg, respectively, at baseline; 2.9 (2.5-3.2 [1.7-4.4]) l.min(-1).m(-2) and 73 (63-81 [51-96]) mmHg following a 5-ml.kg(-1) fluid bolus; and 2.5 (2.2-2.7 [1.4-4.8]) l.min(-1).m(-2) and 69 (62-73 [46-85]) mmHg immediately after turning prone. Turning prone resulted in a median reduction in cardiac index of 0.5 l.min(-1).m(-2) (95% CI 0.3-0.7 l.min(-1).m(-2), p=0.001), or 18.5%, with a large degree of inter-subject variability (+10.3% to -40.9%). The changes in mean arterial blood pressure were not significant. Strategies to predict, prevent and treat decreases in cardiac index need to be developed. PMID:23710730

Brown, Z E; Görges, M; Cooke, E; Malherbe, S; Dumont, G A; Ansermino, J M

2013-07-01

262

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

PubMed Central

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

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

2014-01-01

263

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

PubMed

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

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

2014-09-01

264

Real-time PCR in Food Science: PCR Diagnostics.  

PubMed

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

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

2013-03-19

265

Directed Evolution of Cyanide Degrading Enzymes  

E-print Network

recombination to create recombinant libraries incorporating the products of PCR amplification. This method is useful for generating large pools of randomly mutagenized clones after error-prone PCR mutagenesis. Several parameters were investigated to optimize...

Abou Nader, Mary 1983-

2012-11-12

266

Neural Correlates of Reach Errors  

PubMed Central

Reach errors may be broadly classified into errors arising from unpredictable changes in target location, called target errors, and errors arising from miscalibration of internal models, called execution errors. Execution errors may be caused by miscalibration of dynamics (e.g.. when a force field alters limb dynamics) or by miscalibration of kinematics (e.g., when prisms alter visual feedback). While all types of errors lead to similar online corrections, we found that the motor system showed strong trial-by-trial adaptation in response to random execution errors but not in response to random target errors. We used fMRI and a compatible robot to study brain regions involved in processing each kind of error. Both kinematic and dynamic execution errors activated regions along the central and the post-central sulci and in lobules V, VI, and VIII of the cerebellum, making these areas possible sites of plastic changes in internal models for reaching. Only activity related to kinematic errors extended into parietal area 5. These results are inconsistent with the idea that kinematics and dynamics of reaching are computed in separate neural entities. In contrast, only target errors caused increased activity in the striatum and the posterior superior parietal lobule. The cerebellum and motor cortex were as strongly activated as with execution errors. These findings indicate a neural and behavioral dissociation between errors that lead to switching of behavioral goals, and errors that lead to adaptation of internal models of limb dynamics and kinematics. PMID:16251440

Hashambhoy, Yasmin; Rane, Tushar; Shadmehr, Reza

2005-01-01

267

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

PubMed Central

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

2013-01-01

268

IPTV multicast with peer-assisted lossy error control  

NASA Astrophysics Data System (ADS)

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

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

2010-07-01

269

Error threshold for topological color codes on Union Jack lattices  

NASA Astrophysics Data System (ADS)

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.

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

2010-03-01

270

Is homologous recombination really an error-free process?  

PubMed Central

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

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

2014-01-01

271

Ambiguity and workarounds as contributors to medical error.  

PubMed

Why are some organizations error-prone-regularly subject to interruptions and inconveniences, some of which periodically coalesce catastrophically-whereas other organizations, although similar in the products and services they generate and the process technologies they use, are reliable, adaptable, and continuously self-improving, relentlessly learning from experience to get ever better? Analyzing medical error reports and studies of high-performing, non-health care organizations reveals 2 differences. High performers know how to prevent problems from producing further consequences once they occur and how to prevent their recurrence. They do this by specifying how work is expected to proceed-who will do what for whom, with what purpose, when, where, and how-before work is actually done. Then, when anything contrary to expectations occurs, it is immediately identified as a problem. Through this approach, the effects of problems are contained, the causes are quickly investigated, process knowledge is deepened, and recurrence is prevented. In contrast, error-prone organizations tolerate ambiguity, a prevailing lack of clarity over what is supposed to happen at any given time. Problems are thus hard to identify, and, even when recognized, they are worked around. People "get the job done," but don't initiate efforts to learn from the problem or improve the process. We believe that coupling high degrees of specification with rapid responses to individual problems can improve health care. Superlative manufacturing, service, and military organizations apply this approach to myriad processes and situations, and initial health care trials of this approach have been promising. We discuss how such an approach could be initiated in health care more broadly. PMID:15838069

Spear, Steven J; Schmidhofer, Mark

2005-04-19

272

Human Error In Complex Systems  

NASA Technical Reports Server (NTRS)

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.

Morris, Nancy M.; Rouse, William B.

1991-01-01

273

PCR markers distinguish Plantago major subspecies  

Microsoft Academic Search

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

K. Wolff; M. Morgan-Richards

1998-01-01

274

The polymerase chain reaction (PCR): general methods.  

PubMed

The polymerase chain reaction (PCR) converts very low quantities of DNA into very high quantities and is the foundation of many specialized techniques of molecular biology. PCR utilizes components of the cellular machinery of mitotic cell division in vitro which respond predictably to user inputs. This chapter introduces the principles of PCR and discusses practical considerations from target sequence definition through to optimization and application. PMID:24243196

Waters, Daniel L E; Shapter, Frances M

2014-01-01

275

Inborn errors of metabolism.  

PubMed

Inborn errors of metabolism often cause neurological dysfunction. These disorders are most common in childhood, but adult-onset forms with a different clinical presentation are encountered, examples being Pompe disease, Tay-Sachs disease, metachromatic leukodystrophy, Gaucher disease, and Maroteaux-Lamy disease. In the evaluation of a patient with a possible inborn error of metabolism, simple screening tests may aid in the diagnosis and provide direction for more comprehensive laboratory analysis. In most cases, diagnosis can be established without a brain biopsy through biochemical and ultrastructural analysis of peripheral tissues, blood, and urine. New clinical, genetic, and biochemical variants of inherited metabolic disorders are being recognized through wider application of screening tests, improved specificity of laboratory analysis, cell complementation experiments, and the identification of enzyme activator factors. Accurate diagnosis is important for medical management, determining prognosis, and genetic counseling. PMID:6807191

Kolodny, E H; Cable, W J

1982-03-01

276

Modular error embedding  

DOEpatents

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

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

1999-01-01

277

Modular error embedding  

SciTech Connect

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

Sandford, M.T. II; Handel, T.G.; Ettinger, J.M.

1999-10-19

278

77 FR 41881 - Safety Advisory 2012-03; Buckling-Prone Conditions in Continuous Welded Rail Track  

Federal Register 2010, 2011, 2012, 2013, 2014

...Safety Advisory 2012-03; Buckling-Prone Conditions in Continuous Welded Rail Track AGENCY: Federal Railroad Administration...their employees of the importance of complying with their continuous welded rail (CWR) plan procedures and reviewing their...

2012-07-16

279

The effects of angry and happy expressions on recognition memory for unfamiliar faces in delusion-prone individuals.  

PubMed

Numerous studies suggest a cognitive bias for threat-related material in delusional ideation. However, few studies have examined this bias using a memory task. We investigated the influence of delusion-proneness on identity and expression memory for angry and happy faces. Participants high and low in delusion-proneness were presented with happy and angry faces and were later asked to recognise the same faces displaying a neutral expression. They also had to remember what the initial expressions of the faces had been. Remember/know/guess judgments were asked for both identity and expression memory. Results showed that delusion-prone participants better recognised the identity of angry faces compared to non-delusional participants. Also, this difference between the two groups was mainly due to a greater number of remember responses in delusion-prone participants. These findings extend previous studies by showing that delusions are associated with a memory bias for threat-related stimuli. PMID:16406219

Larøi, Frank; D'Argembeau, Arnaud; Van der Linden, Martial

2006-12-01

280

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

Code of Federal Regulations, 2012 CFR

... 1 2012-10-01 2011-10-01 true Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section...SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...

2012-10-01

281

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

Code of Federal Regulations, 2014 CFR

... 1 2014-10-01 2014-10-01 false Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section...SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...

2014-10-01

282

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

Code of Federal Regulations, 2013 CFR

... 1 2013-10-01 2013-10-01 false Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section...SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND...

2013-10-01

283

Medication errors: immunisation.  

PubMed

Case histories are based on actual medical negligence claims or medicolegal referrals, however certain facts have been omitted or changed by the author to ensure the anonymity of the parties involved. This article outlines a medication error involving childhood immunisation and examines the underlying causes of the incident. Advice about how to deal with a patient and their family when things go wrong is provided. PMID:16969448

Bird, Sara

2006-09-01

284

Error-correction coding  

NASA Technical Reports Server (NTRS)

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.

Hinds, Erold W. (Principal Investigator)

1996-01-01

285

Real-time PCR in microfluidic devices  

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

286

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets  

PubMed Central

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 V3–V5 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

Pinto, Ameet J.; Raskin, Lutgarde

2012-01-01

287

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

Microsoft Academic Search

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

CATHERINE J. FIELD

288

Axillary lymph node dose with tangential whole breast radiation in the prone versus supine position: a dosimetric study  

PubMed Central

Background Prone breast positioning reduces skin reaction and heart and lung dose, but may also reduce radiation dose to axillary lymph nodes (ALNs). Methods Women with early stage breast cancer treated with whole breast irradiation (WBI) in the prone position were identified. Patients treated in the supine position were matched for treating physician, laterality, and fractionation. Ipsilateral breast, tumor bed, and Level I, II, and III ALNs were contoured according to the RTOG breast atlas. Clips marking surgically removed sentinel lymph nodes (SLN)s were contoured. Treatment plans developed for each patient were retrospectively analyzed. V90% and V95% was calculated for each axillary level. When present, dose to axillary surgical clips was calculated. Results Treatment plans for 46 women (23 prone and 23 supine) were reviewed. The mean V90% and V95% of ALN Level I was significantly lower for patients treated in the prone position (21% and 14%, respectively) than in the supine position (50% and 37%, respectively) (p?prone position (p?prone position. Conclusions Standard tangential breast irradiation in the prone position results in substantially reduced dose to the Level I axilla as compared with treatment in the supine position. For women in whom axillary coverage is indicated such as those with positive sentinel lymph node biopsy who do not undergo completion axillary dissection, treatment in the prone position may be inappropriate. PMID:22607612

2012-01-01

289

Depression is an Early Disease Manifestation in Lupus-Prone MRL/lpr Mice  

PubMed Central

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

Gao, Hua-Xin; Campbell, Sean R.; Cui, Min-Hui; Zong, Pu; Hwang, Jong hee; Gulinello, Maria; Putterman, Chaim

2009-01-01

290

Drying of internal-check prone poplar lumber using three different conventional kiln drying schedules  

Microsoft Academic Search

In order to efficiently dry the internal check-prone poplar (Populus nigra) lumber, the 50 mm-thick lumber, freshly cut from Taleghan forest in Iran were dried using three different conventional kiln\\u000a drying schedules (T8-F4, T8-F5 and T9-F4). The initial dry-bulb temperatures for the schedules were adjusted at 54, 54 and\\u000a 60°C, while the final dry-bulb temperatures were 82, 82 and 71°C, respectively.

Soharb Rahimi; Mehdi Faezipour; Asghar Tarmian

291

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

PubMed Central

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

Froggatt, P.

1970-01-01

292

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

PubMed Central

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

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

2010-01-01

293

Linear-After-The-Exponential (LATE)PCR: An advanced method of asymmetric PCR and its  

E-print Network

Linear-After-The-Exponential (LATE)­PCR: An advanced method of asymmetric PCR and its uses August 26, 2003) Conventional asymmetric PCR is inefficient and difficult to optimize because limiting the concentration of one primer lowers its melting temperature below the reaction annealing temperature. Linear

Wangh, Lawrence J.

294

Modeling PCR in Natural Convection Systems  

Microsoft Academic Search

Polymerase chain reaction (PCR) is a biochemical protocol for making many copies of a DNA template by thermal cycling between a hot temperature (where the strands are separated) and a cool temperature (where primers are annealed). In natural convection PCR, the requisite thermal cycling is provided by a buoyancy-driven circulating flow of the carrying buffer between a lower hot plate

Kevin Dorfman; Ehud Yariv; Guy Ben Dov

2007-01-01

295

Testing for Genetically Modified Foods Using PCR  

ERIC Educational Resources Information Center

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…

Taylor, Ann; Sajan, Samin

2005-01-01

296

Skylab water balance error analysis  

NASA Technical Reports Server (NTRS)

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

Leonard, J. I.

1977-01-01

297

Error and Error Mitigation in Low-Coverage Genome Assemblies  

PubMed Central

The recent release of twenty-two new genome sequences has dramatically increased the data available for mammalian comparative genomics, but twenty of these new sequences are currently limited to ?2× coverage. Here we examine the extent of sequencing error in these 2× assemblies, and its potential impact in downstream analyses. By comparing 2× assemblies with high-quality sequences from the ENCODE regions, we estimate the rate of sequencing error to be 1–4 errors per kilobase. While this error rate is fairly modest, sequencing error can still have surprising effects. For example, an apparent lineage-specific insertion in a coding region is more likely to reflect sequencing error than a true biological event, and the length distribution of coding indels is strongly distorted by error. We find that most errors are contributed by a small fraction of bases with low quality scores, in particular, by the ends of reads in regions of single-read coverage in the assembly. We explore several approaches for automatic sequencing error mitigation (SEM), making use of the localized nature of sequencing error, the fact that it is well predicted by quality scores, and information about errors that comes from comparisons across species. Our automatic methods for error mitigation cannot replace the need for additional sequencing, but they do allow substantial fractions of errors to be masked or eliminated at the cost of modest amounts of over-correction, and they can reduce the impact of error in downstream phylogenomic analyses. Our error-mitigated alignments are available for download. PMID:21340033

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

2011-01-01

298

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

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

299

Differences in Irradiated Lung Gene Transcription Between Fibrosis-Prone C57BL/6NHsd and Fibrosis-Resistant C3H/HeNHsd Mice  

PubMed Central

Background/Aim We compared pulmonary irradiation-induced whole lung, gene transcripts, over 200 days after 20 Gy thoracic irradiation in fibrosis-prone C57BL/6NHsd with fibrosis-resistant C3H/HeNHsd female mice. Materials and Methods Lung specimens were analyzed by rt-PCR and changes over time in representative gene transcript levels were correlated with protein levels using Western Blot. Results C3H/HeNHsd mice showed a significantly longer duration of elevation of gene transcripts for stress-response genes (NFk?, Nrf2, Sp1, Ap1), radioprotection gene (SOD2), and endothelial cell associated genes (vWF, VEGFa). C57BL/6NHsd mice showed acute elevation then downregulation and a second elevation in gene transcripts for NFk?, CTGF, IGFbp7, TNF?, collagen1a, and TLR4. There were reciprocal patterns of elevation and decrease in levels of transcripts for epigenetic reader proteins Brd1, 2, 3, and 4 between mouse strains. Conclusions Regulatory pathways linked to radiation pulmonary fibrosis may identify new targets for anti-fibrotic radiation mitigators. PMID:24632969

Kalash, Ronny; Berhane, Hebist; Au, Jeremiah; Rhieu, Byung Han; Epperly, Michael W.; Goff, Julie; Dixon, Tracy; Wang, Hong; Zhang, Xichen; Franicola, Darcy; Shinde, Ashwin; Greenberger, Joel S.

2014-01-01

300

Interactive Histogram with Error Graph  

NSDL National Science Digital Library

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

Kyle Siegrist

301

On KPSS with GARCH errors  

Microsoft Academic Search

In this paper we discuss the finite sample behavior of the KPSS test in the presence of conditionally heteroskedastic errors. We confirm that under stationary GARCH errors the asymptotics of the KPSS remains valid. However, in finite samples we observe a slight size distortion and a power distortion. Interestingly, IGARCH errors do not seem to affect the size of the

Marco Barassi

2005-01-01

302

Angle interferometer cross axis errors  

Microsoft Academic Search

Angle interferometers are commonly used to measure surface plate flatness. An error can exist when the centerline of the double comer cube mirror assembly is not square to the surface plate and the guide bar for the mirror sled is curved. Typical errors can be one to two microns per meter. A similar error can exist in the calibration of

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

1994-01-01

303

A bifactor model of disgust proneness: examination of the disgust emotion scale.  

PubMed

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

Olatunji, Bunmi O; Ebesutani, Chad; Reise, Steven P

2015-04-01

304

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

SciTech Connect

Highlights: {yields} The mitochondrion contains its own protein quality control system. {yields} p62 localizes within the mitochondria and forms mega-dalton sized complexes. {yields} p62 interacts with oxidation-prone proteins and the proteins of quality control. {yields} In vitro delivery of p62 improves mitochondrial functions. {yields} p62 is implicated as a participant in mitochondrial protein quality control. -- Abstract: As the mitochondrion is vulnerable to oxidative stress, cells have evolved several strategies to maintain mitochondrial integrity, including mitochondrial protein quality control mechanisms and autophagic removal of damaged mitochondria. Involvement of an autophagy adaptor, Sqstm1/p62, in the latter process has been recently described. In the present study, we provide evidence that a portion of p62 directly localizes within the mitochondria and supports stable electron transport by forming heterogeneous protein complexes. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) of mitochondrial proteins co-purified with p62 revealed that p62 interacts with several oxidation-prone proteins, including a few components of the electron transport chain complexes, as well as multiple chaperone molecules and redox regulatory enzymes. Accordingly, p62-deficient mitochondria exhibited compromised electron transport, and the compromised function was partially restored by in vitro delivery of p62. These results suggest that p62 plays an additional role in maintaining mitochondrial integrity at the vicinity of target machineries through its function in relation to protein quality control.

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

2011-09-16

305

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

PubMed

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

Kim, Kyung Hoon

2014-10-01

306

Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip.  

PubMed

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

Chan, Yujia A; Aristizabal, Maria J; Lu, Phoebe Y T; Luo, Zongli; Hamza, Akil; Kobor, Michael S; Stirling, Peter C; Hieter, Philip

2014-04-01

307

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

PubMed Central

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

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

2014-01-01

308

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

PubMed

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

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

2015-04-01

309

Depressogenic thinking and shame proneness in the development of internalizing problems.  

PubMed

This study examined depressogenic thinking and shame proneness as factors in the development of internalizing problems in a longitudinal sample of 174 children (99 boys, 75 girls). At 7.6-9.4 years of age (Time 1), mothers assessed general internalizing problems in their children and depressogenic thinking, shame proneness, and anxiety were assessed by child self report. At 10.2-11.8 years of age (Time 2), mothers reassessed internalizing problems, and children reported their anxiety and depression. At 12.3-13.1 years of age (Time 3), children who had been high on any Time 2 measure of internalizing problems were selected for assessment of anxiety and depressive disorders. Depressogenic thinking and shame were significantly correlated and predicted subsequent problems. Depressogenic thinking predicted internalizing problems and anxious and depressive symptoms. Shame directly predicted boys' depressive symptoms, and indirectly predicted boys' general internalizing problems and girls' social anxiety. Depressive disorders in early adolescence were predicted specifically by shame. Findings suggest that both shame and depressive thinking contribute to the development of children's internalizing problems. PMID:24198082

Mills, Rosemary S L; Hastings, Paul D; Serbin, Lisa A; Stack, Dale M; Abela, John R Z; Arbeau, Kimberley A; Lall, Debra I K

2015-04-01

310

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

NASA Technical Reports Server (NTRS)

Pairs of HCMM day-night thermal infrared (IR) data were selected during the 1978-79 winter to examine patterns of surface temperature and thermal inertia (TI) of peninsular Florida. The GOES and NOAA-6 thermal IR, as well as National Climatic Center temperatures and rainfall, were also used. The HCMM apparent thermal inertia (ATI) images closely corresponded to the general soil map of Florida, based on soil drainage classes. Areas with low ATI overlay well-drained soils, such as deep sands and drained organic soils, whereas with high ATI overlay areas with wetlands and bodies of water. The HCMM ATI images also corresponded well with GOES-detected winter nocturnal cold-prone areas. Use of HCMM data with Carlson's energy balance model showed both high moisture availability (MA) and high thermal inertia (TI) of wetland-type surfaces and low MA and low TI of upland, well-drained soils. Since soil areas with low TI develop higher temperatures during the day, then antecedent patterns of highest maximum daytime surface temperature can also be used to predict nocturnal cold-prone areas in Florida.

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

1983-01-01

311

The Effects of Ovariectomy on Binge Eating Proneness in Adult Female Rats  

PubMed Central

Ovarian hormones are associated with binge eating in women, however findings are limited by the lack of experimental control inherent in human studies. Animal research that manipulates ovarian hormone status and examines individual differences in extreme binge eating proneness are needed to model clinical phenotypes in humans and to confirm causal effects. The purpose of this study was to examine the effects of adult ovariectomy on overall binge eating risk and extreme binge eating phenotypes using the binge eating resistant (BER)/ binge eating prone (BEP) rat model. We predicted that palatable food consumption would significantly increase after ovariectomy in all rats because ovarian hormones generally suppress food intake. If differences in responsiveness to ovarian hormones underlie BER/BEP phenotypes, then differences in binge eating between BER and BEP rats would be eliminated or diminished after ovariectomy. Changes in palatable food (PF) intake were compared in BER and BEP rats before and after ovariectomy in two samples of adult females. Findings were highly similar in the two samples. PF intake increased significantly following ovariectomy in all rats. However, BEP rats consistently consumed larger amounts of PF than BER rats, both before and after ovariectomy. The consistency of findings across two samples of rats provides strong support for activational effects of ovarian hormones on binge eating. However, the immunity of extreme binge eating phenotypes to ovarian hormone ablation suggests that other, earlier mechanisms (e.g., organizational hormone effects or hormone-independent effects) determine the expression of binge eating phenotypes. PMID:21376721

Klump, Kelly L.; Suisman, Jessica L.; Culbert, Kristen M.; Kashy, Deborah A.; Keel, Pamela K.; Sisk, Cheryl L.

2011-01-01

312

A 1-D mechanistic model for the evolution of earthflow-prone hillslopes  

NASA Astrophysics Data System (ADS)

In mountainous terrain, deep-seated landslides transport large volumes of material on hillslopes, exerting a dominant control on erosion rates and landscape form. Here, we develop a mathematical landscape evolution model to explore interactions between deep-seated earthflows, soil creep, and gully processes at the drainage basin scale over geomorphically relevant (>103 year) timescales. In the model, sediment flux or incision laws for these three geomorphic processes combine to determine the morphology of actively uplifting and eroding steady state topographic profiles. We apply the model to three sites, one in the Gabilan Mesa, California, with no earthflow activity, and two along the Eel River, California, with different lithologies and varying levels of historic earthflow activity. Representative topographic profiles from these sites are consistent with model predictions in which the magnitude of a dimensionless earthflow number, based on a non-Newtonian flow rheology, reflects the magnitude of recent earthflow activity on the different hillslopes. The model accurately predicts the behavior of earthflow collection and transport zones observed in the field and estimates long-term average sediment fluxes that are due to earthflows, in agreement with historical rates at our field sites. Finally, our model predicts that steady state hillslope relief in earthflow-prone terrain increases nonlinearly with the tectonic uplift rate, suggesting that the mean hillslope angle may record uplift rate in earthflow-prone landscapes even at high uplift rates, where threshold slope processes normally limit further topographic development.

Booth, Adam M.; Roering, Josh J.

2011-12-01

313

Prone positioning reduces mortality from acute respiratory distress syndrome in the low tidal volume era: a meta-analysis  

PubMed Central

Purpose Prone positioning for ARDS has been performed for decades without definitive evidence of clinical benefit. A recent multicenter trial demonstrated for the first time significantly reduced mortality with prone positioning. This meta-analysis was performed to integrate these findings with existing literature and test whether differences in tidal volume explain conflicting results among randomized trials. Methods Studies were identified using MEDLINE, EMBASE, Cochrane Register of Controlled Trials, LILACS, and citation review. Included were randomized trials evaluating the effect on mortality of prone versus supine positioning during conventional ventilation for ARDS. The primary outcome was risk ratio of death at 60 days meta-analyzed using random effects models. Analysis stratified by high (>8 ml/kg predicted body weight) or low (?8 ml/kg PBW) mean baseline tidal volume was planned a priori. Results Seven trials were identified including 2,119 patients, of whom 1,088 received prone positioning. Overall, prone positioning was not significantly associated with the risk ratio of death (RR 0.83; 95 % CI 0.68–1.02; p = 0.073; I2 = 64 %). When stratified by high or low tidal volume, prone positioning was associated with a significant decrease in RR of death only among studies with low baseline tidal volume (RR 0.66; 95 % CI 0.50–0.86; p = 0.002; I2 = 25 %). Stratification by tidal volume explained over half the between-study heterogeneity observed in the unstratified analysis. Conclusions Prone positioning is associated with significantly reduced mortality from ARDS in the low tidal volume era. Substantial heterogeneity across studies can be explained by differences in tidal volume. PMID:24435203

Shaefi, Shahzad; Montesi, Sydney B.; Devlin, Amy; Loring, Stephen H.; Talmor, Daniel; Malhotra, Atul

2014-01-01

314

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

315

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy  

SciTech Connect

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.

Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Gallati, Sabina, E-mail: sabina.gallati@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland)] [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Schaller, Andre, E-mail: andre.schaller@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland)] [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland)

2012-07-06

316

Assessment of surfactants for efficient droplet PCR in mineral oil using the pendant drop technique.  

PubMed

Amplification and detection of nucleic acid sequences within integrated microsystems is routinely conducted using the technique of droplet PCR, wherein the polymerase chain reaction (PCR) is performed in microscale water-in-oil droplets (nanoliter to picoliter volumes). During droplet PCR, interactions at the interface of the droplet tend to dominate. Specifically, adsorption of the polymerase at the droplet interface leads to inefficient amplification. To reduce polymerase adsorption, surfactants such as the silicone-based ABIL EM90 have been commonly used. However, these surfactants have been selected largely through trial and error, and have been only somewhat effective. For example, when using ABIL EM90, 8 times (8 ×) the manufacturer prescribed concentration of polymerase was necessary for amplification. In this report, we use the pendant drop technique to measure adsorption and loss of enzyme at droplet interfaces for various surfactant-oil combinations. Dynamic interfacial tension and surface pressure measurements showed that significant polymerase adsorption occurs when using ABIL EM90. In contrast, much lower polymerase adsorption is observed when using Brij L4, a nonionic surfactant with a C12 tail and an oxyethylene headgroup, which has not yet been reported for droplet PCR. These results correlate strongly with droplet PCR efficiency. Brij L4 enables highly efficient PCR at 2 × polymerase concentration, and still enables effective PCR at 1 × polymerase concentration. Overall, this work introduces a methodology for quantitatively assessing surfactants for use with droplet microreactors, and it demonstrates the practical value of this new approach by identifying a surfactant that can dramatically improve the efficiency of droplet PCR. PMID:25620443

Pandit, Kunal R; Rueger, Paul E; Calabrese, Richard V; Raghavan, Srinivasa R; White, Ian M

2015-02-01

317

PCR as a diagnostic tool for brucellosis.  

PubMed

Numerous PCR-based assays have been developed for the identification of Brucella to improve diagnostic capabilities. Collectively, the repertoire of assays addresses several aspects of the diagnostic process. For some purposes, the simple identification of Brucella is adequate (e.g. diagnosis of human brucellosis or contamination of food products). In these cases, a genus-specific PCR assay is sufficient. Genus-specific assays tend to be simple, robust, and somewhat permissive of environmental influences. The main genetic targets utilized for these applications are the Brucella BCSP31 gene and the 16S-23S rRNA operon. Other instances require identification of the Brucella species involved. For example, most government-sponsored brucellosis eradication programs include regulations that stipulate a species-specific response. For epidemiological trace back, strain-specific identification is helpful. Typically, differential PCR-based assays tend to be more complex and consequently more difficult to perform. Several strategies have been explored to differentiate among Brucella species and strains, including locus specific multiplexing (e.g. AMOS-PCR based on IS711), PCR-RFLP (e.g. the omp2 locus), arbitrary-primed PCR, and ERIC-PCR to name a few. This paper reviews some of the major advancements in molecular diagnostics for Brucella including the development of procedures designed for the direct analysis of a variety of clinical samples. While the progress to date is impressive, there is still room for improvement. PMID:12414163

Bricker, Betsy J

2002-12-20

318

Understanding the effects of leakage in superconducting quantum error detection circuits  

E-print Network

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 work, 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 $\\sigma^z$ 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.

Joydip Ghosh; Austin G. Fowler; John M. Martinis; Michael R. Geller

2013-12-11

319

Error threshold of topological color codes and random three-dimensional color gauge models  

NASA Astrophysics Data System (ADS)

Sensitivity to noise makes most of the current quantum computing schemes prone to error and non-scalable. Topologically-protected quantum computing solves this problem and prevents decoherence effects at the hardware level by encoding quantum states and gates in topological properties of the hardware medium. Recently, a braid-less implementation using brane-net condensates in 3-colexes has been proposed that allows for the implementation of a universal set of quantum gates. The latter is an active scheme for error correction. In this work, we compute the error threshold for a topologically-protected quantum color code in two space dimensions. By mapping the problem onto a new triangular/hexagonal lattice gauge theory with Ising spins and gauge degrees of freedom, we compute the stability of the proposal by randomly perturbing the plaquette interactions between the gauge spins and verifying the existence of a stable broken symmetry phase using Wilson loops.

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

2010-03-01

320

Understanding the effects of leakage in superconducting quantum-error-detection circuits  

NASA Astrophysics Data System (ADS)

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.

Ghosh, Joydip; Fowler, Austin G.; Martinis, John M.; Geller, Michael R.

2013-12-01

321

Real-time PCR detection chemistry.  

PubMed

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

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

2015-01-15

322

Beta systems error analysis  

NASA Technical Reports Server (NTRS)

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

1984-01-01

323

High frequency oscillatory ventilation and prone positioning in a porcine model of lavage-induced acute lung injury  

PubMed Central

Background This animal study was conducted to assess the combined effects of high frequency oscillatory ventilation (HFOV) and prone positioning on pulmonary gas exchange and hemodynamics. Methods Saline lung lavage was performed in 14 healthy pigs (54 ± 3.1 kg, mean ± SD) until the arterial oxygen partial pressure (PaO2) decreased to 55 ± 7 mmHg. The animals were ventilated in the pressure controlled mode (PCV) with a positive endexpiratory pressure (PEEP) of 5 cmH2O and a tidal volume (VT) of 6 ml/kg body weight. After a stabilisation period of 60 minutes, the animals were randomly assigned to 2 groups. Group 1: HFOV in supine position; group 2: HFOV in prone position. After evaluation of prone positioning in group 2, the mean airway pressure (Pmean) was increased by 3 cmH2O from 16 to 34 cmH2O every 20 minutes in both groups accompanied by measurements of respiratory and hemodynamic variables. Finally all animals were ventilated supine with PCV, PEEP = 5 cm H2O, VT = 6 ml/kg. Results Combination of HFOV with prone positioning improves oxygenation and results in normalisation of cardiac output and considerable reduction of pulmonary shunt fraction at a significant (p < 0.05) lower Pmean than HFOV and supine positioning. Conclusion If ventilator induced lung injury is ameliorated by a lower Pmean, a combined treatment approach using HFOV and prone positioning might result in further lung protection. PMID:16584548

Brederlau, Joerg; Muellenbach, Ralf; Kredel, Markus; Greim, Clemens; Roewer, Norbert

2006-01-01

324

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

PubMed Central

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

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

2014-01-01

325

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

PubMed

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

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

2014-07-01

326

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

PubMed Central

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

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

2013-01-01

327

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

NASA Astrophysics Data System (ADS)

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.

Cheung, David J.

328

Input error versus output error model reference adaptive control  

NASA Technical Reports Server (NTRS)

Algorithms for model reference adaptive control were developed in recent years, and their stability and convergence properties have been investigated. Typical algorithms in continuous time involve strictly positive real conditions on the reference model, while similar discrete time algorithms do not require such conditions. It is shown how algorithms differ by the use of an input error versus an output error, and present a continuous time input error adaptive control algorithm which does not involve SPR conditions. The connections with other schemes are discussed. The input error scheme has general stability and ocnvergence properties that are similar to the output error scheme. However, analysis using averaging methods reveals some preferable convergence properties of the input error scheme. Several other advantages are also discussed.

Bodson, Marc; Sastry, Shankar

1987-01-01

329

Accurate Estimation of Nucleic Acids by Amplification Efficiency Dependent PCR  

PubMed Central

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

Chatterjee, Nilanjana; Banerjee, Tanmay; Datta, Santanu

2012-01-01

330

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

PubMed Central

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

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

2015-01-01

331

A Geomagnetic Reference Error Model  

NASA Astrophysics Data System (ADS)

The accuracy of geomagnetic field models, such as the International Geomagnetic Reference Field (IGRF) and the World Magnetic Model (WMM), has benefitted tremendously from the ongoing series of satellite magnetic missions. However, what do we mean by accuracy? When comparing a geomagnetic reference model with a magnetic field measurement (for example of an electronic compass), three contributions play a role: (1) The instrument error, which is not subject of this discussion, (2) the error of commission, namely the error of the model coefficients themselves in representing the geomagnetic main field, and (3) the error of omission, comprising contributions to the geomagnetic field which are not represented in the reference model. The latter can further be subdivided into the omission of the crustal field and the omission of the disturbance field. Several factors have a strong influence on these errors: The error of commission primarily depends on the time elapsed since the last update of the reference model. The omission error for the crustal field depends on altitude of the measurement, while the omission error for the disturbance field has a strong latitudinal dependence, peaking under the auroral electrojets. A further complication arises for the uncertainty in magnetic declination, which is directly dependent on the strength of the horizontal field. Here, we present an error model which takes all of these factors into account. This error model will be implemented as an online-calculator, providing the uncertainty of the magnetic elements at the entered location and time.

Maus, S.; Woods, A. J.; Nair, M. C.

2011-12-01

332

Enumeration of verocytotoxigenic Escherichia coli (VTEC) O157 and O26 in milk by quantitative PCR.  

PubMed

Quantitative real-time polymerase chain reaction (qPCR) can be a convenient alternative to the Most Probable Number (MPN) methods to count VTEC in milk. The number of VTEC is normally very low in milk; therefore with the aim of increasing the method sensitivity a qPCR protocol that relies on preliminary enrichment was developed. The growth pattern of six VTEC strains (serogroups O157 and O26) was studied using enrichment in Buffered Peptone Water (BPW) with or without acriflavine for 4-24h. Milk samples were inoculated with these strains over a five Log concentration range between 0.24-0.50 and 4.24-4.50 Log CFU/ml. DNA was extracted from the enriched samples in duplicate and each extract was analysed in duplicate by qPCR using pairs of primers specific for the serogroups O157 and O26. When samples were pre-enriched in BPW at 37°C for 8h, the relationship between threshold cycles (CT values) and VTEC Log numbers was linear over a five Log concentration range. The regression of PCR threshold cycle numbers on VTEC Log CFU/ml had a slope coefficient equal to -3.10 (R(2)=0.96) which is indicative of a 10-fold difference of the gene copy numbers between samples (with a 100 ± 10% PCR efficiency). The same 10-fold proportion used for inoculating the milk samples with VTEC was observed, therefore, also in the enriched samples at 8h. A comparison of the CT values of milk samples and controls revealed that the strains inoculated in milk grew with 3 Log increments in the 8h enrichment period. Regression lines that fitted the qPCR and MPN data revealed that the error of the qPCR estimates is lower than the error of the estimated MPN (r=0.982, R(2)=0.965 vs. r=0.967, R(2)=0.935). The growth rates of VTEC strains isolated from milk should be comparatively assessed before qPCR estimates based on the regression model are considered valid. Comparative assessment of the growth rates can be done using spectrophotometric measurements of standardized cultures of isolates and reference strains cultured in BPW at 37°C for 8h. The method developed for the serogroups O157 and O26 can be easily adapted to the other VTEC serogroups that are relevant for human health. The qPCR method is less laborious and faster than the standard MPN method and has been shown to be a good technique for quantifying VTEC in milk. PMID:24713473

Mancusi, Rocco; Trevisani, Marcello

2014-08-01

333

DIRECT DNA SEQUENCING OF PCR PRODUCTS  

EPA Science Inventory

Experiments are described which elucidate some of the technical problems associated with the direct sequencing of polymerase chain reaction (PCR) amplified DNA. Sequencing primer purity, labeling methodology, and template preparation were explored. onditions are presented for the...

334

Real time PCR measurement by fluorescence anisotropy  

E-print Network

Real-time polymerase chain reaction (PCR) is the gold-standard for quantitation in both mutation and gene expression analyses. Already this technique has found valuable clinical application in disease diagnosis and progression ...

Crane, Bryan Lee, 1976-

2005-01-01

335

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

SciTech Connect

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.

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

2014-04-01

336

Transgene Detection by Digital Droplet PCR  

PubMed Central

Somatic gene therapy is a promising tool for the treatment of severe diseases. Because of its abuse potential for performance enhancement in sports, the World Anti-Doping Agency (WADA) included the term ‘gene doping’ in the official list of banned substances and methods in 2004. Several nested PCR or qPCR-based strategies have been proposed that aim at detecting long-term presence of transgene in blood, but these strategies are hampered by technical limitations. We developed a digital droplet PCR (ddPCR) protocol for Insulin-Like Growth Factor 1 (IGF1) detection and demonstrated its applicability monitoring 6 mice injected into skeletal muscle with AAV9-IGF1 elements and 2 controls over a 33-day period. A duplex ddPCR protocol for simultaneous detection of Insulin-Like Growth Factor 1 (IGF1) and Erythropoietin (EPO) transgenic elements was created. A new DNA extraction procedure with target-orientated usage of restriction enzymes including on-column DNA-digestion was established. In vivo data revealed that IGF1 transgenic elements could be reliably detected for a 33-day period in DNA extracted from whole blood. In vitro data indicated feasibility of IGF1 and EPO detection by duplex ddPCR with high reliability and sensitivity. On-column DNA-digestion allowed for significantly improved target detection in downstream PCR-based approaches. As ddPCR provides absolute quantification, it ensures excellent day-to-day reproducibility. Therefore, we expect this technique to be used in diagnosing and monitoring of viral and bacterial infection, in detecting mutated DNA sequences as well as profiling for the presence of foreign genetic material in elite athletes in the future. PMID:25375130

Moser, Dirk A.; Braga, Luca; Raso, Andrea; Zacchigna, Serena; Giacca, Mauro; Simon, Perikles

2014-01-01

337

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 ...

338

Assessment of interfractional prostate motion in patients immobilized in the prone position using a thermoplastic shell  

PubMed Central

The aim of this study was to evaluate the interfractional prostate motion of patients immobilized in the prone position using a thermoplastic shell. A total of 24 patients with prostate calcifications detectable using a kilo-voltage X-ray image-guidance system (ExacTrac X-ray system) were examined. Daily displacements of the calcification within the prostate relative to pelvic bony structures were calculated by the ExacTrac X-ray system. The average displacement and standard deviation (SD) in each of the left–right (LR), anterior–posterior (AP), and superior–inferior (SI) directions were calculated for each patient. Based on the results of interfractional prostate motion, we also calculated planning target volume (PTV) margins using the van Herk formula and examined the validity of the PTV margin of our institute (a 9-mm margin everywhere except posteriorly, where a 6-mm margin was applied). In total, 899 data measurements from 24 patients were obtained. The average prostate displacements ± SD relative to bony structures were 2.8 ± 3.3, ?2.0 ± 2.0 and 0.2 ± 0.4 mm, in the SI, AP and LR directions, respectively. The required PTV margins were 9.7, 6.1 and 1.4 mm in the SI, AP and LR directions, respectively. The clinical target volumes of 21 patients (87.5%) were located within the PTV for 90% or more of all treatment sessions. Interfractional prostate motion in the prone position with a thermoplastic shell was equivalent to that reported for the supine position. The PTV margin of our institute is considered appropriate for alignment, based on bony structures. PMID:23860549

Ikeda, Itaru; Mizowaki, Takashi; Sawada, Yohei; Nakata, Manabu; Norihisa, Yoshiki; Ogura, Masakazu; Hiraoka, Masahiro

2014-01-01

339

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

PubMed

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

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

2013-04-01

340

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

PubMed Central

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

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

2014-01-01

341

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

PubMed Central

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

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

2013-01-01

342

Influence of prone positioning on premature newborn infant stress assessed by means of salivary cortisol measurement: pilot study  

PubMed Central

Objective This study sought to assess the influence of prone positioning on the stress of newborn premature infants through the measurement of the salivary cortisol concentration and the evaluation of physiological and behavioral responses before and after changes in body positioning. Methods Saliva samples were collected from newborn infants at two different times: the first (corresponding to the baseline) after a period of 40 minutes during which the infants were not subjected to any manipulation and were placed in the lateral or supine position, and the second 30 minutes after placement in the prone position. Variables including heart rate, respiratory rate, peripheral oxygen saturation, and the Brazelton sleep score were recorded before, during, and at the end of the period in the prone position. Results The sample comprised 16 newborn premature infants (56.3% male) with a gestational age between 26 and 36 weeks, postnatal age between 1 and 33 days, birth weight of 935 to 3,050g, and weight at the time of intervention of 870 to 2,890g. During the intervention, six participants breathed room air, while the remainder received oxygen therapy. The median salivary cortisol concentration was lower in the prone position compared to baseline (0.13 versus 0.20; p=0.003), as was the median Brazelton sleep score (p=0.02). The average respiratory rate was lower after the intervention (54.88±7.15 versus 60±7.59; p=0.0004). The remainder of the investigated variables did not exhibit significant variation. Conclusion Prone positioning significantly reduced the salivary cortisol level, respiratory rate, and Brazelton sleep score, suggesting a correlation between prone positioning and reduction of stress in preterm infants. PMID:25028952

Cândia, Maria Fernanda; Osaku, Erica Fernanda; Leite, Marcela Aparecida; Toccolini, Beatriz; Costa, Nicolle Lamberti; Teixeira, Sandy Nogueira; Costa, Claudia Rejane Lima de Macedo; Piana, Pitágoras Augusto; Cristovam, Marcos Antonio da Silva; Osaku, Nelson Ossamu

2014-01-01

343

Contour Error Map Algorithm  

NASA Technical Reports Server (NTRS)

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.

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

2005-01-01

344

Medication errors in paediatric outpatients  

Microsoft Academic Search

BackgroundMedication errors are common in many settings and have important ramifications. Although there is growing research on rates and characteristics of medication errors in adult ambulatory settings, less is known about the paediatric ambulatory setting.ObjectiveTo assess medication error rates in paediatric patients in ambulatory settings.MethodsThe authors conducted a prospective cohort study of paediatric patients in six outpatient offices in Massachusetts.

Rainu Kaushal; Donald A Goldmann; Carol A Keohane; Erika L Abramson; Seth Woolf; Catherine Yoon; Katherine Zigmont; David W Bates

2010-01-01

345

Learn about PCR Set up PCR reactions using the DNA from  

E-print Network

;Universal rRNA Tree of Life Who is There? © 2012 Pearson Education, Inc. #12;Polymerase Chain Reaction (PCR;PCR Polymerase Chain Reaction © 2012 Pearson Education, Inc. #12;Things you can optimize · Temperature # of reactions final volume Sterile H20 26.8 5X PCR buffer 10 dNTPs (10mM) 1 Taq polymerase (5 Units/µl) 0.2 Tube

Vallino, Joseph J.

346

Specific PCR and real-time PCR assays for detection and quantitation of 'Candidatus Phytoplasma phoenicium'.  

PubMed

Almond witches' broom (AlmWB) is a fast-spreading lethal disease of almond, peach and nectarine associated with 'Candidatus Phytoplasma phoenicium'. The development of PCR and quantitative real-time PCR (qPCR) assays for the sensitive and specific detection of the phytoplasma is of prime importance for early detection of 'Ca. P. phoenicium' and for epidemiological studies. The developed qPCR assay herein uses a TaqMan(®) probe labeled with Black Hole Quencher Plus. The specificity of the PCR and that of the qPCR detection protocols were tested on 17 phytoplasma isolates belonging to 11 phytoplasma 16S rRNA groups, on samples of almond, peach, nectarine, native plants and insects infected or uninfected with the phytoplasma. The developed assays showed high specificity against 'Ca. P. phoenicium' and no cross-reactivity against any other phytoplasma, plant or insect tested. The sensitivity of the developed PCR and qPCR assays was similar to the conventional nested PCR protocol using universal primers. The qPCR assay was further validated by quantitating AlmWB phytoplasma in different hosts, plant parts and potential insect vectors. The highest titers of 'Ca. P. phoenicium' were detected in the phloem tissues of stems and roots of almond and nectarine trees, where they averaged from 10(5) to 10(6) genomic units per nanogram of host DNA (GU/ng of DNA). The newly developed PCR and qPCR protocols are reliable, specific and sensitive methods that are easily applicable to high-throughput diagnosis of AlmWB in plants and insects and can be used for surveys of potential vectors and alternative hosts. PMID:25543009

Jawhari, Maan; Abrahamian, Peter; Sater, Ali Abdel; Sobh, Hana; Tawidian, Patil; Abou-Jawdah, Yusuf

2015-02-01

347

Finding beam focus errors automatically  

SciTech Connect

An automated method for finding beam focus errors using an optimization program called COMFORT-PLUS. The steps involved in finding the correction factors using COMFORT-PLUS has been used to find the beam focus errors for two damping rings at the SLAC Linear Collider. The program is to be used as an off-line program to analyze actual measured data for any SLC system. A limitation on the application of this procedure is found to be that it depends on the magnitude of the machine errors. Another is that the program is not totally automated since the user must decide a priori where to look for errors. (LEW)

Lee, M.J.; Clearwater, S.H.; Kleban, S.D.

1987-01-01

348

A theory of human error  

NASA Technical Reports Server (NTRS)

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

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

1980-01-01

349

Duplex Reverse Transcription-PCR Followed by Nested PCR Assays for Detection and Identification of Brazilian Alphaviruses and Flaviviruses  

Microsoft Academic Search

Received 5 February 2004\\/Returned for modification 2 May 2004\\/Accepted 18 September 2004 A new approach was developed for the rapid detection and identification of Brazilian alphaviruses and flaviviruses. The methodology involves the genus-specific detection of Alphavirus and Flavivirus by a duplex reverse transcription-PCR (D-RT-PCR), followed by multiplex nested PCR (M-N-PCR) or nested PCR (N- PCR) assays for species-specific identification. By

Roberta Vieira de Morais; Rita Maria Ribeiro Nogueira; Marcio Nunes; Luiz Tadeu Moraes Figueiredo

350

An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a 'steric gate' residue for discrimination against ribonucleotides  

Microsoft Academic Search

DNA polymerases of the A and B families, and reverse transcriptases, share a common mechanism for preventing incorporation of ribonucleotides: a highly conserved active site residue obstructing the position that would be occupied by a 2¢ hydroxyl group on the incoming nucleotide. In the family Y (lesion bypass) polymerases, the enzyme active site is more open, with fewer contacts to

Angela M. DeLucia; Nigel D. F. Grindley; Catherine M. Joyce

2003-01-01

351

Error coding simulations in C  

NASA Technical Reports Server (NTRS)

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.

Noble, Viveca K.

1994-01-01

352

Visualizing high error levels during gene expression in living bacterial cells.  

PubMed

To monitor inaccuracy in gene expression in living cells, we designed an experimental system in the bacterium Bacillus subtilis whereby spontaneous errors can be visualized and quantified at a single-cell level. Our strategy was to introduce mutations into a chromosomally encoded gfp allele, such that errors in protein production are reported in real time by the formation of fluorescent GFP molecules. The data reveal that the amount of errors can greatly exceed previous estimates, and that the error rate increases dramatically at lower temperatures and during stationary phase. Furthermore, we demonstrate that when facing an antibiotic threat, an increase in error level is sufficient to allow survival of bacteria carrying a mutated antibiotic-resistance gene. We propose that bacterial gene expression is error prone, frequently yielding protein molecules that differ slightly from the sequence specified by their DNA, thus generating a cellular reservoir of nonidentical protein molecules. This variation may be a key factor in increasing bacterial fitness, expanding the capability of an isogenic population to face environmental challenges. PMID:20534550

Meyerovich, Mor; Mamou, Gideon; Ben-Yehuda, Sigal

2010-06-22

353

Apparent Polyploidization after Gamma Irradiation: Pitfalls in the Use of Quantitative Polymerase Chain Reaction (qPCR) for the Estimation of Mitochondrial and Nuclear DNA Gene Copy Numbers  

PubMed Central

Quantitative polymerase chain reaction (qPCR) has been widely used to quantify changes in gene copy numbers after radiation exposure. Here, we show that gamma irradiation ranging from 10 to 100 Gy of cells and cell-free DNA samples significantly affects the measured qPCR yield, due to radiation-induced fragmentation of the DNA template and, therefore, introduces errors into the estimation of gene copy numbers. The radiation-induced DNA fragmentation and, thus, measured qPCR yield varies with temperature not only in living cells, but also in isolated DNA irradiated under cell-free conditions. In summary, the variability in measured qPCR yield from irradiated samples introduces a significant error into the estimation of both mitochondrial and nuclear gene copy numbers and may give spurious evidence for polyploidization. PMID:23722662

Kam, Winnie W. Y.; Lake, Vanessa; Banos, Connie; Davies, Justin; Banati, Richard

2013-01-01

354

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

PubMed

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

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

2012-01-01

355

Dual Processing and Diagnostic Errors  

ERIC Educational Resources Information Center

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

Norman, Geoff

2009-01-01

356

Correcting errors in shotgun sequences  

Microsoft Academic Search

Sequencing errors in combination with repeated regions cause major problems in shotgun sequen- cing, mainly due to the failure of assembly pro- grams to distinguish single base differences between repeat copies from erroneous base calls. In this paper, a new strategy designed to correct errors in shotgun sequence data using defined nucleotide positions, DNPs, is presented. The method distin- guishes

Martti T. Tammi; Erik Arner; Ellen Kindlund; Bjorn Andersson

2003-01-01

357

Theory Testing and Measurement Error.  

ERIC Educational Resources Information Center

Presents simple and direct demonstrations showing why basic measurement principles require that biases in data created by measurement error be removed. Refutes common objections to the correction for these biases. Also describes substantive psychological processes responsible for some types of measurement error. (SLD)

Schmidt, Frank L.; Hunter, John E.

1999-01-01

358

Medical Error Reduction and PDAs  

Microsoft Academic Search

Numerous studies have revealed that medical errors are respon- sible for tremendous patient suffering, loss of life, and billions of dollars in costs. Research also suggests that children are at much higher risk of these errors than adults. New information technolo- gies, particularly personal digital assistants (PDAs), are able to pro- vide readily accessible medical information at the point-of-care. Al-

Mark Rosenbloom

2003-01-01

359

Eliminating US hospital medical errors  

Microsoft Academic Search

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

Sameer Kumar; Marc Steinebach

2008-01-01

360

Quantifying Potential Error in Painting Breast Excision Specimens  

PubMed Central

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

Godden, Amy

2013-01-01

361

A theory of human error  

NASA Technical Reports Server (NTRS)

Human errors tend to be treated in terms of clinical and anecdotal descriptions, from which remedial measures are difficult to derive. Correction of the sources of human error requires an attempt to reconstruct underlying and contributing causes of error from the circumstantial causes cited in official investigative reports. A comprehensive analytical theory of the cause-effect relationships governing propagation of human error is indispensable to a reconstruction of the underlying and contributing causes. A validated analytical theory of the input-output behavior of human operators involving manual control, communication, supervisory, and monitoring tasks which are relevant to aviation, maritime, automotive, and process control operations is highlighted. This theory of behavior, both appropriate and inappropriate, provides an insightful basis for investigating, classifying, and quantifying the needed cause-effect relationships governing propagation of human error.

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

1981-01-01

362

Does the Perceived Risk of Punishment Deter Criminally Prone Individuals? Rational Choice, Self-Control, and Crime  

ERIC Educational Resources Information Center

Society's efforts to deter crime with punishment may be ineffective because those individuals most prone to commit crime often act impulsively, with little thought for the future, and so they may be unmoved by the threat of later punishment. Deterrence messages they receive, therefore, may fall on deaf ears. This article examines this issue by…

Wright, Bradley R. E.; Caspi, Avshalom; Moffitt, Terrie E.; Paternoster, Ray

2004-01-01

363

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

Microsoft Academic Search

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

N. Tunkuda; A. M. Melesse

2008-01-01

364

Is the spontaneously hypertensive stroke prone rat a pertinent model of sub cortical ischemic stroke? A systematic review.  

PubMed

The spontaneously hypertensive stroke prone rat is best known as an inducible model of large artery stroke. Spontaneous strokes and stroke propensity in the spontaneously hypertensive stroke prone rat are less well characterized; however, could be relevant to human lacunar stroke. We systematically reviewed the literature to assess the brain tissue and small vessel pathology underlying the spontaneous strokes of the spontaneously hypertensive stroke prone rat. We searched systematically three online databases from 1970 to May 2010; excluded duplicates, reviews, and articles describing the consequences of induced middle cerebral artery occlusion or noncerebral pathology; and recorded data describing brain region and the vessels examined, number of animals, age, dietary salt intake, vascular and tissue abnormalities. Among 102 relevant studies, animals sacrificed after developing stroke-like symptoms displayed arteriolar wall thickening, subcortical lesions, enlarged perivascular spaces and cortical infarcts and hemorrhages. Histopathology, proteomics and imaging studies suggested that the changes not due simply to hypertension. There may be susceptibility to endothelial permeability increase that precedes arteriolar wall thickening, degeneration and perivascular tissue changes; systemic inflammation may also precede cerebrovascular changes. There were very few data on venules or tissue changes before hypertension. The spontaneously hypertensive stroke prone rat shows similar features to human lacunar stroke and may be a good spontaneous model of this complex human disorder. Further studies should focus on structural changes at early ages and genetics to identify factors that predispose to vascular and brain damage. PMID:21951409

Bailey, Emma L; Smith, Colin; Sudlow, Cathie L M; Wardlaw, Joanna M

2011-10-01

365

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

Microsoft Academic Search

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

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

2002-01-01

366

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

EPA Science Inventory

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

367

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

E-print Network

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

Paris-Sud XI, Université de

368

Overexpression of matrix metalloproteinase 1 in dermal fibroblasts from DNA repair-deficient\\/cancer-prone xeroderma pigmentosum group C patients  

Microsoft Academic Search

Xeroderma pigmentosum (XP) is a rare, recessively inherited genetic disease characterized by skin cancer proneness and premature aging in photoexposed area. The disease results from defective nucleotide excision repair of ultraviolet (UV)-induced DNA lesions. Reconstruction of group C (XP-C) skin in vitro previously suggested that patients' dermal fibroblasts might be involved in promoting skin cancer development, as they elicited microinvasions

M Fréchet; E Warrick; C Vioux; O Chevallier; A Spatz; S Benhamou; A Sarasin; F Bernerd; T Magnaldo

2008-01-01

369

Linking Self-Regulation and Risk Proneness to Risky Sexual Behavior: Pathways through Peer Pressure and Early Substance Use  

ERIC Educational Resources Information Center

The linkages between self-regulation in childhood, risk proneness in early adolescence, and risky sexual behavior in mid-adolescence were examined in a cohort of children (N=518) from the National Longitudinal Survey of Youth. The possible mediating role of two early adolescent variables (substance use and negative peer pressure) was also…

Crockett, Lisa J.; Raffaelli, Marcela; Shen, Yuh-Ling

2006-01-01

370

Congenital disorders sharing oxidative stress and cancer proneness as phenotypic hallmarks: prospects for joint research in pharmacology  

Microsoft Academic Search

In spite of very distinct genotypic assets, a number of congenital conditions include oxidative stress as a phenotypic hallmark. These disorders include Fanconi's aneemia, ataxia telangiectasia, xeroderma pigmentosum and Bloom's syndrome, as well as two frequent congenital conditions: Down's syndrome and cystic fibrosis. Cancer proneness is a clinical feature shared by these disorders, while other manifestations include early ageing, neurological

G. Pagano; L. G. Korkina; U. T. Brunk; L. Chessa; P. Degan; D. del Principe; F. J. Kelly; W. Malorni; F. Pallardó; C. Pasquier; I. Scovassi; A. Zatterale; C. Franceschi

1998-01-01

371

Prediction of Delinquency, Adjustment, and Academic Achievement Over a Five Year Period with the Kvaraceus Delinquency Proneness Scale.  

ERIC Educational Resources Information Center

The Kvaraceus Delinquency Proneness Scale (KD Scale) was developed as an instrument designed to aid in prediction of future juvenile delinquents. The purpose of this research was to evaluate the predictive validity of the instrument over a 5-year period. Indexes of delinquency adjustment and academic achievement served as the validational…

Benning, James J.; And Others

372

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

Microsoft Academic Search

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

Johan Rockström

373

The effects of discount level, price consciousness and sale proneness on consumers' price perception and behavioral intention  

Microsoft Academic Search

Previous research concerning external reference prices focused on outcome variables and contextual variables that influence them. Missing from the literature is sufficient assessment of the effect of individual difference variables. The current research examines two individual difference variables (price consciousness and sale proneness) along with discount level and their relationship with consumers' outcome evaluations of offer value, search intention and

Bruce L. Alford; Abhijit Biswas

2002-01-01

374

Injury-Proneness of Youth with Attention-Deficit Hyperactivity Disorder: A National Clinical Data Analysis in Taiwan  

ERIC Educational Resources Information Center

Limited literature documents injury-proneness of attention-deficit hyperactivity disorder in western population. However, only a few studies prospectively investigated the prediction of ADHD to injuries without considering other psychiatric and physical conditions and there is lack of such data in Asian population. To prospectively examine the…

Tai, Yueh-Ming; Gau, Susan Shur-Fen; Gau, Churn-Shiouh

2013-01-01

375

Automated High-Content Live Animal Drug Screening Using C. elegans Expressing the Aggregation Prone Serpin ?1-antitrypsin Z  

Microsoft Academic Search

The development of preclinical models amenable to live animal bioactive compound screening is an attractive approach to discovering effective pharmacological therapies for disorders caused by misfolded and aggregation-prone proteins. In general, however, live animal drug screening is labor and resource intensive, and has been hampered by the lack of robust assay designs and high throughput work-flows. Based on their small

Sager J. Gosai; Joon Hyeok Kwak; Cliff J. Luke; Olivia S. Long; Dale E. King; Kevin J. Kovatch; Paul A. Johnston; Tong Ying Shun; John S. Lazo; David H. Perlmutter; Gary A. Silverman; Stephen C. Pak

2010-01-01

376

Errors as allies: error management training in health professions education.  

PubMed

This paper adopts methods from the organisational team training literature to outline how health professions education can improve patient safety. We argue that health educators can improve training quality by intentionally encouraging errors during simulation-based team training. Preventable medical errors are inevitable, but encouraging errors in low-risk settings like simulation can allow teams to have better emotional control and foresight to manage the situation if it occurs again with live patients. Our paper outlines an innovative approach for delivering team training. PMID:23293120

King, Aimee; Holder, Michael G; Ahmed, Rami A

2013-06-01

377

Multiplex PCR Assay Design by Hybrid Multiobjective Evolutionary Algorithm  

E-print Network

Polymerase Chain Reaction (PCR) assay is to am- plify multiple target DNAs simultaneously using different sequences. 1 Introduction The Polymerase Chain Reaction (PCR) is a very powerful biological technique which polymerase chain reaction (PCR). The region between primers in A (the dashed box) is amplified by PCR. (b

378

Real-time PCR in the microbiology laboratory  

Microsoft Academic Search

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

I. M. Mackay

2004-01-01

379

Chronic exposure of cancer-prone mice to low-level 2450 MHz radiofrequency radiation.  

PubMed

The purpose of this study was to determine whether chronic, low-level exposure of mammary-tumor-prone mice to 2450 MHz radiofrequency radiation (RFR) promotes an earlier onset (decreased latency), a greater total incidence, or a faster growth rate of mammary tumors. One hundred C3H/ HeJ mice were exposed in circularly polarized waveguides (CWG) for 18 months (20 h/day, 7 days/wk) to continuous-wave, 2450 MHz RFR at a whole body average specific absorption rate (SAR) of 0.3 W/kg; 100 mice were sham exposed. Before exposure, SARs were determined calorimetrically; during experimentation, SARs were monitored by differential power measurement. All animals were visually inspected twice daily and were removed from the CWG cages for a weekly inspection, palpation, and weighing. From the time of detection, tumor size was measured weekly. Animals that died spontaneously, became moribund, or were killed after 18 months of exposure were completely necropsied; tissues were fixed and subjected to histopathological evaluations. Results showed no significant difference in weight profiles between sham-irradiated and irradiated mice. Concerning mammary carcinomas, there was no significant difference between groups with respect to palpated tumor incidence (sham = 52%; irradiated = 44%), latency to tumor onset (sham = 62.3 +/- 1.2 wk; irradiated = 64.0 +/- 1.6 wk), and rate of tumor growth. In general, histopathological examination revealed no significant differences in numbers of malignant, metastatic, or benign neoplasms between the two groups; a significantly greater incidence of alveolar-bronchiolar adenoma in the sham-irradiated mice was the only exception. In addition, survival analysis showed no significant difference in cumulative percent survival between sham and irradiated animals. Thus, results indicate that under the conditions of this study, long-term, low-level exposure of mammary-tumor-prone mice to 2450 MHz RFR did not affect mammary tumor incidence, latency to tumor onset, tumor growth rate, or animal longevity when compared with sham-irradiated controls. PMID:9453703

Frei, M R; Berger, R E; Dusch, S J; Guel, V; Jauchem, J R; Merritt, J H; Stedham, M A

1998-01-01

380

Rainwater management for increased productivity among small-holder farmers in drought prone environments  

NASA Astrophysics Data System (ADS)

A critical analysis of conventional water resources assessments and re-visiting the on-farm water balance suggests large scopes for water productivity improvements in small-holder rainfed farming systems in drought prone environments of Eastern and Southern Africa. The paper addresses key management challenges in trying to upgrade rainfed agriculture, and presents a set of field experiences on system options for increased water productivity in small-holder farming. Implications for watershed management are discussed, and the links between water productivity for food and securing of water flow to sustain ecosystem services are briefly analysed. Focus is on sub-Saharan Africa hosting the largest food deficit and water scarcity challenges. The paper shows that there are no agro-hydrological limitations to doubling on-farm staple food yields even in drought prone environments, by producing more “crop per drop” of rain. Field evidence is presented suggesting that meteorological dry spells are an important cause for low yield levels and it is hypothesised that this may constitute a core driver behind farmers risk aversion strategies. The dry spell induced risk perceptions contribute amongst others to soil nutrient mining due to insignificant investments in fertilisation. For many small-holder farmers in the semi-arid tropics it is simply not worth investing in fertilisation (and other external inputs) as long as the risk for crop failure remains a reality every fifth year with risk of yield reductions every second year, due to periodic water scarcity during the growing season (i.e., not necessarily cumulative water scarcity). Results are presented from field research on small-holder system innovations in the field of water harvesting and conservation tillage. Upgrading rainfed production systems through supplemental irrigation during short dry-spells is shown to dramatically increase water productivity. Downstream implications of increased upstream withdrawals of water for upgrading of rainfed food production are discussed. Finally it is argued that some of the most exciting opportunities for water productivity enhancements in rainfed agriculture are found in the realm of integrating components of irrigation management within the context of rainfed farming, e.g., supplemental or micro irrigation for dry spell mitigation. Combining such practices with management strategies that enhance soil infiltration, improve water holding capacity and plant water uptake potential, can have strong impact on agricultural water productivity. This suggests that it is probably time to abandon the largely obsolete distinction between irrigated and rainfed agriculture, and instead focus on integrated rainwater management.

Rockström, Johan; Barron, Jennie; Fox, Patrick

381

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

NASA Technical Reports Server (NTRS)

During the Orion landing and recovery subsystem design review, June 2009, it was noted that the human system and various vehicle systems, the environmental control and life support (ECLSS) and guidance, navigation and control (GN&C) systems for example, are negatively affected by Orion assuming a stable 2 (upside down; Figure A) configuration post landing. The stable 2 configuration is predicted to occur about 50% of the time based on Apollo landing data and modeling of the current capsule. The stable 2 configuration will be countered by an active up-righting system (crew module up-righting system; CMUS). Post landing balloons will deploy and inflate causing the vehicle to assume or maintain the stable 1 (up-right; Figure B) configuration. During the design review it was proposed that the up-righting system could be capable of righting the vehicle within 60 seconds. However, this time limit posed a series of constraints on the design which made it less robust than desired. The landing and recovery subsystem team requested an analysis of Orion vehicle systems as well as the human system with regard to the effect of stable 2 in order to determine if an up-righting response time greater than 60 seconds could be tolerated. The following report focuses on the assessment of the human system in the posture assumed when Orion is in the stable 2 configuration. Stable 2 will place suited, seated, and restrained crewmembers in a prone (facedown), head-up position for a period of time dependent on the functionality of the up-righting systems, ability of the crew to release themselves from the seat and restraints, and/or time to arrival of rescue forces. Given that the Orion seat and restraint system design is not complete and therefore, not available for evaluation, Space Medicine assessed how long a healthy but deconditioned crewmember could stay in this prone, restrained position and the physiological consequences of this posture by researching terrestrial analogs and considered the known physiological alterations and deconditioning experienced by long duration crewmembers.

Barr, Yael; Fogarty, Jennifer

2010-01-01

382

A comparative analysis of MODIS based spectral indices for drought monitoring over fire prone vegetation types  

NASA Astrophysics Data System (ADS)

Drought is a complex natural hazard with severe impacts on ecosystems. Several studies have highlighted links between drought spatio-temporal patterns and wildfire behaviour. Recent research showed drought can affect the development of catastrophic fires through influence on the spatial connectivity of dry fuel patches. Wildfires that are initiated at isolated ignition points (‘within patch scale’) can propagate non-linearly across landscapes (“among-patches”) if fuels are sufficiently dry and connected. Consequently, accurate mapping of drought at fine spatial resolution represents a priority to monitor “among-patches” continuity of flammable fuels in fire prone regions. Traditional methods of drought monitoring are based on meteorological indices (MI) calculated from weather stations data. The network of weather stations is often sparse and inadequate to produce fine spatial resolution surfaces of MI especially across remote forested areas. Spectral indices (SI) based on satellite data provide sound and cost-effective alternatives to MI, offering spatially dense information regularly recorded over large areas across a wide range of wavelengths. Since a considerable number of SI have been proposed as drought monitoring tool, the selection of the most appropriate index for a specific region represents an essential operation to ensure efficiency in drought mapping. In this study we propose a comprehensive analysis to evaluate the performance of a wide range of Vis, NIR and SWIR based SI towards drought condition monitoring over fire prone vegetation types, using the Sydney Basin bioregion (Australia) as case study. All spectral indices were derived from reflectance data sets obtained from MODIS Terra time series (2000-2009). The relationships between SI and drought conditions were analysed using a meteorological index (Standardized Precipitation Index, SPI) as rainfall deficiency indicator. The spatial and temporal co-variability between SPI and spectral indices was analysed and the sensitivity of MODIS indices to drought-related vegetation conditions was tested against a series of dry/wet years. Strong relationships between MODIS data and drought conditions were found. All spectral indices showed strong temporal and spatial correlations with SPI, with higher sensitivity to drought among SWIR based indices. The results revealed also that the spectral index routinely used by bushfire authorities in the Sydney Basin for drought monitoring is not the best indicator available, and there are potentials for the development of an enhanced MODIS-based monitoring tool. Our findings confirmed that extensive comparative analysis is necessary prior to implementation of SI in drought monitoring systems.

Caccamo, G.; Chisholm, L. A.; Bradstock, R.; Puotinen, M. L.

2010-12-01

383

Registration of central paths and colonic polyps between supine and prone scans in computed tomography colonography: Pilot study  

SciTech Connect

Computed tomography colonography (CTC) is a minimally invasive method that allows the evaluation of the colon wall from CT sections of the abdomen/pelvis. The primary goal of CTC is to detect colonic polyps, precursors to colorectal cancer. Because imperfect cleansing and distension can cause portions of the colon wall to be collapsed, covered with water, and/or covered with retained stool, patients are scanned in both prone and supine positions. We believe that both reading efficiency and computer aided detection (CAD) of CTC images can be improved by accurate registration of data from the supine and prone positions. We developed a two-stage approach that first registers the colonic central paths using a heuristic and automated algorithm and then matches polyps or polyp candidates (CAD hits) by a statistical approach. We evaluated the registration algorithm on 24 patient cases. After path registration, the mean misalignment distance between prone and supine identical anatomic landmarks was reduced from 47.08 to 12.66 mm, a 73% improvement. The polyp registration algorithm was specifically evaluated using eight patient cases for which radiologists identified polyps separately for both supine and prone data sets, and then manually registered corresponding pairs. The algorithm correctly matched 78% of these pairs without user input. The algorithm was also applied to the 30 highest-scoring CAD hits in the prone and supine scans and showed a success rate of 50% in automatically registering corresponding polyp pairs. Finally, we computed the average number of CAD hits that need to be manually compared in order to find the correct matches among the top 30 CAD hits. With polyp registration, the average number of comparisons was 1.78 per polyp, as opposed to 4.28 comparisons without polyp registration.

Li Ping; Napel, Sandy; Acar, Burak; Paik, David S.; Jeffrey, R. Brooke Jr.; Beaulieu, Christopher F. [Department of Statistics, Stanford University, Stanford, California 94305 (United States); Department of Radiology, Stanford University, Stanford, California 94305 (United States); Electrical and Electronics Engineering Department, Bogazici University 34342 Bebek, Istanbul (Turkey); Department of Radiology, Stanford University, Stanford, California 94305 (United States); Department of Radiology, Stanford University, Stanford, California 94305 (United States); Department of Radiology, Stanford University, Stanford, California 94305 (United States)

2004-10-01

384

Prospective Assessment of Optimal Individual Position (Prone Versus Supine) for Breast Radiotherapy: Volumetric and Dosimetric Correlations in 100 Patients  

SciTech Connect

Purpose: Damage to heart and lung from breast radiotherapy is associated with increased cardiovascular mortality and lung cancer development. We conducted a prospective study to evaluate which position is best to spare lung and heart from radiotherapy exposure. Methods and Materials: One hundred consecutive Stage 0-IIA breast cancer patients consented to participate in a research trial that required two computed tomography simulation scans for planning both supine and prone positions. The optimal position was defined as that which best covered the contoured breast and tumor bed while it minimized critical organ irradiation, as quantified by the in-field heart and lung volume. The trial was designed to plan the first 100 patients in each position to study correlations between in-field volumes of organs at risk and dose. Results: Fifty-three left and 47 right breast cancer patients were consecutively accrued to the trial. In all patients, the prone position was optimal for sparing lung volume compared to the supine setup (mean lung volume reduction was 93.5 cc for right and 103.6 cc for left breast cancer patients). In 46/53 (87%) left breast cancer patients best treated prone, in-field heart volume was reduced by a mean of 12 cc and by 1.8 cc for the other 7/53 (13%) patients best treated supine. As predicted, supine-prone differences in in-field volume and mean dose of heart and lung were highly correlated (Spearman's correlation coefficient for left breast cancer patients was 0.90 for heart and 0.94 for lung and 0.92 for right breast cancer patients for lung). Conclusions: Prone setup reduced the amount of irradiated lung in all patients and reduced the amount of heart volume irradiated in 87% of left breast cancer patients. In-field organ volume is a valid surrogate for predicting dose; the trial continued to the planned target of 400.

Lymberis, Stella C.; Wyngaert, John Keith de; Parhar, Preeti; Chhabra, Arpit M.; Fenton-Kerimian, Maria; Chang Jengwha [Department of Radiation Oncology, New York University School of Medicine and Langone Medical Center, New York, New York (United States)] [Department of Radiation Oncology, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Hochman, Tsivia [Division of Biostatistics, New York University School of Medicine and Langone Medical Center, New York, New York (United States) [Division of Biostatistics, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Department of Environmental Medicine, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Guth, Amber; Roses, Daniel [Department of Surgery, New York University School of Medicine and Langone Medical Center, New York, New York (United States)] [Department of Surgery, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Goldberg, Judith D. [Division of Biostatistics, New York University School of Medicine and Langone Medical Center, New York, New York (United States) [Division of Biostatistics, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Department of Environmental Medicine, New York University School of Medicine and Langone Medical Center, New York, New York (United States); Formenti, Silvia C., E-mail: silvia.formenti@nyumc.org [Department of Radiation Oncology, New York University School of Medicine and Langone Medical Center, New York, New York (United States)

2012-11-15

385

Development, Evaluation, and Standardization of a Real-Time TaqMan Reverse Transcription-PCR Assay for Quantification of Hepatitis A Virus in Clinical and Shellfish Samples  

PubMed Central

A standardized real-time reverse transcription-PCR (RT-PCR) assay has been developed for an accurate estimation of the number of genome copies of hepatitis A virus (HAV) in clinical and shellfish samples. Real-time procedures were based on the amplification of a fragment of the highly conserved 5? noncoding region and detection through an internal fluorescent probe, including TaqMan and beacon chemistries, in one- and two-step RT-PCR formats. The best performance in terms of sensitivity and reproducibility was achieved by a one-step TaqMan RT-PCR, with a sensitivity enabling the detection of 0.05 infectious unit and 10 copies of a single-stranded RNA (ssRNA) synthetic transcript. Standard reagents, such as a mengovirus strain and an ssRNA transcript, were employed as controls of nucleic acid extraction and RT-PCR, respectively. The test proved to be highly specific after a broad panel of enteric viruses was tested. Sequence alignment of target regions of the primers and probe proved them to be adequate for the quantification of all HAV genotypes. In addition, a quasispecies analysis of the mutant spectrum indicated that these regions are not prone to variability, thus confirming their robustness. PMID:16751488

Costafreda, M. Isabel; Bosch, Albert; Pintó, Rosa M.

2006-01-01

386

Quantitative real-time PCR in aDNA research.  

PubMed

Quantitative real-time PCR (qPCR) is a technique that is widely used in the field of ancient DNA (aDNA). Quantitative PCR can be used to optimize aDNA extraction methodologies, to detect PCR inhibition, and to quantify aDNA libraries for use in high-throughput sequencing. In this chapter, we outline factors that need to be considered when developing efficient SYBR Green qPCR assays. We describe how to setup qPCR standards of known copy number and provide some useful tips regarding interpretation of qPCR data generated from aDNA templates. PMID:22237530

Bunce, Michael; Oskam, Charlotte L; Allentoft, Morten E

2012-01-01

387

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

USGS Publications Warehouse

Non-invasive genetic sampling (NGS) is becoming a popular tool for population estimation. However, multiple NGS studies have demonstrated that polymerase chain reaction (PCR) genotyping errors can bias demographic estimates. These errors can be detected by comprehensive data filters such as the multiple-tubes approach, but this approach is expensive and time 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.

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

2005-01-01

388

Photometric Redshifts and Photometry Errors  

E-print Network

We examine the impact of non-Gaussian photometry errors on photometric redshift performance. We find that they greatly increase the scatter, but this can be mitigated to some extent by incorporating the correct noise model into the photometric redshift estimation process. However, the remaining scatter is still equivalent to that of a much shallower survey with Gaussian photometry errors. We also estimate the impact of non-Gaussian errors on the spectroscopic sample size required to verify the photometric redshift rms scatter to a given precision. Even with Gaussian {\\it photometry} errors, photometric redshift errors are sufficiently non-Gaussian to require an order of magnitude larger sample than simple Gaussian statistics would indicate. The requirements increase from this baseline if non-Gaussian photometry errors are included. Again the impact can be mitigated by incorporating the correct noise model, but only to the equivalent of a survey with much larger Gaussian photometry errors. However, these requirements may well be overestimates because they are based on a need to know the rms, which is particularly sensitive to tails. Other parametrizations of the distribution may require smaller samples.

D. Wittman; P. Riechers; V. E. Margoniner

2007-09-21

389

Errors In Short Distance Photometry  

NASA Astrophysics Data System (ADS)

The errors involved in the short-distance photometry of projectors are evaluated and the same conclusions have been shown to apply to general purpose luminaires. The mathematical analysis from which the equations were derived has been published in Lighting Research and Technology (1981). The illuminance at a short distance from the projector does not follow the inverse square law; the errors depend on the angular subtense of the aperture of the projector relative to the divergence of the beam, and on the distribution of luminance across the aperture of the projector. At any particular distance, the errors are least in directions in which the curvature of the intensity distribution curve is least; the errors may therefore be greatest in the axial direction or in the direction of a shoulder on the curve, and they may change sign where the intensity distribution curve changes from convex to concave. In any particular direction, the error is greater if the outer zones of the projector have higher luminance or give a narrower relative spread; the worst case is a ring-shaped luminaire. If the relative error is less than 10 per cent, it is inversely proportional to the square of the distance of measurement. For general guidance, a nomogram relates the maximum likely percentage error to the beam divergence and to the relative distance of measurement; an empirical reference distance, to be known as the Beam Cross-over Distance, is suggested to replace the traditional 'cross-over distance' of a projector.

Holmes, J. G.; Moermann, J. J. B.

1982-02-01

390

Quantum rms error and Heisenberg's error-disturbance relation  

NASA Astrophysics Data System (ADS)

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.

Busch, Paul

2014-09-01

391

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

392

Trunk and hip muscle recruitment patterns during the prone leg extension following a lateral ankle sprain: A prospective case study pre and post injury  

Microsoft Academic Search

BACKGROUND AND CASE PRESENTATION: The prone leg extension (PLE) is commonly used to identify dysfunction of muscle recruitment patterns. The prone leg extension is theorized to identify proximal muscle disturbances which are a result of distal injury or dysfunction (i.e. an ankle sprain). This case study compares the trunk and hip muscle (bilateral lower erector spine, ipsilateral hamstring and ipsilateral

Gregory J Lehman

2006-01-01

393

Individual differences in the proneness to have flow experiences are linked to dopamine D2-receptor availability in the dorsal striatum.  

PubMed

Flow is a subjective experience of high but effortless attention, enjoyment, and low self-awareness that can occur during the active performance of challenging tasks. The dispositional proneness to experience flow is associated with personality traits that are known to be influenced by dopaminergic neural systems. Here, for the first time, we investigated relations between flow proneness and dopaminergic function. Specifically, we tested the hypothesis that the availability of dopamine D2-receptors in the striatum is positively associated with flow proneness. Striatal D2-receptor availability was measured in a sample of 25 healthy adults using positron emission tomography and [(11)C]raclopride. Flow proneness was measured using the Swedish Flow Proneness Questionnaire. As hypothesized, there was a significant correlation (r=.41) between striatal D2-receptor availability and flow proneness. An exploratory analysis of striatal subregions showed that the relation was mainly driven by the dorsal striatum, with a significantly higher correlation in the putamen than in the ventral striatum. The findings constitute the first demonstration of an association between flow proneness and dopaminergic function. We suggest that the proneness to experience flow is related to personality dimensions that are under dopaminergic control and characterized by low impulsiveness, stable emotion, and positive affect. PMID:23128075

de Manzano, Örjan; Cervenka, Simon; Jucaite, Aurelija; Hellenäs, Oscar; Farde, Lars; Ullén, Fredrik

2013-02-15

394

Stay cables, such as used in cable-stayed bridges, are prone to vibration due to their low inherent damping characteristics.  

E-print Network

1 ABSTRACT Stay cables, such as used in cable-stayed bridges, are prone to vibration due steel cables, such as are used in cable-stayed bridges and other structures, are prone to vibration in such cables, typically on the order of a fraction of a percent, is insufficient to eliminate this vibration

Johnson, Erik A.

395

Jumping to Conclusions Style along the Continuum of Delusions: Delusion-Prone Individuals Are Not Hastier in Decision Making than Healthy Individuals  

PubMed Central

Literature comparing ‘jumping to conclusions’ (JTC) between patients and healthy controls has demonstrated the importance of the reasoning bias in the development of delusions. When groups that vary along the entire delusional continuum are included, the relationship between JTC and delusionality is less clear. This study compared JTC and delusional dimensions between 28 patients with delusions, 35 delusion-prone individuals and 32 non-delusion-prone individuals. Delusion proneness was defined by an established threshold based on the Peters et al. Delusions Inventory. Two versions of the beads task (85:15 and 60:40) were used to measure JTC. As hypothesized, patients manifested hastier data gathering than the two non-clinical groups on both beads tasks. However, delusion-prone individuals did not manifest a hastier decision making style than non-delusion prone individuals. Instead, non-delusion-prone participants showed more JTC bias than delusion-prone individuals on the easier beads task. There was no evidence for a dose-response relationship between JTC and delusional dimensions, with correlations between JTC and PDI scores found in the non-delusion-prone group only. The present finding confirms the link between an extreme JTC bias and the presence of clinical delusions, and argues against a linear relationship between JTC and delusionality along the symptomatic continuum. PMID:25793772

So, Suzanne Ho-wai; Kwok, Nate Tsz-kit

2015-01-01

396

Eye-mediated immune tolerance to Type II collagen in arthritis-prone strains of mice  

PubMed Central

Type II collagen (CII) is a cartilage structural protein that plays important roles in joint function, arthritis and ageing. In studying the ability of CII to induce eye-mediated specific immune tolerance, we have recently proven that CII is capable of inducing anterior chamber-associated immune deviation (ACAID) in Balb/c mice. Here, we study the ability of CII to induce eye-mediated immune tolerance in strains of mice that are prone to the induction of rheumatoid arthritis. Thus, we hypothesized that CII induces ACAID in DBA/1 mice and in C57BL/6 mice through the AC route (direct injection) or the intravenous route (adoptive transfer of in vitro-generated CII-specific ACAID macrophages or of CII-specific in vitro-generated T regulatory cells). Specific immune tolerance induction was assessed using both delayed-type hypersensitivity (DTH) and local adoptive transfer (LAT) assays. Results indicated the ability of CII to generate CII-specific ACAID-mediated immune tolerance in vivo and in vitro in both DBA/1 mice and C57BL/6 mice. These findings could be beneficial in studies of immune tolerance induction using CII. PMID:25211510

Farooq, Shukkur M; Kumar, Ashok; Ashour, Hossam M

2014-01-01

397

Landslide susceptibility mapping of a landside-prone area from Turkey by decision tree analysis  

NASA Astrophysics Data System (ADS)

The landslides are accepted as one of the important natural hazards throughout the world. Besides, the regional landslide susceptibility assessments is one of the first stages of the landslide hazard mitigation efforts. For this purpose, various methods have been applied to produce landslide susceptibility maps for many years. However, application of decision tree to landslide susceptibility mapping, one of data mining methods, is not common. Considering this lack in the landslide literature,an application of decision tree method to landslide susceptibility mapping is the main purpose of the present study. As the study area, the Inegol region (Northwestern Turkey) is selected. In the first stage of the study, a landslide inventory is produced by aerial-photo interpretations and field studies. Employing 16 topographic and lithologic variables, the landslide susceptibility analyses are performed by decision tree method. The AUC (Area Under Curve) values for ROC (Receiver-Operating Characteristics) curves are calculated as 0.942 for the landslide susceptibility model obtained from the decision tree analysis. According to the AUC values, the decision tree analysis presents a considerable performance. As a result of the present study, it may be concluded that the decision tree method presents promising results for the regional landslide susceptibility assessment. However, the technique should be studied for different landslide-prone areas and compared with other prediction techniques such as logistic regression, artificial neural networks, fuzzy approaches, etc.

Gorum, Tolga; Celal Tunusluoglu, M.; Sezer, Ebru; Nefeslioglu, Hakan A.; Bozkir, A. Selman; Gokceoglu, Candan

2010-05-01

398

Effect of Diet on Preference and Intake of Sucrose in Obese Prone and Resistant Rats  

PubMed Central

Increased orosensory stimulation from palatable diets and decreased feedback from gut signals have been proposed as contributing factors to obesity development. Whether altered taste functions associated with obesity are common traits or acquired deficits to environmental factors, such as a high-energy (HE)-diet, however, is not clear. To address this, we examined preference and sensitivity of increasing concentrations of sucrose solutions in rats prone (OP) and resistant (OR) to obesity during chow and HE feeding and measured lingual gene expression of the sweet taste receptor T1R3. When chow-fed, OP rats exhibited reduced preference and acceptance of dilute sucrose solutions, sham-fed less sucrose compared to OR rats, and had reduced lingual T1R3 gene expression. HE-feeding abrogated differences in sucrose preference and intake and lingual T1R3 expression between phenotypes. Despite similar sucrose intakes however, OP rats consumed significantly more total calories during 48-h two-bottle testing compared to OR rats. The results demonstrate that OP rats have an innate deficit for sweet taste detection, as illustrated by a reduction in sensitivity to sweets and reduced T1R3 gene expression; however their hyperphagia and subsequent obesity during HE-feeding is most likely not due to altered consumption of sweets. PMID:25329959

Duca, Frank A.; Swartz, Timothy D.; Covasa, Mihai

2014-01-01

399

How Different Knee Flexion Angles Influence the Hip Extensor in the Prone Position  

PubMed Central

[Purpose] The present study examined the effects of knee flexion angle on hip extensor muscle activity. [Subjects and Methods] Twenty healthy subjects maintained knee flexion angles of 0°, 30°, 60°, 90° and 110° in the prone position and performed maximal voluntary contraction in hip extension. Maximum torque in hip extension at the different angles was measured, and surface electromyogram activities of the gluteus maximus (GM), biceps femoris (BF) and semitendinosus (ST) were recorded and normalized by the maximum voluntary isometric contraction (MVIC). [Results] The maximum torque of the hip extensor showed significant decreases between 0°and 60°, 90° and 110° of knee flexion. The muscle activity of BF was significantly high at 0°, and GM showed a significantly higher activity than both BF and ST at 60°, 90°and 110° of knee flexion. [Conclusion] The maximum torque in hip extension and muscle activities of BF and ST were significantly high at 0° but they decreased at knee flexion angles of more than 60°. Therefore, we consider that more than 60° of knee joint flexion is required to increase GM activity, and to reduce the muscle activities of BF and ST. PMID:24259779

Kwon, Yu-Jeong; Lee, Hyun-Ok

2013-01-01

400

Astaxanthin inhibits thrombosis in cerebral vessels of stroke-prone spontaneously hypertensive rats.  

PubMed

It is known that vitamin E and some carotenoids have antioxidant activities that alleviate endothelial dysfunction and play a protective role against cardiovascular disease. The current study was designed to examine the hypothesis that astaxanthin, a red pigment carotenoid found in salmonid and crustacean aquaculture, protects stroke-prone spontaneously hypertensive rats (SHRSP) from vascular oxidative damage, hypertension, and cerebral thrombosis. Male 6-week-old SHRSP were classified into 4 groups: a control group, 2 astaxanthin groups, and a vitamin E group. The treated animals were given either astaxanthin or vitamin E for 3 weeks. Body weights in each group were not significantly different from control group during the treatment period, but the usual increase in systolic blood pressure in SHRSP observed with age was significantly suppressed by treatment. Thrombogenesis, assessed using a helium-neon (He-Ne) laser technique in pial blood vessels, together with antioxidant activity, assessed by measuring urinary 8-OHdG levels, were significantly moderated. Urinary nitric oxide (NO) metabolites were increased after treatment. These results supported our hypothesis and strongly suggested that the antithrombotic and antihypertensive effects of astaxanthin or vitamin E may be related to an increase in bioavailable NO, possibly mediated by decreased inactivation of NO by reactive oxygen species. PMID:22074803

Sasaki, Yasuto; Kobara, Nozomi; Higashino, Saori; Giddings, John C; Yamamoto, Junichiro

2011-10-01

401

Automated landform classification in a rockfall-prone area, Gunung Kelir, Java  

NASA Astrophysics Data System (ADS)

This paper presents an automated landform classification in a rockfall-prone area. Digital terrain models (DTMs) and a geomorphological inventory of rockfall deposits were the basis of landform classification analysis. Several data layers produced solely from DTMs were slope, plan curvature, stream power index, and shape complexity index; whereas layers produced from DTMs and rockfall modeling were velocity and energy. Unsupervised fuzzy k means was applied to classify the generic landforms into seven classes: interfluve, convex creep slope, fall face, transportational middle slope, colluvial foot slope, lower slope and channel bed. We draped the generic landforms over DTMs and derived a power-law statistical relationship between the volume of the rockfall deposits and number of events associated with different landforms. Cumulative probability density was adopted to estimate the probability density of rockfall volume in four generic landforms, i.e., fall face, transportational middle slope, colluvial foot slope and lower slope. It shows negative power laws with exponents 0.58, 0.73, 0.68, and 0.64 for fall face, transportational middle slope, colluvial foot slope and lower slope, respectively. Different values of the scaling exponents in each landform reflect that geomorphometry influences the volume statistics of rockfall. The methodology introduced in this paper has possibility to be used for preliminary rockfall risk analyses; it reveals that the potential high risk is located in the transportational middle slope and colluvial foot slope.

Samodra, G.; Chen, G.; Sartohadi, J.; Hadmoko, D. S.; Kasama, K.

2014-06-01

402

Fear conditioning and extinction in anxiety- and depression-prone persons.  

PubMed

Anxiety and depression frequently co-occur and may share similar deficits in the processing of emotional stimuli. High anxiety is associated with a failure in the acquisition and extinction of fear conditioning. Despite the supposed common deficits, no research has been conducted on fear acquisition and extinction in depression. The main aim of the present study was to investigate and compare fear acquisition and extinction in anxiety- and depression-prone participants. Non-clinical anxious, depressive, anxious-depressive and control participants performed a fear discrimination task. During acquisition, the CS+ predicted an aversive event (unconditioned stimulus, US) and the CS- safety (no US). During extinction, the CS+ was no longer followed by the US, rendering it (temporarily) into a safety signal. On each CS participants rated their US expectancy; skin conductance responses (SCRs) were measured throughout. The expectancy scores indicated that high anxiety resulted in less safety learning during acquisition and extinction; no effect of depression was observed. SCRs showed that high-anxiety persons displayed less discrimination learning (CS+ minus CS-) during acquisition than low-anxiety persons. During extinction, high-depression persons demonstrated more discriminative SCR than low-depression persons. The observed discrepancies in response patterns of high-anxiety and -depression persons seem to indicate distinctive information processing of emotional stimuli. PMID:24601711

Dibbets, Pauline; van den Broek, Anne; Evers, Elisabeth A T

2015-04-01

403

Index Cohesive Force Analysis Reveals That the US Market Became Prone to Systemic Collapses Since 2002  

PubMed Central

Background The 2007–2009 financial crisis, and its fallout, has strongly emphasized the need to define new ways and measures to study and assess the stock market dynamics. Methodology/Principal Findings The S&P500 dynamics during 4/1999–4/2010 is investigated in terms of the index cohesive force (ICF - the balance between the stock correlations and the partial correlations after subtraction of the index contribution), and the Eigenvalue entropy of the stock correlation matrices. We found a rapid market transition at the end of 2001 from a flexible state of low ICF into a stiff (nonflexible) state of high ICF that is prone to market systemic collapses. The stiff state is also marked by strong effect of the market index on the stock-stock correlations as well as bursts of high stock correlations reminiscence of epileptic brain activity. Conclusions/Significance The market dynamical states, stability and transition between economic states was studies using new quantitative measures. Doing so shed new light on the origin and nature of the current crisis. The new approach is likely to be applicable to other classes of complex systems from gene networks to the human brain. PMID:21556323

Kenett, Dror Y.; Shapira, Yoash; Madi, Asaf; Bransburg-Zabary, Sharron; Gur-Gershgoren, Gitit; Ben-Jacob, Eshel

2011-01-01

404

Quantitative phosphoproteomic analysis of T cell receptor signaling in diabetes prone and resistant mice.  

PubMed

Type 1 diabetes, in human patients and NOD mice, results from an immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the altered responses of T cells, manifest as inefficient induction of apoptosis after recognition of self-antigens in the thymus or as perturbed reactivity of mature T cells in peripheral organs. To map this signaling difference(s), we have used mass spectrometry-based quantitative phosphoproteomics to compare the activation of primary CD4(+) T cells of diabetes-prone NOD and -resistant B6.H2g7 mice. Immunoprecipitation and IMAC purification of tyrosine-phosphorylated peptides, combined with a stable-isotope iTRAQ labeling, enabled us to identify and quantify over 77 phosphorylation events in 54 different proteins downstream of TCR stimulation of primary CD4(+) T cells. This analysis showed a generally higher level of phosphotyrosine in activated NOD cells, as well as several phosphorylation sites that appeared to be differentially regulated in these two strains (involving TXK, CD5, PAG1, and ZAP-70). These data highlight the differences in signaling between CD4(+) T cell compartments of NOD and B6g7 mice and may underlie the dysregulation of T cells in NOD mice. PMID:20438120

Iwai, Leo K; Benoist, Christophe; Mathis, Diane; White, Forest M

2010-06-01

405

QUANTITATIVE PHOSPHOPROTEOMIC ANALYSIS OF T CELL RECEPTOR SIGNALING IN DIABETES PRONE AND RESISTANT MICE  

PubMed Central

Type 1 diabetes, in human patients and NOD mice, results from immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically-controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the altered responses of T cells, manifest as inefficient induction of apoptosis after recognition of self-antigens in the thymus, or as perturbed reactivity of mature T cells in peripheral organs. To map this signaling difference(s), we have used mass spectrometry-based quantitative phosphoproteomics to compare the activation of primary CD4+ T cells of diabetes-prone NOD and -resistant B6.H2g7 mice. Immunoprecipitation and IMAC purification of tyrosine-phosphorylated peptides, combined with a stable-isotope iTRAQ labeling, enabled us to identify and quantify over 77 phosphorylation events in 54 different proteins downstream of TCR stimulation of primary CD4+ T cells. This analysis showed a generally higher level of phosphotyrosine in activated NOD cells, as well as several phosphorylation sites that appeared to be differentially regulated in these two strains (involving TXK, CD5, PAG1, and ZAP-70). These data highlight the differences in signaling between CD4+ T cell compartments of NOD and B6g7 mice, and may underlie the dysregulation of T cells in NOD mice. PMID:20438120

Iwai, Leo K.; Benoist, Christophe; Mathis, Diane; White, Forest M

2012-01-01

406

Structural studies of "aggregation-prone" peptide-analogues of teleostean egg chorion ZPB proteins.  

PubMed

Egg envelopes of vertebrates are composed of a family of proteins called zona pellucida (ZP) proteins, which are distinguished by the presence of a common structural polymerizing motif, known as ZP domain. Teleostean fish chorion is a fibrous structure, consisting of protein members of the ZPB/ZP1 and the ZPC/ZP3 families, which are incorporated as tandemly repeating heterodimers inside chorion fibers. Computational analysis of multiple ZPB/ZP1 proteins from several teleostean species, reveals two potential "aggregation-prone" sequence segments, forming a specific polymerization interface (AG interface). These two peptides were synthesized and results are presented in this work from transmission electron microscopy, Congo red staining, X-ray fiber diffraction and ATR FT-IR, which clearly display the ability of these peptides to self-aggregate, forming amyloid-like fibrils. This, most probably implies that the AG interface of ZPB/ZP1 proteins plays an important role for the formation of the repeating ZPB-ZPC heterodimers, which constitute teleostean chorion fibrils. © 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 427-436, 2014. PMID:25229478

Louros, Nikolaos N; Petronikolou, Nektaria; Karamanos, Theodoros; Cordopatis, Paul; Iconomidou, Vassiliki A; Hamodrakas, Stavros J

2014-11-01

407

Effects of dietary Angelica keiskei on lipid metabolism in stroke-prone spontaneously hypertensive rats.  

PubMed

1. The effect of dietary Angelica keiskei on lipid metabolism was examined in stroke-prone spontaneously hypertensive rats (SHRSP). 2. Six-week-old male SHRSP were fed diets containing 0.2% A. keiskei extract (ethyl acetate extract from the yellow liquid of stems) for 6 weeks with free access to the diet and water. 3. Elevation of systolic blood pressure tended to be suppressed on and after 2 weeks; however, this effect was not statistically significant. 4. Serum levels of cholesterol and phospholipid in SHRSP were significantly elevated after treatment with A. keiskei extract and this effect was accompanied by significant increases in serum apolipoprotein (Apo) A-I and ApoE concentrations. These changes in the serum were due to increases in high-density lipoprotein (HDL) containing ApoA-I and ApoE. 5. In the liver, significant decreases in relative weight and triglyceride content were observed in SHRSP after treatment with A. keiskei extract. An investigation of mRNA expression of enzymes involved in hepatic triglyceride metabolism indicated a decreased level of hepatic Acyl-coenzyme A synthetase mRNA expression. 6. In conclusion, dietary A. keiskei produces elevation of serum HDL levels and a reduction of liver triglyceride levels in SHRSP. PMID:12680848

Ogawa, Hiroshi; Nakashima, Seiji; Baba, Kimiye

2003-04-01

408

Seroprevalence of leptospirosis in a rural flood prone district of Bangladesh.  

PubMed Central

Leptospirosis is a worldwide zoonotic disease. In the present investigation, a total of 89 human sera from a flood prone district of Bangladesh was screened by a one-point microscapsule agglutination test (MCAT). MCAT-positive and -doubtful sera were further tested by microscopic agglutination test (MAT) against 16 reference serovars of Leptospira interrogans, and the antibody titres determined. In MCAT, 34 sera were positive and 22 were doubtful. Among those positive and doubtful sera, 33 and 20, respectively were tested by MAT. Thirty-four out of 53 MCAT-screened samples were MAT-positive. The titres ranged from 20 to 1600 with antibodies to serovars copenhageni, australis, cynopteri and icterohaemorrhagiae being the most prevalent. Eleven MCAT-positive samples failed to react with any strains used by MAT, suggesting the presence of new or untested serovars. Among the MAT-positive samples, the presence of antibody against two or more serovars was more common than that of a single serovar. The present study suggests that rural people in Bangladesh are at high risk to leptospiral infection. PMID:8005218

Morshed, M. G.; Konishi, H.; Terada, Y.; Arimitsu, Y.; Nakazawa, T.

1994-01-01

409

Individual Differences in Gambling Proneness among Rats and Common Marmosets: An Automated Choice Task  

PubMed Central

Interest is rising for animal modeling of pathological gambling. Using the operant probabilistic-delivery task (PDT), gambling proneness can be evaluated in laboratory animals. Drawing a comparison with rats, this study evaluated the common marmoset (Callithrix jacchus) using a PDT. By nose- or hand-poking, subjects learnt to prefer a large (LLL, 5-6 pellets) over a small (SS, 1-2 pellets) reward and, subsequently, the probability of occurrence of large-reward delivery was decreased progressively to very low levels (from 100% to 17% and 14%). As probability decreased, subjects showed a great versus little shift in preference from LLL to SS reinforcer. Hence, two distinct subpopulations (“non-gambler” versus “gambler”) were differentiated within each species. A proof of the model validity comes from marmosets' reaction to reward-delivery omission. Namely, depending on individual temperament (“gambler” versus “non-gambler”), they showed either persistence (i.e., inadequate pokes towards LLL) or restlessness (i.e., inadequate pokes towards SS), respectively. In conclusion, the marmoset could be a suitable model for preclinical gambling studies. Implementation of the PDT to species other than rats may be relevant for determining its external validity/generalizability and improving its face/construct validity. PMID:24971360

Manciocco, Arianna; Vitale, Augusto; Laviola, Giovanni

2014-01-01

410

Toso regulates differentiation and activation of inflammatory dendritic cells during persistence-prone virus infection.  

PubMed

During virus infection and autoimmune disease, inflammatory dendritic cells (iDCs) differentiate from blood monocytes and infiltrate infected tissue. Following acute infection with hepatotropic viruses, iDCs are essential for re-stimulating virus-specific CD8(+) T cells and therefore contribute to virus control. Here we used the lymphocytic choriomeningitis virus (LCMV) model system to identify novel signals, which influence the recruitment and activation of iDCs in the liver. We observed that intrinsic expression of Toso (Faim3, Fc?R) influenced the differentiation and activation of iDCs in vivo and DCs in vitro. Lack of iDCs in Toso-deficient (Toso(-/-)) mice reduced CD8(+) T-cell function in the liver and resulted in virus persistence. Furthermore, Toso(-/-) DCs failed to induce autoimmune diabetes in the rat insulin promoter-glycoprotein (RIP-GP) autoimmune diabetes model. In conclusion, we found that Toso has an essential role in the differentiation and maturation of iDCs, a process that is required for the control of persistence-prone virus infection. PMID:25257173

Lang, P A; Meryk, A; Pandyra, A A; Brenner, D; Brüstle, A; Xu, H C; Merches, K; Lang, F; Khairnar, V; Sharma, P; Funkner, P; Recher, M; Shaabani, N; Duncan, G S; Duhan, V; Homey, B; Ohashi, P S; Häussinger, D; Knolle, P A; Honke, N; Mak, T W; Lang, K S

2015-01-01

411

Renal hemodynamics and sodium excretion in stroke-prone spontaneously hypertensive rats.  

PubMed

Renal blood flow (RBF), renal vascular resistance (RVR), glomerular filtration rate (GFR), and sodium and water excretion were measured in anesthetized stroke-prone spontaneously hypertensive rats (SHRSP), spontaneously hypertensive rats (SHR), and control Wistar-Kyoto rats (WKY) at 9 wk of age. Mean arterial pressure in SHRSP and SHR was significantly higher than that in WKY. RBF was slightly increased in SHR and decreased in SHRSP. RVR was markedly elevated only in SHRSP. In both strains of SHR, GFR was significantly increased but water and sodium excretion were similar. When renal perfusion pressure in both strains of SHR was reduced to a level similar to that of WKY by aortic constriction, RBF was slightly but significantly reduced in both SHRSP and SHR, and GFR only in SHRSP. RVR in SHRSP was still higher. Sodium and water excretion were markedly decreased in both SHR and SHRSP. The data suggest that SHRSP are characterized by an alteration in renal hemodynamics at a young age and support the hypothesis that kidneys of SHR require a higher arterial pressure than kidneys of WKY to excrete a given amount of salt and water. PMID:7282927

Nagaoka, A; Kakihana, M; Suno, M; Hamajo, K

1981-09-01

412

Error bounds in cascading regressions  

USGS Publications Warehouse

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

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

1985-01-01

413

Stochastic Models of Human Errors  

NASA Technical Reports Server (NTRS)

Humans play an important role in the overall reliability of engineering systems. More often accidents and systems failure are traced to human errors. Therefore, in order to have meaningful system risk analysis, the reliability of the human element must be taken into consideration. Describing the human error process by mathematical models is a key to analyzing contributing factors. Therefore, the objective of this research effort is to establish stochastic models substantiated by sound theoretic foundation to address the occurrence of human errors in the processing of the space shuttle.

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

2002-01-01

414

Mars gravitational field estimation error  

NASA Technical Reports Server (NTRS)

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

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

1972-01-01

415

Body-related state shame and guilt in women: do causal attributions mediate the influence of physical self-concept and shame and guilt proneness.  

PubMed

Guided by the process model of self-conscious emotions, this study examined whether physical self-concept (PSC) and shame and guilt proneness were associated with body-related self-conscious emotions of state shame and guilt and if these relationships were mediated by attributions of stability, globality, and controllability. Female participants (N=284; Mean age=20.6±1.9 years) completed measures of PSC and shame and guilt proneness before reading a hypothetical scenario. Participants completed measures of attributions and state shame and guilt in response to the scenario. Significant relationships were noted between state shame and attributions of globality and controllability, and shame proneness, guilt proneness, and PSC. Similar relationships, with the additional predictor of stability, were found for state guilt. Mediation analysis partially supported the process model hypotheses for shame. Results indicate PSC and shame proneness are important in predicting body-related emotions, but the role of specific attributions are still unclear. PMID:24035310

Crocker, Peter R E; Brune, Sara M; Kowalski, Kent C; Mack, Diane E; Wilson, Philip M; Sabiston, Catherine M

2014-01-01

416

Amp-PCR: Combining a Random Unbiased Phi29Amplification with a Specific Real-Time PCR, Performed in One Tube to Increase PCR Sensitivity  

Microsoft Academic Search

In clinical situations where a diagnostic real-time PCR assay is not sensitive enough, leading to low or falsely negative results, or where detection earlier in a disease progression would benefit the patient, an unbiased pre-amplification prior to the real-time PCR could be beneficial. In Amp-PCR, an unbiased random Phi29 pre-amplification is combined with a specific real-time PCR reaction. The two

Lena Erlandsson; Lars Peter Nielsen; Anders Fomsgaard

2010-01-01

417

New PCR systems to confirm real-time PCR detection of Mycobacterium avium subsp. paratuberculosis  

PubMed Central

Background Johne's disease, a serious chronic form of enteritis in ruminants, is caused by Mycobacterium avium subsp. paratuberculosis (MAP). As the organism is very slow-growing and fastidious, several PCR-based methods for detection have been developed, based mainly on the MAP-specific gene IS900. However, because this gene is similar to genes in other mycobacteria, there is a need for sensitive and reliable methods to confirm the presence of MAP. As described here, two new real-time PCR systems on the IS900 gene and one on the F57 gene were developed and carefully validated on 267 strains and 56 positive clinical faecal samples. Results Our confirmatory PCR systems on IS900 were found sensitive and specific, only yielding weak false positive reactions in one strain for each system. The PCR system on F57 did not elicit any false positives and was only slightly less sensitive than our primary IS900-system. DNA from both naturally infected and spiked faeces that tested positive with our primary system could be confirmed with all new systems, except one low-level infected sample that tested negative with the F57 system. Conclusion We recommend using the newly constructed DH3 PCR system on the F57 gene as the primary confirmatory test for PCR positives, but should it fail due to its lower sensitivity, the DH1 and DH2 PCR systems should be used. PMID:17020599

Herthnek, David; Bölske, Göran

2006-01-01

418

How Many Microorganisms Are Present? Quantitative Reverse Transcription PCR (qRT-PCR)  

NASA Astrophysics Data System (ADS)

Quantitative reverse transcription PCR (qRT-PCR) is a variation of conventional quantitative or real-time PCR, whereby mRNA is first converted into the complementary DNA (cDNA) by reverse transcription, the cDNA is then subsequently quantified by qPCR. The use of mRNA as the initial template allows the quantification of gene transcripts, rather than gene copy numbers. mRNA is only produced by actively metabolising cells and is produced by its corresponding gene to provide a 'blueprint' in order for a cell to manufacture a specific protein. Conventional qPCR detects not only DNA present in actively metabolising cells but also inactive and dead cells. qRT-PCR has the advantage that only actively metabolising cells are detected, hence provides a more reliable measure of microbial activity in oilfield samples. When qRT-PCR is combined with primers and probes for specific genes, the activity of microbial processes important in the oilfield, such as sulphate reduction, methanogenesis and nitrate reduction can be monitored.

Price, Andy; Álvarez, Laura Acuña; Whitby, Corinne; Larsen, Jan

419

Using Block-local Atomicity to Detect Stale-value Concurrency Errors  

NASA Technical Reports Server (NTRS)

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.

Artho, Cyrille; Havelund, Klaus; Biere, Armin

2004-01-01

420

Orbital and Geodetic Error Analysis  

NASA Technical Reports Server (NTRS)

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

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

1985-01-01

421

Static Detection of Disassembly Errors  

SciTech Connect

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

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

2009-10-13

422

Prospective errors determine motor learning.  

PubMed

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 model's 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

Takiyama, Ken; Hirashima, Masaya; Nozaki, Daichi

2015-01-01

423

Prospective errors determine motor learning  

PubMed Central

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 model’s 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

Takiyama, Ken; Hirashima, Masaya; Nozaki, Daichi

2015-01-01

424

Human errors and measurement uncertainty  

NASA Astrophysics Data System (ADS)

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.

Kuselman, Ilya; Pennecchi, Francesca

2015-04-01

425

Modeling PCR in Natural Convection Systems  

NASA Astrophysics Data System (ADS)

Polymerase chain reaction (PCR) is a biochemical protocol for making many copies of a DNA template by thermal cycling between a hot temperature (where the strands are separated) and a cool temperature (where primers are annealed). In natural convection PCR, the requisite thermal cycling is provided by a buoyancy-driven circulating flow of the carrying buffer between a lower hot plate (at the denaturing temperature) and an upper cold plate (at the annealing temperature). We present a multi-component convection-diffusion-reaction model for natural convection-driven PCR when both primers and PCR enzyme are in excess. The evolution of the DNA population achieves a stationary state, wherein the problem is recast as an eigenvalue problem for computing the exponential amplification rate. With a realistic choice of parameters, the model predicts a doubling time on the order of two minutes, in agreement with experiments and much slower than the fluid cycling time. In contrast to what might be expected, the doubling time increases monotonically with the diffusion coefficient.

Dorfman, Kevin; Yariv, Ehud; Ben Dov, Guy

2007-03-01

426

DNA profiles from fingernails using direct PCR.  

PubMed

We report on the successful routine amplification of DNA profiles from small sections of fingernails using direct PCR. The data are from 40 nail clippings from eight donors where approximately 4 mm(2) of nail is added directly to the PCR. The NGM™ kit was used that amplifies 15 STR loci plus amelogenin. No increase in cycle number was used and no enrichment of the PCR products was performed. Full DNA profiles were observed in 17 of the 40 profiles with 21 generating partial DNA profiles. The process omits the DNA extraction process, and hence there is no opportunity to quantify the DNA prior to amplifying the STRs, but by not performing a DNA extraction step, the amount of DNA available for PCR is maximized. Single source DNA profiles were observed in 29 of the 38 profiles obtained. The source of the DNA is assumed to be adhering to the underside of the nail. This simple method offers a significant reduction in time to generate DNA profiles from nail clippings, such as those taken from victims of mass disasters, and should be included into a forensic process relatively easily as it requires no change to manufacturer's instructions for amplification. PMID:25391459

Ottens, Renée; Taylor, Duncan; Linacre, Adrian

2015-03-01

427

Hybridization Screening of Very Short PCR  

E-print Network

Hybridization Screening of Very Short PCR Products for Paleoepi- demiological Studies of Chagas the kinetoplast of Try- panosoma cruzi, the infectious agent of Chagas' disease (American Trypanosomia- sis and report here is part of our major paleoepidemio- logical study of Chagas' disease (Amer- ican

428

PCR detection of potato cyst nematode.  

PubMed

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

Reid, Alex

2009-01-01

429

PCR and recombinant DNA Joan Camuas  

E-print Network

de Barcelona #12;Topics to be covered Introduction (DNA isolation, modification enzymes) PCR DNA Koolman, Klaus-Heinrich Rohm #12;Modification enzymes in molecular biology III Major types: -T4 DNAPCR and recombinant DNA techniques Joan Camuñas Felix Ritort Group Small Biosystems Lab Universitat

Ritort, Felix

430

The Power of Real-Time PCR  

ERIC Educational Resources Information Center

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

Valasek, Mark A.; Repa, Joyce J.

2005-01-01

431

PCR Assay Specific for Chicken Feces.  

PubMed

Bacteroidales are fecal anaerobic bacteria that are common in the digestive systems and feces of warm-blooded animals. Some strains of Bacteroidales have been reported to be host-specific. In this study, Bacteroidales strains from chicken feces were examined for their potential use as indicators of chicken fecal contamination. Bacteroidales 16S rRNA gene sequences from chicken feces were amplified, cloned and sequenced. Phylogenetic analysis was performed using these sequences and published Bacteroidales 16S rRNA gene sequences from human and bovine feces. Primers were designed based on putative chicken feces-specific 16S rRNA gene sequences and the primer pairs were tested for specificity in PCR assays. One set of primers, chBact F1 and chBact R16, specifically amplified DNA from chicken feces in a PCR assay, but did not amplify wild turkey, cat, bovine, or deer fecal DNAs. In addition, DNA from feces contaminated straw-based chicken litter produced a product in the PCR assay. However, DNA from feces contaminated wood shavings-based chicken litter was not amplified. The PCR assay described here may prove a useful tool for the detection of chicken feces and for source tracking in watersheds with fecal contamination. PMID:24839330

Cisar, Cindy R; Akiyama, Tatsuya; Hatley, Jonathan; Arney, Lori; Kezunovic, Nebojsa; Owen, Daniel

2010-01-01

432

Identification of Lactococcus garvieae by PCR  

Microsoft Academic Search

Lactococcus garvieae (junior synonym Enterococcus seriolicida) is an emerging zoonotic agent isolated from economically important fish (rainbow trout and yellowtail), from cattle, and from humans. Clindamycin susceptibility is the only phenotypic test which can differentiate L. garvieae from Lactococcus lactis, another emerging agent in humans. A PCR assay for the identification of L. garvieae was developed and resulted in an

AMIR ZLOTKIN; AVI ELDAR; CLAUDIO GHITTINO; HERVE BERCOVIER; Beit Dagan

433

Quantum error correction for beginners.  

PubMed

Quantum error correction (QEC) and fault-tolerant quantum computation represent one of the most vital theoretical aspects of quantum information processing. It was well known from the early developments of this exciting field that the fragility of coherent quantum systems would be a catastrophic obstacle to the development of large-scale quantum computers. The introduction of quantum error correction in 1995 showed that active techniques could be employed to mitigate this fatal problem. However, quantum error correction and fault-tolerant computation is now a much larger field and many new codes, techniques, and methodologies have been developed to implement error correction for large-scale quantum algorithms. In response, we have attempted to summarize the basic aspects of quantum error correction and fault-tolerance, not as a detailed guide, but rather as a basic introduction. The development in this area has been so pronounced that many in the field of quantum information, specifically researchers who are new to quantum information or people focused on the many other important issues in quantum computation, have found it difficult to keep up with the general formalisms and methodologies employed in this area. Rather than introducing these concepts from a rigorous mathematical and computer science framework, we instead examine error correction and fault-tolerance largely through detailed examples, which are more relevant to experimentalists today and in the near future. PMID:23787909

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

2013-07-01

434

Orthosis reduces breast pain and mechanical forces through natural and augmented breast tissue in women lying prone  

PubMed Central

Background Breast implant displacement or rupture can cause aesthetic problems and serious medical complications. Activities with prone positioning and loading of the anterior chest wall, such as massage, chiropractic or osteopathic therapies may increase the risk of implant failure and can also cause discomfort in women with natural breast tissue. Here we test the effectiveness of a newly developed orthosis on pain, mechanical pressure and displacement of breast tissue in women with cosmetic augmentation, post-mastectomy reconstruction, lactating or natural breast tissue. Methods Thirty-two females volunteers, aged 25–56 years with augmented, reconstructed, natural or lactating breast tissue and cup sizes B-F, participated in this open-label clinical trial. We measured pain perception, peak pressure, maximum force, and breast tissue displacement using different sizes of the orthosis compared to no orthosis. Different densities of the orthosis were also tested in a subgroup of women (n?=?7). Pain perception was rated using a validated 11-point visual-analogue scale. Peak pressure and maximum force were assessed using a bilateral set of capacitance-pliance® sensor strips whilst participants were load bearing in a prone position, and breast displacement was measured by magnetic-resonance-imaging. Results The orthosis significantly reduced pain, breast displacement and mechanical pressures in women with natural and augmented breast tissue in prone position. Greater relief of pain and greater reduction in mechanical forces were found with increased size and density of the orthosis. Use of the orthosis improved overall comfort by 64-100%, lowered peak pressure by up to 85% and maximum force by up to 96%. Medio-lateral displacement of breast tissue was reduced by 16%, resulting in a 51% desirable increase of breast tissue height. Conclusion Our study demonstrated that the newly developed orthosis significantly reduced pain, mechanical pressure and breast tissue displacement in women with augmented and natural breast tissue when lying prone. Our findings are of clinical significance, potentially reducing the risk of complication from prone activities in women with breast augmentation or reconstruction, as well as improving comfort whilst undergoing prone procedures. Trial registration Australia and New Zealand Clinical Trials Register, ACTRN12613000541707. PMID:24410925

2014-01-01

435

Quantum Error Correction and Orthogonal Geometry  

Microsoft Academic Search

A group theoretic framework is introduced that simplifies the description of known quantum error-correcting codes and greatly facilitates the construction of new examples. Codes are given which map 3 qubits to 8 qubits correcting 1 error, 4 to 10 qubits correcting 1 error, 1 to 13 qubits correcting 2 errors, and 1 to 29 qubits correcting 5 errors. {copyright} {ital

A. R. Calderbank; P. Shor; N. Sloane; E. Rains

1997-01-01

436

Critical evaluation of HPV16 gene copy number quantification by SYBR green PCR  

PubMed Central

Background Human papilloma virus (HPV) load and physical status are considered useful parameters for clinical evaluation of cervical squamous cell neoplasia. However, the errors implicit in HPV gene quantification by PCR are not well documented. We have undertaken the first rigorous evaluation of the errors that can be expected when using SYBR green qPCR for quantification of HPV type 16 gene copy numbers. We assessed a modified method, in which external calibration curves were generated from a single construct containing HPV16 E2, HPV16 E6 and the host gene hydroxymethylbilane synthase in a 1:1:1 ratio. Results When testing dilutions of mixed HPV/host DNA in replicate runs, we observed errors in quantifying E2 and E6 amplicons of 5–40%, with greatest error at the lowest DNA template concentration (3 ng/?l). Errors in determining viral copy numbers per diploid genome were 13–53%. Nevertheless, in cervical keratinocyte cell lines we observed reasonable agreement between viral loads determined by qPCR and Southern blotting. The mean E2/E6 ratio in episome-only cells was 1.04, but with a range of 0.76–1.32. In three integrant-only lines the mean E2/E6 ratios were 0.20, 0.72 and 2.61 (values confirmed by gene-specific Southern blotting). When E2/E6 ratios in fourteen HPV16-positive cervical carcinomas were analysed, conclusions regarding viral physical state could only be made in three cases, where the E2/E6 ratio was ? 0.06. Conclusion Run-to-run variation in SYBR green qPCR produces unavoidable inaccuracies that should be allowed for when quantifying HPV gene copy number. While E6 copy numbers can be considered to provide a useable indication of viral loads, the E2/E6 ratio is of limited value. Previous studies may have overestimated the frequency of mixed episomal/integrant HPV infections. PMID:18652663

Roberts, Ian; Ng, Grace; Foster, Nicola; Stanley, Margaret; Herdman, Michael T; Pett, Mark R; Teschendorff, Andrew; Coleman, Nicholas

2008-01-01

437

DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity  

PubMed Central

DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability. PMID:24473148

Gonzalez-Huici, Victor; Szakal, Barnabas; Urulangodi, Madhusoodanan; Psakhye, Ivan; Castellucci, Federica; Menolfi, Demis; Rajakumara, Eerappa; Fumasoni, Marco; Bermejo, Rodrigo; Jentsch, Stefan; Branzei, Dana

2014-01-01

438

The best of both worlds: emotional cues improve prospective memory execution and reduce repetition errors.  

PubMed

Prospective memory (PM) errors are commonly investigated as failures to execute an intended task (e.g., taking medication), and some studies suggest that emotional PM cues significantly reduce such failures. In Experiment 1, we extended these findings and additionally explored whether improved PM performance with emotional cues comes at the expense of performance on the ongoing task. Our results indicated that both younger and older adults are more likely to respond to emotional than to neutral PM cues, but the emotional cues did not differentially disrupt the performance on the ongoing task for either age group. Because older adults are also prone to mistakenly repeating a completed PM task, in Experiment 2 we further examined whether emotional PM cues increased repetition errors for older adults. Despite equivalent opportunity for repetition errors across cue type, older adults committed significantly fewer repetition errors with emotional than with neutral cues. Thus, these experiments demonstrated that older adults can effectively use emotional cues to help them initiate actions and to minimize repetition errors. PMID:25175608

May, Cynthia P; Manning, Michelle; Einstein, Gilles O; Becker, Lauren; Owens, Max