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1

One-step generation of error-prone PCR libraries using Gateway® technology  

PubMed Central

Background Error-prone PCR (epPCR) libraries are one of the tools used in directed evolution. The Gateway® technology allows constructing epPCR libraries virtually devoid of any background (i.e., of insert-free plasmid), but requires two steps: the BP and the LR reactions and the associated E. coli cell transformations and plasmid purifications. Results We describe a method for making epPCR libraries in Gateway® plasmids using an LR reaction without intermediate BP reaction. We also describe a BP-free and LR-free sub-cloning method for in-frame transferring the coding sequence of selected clones from the plasmid used to screen the library to another one devoid of tag used for screening (such as the green fluorescent protein). We report preliminary results of a directed evolution program using this method. Conclusions The one-step method enables producing epPCR libraries of as high complexity and quality as does the regular, two-step, protocol for half the amount of work. In addition, it contributes to preserve the original complexity of the epPCR product. PMID:22289297

2012-01-01

2

[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

3

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

4

Optimal Audio Transmission over Error-Prone Wireless Links  

E-print Network

1 Optimal Audio Transmission over Error-Prone Wireless Links Ala' Khalifeh, Student Member IEEE for transmitting high quality audio sequences over error-prone wireless links. Our framework introduces apparatus and technique to optimally protect a stored audio sequence transmitted over a wireless link while considering

Yousefi'zadeh, Homayoun

5

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

6

Error Free Self-assembly Using Error Prone Tiles  

Microsoft Academic Search

DNA self-assembly is emerging as a key paradigm for nano-technology, nano-computation, and several related disciplines. In nature, DNA self-assembly is often equipped with explicit mechanisms for both error prevention and error correction. For artificial self-assembly, these problems are even more important since we are interested in assembling large systems with great precision. We present an error-correction scheme, called snaked proof-reading,

Ho-lin Chen; Ashish Goel

2004-01-01

7

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

8

Error Free Self-Assembly using Error Prone Tiles Ho-Lin Chen  

E-print Network

Error Free Self-Assembly using Error Prone Tiles Ho-Lin Chen Stanford University Ashish Goel Stanford University Abstract. DNA self-assembly is emerging as a key paradigm for nano-technology, nano-computation, and several related disciplines. In nature, DNA self-assembly is often equipped with explicit mechanisms

Batzoglou, Serafim

9

Error-prone polymerase activity causes multinucleotide mutations in humans.  

PubMed

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

Harris, Kelley; Nielsen, Rasmus

2014-09-01

10

Error-prone DNA polymerases: when making a mistake is the only way to get ahead.  

PubMed

Cells have high-fidelity polymerases whose task is to accurately replicate the genome, and low-fidelity polymerases with specialized functions. Although some of these low-fidelity polymerases are exceptional in their ability to replicate damaged DNA and restore the undamaged sequence, they are error prone on undamaged DNA. In fact, these error-prone polymerases are sometimes used in circumstances where the capacity to make errors has a selective advantage. The mutagenic potential of the error-prone polymerases requires that their expression, activity, and access to undamaged DNA templates be regulated. Here we review these specialized polymerases with an emphasis on their biological roles. PMID:14616055

Rattray, Alison J; Strathern, Jeffrey N

2003-01-01

11

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

12

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

PubMed

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

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

2013-08-15

13

A QUANTITATIVE MODEL OF ERROR ACCUMULATION DURING PCR AMPLIFICATION  

PubMed Central

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

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

2006-01-01

14

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

15

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

PubMed

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

16

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

17

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

PubMed Central

The induction of skin cancer involves both mutagenic and proliferative responses of the epidermis to ultraviolet (UV) light. It is believed that tumor initiation requires the mutagenic replication of damaged DNA by translesion synthesis (TLS) pathways. The mechanistic basis for the induction of proliferation, providing tumor promotion, is poorly understood. Here, we have investigated the role of TLS in the initiation and promotion of skin carcinogenesis, using a sensitive nucleotide excision repair-deficient mouse model that carries a hypomorphic allele of the error-prone TLS gene Rev1. Despite a defect in UV-induced mutagenesis, skin carcinogenesis was accelerated in these mice. This paradoxical phenotype was caused by the induction of inflammatory hyperplasia of the mutant skin that provides strong tumor promotion. The induction of hyperplasia was associated with mild and transient replicational stress of the UV-damaged genome, triggering DNA damage signaling and senescence. The concomitant expression of Interleukin-6 (IL-6) is in agreement with an executive role for IL-6 and possibly other cytokines in the autocrine induction of senescence and the paracrine induction of inflammatory hyperplasia. In conclusion, error-prone TLS suppresses tumor-promoting activities of UV light, thereby controlling skin carcinogenesis. PMID:20007784

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

2009-01-01

18

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

PubMed

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

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

2014-05-15

19

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

20

Error-Prone DNA Repair System in Enteroaggregative Escherichia coli Identified by Subtractive Hybridization? †  

PubMed Central

Enteroaggregative Escherichia coli (EAEC) are etiologic agents of diarrhea. The EAEC category is heterogeneous, but most in-depth experimentation has focused on prototypical strain, 042. We hypothesized that 60A, another EAEC strain, might posses virulence or fitness genes that 042 does not have. Through subtractive hybridization we identified 60A-specific sequences, including loci present in other E. coli and phage DNA. One locus thus identified was impB, a LexA repressed error-prone DNA repair gene that has been identified in plasmids from other enteric organisms and which we detected in 21 of 34 EAEC strains. An isogenic 60A impB mutant showed decreased survival and mutagenesis after exposure to UV, as well as bile salt exposure, compared to the wild-type strain, and these phenotypes could be complemented in trans. The EAEC strain 60A imp operon differs structurally from previously described homologs. A cryptic gene, impC, present in other imp operons, is absent from 60A. In addition, transcription of impAB in strain 60A occurs from a promoter that is dissimilar to the previously described impC promoter but is still triggered by UV-mediated damage. In strain 60A the impAB and the aggregative adherence fimbriae I (AAF/I)-encoding genes are on the same large plasmid, and the 60A version of the operon is predominantly seen in AAF/I-positive EAEC. Supplementary imp SOS-inducible error-prone repair systems are common among EAEC even though they are absent in prototypical strain 042. PMID:17351038

Joo, Lucy M.; Macfarlane-Smith, Louissa R.; Okeke, Iruka N.

2007-01-01

21

Error-prone DNA repair system in enteroaggregative Escherichia coli identified by subtractive hybridization.  

PubMed

Enteroaggregative Escherichia coli (EAEC) are etiologic agents of diarrhea. The EAEC category is heterogeneous, but most in-depth experimentation has focused on prototypical strain, 042. We hypothesized that 60A, another EAEC strain, might posses virulence or fitness genes that 042 does not have. Through subtractive hybridization we identified 60A-specific sequences, including loci present in other E. coli and phage DNA. One locus thus identified was impB, a LexA repressed error-prone DNA repair gene that has been identified in plasmids from other enteric organisms and which we detected in 21 of 34 EAEC strains. An isogenic 60A impB mutant showed decreased survival and mutagenesis after exposure to UV, as well as bile salt exposure, compared to the wild-type strain, and these phenotypes could be complemented in trans. The EAEC strain 60A imp operon differs structurally from previously described homologs. A cryptic gene, impC, present in other imp operons, is absent from 60A. In addition, transcription of impAB in strain 60A occurs from a promoter that is dissimilar to the previously described impC promoter but is still triggered by UV-mediated damage. In strain 60A the impAB and the aggregative adherence fimbriae I (AAF/I)-encoding genes are on the same large plasmid, and the 60A version of the operon is predominantly seen in AAF/I-positive EAEC. Supplementary imp SOS-inducible error-prone repair systems are common among EAEC even though they are absent in prototypical strain 042. PMID:17351038

Joo, Lucy M; Macfarlane-Smith, Louissa R; Okeke, Iruka N

2007-05-01

22

Error-prone DNA repair and translesion DNA synthesis. II: The inducible SOS hypothesis.  

PubMed

Evelyn Witkin hypothesized in 1967 that bacterial cell division is controlled by a repressor which, like the lambda repressor, is inactivated by a complex process that starts with the presence of replication-blocking lesions in the DNA. She further suggested that this might not be the only cellular function to show induction by DNA damage. Three years later, Miroslav Radman, in a privately circulated note, proposed that one such function might be an inaccurate (mutation-prone) DNA polymerase under the control of the recA and lexA genes. Thus was born the SOS hypothesis. PMID:15907776

Bridges, Bryn A

2005-06-01

23

Modification of PCNA by ISG15 plays a crucial role in termination of error-prone translesion DNA synthesis.  

PubMed

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

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

2014-05-22

24

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

PubMed Central

Summary Occupational, environmental, and nutritional epidemiologists are often interested in estimating the prospective effect of time-varying exposure variables such as cumulative exposure or cumulative updated average exposure, in relation to chronic disease endpoints such as cancer incidence and mortality. From exposure validation studies, it is apparent that many of the variables of interest are measured with moderate to substantial error. Although the ordinary regression calibration approach is approximately valid and efficient for measurement error correction of relative risk estimates from the Cox model with time-independent point exposures when the disease is rare, it is not adaptable for use with time-varying exposures. By re-calibrating the measurement error model within each risk set, a risk set regression calibration method is proposed for this setting. An algorithm for a bias-corrected point estimate of the relative risk using an RRC approach is presented, followed by the derivation of an estimate of its variance, resulting in a sandwich estimator. Emphasis is on methods applicable to the main study/external validation study design, which arises in important applications. Simulation studies under several assumptions about the error model were carried out, which demonstrated the validity and efficiency of the method in finite samples. The method was applied to a study of diet and cancer from Harvard’s Health Professionals Follow-up Study (HPFS). PMID:20486928

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

2010-01-01

25

FragGeneScan: predicting genes in short and error-prone reads.  

PubMed

The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging problem in annotating metagenomes, since the assembly of metagenomes is often not available. Gene predictors developed for whole genomes (e.g. Glimmer) and recently developed for metagenomic sequences (e.g. MetaGene) show a significant decrease in performance as the sequencing error rates increase, or as reads get shorter. We have developed a novel gene prediction method FragGeneScan, which combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads. The performance of FragGeneScan was comparable to Glimmer and MetaGene for complete genomes. But for short reads, FragGeneScan consistently outperformed MetaGene (accuracy improved ?62% for reads of 400 bases with 1% sequencing errors, and ?18% for short reads of 100 bases that are error free). When applied to metagenomes, FragGeneScan recovered substantially more genes than MetaGene predicted (>90% of the genes identified by homology search), and many novel genes with no homologs in current protein sequence database. PMID:20805240

Rho, Mina; Tang, Haixu; Ye, Yuzhen

2010-11-01

26

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

PubMed

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

2015-01-30

27

A Bayesian approach to strengthen inference for case-control studies with multiple error-prone exposure assessments  

PubMed Central

In case-control studies, exposure assessments are almost always error-prone. In the absence of a gold standard, two or more assessment approaches are often used to classify people with respect to exposure. Each imperfect assessment tool may lead to misclassification of exposure assignment; the exposure misclassification may be differential with respect to case status or not; and, the errors in exposure classification under the different approaches may be independent (conditional upon the true exposure status) or not. Although methods have been proposed to study diagnostic accuracy in the absence of a gold standard, these methods are infrequently used in case-control studies to correct exposure misclassification that is simultaneously differential and dependent. In this paper, we proposed a Bayesian method to estimate the measurement-error corrected exposure-disease association, accounting for both differential and dependent misclassification. The performance of the proposed method is investigated using simulations, which show that the proposed approach works well, as well as an application to a case-control study assessing the association between asbestos exposure and mesothelioma. PMID:23661263

Zhang, Jing; Cole, Stephen R.; Richardson, David B.; Chu, Haitao

2013-01-01

28

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

29

The Escherichia coli UVM response is accompanied by an SOS-independent error-prone DNA replication activity demonstrable in vitro.  

PubMed

UVM is an SOS-independent inducible response characterized by elevated mutagenesis at a site-specific 3, N4-ethenocytosine (epsilonC) residue borne on M13 single-stranded DNA transfected into Escherichia coli cells pretreated with DNA-damaging agents. By constructing and using E. coli strain AM124 (polA polB umuDC dinB lexA1[Ind-]), we show here that the UVM response is manifested in cells deficient for SOS induction, as well as for all four of the 'non-replicative' DNA polymerases, namely DNA polymerase I (polA), II (polB), IV (dinB) and V (umuDC). These results confirm that UVM represents a novel, previously unidentified cellular response to DNA-damaging agents. To address the question as to whether the UVM response is accompanied by an error-prone DNA replication activity, we applied a newly developed in vitro replication assay coupled to an in vitro mutation analysis system. In the assay, circular M13 single-stranded DNA bearing a site-specific lesion is converted to circular double-stranded replicative-form DNA in the presence of cell extracts and nucleotide precursors under conditions that closely mimic M13 replication in vivo. The newly synthesized (minus) DNA strand is selectively amplified by ligation-mediated polymerase chain reaction (LM-PCR), followed by a multiplex sequence analysis to determine the frequency and specificity of mutations. Replication of DNA bearing a site-specific epsilonC lesion by cell extracts from uninduced E. coli AM124 cells results in a mutation frequency of about 13%. Mutation frequency is elevated fivefold (to 58%) in cell extracts from UVM-induced AM124 cells, with C --> A mutations predominating over C --> T mutations, a specificity similar to that observed in vivo. These results, together with previously reported data, suggest that the UVM response is mediated through the induction of a transient error-prone DNA replication activity and that a modification of DNA polymerase III or the expression of a previously unidentified DNA polymerase may account for the UVM phenotype. PMID:11069662

Al Mamun, A A; Yadava, R S; Ren, L; Humayun, M Z

2000-10-01

30

Escherichia coli DNA polymerase V subunit exchange: a post-SOS mechanism to curtail error-prone DNA synthesis.  

PubMed

DNA polymerase V consisting of a heterotrimer composed of one molecule of UmuC and two molecules of UmuD' (UmuD'2C) is responsible for SOS damage-induced mutagenesis in Escherichia coli. Here we show that although the UmuD'2C complex remains intact through multiple chromatographic steps, excess UmuD, the precursor to UmuD', displaces UmuD' from UmuD'2C by forming a UmuDD' heterodimer, while UmuC concomitantly aggregates as an insoluble precipitate. Although soluble UmuD'2C is readily detected when the two genes are co-transcribed and translated in vitro, soluble UmuD2C or UmuDD'C are not detected. The subunit exchange between UmuD'2C and UmuD offers a biological means to inactivate error-prone polymerase V following translesion synthesis, thus preventing mutations from occurring on undamaged DNA. PMID:14573598

Shen, Xuan; Woodgate, Roger; Goodman, Myron F

2003-12-26

31

Error-prone ZW pairing and no evidence for meiotic sex chromosome inactivation in the chicken germ line.  

PubMed

In the male mouse the X and Y chromosomes pair and recombine within the small pseudoautosomal region. Genes located on the unsynapsed segments of the X and Y are transcriptionally silenced at pachytene by Meiotic Sex Chromosome Inactivation (MSCI). The degree to which MSCI is conserved in other vertebrates is currently unclear. In the female chicken the ZW bivalent is thought to undergo a transient phase of full synapsis at pachytene, starting from the homologous ends and spreading through the heterologous regions. It has been proposed that the repair of the ZW DNA double-strand breaks (DSBs) is postponed until diplotene and that the ZW bivalent is subject to MSCI, which is independent of its synaptic status. Here we present a distinct model of meiotic pairing and silencing of the ZW pair during chicken oogenesis. We show that, in most oocytes, DNA DSB foci on the ZW are resolved by the end of pachytene and that the ZW desynapses in broad synchrony with the autosomes. We unexpectedly find that ZW pairing is highly error prone, with many oocytes failing to engage in ZW synapsis and crossover formation. Oocytes with unsynapsed Z and W chromosomes nevertheless progress to the diplotene stage, suggesting that a checkpoint does not operate during pachytene in the chicken germ line. Using a combination of epigenetic profiling and RNA-FISH analysis, we find no evidence for MSCI, associated with neither the asynaptic ZW, as described in mammals, nor the synaptic ZW. The lack of conservation of MSCI in the chicken reopens the debate about the evolution of MSCI and its driving forces. PMID:22412389

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

2012-01-01

32

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

33

Removal of PCR Error Products and Unincorporated Primers by Metal-Chelate Affinity Chromatography  

PubMed Central

Immobilized Metal Affinity Chromatography (IMAC) has been used for decades to purify proteins on the basis of amino acid content, especially surface-exposed histidines and “histidine tags” genetically added to recombinant proteins. We and others have extended the use of IMAC to purification of nucleic acids via interactions with the nucleotide bases, especially purines, of single-stranded RNA and DNA. We also have demonstrated the purification of plasmid DNA from contaminating genomic DNA by IMAC capture of selectively-denatured genomic DNA. Here we describe an efficient method of purifying PCR products by specifically removing error products, excess primers, and unincorporated dNTPs from PCR product mixtures using flow-through metal-chelate affinity adsorption. By flowing a PCR product mixture through a Cu2+-iminodiacetic acid (IDA) agarose spin column, 94–99% of the dNTPs and nearly all the primers can be removed. Many of the error products commonly formed by Taq polymerase also are removed. Sequencing of the IMAC-processed PCR product gave base-calling accuracy comparable to that obtained with a commercial PCR product purification method. The results show that IMAC matrices (specifically Cu2+-IDA agarose) can be used for the purification of PCR products. Due to the generality of the base-specific mechanism of adsorption, IMAC matrices may also be used in the purification of oligonucleotides, cDNA, mRNA and micro RNAs. PMID:21264292

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

2011-01-01

34

Removal of PCR Error Products and Unincorporated Primers by Metal-Chelate Affinity Chromatography  

E-print Network

Removal of PCR Error Products and Unincorporated Primers by Metal-Chelate Affinity Chromatography of America Abstract Immobilized Metal Affinity Chromatography (IMAC) has been used for decades to purify Products and Unincorporated Primers by Metal-Chelate Affinity Chromatography. PLoS ONE 6(1): e14512. doi:10

Fox, George

35

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

36

Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli  

PubMed Central

DNA polymerase V, composed of a heterotrimer of the DNA damage-inducible UmuC and UmuD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}{\\mathrm{_{2}^{^{\\prime}}}}\\end{equation*}\\end{document} proteins, working in conjunction with RecA, single-stranded DNA (ssDNA)-binding protein (SSB), ? sliding clamp, and ? clamp loading complex, are responsible for most SOS lesion-targeted mutations in Escherichia coli, by catalyzing translesion synthesis (TLS). DNA polymerase II, the product of the damage-inducible polB (dinA ) gene plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Replication-restart takes place almost immediately after the DNA is damaged (?2 min post-UV irradiation), whereas TLS occurs after pol V is induced ?50 min later. We discuss recent data for pol V-catalyzed TLS and pol II-catalyzed replication-restart. Specific roles during TLS for pol V and each of its accessory factors have been recently determined. Although the precise molecular mechanism of pol II-dependent replication-restart remains to be elucidated, it has recently been shown to operate in conjunction with RecFOR and PriA proteins. PMID:11459974

Pham, Phuong; Rangarajan, Savithri; Woodgate, Roger; Goodman, Myron F.

2001-01-01

37

Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli.  

PubMed

DNA polymerase V, composed of a heterotrimer of the DNA damage-inducible UmuC and UmuD(2)(') proteins, working in conjunction with RecA, single-stranded DNA (ssDNA)-binding protein (SSB), beta sliding clamp, and gamma clamp loading complex, are responsible for most SOS lesion-targeted mutations in Escherichia coli, by catalyzing translesion synthesis (TLS). DNA polymerase II, the product of the damage-inducible polB (dinA ) gene plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Replication-restart takes place almost immediately after the DNA is damaged (approximately 2 min post-UV irradiation), whereas TLS occurs after pol V is induced approximately 50 min later. We discuss recent data for pol V-catalyzed TLS and pol II-catalyzed replication-restart. Specific roles during TLS for pol V and each of its accessory factors have been recently determined. Although the precise molecular mechanism of pol II-dependent replication-restart remains to be elucidated, it has recently been shown to operate in conjunction with RecFOR and PriA proteins. PMID:11459974

Pham, P; Rangarajan, S; Woodgate, R; Goodman, M F

2001-07-17

38

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

39

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

PubMed

DNA-protein crosslinks (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 the present 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 cycloaddition 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 hPol ? and ? can incorporate A, G, C, or T opposite the C5-dT-conjugated DNA-peptide conjugates, while hPol ? preferentially inserts G opposite the lesion. Furthermore, HPLC-ESI--MS/MS sequencing of the extension products has revealed that postlesion 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 C-5 position of thymine by human TLS 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

2014-11-12

40

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

41

Involvement of Nucleotide Excision Repair in a Recombination-Independent and Error-Prone Pathway of DNA Interstrand Cross-Link Repair  

PubMed Central

DNA interstrand cross-links (ICLs) block the strand separation necessary for essential DNA functions such as transcription and replication and, hence, represent an important class of DNA lesion. Since both strands of the double helix are affected in cross-linked DNA, it is likely that conservative recombination using undamaged homologous regions as a donor may be required to repair ICLs in an error-free manner. However, in Escherichia coli and yeast, recombination-independent mechanisms of ICL repair have been identified in addition to recombinational repair pathways. To study the repair mechanisms of interstrand cross-links in mammalian cells, we developed an in vivo reactivation assay to examine the removal of interstrand cross-links in cultured cells. A site-specific psoralen cross-link was placed between the promoter and the coding region to inactivate the expression of green fluorescent protein or luciferase genes from reporter plasmids. By monitoring the reactivation of the reporter gene, we showed that a single defined psoralen cross-link was removed in repair-proficient cells in the absence of undamaged homologous sequences, suggesting the existence of an ICL repair pathway that is independent of homologous recombination. Mutant cell lines deficient in the nucleotide excision repair pathway were examined and found to be highly defective in the recombination-independent repair of ICLs, while mutants deficient in homologous recombination were found to be proficient. Mutation analysis of plasmids recovered from transfected cells showed frequent base substitutions at or near positions opposing a cross-linked thymidine residue. Based on these results, we suggest a distinct pathway for DNA interstrand cross-link repair involving nucleotide excision repair and a putative lesion bypass mechanism. PMID:11154259

Wang, Xin; Peterson, Carolyn A.; Zheng, Huyong; Nairn, Rodney S.; Legerski, Randy J.; Li, Lei

2001-01-01

42

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

Microsoft Academic Search

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

R. G. Rutledge

2004-01-01

43

Reducing medication errors.  

PubMed

Most nurses are involved in medicines management, which is integral to promoting patient safety. Medicines management is prone to errors, which depending on the error can cause patient injury, increased hospital stay and significant legal expenses. This article describes a new approach to help minimise drug errors within healthcare settings where medications are prescribed, dispensed or administered. The acronym DRAINS, which considers all aspects of medicines management before administration, was devised to reduce medication errors on a cardiothoracic intensive care unit. PMID:25408048

Nute, Christine

2014-11-19

44

Serial Subtraction Errors Revealed  

E-print Network

A fine-grained analysis of errors and their frequency during the performance of a mental multi-digit serial subtraction task reveals the cognitive processes most prone to failure. Example serial subtraction problems from the experimental problem set are utilized in illustrating different types of errors and their probable causes. A list of considerations is presented for future descriptive and computational modeling of the errors committed during performance of the task.

Sue E. Kase; Frank E. Ritter; Michael Schoelles

45

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

46

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

47

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

48

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

MedlinePLUS

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

49

Building a reliable internet core using soft error prone electronics  

Microsoft Academic Search

This paper describes a methodology for building a reliable internet core router that considers the vulnerability of its electronic components to single event upset (SEU). It begins with a set of meaningful system level metrics that can be related to product reliability requirements. A specification is then defined that can be effectively used during the system architecture, silicon and software

Allan L. Silburt; Adrian Evans; Ana Burghelea; Shi-Jie Wen; D. Ward; R. Norrish; D. Hogle

2008-01-01

50

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

51

PCR detection of nearly any dengue virus strain using a highly sensitive primer `cocktail'  

E-print Network

PCR detection of nearly any dengue virus strain using a highly sensitive primer `cocktail' Charul to target effectively. This problem is espe- cially pronounced with the mutation-prone RNA viruses. Dengue Keywords cocktail PCR; dengue virus; diagnostic; PCR; primer Correspondence R. C. Willson, Department

Fox, George

52

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

53

Associations between intrusive thoughts, reality discrimination and hallucination-proneness in healthy young adults.  

PubMed

Introduction. People who experience intrusive thoughts are at increased risk of developing hallucinatory experiences, as are people who have weak reality discrimination skills. No study has yet examined whether these two factors interact to make a person especially prone to hallucinatory experiences. The present study examined this question in a non-clinical sample. Methods. Participants were 160 students, who completed a reality discrimination task, as well as self-report measures of cannabis use, negative affect, intrusive thoughts and auditory hallucination-proneness. The possibility of an interaction between reality discrimination performance and level of intrusive thoughts was assessed using multiple regression. Results. The number of reality discrimination errors and level of intrusive thoughts were independent predictors of hallucination-proneness. The reality discrimination errors × intrusive thoughts interaction term was significant, with participants who made many reality discrimination errors and reported high levels of intrusive thoughts being especially prone to hallucinatory experiences. Conclusions. Hallucinatory experiences are more likely to occur in people who report high levels of intrusive thoughts and have weak reality discrimination skills. If applicable to clinical samples, these findings suggest that improving patients' reality discrimination skills and reducing the number of intrusive thoughts they experience may reduce the frequency of hallucinatory experiences. PMID:25345759

Smailes, David; Meins, Elizabeth; Fernyhough, Charles

2015-01-01

54

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

55

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

56

Psychosis-proneness and socially relevant reasoning.  

PubMed

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

Young, Eliane; Mason, Oliver

2007-03-30

57

Potential aggregation prone regions in biotherapeutics  

PubMed Central

Aggregation of a biotherapeutic is of significant concern and judicious process and formulation development is required to minimize aggregate levels in the final product. Aggregation of a protein in solution is driven by intrinsic and extrinsic factors. In this work we have focused on aggregation as an intrinsic property of the molecule. We have studied the sequences and Fab structures of commercial and non-commercial antibody sequences for their vulnerability towards aggregation by using sequence based computational tools to identify potential aggregation-prone motifs or regions. The mAbs in our dataset contain 2 to 8 aggregation-prone motifs per heavy and light chain pair. Some of these motifs are located in variable domains, primarily in CDRs. Most aggregation-prone motifs are rich in ? branched aliphatic and aromatic residues. Hydroxyl-containing Ser/Thr residues are also found in several aggregation-prone motifs while charged residues are rare. The motifs found in light chain CDR3 are glutamine (Q)/asparagine (N) rich. These motifs are similar to the reported aggregation promoting regions found in prion and amyloidogenic proteins that are also rich in Q/N, aliphatic and aromatic residues. The implication is that one possible mechanism for aggregation of mAbs may be through formation of cross-? structures and fibrils. Mapping on the available Fab—receptor/antigen complex structures reveals that these motifs in CDRs might also contribute significantly towards receptor/antigen binding. Our analysis identifies the opportunity and tools for simultaneous optimization of the therapeutic protein sequence for potency and specificity while reducing vulnerability towards aggregation. PMID:20065649

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

2009-01-01

58

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

PubMed

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

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

2014-01-01

59

Action simulation in hallucination-prone adolescents  

PubMed Central

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

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

2013-01-01

60

New fire-prone areas in Europe  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

61

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

62

Extralevator abdominoperineal resection in the prone position.  

PubMed

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

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

2014-03-01

63

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

Code of Federal Regulations, 2012 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...

2012-10-01

64

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

...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...

2014-10-01

65

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

Code of Federal Regulations, 2013 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...

2013-10-01

66

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

67

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

Code of Federal Regulations, 2012 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...

2012-10-01

68

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

69

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

70

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

Code of Federal Regulations, 2013 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...

2013-10-01

71

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

Code of Federal Regulations, 2010 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...

2010-10-01

72

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

...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...

2014-10-01

73

Estimating genetic variability in non-model taxa: a general procedure for discriminating sequence errors from actual variation.  

PubMed

Genetic variation is the driving force of evolution and as such is of central interest for biologists. However, inadequate discrimination of errors from true genetic variation could lead to incorrect estimates of gene copy number, population genetic parameters, phylogenetic relationships and the deposition of gene and protein sequences in databases that are not actually present in any organism. Misincorporation errors in multi-template PCR cloning methods, still commonly used for obtaining novel gene sequences in non-model species, are difficult to detect, as no previous information may be available about the number of expected copies of genes belonging to multi-gene families. However, studies employing these techniques rarely describe in any great detail how errors arising in the amplification process were detected and accounted for. Here, we estimated the rate of base misincorporation of a widely-used PCR-cloning method, using a single copy mitochondrial gene from a single individual to minimise variation in the template DNA, as 1.62×10(-3) errors per site, or 9.26×10(-5) per site per duplication. The distribution of errors among sequences closely matched that predicted by a binomial distribution function. The empirically estimated error rate was applied to data, obtained using the same methods, from the Phospholipase A(2) toxin family from the pitviper Ovophis monticola. The distribution of differences detected closely matched the expected distribution of errors and we conclude that, when undertaking gene discovery or assessment of genetic diversity using this error-prone method, it will be informative to empirically determine the rate of base misincorporation. PMID:21151906

Dawson, Karen; Thorpe, Roger S; Malhotra, Anita

2010-01-01

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

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

76

FLOOD-PLAIN DELINEATION IN ICE JAM PRONE REGIONS  

E-print Network

FLOOD-PLAIN DELINEATION IN ICE JAM PRONE REGIONS By Richard M. Vogel,1 S. M. ASCE and Jery R. Stedinger,2 A. M. ASCE ABSTRACT:Flood-plain delineation in ice jam prone regions is in its infancy .A-plain boundaries. These results document the need to consider the probability of ice jam flood events

Vogel, Richard M.

77

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

78

Pathogenesis of A??? ketosis-prone diabetes.  

PubMed

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

2013-03-01

79

Explanatory chapter: quantitative PCR.  

PubMed

Quantitative PCR (qPCR), also called real-time PCR or quantitative real-time PCR, is a PCR-based technique that couples amplification of a target DNA sequence with quantification of the concentration of that DNA species in the reaction. This method enables calculation of the starting template concentration and is therefore a frequently used analytical tool in evaluating DNA copy number, viral load, SNP detection, and allelic discrimination. When preceded by reverse-transcription PCR, qPCR is a powerful tool to measure mRNA expression and is the gold standard for microarray gene expression data confirmation. Given the broad applications of qPCR and the many technical variations that have been developed, a brief survey of qPCR, including technical background, available chemistries, and data analysis techniques will provide a framework for both experimental design and evaluation. PMID:24011054

Dymond, Jessica S

2013-01-01

80

Piezoelectric control of structures prone to instabilities  

NASA Astrophysics Data System (ADS)

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

Kim, Sunjung

81

Refractive Errors  

MedlinePLUS

... your eye helps you focus. Refractive errors are vision problems that happen when the shape of the ... common refractive errors are Myopia, or nearsightedness - clear vision close up but blurry in the distance Hyperopia, ...

82

Sampling Error  

NSDL National Science Digital Library

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

2009-01-07

83

Pre-PCR processing  

Microsoft Academic Search

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

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

2004-01-01

84

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

85

Correlates of prone infant sleeping position by period of birth.  

PubMed Central

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

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

1995-01-01

86

Determination of radon prone areas by optimized binary classification.  

PubMed

Geogenic radon prone areas are regions in which for natural reasons elevated indoor radon concentrations must be expected. Their identification is part of radon mitigation policies in many countries, as radon is acknowledged a major indoor air pollutant, being the second cause of lung cancer after smoking. Defining and estimating radon prone areas is therefore of high practical interest. In this paper a method is presented which uses the geogenic radon potential as predictor and thresholds of indoor radon concentration for defining radon prone areas, from which thresholds for the geogenic radon potential are deduced which decide whether a location is flagged radon prone or not, in the absence of actual indoor observations. The overall results are different maps of radon prone areas, derived from the geogenic radon map, and depending (1) on the criterion which defines what a radon prone area is; and (2) on the choice of score whose maximization defines the optimal classifier. Such map is not the result of a transfer model (geogenic to indoor radon), but of the optimization of a classification rule. The method is computationally simple but has its caveats and statistical traps, some of which are also addressed. PMID:24412776

Bossew, P

2014-03-01

87

The prone position in ARDS patients. A clinical study.  

PubMed

The gas exchange and hemodynamics were evaluated before, during, and after a two-hour period of prone position in 13 moderate-severe ARDS patients. Lung computerized tomography was obtained in both the supine and prone positions in two of these patients. Average arterial oxygenation improved after prone positioning (p less than 0.01). A PaO2 improvement of at least 10 mm Hg after 30 minutes of prone position was used as a criterion to discriminate between responders and nonresponders to the postural change. Eight patients met the "responders" group criterion, and in the five nonresponder patients, the PaO2 did not change significantly throughout the study. Computerized tomograms in the prone position showed disappearance of posterobasal densities and appearance of new densities in the anterior regions, in both patients studied. One of these was a responder, the other a nonresponder. A brief test period in prone position is indicated in ARDS patients to identify those who may benefit from this postural treatment. The definite mechanism of the arterial oxygenation improvement observed remains to be clarified. PMID:3383620

Langer, M; Mascheroni, D; Marcolin, R; Gattinoni, L

1988-07-01

88

CODEHOP PCR and CODEHOP PCR primer design.  

PubMed

While PCR primer design for the amplification of known sequences is usually quite straightforward, the design, and successful application of primers aimed at the detection of as yet unknown genes is often not. The search for genes that are presumed to be distantly related to a known gene sequence, such as homologous genes in different species, paralogs in the same genome, or novel pathogens in diverse hosts, often turns into the proverbial search for the needle in the haystack. PCR-based methods commonly used to address this issue involve the use of either consensus primers or degenerate primers, both of which have significant shortcomings regarding sensitivity and specificity. We have developed a novel primer design approach that diminishes these shortcomings and instead takes advantage of the strengths of both consensus and degenerate primer designs, by combining the two concepts into a Consensus-Degenerate Hybrid Oligonucleotide Primer (CODEHOP) approach. CODEHOP PCR primers contain a relatively short degenerate 3' core and a 5' nondegenerate clamp. The 3' degenerate core consists of a pool of primers containing all possible codons for a 3-4 aminoacid motif that is highly conserved in multiply aligned sequences from known members of a protein family. Each primer in the pool also contains a single 5' nondegenerate nucleotide sequence derived from a codon consensus across the aligned aminoacid sequences flanking the conserved motif. During the initial PCR amplification cycles, the degenerate core is responsible for specific binding to sequences encoding the conserved aminoacid motif. The longer consensus clamp region serves to stabilize the primer and allows the participation of all primers in the pool in the efficient amplification of products during later PCR cycles. We have developed an interactive web site and algorithm (iCODEHOP) for designing CODEHOP PCR primers from multiply aligned protein sequences, which is freely available online. Here, we describe the workflow of a typical CODEHOP PCR assay design and optimization and give a specific implementation example along with "best-practice" advice. PMID:20967601

Staheli, Jeannette P; Boyce, Richard; Kovarik, Dina; Rose, Timothy M

2011-01-01

89

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

90

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.

91

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

PubMed Central

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

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

2008-01-01

92

Digital PCR and Quantitation  

E-print Network

Group Forensics@NIST 2012 Meeting Gaithersburg, MD November 28, 2012 #12;Applied Genetics Agenda · Why with qPCR · Forensic samples often have non-human DNA ­ Forensic standards require human specific DNA · Predicted Major Uses of Digital PCR: ­ Quantify higher order reference materials · Standard Reference

Perkins, Richard A.

93

Medication Errors  

MedlinePLUS

... for Healthcare Research and Quality: Medical Errors and Patient Safety Centers for Disease Control and Prevention: Medication Safety Department of Veterans Affairs National Center for Patient Safety Institute for Safe Medication Practices To Err is ...

94

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 ...

95

Discovering motifs that induce sequencing errors  

PubMed Central

Background Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS). Beyond routinely handled generic sources of errors, certain base calling errors relate to specific sequence patterns. Statistically principled ways to associate sequence patterns with base calling errors have not been previously described. Extant approaches either incur decisive losses in power, due to relating errors with individual genomic positions rather than motifs, or do not properly distinguish between motif-induced and sequence-unspecific sources of errors. Results Here, for the first time, we describe a statistically rigorous framework for the discovery of motifs that induce sequencing errors. We apply our method to several datasets from Illumina GA IIx, HiSeq 2000, and MiSeq sequencers. We confirm previously known error-causing sequence contexts and report new more specific ones. Conclusions Checking for error-inducing motifs should be included into SNP calling pipelines to avoid false positives. To facilitate filtering of sets of putative SNPs, we provide tracks of error-prone genomic positions (in BED format). Availability http://discovering-cse.googlecode.com PMID:23735080

2013-01-01

96

Intra-patient Prone to Supine Colon Registration  

E-print Network

Intra-patient Prone to Supine Colon Registration for Synchronized Virtual Colonoscopy Delphine Nain,hooni,kikinis,westin}@bwh.harvard.edu http://www.spl.harvard.edu Abstract. 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

97

The Validity and Utility of the Depression Proneness Rating Scale.  

ERIC Educational Resources Information Center

The development of the Depression Proneness Rating Scale (DPRS) and three investigations into its reliability, validity, and factor structure are described. Subjects of all three studies were university undergraduates. The first study (n=100) found a stability coefficient of 0.82 for the DPRS over a test-retest (Time 1-Time 2) interval of 9 weeks.…

Zemore, Robert; And Others

98

Managing fire-prone forests in the western United States  

Microsoft Academic Search

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

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

2006-01-01

99

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

100

Automatic prone to supine haustral fold matching in CT colonography using a Markov random field model.  

PubMed

CT colonography is routinely performed with the patient prone and supine to differentiate fixed colonic pathology from mobile faecal residue. We propose a novel method to automatically establish correspondence. Haustral folds are detected using a graph cut method applied to a surface curvature-based metric, where image patches are generated using endoluminal CT colonography surface rendering. The intensity difference between image pairs, along with additional neighbourhood information to enforce geometric constraints, are used with a Markov Random Field (MRF) model to estimate the fold labelling assignment. The method achieved fold matching accuracy of 83.1% and 88.5% with and without local colonic collapse. Moreover, it improves an existing surface-based registration algorithm, decreasing mean registration error from 9.7mm to 7.7mm in cases exhibiting collapse. PMID:22003656

Hampshire, Thomas; Roth, Holger; Hu, Mingxing; Boone, Darren; Slabaugh, Greg; Punwani, Shonit; Halligan, Steve; Hawkes, David

2011-01-01

101

A novel still image error concealment using fragile watermarking in wireless image transmission and packet-switched networks  

Microsoft Academic Search

Images transmitted over unreliable channels are highly prone to errors. Produces distortion in transmitted images is usually repaired using post processing techniques called error concealment. Error concealment techniques provide a simple framework to compensate the produced distortions without incurring additional delays and wasting bandwidth resources which are crucial for real-time applications over networks with limited resources. Utilizing data hiding techniques

Davood Bashiri; Ali Aghagolzadeh; Javad Museviniya; Mehdi Nooshyar

2008-01-01

102

Atypical diabetes in children: ketosis-prone type 2 diabetes  

PubMed Central

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

103

Enhancing disaster management by mapping disaster proneness and preparedness.  

PubMed

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

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

2012-07-01

104

Sulphamethoxazole prophylaxis in the otitis-prone child  

Microsoft Academic Search

A bedtime dose of sulphamethoxazole was effective in preventing ear infections in otitis-prone young children. Thirty-three such children were studied by means of a random, double-blind, placebo-controlled, cross-over protocol. Nine (27%) of 33 children treated with sulphamethoxazole experienced 10 episodes of acute suppurative otitis media or otitis media with effusion while 19 (58%) of 33 children given a placebo experienced

R H Schwartz; J Puglise; W J Rodriguez

1982-01-01

105

Mapping radon-prone areas - a geophysical approach  

Microsoft Academic Search

Radon-prone areas in Israel were mapped on the basis of direct measurements of radon (222Rn) in the soil\\/rock gas of all exposed geological units, supported by the accumulated knowledge of local stratigraphy and\\u000a sub-surface geology. Measurements were carried out by a modified alpha-track detection system, resulting in high radon levels\\u000a mainly in rocks of the Senonian-Paleocene-aged Mount Scopus Group, comprised

U. Vulkan

1997-01-01

106

Thoracoscopic and laparoscopic radical esophagectomy with lateral-prone position  

PubMed Central

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

Ma, Zheng; Niu, Huijun

2014-01-01

107

Breakdown-prone volume in terahertz wave beams  

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

108

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

PubMed Central

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

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

2012-01-01

109

Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase  

PubMed Central

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

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

2014-01-01

110

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...

111

Revisiting the prone position in video-assisted thoracoscopic surgery.  

PubMed

The fully prone position, once used in surgery for chronic inflammatory lung diseases, has become obsolete. In the last 2 years, a modified semiprone position was used for video-assisted thoracoscopic surgery in 358 patients undergoing lobectomy with mediastinal complete lymphadenectomy The ports were placed with the patient in the lateral decubitus position. The patient was rotated 45-60 degrees towards the surgeon, giving enhanced exposure of the posterior mediastinum, esophagus, subcarinal and paratracheal spaces, due to displacement of the lung under gravity away from the operative field. This position is safe, well-tolerated, and allows more ergonomic and anatomical placement of the ports. PMID:20719788

Agasthian, Thirugnanam

2010-08-01

112

Ultrasound to reduce cognitive errors in the ED.  

PubMed

Emergency medicine setting is intrinsically prone to a greater risk of medical errors than other specialties. Cognitive errors are particularly frequent when the clinical decision-making process heavily relies on heuristics. These could be defined as "mental shortcuts," which enable physicians to rapidly overcome both time and efforts required by the normative reasoning. Our article demonstrates how emergency physicians' thinking may be affected by failed heuristics, through the description of 3 real clinical cases. We aimed to show how the proper use of a widespread and easy-learning technology, such as goal-directed, focused ultrasonography, may both counteract cognitive errors and favor the right interpretation of other examinations. PMID:22795417

Elia, Fabrizio; Panero, Francesco; Molino, Paola; Ferrari, Giovanni; Aprà, Franco

2012-11-01

113

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

2014-12-10

114

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...

115

Predicting Fault-Prone Modules: A Comparative Study  

NASA Astrophysics Data System (ADS)

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

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

116

Measurement of vertebral rotation in adolescent idiopathic scoliosis with low-dose CT in prone position - method description and reliability analysis  

PubMed Central

Background To our knowledge there is no report in the literature on measurements of vertebral rotation with low-dose computed tomography (CT) in prone position. Aims To describe and test the reliability of this new method, compare it with other methods in use and evaluate the influence of body position on the degree of vertebral rotation measured by different radiological methods. Study design Retrospective study. Methods 25 consecutive patients with adolescent idiopathic scoliosis scheduled for surgery (17 girls, 8 boys) aged 15 ± 2 years (mean ± SD) were included in the analysis of this study. The degree of the vertebral rotation was in all patients measured according to the method of Perdriolle on standing plain radiographs and on supine CT scanogram, and according to the method of Aaro and Dahlborn on axial CT images in prone position and on magnetic resonance imaging (MRI) in supine position. The measurements were done by one neuroradiologist at two different occasions. Bland and Altman statistical approach was used in the reliability assessment. Results The reliability of measuring vertebral rotation by axial CT images in prone position was almost perfect with an intraclass correlation coefficient of 0.95, a random error of the intraobserver differences of 2.3°, a repeatability coefficient of 3.2° and a coefficient of variation of 18.4%. Corresponding values for measurements on CT scanogram were 0.83, 5.1°, 7.2°, and 32.8%, respectively, indicating lower reliability of the latter modality and method. The degree of vertebral rotation measured on standing plain radiographs, prone CT scanogram, axial images on CT in prone position and on MRI in supine position were 25.7 ± 9.8°, 21.9 ± 8.3°, 17.4 ± 7.1°, and 16.1 ± 6.5°, respectively. The vertebral rotation measured on axial CT images in prone position was in average 7.5% larger than that measured on axial MRI in supine position. Conclusions This study has shown that measurements of vertebral rotation in prone position were more reliable on axial CT images than on CT scanogram. The measurement of vertebral rotation on CT (corrected to the pelvic tilt) in prone position imposes lower impact of the recumbent position on the vertebral rotation than did MRI in supine position. However, the magnitude of differences is of doubtful clinical significance. PMID:20178610

2010-01-01

117

Facts about Refractive Errors  

MedlinePLUS

... NEI Education Programs Training and Jobs Facts About Refractive Errors Listen This information was developed by the National ... is the best person to answer specific questions. Refractive Errors Defined What are refractive errors? Refractive errors occur ...

118

Shock wave lithotripsy for distal ureteric stones: supine or prone.  

PubMed

Shock wave lithotripsy (SWL) has become the preferred first-line approach to most patients with symptomatic urolithiasis. The purpose of this study is to assess the ideal patient position during SWL for the treatment of distal ureter stones. A total of 342 patients included in this retrospective study. 148 (108 men, 40 women) patients were included in the first group and were treated in supine position. The remaining 194 (143 men, 51 women) patients were included to second group and were treated in prone position. This study designed retrospectively. The procedure was accepted as a success if the patient was stone free or had only clinically insignificant fragments (?3 mm) for 3 months or more after the last SWL session. Before SWL, the mean is one area in the first group was 61.32 mm2 while the mean stone area in the second group was 59.04 mm2 (p = 0.208). Mean energy, Mean energy maximum and mean number of applied shock waves of the first group was 4.65, 3.19 and 3,960, respectively. The same parameters in second group were 4.26, 3.03 and 2,953, respectively. These results show that there are statistically significant differences between two groups with respect to mean energy, mean energy maximum and mean number of applied shock waves (p = 0.003, p = 0.010, p = 0.000, respectively). Success rate was 85.1% in group 1 and 72.7% in group 2 (p = 0.006). Our results suggest that supine position is effective and better than prone position for SWL in patients with distal ureteric stones. PMID:20963407

Istanbulluoglu, Mustafa Okan; Hoscan, Mustafa Burak; Tekin, Mehmet Ilteris; Cicek, Tufan; Ozturk, Bulent; Ozkardes, Hakan

2011-06-01

119

Using Faults-Slip-Through Metric as a Predictor of Fault-Proneness  

Microsoft Academic Search

Background: The majority of software faults are present in small number of modules, therefore accurate prediction of fault-prone modules helps improve software quality by focusing testing efforts on a subset of modules. Aims: This paper evaluates the use of the faults-slip-through (FST) metric as a potential predictor of fault-prone modules. Rather than predicting the fault-prone modules for the complete test

Wasif Afzal

2010-01-01

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

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

PubMed Central

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

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

2013-01-01

122

3D supine and prone colon registration for computed tomographic colonography scans based on graph matching  

NASA Astrophysics Data System (ADS)

In this paper, we propose a new registration method for supine and prone computed tomographic colonography scans based on graph matching. We first formulated 3D colon registration as a graph matching problem and utilized a graph matching algorithm based on mean field theory. During the iterative optimization process, one-to-one matching constraints were added to the system step-by-step. Prominent matching pairs found in previous iterations are used to guide subsequent mean field calculations. The advantage of the proposed method is that it does not require a colon centerline for registration. We tested the algorithm on a CTC dataset of 19 patients with 19 polyps. The average registration error of the proposed method was 4.0cm (std. 2.1cm). The 95% confidence intervals were [3.0cm, 5.0mm]. There was no significant difference between the proposed method and our previous method based on the normalized distance along the colon centerline (p=0.1).

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

2011-03-01

123

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

PubMed

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

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

2013-01-01

124

Unforced errors and error reduction in tennis  

PubMed Central

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

Brody, H

2006-01-01

125

ExCyto PCR Amplification  

Microsoft Academic Search

BackgroundExCyto PCR cells provide a novel and cost effective means to amplify DNA transformed into competent bacterial cells. ExCyto PCR uses host E. coli with a chromosomally integrated gene encoding a thermostable DNA polymerase to accomplish robust, hot-start PCR amplification of cloned sequences without addition of exogenous enzyme.ResultsBecause the thermostable DNA polymerase is stably integrated into the bacterial chromosome, ExCyto

Vinay Dhodda; Ronald Godiska; Jeffrey D. Vanwye; David Mead; Rebecca Hochstein; Lynne Sheets; Sarah Vande Zande; Chris Niebauer; Douglas L. Crawford; Marjorie F. Oleksiak; Ching-Hong Yang

2010-01-01

126

Uncertainties and Error Propagation  

NSDL National Science Digital Library

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

Lindberg, Vern

2008-07-22

127

Errors in Copy Typewriting  

Microsoft Academic Search

An analysis of the errors made by a skilled female typist led to the identification of error factors that often act conjointly. Substitution errors indicated that she had acquired a cognitive map of the keyboard and then controlled her fingers by spelling the to-be-typed words covertly. Accordingly, some typographical errors were attributed in part to errors of inner speech. Intrusion

Frank A. Logan

1999-01-01

128

Background and Related Work Data Encoding for Failure-Prone Sensor Networks  

E-print Network

Outline Background and Related Work Data Encoding for Failure-Prone Sensor Networks Encoding for Persistent Sensor Networks Abhinav Kamra1, Jon Feldman3, Vishal Misra1,2 and Dan Rubenstein2,1 1Department for Persistent Sensor Networks #12;Outline Background and Related Work Data Encoding for Failure-Prone Sensor

129

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

ERIC Educational Resources Information Center

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

Gerdes, Eugenia Proctor; Sidler, John P.

130

Intra-Patient Supine-Prone Colon Registration in CT Colonography Using Shape Spectrum  

E-print Network

screening technique for colorectal polyps and colon cancer. Since electronic colon cleansing (ECC) cannotIntra-Patient Supine-Prone Colon Registration in CT Colonography Using Shape Spectrum Zhaoqiang Lai develop a fully automatic method for registering colon surfaces extracted from prone and supine images

Hua, Jing

131

Prone Position Is Associated with Mild Cerebral Oxygen Desaturation in Elderly Surgical Patients  

PubMed Central

Purpose A variety of hemodynamic and respiratory alterations accompany patients in the prone position; however the effect of the prone position on intraoperative cerebral saturation has not been studied. We sought to examine whether the incidence of cerebral oxygen desaturation in elderly patients (?68 years of age) undergoing spine surgery in the prone position was more common than patients undergoing major surgery in the supine position. Methods We performed a retrospective cohort study of 205 patients; 63 patients underwent surgery in the prone position and 142 in the supine position. Patients were evaluated for cerebral desaturation with bilateral cerebral oximetry. The primary predictor was position, secondary were: length of the surgery, incidence and duration of cerebral desaturation episodes at several thresholds, average time of Bispectral index below threshold of 45 in minutes, average electroencephalogram suppression ratio >0, amount of blood transfused, and the incidence of hypotension and hypertension. Results Elderly spine surgery patients in the prone position were more than twice as likely to experience mild cerebral desaturation as patients in the supine position. Patients in the prone position had longer surgeries; however cerebral desaturation in the prone position was significantly more common even when adjusted for surgery time and the occurrence of intraoperative hypotension. Conclusion Cerebral desaturation is related to the prone position in elderly surgery patients. Future studies are necessary to determine whether this translates to a higher incidence of postoperative cognitive dysfunction and delirium. PMID:25216265

Deiner, Stacie; Chu, Isaac; Mahanian, Michelle; Lin, Hung-Mo; Hecht, Andrew C.; Silverstein, Jeffrey H.

2014-01-01

132

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

133

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

134

Effect of Prone and Supine Position on Sleep, Apneas, and Arousal in Preterm Infants  

Microsoft Academic Search

OBJECTIVE.Prematurely born compared with term born infants are at increased risk of sudden infant death syndrome, particularly if slept prone. The purpose of this work was to test the hypothesis that preterm infants with or without broncho- pulmonary dysplasia being prepared for neonatal unit discharge would sleep longer and have less arousals and more central apneas in the prone position.

Ravindra Y. Bhat; Simon Hannam; Ronit Pressler; Gerrard F. Rafferty; Janet L. Peacock; Anne Greenough

2010-01-01

135

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

E-print Network

the fault- and change-proneness of APIs used by 7,097 (free) Android apps relates to applications' lackAPI Change and Fault Proneness: A Threat to the Success of Android Apps Mario Linares-Vásquez1+ apps for Android and 900K+ for iOS. Availability, cost, functionality, and usability are just some

Poshyvanyk, Denys

136

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

137

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

138

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

139

Genome-Wide Association Study of Proneness to Anger  

PubMed Central

Background Community samples suggest that approximately 1 in 20 children and adults exhibit clinically significant anger, hostility, and aggression. Individuals with dysregulated emotional control have a greater lifetime burden of psychiatric morbidity, severe impairment in role functioning, and premature mortality due to cardiovascular disease. Methods With publically available data secured from dbGaP, we conducted a genome-wide association study of proneness to anger using the Spielberger State-Trait Anger Scale in the Atherosclerosis Risk in Communities (ARIC) study (n?=?8,747). Results Subjects were, on average, 54 (range 45–64) years old at baseline enrollment, 47% (n?=?4,117) were male, and all were of European descent by self-report. The mean Angry Temperament and Angry Reaction scores were 5.8±1.8 and 7.6±2.2. We observed a nominally significant finding (p?=?2.9E-08, ??=?1.027 - corrected pgc?=?2.2E-07, ??=?1.0015) on chromosome 6q21 in the gene coding for the non-receptor protein-tyrosine kinase, Fyn. Conclusions Fyn interacts with NDMA receptors and inositol-1,4,5-trisphosphate (IP3)-gated channels to regulate calcium influx and intracellular release in the post-synaptic density. These results suggest that signaling pathways regulating intracellular calcium homeostasis, which are relevant to memory, learning, and neuronal survival, may in part underlie the expression of Angry Temperament. PMID:24489884

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

2014-01-01

140

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

141

Complementary sex determination substantially increases extinction proneness of haplodiploid populations.  

PubMed

The role of genetic factors in extinction is firmly established for diploid organisms, but haplodiploids have been considered immune to genetic load impacts because deleterious alleles are readily purged in haploid males. However, we show that single-locus complementary sex determination ancestral to the haplodiploid Hymenoptera (ants, bees, and wasps) imposes a substantial genetic load through homozygosity at the sex locus that results in the production of inviable or sterile diploid males. Using stochastic modeling, we have discovered that diploid male production (DMP) can initiate a rapid and previously uncharacterized extinction vortex. The extinction rate in haplodiploid populations with DMP is an order of magnitude greater than in its absence under realistic but conservative demographic parameter values. Furthermore, DMP alone can elevate the base extinction risk in haplodiploids by over an order of magnitude higher than that caused by inbreeding depression in threatened diploids. Thus, contrary to previous expectations, haplodiploids are more, rather than less, prone to extinction for genetic reasons. Our findings necessitate a fundamental shift in approaches to the conservation and population biology of these ecologically and economically crucial insects. PMID:16020532

Zayed, Amro; Packer, Laurence

2005-07-26

142

Is abdomen release really necessary for prone ventilation in acute respiratory distress syndrome?  

PubMed

Prone ventilation for refractory acute respiratory distress syndrome (ARDS) mandates free abdomen by rolls in between chest wall and pelvic bones for better ventilation and control of airway pressure. We observed that, in patients with severe ARDS, prone ventilation with movable free abdomen produced high plateau pressure reduced by applying simple support to abdominal wall. Here, we have proposed a possible hypothesis to explain the paradoxical event in this particular group of patients. The increased alveolar volume in prone position is counteracted by reduction in rib cage diameter caused by weight of abdomen. In patients with severe ARDS in prone position, gravitational pressure transmits through abdominal support, resulting in better chest wall expansion and leading to more oxygenation and opening of the alveoli in ventral lung along with the dorsal lung portion that is usually better ventilated in prone position. There is no clinical trial regarding this particular observation. We suggest randomized trials to prove our observational findings. PMID:24768337

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

2014-10-01

143

Scalable, error-resilient, and high-performance video communications in mobile wireless environments  

Microsoft Academic Search

A novel mobile communications system is proposed, which provides not only effective but also efficient video access for mobile users when communicating over low-bandwidth error-prone wireless links. The middleware implemented by a mobile proxy server at the mobile support station is designed for the seamless integration of mobile users with video servers, so the specific details of the underlying protocols

Jozsef Vass; Shelley Zhuang; Xinhua Zhuang

2001-01-01

144

Cognitive Deficits Specific to Depression-Prone Smokers During Abstinence  

PubMed Central

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

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

2014-01-01

145

Equation error versus output error methods  

Microsoft Academic Search

For the identification of linear processes on the basis of ARX-models, equation error least squares (EELS) (often indicated as the one step ahead prediction error method) is frequently used rather than output error least squares (OELS). This is mainly because the minimum of the convex EE-criterion can easily be found, in contrast to the OE-criterion, which often displays multiple local

YUTAKA TOMITA; AD A. H. DAMEN; PAUL M. J. VAN DEN HOF

1992-01-01

146

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

147

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

148

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

149

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

PubMed Central

Background. The prone position is applied to facilitate surgery of the back and to improve oxygenation in the respirator-treated patient. In particular, with positive pressure ventilation the prone position reduces venous return to the heart and in turn cardiac output (CO) with consequences for cerebral blood flow. We tested in healthy subjects the hypothesis that rotating the head in the prone position reduces cerebral blood flow. Methods. Mean arterial blood pressure (MAP), stroke volume (SV), and CO were determined, together with the middle cerebral artery mean blood velocity (MCA Vmean) and jugular vein diameters bilaterally in 22 healthy subjects in the prone position with the head centered, respectively, rotated sideways, with and without positive pressure breathing (10?cmH2O). Results. The prone position reduced SV (by 5.4 ± 1.5%; P < 0.05) and CO (by 2.3 ± 1.9 %), and slightly increased MAP (from 78 ± 3 to 80 ± 2?mmHg) as well as bilateral jugular vein diameters, leaving MCA Vmean unchanged. Positive pressure breathing in the prone position increased MAP (by 3.6 ± 0.8?mmHg) but further reduced SV and CO (by 9.3 ± 1.3 % and 7.2 ± 2.4 % below baseline) while MCA Vmean was maintained. The head-rotated prone position with positive pressure breathing augmented MAP further (87 ± 2?mmHg) but not CO, narrowed both jugular vein diameters, and reduced MCA Vmean (by 8.6 ± 3.2 %). Conclusion. During positive pressure breathing the prone position with sideways rotated head reduces MCA Vmean ~10% in spite of an elevated MAP. Prone positioning with rotated head affects both CBF and cerebrovenous drainage indicating that optimal brain perfusion requires head centering. PMID:22988456

Højlund, Jakob; Sandmand, Marie; Sonne, Morten; Mantoni, Teit; Jørgensen, Henrik L.; Belhage, Bo; van Lieshout, Johannes J.; Pott, Frank C.

2012-01-01

150

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

PubMed

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

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

2013-09-01

151

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

PubMed

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

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

2014-12-01

152

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

PubMed

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

Goodman, Myron F

2014-09-26

153

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

PubMed Central

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

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

2014-01-01

154

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

PubMed

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

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

2014-12-26

155

Feeling socially powerless makes you more prone to bumping into things on the right and induces leftward line bisection error.  

PubMed

Social power affects the manner in which people view themselves and act toward others, a finding that has attracted broad interest from the social and political sciences. However, there has been little interest from those within cognitive neuroscience. Here, we demonstrate that the effects of power extend beyond social interaction and invoke elementary spatial biases in behavior consistent with preferential hemispheric activation. In particular, participants who felt relatively powerless, compared with those who felt more powerful, were more likely to bisect horizontal lines to the left of center, and bump into the right-hand (as opposed to the left-hand) side when walking through a narrow passage. These results suggest that power induces hemispheric differences in visuomotor behavior, indicating that this ubiquitous phenomenon affects not only how we interact with one another, but also how we interact with the physical world. PMID:21169589

Wilkinson, David; Guinote, Ana; Weick, Mario; Molinari, Rosanna; Graham, Kylee

2010-12-01

156

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

Code of Federal Regulations, 2013 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....

2013-10-01

157

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

...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....

2014-10-01

158

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

Code of Federal Regulations, 2012 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....

2012-10-01

159

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

160

Prevention of medication errors.  

PubMed

Medication error is the most frequent source of medical error that is associated with adverse events, and, in many cases, is preventable. Medication errors can occur at any step in the medication process. Medication error prevention and reduction begins with a systematic approach to their detection. An important approach to mitigating errors involves the reduction of variation in task performance using tested techniques and technologies from other industries. The most important component of error prevention and reduction is the proactive promotion of a safety culture by organizational leadership, with sustained education and support for users. PMID:15777824

Lehmann, Christoph U; Kim, George R

2005-03-01

161

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

162

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

PubMed Central

Although quantitative PCR (qPCR) is becoming the method of choice for expression profiling of selected genes, accurate and straightforward processing of the raw measurements remains a major hurdle. Here we outline advanced and universally applicable models for relative quantification and inter-run calibration with proper error propagation along the entire calculation track. These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data. PMID:17291332

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

2007-01-01

163

CyberKnife robotic spinal radiosurgery in prone position: dosimetric advantage due to posterior radiation access?  

PubMed

CyberKnife spinal radiosurgery suffers from a lack of posterior beams due to workspace limitations. This is remedied by a newly available tracking modality for fiducial-free, respiration-compensated spine tracking in prone patient position. We analyzed the potential dosimetric benefit in a planning study. Fourteen exemplary cases were compared in three scenarios: supine (PTV=CTV), prone (PTV=CTV), and prone position with an additional margin (PTV=CTV+2 mm), to incorporate reduced accuracy of respiration-compensated tracking. Target and spinal cord constraints were chosen according to RTOG 0631 protocol for spinal metastases. Plan quality was scored based on four predefined parameters: dose to cord (D0.1cc and D1cc), high dose (V10Gy), and low dose (V4Gy) volume of healthy tissue. Prescription dose was 16 Gy to the highest isodose line encompassing 90% of the target. Results were related to target size and position. All plans fulfilled RTOG 0631 constraints for coverage and dose to cord. When no additional margin was applied, a majority of eight cases benefitted from prone position, mainly due to a reduction of V4Gy by 23% ± 26%. In the 2 mm prone scenario, the benefit was nullified by an average increase of V10Gy by 43% ± 24%, and an increase of D1cc to cord (four cases). Spinal cord D0.1cc was unchanged (< ± 1 Gy) in all but two cases for both prone scenarios. Conformity (nCI) and number of beams were equivalent in all scenarios, but supine plans used a significantly higher number of monitor units (+16%) than prone. Posterior beam access can reduce dose to healthy tissue in CyberKnife spinal radiosurgery when no additional margin is applied. When a target margin of 2 mm is added, this potential gain is lost. Relative anterior-posterior position and size of the target are selection criteria for prone treatment. PMID:25207392

Fürweger, Christoph; Drexler, Christian; Muacevic, Alexander; Wowra, Berndt; de Klerck, Erik C; Hoogeman, Mischa S

2014-01-01

164

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

Microsoft Academic Search

Purpose: To determine the dosimetric and toxicity differences between prone and supine position intensity-modulate radiotherapy in endometrial cancer patients treated with adjuvant radiotherapy. Methods: Forty-seven consecutive endometrial cancer patients treated with adjuvant RT were analyzed. Of these, 21 were treated in prone position and 26 in the supine position. Dose-volume histograms for normal tissue structures and targets were compared between

Sushil. Beriwal; Sheena K. Jain; Dwight E. Heron; Regiane S. de Andrade; Chyonghiou J. Lin; Hayeon Kim

2007-01-01

165

Temporal disparity between reduction of cot death and reduction of prone sleeping prevalence.  

PubMed

According to several reports sudden infant death rates have decreased significantly after public campaigns aimed at reducing the incidence of sleeping in a prone position. The Styrian population (1.2 million inhabitants), who have been studied from 1984, also showed a significant drop in the incidence of cot death during 1989 (from 2/1000 to 1/1000%). The year before, a campaign for the prevention of cot death had been launched. This included the recommendation to prevent infants from lying in a prone position during sleep. Part of the prevention programme consisted of a detailed questionnaire filled in and returned by the parents. These data, on 29970 infants from 1989 to 1994, provided information on the frequency of prone sleeping in 37% of our total population and as a consequence on parental response to the campaign. Calculating the data per year led to the surprising result that the reduction by half (from 50% to 25%) in the prevalence of sleeping in a prone position did not occur in 1989, when the drop in the incidence of cot death occurred, but 3 years later, in 1992. The following years saw a further decrease of prone position to 7% but no appreciable change in the incidence of cot death. However, during those 11 years of study about 80% of the victims were consistently found dead lying in a prone position. Our results show a temporal disparity between the reduction of sudden infant death and the decrease of prone sleeping in a population. Although we do not deny sleeping in a prone position as a risk factor for cot death, there cannot be a simple relationship between sleeping habits in the population and incidence of cot death. PMID:9226119

Einspieler, C; Kerbl, R; Kenner, T

1997-09-19

166

The prone hip extension test: a method of measuring hip flexion deformity.  

PubMed

The "prone hip extension test" is described as a simple, convenient, and reliable method of measuring hip flexion contracture. The test may be performed on a padded examining table or bed, it is applicable to the spastic patient, and as the patient is examined prone, it provides a method of flattening the lumbar spine under visual control to avoid obtaining either a falsely high or low value. It, therefore, circumvents the problems commonly associated with the traditional "Thomas Test". PMID:852171

Staheli, L T

1977-01-01

167

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

PubMed Central

Purpose Post-implant dosimetric assessment is essential for optimal care of patients receiving prostate brachytherapy. In most institutions, post-implant computed tomography (CT) is performed in the supine position. This study aimed to assess variability in dosimetric parameters with postural changes during acquisition of post-implant CT scans. Material and methods In total, 85 consecutive patients were enrolled in this study. Fifty-three patients underwent seed implantation alone, and the remaining 32 received a combination of seed implantation and external beam radiotherapy. For post-implant analyses, CT scans were obtained in two patient positions, supine and prone. To evaluate differences in dosimetric parameters associated with postural change, the dosimetric data obtained in the supine position were defined as the standard. Results The median prostate volume was 22.4 ml in the supine and 22.5 ml in the prone position (p = 0.51). The median prostate D90 was 120.1% in the supine and 120.3% in the prone position, not significantly different. The mean prostate V100 was 97.1% in the supine and 97.0% in the prone position, again not significantly different. Median rectal V100 in supine and prone positions were 0.42 ml and 0.33 ml, respectively (p < 0.01). Rectal D2cc was also significantly decreased in the prone as compared with the supine position (median, 59.1% vs. 63.6%; p < 0.01). A larger post-implant prostate volume was associated with decreased rectal doses in the prone position. Conclusions Though there were no significant differences among prostate D90 assessments according to postural changes, our results suggest that post-implant rectal doses decreased in the prone position. PMID:24143145

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

2013-01-01

168

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

169

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

2014-05-20

170

Sigh in supine and prone position during acute respiratory distress syndrome.  

PubMed

Interventions aimed at recruiting the lung of patients with acute respiratory distress syndrome (ARDS) are not uniformly effective. Because the prone position increases homogeneity of inflation of the lung, we reasoned that it might enhance its potential for recruitment. We ventilated 10 patients with early ARDS (PaO2/FIO2, 121 +/- 46 mm Hg; positive end-expiratory pressure, 14 +/- 3 cm H2O) in supine and prone, with and without the addition of three consecutive "sighs" per minute to recruit the lung. Inspired oxygen fraction, positive end-expiratory pressure, and minute ventilation were kept constant. Sighs increased PaO2 in both supine and prone (p < 0.01). The highest values of PaO2 (192 +/- 41 mm Hg) and end-expiratory lung volume (1840 +/- 790 ml) occurred with the addition of sighs in prone and remained significantly elevated 1 hour after discontinuation of the sighs. The increase in PaO2 associated with the sighs, both in supine and prone, correlated linearly with the respective increase of end-expiratory lung volume (r = 0.82, p < 0.001). We conclude that adding a recruitment maneuver such as cyclical sighs during ventilation in the prone position may provide optimal lung recruitment in the early stage of ARDS. PMID:12493644

Pelosi, Paolo; Bottino, Nicola; Chiumello, Davide; Caironi, Pietro; Panigada, Mauro; Gamberoni, Chiara; Colombo, Giorgia; Bigatello, Luca M; Gattinoni, Luciano

2003-02-15

171

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.

Nielsen-Gammon, John

1996-01-01

172

PEC: Period Error Calculator  

NASA Astrophysics Data System (ADS)

The PEC (Period Error Calculator) algorithm estimates the period error for eclipsing binaries observed by the Kepler Mission. The algorithm is based on propagation of error theory and assumes that observation of every light curve peak/minimum in a long time-series observation can be unambiguously identified. A simple C implementation of the PEC algorithm is available.

Mighell, Kenneth J.

2013-04-01

173

[Medication errors: prevention strategies].  

PubMed

Medication errors are an important aspect of health care. The American Institute of Medicine informs that 44,000 to 98,000 Americans die annually as a result of medication errors and that such errors affect 2 to 14% of hospitalized patients. The American Society of Hospital Pharmacists presents strategies that, if implemented, can prevent or reduce medication errors. This review discusses four strategies: electronic prescription, the pharmacist's role, the report of errors and the patient's role. A non-punitive culture that prioritizes patient's safety should be stimulated in institutions. PMID:12138424

Cassiani, S H

2000-01-01

174

Computer program for the proportional hazards measurement error model.  

PubMed

The Cox-regression analysis based on the partial likelihood assumes that the covariates, or independent variables, are exactly measured without error. If the covariates are subject to measurement error and the error-prone observed values are used in the analysis by simply ignoring the measurement error, the results are generally biased and misleading; the bias does not diminish as the sample size is increased. The objective of the paper is to briefly describe a method searching for asymptotically unbiased estimates of the parameters correcting for the measurement error in the Cox-regression model and to present a FORTRAN program to perform the correction method; asymptotic standard errors of the corrected estimates are also obtained. The measurement error distribution, that is the conditional distribution of the observed values given the true value, must be specified. An advantage of the method described is that it does not require any assumption on the distribution of the true values; in other words, <--> values are treated as unknown fixed constants. It can accommodate tied failure times unless ties are very frequent, and any censorship or loss to follow-up are allowed as long as they are 'independent of survival'. PMID:7705078

Nakamura, T; Akazawa, K

1994-11-01

175

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

SciTech Connect

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

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

2012-07-01

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

PCR for Diagnosis of Paracoccidioidomycosis  

PubMed Central

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 standardized conditions, it could detect 10 cells/ml of sputum, providing sufficient accuracy to be useful for diagnosis of paracoccidioidomycosis. PMID:10970409

Gomes, Glauce M.; Cisalpino, Patrícia S.; Taborda, Carlos P.; de Camargo, Zoilo P.

2000-01-01

178

Telomere measurement by quantitative PCR  

Microsoft Academic Search

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

Richard M. Cawthon

2002-01-01

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

Serial Subtraction Errors Revealed Sue E. Kase (skase@ist.psu.edu), Frank E. Ritter (frank.ritter@psu.edu)  

E-print Network

Serial Subtraction Errors Revealed Sue E. Kase (skase@ist.psu.edu), Frank E. Ritter (frank the performance of a mental multi-digit serial subtraction task reveals the cognitive processes most prone to failure. Example serial subtraction problems from the experimental problem set are utilized

Ritter, Frank

181

Post-Error Adjustments  

PubMed Central

When our brain detects an error, this process changes how we react on ensuing trials. People show post-error adaptations, potentially to improve their performance in the near future. At least three types of behavioral post-error adjustments have been observed. These are post-error slowing (PES), post-error reduction of interference, and post-error improvement in accuracy (PIA). Apart from these behavioral changes, post-error adaptations have also been observed on a neuronal level with functional magnetic resonance imaging and electroencephalography. Neuronal post-error adaptations comprise activity increase in task-relevant brain areas, activity decrease in distracter-encoding brain areas, activity modulations in the motor system, and mid-frontal theta power increases. Here, we review the current literature with respect to these post-error adjustments, discuss under which circumstances these adjustments can be observed, and whether the different types of adjustments are linked to each other. We also evaluate different approaches for explaining the functional role of PES. In addition, we report reanalyzed and follow-up data from a flanker task and a moving dots interference task showing (1) that PES and PIA are not necessarily correlated, (2) that PES depends on the response–stimulus interval, and (3) that PES is reliable on a within-subject level over periods as long as several months. PMID:21954390

Danielmeier, Claudia; Ullsperger, Markus

2011-01-01

182

The error in total error reduction.  

PubMed

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

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

2014-02-01

183

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

Microsoft Academic Search

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

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

2011-01-01

184

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

185

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

186

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

PubMed

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

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

1998-02-01

187

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

PubMed Central

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

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

2010-01-01

188

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

189

Prone breast radiotherapy in a patient with early stage breast cancer and a large pendulous breast.  

PubMed

In women with large and pendulous breasts postoperative radiotherapy in the supine position could represent a technical challenge because of the resulting dose inhomogeneity and the large amount of lung and heart receiving a high percentage of the prescribed dose. Breast-conserving surgery is therefore relatively contraindicated in these patients. Alternative positions for radiation therapy treatment have been proposed, and prone breast irradiation in particular has been recognized as a useful alternative to conventional treatment in the supine position. We report the case of a large-breasted patient treated in prone position in our radiation therapy division. PMID:19688985

Ferrari, Annamaria; Ivaldi, Giovanni; Leonardi, Maria Cristina; Rondi, Elena; Orecchia, Roberto

2009-01-01

190

Everyday Scale Errors  

ERIC Educational Resources Information Center

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

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

2010-01-01

191

Errors in microdensitometry  

Microsoft Academic Search

Summary  Microdensitometric errors can originate in the instrument, in the specimen or in the human operator. Instrumental sources of systematic error mostly reduce the apparent integrated absorbance, especially of relatively small and highly absorbing objects. They can be assessed, minimized or eliminated by available techniques, but with modern apparatus are in general important only if results of high accuracy are required.

D. J. Goldstein

1981-01-01

192

Mutation Detection by Real-Time PCR: A Simple, Robust and Highly Selective Method  

PubMed Central

Background Molecular tests for diagnosis of disease, particularly cancer, are gaining increased acceptance by physicians and their patients for disease prognosis and selection of treatment options. Gene expression profiles and genetic mutations are key parameters used for the molecular characterization of tumors. A variety of methods exist for mutation analysis but the development of assays with high selectivity tends to require a process of trial and error, and few are compatible with real-time PCR. We sought to develop a real-time PCR-based mutation assay methodology that successfully addresses these issues. Methodology/Principal Findings The method we describe is based on the widely used TaqMan® real-time PCR technology, and combines Allele-Specific PCR with a Blocking reagent (ASB-PCR) to suppress amplification of the wildype allele. ASB-PCR can be used for detection of germ line or somatic mutations in either DNA or RNA extracted from any type of tissue, including formalin-fixed paraffin-embedded tumor specimens. A set of reagent design rules was developed enabling sensitive and selective detection of single point substitutions, insertions, or deletions against a background of wild-type allele in thousand-fold or greater excess. Conclusions/Significance ASB-PCR is a simple and robust method for assaying single nucleotide mutations and polymorphisms within the widely used TaqMan® protocol for real time RT-PCR. The ASB-PCR design rules consistently produce highly selective mutation assays while obviating the need for redesign and optimization of the assay reagents. The method is compatible with formalin-fixed tissue and simultaneous analysis of gene expression by RT-PCR on the same plate. No proprietary reagents other than those for TaqMan chemistry are required, so the method can be performed in any research laboratory with real-time PCR capability. PMID:19240792

Morlan, John; Baker, Joffre; Sinicropi, Dominick

2009-01-01

193

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

194

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

195

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

196

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

197

[Prone position and severe pneumopathy in a patient with head injuries and intracranial hypertension].  

PubMed

The treatment of hypoxaemia is one of the main goals of intensive care to patients with severe head injury. In the case reported here, the appearance of early pneumonia was accompanied by a severe deterioration of blood gases with worsening of intracranial hypertension. Prone position allowed rapid improvement of blood gases which contributed to the control of intracranial hypertension. PMID:11098325

Beuret, P; Ghesquieres, H; Fol, S; Pirel, M; Nourdine, K; Ducreux, J C

2000-10-01

198

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...

199

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.

200

Dynamic testing of the motor stereotype in prone hip extension from neutral position  

Microsoft Academic Search

Objective. The purpose of the study was to identify a sequential activation of lumbar and hip muscles in active prone hip extension from neutral position in subjects without a history of low back pain.Design. Using surface electromyography, the myoelectric activity onsets of agonistic and antagonistic hip muscles were recorded.Background. The development of low back pain is ascribed to changes of

L Vogt; W Banzer

1997-01-01

201

Classification of Atrial Fibrillation prone Patients using Electrocardiographic Parameters in Neuro-Fuzzy Modeling  

E-print Network

of statistics-based attempts to predict AF occurrence may be overcome using a hybrid neuro-fuzzy predictionClassification of Atrial Fibrillation prone Patients using Electrocardiographic Parameters in Neuro-Fuzzy postoperative AF often lead to longer hospital stays and higher heath care costs. The literature showed that AF

Simon, Dan

202

CLASSIFICATION OF ATRIAL FIBRILLATION PRONE PATIENTS USING ELECTROCARDIOGRAPHIC PARAMETERS IN NEURO-FUZZY MODELING  

E-print Network

CLASSIFICATION OF ATRIAL FIBRILLATION PRONE PATIENTS USING ELECTROCARDIOGRAPHIC PARAMETERS IN NEURO-FUZZY hospital stays and higher heath care costs. The literature showed that AF may be preceded by changes in electrocardiogram (ECG) characteristics such as premature atrial activity, heart rate variability (HRV), and P- wave

Simon, Dan

203

"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

204

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

205

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

206

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

ERIC Educational Resources Information Center

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

Comer, David W.; And Others

207

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

208

Insulin use: preventable errors.  

PubMed

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

2014-01-01

209

Surprise beyond prediction error  

PubMed Central

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

2014-01-01

210

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

211

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;

212

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

213

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

214

Quality assessment and error concealment for SVC transmission over unreliable channels  

Microsoft Academic Search

Scalable video coding (SVC) has aroused a wide interest in the areas of video coding and transmission technology, since it provides desirable features for heterogeneous error-prone network environments. The layered video structure allows not only adaptation to the available bandwidth but also a device adaptation capability via multiple decodable sub-streams. In this paper, we focus on SVC MediumGrain Scalability (MGS)

Marco Brandas; Maria G. Martini; Mikko Uitto; Janne Vehkapera

2011-01-01

215

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.

216

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

217

Quantum Error Correction  

NASA Astrophysics Data System (ADS)

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

Lidar, Daniel A.; Brun, Todd A.

2013-09-01

218

Prone positioning to treat acute severe pulmonary edema in the post-cardiac surgical patient: a case report.  

PubMed

Noncardiogenic pulmonary edema can be fatal without adequate resuscitation. We report, for the first time, the use of prone positioning in the immediate post-cardiac surgical period to treat a patient with profound hypoxemia secondary to massive (noncardiogenic) pulmonary edema. Prone positioning corrects ventilation-perfusion mismatch and allows gravity-dependent drainage of capillary leak-mediated endobronchial pulmonary fluid. PMID:16844634

Atluri, Pavan; Neligan, Patrick J; Acker, Michael A; Bensall, Dean L; Horak, Jiri

2006-01-01

219

Clinical applications using digital PCR.  

PubMed

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

Bizouarn, Francisco

2014-01-01

220

Smoothing error pitfalls  

NASA Astrophysics Data System (ADS)

The difference due to the content of a priori information between a constrained retrieval and the true atmospheric state is usually represented by the so-called smoothing error. In this paper it is shown that the concept of the smoothing error is questionable because it is not compliant with Gaussian error propagation. The reason for this is that the smoothing error does not represent the expected deviation of the retrieval from the true state but the expected deviation of the retrieval from the atmospheric state sampled on an arbitrary grid, which is itself a smoothed representation of the true state. The idea of a sufficiently fine sampling of this reference atmospheric state is untenable because atmospheric variability occurs on all scales, implying that there is no limit beyond which the sampling is fine enough. Even the idealization of infinitesimally fine sampling of the reference state does not help because the smoothing error is applied to quantities which are only defined in a statistical sense, which implies that a finite volume of sufficient spatial extent is needed to meaningfully talk about temperature or concentration. Smoothing differences, however, which play a role when measurements are compared, are still a useful quantity if the involved a priori covariance matrix has been evaluated on the comparison grid rather than resulting from interpolation. This is, because the undefined component of the smoothing error, which is the effect of smoothing implied by the finite grid on which the measurements are compared, cancels out when the difference is calculated.

von Clarmann, T.

2014-04-01

221

Twenty questions about student errors  

Microsoft Academic Search

Errors in science learning (errors in expression of organized, purposeful thought within the domain of science) provide a window through which glimpses of mental functioning can be obtained. Errors are valuable and normal occurrences in the process of learning science. A student can use his\\/her errors to develop a deeper understanding of a concept as long as the error can

Kathleen M. Fisher; Joseph Isaac Lipson

1986-01-01

222

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

223

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

224

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

225

Estimating GPS Positional Error  

NSDL National Science Digital Library

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

Witte, Bill

226

Examine gels from PCR Learn about more molecular methods in  

E-print Network

;Quantitative (Real Time) PCR Real time PCR monitors the fluorescence emitted during the reactions as an indicator of amplicon production at each PCR cycle (in real time) as opposed to the endpoint detection #12/dye Quantitative (Real Time) PCR #12;Quantitative PCR · Used qPCR to quantify total bacteria (16S rRNA) and total

Vallino, Joseph J.

227

In situ prone ESWL for the treatment of lower ureteral stones: experience with 28 patients.  

PubMed

Twenty-eight patients with lower ureteral stones underwent in situ extracorporeal shock wave lithotripsy (ESWL) in the prone position over the period of 7 months between March 1990 and September 1990. For stone disintegration the spark gap shock wave lithotripter Tripter XI (Direx) was used. Satisfactory disintegration was achieved in 93 per cent of patients. The stone-free rate at 12 weeks was 82 per cent, and 11 per cent had residual fragments less than or equal to 4 mm in diameter. Twenty-one per cent of patients required repeat treatments. For only 2 patients general anaesthesia was required (7 per cent). There were no remarkable complications except for haemospermia which resolved spontaneously 15 days after treatment. It was concluded that in situ prone ESWL is an effective and safe procedure for the treatment of lower ureteral stones. PMID:1459811

Ba?ar, I; Gürpinar, T; Erkan, A

1992-01-01

228

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

229

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

PubMed

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

Bowler, Jennifer L; Bowler, Mark C

2014-10-01

230

Memory efficient error diffusion.  

PubMed

Because of its good image quality and moderate computational requirements, error diffusion has become a popular halftoning solution for desktop printers, especially inkjet printers. By making the weights and thresholds tone-dependent and using a predesigned halftone bitmap for tone-dependent threshold modulation, it is possible to achieve image quality very close to that obtained with far more computationally complex iterative methods. However, the ability to implement error diffusion in very low cost or large format products is hampered by the requirement to store the tone-dependent parameters and halftone bitmap, and also the need to store error information for an entire row of the image at any given point during the halftoning process. For the first problem, we replace the halftone bitmap by deterministic bit flipping, which has been previously applied to halftoning, and we linearly interpolate the tone-dependent weights and thresholds from a small set of knot points. We call this implementation a reduced lookup table. For the second problem, we introduce a new serial block-based approach to error diffusion. This approach depends on a novel intrablock scan path and the use of different parameter sets at different points along that path. We show that serial block-based error diffusion reduces off-chip memory access by a factor equal to the block height. With both these solutions, satisfactory image quality can only be obtained with new cost functions that we have developed for the training process. With these new cost functions and moderate block size, we can obtain image quality that is very close to that of the original tone-dependent error diffusion algorithm. PMID:18244693

Chang, Ti-chiun; Allebach, Jan P

2003-01-01

231

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

232

Clinical review: Intra-abdominal hypertension: does it influence the physiology of prone ventilation?  

Microsoft Academic Search

Prone ventilation (PV) is a ventilatory strategy that frequently improves oxygenation and lung mechanics in critical illness,\\u000a yet does not consistently improve survival. While the exact physiologic mechanisms related to these benefits remain unproven,\\u000a one major theoretical mechanism relates to reducing the abdominal encroachment upon the lungs. Concurrent to this experience\\u000a is increasing recognition of the ubiquitous role of intra-abdominal

Andrew W Kirkpatrick; Paolo Pelosi; Jan J De Waele; Manu LNG Malbrain; Chad G Ball; Maureen O Meade; Henry T Stelfox; Kevin B Laupland

2010-01-01

233

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

Microsoft Academic Search

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

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

2011-01-01

234

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

PubMed

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

235

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

236

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

237

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

PubMed Central

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

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

2014-01-01

238

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

PubMed Central

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

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

2014-01-01

239

Accelerated partial breast irradiation in the prone position with helical tomotherapy  

NASA Astrophysics Data System (ADS)

A new method for treating early stage breast cancer, called accelerated partial breast irradiation (APBI), is described. This method is mostly being accomplished through the use of brachytherapy, whether it be interstitial or using the Mammosite(c) devise. APBI has proven to be effective but costly in a fiscal and physical sense. APBI is more time intensive for the staff and requires an extra operation. Brachytherapy is used instead of external beam partially because of a lack of image guidance and the inability to easily set up the patient in the prone position. In order to perform high precision IMRT on the breast image guidance and delivery verification is necessary. With the advent of helical tomotherapy, another external beam approach is now possible. Tomotherapy allows for an easier method of setting up the patient and verifying her location in the prone position, and it has the ability to track the position of the target on a daily basis. These and other aspects of external beam APBI such as breathing motion, dosimetry differences, and setup differences have been explored. Results show that treating APBI with external beam is not only possible but may be beneficial. Also an entire new modality based on the helical tomotherapy machine is explored. This would specialize the tomotherapy machine for use on the prone breast taking advantage of its unique geometry.

Becker, Stewart J.

240

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

241

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

242

Dynamic testing of the motor stereotype in prone hip extension from neutral position.  

PubMed

OBJECTIVE: The purpose of the study was to identify a sequential activation of lumbar and hip muscles in active prone hip extension from neutral position in subjects without a history of low back pain. DESIGN: Using surface electromyography, the myoelectric activity onsets of agonistic and antagonistic hip muscles were recorded. BACKGROUND: The development of low back pain is ascribed to changes of the muscle firing order in prone hip extension. There appeared to be no normative data on muscle firing order of the lumbar and hip musculature to provide a basis for recognizing variations. METHODS: Fifteen healthy subjects performed standardized right hip extensions. Time-normalized onset of EMG activity in each muscle was measured for each trial. RESULTS: A MANOVA revealed significant (P < 0.01) differences between the activity onsets of synergistic muscles in hip extension. CONCLUSIONS: On the results it was concluded that the consistent muscle firing order of ipsilateral lumbar erector spinae, semitendinosus, contralateral lumbar erector spinae, tensor fasciae latae, and gluteus maximus demonstrate the characteristic pattern in prone hip extension. In future studies it is essential to evaluate also the hip extension pattern in functional upright conditions during gait and their relationship to spinal mechanics. PMID:11415681

Vogt, L; Banzer, W

1997-03-01

243

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

244

Prenatal diagnosis of fetal aneuploidies using QF-PCR: the egyptian study  

PubMed Central

Background The most common chromosomal abnormalities identified at birth are aneuploidies of chromosome 21, 18, 13, X and Y. Prenatal diagnosis of fetal aneuploidies is routinely done by traditional cytogenetic culture; a major drawback of this technique is the long period of time required to reach a diagnosis. In this study we evaluated the QF-PCR as a rapid technique for prenatal diagnosis of common aneuploidies. Method This work was carried out on Sixty amniotic fluid samples taken from patients with one or more of the following indications: advanced maternal age (3 case), abnormal biochemical markers (6 cases), abnormal ultrasound (12 cases) or previous history of abnormal child (39 cases). Each sample was tested by QF-PCR and traditional cytogenetic. Aneuploidy screenings were performed amplifying four STRs on chromosomes 21, 18, 13, two pseudoautosomal, one X linked, as well as the AMXY and SRY. Markers were distributed in two multiplex QFPCR assays (S1 and S2) in order to reduce the risk of sample mishandling. Results All the QF-PCR results were successful, while there were two culture failures, only one of them was repeated. No discrepancy was seen between the results of both techniques. Fifty six samples showed normal patterns, three samples showed trisomy 21, successfully detected by both techniques and one sample showed normal pattern by QF-PCR but could not be compared to the cytogenetic due to culture failure, the pregnancy outcome of this case was a normal baby. Conclusion Our study concluded that QF-PCR is a reliable technique for prenatal diagnosis of the common chromosomal aneuploidies. It has the advantages over the cytogenetic culture of being faster with the results appearing within 24–48 hours, simpler, doesn’t need a highly qualified staff, less prone to failure and more cost effective. PMID:22905299

Atef, Shereen H.; Hafez, Sawsan S.; Mahmoud, Nermein H.; Helmy, Sanaa M.

2011-01-01

245

Orwell's Instructive Errors  

ERIC Educational Resources Information Center

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

Julian, Liam

2009-01-01

246

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

247

Involvement in Intimate Partner Psychological Abuse and Suicide Proneness in College Women: Alcohol Related Problems as a Potential Mediator  

PubMed Central

This study examined the relations among involvement in intimate partner psychological abuse, alcohol-related problems, and suicide proneness as measured by the Life Attitudes Schedule – Short Form (LAS-SF) in college women (N = 709). Results revealed that, as expected, being involved in a psychologically abusive relationship was significantly and positively correlated with alcohol-related problems and alcohol-related problems were significantly and positively correlated with suicide proneness. Additionally, the intimate partner psychological abuse involvement-suicide proneness link was significantly mediated by alcohol-related problems. Implications are offered for the improved identification and treatment of young women at risk for suicidal and health-diminishing behaviors. PMID:20544000

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

2010-01-01

248

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

249

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

250

Control by model error estimation  

NASA Technical Reports Server (NTRS)

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

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

1976-01-01

251

Automatic Error Analysis Using Intervals  

ERIC Educational Resources Information Center

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

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

2012-01-01

252

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

253

Comparison of droplet digital PCR to real-time PCR for quantitative detection of cytomegalovirus.  

PubMed

Quantitative real-time PCR (QRT-PCR) has been widely implemented for clinical viral load testing, but a lack of standardization and relatively poor precision have hindered its usefulness. Digital PCR offers highly precise, direct quantification without requiring a calibration curve. Performance characteristics of real-time PCR were compared to those of droplet digital PCR (ddPCR) for cytomegalovirus (CMV) load testing. Tenfold serial dilutions of the World Health Organization (WHO) and the National Institute of Standards and Technology (NIST) CMV quantitative standards were tested, together with the AcroMetrix CMV tc panel (Life Technologies, Carlsbad, CA) and 50 human plasma specimens. Each method was evaluated using all three standards for quantitative linearity, lower limit of detection (LOD), and accuracy. Quantitative correlation, mean viral load, and variability were compared. Real-time PCR showed somewhat higher sensitivity than ddPCR (LODs, 3 log(10) versus 4 log(10) copies/ml and IU/ml for NIST and WHO standards, respectively). Both methods showed a high degree of linearity and quantitative correlation for standards (R(2) ? 0.98 in each of 6 regression models) and clinical samples (R(2) = 0.93) across their detectable ranges. For higher concentrations, ddPCR showed less variability than QRT-PCR for the WHO standards and AcroMetrix standards (P < 0.05). QRT-PCR showed less variability and greater sensitivity than did ddPCR in clinical samples. Both digital and real-time PCR provide accurate CMV load data over a wide linear dynamic range. Digital PCR may provide an opportunity to reduce the quantitative variability currently seen using real-time PCR, but methods need to be further optimized to match the sensitivity of real-time PCR. PMID:23224089

Hayden, R T; Gu, Z; Ingersoll, J; Abdul-Ali, D; Shi, L; Pounds, S; Caliendo, A M

2013-02-01

254

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

255

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

256

Error-Free Software  

NASA Technical Reports Server (NTRS)

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

1989-01-01

257

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

258

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

259

Nature of Human Error  

PubMed Central

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

Cuschieri, Alfred

2006-01-01

260

Airborne Gradiometry Error Analysis  

NASA Astrophysics Data System (ADS)

Gravity gradiometry is one of the older methods of determining the Earth’s local gravitational field, but lies in the shadow of more conventional static and moving-base gravimeter-based systems. While the static torsion balance appears to have been relegated to the museum, support for the airborne and space-borne differential accelerometer (gradiometer) continues so as to overcome limitations in spatial resolution and accuracy inherent in ordinary moving-base gravimetry. One airborne system exists, building on 30 year old technology concepts, and new technologies (e.g., cold-atom interferometry) promise significant improvements. Concomitant advances are required to measure accurately the angular velocity and angular acceleration of the platform, which inseparably combine (in an absolute sense) with the Earth’s gravitational gradients. A numerical analysis of instrument errors, with simulated aircraft dynamics, shows that navigation-grade gyros are just sufficient to account for these effects in gradiometers with 1E/ sqrt{Hz} sensitivity. More accurate instruments, with 0.1 E/sqrt{Hz} sensitivity, require commensurate sensitivity in the gyros, of the order of 0.01°/h/sqrt{Hz} = 1.5×10-4 ° sqrt{{Hz}} for typical survey aircraft dynamics. On the other hand, typical orientation errors in the platform, which are problematic for vector gravimetry, are much less of a concern in gradiometry. They couple to the gradient signals and affect only the very low frequencies of the total gradient error.

Jekeli, Christopher

2006-03-01

261

Prescribing errors in hospital practice  

PubMed Central

Prescribing errors that occur in hospitals have been a source of concern for decades. This narrative review describes some of the recent work in this field. There is considerable heterogeneity in definitions and methods used in research on prescribing errors. There are three definitions that are used most frequently (one for prescribing errors specifically and two for the broader arena of medication errors), although many others have also been used. Research methods used focus primarily on investigating either the prescribing process (such as errors in the dose prescribed) or the outcomes for the patient (such as preventable adverse drug events). This complicates attempts to calculate the overall prevalence or incidence of errors. Errors have been reported in handwritten descriptions of almost 15% and with electronic prescribing of up to 8% of orders. Errors are more likely to be identified on admission to hospital than at any other time (usually failure to continue ongoing medication) and errors of dose occur most commonly throughout the patients' stay. Although there is evidence that electronic prescribing reduces the number of errors, new types of errors also occur. The literature on causes of error shows some commonality with both handwritten and electronic prescribing but there are also causes that are unique to each. A greater understanding of the prevalence of the complex causal pathways found and the differences between the pathways of minor and severe errors is necessary. Such an understanding would underpin theoretically-based interventions to reduce the occurrence of prescribing errors. PMID:22554316

Tully, Mary P

2012-01-01

262

Mal-adaptation of event-related EEG responses preceding performance errors.  

PubMed

Recent EEG and fMRI evidence suggests that behavioral errors are foreshadowed by systematic changes in brain activity preceding the outcome by seconds. In order to further characterize this type of error precursor activity, we investigated single-trial event-related EEG activity from 70 participants performing a modified Eriksen flanker task, in particular focusing on the trial-by-trial dynamics of a fronto-central independent component that previously has been associated with error and feedback processing. The stimulus-locked peaks in the N2 and P3 latency range in the event-related averages showed expected compatibility and error-related modulations. In addition, a small pre-stimulus negative slow wave was present at erroneous trials. Significant error-preceding activity was found in local stimulus sequences with decreased conflict in the form of less negativity at the N2 latency (310-350 ms) accumulating across five trials before errors; concomitantly response times were speeding across trials. These results illustrate that error-preceding activity in event-related EEG is associated with the performance monitoring system and we conclude that the dynamics of performance monitoring contribute to the generation of error-prone states in addition to the more remote and indirect effects in ongoing activity such as posterior alpha power in EEG and default mode drifts in fMRI. PMID:20740080

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

2010-01-01

263

Error, Error-Statistics and Self-Directed Anticipative Learning  

Microsoft Academic Search

Error is protean, ubiquitous and crucial in scientific process. In this paper it is argued that understanding scientific process\\u000a requires what is currently absent: an adaptable, context-sensitive functional role for error in science that naturally harnesses error identification and avoidance to positive, success-driven, science. This\\u000a paper develops a new account of scientific process of this sort, error and success driving

R. P. Farrell; C. A. Hooker

2009-01-01

264

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

265

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

266

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

267

Wavefront error sensing  

NASA Technical Reports Server (NTRS)

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

Tubbs, Eldred F.

1986-01-01

268

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

269

Error Sources in Asteroid Astrometry  

NASA Technical Reports Server (NTRS)

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

Owen, William M., Jr.

2000-01-01

270

Error resilient video coding techniques  

Microsoft Academic Search

We review error resilience techniques for real-time video transport over unreliable networks. Topics covered include an introduction to today's protocol and network environments and their characteristics, encoder error resilience tools, decoder error concealment techniques, as well as techniques that require cooperation between encoder, decoder, and the network. We provide a review of general principles of these techniques as well as

Yao Wang; S. Wenger; Jiantao Wen; A. K. Katsaggelos

2000-01-01

271

Interactive Histogram with Error Graph  

NSDL National Science Digital Library

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

Siegrist, Kyle

272

Tolerability and cosmetic acceptability of a body wash in atopic dermatitis-prone subjects.  

PubMed

Atopic dermatitis is a common skin disease characterized by eczematous eruptions and impaired skin barrier function. Patients, as well as their families, frequently report reductions in quality of life. Pruritus, lack of sleep, and impaired social functioning all contribute to this reduction. A skincare regimen of gentle cleansing and daily moisturization is integral to managing atopic dermatitis. While there are a multitude of reports supporting the use of moisturizers, there is a paucity regarding the use of cleansers, especially cleansers formulated with ingredients known to improve skin hydration. A clinical study was conducted to assess the tolerability and cosmetic acceptability of a body wash formulated with the filaggrin break-down products arginine and pyrrolidone carboxylic acid in subjects with atopic dermatitis-prone skin (Cetaphil® RestoraDerm® Body Wash). The results of this study indicate that Cetaphil RestoraDerm Body Wash was well tolerated, reduced itch, improved quality of life, and was well-liked by subjects with atopic dermatitis-prone skin. PMID:25226012

Brandt, Staci; Meckfessel, Matthew H; Lio, Peter A

2014-09-01

273

A consensus method for the prediction of 'aggregation-prone' peptides in globular proteins.  

PubMed

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

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

2013-01-01

274

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

PubMed Central

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

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

2013-01-01

275

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

276

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

PubMed Central

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

2014-01-01

277

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

278

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

279

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

280

Current applications of single-cell PCR  

Microsoft Academic Search

Abstract. The advent of the polymerase chain reaction applications, single-cell PCR has proven to be of enor- (PCR) has revolutionised the way in which molecular mous use to basic scientists, addressing diverse immuno- logical, neurological and developmental questions, biologists view their task at hand, for it is now possible to amplify,and examine,minute,quantities of rare genetic,where,both the genome,but also messenger,RNA expres-

S. Hahn; X. Y. Zhong; C. Troeger

2000-01-01

281

Identification of Lactococcus garvieae by PCR  

PubMed Central

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 amplified fragment of 1,100 bp in size. The PCR assay was shown to be specific to L. garvieae. The PCR assay was positive for all the L. garvieae strains tested, which originated from three different continents (Asia, Australia, and Europe). The PCR assay was negative for the phenotypically similar L. lactis and for all the other fish pathogens tested, including Streptococcus iniae and Aeromonas salmonicida. The PCR assay was applied to plasma obtained from diseased animals and was found sensitive enough to detect bacteria from 1 ?l of plasma. The PCR assay that was developed is the only practical test besides the clindamycin test which can specifically identify the zoonotic agent L. garvieae and which can differentiate it from L. lactis. PMID:9542921

Zlotkin, Amir; Eldar, Avi; Ghittino, Claudio; Bercovier, Herve

1998-01-01

282

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

283

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

284

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

285

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

SciTech Connect

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

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

2010-03-24

286

Cognitive demands of error processing.  

PubMed

This study used a dual-task methodology to assess attention demands associated with error processing during an anticipation-timing task. A difference was predicted in attention demands during feedback on trials with correct responses and errors. This was addressed by requiring participants to respond to a probe reaction-time stimulus after augmented feedback presentation. 16 participants (8 men, 8 women) completed two phases, the reaction time task only and the anticipation-timing task with the probe RT task. False feedback indicating error and a financial reward manipulation were used to increase relevance of errors. Data supported the hypothesis that error processing is associated with higher cognitive demands than processing feedback denoting a correct response. Individuals responded with quicker probe reaction times during presentation of feedback on correct trials than on error trials. These results are discussed with respect to the cognitive processes which might occur during error processing and their role in motor learning. PMID:18567222

Koehn, J D; Dickinson, J; Goodman, D

2008-04-01

287

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

288

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

PubMed Central

Inner speech is a commonly experienced but poorly understood phenomenon. The Varieties of Inner Speech Questionnaire (VISQ; McCarthy-Jones & Fernyhough, 2011) assesses four characteristics of inner speech: dialogicality, evaluative/motivational content, condensation, and the presence of other people. Prior findings have linked anxiety and proneness to auditory hallucinations (AH) to these types of inner speech. This study extends that work by examining how inner speech relates to self-esteem and dissociation, and their combined impact upon AH-proneness. 156 students completed the VISQ and measures of self-esteem, dissociation and AH-proneness. Correlational analyses indicated that evaluative inner speech and other people in inner speech were associated with lower self-esteem and greater frequency of dissociative experiences. Dissociation and VISQ scores, but not self-esteem, predicted AH-proneness. Structural equation modelling supported a mediating role for dissociation between specific components of inner speech (evaluative and other people) and AH-proneness. Implications for the development of “hearing voices” are discussed. PMID:24980910

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

2014-01-01

289

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

290

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

291

PRONE ACCELERATED PARTIAL BREAST IRRADIATION AFTER BREAST-CONSERVING SURGERY: FIVE YEAR RESULTS OF 100 PATIENTS  

PubMed Central

Purpose To report the 5-year results of a prospective trial of three-dimensional conformal external beam radiotherapy (3D-CRT) to deliver accelerated partial breast irradiation in the prone position (P-APBI). Methods Post-menopausal patients with Stage I breast cancer with non palpable <2 cm tumors, negative margins, and negative nodes, positive hormonal receptors, and no extensive intraductal component (EIC) were eligible. The trial was offered only once eligible patients had refused to undergo standard whole-breast radiotherapy. Patients were simulated and treated on a dedicated table for prone set-up. The 3D-CRT delivered was 30 Gy in five 6 Gy/daily fractions over 10 days with port film verification at each treatment. Ipsilateral breast, ipsilateral nodal, contralateral breast, and distant failure (IBF, INF, CBF, DF) were estimated using the cumulative incidence method. Disease-free, overall, and cancer-specific survival (DFS, OS, CSS) were recorded. Results One hundred patients accrued to this IRB- approved prospective trial, one with bilateral breast cancer. One patient withdrew consent after simulation and another elected to interrupt radiotherapy after receiving two treatments. Ninety-eight patients are evaluable for toxicity and, in one case, both breasts were treated with PBI. Median patient age was 68 years (range 53–88 years); in 55% the tumor size was <1 cm. All patients had hormonal receptor positive cancers: 87% underwent adjuvant anti-hormonal therapy. At a median follow-up of 64 months (range, 2–125 months), there was one local recurrence (1% IBF) and one contralateral breast cancer (1% CBF). There were no deaths due to breast cancer by 5 years. Grade 3 late toxicities occurred in 2 patients (1 breast edema, 1 transient breast pain). Cosmesis was rated good/excellent in 89% of patients with at least 36 months follow-up. Conclusions Five-year efficacy and toxicity of 3D-CRT to deliver prone-PBI are comparable to other experiences with similar follow-up. PMID:22494589

Formenti, Silvia C.; Hsu, Howard; Fenton-Kerimian, Maria; Roses, Daniel; Guth, Amber; Jozsef, Gabor; Goldberg, Judith D.; DeWyngaert, J. Keith

2013-01-01

292

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

293

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

PubMed

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

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

2008-07-23

294

Can perspective-taking reduce crime? Examining a pathway through empathic-concern and guilt-proneness.  

PubMed

We describe and appraise a theoretical model in which individual differences in perspective-taking eventuate in crime reduction. Specifically, it is hypothesized that perspective-taking propensities influence the tendency to feel empathic-concern, thereby heightening proneness for guilt, which ultimately inhibits criminal behavior (perspective-taking ? empathic-concern ? guilt-proneness ? crime desistance). Data from two sources were analyzed: (a) a cross-sectional college sample and (b) a longitudinal sample of jail inmates. Overall, results lend credence to this theoretical model: Perspective-taking propensities ultimately "put the brakes" on criminal behavior-via an emotional pathway of empathic-concern and then guilt-proneness. Discussion focuses on the nature of perspective-taking, its generative role for moral emotion and behavior, as well as potential applications for crime reduction. PMID:25324328

Martinez, Andres G; Stuewig, Jeffrey; Tangney, June P

2014-12-01

295

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

296

The Violence Proneness Scale of the DUSI-R predicts adverse outcomes associated with substance abuse.  

PubMed

Accuracy of the Violence Proneness Scale (VPS) of the Drug Use Screening Inventory (DUSI-R) was evaluated in 328 boys for predicting use of illegal drugs, DUI, selling drugs, sexually transmitted disease, car accident while under acute effects of drugs/alcohol, trading drugs for sex, injuries from a fight, and traumatic head injury. Boys were prospectively tracked from age 16 to 19 at which time these outcomes were documented in the interim period. The results demonstrated that the VPS score is a significant predictor of all outcomes. Prediction accuracy ranged between 62%-83%. These findings suggest that the VPS may be useful for identifying youths who are at high risk for using illicit drugs and commonly associated adverse outcomes. PMID:19283571

Kirisci, Levent; Tarter, Ralph; Reynolds, Maureen

2009-01-01

297

The Violence Proneness Scale of the DUSI-R Predicts Adverse Outcomes Associated with Substance Abuse  

PubMed Central

Accuracy of the Violence Proneness Scale (VPS) of the Drug Use Screening Inventory (DUSI-R)1 was evaluated in 328 boys for predicting use of illegal drugs, DUI, selling drugs, sexually transmitted disease, car accident while under acute effects of drugs/alcohol, trading drugs for sex, injuries from a fight, and traumatic head injury. Boys were prospectively tracked from age 16 to 19 at which time these outcomes were documented in the interim period. The results demonstrated that the VPS score is a significant predictor of all outcomes. Prediction accuracy ranged between 62%-83%. These findings suggest that the VPS may be useful for identifying youths who are at high risk for using illicit drugs and commonly associated adverse outcomes. PMID:19283571

Kirisci, Levent; Tarter, Ralph; Reynolds, Maureen

2009-01-01

298

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

299

Chronic dietary Kudzu Isoflavones Improve Components of Metabolic Syndrome in Stroke-prone Spontaneously Hypertensive Rats  

PubMed Central

The present study tested the long-term effects of dietary kudzu root extract supplementation on the regulation of arterial pressure, plasma glucose and circulating cholesterol in stroke-prone spontaneously hypertensive rats (SP-SHR). Female SP-SHR were maintained for 2 months on a polyphenol-free diet, with or without the addition of 0.2% kudzu root extract. One-half of the rats in each diet group were ovariectomized while the other half remained intact. Following 2 months on the diets, the 0.2% kudzu root extract supplementation (compared to control diet) significantly lowered arterial pressure (11–15 mm Hg), plasma cholesterol, fasting blood glucose (20%–30%) and fasting plasma insulin in both the ovariectomized and intact SP-SHR. These results indicate that long-term dietary kudzu root extract supplementation can improve glucose, lipid and blood pressure control in intact and ovariectomized SP-SHR. PMID:19938872

Peng, Ning; Prasain, Jeevan K.; Dai, Yanying; Moore, Ray; Arabshahi, Alireza; Barnes, Stephen; Carlson, Scott; Wyss, J. Michael

2009-01-01

300

Chronic dietary kudzu isoflavones improve components of metabolic syndrome in stroke-prone spontaneously hypertensive rats.  

PubMed

The present study tested the long-term effects of dietary kudzu root extract supplementation on the regulation of arterial pressure, plasma glucose, and circulating cholesterol in stroke-prone spontaneously hypertensive rats (SP-SHR). Female SP-SHR were maintained for 2 months on a polyphenol-free diet, with or without the addition of 0.2% kudzu root extract. Half of the rats in each diet group were ovariectomized, whereas the other half remained intact. Following 2 months on the diets, the 0.2% kudzu root extract supplementation (compared to control diet) significantly lowered arterial pressure (11-15 mmHg), plasma cholesterol, fasting blood glucose (20-30%), and fasting plasma insulin in both the ovariectomized and intact SP-SHR. These results indicate that long-term dietary kudzu root extract supplementation can improve glucose, lipid, and blood pressure control in intact and ovariectomized SP-SHR. PMID:19938872

Peng, Ning; Prasain, Jeevan K; Dai, Yanying; Moore, Ray; Arabshahi, Alireza; Barnes, Stephen; Carlson, Scott; Wyss, J Michael

2009-08-26

301

Marked differences between prone and supine sheep in effect of PEEP on perfusion distribution in zone II lung.  

PubMed

The classic four-zone model of lung blood flow distribution has been questioned. We asked whether the effect of positive end-expiratory pressure (PEEP) is different between the prone and supine position for lung tissue in the same zonal condition. Anesthetized and mechanically ventilated prone (n = 6) and supine (n = 5) sheep were studied at 0, 10, and 20 cm H2O PEEP. Perfusion was measured with intravenous infusion of radiolabeled 15-microm microspheres. The right lung was dried at total lung capacity and diced into pieces (approximately 1.5 cm3), keeping track of the spatial location of each piece. Radioactivity per unit weight was determined and normalized to the mean value for each condition and animal. In the supine posture, perfusion to nondependent lung regions decreased with little relative perfusion in nondependent horizontal lung planes at 10 and 20 cm H2O PEEP. In the prone position, the effect of PEEP was markedly different with substantial perfusion remaining in nondependent lung regions and even increasing in these regions with 20 cm H2O PEEP. Vertical blood flow gradients in zone II lung were large in supine, but surprisingly absent in prone, animals. Isogravitational perfusion heterogeneity was smaller in prone than in supine animals at all PEEP levels. Redistribution of pulmonary perfusion by PEEP ventilation in supine was largely as predicted by the zonal model in marked contrast to the findings in prone. The differences between postures in blood flow distribution within zone II strongly indicate that factors in addition to pulmonary arterial, venous, and alveolar pressure play important roles in determining perfusion distribution in the in situ lung. We suggest that regional variation in lung volume through the effect on vascular resistance is one such factor and that chest wall conformation and thoracic contents determine regional lung volume. PMID:15774701

Walther, Sten M; Johansson, Mats J; Flatebø, Torun; Nicolaysen, Anne; Nicolaysen, Gunnar

2005-09-01

302

Macrophages from lupus-prone MRL mice have a conditional signaling abnormality that leads to dysregulated expression of numerous genes  

PubMed Central

Macrophages (m?) from pre-diseased mice of the major murine inbred models of spontaneous autoimmunity (AI), including multiple lupus-prone strains and the type I diabetes-prone NOD (non-obese diabetic) strain, have identical apoptotic target-dependent abnormalities. This characteristic feature of m? from AI-prone mice suggests that abnormal signaling events induced within m? following their interaction with apoptotic targets may predispose to AI. Such signaling abnormalities would affect predominantly the processing and presentation of self-antigen (i.e., derived from apoptotic targets), while sparing the processing and presentation of foreign antigen (i.e., derived from non-apoptotic sources). Here, we used DNA microarrays to test the hypothesis that m? from AI-prone mice (MRL/MpJ [MRL/+] or MRL/MpJ-Tnfrsf6lpr [MRL/lpr]) differentially express multiple genes in comparison to non-AI m? (BALB/c), but do so in a largely apoptotic cell-dependent manner. M? were stimulated with lipopolysaccharide, a potent innate stimulus, in the presence or absence of serum (an experimental surrogate for apoptotic targets). In accord with our hypothesis, the number of genes differentially expressed by MRL m? was significantly increased in the presence vs. the absence of serum, the apoptotic target surrogate (n=401 vs. n=201). Notably, for genes differentially expressed by MRL m? in the presence of serum, serum-free culture normalized their expression to a level statistically indistinguishable from that by non-AI m?. Comparisons of m? from AI-prone NOD and non-AI C57BL/6 mice corroborated these findings. Together, these data support the hypothesis that m? from MRL and other AI-prone mice are characterized by a conditional abnormality elicited by serum lipids or apoptotic targets. PMID:21229240

Antoni, Angelika; Patel, Vimal A.; Fan, Hanli; Lee, Daniel J.; Graham, Lee H.; Rosch, Cristen L.; Spiegel, Daniel S.; Rauch, Joyce

2012-01-01

303

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

304

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

305

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

306

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

307

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

PubMed

Protein conformational disorders (PCDs), such as Alzheimer's disease, Huntington's disease (HD), Parkinson's disease and oculopharyngeal muscular dystrophy, are associated with proteins that misfold and aggregate. Here we have used exon 1 of the HD gene with expanded polyglutamine [poly(Q)] repeats and enhanced green fluorescent protein tagged to 19 alanines as models for aggregate-prone proteins, to investigate the pathways mediating their degradation. Autophagy is involved in the degradation of these model proteins, since they accumulated when cells were treated with different inhibitors acting at distinct stages of the autophagy-lysosome pathway, in two different cell lines. Furthermore, rapamycin, which stimulates autophagy, enhanced the clearance of our aggregate-prone proteins. Rapamycin also reduced the appearance of aggregates and the cell death associated with the poly(Q) and polyalanine [poly(A)] expansions. Since rapamycin is used clinically, this drug or related analogues may be suitable candidates for therapeutic investigation in HD and related diseases. We have also re-examined the role of the proteasome, since previous studies in poly(Q) diseases have used lactacystin as an inhibitor--recent studies have shown that lactacystin may also affect lysosomal function. Both lactacystin and the specific proteasomal inhibitor epoxomicin increased soluble protein levels of the poly(Q) constructs, suggesting that these are also cleared by the proteasome. However, while poly(Q) aggregation was enhanced by lactacystin in our inducible PC12 cell model, aggregation was reduced by epoxomicin, suggesting that some other protein(s) induced by epoxomicin may regulate poly(Q) aggregation. PMID:11978769

Ravikumar, Brinda; Duden, Rainer; Rubinsztein, David C

2002-05-01

308

Effect of Prone Positioning on Clinical Outcomes in Children with Acute Lung Injury: A Randomized Controlled Trial  

PubMed Central

Context In uncontrolled clinical studies, prone positioning appeared to be safe and to improve oxygenation in pediatric patients with acute lung injury. However, the effect of prone positioning on clinical outcomes in children is not known. Objective To test the hypothesis that, at the end of 28 days, infants and children with acute lung treated with prone positioning would have more ventilator-free days than those treated with supine positioning. Design Multi-center, randomized, controlled clinical trial of supine versus prone positioning. Randomization was concealed. Group assignment was not blinded. Patients and Setting We enrolled 102 pediatric patients, 42-weeks post-conceptual age to 18 years, within 48 hours of meeting acute lung injury criteria from seven Pediatric Intensive Care units. Interventions Patients randomized to the supine position remained supine. Patients randomized to the prone group were positioned within 4 hours of randomization and remained prone for 20 hours each day during the acute phase of their illness for a maximum of 7 days then remained supine. Both groups were managed using lung protective ventilator and sedation protocols, extubation readiness testing and hemodynamic, nutrition and skin care guidelines. Main Outcome Measure Ventilator-free days to day 28. Analyses were carried out on an intention-to-treat basis. Results The trial was stopped at the planned interim analysis on the basis of the pre-specified futility stopping rule. There were no differences in the number of ventilator-free days between the two groups (15.8 ± 8.5 supine versus 15.6 ± 8.6 prone group, difference ?0.2 days, 95 percent confidence interval, ?3.6 to 3.2, P=0.91). After controlling for age, Pediatric Risk of Mortality III score, direct versus indirect acute lung injury and mode of mechanical ventilation at enrollment, the adjusted difference in ventilator-free days was 0.3 days (95% confidence interval, ?3.0 to 3.5; P=0.87). There were no differences in the secondary endpoints including proportion alive and ventilator-free on day 28, mortality from all causes, the time to recovery of lung injury, organ-failure-free days, and functional health. Conclusions Prone positioning does not significantly improve ventilator-free days or other clinical outcomes in pediatric patients with acute lung injury. PMID:16014597

Curley, Martha A.Q.; Hibberd, Patricia L.; Fineman, Lori D.; Wypij, David; Shih, Mei-Chiung; Thompson, John E.; Grant, Mary Jo C.; Barr, Frederick E.; Cvijanovich, Natalie Z.; Sorce, Lauren; Luckett, Peter M.; Matthay, Michael A.; Arnold, John H.

2005-01-01

309

Nebular Abundance Errors  

E-print Network

The errors inherent to the use of the standard "ionization correction factor" ("i_CF") method of calculating nebular conditions and relative abundances of H, He, N, O, Ne, S, and Ar in emission line nebulae have been investigated under conditions typical for planetary nebulae. The photoionization code CLOUDY was used to construct a series of model nebulae with properties spanning the range typical of PNe. Its radial "profiles" of bright, frequently observed optical emission lines were then summed over a variety of "apertures" to generate sets of emission line measurements. These resulting line ratios were processed using the i_CF method to "derive" nebular conditions and abundances. We find that for lines which are summed over the entire nebula the i_CF-derived abundances differ from the input abundances by less than 5% for He and O up to 25% or more for Ne, S, and Ar. For resolved observations, however, the discrepancies are often much larger and are systematically variable with radius. This effect is especially pronounced in low-ionization zones where nitrogen and oxygen are neutral or once-ionized such as in FLIERs, ansae and ionization fronts. We argue that the reports of stellar-enriched N in the FLIERs of several PNe are probably specious.

J. Alexander; B. Balick

1997-05-01

310

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

311

Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance  

PubMed Central

The polymerase chain reaction (PCR) is widely used for applications which require a high level of specificity and reliability, such as genetic testing, clinical diagnostics, blood screening, forensics and biodefense. Great improvements to PCR performance have been achieved by the use of Hot Start activation strategies that aim to prevent DNA polymerase extension until more stringent, higher temperatures are reached. Herein we present a novel Hot Start activation approach in PCR where primers contain one or two thermolabile, 4-oxo-1-pentyl (OXP) phosphotriester (PTE) modification groups at 3?-terminal and 3?-penultimate internucleotide linkages. Studies demonstrated that the presence of one or more OXP PTE modifications impaired DNA polymerase primer extension at the lower temperatures that exist prior to PCR amplification. Furthermore, incubation of the OXP-modified primers at elevated temperatures was found to produce the corresponding unmodified phosphodiester (PDE) primer, which was then a suitable DNA polymerase substrate. The OXP-modified primers were tested in conventional PCR with endpoint detection, in one-step reverse transcription (RT)–PCR and in real-time PCR with SYBR Green I dye and Taqman® probe detection. When OXP-modified primers were used as substitutes for unmodified PDE primers in PCR, significant improvement was observed in the specificity and efficiency of nucleic acid target amplification. PMID:18796527

Lebedev, Alexandre V.; Paul, Natasha; Yee, Joyclyn; Timoshchuk, Victor A.; Shum, Jonathan; Miyagi, Kei; Kellum, Jack; Hogrefe, Richard I.; Zon, Gerald

2008-01-01

312

PCR melting profile (PCR MP) - a new tool for differentiation of Candida albicans strains  

PubMed Central

Background We have previously reported the use of PCR Melting Profile (PCR MP) technique based on using low denaturation temperatures during ligation mediated PCR (LM PCR) for bacterial strain differentiation. The aim of the current study was to evaluate this method for intra-species differentiation of Candida albicans strains. Methods In total 123 Candida albicans strains (including 7 reference, 11 clinical unrelated, and 105 isolates from patients of two hospitals in Poland) were examined using three genotyping methods: PCR MP, macrorestriction analysis of the chromosomal DNA by pulsed-field gel electrophoresis (REA-PFGE) and RAPD techniques. Results The genotyping results of the PCR MP were compared with results from REA-PFGE and RAPD techniques giving 27, 26 and 25 unique types, respectively. The results showed that the PCR MP technique has at least the same discriminatory power as REA-PFGE and RAPD. Conclusion Data presented here show for the first time the evaluation of PCR MP technique for candidial strains differentiation and we propose that this can be used as a relatively simple and cheap technique for epidemiological studies in short period of time in hospital. PMID:19906294

2009-01-01

313

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

E-print Network

the host animal source of fecal contamination is based on the assumption that certain strains of fecalAnalyzing Water Samples for Sources of Contamination using PCR and qPCR Berenise Rivera Advisor: Dr or full body contact) and public water supplies from fecal contamination have become challenging

Fay, Noah

314

Numerical Error Estimation with UQ  

NASA Astrophysics Data System (ADS)

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

Ackmann, Jan; Korn, Peter; Marotzke, Jochem

2014-05-01

315

Forensic implications of PCR inhibition—A review  

Microsoft Academic Search

Polymerase chain reaction (PCR) is currently the method of choice for the identification of human remains in forensic coursework. DNA samples from crime scenes often contain co-purified impurities which inhibit PCR. PCR inhibition is the most common cause of PCR failure when adequate copies of DNA are present. Inhibitors have been routinely reported in forensic investigations of DNA extracted from

Reza Alaeddini

316

Real-time PCR: Advanced technologies and applications  

Technology Transfer Automated Retrieval System (TEKTRAN)

This book brings together contributions from 20 experts in the field of PCR, providing a broad perspective of the applications of quantitative real-time PCR (qPCR). The editors state in the preface that the aim is to provide detailed insight into underlying principles and methods of qPCR to provide ...

317

Kinetic Outlier Detection (KOD) in real-time PCR  

Microsoft Academic Search

Real-time PCR is becoming the method of choice for precise quantification of minute amounts of nucleic acids. For proper comparison of samples, almost all quantification methods assume similar PCR effi- ciencies in the exponential phase of the reaction. However, inhibition of PCR is common when work- ing with biological samples and may invalidate the assumed similarity of PCR efficiencies. Here

Tzachi Bar; Anders Stahlberg; Anders Muszta; Mikael Kubista

2003-01-01

318

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

319

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

320

Urine PCR Evaluation to Diagnose Pulmonary Tuberculosis  

PubMed Central

Background: Culture and specific staining (including Zeil-Nelson and fluorescent methods) are standard measures for the diagnosis of tuberculosis (TB). These methods are time-consuming and sometimes have a low level of accuracy. In addition, in some cases obtaining samples for smear and culture involves invasive procedures; while in other cases there is no suitable sample for evaluation. Therefore, there is a need for faster and more accurate diagnostic methods. Objectives: The current study investigated the diagnostic value of tuberculosis-polymerase chain reaction (TB-PCR) of urine in the diagnosis of pulmonary tuberculosis (PTB). Patients and Methods: This case-control study included; 77 proven pulmonary tuberculosis cases (according to the national TB protocol), and 30 subjects who were completely healthy. The urine samples (50 mL) were mixed with 0.5 mL Ethylene diamine tetraacetic acid. DNA extraction and PCR testing were performed on all blood samples using SI 6110 primers. Mycobacterium tuberculosis was also cultivated in the sputum and urine samples of the patients. Results: Results of the current study indicated that 48 (62.3%) patients out of 77 had a positive sputum culture. Urine cultures and acid-fast smears were negative. Urine PCR-TB was positive in 48.0% (37/77) of the patients. The speci?c TBPCR complex was positive in 56.2% (27/48) of the positive cultures and 34.4% (10/29) of the negative culture PTB patients. The control group had negative urine PCR (sensitivity 56.2% and specificity 100%). Conclusions: With regard to the ease of urine sample preparation and the 100% specificity the PCR method, performing urine PCR could be used as a diagnostic aid in PTB cases obtaining sputum samples is problematic. PMID:25147688

Heydari, Ali Akbar; Movahhede Danesh, Masood Reza; Ghazvini, Kiarash

2014-01-01

321

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

322

Application of a Nested, Multiplex PCR to Psittacosis Outbreaks  

Microsoft Academic Search

We developed a nested, multiplex PCR for simultaneous detection of three species of chlamydiae in human and avian specimens. The PCR was designed to increase sensitivity and to circumvent inhibitors of PCR present in clinical specimens. The target sequence was the 16S rRNA gene. The first-step PCR was genus specific, and the second-step PCR was multiplexed (i.e., had multiple primer

TRUDY O. MESSMER; STEPHEN K. SKELTON; JOHN F. MORONEY; HARRY DAUGHARTY; BARRY S. FIELDS

323

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 ...

324

Children's Scale Errors with Tools  

ERIC Educational Resources Information Center

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

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

2011-01-01

325

Twenty questions about student errors  

NASA Astrophysics Data System (ADS)

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

Fisher, Kathleen M.; Lipson, Joseph Isaac

326

Human error in recreational boating  

Microsoft Academic Search

Each year over 600 people die and more than 4000 are reported injured in recreational boating accidents. As with most other accidents, human error is the major contributor. U.S. Coast Guard reports of 3358 accidents were analyzed to identify errors in each of the boat types by which statistics are compiled: auxiliary (motor) sailboats, cabin motorboats, canoes and kayaks, house

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

2007-01-01

327

A Trio of Turmoil for Internet Sexually Addicted Men Who Have Sex with Men: Boredom Proneness, Social Connectedness, and Dissociation  

Microsoft Academic Search

This article explores the impact of boredom proneness, social connectedness, and online dissociation in Internet sexually addicted men who have sex with men (MSM). Increased levels of boredom, diminished social connections, and dissociative symptoms while engaged in excessive online sexual activities are conceptualized as components that facilitate and maintain Internet sexual addiction. An overview of the literature pertaining to extreme

MICHAEL P. CHANEY; CATHERINE Y. CHANG

2005-01-01

328

Boredom-proneness, loneliness, social engagement and depression and their association with cognitive function in older people: A population study  

Microsoft Academic Search

In this study, we use data from a population survey of persons aged 65 and over living in the Irish Republic to examine the relationship of cognitive impairment, assessed using the Abbreviated Mental Test, with loneliness, boredom-proneness, social relations, and depression. Participants were randomly selected community-dwelling Irish people aged 65+ years. An Abbreviated Mental Test score of 8 or 9

Ronán M. Conroy; Jeannette Golden; Isabelle Jeffares; Desmond ONeill; Hannah McGee

2010-01-01

329

Boredom-proneness, loneliness, social engagement and depression and their association with cognitive function in older people: a population study.  

PubMed

In this study, we use data from a population survey of persons aged 65 and over living in the Irish Republic to examine the relationship of cognitive impairment, assessed using the Abbreviated Mental Test, with loneliness, boredom-proneness, social relations, and depression. Participants were randomly selected community-dwelling Irish people aged 65+ years. An Abbreviated Mental Test score of 8 or 9 out of 10 was classified as 'low normal', and a score of less than 8 as 'possible cognitive impairment'. We used clustering around latent variables analysis (CLV) to identify families of variables associated with reduced cognitive function. The overall prevalence of possible cognitive impairment was 14.7% (95% CI 12.4-17.3%). Low normal scores had a prevalence of 30.5% (95% CI 27.2-33.7%). CLV analysis identified three groups of predictors: 'Low social support' (widowed, living alone, low social support), 'personal cognitive reserve' (low social activity, no leisure exercise, never having married, loneliness and boredom-proneness), and 'sociodemographic cognitive reserve' (primary education, rural domicile). In multivariate analysis, both cognitive reserve clusters, but not social support, were independently associated with cognitive function. Loneliness and boredom-proneness are associated with reduced cognitive function in older age, and cluster with other factors associated with cognitive reserve. Both may have a common underlying mechanism in the failure to select and maintain attention on particular features of the social environment (loneliness) or the non-social environment (boredom-proneness). PMID:20677084

Conroy, Ronan M; Golden, Jeannette; Jeffares, Isabelle; O'Neill, Desmond; McGee, Hannah

2010-08-01

330

A Longitudinal Study of Drug and Alcohol Use by Psychosis-Prone and Impulsive–Nonconforming Individuals  

Microsoft Academic Search

The rates of substance use and abuse are higher among psychotic patients and antisocial individuals than in the general population. In a 10-year longitudinal study, psychosis-prone individuals identified by the Perceptual Aberration (L. J. Chapman, J. P. Chapman, M. L. Raulin, 1976) and Magical Ideation (Per-Mag) scales (M. Eckblad & L. J. Chapman, 1983), and individuals with antisocial traits, identified

Thomas R. Kwapil

1996-01-01

331

Applications of Physics to Measuring and Improving the Performance of Buildings in Hot, Humid, Hurricane-Prone Climates  

NASA Astrophysics Data System (ADS)

In this presentation we will present topics showing how physics can be applied to measuring and improving the performance (energy efficiency and durability of the structure, health, safety, and comfort of the occupants) of buildings in hot, humid, hurricane-prone climates representative of the climate in New Orleans and the Gulf Coast.

Witriol, Norman; Katz, Myron; Faust, Christophor; Erinjeri, Jinson

2008-03-01

332

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 ...

333

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

334

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

335

Determination of radon prone areas by probabilistic analysis of indoor survey results and geological prognostic maps in the Czech Republic  

Microsoft Academic Search

The determination of radon prone areas is usually based on indoor radon surveys and prognoses of occurrence of houses above action level [CRP Publication 65, Protection against Radon at Home and at Work]. The sample of houses in the survey must be representative and large enough, if accurate results are to be obtained. However, even if such condition are fulfilled,

Josef Thomas; Ji??? H?lka; Ladislav Tomášek; Ivana Fojt??ková; Ivan Barnet

2002-01-01

336

Optimal PHP control of multiple part-types on a failure-prone machine with quadratic buffer costs  

Microsoft Academic Search

We consider a single, failure-prone machine, producing multiple part-types. The goal is to minimize the expected sum of quadratic buffer costs. In general, the optimal solution to this problem is unknown. However, by restricting the allowable set of control policies to the class of prioritized hedging point policies, we are able to determine simple, analytical expressions for the optimal hedging

Chang Shu; James R. Perkins

1998-01-01

337

Optimal PHP production of multiple part-types on a failure-prone machine with quadratic buffer costs  

Microsoft Academic Search

We consider a single, failure-prone machine, producing multiple part-types The objective is to minimize the expected sum of quadratic buffer costs. In general, the optimal solution to this problem is unknown. However, by restricting the allowable set of control policies to the class of prioritized hedging point (PHP) policies, we are able to determine simple, analytical expressions for the optimal

Chang Shu; James R. Perkins

2001-01-01

338

Preterm Infants Who Are Prone to Distress: Differential Effects of Parenting on 36-Month Behavioral and Cognitive Outcomes  

ERIC Educational Resources Information Center

Background: The differential susceptibility (DS) model suggests that temperamentally prone-to-distress infants may exhibit adverse outcomes in negative environments but optimal outcomes in positive environments. This study explored temperament, parenting, and 36-month cognition and behavior in preterm infants using the DS model. We hypothesized…

Poehlmann, Julie; Hane, Amanda; Burnson, Cynthia; Maleck, Sarah; Hamburger, Elizabeth; Shah, Prachi E.

2012-01-01

339

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

340

Angle interferometer cross axis errors  

SciTech Connect

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

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

1994-01-01

341

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

342

PCR-based detection of Mycoplasma species.  

PubMed

In this study, we describe our newly-developed sensitive two-stage PCR procedure for the detection of 13 common mycoplasmal contaminants (M. arthritidis, M. bovis, M. fermentans, M. genitalium, M. hominis, M. hyorhinis, M. neurolyticum, M. orale, M. pirum, M. pneumoniae, M. pulmonis, M. salivarium, U. urealyticum). For primary amplification, the DNA regions encompassing the 16S and 23S rRNA genes of 13 species were targeted using general mycoplasma primers. The primary PCR products were then subjected to secondary nested PCR, using two different primer pair sets, designed via the multiple alignment of nucleotide sequences obtained from the 13 mycoplasmal species. The nested PCR, which generated DNA fragments of 165-353 bp, was found to be able to detect 1-2 copies of the target DNA, and evidenced no cross-reactivity with the genomic DNA of related microorganisms or of human cell lines, thereby confirming the sensitivity and specificity of the primers used. The identification of contaminated species was achieved via the performance of restriction fragment length polymorphism (RFLP) coupled with Sau3AI digestion. The results obtained in this study furnish evidence suggesting that the employed assay system constitutes an effective tool for the diagnosis of mycoplasmal contamination in cell culture systems. PMID:16554716

Sung, Hyeran; Kang, Seung Hye; Bae, Yoon Jin; Hong, Jin Tae; Chung, Youn Bok; Lee, Chong-Kil; Song, Sukgil

2006-02-01

343

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

344

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

345

Effects of electroacupuncture Zusanli (ST36) on food intake and expression of POMC and TRPV1 through afferents-medulla pathway in Obese Prone Rats  

PubMed Central

Objective The purpose of this study was to determine the effects of electroacupuncture (EA) ST36 on food intake and body weight in Obese Prone (OP) rats compared to obese resistant (OR) strain on a high fat diet. The influences of EA on mRNA levels of pro-opiomelanocortin (POMC), transient receptor potential vanilloid type-1 (TRPV1), and neuronal nitric oxide synthase (nNOS) were also examined in the medulla regions and ST36 skin tissue. Methods Advanced EA ST36 was conducted in two sessions of 20 min separated by an 80 min interval for 7 days. Food intake and body weight were recorded in conscious rats every day. Real time PCR was conducted in the micropunches of the medulla regions and skin tissues at the end of the treatment. Results Food intake and body weight were significantly reduced by advanced EA ST36 in OP rats, but slightly decreased in OR strain and sham-EA rats. Advanced EA ST36 produced a marked increase in POMC mRNA level in the nucleus tractus solitarius (NTS) and hypoglossal nucleus (HN) regions. TRPV1 and nNOS mRNAs were simultaneously increased in the NTS/gracile nucleus regions and in the ST36 skin regions by the EA treatment in OP rats. Conclusions We conclude that advanced EA ST36 produces an up-regulation of anorexigenic factor POMC production in the NTS/HN, which inhibits food intake and reduces body weight. EA-induced expression of TRPV1-nNOS in the ST36 and the NTS/gracile nucleus is involved in the signal transduction of EA stimuli via somatosensory afferents-medulla pathways. PMID:23116614

Ji, Bo; Hu, Jay; Ma, Shengxing

2013-01-01

346

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

347

Gene expression analysis in early embryos through reverse transcription quantitative PCR (RT-qPCR).  

PubMed

Real-time, reverse transcription quantitative PCR (RT-qPCR) is a highly sensitive and reproducible technology for the analysis of gene expression patterns. Its ability to detect minute quantities of nucleic acid from multifarious sources makes it an ideal technique for embryonic transcript quantification. However, complex cellular diversity and active transcriptome dynamics in early embryos necessitate particular caution to avoid erroneous results. This chapter is intended to outline basic methodology to design and execute RT-qPCR experiments in pre-implantation embryos. PMID:25287347

Peynot, Nathalie; Duranthon, Véronique; Khan, Daulat Raheem

2015-01-01

348

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

349

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

350

Comparison of dose volume histograms for supine and prone position in patients irradiated for prostate cancer—A preliminary study  

PubMed Central

Aim To compare DVHs for OARs in two different positions – prone and supine – for prostate cancer patients irradiated with a Tomotherapy unit. Background In the era of dose escalation, the choice of optimal patient immobilization plays an essential role in radiotherapy of prostate cancer. Materials and methods The study included 24 patients who were allocated to 3 risk groups based on D’Amico criteria; 12 patients represented a low or intermediate and 12 a high risk group. For each patient two treatment plans were performed: one in the supine and one in the prone position. PTV included the prostate, seminal vesicles and lymph nodes for the high risk group and the prostate and seminal vesicles for the intermediate or low risk groups. DVHs for the two positions were compared according to parameters: Dmean, D70, D50 and D20 for the bladder and rectum and Dmean, D10 for the intestine. The position accuracy was verified using daily MVCT. Results Prone position was associated with lower doses in OARs, especially in the rectum. Despite the fact that in the entire group the differences between tested parameters were not large, the Dmean and D10 for the intestine were statistically significant. In the case of irradiation only to the prostate and seminal vesicles, the prone position allowed for substantial reduction of all tested DVH parameters in the bladder and rectum, except D20 for bladder. Moreover, the Dmean and D50 parameter differences for the bladder were statistically significant. No significant differences between positions reproducibility were demonstrated. Conclusion In patients irradiated to prostate and seminal vesicles, the prone position may support sparing of the rectum and bladder. The reproducibility of position arrangement in both positions is comparable. PMID:24376959

Bajon, Tomasz; Piotrowski, Tomasz; Antczak, Andrzej; B?k, Bartosz; B?asiak, Barbara; Ka?mierska, Joanna

2011-01-01

351

Dopaminergic basis of the psychosis-prone personality investigated with functional magnetic resonance imaging of procedural learning  

PubMed Central

Previous evidence shows a reliable association between psychosis-prone (especially schizotypal) personality traits and performance on dopamine (DA)-sensitive tasks (e.g., prepulse inhibition and antisaccade). Here, we used blood oxygen level-dependent (BOLD) fMRI and an established procedural learning (PL) task to examine the dopaminergic basis of two aspects of psychosis-proneness (specific schizotypy and general psychoticism). Thirty healthy participants (final N = 26) underwent fMRI during a blocked, periodic sequence-learning task which, in previous studies, has been shown to reveal impaired performance in schizophrenia patients given drugs blocking the DA D2 receptor subtype (DRD2), and to correspond with manipulation of DA activity and elicit fronto-striatal-cerebellar activity in healthy people. Psychosis-proneness was indexed by the Psychoticism (P) scale of the Eysenck Personality Questionnaire-Revised (EPQ-R; 1991) and the Schizotypal Personality Scale (STA; 1984). EPQ-R Extraversion and Neuroticism scores were also examined to establish discriminant validity. We found a positive correlation between the two psychosis-proneness measures (r = 0.43), and a robust and unique positive association between EPQ-R P and BOLD signal in the putamen, caudate, thalamus, insula, and frontal regions. STA schizotypy score correlated positively with activity in the right middle temporal gyrus. As DA is a key transmitter in the basal ganglia, and the thalamus contains the highest levels of DRD2 receptors of all extrastriatal regions, our results support a dopaminergic basis of psychosis-proneness as measured by the EPQ-R Psychoticism. PMID:23596404

Ettinger, Ulrich; Corr, Philip J.; Mofidi, Ardeshier; Williams, Steven C. R.; Kumari, Veena

2013-01-01

352

Dopaminergic basis of the psychosis-prone personality investigated with functional magnetic resonance imaging of procedural learning.  

PubMed

Previous evidence shows a reliable association between psychosis-prone (especially schizotypal) personality traits and performance on dopamine (DA)-sensitive tasks (e.g., prepulse inhibition and antisaccade). Here, we used blood oxygen level-dependent (BOLD) fMRI and an established procedural learning (PL) task to examine the dopaminergic basis of two aspects of psychosis-proneness (specific schizotypy and general psychoticism). Thirty healthy participants (final N = 26) underwent fMRI during a blocked, periodic sequence-learning task which, in previous studies, has been shown to reveal impaired performance in schizophrenia patients given drugs blocking the DA D2 receptor subtype (DRD2), and to correspond with manipulation of DA activity and elicit fronto-striatal-cerebellar activity in healthy people. Psychosis-proneness was indexed by the Psychoticism (P) scale of the Eysenck Personality Questionnaire-Revised (EPQ-R; 1991) and the Schizotypal Personality Scale (STA; 1984). EPQ-R Extraversion and Neuroticism scores were also examined to establish discriminant validity. We found a positive correlation between the two psychosis-proneness measures (r = 0.43), and a robust and unique positive association between EPQ-R P and BOLD signal in the putamen, caudate, thalamus, insula, and frontal regions. STA schizotypy score correlated positively with activity in the right middle temporal gyrus. As DA is a key transmitter in the basal ganglia, and the thalamus contains the highest levels of DRD2 receptors of all extrastriatal regions, our results support a dopaminergic basis of psychosis-proneness as measured by the EPQ-R Psychoticism. PMID:23596404

Ettinger, Ulrich; Corr, Philip J; Mofidi, Ardeshier; Williams, Steven C R; Kumari, Veena

2013-01-01

353

Clinical Utility of Droplet Digital PCR for Human Cytomegalovirus  

PubMed Central

Human cytomegalovirus (CMV) has historically been the major infectious cause of morbidity and mortality among patients receiving hematopoietic cell or organ transplant. Standard care in a transplant setting involves frequent monitoring of CMV viral load over weeks to months to determine when antiviral treatment may be required. Quantitative PCR (qPCR) is the standard molecular diagnostic method for monitoring. Recently, digital PCR (dPCR) has shown promise in viral diagnostics, although current dPCR systems have lower throughput than qPCR systems. Here, we compare qPCR and droplet digital PCR (ddPCR) for CMV detection in patient plasma samples. Droplet digital PCR exhibits increased precision over qPCR at viral loads of ?4 log10 with equivalent sensitivity. However, retrospective analysis of longitudinal samples from transplant patients with CMV viral loads near therapeutic thresholds did not provide evidence that the improved precision of ddPCR would be of clinical benefit. Given the throughput advantages of current qPCR systems, a widespread switch to dPCR for CMV monitoring would appear premature. PMID:24871214

Sedlak, Ruth Hall; Cook, Linda; Cheng, Anqi; Magaret, Amalia

2014-01-01

354

[Medication errors: who is responsible?].  

PubMed

New diagnostic and therapeutic technologies are used with growing frequency, improving the quality of medical assistance and increasing life expectancy. Health care, however, is becoming progressively more expensive and complex. Adverse events related to medical assistance, particularly errors, are becoming public, being debated and judged in courts. Given their training, health workers are not prepared to deal with errors, which are associated with shame, fear and punishment. The approach to errors in the health system is usually individualistic, considering such events as acts of insecurity performed by careless, non-motivated and ill-trained persons. The tendency is to hide errors when they occur, with the result that an important learning opportunity is lost. There is another way to deal with errors, a systemic view that has obtained positive results in sectors such as aviation, anesthesiology and unit-dose drug distribution systems. These systems have varied degrees of safety and should take into account human limitations when designed and applied. A change in paradigm is needed when dealing with drugs, as it is not enough for a drug to have quality assurance, but the complete process of drug use should be safe. Medication errors, avoidable by definition, are at present a serious public health issue, leading to loss of lives and significant financial losses. A systemic approach to medication errors may disclose failures in the process as a whole, and improvements can be implemented to reduce their occurrence. PMID:14666362

Rosa, Mário Borges; Perini, Edson

2003-01-01

355

Error-resilient video compression  

NASA Astrophysics Data System (ADS)

Video compression reduces the required bit rate and thereby enables a number of applications such as digital television and video over the Internet. However, compression also makes the video much more susceptible to errors, e.g. bit errors or packet loss. Generally there is a tradeoff between the compression of a signal and the error resilience of the compressed representation. However, recently there have been a number of developments which provide significant improvements in error-resilience while resulting in relatively small reductions in compression. This paper provides an overview of current error-resilient compression methods and also proposes an error-resilient coding scheme referred to as Multiple State Streams (MSS). Conventional video compression standards employ a similar architecture which we refer to as single-state systems since they have a single state (e.g. the previously decoded frame) which if lost or corrupted adversely affects all subsequent frames until the state is reinitialized (the prediction is refreshed). We propose to combat this problem of incorrect state at the decoder with MSS by coding the video into multiple independently decodable streams, each with its own prediction process and state, such that if one stream is lost the other streams can still be used to produce usable video. More importantly, the correctly received streams provide improved error concealment and enable faster state recovery for the lost stream.

Apostolopoulos, John G.

1999-11-01

356

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

357

Numerical Errors in DNS: Total Run-Time Error  

SciTech Connect

Understanding numerical errors in simulations is critical for many reasons. First and foremost, one must some estimate concerning the reliability of the final result. Simply put, numerical errors add up over time and in most cases the increase is a linear process. It is quite possible that running a code for a very long time can lead to a solution which is completely meaningless even though it may look reasonable. This manuscript will begin a technical discussion on these issues.

Jameson, L.

2000-06-06

358

Piezoelectric control of columns prone to instabilities and nonlinear modal interaction  

NASA Astrophysics Data System (ADS)

This paper attempts to unravel the issues of piezoelectric control of structures prone to nonlinear static and dynamic instabilities. A simple yet typical example is considered, namely the problem of a simply supported axially compressed imperfect column on an elastic softening foundation. Here the significant nonlinearity arises from the softening foundation. The column is so designed as to have coincident critical loads for the first two modes of buckling. Piezoelectric actuators/sensors are deemed to be attached to a column in regions of maximum strain at several locations along the length of the column. The issues involved in (i) enhancing the static buckling load, (ii) suppression of vibrations as the column is compressed to a load close to its dynamic instability load and (iii) enhancing the dynamic instability load are investigated and discussed. It is shown that there is a premium price to pay for enhancing the buckling capacity of the column, be it static or dynamic. The paper concludes by alluding to the possibility of a failure of patch control if a higher-order shortwave mode happens to be the governing principal mode of the structure.

Sridharan, Srinivasan; Kim, Sunjung

2008-06-01

359

Intravital imaging in spontaneously hypertensive stroke-prone rats-a pilot study  

PubMed Central

Background There is growing evidence that endothelial failure and subsequent blood brain barrier (BBB) breakdown initiate cerebral small vessel disease (CSVD) pathology. In spontaneously hypertensive stroke-prone rats (SHRSP) endothelial damage is indicated by intraluminal accumulations of erythrocytes (erythrocyte thrombi) that are not observed with current magnetic resonance imaging techniques. Two-photon microscopy (2 PM) offers the potential for real-time direct detection of the small vasculature. Thus, within this pilot study we investigated the sensitivity of 2 PM to detect erythrocyte thrombi expressing initiating CSVD phenomena in vivo. Methods Eight SHRSP and 13 Wistar controls were used for in vivo imaging and subsequent histology with haematoxylin-eosin (HE). For 2 PM, cerebral blood vessels were labeled by fluorescent Dextran (70 kDa) applied intraorbitally. The correlation between vascular erythrocyte thrombi observed by 2 PM and HE-staining was assessed. Artificial surgical damage and parenchymal Dextran distribution were analyzed postmortem. Results Dextran was distributed within the small vessel walls and co-localized with IgG. Artificial surgical damage was comparable between SHRSP and Wistar controls and mainly affected the small vasculature. In fewer than 20% of animals there was correlation between erythrocyte thrombi as observed with 2 PM and histologically with HE. Conclusions Contrary to our initial expectations, there was little agreement between intravital 2 PM imaging and histology for the detection of erythrocyte thrombi. Two-photon microscopy is a valuable technique that complements but does not replace the value of conventional histology. PMID:24461046

2014-01-01

360

Matching 3-D prone and supine CT colonography scans using graphs.  

PubMed

In this paper, we propose a new registration method for prone and supine computed tomographic colonography scans using graph matching. We formulate 3-D colon registration as a graph matching problem and propose a new graph matching algorithm based on mean field theory. In the proposed algorithm, we solve the matching problem in an iterative way. In each step, we use mean field theory to find the matched pair of nodes with highest probability. During iterative optimization, one-to-one matching constraints are added to the system in a step-by-step approach. Prominent matching pairs found in previous iterations are used to guide subsequent mean field calculations. The proposed method was found to have the best performance with smallest standard deviation compared with two other baseline algorithms called the normalized distance along the colon centerline (NDACC) ( p = 0.17) with manual colon centerline correction and spectral matching ( p < 1e-5). A major advantage of the proposed method is that it is fully automatic and does not require defining a colon centerline for registration. For the latter NDACC method, user interaction is almost always needed for identifying the colon centerlines. PMID:22552585

Wang, Shijun; Petrick, Nicholas; Van Uitert, Robert L; Periaswamy, Senthil; Wei, Zhuoshi; Summers, Ronald M

2012-07-01

361

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

362

Prophylactic effects of ajoene on cerebral injury in stroke-prone spontaneously hypertensive rats (SHRSP).  

PubMed

As part of a basic study on the prevention of cerebral injury, ajoene (0.5 mg/d) and oil-macerated garlic extract (OMGE, containing 0.5 mg ajoene/d) were administrated to stroke-prone spontaneously hypertensive rats (SHRSP) among 8 weeks from 9 weeks of age. In the control group, 3 of 10 rats died (30%), whereas all SHRSP treated by ajoene or OMGE survived. Our results suggested that ajoene and OMGE-treatment reduced the mortality and cerebral injury in SHRSP. The levels of thiobarbituric acid reactive substance (TBARS) and the enzymatic activities of glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) and catalase (CAT) in the serum of stroke stage of SHRSP were measured. The results obtained were as follows; the TBARS level of the ajoene and OMGE-treated groups were lower than those of control groups. On the other hand, the GSH-Px and SOD activities of the ajoene and OMGE-treated groups were higher. Our results suggested that ajoene and OMGE were capable of having prophylactic effects on cerebral injury in SHRSP. PMID:16595890

Yamada, Norihiko; Hattori, Atsuhiko; Nishikawa, Tomoaki; Fukuda, Hiroyuki; Fujino, Tsuchiyoshi

2006-04-01

363

Dietary pattern and state of nutrition among children in drought-prone areas of southern Ethiopia.  

PubMed

To assess dietary habits and nutritional state in drought-prone areas of southern Ethiopia, we studied 334 households in a pastoral and 282 in an agricultural community. Milk and cereals were the main sources of food among children of the pastoral Boran in Dubluk, while cereals with limited supplements of animal products or legumes formed the main sources of food among children of the agricultural population of Elka in the Rift valley. Of the children in Elka, 54.9% were stunted, as compared with 19.5% among children in Dubluk. Also, stunting occurred at an earlier age among the Elka children. Prevalences of wasting were less than 5% in both communities. Improvement in the state of nutrition of the pastoral children followed soon after the main rains, but occurred later and after the main harvest among the agricultural children. In contrast to arm circumference, the weight-for-height measure showed marked seasonal variation. Socio-economic factors, such as family wealth and crowding, significantly influenced the state of nutrition among the children. Nutritional recovery following the prolonged drought among the agricultural children was slow and associated with families acquiring more wealth. PMID:7681641

Lindtjørn, B; Alemu, T; Bjorvatn, B

1993-01-01

364

Population growth, fertility, mortality and migration in drought prone areas in Ethiopia.  

PubMed

To assess the population dynamics of drought-prone communities, we investigated 605 households in the pastoralist Boran community of Dubluk and in the agricultural community of Elka, both located in southern Ethiopia. The age and sex composition of the population as well as records of births, deaths and patterns of migration were observed for 2 consecutive years. Repeated surveys of the same households revealed much higher rates for deaths and births than did cross-sectional surveys with a one-year recall period. Indirect mortality estimates showed that the under 5 years mortality rates (per 1000 births) were 135 in Dubluk and 219 in Elka. Highest crude death rates were observed in Elka during periods of meningitis and malaria epidemics. During the period of observation, death rates fluctuated to a greater extent than birth rates. Both communities had very high rates of natural increase: in Dubluk 39.0/1000 and in Elka 37.1/1000. In Dubluk, this rate was far higher than any previously recorded and may have indicated that fertility regulating mechanisms, traditionally inherent in the pastoralist social organization, had become weaker as part of cultural changes. Dubluk represented a semi-nomadic society with a moderately high mobility pattern. Peak periods of migration coincided with times of food scarcity in Elka. PMID:8465386

Lindtjørn, B; Alemu, T; Bjorvatn, B

1993-01-01

365

Group VII ethylene response factor diversification and regulation in four species from flood-prone environments.  

PubMed

Flooding events negatively affect plant performance and survival. Flooding gradients thereby determine the dynamics in vegetation composition and species abundance. In adaptation to flooding, the group VII Ethylene Response Factor genes (ERF-VIIs) play pivotal roles in rice and Arabidopsis through regulation of anaerobic gene expression and antithetical survival strategies. We investigated if ERF-VIIs have a similar role in mediating survival strategies in eudicot species from flood-prone environments. Here, we studied the evolutionary origin and regulation of ERF-VII transcript abundance and the physiological responses in species from two genera of divergent taxonomic lineages (Rumex and Rorippa). Synteny analysis revealed that angiosperm ERF-VIIs arose from two ancestral loci and that subsequent diversification and duplication led to the present ERF-VII variation. We propose that subtle variation in the regulation of ERF-VII transcript abundance could explain variation in tolerance among Rorippa species. In Rumex, the main difference in flood tolerance correlated with the genetic variation in ERF-VII genes. Large transcriptional differences were found by comparing the two genera: darkness and dark submergence-induced Rumex?ERF-VIIs, whereas HRE2 expression was increased in submerged Rorippa roots. We conclude that the involvement of ERF-VIIs in flooding tolerance developed in a phylogenetic-dependent manner, with subtle variations within taxonomic clades. PMID:24548060

van Veen, Hans; Akman, Melis; Jamar, Diaan C L; Vreugdenhil, Dick; Kooiker, Maarten; van Tienderen, Peter; Voesenek, Laurentius A C J; Schranz, M Eric; Sasidharan, Rashmi

2014-10-01

366

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 (DTM) and geomorphological inventory of rockfall deposits were the basis of landform classification analysis. DTM pre-processing was applied to improve the quality of DTM-derived products. Several data layers produced merely from DTM were slope, plan curvature, stream power index, shape complexity index; whereas layers produced from DTM and rockfall modeling were velocity and energy. Unsupervised fuzzy k-means was applied to classify the generic landforms. It was classified into seven classes: interfluve, convex creep slope, fall face, transportational middle slope, colluvial foot slope, lower slope and channel bed. The classification result was analyzed by draping it over DTMs and performing probability distribution of rockfall volume. Cumulative probability density was adopted to estimate the probability density of rockfall volume in four generic landforms i.e. fall face, transportational middle slope, colluvial foot slope and lower slope. It shows negative power laws, with exponents 0.58, 0.73, 0.68, 0.64; for fall face, transportational middle slope, colluvial foot slope and lower slope, respectively. Different values of the scaling exponents in each landform reflect that geomorphometry influences the volume statistics of rockfall. The methodology introduced in this paper has possibility for preliminary rockfall risk analysis. It reveals that the potential high risk is located in the transportational middle slope and colluvial footslope. This is useful information to account for the prioritization action of countermeasures policy and design.

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

2014-01-01

367

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

368

Anticardiolipin antibodies in spontaneously hypertensive rats (SHR), stroke-prone SHR and normal Wistar rats.  

PubMed

1. Anticardiolipin antibodies (ACA) can be detected in the serum of patients with autoimmune disturbances, ischaemic heart disease, myocardial infarction, neurological disorders and other medical conditions. Elevated values of these autoantibodies can be associated with recurrent fetal loss, arterial and venous thrombosis and thrombocytopenia. 2. In the present study, we investigated the presence of ACA in three rat strains, namely normal Wistar rats (WR), spontaneously hypertensive rats Okamoto-Aoki (SHR) and stroke-prone SHR (SHRSP). All animals were examined at four ages: 1, 4, 10 and 12 months of age. Anticardiolipin antibodies were determined by ELISA. 3. Anticardiolipin antibody levels in normal WR, which were used as controls, were lowest at 1 month and increased significantly from the 4th month on. At the prehypertensive age (1 month), ACA levels in SHR and SHRSP were significantly higher compared with control WR, decreased with age and were significantly lower at 4, 10 and 12 months compared with age-matched WR. 4. These differences may be a result of immunological disorders in SHR. PMID:10972537

Todorova, M; Baleva, M; Nikolov, K; Higashino, H; Kamenov, Z

2000-09-01

369

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

370

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

371

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

372

Investigation on the use of geomorphic approaches for the delineation of flood prone areas  

NASA Astrophysics Data System (ADS)

Three different geomorphic approaches to the identification of flood prone areas are investigated by means of a comparative analysis of the input parameters, the performances and the range of applicability. The selected algorithms are: the method proposed by Manfreda et al. (2011) based on a modified version of the Topographic Index (TIm); the linear binary classifier proposed by Degiorgis et al. (2012), which uses different geomorphic features related to the location of the site under exam with respect to the nearest hazard source; the hydro-geomorphic method by Nardi et al. (2006) simulating inundation flow depths along the river valley with the associated extent of surrounding inundated areas. Comparison has been carried out on two sub-catchments of the Tiber River in Central Italy. The simulated flooded areas, obtained using the selected three methods, are evaluated using as a reference the Tiber River Basin Authority standard flood maps. The aim of the research is to deepen our understanding on the potential of geomorphic algorithms and to define new strategies for prompt hydraulic risk mapping and preliminary flood hazard graduation. This is of foremost importance when detailed hydrologic and hydraulic studies are not available, e.g., over large regions and for ungauged basins.

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

2014-09-01

373

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

PubMed

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

2014-12-01

374

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

375

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

376

Co-chaperone CHIP stabilizes aggregate-prone malin, a ubiquitin ligase mutated in Lafora disease.  

PubMed

Lafora disease (LD) is an autosomal recessive neurodegenerative disorder caused by mutation in either the dual specificity phosphatase laforin or ubiquitin ligase malin. A pathological hallmark of LD is the accumulation of cytoplasmic polyglucosan inclusions commonly known as Lafora bodies in both neuronal and non-neuronal tissues. How mutations in these two proteins cause disease pathogenesis is not well understood. Malin interacts with laforin and recruits to aggresomes upon proteasome inhibition and was shown to degrade misfolded proteins. Here we report that malin is spontaneously misfolded and tends to be aggregated, degraded by proteasomes, and forms not only aggresomes but also other cytoplasmic and nuclear aggregates in all transfected cells upon proteasomal inhibition. Malin also interacts with Hsp70. Several disease-causing mutants of malin are comparatively more unstable than wild type and form aggregates in most transfected cells even without the inhibition of proteasome function. These cytoplasmic and nuclear aggregates are immunoreactive to ubiquitin and 20 S proteasome. Interestingly, progressive proteasomal dysfunction and cell death is also most frequently observed in the mutant malin-overexpressed cells compared with the wild-type counterpart. Finally, we demonstrate that the co-chaperone carboxyl terminus of the Hsc70-interacting protein (CHIP) stabilizes malin by modulating the activity of Hsp70. All together, our results suggest that malin is unstable, and the aggregate-prone protein and co-chaperone CHIP can modulate its stability. PMID:19892702

Rao, Sudheendra N R; Sharma, Jaiprakash; Maity, Ranjan; Jana, Nihar Ranjan

2010-01-01

377

Geophysical modeling of collapse-prone zones at Rumble III seamount, southern Pacific Ocean, New Zealand  

NASA Astrophysics Data System (ADS)

Catastrophic collapses of submarine volcanoes have the potential to generate major tsunami, threatening many coastal populations. Recognizing the difficulties surrounding anticipations of these events, quantitative assessment of collapse-prone regions based on detailed morphological, geological, and geophysical mapping can still provide important information about the hazards associated with these collapses. Rumble III is one of the shallowest, and largest, submarine volcanoes found along the Kermadec arc, and is both volcanically and hydrothermally active. Previous surveys have delineated major collapse features at Rumble III; based on time-lapse bathymetry, dramatic changes in the volcano morphology have been shown to have occurred over the interval 2007-2009. Furthermore, this volcano is located just ˜300 km from the east coast of the North Island of New Zealand. Here, we present a geophysical model for Rumble III that provides the locations and sizes of potential weak regions of this volcano. Shipborne and near-seafloor geological and geophysical data collected by the AUV Sentry are used to determine the subsurface distribution of weak and unstable volcanic rocks. The resulting model provides evidence for potentially unstable areas located in the Southeastern flank of this volcano which should be included in future hazard predictions.

Tontini, F. Caratori; Ronde, C. E. J.; Kinsey, J. C.; Soule, A.; Yoerger, D.; Cocchi, L.

2013-10-01

378

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

379

Improved PCR-based gene synthesis method and its application to the Citrobacter freundii phytase gene codon modification.  

PubMed

Gene synthesis technologies provide a powerful tool for increasing protein expression through codon optimization and gene modification. Here we describe an improved PCR-based gene synthesis technology, which is accurate, simple and cheap. The improved PCR-based gene synthesis (IPS) method consists of two steps. The first one is the synthesis of 300-400bp fragments by PCR reaction with Pfu DNA polymerase from 60-mer and 30-mer oligonucleotides with a 15bp overlap. The second one is assembling of fragments from the first step into the full-length gene by PCR reaction. Using this approach, we have successfully synthesized a modified phytase gene with 1256bp in length with optimal codons for expression in Pichia pastoris. P. pastoris strain that expressed the modified phytase gene (phyA-mod) showed a 50% increase in phytase activity level. In addition, we propose an inexpensive method for error correction, based on overlap-extension PCR (OE-PCR). PMID:20226218

Gordeeva, Tatiana L; Borschevskaya, Larisa N; Sineoky, Sergei P

2010-05-01

380

Discrete-error transport equation for error estimation in CFD  

NASA Astrophysics Data System (ADS)

With computational fluid dynamics (CFD) becoming more accepted and more widely used in industry for design and analysis, there is increasing demand for not just more accurate solutions, but also error bounds on the solutions. One major source of error is from the grid or mesh. A number of methods have been developed to quantify errors in solutions of partial differential equations (PDEs) that arise from poor-quality or insufficiently fine grids/meshes. For PDEs of interest to CFD, it has been shown that the error at one location could be generated elsewhere and then transported there, and thus is not a function of the local mesh quality and the local solution. So, a transport equation for error is needed to understand the generation and evolution of errors. Error transport equations have been developed for finite-element methods but not for finite-difference (FD) and finite-volume (FV) methods. In this study, a method is developed for deriving error-transport equations for estimating grid-induced errors in solutions obtained by using FD and FV methods. The error-transport equations derived are discrete in that they depend only on the FD or FV equations and are independent of the PDEs that the FD or FV equations are intended to represent. The usefulness of the DETEs developed was evaluated through test problems based on four one-dimensional (1-D) and two two-dimensional (2-D) PDES. The four 1-D PDEs are the advection-diffusion equation, the wave equation, the inviscid Burgers equation, and the steady Burgers equation. The two 2-D PDEs are the 2-D advection-diffusion equation and the system of Euler equations. For PDEs that are not linear, linearization procedures were proposed and examined. For all test problems based on 1-D PDEs, the residual is modeled by the leading term of the remainder in the modified equation for the FD or FV equation. The residual was also modeled by using functional relationship suggested by data mining, where actual residuals generated by the numerical experiments were fitted by using least-square minimization. For all test problems, grid-independent solutions were generated to assess how well the residuals are modeled and how well grid-induced errors are predicted by the DETEs. Results obtained show that if the actual residuals are used, then the DETEs can predict the grid-induced errors perfectly. This is true for all test problems evaluated, including those based on PDEs that are nonlinear and have time derivatives and for test problems with weak solutions. Results obtained also show that the leading terms of the modified equation is useful in modeling the residual if the grid spacing or cell size is sufficiently small so that the leading terms are bounded, a condition that is often not satisfied in practice. The usefulness of data mining in constructing residuals show the power-law to produce better fit than local linear least square of smoothness, resolution, aspect ratio and solution gradient. However, a more extensive database is needed before this approach can be expected to yield a more generally applicable models for the residual. The usefulness of Euler DETE in predicting grid-induced errors in the Navier-Stokes solutions was also examined. Results obtained show that error predicted by Euler DETE matches very well with the actual error for the high-Reynolds-number Navier-Stokes solutions.

Qin, Yuehui

381

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

382

Errors in performance testing: a comparison of ethanol and temazepam.  

PubMed

Both ethanol and benzodiazepines impair psychomotor function. Previous work has suggested that ethanol may have a greater effect on errors while benzodiazepines may cause greater slowing, but this has not been tested in a direct comparison. We assessed the effects of ethanol, at blood concentrations of approximately 80-100 mg/100 ml, compared to two doses of temazepam (20 mg and 30 mg) on psychomotor speed and accuracy and on long-term memory. Sixteen healthy volunteers (eight male, aged 20-25 years) took part in a four-period, placebo-controlled cross-over study. Performance was evaluated using analysis of covariance (critical significance level, p = 0.05) comparing the areas under the response-time curves. Performance on a psychomotor maze showed an almost complete dissociation, with ethanol leading to a substantial and significant increase in errors with little effect on speed, while temazepam slowed performance with no significant change in accuracy. Other tasks showed a similar pattern, but the dissociation was less complete. Handwriting size was substantially increased by ethanol, but not by temazepam. Information processing capacity and long-term memory formation were reduced by a similar amount both for ethanol and 30 mg temazepam. The faster, more error-prone, behaviour on ethanol than with a similarly impairing dose of temazepam has clear implications for the relative potential of the two drugs to contribute to accidents. The results are also important in understanding the differential effects of drugs with different mechanisms of action on human performance. PMID:12680738

Tiplady, B; Hiroz, J; Holmes, L; Drummond, G

2003-03-01

383

Comparison of PCR-Ribotyping, Arbitrarily Primed PCR, and Pulsed-Field Gel Electrophoresis for Typing Clostridium difficile  

PubMed Central

Clostridium difficile is now recognized as the major agent responsible for nosocomial diarrhea in adults. Among the genotyping methods available, arbitrarily primed PCR (AP-PCR), PCR-ribotyping, and pulsed-field gel electrophoresis (PFGE) have been widely used for investigating outbreaks of C. difficile infections. However, the comparative typing ability, reproducibility, discriminatory power, and efficiency of these methods have not been fully investigated. We compared the results of three methods—AP-PCR with three different primers (AP3, AP4, and AP5), PCR-ribotyping, and PFGE (with SmaI endonuclease)—to differentiate 99 strains of C. difficile that had been previously serogrouped. Typing abilities were 100% for PCR-ribotyping and AP-PCR with AP3 and 90% for PFGE, due to early DNA degradation in strains from serogroup G. Reproducibilities were 100% for PCR-ribotyping and PFGE but only 88% for AP-PCR with AP3, 67% for AP-PCR with AP4, and 33% for AP-PCR with AP5. Discriminatory power for unrelated strains was >0.95 for all the methods but was lower for PCR-ribotyping among serogroups D and C. PCR-based methods were easier and quicker to perform, but their fingerprints were more difficult to interpret than those of PFGE. We conclude that PCR-ribotyping offers the best combination of advantages as an initial typing tool for C. difficile. PMID:10878030

Bidet, Philippe; Lalande, Valérie; Salauze, Béatrice; Burghoffer, Béatrice; Avesani, Véronique; Delmée, Michel; Rossier, Anne; Barbut, Frédéric; Petit, Jean-Claude

2000-01-01

384

Guiding Intellect for Occlusal Errors  

PubMed Central

Purpose: The purpose of the study is to quantify occlusal errors seen, during the processing of complete denture. Material and Methods: Maxillary and mandibular complete dentures were fabricated for 30 subjects. Anterior and posterior markings were made on articulator and the distance was measured from these points before and after processing of complete dentures. Occlusal errors following processing of complete dentures was determined by subjecting the values obtained to statistical analysis using paired t-test. Results: The results indicated the existence of discrepant amount of occlusal errors following processing of complete denture and statistical test applied was paired t-test, p-values obtained are, p=0.00 anterior reference markings and p=0.006 for posterior reference markings (p ? 0.001 highly significant). Conclusion: The processing errors are inevitable. Hence for patient comfort, laboratory remounting is an important procedure that needs to be followed as a regular step after processing of each and every denture. PMID:24392422

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

2013-01-01

385

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

386

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

387

Block Interlaced Pinwheel Error Diffusion  

Microsoft Academic Search

Error diffusion is a popular halftoning algorithm that in its most widely used form, is inherently serial. As a se- rial algorithm, error diffusion offers limited opportunity for large-scale parallelism. In some implementations, it may result in excessive bus traffic between the on-chip pro- cessor and the off-chip memory used to store the modified continuous-tone image and the halftone image.

Pingshan Li; Jan P. Allebach

2002-01-01

388

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

389

The Rad5 helicase activity is dispensable for error-free DNA post-replication repair.  

PubMed

DNA post-replication repair (PRR) functions to bypass replication-blocking lesions and is subdivided into two parallel pathways: error-prone translesion DNA synthesis and error-free PRR. While both pathways are dependent on the ubiquitination of PCNA, error-free PRR utilizes noncanonical K63-linked polyubiquitinated PCNA to signal lesion bypass through template switch, a process thought to be dependent on Mms2-Ubc13 and a RING finger motif of the Rad5 ubiquitin ligase. Previous in vitro studies demonstrated the ability of Rad5 to promote replication fork regression, a function dependent on its helicase activity. To investigate the genetic and mechanistic relationship between fork regression in vitro and template switch in vivo, we created and characterized site-specific mutations defective in the Rad5 RING or helicase activity. Our results indicate that both the Rad5 ubiquitin ligase and the helicase activities are exclusively involved in the same error-free PRR pathway. Surprisingly, the Rad5 helicase mutation abolishes its physical interaction with Ubc13 and the K63-linked PCNA polyubiquitin chain assembly. Indeed, physical fusions of Rad5 with Ubc13 bypass the requirement for either the helicase or the RING finger domain. Since the helicase domain overlaps with the SWI/SNF chromatin-remodelling domain, our findings suggest a structural role of this domain and that the Rad5 helicase activity is dispensable for error-free lesion bypass. PMID:24674630

Ball, Lindsay G; Xu, Xin; Blackwell, Susan; Hanna, Michelle D; Lambrecht, Amanda D; Xiao, Wei

2014-04-01

390

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

2015-05-01

391

Replaceable Microfluidic Cartridges for a PCR Biosensor  

NASA Technical Reports Server (NTRS)

The figure depicts a replaceable microfluidic cartridge that is a component of a miniature biosensor that detects target deoxyribonucleic acid (DNA) sequences. The biosensor utilizes (1) polymerase chain reactions (PCRs) to multiply the amount of DNA to be detected, (2) fluorogenic polynucleotide probe chemicals for labeling the target DNA sequences, and (3) a high-sensitivity epifluorescence-detection optoelectronic subsystem. Microfluidics is a relatively new field of device development in which one applies techniques for fabricating microelectromechanical systems (MEMS) to miniature systems for containing and/or moving fluids. Typically, microfluidic devices are microfabricated, variously, from silicon or polymers. The development of microfluidic devices for applications that involve PCR and fluorescence-based detection of PCR products poses special challenges

Francis, Kevin; Sullivan, Ron

2005-01-01

392

The usability-error ontology.  

PubMed

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

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

2013-01-01

393

PCR microfluidic devices for DNA amplification  

Microsoft Academic Search

The miniaturization of biological and chemical analytical devices by micro-electro-mechanical-systems (MEMS) technology has posed a vital influence on such fields as medical diagnostics, microbial detection and other bio-analysis. Among many miniaturized analytical devices, the polymerase chain reaction (PCR) microchip\\/microdevices are studied extensively, and thus great progress has been made on aspects of on-chip micromachining (fabrication, bonding and sealing), choice of

Chunsun Zhang; Jinliang Xu; Wenli Ma; Wenling Zheng

2006-01-01

394

Identification of Haemophilus influenzae Serotypes by Standard Slide Agglutination Serotyping and PCR-Based Capsule Typing  

PubMed Central

To resolve discrepancies in slide agglutination serotyping (SAST) results from state health departments and the Centers for Disease Control and Prevention (CDC), we characterized 141 of 751 invasive Haemophilus influenzae isolates that were identified in the United States from January 1998 to December 1999 through an active, laboratory-based, surveillance program coordinated by the CDC. We found discrepancies between the results of SAST performed at state health departments and those of PCR capsule typing performed at the CDC for 56 (40%) of the isolates characterized: 54 isolates that were identified as a particular serotype by SAST were shown to be unencapsulated by PCR, and two isolates that were reported as serotypes b and f were found to be serotypes f and e, respectively, by PCR. The laboratory error most likely to affect the perceived efficacy of the conjugate H. influenzae type b (Hib) vaccine was the misidentification of isolates as serotype b: of 40 isolates identified as serotype b by SAST, 27 (68%) did not contain the correlating capsule type genes. The frequency of errors fell substantially when standardized reagents and routine quality control of SAST were used during a study involving three laboratories. An overall 94% agreement between SAST and PCR results showed that slide agglutination could be a valid and reliable method for serotyping H. influenzae if the test was performed correctly, in accordance with standardized and recommended procedures. An ongoing prospective analysis of all H. influenzae surveillance isolates associated with invasive disease in children less than 5 years old will provide more accurate national figures for the burden of invasive disease caused by Hib and other H. influenzae serotypes. PMID:12517878

LaClaire, Leslye L.; Tondella, Maria Lucia C.; Beall, David S.; Noble, Corie A.; Raghunathan, Pratima L.; Rosenstein, Nancy E.; Popovic, Tanja

2003-01-01

395

A Disposable, Self-Contained PCR Chip  

PubMed Central

A disposable, self-contained polymerase chain reaction (PCR) chip with on-board stored, just on time releasable, paraffin-passivated, dry reagents is described. During both storage and sample preparation, the paraffin immobilizes and protects the stored reagents. Fluid flow through the reactor leaves the reagents undisturbed. Prior to the amplification step, the chamber is filled with target analyte suspended in water. Upon heating the PCR chamber to the DNA’s denaturation temperature, the paraffin melts and moves out of the way, and the reagents are released and hydrated. To better understand the reagent release process, a scaled up model of the reactor was constructed and the paraffin migration was visualized. Experiments were carried out with a 30 ?l reactor demonstrating detectable amplification (with agarose gel electrophoresis) of 10 fg (~200 copies) of lambda DNA template. The in-reactor storage and on-time release of the PCR reagents reduce the number of needed operations and significantly simplify the flow control that would, otherwise, be needed in lab-on-chip devices. PMID:19190797

Kim, Jitae; Byun, Doyoung; Mauk, Michael G.; Bau, Haim H.

2009-01-01

396

Diagnostic value of PCR in genitourinary tuberculosis.  

PubMed

Genitourinary tuberculosis is a disease of the genitourinary system which includes the entire urinary tract and reproductive system. Genital tuberculosis is an important cause of female infertility, especially in developing nations like India. In the present study, a total of 257 clinical specimens comprising of endometrial biopsy (109), endometrial curetting (42), menstrual blood (8), semen (17), placenta (11) and urine (70) were collected from patients and subjected for PCR, Culture and AFB detection. The endometrial biopsy, endometrial curetting, menstrual blood, semen, placenta, urine showed 30.2, 45.2,12.5, 5.8, 27.2, 31.4 %, positivity rate for tuberculosis by PCR, 7.3, 9.5, 25.0, 0, 9, 8.5 % by culture and 1.8, 2.3, 0, 0, 0, 2.8 % respectively by AFB smear. Being a novel, rapid technique, PCR is the method of choice for rapid diagnosis and management of genitourinary tuberculosis shared with the other concerned tests. This study reveals that genital tuberculosis can occur in any age group, however, the majority of patients were from reproductive age (nearly 75 % of them were from 20-45 years of age) group. PMID:24426229

Sharma, Narotam; Sharma, Veena; Singh, Prem Raj; Sailwal, Shivani; Kushwaha, Rajeev S; Singh, Rajesh K; Nautiyal, Satish C; Mishra, Pankaj; Masood, Tariq; Singh, R K

2013-07-01

397

Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy  

E-print Network

: Digital PCR accurately identified all cases of fetal trisomy (3 cases of trisomy 21, 3 cases of trisomy 18 and sixty PCR reactions were performed for each of the target chromosomes (X, Y, 13, 18, and 21

Quake, Stephen R.

398

New developments in ambient noise analysis to characterise the seismic response of landslide prone slopes  

NASA Astrophysics Data System (ADS)

We report on new developments in the application of ambient noise analysis applied to investigate the dynamic response of landslide prone slopes to seismic shaking with special attention to the directional resonance phenomena recognised in previous studies. Investigations relying on the calculation of horizontal-to-vertical noise spectral ratio (HVNR) were carried out in the area of Caramanico Terme (central Italy) where an ongoing accelerometer monitoring on slopes with different characteristics offers the possibility of validation of HVNR analysis. The noise measurements, carried out in different times to test the result repeatability, revealed that sites affected by response directivity persistently show major peaks with a common orientation consistent with the resonance direction inferred from accelerometer data. At sites where directivity is absent, the HVNR peaks do not generally show a preferential orientation, with rare exceptions that could be linked to the presence of temporarily active sources of polarised noise. The observed spectral ratio amplitude variations can be related to temporal changes in site conditions, which can hinder the recognition of main resonance frequencies. Therefore, it is recommended to conduct simultaneous measurements at nearby sites within the same study area and to repeat measurements at different times in order to distinguish significant systematic polarisation caused by site specific response directivity from polarisation controlled by properties of noise sources. Furthermore, an analysis of persistence in noise recordings of signals with systematic directivity showed that only a~portion of recordings contains wave trains having a clear polarisation representative of site directional resonance. Thus a careful selection of signals for HVNR analysis is needed for a correct characterisation of site directional properties.

Del Gaudio, V.; Wasowski, J.; Muscillo, S.

2013-04-01

399

Cholinergic control over attention in rats prone to attribute incentive salience to reward cues  

PubMed Central

Some rats (sign-trackers, ST) are especially prone to attribute incentive salience to reward cues, relative to others (goal-trackers, GT). Thus, reward cues are more likely to promote maladaptive reward-seeking behavior in ST than GT. Here, we asked whether ST and GT differ on another trait that can contribute to poor restraint over behavior evoked by reward cues. We report that, relative to GT, ST have poor control over attentional performance, due in part to insufficient cholinergic stimulation of cortical circuitry. We found that, relative to GT, ST showed poor performance on a sustained attention task (SAT). Furthermore, their performance fluctuated rapidly between periods of good to near-chance performance. This finding was reproduced using a separate cohort of rats. As demonstrated earlier, performance on the SAT was associated with increases in extracellular levels of cortical acetylcholine (ACh); however, SAT performance-associated increases in ACh levels were significantly attenuated in ST relative to GT. Consistent with the view that the modulatory effects of ACh involves stimulation of ?4?2* nicotinic acetylcholine receptors (nAChRs), systemic administration of the partial nAChR agonist ABT-089 improved SAT performance in ST and abolished the difference between SAT-associated ACh levels in ST and GT. Neither the nonselective nAChR agonist nicotine nor the psychostimulant amphetamine improved SAT performance. These findings suggest that individuals who have a propensity to attribute high incentive salience to reward cues also exhibit relatively poor attentional control. A combination of these traits may render individuals especially vulnerable to disorders such as obesity and addiction. PMID:23658172

Paolone, Giovanna; Angelakos, Christopher C.; Meyer, Paul J.; Robinson, Terry E.; Sarter, Martin

2013-01-01

400

Quantification of quaternary structure stability in aggregation-prone proteins under physiological conditions: the transthyretin case.  

PubMed

The quaternary structure stability of proteins is typically studied under conditions that accelerate their aggregation/unfolding processes on convenient laboratory time scales. Such conditions include high temperature or pressure, chaotrope-mediated unfolding, or low or high pH. These approaches have the limitation of being nonphysiological and that the concentration of the protein in solution is changing as the reactions proceed. We describe a methodology to define the quaternary structure stability of the amyloidogenic homotetrameric protein transthyretin (TTR) under physiological conditions. This methodology expands from a described approach based on the measurement of the rate of subunit exchange of TTR with a tandem flag-tagged (FT?) TTR counterpart. We demonstrate that subunit exchange of TTR with FT?·TTR can be analyzed and quantified using a semi-native polyacrylamide gel electrophoresis technique. In addition, we biophysically characterized two FT?·TTR variants derived from wild-type and the amyloidogenic variant Val122Ile TTR, both of which are associated with cardiac amyloid deposition late in life. The FT?·TTR variants have similar amyloidogenic potential and similar thermodynamic and kinetic stabilities compared to those of their nontagged counterparts. We utilized the methodology to study the potential of the small molecule SOM0226, a repurposed drug under clinical development for the prevention and treatment of the TTR amyloidoses, to stabilize TTR. The results enabled us to characterize the binding energetics of SOM0226 to TTR. The described technique is well-suited to study the quaternary structure of other human aggregation-prone proteins under physiological conditions. PMID:25245430

Robinson, Lei Z; Reixach, Natàlia

2014-10-21

401

Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.  

PubMed

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure. PMID:22202889

Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

2012-07-01

402

Psychosis-Proneness and Neural Correlates of Self-Inhibition in Theory of Mind  

PubMed Central

Impaired Theory of Mind (ToM) has been repeatedly reported as a feature of psychotic disorders. ToM is crucial in social interactions and for the development of social behavior. It has been suggested that reasoning about the belief of others, requires inhibition of the self-perspective. We investigated the neural correlates of self-inhibition in nineteen low psychosis prone (PP) and eighteen high PP subjects presenting with subclinical features. High PP subjects have a more than tenfold increased risk of developing a schizophrenia-spectrum disorder. Brain activation was measured with functional Magnetic Resonance Imaging during a ToM task differentiating between self-perspective inhibition and belief reasoning. Furthermore, to test underlying inhibitory mechanisms, we included a stop-signal task. We predicted worse behavioral performance for high compared to low PP subjects on both tasks. Moreover, based on previous neuroimaging results, different activation patterns were expected in the inferior frontal gyrus (IFG) in high versus low PP subjects in self-perspective inhibition and simple response inhibition. Results showed increased activation in left IFG during self-perspective inhibition, but not during simple response inhibition, for high PP subjects as compared to low PP subjects. High and low PP subjects showed equal behavioral performance. The results suggest that at a neural level, high PP subjects need more resources for inhibiting the self-perspective, but not for simple motor response inhibition, to equal the performance of low PP subjects. This may reflect a compensatory mechanism, which may no longer be available for patients with schizophrenia-spectrum disorders resulting in ToM impairments. PMID:23874445

van der Meer, Lisette; Groenewold, Nynke A.; Pijnenborg, Marieke; Aleman, André

2013-01-01

403

True colors - experimental identification of hydrological processes at a hillslope prone to slide  

NASA Astrophysics Data System (ADS)

This study investigated runoff formation processes of a pre-alpine hillslope prone to slide. The experimental pasture plot (40 m × 60 m) is located in the northern front range of the Swiss Alps on a 30° steep hillslope (1180 m a.s.l., 1500 + mm annual precipitation). A gleysol (H-Go-Gr) overlies weathered marlstone and conglomerate of subalpine molasse. We conducted sprinkling experiments on a subplot (10 m × 10 m) with variable rainfall intensities. During both experiments fluorescein line-tracer injections into the topsoil, and sodium chloride (NaCl) injections into the sprinkling water were used to monitor flow velocities in the soil. The observed flow velocities for fluorescein in the soil were 1.2 and 1.4 × 10-3 m s-1. The NaCl breakthrough occurred almost simultaneously in all monitored discharge levels (0.05, 0.25 and 1.0 m depth), indicating a high-infiltration capacity and efficient drainage of the soil. These initial observations suggested "transmissivity feedback", a form of subsurface stormflow, as the dominant runoff process. However, the results of a brilliant blue dye tracer experiment completely changed our perceptions of the hillslope's hydrological processes. Excavation of the dye-stained soils highlighted the dominance of "organic layer interflow", a form of shallow subsurface stormflow. The dye stained the entire H horizon, vertical soil fractures, and macropores (mostly worm burrows) up to 0.5 m depth. Lateral drainage in the subsoil or at the soil-bedrock interface was not observed, and thus was limited to the organic topsoil. In the context of shallow landslides, the subsoil (Go/Gr) acted as an infiltration and exfiltration barrier, which produced significant lateral saturated drainage in the topsoil (H) and possibly a confined aquifer in the bedrock.

Schneider, P.; Pool, S.; Strouhal, L.; Seibert, J.

2014-02-01

404

Kidney Pathology Precedes and Predicts the Pathological Cascade of Cerebrovascular Lesions in Stroke Prone Rats  

PubMed Central

Introduction Human cerebral small vessel disease (CSVD) has been hypothesized to be an age-dependent disease accompanied by similar vascular changes in other organs. SHRSP feature numerous vascular risk factors and may be a valid model of some aspects of human CSVD. Here we compare renal histopathological changes with the brain pathology of spontaneously hypertensive stroke-prone rats (SHRSP). Material and Methods We histologically investigated the brains and kidneys of 61 SHRSP at different stages of age (12 to 44 weeks). The brain pathology (aggregated erythrocytes in capillaries and arterioles, microbleeds, microthromboses) and the kidney pathology (aggregated erythrocytes within peritubular capillaries, tubular protein cylinders, glomerulosclerosis) were quantified separately. The prediction of the brain pathology by the kidney pathology was assessed by creating ROC-curves integrating the degree of kidney pathology and age of SHRSP. Results Both, brain and kidney pathology, show an age-dependency and proceed in definite stages whereas an aggregation of erythrocytes in capillaries and arterioles, we parsimoniously interpreted as stases, represent the initial finding in both organs. Thus, early renal tubulointerstitial damage characterized by rather few intravasal erythrocyte aggregations and tubular protein cylinders predicts the initial step of SHRSPs' cerebral vascular pathology marked by accumulated erythrocytes. The combined increase of intravasal erythrocyte aggregations and protein cylinders accompanied by glomerulosclerosis and thrombotic renal microangiopathy in kidneys of older SHRSP predicts the final stages of SHRSPs' cerebrovascular lesions marked by microbleeds and thrombotic infarcts. Conclusion Our results illustrate a close association between structural brain and kidney pathology and support the concept of small vessel disease to be an age-dependent systemic pathology. Further, an improved joined nephrologic and neurologic diagnostic may help to identify patients with CSVD at an early stage. PMID:22031827

Schreiber, Stefanie; Bueche, Celine Z.; Garz, Cornelia; Kropf, Siegfried; Kuester, Doerthe; Amann, Kerstin; Heinze, Hans-Jochen; Goertler, Michael; Reymann, Klaus G.; Braun, Holger

2011-01-01

405

Spatial task context makes short-latency reaches prone to induced Roelofs illusion  

PubMed Central

The perceptual localization of an object is often more prone to illusions than an immediate visuomotor action towards that object. The induced Roelofs effect (IRE) probes the illusory influence of task-irrelevant visual contextual stimuli on the processing of task-relevant visuospatial instructions during movement preparation. In the IRE, the position of a task-irrelevant visual object induces a shift in the localization of a visual target when subjects indicate the position of the target by verbal response, key-presses or delayed pointing to the target (“perception” tasks), but not when immediately pointing or reaching towards it without instructed delay (“action” tasks). This discrepancy was taken as evidence for the dual-visual-stream or perception-action hypothesis, but was later explained by a phasic distortion of the egocentric spatial reference frame which is centered on subjective straight-ahead (SSA) and used for reach planning. Both explanations critically depend on delayed movements to explain the IRE for action tasks. Here we ask: first, if the IRE can be observed for short-latency reaches; second, if the IRE in fact depends on a distorted egocentric frame of reference. Human subjects were tested in new versions of the IRE task in which the reach goal had to be localized with respect to another object, i.e., in an allocentric reference frame. First, we found an IRE even for immediate reaches in our allocentric task, but not for an otherwise similar egocentric control task. Second, the IRE depended on the position of the task-irrelevant frame relative to the reference object, not relative to SSA. We conclude that the IRE for reaching does not mandatorily depend on prolonged response delays, nor does it depend on motor planning in an egocentric reference frame. Instead, allocentric encoding of a movement goal is sufficient to make immediate reaches susceptible to IRE, underlining the context dependence of visuomotor illusions. PMID:25221500

Taghizadeh, Bahareh; Gail, Alexander

2014-01-01

406

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

NASA Astrophysics Data System (ADS)

Two underground coal mines in the Sydney Coalfield, Nova Scotia, Canada have encountered gas outbursts from sandstone formations overlying the coal seams. These have consistently occurred while driving mine roadways into virgin ground at and below mining depths of 700 m. In this investigation, triaxial compression tests were conducted on samples of the outburst-prone sandstone from one of these mines, the Phalen Colliery, while simultaneously measuring gas permeability, acoustic emissions and ultrasonic P-wave velocity and attenuation. Experimental results characterized these sandstone properties over the full range of axial stresses up to compressive failure. These data were intended to assist with (i) evaluating the potential for degassing the sandstone and (ii) evaluating the results of in-seam seismic surveys, which were conducted to map the sandstone ahead of mining. At the estimated in situ conditions in virgin rock at 700 m depth, the sandstone permeability is expected to be in the 0.005 to 0.04 mD range, the P-wave velocity is approximately 4000 m/s and the attenuation quality factor in the 20 to 25 range. Near mine openings at 700 m depth, where the lateral confining pressures are reduced, the permeability can be several orders of magnitude higher in the 4 to 15 mD range, the P-wave velocity is 3800 m/s and the attenuation quality factor is in the 10 to 15 range. Experimental data suggests that microcracking in the sandstone prior to compressive failure does not significantly enhance permeability but there may be local pockets of higher permeability within the sandstone.

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

2005-08-01

407

System-wide Analysis Reveals Intrinsically Disordered Proteins Are Prone to Ubiquitylation after Misfolding Stress*  

PubMed Central

Damaged and misfolded proteins that are no longer functional in the cell need to be eliminated. Failure to do so might lead to their accumulation and aggregation, a hallmark of many neurodegenerative diseases. Protein quality control pathways play a major role in the degradation of these proteins, which is mediated mainly by the ubiquitin proteasome system. Despite significant focus on identifying ubiquitin ligases involved in these pathways, along with their substrates, a systems-level understanding of these pathways has been lacking. For instance, as misfolded proteins are rapidly ubiquitylated, unconjugated ubiquitin is rapidly depleted from the cell upon misfolding stress; yet it is unknown whether certain targets compete more efficiently to be ubiquitylated. Using a system-wide approach, we applied statistical and computational methods to identify characteristics enriched among proteins that are further ubiquitylated after heat shock. We discovered that distinct populations of structured and, surprisingly, intrinsically disordered proteins are prone to ubiquitylation. Proteomic analysis revealed that abundant and highly structured proteins constitute the bulk of proteins in the low-solubility fraction after heat shock, but only a portion is ubiquitylated. In contrast, ubiquitylated, intrinsically disordered proteins are enriched in the low-solubility fraction after heat shock. These proteins have a very low abundance in the cell, are rarely encoded by essential genes, and are enriched in binding motifs. In additional experiments, we confirmed that several of the identified intrinsically disordered proteins were ubiquitylated after heat shock and demonstrated for two of them that their disordered regions are important for ubiquitylation after heat shock. We propose that intrinsically disordered regions may be recognized by the protein quality control machinery and thereby facilitate the ubiquitylation of proteins after heat shock. PMID:23716602

Ng, Alex H. M.; Fang, Nancy N.; Comyn, Sophie A.; Gsponer, Jörg; Mayor, Thibault

2013-01-01

408

Arterial smooth muscle cell phenotype in stroke-prone spontaneously hypertensive rats.  

PubMed

The aim of this study was to determine the phenotype of smooth muscle cells in the arteries of chronically hypertensive animals and to analyze the effects of treatments known to increase the survival of the animal without a clear effect on its hypertensive state. Stroke-prone spontaneously hypertensive rats (SHRSP) kept on a 1% sodium drinking solution were untreated or treated with one of two diuretics, indapamide (3 mg/kg per day) or hydrochlorothiazide (20 mg/kg per day), from 6 to 13 weeks of age. Phenotype was characterized by the immunolabeling of arteries with antibodies raised against a cellular form (EIIIA) of fibronectin, alpha-smooth muscle actin, and nonmuscle myosin. We demonstrated that phenotypes of smooth muscle cells of the SHRSP differ from those found in Wistar-Kyoto rats. The difference in phenotype is specific for the vessel type: ie, an increased expression of nonmuscle myosin in the aorta and of both EIIIA fibronectin and nonmuscle myosin in the coronary arteries. The two diuretics (1) had no effect on blood pressure, (2) prevented or did not prevent the increase in medial thickness, and (3) prevented changes in both smooth muscle cell phenotype and ischemic tissular lesions. Taken together, the results suggest that in SHRSP the changes in the phenotype of smooth muscle cells and the thickness of arteries are unrelated events. We propose that the maintenance of the contractile phenotype of the arterial smooth muscle cells could be an essential parameter involved in the prevention of the deleterious consequences characteristic of a severe hypertensive state. PMID:8225526

Contard, F; Sabri, A; Glukhova, M; Sartore, S; Marotte, F; Pomies, J P; Schiavi, P; Guez, D; Samuel, J L; Rappaport, L

1993-11-01

409

Inhibition of ERK1/2 signaling prevents epileptiform behavior in rats prone to audiogenic seizures.  

PubMed

It has recently been proposed that extracellular signal-regulated kinases 1 and 2 (ERK1/2) are one of the factors mediating seizure development. We hypothesized that inhibition of ERK1/2 activity could prevent audiogenic seizures by altering GABA and glutamate release mechanisms. Krushinsky-Molodkina rats, genetically prone to audiogenic seizure, were recruited in the experiments. Animals were i.p. injected with an inhibitor of ERK1/2 SL 327 at different doses 60 min before audio stimulation. We demonstrated for the first time that inhibition of ERK1/2 activity by SL 327 injections prevented seizure behavior and this effect was dose-dependent and correlated with ERK1/2 activity. The obtained data also demonstrated unchanged levels of GABA production, and an increase in the level of vesicular glutamate transporter 2. The study of exocytosis protein expression showed that SL 327 treatment leads to downregulation of vesicle-associated membrane protein 2 and synapsin I, and accumulation of synaptosomal-associated protein 25 (SNAP-25). The obtained data indicate that the inhibition of ERK1/2 blocks seizure behavior presumably by altering the exocytosis machinery, and identifies ERK1/2 as a potential target for the development of new strategies for seizure treatment. Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are one of the factors mediating seizure development. Here we report that inhibition of ERK1/2 by SL 327 prevented seizure behavior and this effect was dose-dependent and correlated with ERK1/2 activity. Accumulation of VGLUT2 was associated with differential changing of synaptic proteins VAMP2, SNAP-25 and synapsin I. The obtained data indicate that the inhibition of ERK1/2 alters neurotransmitter release by changing the exocytosis machinery, thus preventing seizures. PMID:25351927

Glazova, Margarita V; Nikitina, Liubov S; Hudik, Kirill A; Kirillova, Olga D; Dorofeeva, Nadezhda A; Korotkov, Anatoly A; Chernigovskaya, Elena V

2015-01-01

410

Regulation of synaptic Pumilio function by an aggregation-prone domain  

PubMed Central

We identified Pumilio (Pum), a Drosophila translational repressor, in a computational search for metazoan proteins whose activities might be regulated by assembly into ordered aggregates. The search algorithm was based on evolutionary sequence conservation patterns observed for yeast prion proteins, which contain aggregation-prone glutamine/asparagine (Q/N)-rich domains attached to functional domains of normal amino acid composition. We examined aggregation of Pum and its nematode ortholog PUF-9 by expression in yeast. A domain of Pum containing the Q/N-rich sequence, denoted as NQ1, the entire Pum N-terminus, and the complete PUF-9 protein localize to macroscopic aggregates (foci) in yeast. NQ1 and PUF-9 can generate the yeast Pin+ trait, which is transmitted by a heritable aggregate. NQ1 also assembles into amyloid fibrils in vitro. In Drosophila, Pum regulates postsynaptic translation at neuromuscular junctions (NMJs). To assess whether NQ1 affects synaptic Pum activity in vivo, we expressed it in muscles. We found that it negatively regulates endogenous Pum, producing gene dosage-dependent pum loss-of-function NMJ phenotypes. NQ1 coexpression also suppresses lethality and NMJ phenotypes caused by overexpression of Pum in muscles. The Q/N block of NQ1 is required for these phenotypic effects. Negative regulation of Pum by NQ1 might be explained by formation of inactive aggregates, but we have been unable to demonstrate that NQ1 aggregates in Drosophila. NQ1 could also regulate Pum by a “dominant-negative” effect, in which it would block Q/N-mediated interactions of Pum with itself or with cofactors required for translational repression. PMID:20071514

Salazar, Anna M.; Silverman, Edward J.; Menon, Kaushiki P.; Zinn, Kai

2010-01-01

411

Identification of histone methylation multiplicities patterns in the brain of senescence-accelerated prone mouse 8.  

PubMed

Histone post-translational modifications (PTMs) are involved in diverse biological processes and methylation was regarded as a long-term epigenetic mark. Though aging represented one of the major risk factors for neurodegenerative diseases, no systematic investigations had correlated the patterns of histone PTMs in the brain with aging and the roles of such concerted histone PTMs in brain aging are still unknown. In this study, enzyme digestion, nano-LC, MALDI-TOF/TOF MS analysis and Western blotting were combined to investigate the defined methylation of core histones (H2A, H2B, H3 and H4) in the brain of 12-month-old senescence accelerated mouse prone 8 (SAMP8). The expression of several modified histones in the brain of 3-, and 12-month-old SAMP8 mice as well as that of the age-matched control senescence accelerated-resistant mouse (SAMR1) was compared. In the brain of 12-month-old SAMP8 mice, seven methylation sites (H3K24, H3K27, H3K36, H3K79, H3R128, H4K20 and H2A R89) were detected and most PTMs sites were located on histone H3. Mono-methylated H4K20 decreased significantly in the brain of 12-month-old SAMP8 mice. Methylated H3K27 and H3K36 coexisted in the aged brain with different methylation multiplicities. Di-methylated H3K79 expressed in the neurons of cerebral cortex and hippocampus. This study showed histone methylation patterns in the aged SAMP8 mice brain and provided the experimental evidences for further research on histone PTMs in the aged brain. We hope these results could initiate a platform for the exchange of comprehensive information concerning aging or neurodegenerative disease and help us interpret the change of gene expression and DNA repair ability at epigenetic level. PMID:19434510

Wang, Chun Mei; Tsai, Sau Na; Yew, Tai Wai; Kwan, Yiu Wa; Ngai, Sai Ming

2010-02-01

412

VITAMIN D DEFICIENCY IN THE SPONTANEOUSLY HYPERTENSIVE HEART FAILURE [SHHF] PRONE RAT  

PubMed Central

Background and Aims Vitamin D deficiency has been associated with the etiology and pathogenesis of heart disease including congestive heart failure. We previously observed cardiac hypertrophy in vitamin D deficient rats and vitamin D-receptor knockout mice. These studies indicate that the absence of vitamin D-mediated signal transduction and genomic activation results in increased sensitivity of the heart to ionotropic stimuli and cardiomyocyte hypertrophy. This study’s aim is to investigate the relationship between vitamin D status and the heart failure phenotype in the rat. Methods and Results Vitamin D status was assessed by measuring 25-hydroxyvitamin D levels and related to heart weight in young, middle-aged and aging spontaneously hypertensive, heart failure-prone (SHHF) rats. We also measured the effects of the vitamin D hormone,1,25(OH)2D3, on cardiac function in SHHF rats. Cardiac hypertrophy in this model of the failing heart increased with age and related to decreasing vitamin D status. Vitamin D deficiency presented after cardiac hypertrophy was first observed. Additionally, we found that 1,25(OH)2D3 treatment between 4.0–7.0 months of age prevented cardiac hypertrophy and permits decreased workload for the heart while allowing adequate blood perfusion and pressure, resulting in reduced cardiac index. Conclusions Our findings suggest that low vitamin D status is associated with the progression and final terminal phase of the heart failure phenotype and not with initial heart hypertrophy. Also, we report that in the vitamin D sufficient SHHF rat, 1,25(OH)2D3 treatment provided protection against the progression of the heart failure phenotype. PMID:19836216

Przybylski, Robert; Mccune, Sylvia; Hollis, Bruce; Simpson, Robert U.

2009-01-01

413

Acylation Stimulating Protein, Complement C3 and Lipid Metabolism in Ketosis-Prone Diabetic Subjects  

PubMed Central

Background Ketosis-prone diabetes (KPDM) is new-onset diabetic ketoacidosis without precipitating factors in non-type 1 diabetic patients; after management, some are withdrawn from exogenous insulin, although determining factors remain unclear. Methods Twenty KPDM patients and twelve type 1 diabetic patients (T1DM), evaluated at baseline, 12 and 24 months with/without insulin maintenance underwent a standardized mixed-meal tolerance test (MMTT) for 2 h. Results At baseline, triglyceride and C3 were higher during MMTT in KPDM vs. T1DM (p<0.0001) with no differences in non-esterified fatty acids (NEFA) while Acylation Stimulating Protein (ASP) tended to be higher. Within 12 months, 11 KPDM were withdrawn from insulin treatment (KPDM-ins), while 9 were maintained (KPDM+ins). NEFA was lower in KPDM-ins vs. KPDM+ins at baseline (p?=?0.0006), 12 months (p<0.0001) and 24 months (p<0.0001) during MMTT. NEFA in KPDM-ins decreased over 30–120 minutes (p<0.05), but not in KPDM+ins. Overall, C3 was higher in KPDM-ins vs KPDM+ins at 12 months (p?=?0.0081) and 24 months (p?=?0.0019), while ASP was lower at baseline (p?=?0.0024) and 12 months (p?=?0.0281), with a decrease in ASP/C3 ratio. Conclusions Notwithstanding greater adiposity in KPDM-ins, greater NEFA decreases and lower ASP levels during MMTT suggest better insulin and ASP sensitivity in these patients. PMID:25275325

Liu, Yan; Gupta, Priyanka; Lapointe, Marc; Yotsapon, Thewjitcharoen; Sarat, Sunthornyothin; Cianflone, Katherine

2014-01-01

414

Microfluidic gradient PCR (MG-PCR): a new method for microfluidic DNA amplification.  

PubMed

This study develops a new microfluidic DNA amplification strategy for executing parallel DNA amplification in the microfluidic gradient polymerase chain reaction (MG-PCR) device. The developed temperature gradient microfluidic system is generated by using an innovative fin design. The device mainly consists of modular thermally conductive copper flake which is attached onto a finned aluminum heat sink with a small fan. In our microfluidic temperature gradient prototype, a non-linear temperature gradient is produced along the gradient direction. On the copper flake of length 45 mm, width 40 mm and thickness 4 mm, the temperature gradient easily spans the range from 97 to 52 degrees Celsius. By making full use of the hot (90-97 degrees Celsius) and cold (60-70 degrees Celsius) regions on the temperature gradient device, the parallel, two-temperature MG-PCR amplification is feasible. As a demonstration, the MG-PCR from three parallel reactions of 112-bp Escherichia coli DNA fragment is performed in a continuous-flow format, in which the flow of the PCR reagent in the closed loop is induced by the buoyancy-driven nature convection. Although the prototype is not optimized, the MG-PCR amplification can be completed in less than 45 min. However, the MG-PCR thermocycler presented herein can be further scaled-down, and thus the amplification times and reagent consumption can be further reduced. In addition, the currently developed temperature gradient technology can be applied onto other continuous-flow MG-PCR systems or used for other analytical purposes such as parallel and combination measurements, and fluorescent melting curve analysis. PMID:19757072

Zhang, Chunsun; Xing, Da

2010-02-01

415

People who expect to enter psychotherapy are prone to believing that they have forgotten memories of childhood trauma and abuse.  

PubMed

We asked 1004 undergraduates to estimate both the probability that they would enter therapy and the probability that they experienced but could not remember incidents of potentially life-threatening childhood traumas or physical and sexual abuse. We found a linear relation between the expectation of entering therapy and the belief that one had, but cannot now remember, childhood trauma and abuse. Thus individuals who are prone to seek psychotherapy are also prone to accept a suggested memory of childhood trauma or abuse as fitting their expectations. In multiple regressions predicting the probability of forgotten memories of childhood traumas and abuse, the expectation of entering therapy remained as a substantial predictor when self-report measures of mood, anxiety, post-traumatic stress disorder symptom severity, and trauma exposure were included. PMID:20623421

Rubin, David C; Boals, Adriel

2010-07-01

416

Smooth pursuit eye tracking and visual fixation in psychosis-prone individuals  

Microsoft Academic Search

Subjects identified by Perceptual Aberration-Magical Ideation (Per-Mag) scores (n=97), Social Anhedonia (SocAnh) scores (n=45), and Physical Anhedonia (PhysAnh) scores (n=31) as well as normal controls (n=94), underwent psychophysiological and clinical assessment. This is the first published investigation of pursuit system functioning in three groups of questionnaire-identified at-risk individuals. Pursuit during a simple non-monitor tracking task was measured using root-mean-square error

Diane C Gooding; Meghan D Miller; Thomas R Kwapil

2000-01-01

417

Administration Errors-An Observation and  

E-print Network

Medication Administration Errors- An Observation and Intervention Study (An Ongoing Study). Non health outcomes. Errors in medication administration can lead to tremendous health issues and major processes during medication administration leads to medication errors. · Research hypothesis: Observing

Connor, Ed

418

Efficient experimental design and analysis of real-time PCR assays  

PubMed Central

Real-time polymerase chain reaction (qPCR) is currently the standard for gene quantification studies and has been extensively used in large-scale basic and clinical research. The operational costs and technical errors can become a significant issue due to the large number of sample reactions. In this paper, we present an experimental design strategy and an analysis procedure that are more efficient requiring fewer sample reactions than the traditional approach. We verified mathematically and experimentally the new design on a well-characterized model, to evaluate the gene expression levels of CACNA1C and CACNA1G in hypertrophic ventricular myocytes induced by phenylephrine treatment. PMID:23510941

Hui, Kwokyin; Feng, Zhong-Ping

2013-01-01

419

Design considerations and effects of LNA in PCR primers  

Microsoft Academic Search

The effects of comprehensive LNA substitution in PCR primers for amplification of human genomic DNA targets are presented in this report. Previous research with LNA in other applications has shown interesting properties for molecular hybridization including enhanced specificity in allele-specific PCR. Here we systematically modified PCR primers and conditions for the human genomic DNA targets APOB and PAH, along with

David Latorra; Khalil Arar; J. Michael Hurley

2003-01-01

420

Updating SRM 2391c: PCR-Based DNA Profiling Standard  

E-print Network

Updating SRM 2391c: PCR-Based DNA Profiling Standard Why and When? Becky Hill, Margaret Kline profiling SRM 2391 SRM 2391a SRM 2391b SRM 2391c SRM 2390 DNA profiling 2391 series PCR-based DNA profiling #12;SRM 2391c: PCR-Based DNA Profiling Standard · Standard Reference Material 2391c is intended

421

Age-related changes in anxiety are task-specific in the senescence-accelerated prone mouse 8  

Microsoft Academic Search

In the senescence-accelerated prone mouse 8 (SAMP8), an excellent model of brain aging, aged individuals have impairments in learning and memory. One study has indicated that the anxiety is also reduced in those mice. However, increased anxiety with aging has been observed in other models, such as C57BL mice and rats. Altered emotion is linked to impairments in learning and

Gui-Hai Chen; Cheng Wang; Han-Yu Yangcheng; Rong-Yu Liu; Jiang-Ning Zhou

2007-01-01

422

Reduction of diabetes incidence of BB Wistar rats by early prophylactic insulin treatment of diabetes-prone animals  

Microsoft Academic Search

Summary  A group of 36 diabetes-prone BB Wistar rats were given prophylactic insulin treatment with heat-treated bovine ultralente insulin (15 IU · kg–1 · day–1) from 50 to 142 days of age. The incidence of Type 1 (insulin-dependent) diabetes at the end of the treatment period was compared to that of 36 control animals given insulin only from the first day

C. F. Gotfredsen; K. Buschard; E. K. Frandsen

1985-01-01

423

Overeating by Young Obesity-prone and Lean Rats Caused by Tastes Associated With Low Energy Foods  

Microsoft Academic Search

Objective: Childhood obesity is a prominent health problem that may involve early learning about tastes and the energy content of foods. We tested the hypothesis that food tastes predictive of low energy content cause overeating in young animals.Research Methods and Procedures: Juvenile and adolescent (4- and 8-week-old) male JCR:LA-cp lean (+\\/cp or +\\/+) and obesity-prone (cp\\/cp) rats were given sweet

W. David Pierce; C. Donald Heth; Joanna C. Owczarczyk; James C. Russell; Spencer D. Proctor

2007-01-01

424

Increased density of fluorescent adrenergic fibers around the middle cerebral arteries of stroke-prone spontaneously hypertensive rats  

Microsoft Academic Search

Summary  The distribution of fluorescent adrenergic nerve fibers in the proximal portion (horizontal segment, Hs) and the three distal\\u000a portions (major branches) of the middle cerebral arteries (MCA) was examined in stroke-prone spontaneously hypertensive rats\\u000a (SHRSP) aged 10, 30, 60, 90, and 180 days, by the glyoxylic acid method. The results were compared with those in agematched\\u000a normotensive Wistar Kyoto (WKY)

Mari Kondo; Tatsuhiko Miyazaki; Takashi Fujiwara; Akemi Yano; Ryo Tabei

1992-01-01

425

Recovery and purification of highly aggregation-prone disulfide-containing peptides: Application to islet amyloid polypeptide  

Microsoft Academic Search

Islet amyloid polypeptide (IAPP) is a 37-residue pancreatic hormone. It is responsible for the formation of islet amyloid in vivo and is very insoluble and aggregation-prone in vitro, particularly at basic pH. The peptide contains a disulfide bridge between residues two and seven and an amidated C terminus. There is no reported expression system for the production of amidated IAPP.

Andisheh Abedini; Gagandeep Singh; Daniel P. Raleigh

2006-01-01

426