Sample records for error prone pcr

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

    PubMed

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

    2003-07-01

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

  2. A multiplexed droplet digital PCR assay performs better than qPCR on inhibition prone samples.

    PubMed

    Sedlak, Ruth Hall; Kuypers, Jane; Jerome, Keith R

    2014-12-01

    We demonstrate the development of a multiplex droplet digital PCR assay for human cytomegalovirus (CMV), human adenovirus species F, and an internal plasmid control that may be useful for PCR inhibition-prone clinical samples. This assay performs better on inhibition-prone stool samples than a quantitative PCR assay for CMV and is the first published clinical virology droplet digital PCR assay to incorporate an internal control. Copyright © 2014 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2014-01-01

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

  4. Error-prone PCR mutation of Ls-EPSPS gene from Liriope spicata conferring to its enhanced glyphosate-resistance.

    PubMed

    Mao, Chanjuan; Xie, Hongjie; Chen, Shiguo; Valverde, Bernal E; Qiang, Sheng

    2017-09-01

    Liriope spicata (Thunb.) Lour has a unique LsEPSPS structure contributing to the highest-ever-recognized natural glyphosate tolerance. The transformed LsEPSPS confers increased glyphosate resistance to E. coli and A. thaliana. However, the increased glyphosate-resistance level is not high enough to be of commercial value. Therefore, LsEPSPS was subjected to error-prone PCR to screen mutant EPSPS genes capable of endowing higher resistance levels. A mutant designated as ELs-EPSPS having five mutated amino acids (37Val, 67Asn, 277Ser, 351Gly and 422Gly) was selected for its ability to confer improved resistance to glyphosate. Expression of ELs-EPSPS in recombinant E. coli BL21 (DE3) strains enhanced resistance to glyphosate in comparison to both the LsEPSPS-transformed and -untransformed controls. Furthermore, transgenic ELs-EPSPS A. thaliana was about 5.4 fold and 2-fold resistance to glyphosate compared with the wild-type and the Ls-EPSPS-transgenic plants, respectively. Therefore, the mutated ELs-EPSPS gene has potential value for has potential for the development of glyphosate-resistant crops. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Furfural-tolerant Zymomonas mobilis derived from error-prone PCR-based whole genome shuffling and their tolerant mechanism.

    PubMed

    Huang, Suzhen; Xue, Tingli; Wang, Zhiquan; Ma, Yuanyuan; He, Xueting; Hong, Jiefang; Zou, Shaolan; Song, Hao; Zhang, Minhua

    2018-04-01

    Furfural-tolerant strain is essential for the fermentative production of biofuels or chemicals from lignocellulosic biomass. In this study, Zymomonas mobilis CP4 was for the first time subjected to error-prone PCR-based whole genome shuffling, and the resulting mutants F211 and F27 that could tolerate 3 g/L furfural were obtained. The mutant F211 under various furfural stress conditions could rapidly grow when the furfural concentration reduced to 1 g/L. Meanwhile, the two mutants also showed higher tolerance to high concentration of glucose than the control strain CP4. Genome resequencing revealed that the F211 and F27 had 12 and 13 single-nucleotide polymorphisms. The activity assay demonstrated that the activity of NADH-dependent furfural reductase in mutant F211 and CP4 was all increased under furfural stress, and the activity peaked earlier in mutant than in control. Also, furfural level in the culture of F211 was also more rapidly decreased. These indicate that the increase in furfural tolerance of the mutants may be resulted from the enhanced NADH-dependent furfural reductase activity during early log phase, which could lead to an accelerated furfural detoxification process in mutants. In all, we obtained Z. mobilis mutants with enhanced furfural and high concentration of glucose tolerance, and provided valuable clues for the mechanism of furfural tolerance and strain development.

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

    PubMed Central

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

    2013-01-01

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

  7. Structure-Function Analysis of Chloroplast Proteins via Random Mutagenesis Using Error-Prone PCR.

    PubMed

    Dumas, Louis; Zito, Francesca; Auroy, Pascaline; Johnson, Xenie; Peltier, Gilles; Alric, Jean

    2018-06-01

    Site-directed mutagenesis of chloroplast genes was developed three decades ago and has greatly advanced the field of photosynthesis research. Here, we describe a new approach for generating random chloroplast gene mutants that combines error-prone polymerase chain reaction of a gene of interest with chloroplast complementation of the knockout Chlamydomonas reinhardtii mutant. As a proof of concept, we targeted a 300-bp sequence of the petD gene that encodes subunit IV of the thylakoid membrane-bound cytochrome b 6 f complex. By sequencing chloroplast transformants, we revealed 149 mutations in the 300-bp target petD sequence that resulted in 92 amino acid substitutions in the 100-residue target subunit IV sequence. Our results show that this method is suited to the study of highly hydrophobic, multisubunit, and chloroplast-encoded proteins containing cofactors such as hemes, iron-sulfur clusters, and chlorophyll pigments. Moreover, we show that mutant screening and sequencing can be used to study photosynthetic mechanisms or to probe the mutational robustness of chloroplast-encoded proteins, and we propose that this method is a valuable tool for the directed evolution of enzymes in the chloroplast. © 2018 American Society of Plant Biologists. All rights reserved.

  8. Designing an algorithm to preserve privacy for medical record linkage with error-prone data.

    PubMed

    Pal, Doyel; Chen, Tingting; Zhong, Sheng; Khethavath, Praveen

    2014-01-20

    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. 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. 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. 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

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

    PubMed Central

    Pal, Doyel; Chen, Tingting; Khethavath, Praveen

    2014-01-01

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

  10. Error minimization algorithm for comparative quantitative PCR analysis: Q-Anal.

    PubMed

    OConnor, William; Runquist, Elizabeth A

    2008-07-01

    Current methods for comparative quantitative polymerase chain reaction (qPCR) analysis, the threshold and extrapolation methods, either make assumptions about PCR efficiency that require an arbitrary threshold selection process or extrapolate to estimate relative levels of messenger RNA (mRNA) transcripts. Here we describe an algorithm, Q-Anal, that blends elements from current methods to by-pass assumptions regarding PCR efficiency and improve the threshold selection process to minimize error in comparative qPCR analysis. This algorithm uses iterative linear regression to identify the exponential phase for both target and reference amplicons and then selects, by minimizing linear regression error, a fluorescence threshold where efficiencies for both amplicons have been defined. From this defined fluorescence threshold, cycle time (Ct) and the error for both amplicons are calculated and used to determine the expression ratio. Ratios in complementary DNA (cDNA) dilution assays from qPCR data were analyzed by the Q-Anal method and compared with the threshold method and an extrapolation method. Dilution ratios determined by the Q-Anal and threshold methods were 86 to 118% of the expected cDNA ratios, but relative errors for the Q-Anal method were 4 to 10% in comparison with 4 to 34% for the threshold method. In contrast, ratios determined by an extrapolation method were 32 to 242% of the expected cDNA ratios, with relative errors of 67 to 193%. Q-Anal will be a valuable and quick method for minimizing error in comparative qPCR analysis.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2015-01-01

    Thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. In this study, we constructed an error-prone strain of the thermophile Geobacillus kaustophilus HTA426 and investigated thermoadaptation-directed enzyme evolution using the strain. A mutation frequency assay using the antibiotics rifampin and streptomycin revealed that G. kaustophilus had substantially higher mutability than Escherichia coli and Bacillus subtilis. The predominant mutations in G. kaustophilus were A · T→G · C and C · G→T · A transitions, implying that the high mutability of G. kaustophilus was attributable in part to high-temperature-associated DNA damage during growth. Among the genes that may be involved in DNA repair in G. kaustophilus, deletions of the mutSL, mutY, ung, and mfd genes markedly enhanced mutability. These genes were subsequently deleted to construct an error-prone thermophile that showed much higher (700- to 9,000-fold) mutability than the parent strain. The error-prone strain was auxotrophic for uracil owing to the fact that the strain was deficient in the intrinsic pyrF gene. Although the strain harboring Bacillus subtilis pyrF was also essentially auxotrophic, cells became prototrophic after 2 days of culture under uracil starvation, generating B. subtilis PyrF variants with an enhanced half-denaturation temperature of >10°C. These data suggest that this error-prone strain is a promising host for thermoadaptation-directed evolution to generate thermostable variants from thermolabile enzymes. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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

    PubMed

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

    2013-05-01

    Acid tolerance of Lactobacillus pentosus ATCC 8041 was improved by error-prone amplification of its genomic DNA using random primers and Taq DNA polymerase. The resulting amplification products were transferred into wild-type L. pentosus by electroporation and the transformants were screened for growth on low-pH agar plates. After only one round of mutation, one mutant (MT3) was identified that was able to completely consume 20 g/L of glucose to produce lactic acid at a yield of 95% in 1L MRS medium at pH 3.8 within 36 h, whereas no growth or lactic acid production was observed for the wild-type strain under the same conditions. The acid tolerance of mutant MT3 remained genetically stable for at least 25 subcultures. Therefore, the error-prone whole genome amplification technique is a very powerful tool for improving phenotypes of this lactic acid bacterium and may also be applicable for other microorganisms. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Producing good font attribute determination using error-prone information

    NASA Astrophysics Data System (ADS)

    Cooperman, Robert

    1997-04-01

    A method to provide estimates of font attributes in an OCR system, using detectors of individual attributes that are error-prone. For an OCR system to preserve the appearance of a scanned document, it needs accurate detection of font attributes. However, OCR environments have noise and other sources of errors, tending to make font attribute detection unreliable. Certain assumptions about font use can greatly enhance accuracy. Attributes such as boldness and italics are more likely to change between neighboring words, while attributes such as serifness are less likely to change within the same paragraph. Furthermore, the document as a whole, tends to have a limited number of sets of font attributes. These assumptions allow a better use of context than the raw data, or what would be achieved by simpler methods that would oversmooth the data.

  15. Inhibiting HER3-mediated tumor cell growth with affibody molecules engineered to low picomolar affinity by position-directed error-prone PCR-like diversification.

    PubMed

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

    2013-01-01

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

  16. Validation, Edits, and Application Processing Phase II and Error-Prone Model Report.

    ERIC Educational Resources Information Center

    Gray, Susan; And Others

    The impact of quality assurance procedures on the correct award of Basic Educational Opportunity Grants (BEOGs) for 1979-1980 was assessed, and a model for detecting error-prone applications early in processing was developed. The Bureau of Student Financial Aid introduced new comments into the edit system in 1979 and expanded the pre-established…

  17. Two-Step Fair Scheduling of Continuous Media Streams over Error-Prone Wireless Channels

    NASA Astrophysics Data System (ADS)

    Oh, Soohyun; Lee, Jin Wook; Park, Taejoon; Jo, Tae-Chang

    In wireless cellular networks, streaming of continuous media (with strict QoS requirements) over wireless links is challenging due to their inherent unreliability characterized by location-dependent, bursty errors. To address this challenge, we present a two-step scheduling algorithm for a base station to provide streaming of continuous media to wireless clients over the error-prone wireless links. The proposed algorithm is capable of minimizing the packet loss rate of individual clients in the presence of error bursts, by transmitting packets in the round-robin manner and also adopting a mechanism for channel prediction and swapping.

  18. Update: Validation, Edits, and Application Processing. Phase II and Error-Prone Model Report.

    ERIC Educational Resources Information Center

    Gray, Susan; And Others

    An update to the Validation, Edits, and Application Processing and Error-Prone Model Report (Section 1, July 3, 1980) is presented. The objective is to present the most current data obtained from the June 1980 Basic Educational Opportunity Grant applicant and recipient files and to determine whether the findings reported in Section 1 of the July…

  19. Error-proneness as a handicap signal.

    PubMed

    De Jaegher, Kris

    2003-09-21

    This paper describes two discrete signalling models in which the error-proneness of signals can serve as a handicap signal. In the first model, the direct handicap of sending a high-quality signal is not large enough to assure that a low-quality signaller will not send it. However, if the receiver sometimes mistakes a high-quality signal for a low-quality one, then there is an indirect handicap to sending a high-quality signal. The total handicap of sending such a signal may then still be such that a low-quality signaller would not want to send it. In the second model, there is no direct handicap of sending signals, so that nothing would seem to stop a signaller from always sending a high-quality signal. However, the receiver sometimes fails to detect signals, and this causes an indirect handicap of sending a high-quality signal that still stops the low-quality signaller of sending such a signal. The conditions for honesty are that the probability of an error of detection is higher for a high-quality than for a low-quality signal, and that the signaller who does not detect a signal adopts a response that is bad to the signaller. In both our models, we thus obtain the result that signal accuracy should not lie above a certain level in order for honest signalling to be possible. Moreover, we show that the maximal accuracy that can be achieved is higher the lower the degree of conflict between signaller and receiver. As well, we show that it is the conditions for honest signalling that may be constraining signal accuracy, rather than the signaller trying to make honest signals as effective as possible given receiver psychology, or the signaller adapting the accuracy of honest signals depending on his interests.

  20. One-step random mutagenesis by error-prone rolling circle amplification

    PubMed Central

    Fujii, Ryota; Kitaoka, Motomitsu; Hayashi, Kiyoshi

    2004-01-01

    In vitro random mutagenesis is a powerful tool for altering properties of enzymes. We describe here a novel random mutagenesis method using rolling circle amplification, named error-prone RCA. This method consists of only one DNA amplification step followed by transformation of the host strain, without treatment with any restriction enzymes or DNA ligases, and results in a randomly mutated plasmid library with 3–4 mutations per kilobase. Specific primers or special equipment, such as a thermal-cycler, are not required. This method permits rapid preparation of randomly mutated plasmid libraries, enabling random mutagenesis to become a more commonly used technique. PMID:15507684

  1. Digital Droplet PCR: CNV Analysis and Other Applications.

    PubMed

    Mazaika, Erica; Homsy, Jason

    2014-07-14

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

  2. A false positive food chain error associated with a generic predator gut content ELISA

    USDA-ARS?s Scientific Manuscript database

    Conventional prey-specific gut content ELISA and PCR assays are useful for identifying predators of insect pests in nature. However, these assays are prone to yielding certain types of food chain errors. For instance, it is possible that prey remains can pass through the food chain as the result of ...

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

    PubMed

    Goomber, Shelly; Kumar, Arbind; Kaur, Jagdeep

    2016-01-15

    Cold adapted enzymes have applications in detergent, textile, food, bioremediation and biotechnology processes. Bacillus lipases are 'generally recognized as safe' (GRAS) and hence are industrially attractive. Bacillus lipase of 1.4 subfamily are of lowest molecular weight and are reversibly unfolded due to absence of disulphide bonds. Therefore these are largely used to study energetic of protein stability that represents unfolding of native protein to fully unfolded state. In present study, metagenomically isolated Bacillus LipJ was laboratory evolved for cold adaptation by error Prone PCR. Library of variants were screened for high relative activity at low temperature of 10°C compared to native protein LipJ. Point mutant sequenced as Phe19→Leu was determined to be active at cold and was selected for extensive biochemical, biophysical characterization. Variant F19L showed its maximum activity at 10°C where parent protein LipJ had 20% relative activity. Psychrophilic nature of F19L was established with about 50% relative active at 5°C where native protein was frozen to act. Variant F19L showed no activity at temperature 40°C and above, establishing its thermolabile nature. Thermostability studies determined mutant to be unstable above 20°C and three fold decrease in its half life at 30°C compared to native protein. Far UV-CD and intrinsic fluorescence study demonstrated unstable tertiary structure of point variant F19L leading to its unfolding at low temperature of 20°C. Cold adaptation of mutant F19L is accompanied with increased specific activity. Mutant was catalytically more efficient with 1.3 fold increase in kcat. Homologue structure modelling predicted disruption of intersecondary hydrophobic core formed by aromatic ring of Phe19 with non polar residues placed at β3, β4, β5, β6, αF. Increased local flexibility of variant F19L explains molecular basis of its psychrophilic nature. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. [Effect of Mn(II) on the error-prone DNA polymerase iota activity in extracts from human normal and tumor cells].

    PubMed

    Lakhin, A V; Efremova, A S; Makarova, I V; Grishina, E E; Shram, S I; Tarantul, V Z; Gening, L V

    2013-01-01

    The DNA polymerase iota (Pol iota), which has some peculiar features and is characterized by an extremely error-prone DNA synthesis, belongs to the group of enzymes preferentially activated by Mn2+ instead of Mg2+. In this work, the effect of Mn2+ on DNA synthesis in cell extracts from a) normal human and murine tissues, b) human tumor (uveal melanoma), and c) cultured human tumor cell lines SKOV-3 and HL-60 was tested. Each group displayed characteristic features of Mn-dependent DNA synthesis. The changes in the Mn-dependent DNA synthesis caused by malignant transformation of normal tissues are described. It was also shown that the error-prone DNA synthesis catalyzed by Pol iota in extracts of all cell types was efficiently suppressed by an RNA aptamer (IKL5) against Pol iota obtained in our work earlier. The obtained results suggest that IKL5 might be used to suppress the enhanced activity of Pol iota in tumor cells.

  5. Error-prone meiotic division and subfertility in mice with oocyte-conditional knockdown of pericentrin.

    PubMed

    Baumann, Claudia; Wang, Xiaotian; Yang, Luhan; Viveiros, Maria M

    2017-04-01

    Mouse oocytes lack canonical centrosomes and instead contain unique acentriolar microtubule-organizing centers (aMTOCs). To test the function of these distinct aMTOCs in meiotic spindle formation, pericentrin (Pcnt), an essential centrosome/MTOC protein, was knocked down exclusively in oocytes by using a transgenic RNAi approach. Here, we provide evidence that disruption of aMTOC function in oocytes promotes spindle instability and severe meiotic errors that lead to pronounced female subfertility. Pcnt-depleted oocytes from transgenic (Tg) mice were ovulated at the metaphase-II stage, but show significant chromosome misalignment, aneuploidy and premature sister chromatid separation. These defects were associated with loss of key Pcnt-interacting proteins (γ-tubulin, Nedd1 and Cep215) from meiotic spindle poles, altered spindle structure and chromosome-microtubule attachment errors. Live-cell imaging revealed disruptions in the dynamics of spindle assembly and organization, together with chromosome attachment and congression defects. Notably, spindle formation was dependent on Ran GTPase activity in Pcnt-deficient oocytes. Our findings establish that meiotic division is highly error-prone in the absence of Pcnt and disrupted aMTOCs, similar to what reportedly occurs in human oocytes. Moreover, these data underscore crucial differences between MTOC-dependent and -independent meiotic spindle assembly. © 2017. Published by The Company of Biologists Ltd.

  6. Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway

    PubMed Central

    Weeden, Clare E.; Chen, Yunshun; Ma, Stephen B.; Hu, Yifang; Ramm, Georg; Sutherland, Kate D.; Smyth, Gordon K.

    2017-01-01

    Lung squamous cell carcinoma (SqCC), the second most common subtype of lung cancer, is strongly associated with tobacco smoking and exhibits genomic instability. The cellular origins and molecular processes that contribute to SqCC formation are largely unexplored. Here we show that human basal stem cells (BSCs) isolated from heavy smokers proliferate extensively, whereas their alveolar progenitor cell counterparts have limited colony-forming capacity. We demonstrate that this difference arises in part because of the ability of BSCs to repair their DNA more efficiently than alveolar cells following ionizing radiation or chemical-induced DNA damage. Analysis of mice harbouring a mutation in the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a key enzyme in DNA damage repair by nonhomologous end joining (NHEJ), indicated that BSCs preferentially repair their DNA by this error-prone process. Interestingly, polyploidy, a phenomenon associated with genetically unstable cells, was only observed in the human BSC subset. Expression signature analysis indicated that BSCs are the likely cells of origin of human SqCC and that high levels of NHEJ genes in SqCC are correlated with increasing genomic instability. Hence, our results favour a model in which heavy smoking promotes proliferation of BSCs, and their predilection for error-prone NHEJ could lead to the high mutagenic burden that culminates in SqCC. Targeting DNA repair processes may therefore have a role in the prevention and therapy of SqCC. PMID:28125611

  7. Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes.

    PubMed

    Supek, Fran; Lehner, Ben

    2017-07-27

    Many processes can cause the same nucleotide change in a genome, making the identification of the mechanisms causing mutations a difficult challenge. Here, we show that clustered mutations provide a more precise fingerprint of mutagenic processes. Of nine clustered mutation signatures identified from >1,000 tumor genomes, three relate to variable APOBEC activity and three are associated with tobacco smoking. An additional signature matches the spectrum of translesion DNA polymerase eta (POLH). In lymphoid cells, these mutations target promoters, consistent with AID-initiated somatic hypermutation. In solid tumors, however, they are associated with UV exposure and alcohol consumption and target the H3K36me3 chromatin of active genes in a mismatch repair (MMR)-dependent manner. These regions normally have a low mutation rate because error-free MMR also targets H3K36me3 chromatin. Carcinogens and error-prone repair therefore redistribute mutations to the more important regions of the genome, contributing a substantial mutation load in many tumors, including driver mutations. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. DNA double strand break repair in human bladder cancer is error prone and involves microhomology-associated end-joining

    PubMed Central

    Bentley, Johanne; Diggle, Christine P.; Harnden, Patricia; Knowles, Margaret A.; Kiltie, Anne E.

    2004-01-01

    In human cells DNA double strand breaks (DSBs) can be repaired by the non-homologous end-joining (NHEJ) pathway. In a background of NHEJ deficiency, DSBs with mismatched ends can be joined by an error-prone mechanism involving joining between regions of nucleotide microhomology. The majority of joins formed from a DSB with partially incompatible 3′ overhangs by cell-free extracts from human glioblastoma (MO59K) and urothelial (NHU) cell lines were accurate and produced by the overlap/fill-in of mismatched termini by NHEJ. However, repair of DSBs by extracts using tissue from four high-grade bladder carcinomas resulted in no accurate join formation. Junctions were formed by the non-random deletion of terminal nucleotides and showed a preference for annealing at a microhomology of 8 nt buried within the DNA substrate; this process was not dependent on functional Ku70, DNA-PK or XRCC4. Junctions were repaired in the same manner in MO59K extracts in which accurate NHEJ was inactivated by inhibition of Ku70 or DNA-PKcs. These data indicate that bladder tumour extracts are unable to perform accurate NHEJ such that error-prone joining predominates. Therefore, in high-grade tumours mismatched DSBs are repaired by a highly mutagenic, microhomology-mediated, alternative end-joining pathway, a process that may contribute to genomic instability observed in bladder cancer. PMID:15466592

  9. Improvement of enzyme activity of β-1,3-1,4-glucanase from Paenibacillus sp. X4 by error-prone PCR and structural insights of mutated residues.

    PubMed

    Baek, Seung Cheol; Ho, Thien-Hoang; Lee, Hyun Woo; Jung, Won Kyeong; Gang, Hyo-Seung; Kang, Lin-Woo; Kim, Hoon

    2017-05-01

    β-1,3-1,4-Glucanase (BGlc8H) from Paenibacillus sp. X4 was mutated by error-prone PCR or truncated using termination primers to improve its enzyme properties. The crystal structure of BGlc8H was determined at a resolution of 1.8 Å to study the possible roles of mutated residues and truncated regions of the enzyme. In mutation experiments, three clones of EP 2-6, 2-10, and 5-28 were finally selected that exhibited higher specific activities than the wild type when measured using their crude extracts. Enzyme variants of BG 2-6 , BG 2-10 , and BG 5-28 were mutated at two, two, and six amino acid residues, respectively. These enzymes were purified homogeneously by Hi-Trap Q and CHT-II chromatography. Specific activity of BG 5-28 was 2.11-fold higher than that of wild-type BG wt , whereas those of BG 2-6 and BG 2-10 were 0.93- and 1.19-fold that of the wild type, respectively. The optimum pH values and temperatures of the variants were nearly the same as those of BG wt (pH 5.0 and 40 °C, respectively). However, the half-life of the enzyme activity and catalytic efficiency (k cat /K m ) of BG 5-28 were 1.92- and 2.12-fold greater than those of BG wt at 40 °C, respectively. The catalytic efficiency of BG 5-28 increased to 3.09-fold that of BG wt at 60 °C. These increases in the thermostability and catalytic efficiency of BG 5-28 might be useful for the hydrolysis of β-glucans to produce fermentable sugars. Of the six mutated residues of BG 5-28 , five residues were present in mature BGlc8H protein, and two of them were located in the core scaffold of BGlc8H and the remaining three residues were in the substrate-binding pocket forming loop regions. In truncation experiments, three forms of C-terminal truncated BGlc8H were made, which comprised 360, 286, and 215 amino acid residues instead of the 409 residues of the wild type. No enzyme activity was observed for these truncated enzymes, suggesting the complete scaffold of the α 6 /α 6 -double-barrel structure is

  10. Statistical approaches to account for false-positive errors in environmental DNA samples.

    PubMed

    Lahoz-Monfort, José J; Guillera-Arroita, Gurutzeta; Tingley, Reid

    2016-05-01

    Environmental DNA (eDNA) sampling is prone to both false-positive and false-negative errors. We review statistical methods to account for such errors in the analysis of eDNA data and use simulations to compare the performance of different modelling approaches. Our simulations illustrate that even low false-positive rates can produce biased estimates of occupancy and detectability. We further show that removing or classifying single PCR detections in an ad hoc manner under the suspicion that such records represent false positives, as sometimes advocated in the eDNA literature, also results in biased estimation of occupancy, detectability and false-positive rates. We advocate alternative approaches to account for false-positive errors that rely on prior information, or the collection of ancillary detection data at a subset of sites using a sampling method that is not prone to false-positive errors. We illustrate the advantages of these approaches over ad hoc classifications of detections and provide practical advice and code for fitting these models in maximum likelihood and Bayesian frameworks. Given the severe bias induced by false-negative and false-positive errors, the methods presented here should be more routinely adopted in eDNA studies. © 2015 John Wiley & Sons Ltd.

  11. A nucleotide-analogue-induced gain of function corrects the error-prone nature of human DNA polymerase iota.

    PubMed

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

    2012-06-27

    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 ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι 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 ι. 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 ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

  12. A nucleotide analogue induced gain of function corrects the error-prone nature of human DNA polymerase iota

    PubMed Central

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

    2012-01-01

    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 ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2′-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2′-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle (χ), which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol ι. 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 ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-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. PMID:22632140

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

    PubMed

    Cooperstein, Robert; Young, Morgan

    2014-01-01

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

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

    PubMed

    Mallik, Sarita; Popodi, Ellen M; Hanson, Andrew J; Foster, Patricia L

    2015-09-01

    Escherichia coli's DNA polymerase IV (Pol IV/DinB), a member of the Y family of error-prone polymerases, is induced during the SOS response to DNA damage and is responsible for translesion bypass and adaptive (stress-induced) mutation. In this study, the localization of Pol IV after DNA damage was followed using fluorescent fusions. After exposure of E. coli to DNA-damaging agents, fluorescently tagged Pol IV localized to the nucleoid as foci. Stepwise photobleaching indicated ∼60% of the foci consisted of three Pol IV molecules, while ∼40% consisted of six Pol IV molecules. Fluorescently tagged Rep, a replication accessory DNA helicase, was recruited to the Pol IV foci after DNA damage, suggesting that the in vitro interaction between Rep and Pol IV reported previously also occurs in vivo. Fluorescently tagged RecA also formed foci after DNA damage, and Pol IV localized to them. To investigate if Pol IV localizes to double-strand breaks (DSBs), an I-SceI endonuclease-mediated DSB was introduced close to a fluorescently labeled LacO array on the chromosome. After DSB induction, Pol IV localized to the DSB site in ∼70% of SOS-induced cells. RecA also formed foci at the DSB sites, and Pol IV localized to the RecA foci. These results suggest that Pol IV interacts with RecA in vivo and is recruited to sites of DSBs to aid in the restoration of DNA replication. DNA polymerase IV (Pol IV/DinB) is an error-prone DNA polymerase capable of bypassing DNA lesions and aiding in the restart of stalled replication forks. In this work, we demonstrate in vivo localization of fluorescently tagged Pol IV to the nucleoid after DNA damage and to DNA double-strand breaks. We show colocalization of Pol IV with two proteins: Rep DNA helicase, which participates in replication, and RecA, which catalyzes recombinational repair of stalled replication forks. Time course experiments suggest that Pol IV recruits Rep and that RecA recruits Pol IV. These findings provide in vivo evidence

  15. The Concept of Accident Proneness: A Review

    PubMed Central

    Froggatt, Peter; Smiley, James A.

    1964-01-01

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yasbin, R. E.

    1981-06-01

    The research performed under this contract has been concentrated on the relationship between inducible DNA repair systems, mutagenesis and the competent state in the gram positive bacterium Bacillus subtilis. The following results have been obtained from this research: (1) competent Bacillus subtilis cells have been developed into a sensitive tester system for carcinogens; (2) competent B. subtilis cells have an efficient excision-repair system, however, this system will not function on bacteriophage DNA taken into the cell via the process of transfection; (3) DNA polymerase III is essential in the mechanism of the process of W-reactivation; (4) B. subtilis strains curedmore » 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.« less

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

    ERIC Educational Resources Information Center

    Saavedra, Pedro; And Others

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

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

    PubMed Central

    2014-01-01

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

  19. Gene-targeted Random Mutagenesis to Select Heterochromatin-destabilizing Proteasome Mutants in Fission Yeast.

    PubMed

    Seo, Hogyu David; Lee, Daeyoup

    2018-05-15

    Random mutagenesis of a target gene is commonly used to identify mutations that yield the desired phenotype. Of the methods that may be used to achieve random mutagenesis, error-prone PCR is a convenient and efficient strategy for generating a diverse pool of mutants (i.e., a mutant library). Error-prone PCR is the method of choice when a researcher seeks to mutate a pre-defined region, such as the coding region of a gene while leaving other genomic regions unaffected. After the mutant library is amplified by error-prone PCR, it must be cloned into a suitable plasmid. The size of the library generated by error-prone PCR is constrained by the efficiency of the cloning step. However, in the fission yeast, Schizosaccharomyces pombe, the cloning step can be replaced by the use of a highly efficient one-step fusion PCR to generate constructs for transformation. Mutants of desired phenotypes may then be selected using appropriate reporters. Here, we describe this strategy in detail, taking as an example, a reporter inserted at centromeric heterochromatin.

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

    PubMed

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

    2016-01-01

    Stringently defined otitis-prone (sOP) children represent a new classification of the otitis-prone condition. Previous studies showed dysfunction in Ab, B-cell memory and T-cell memory responses. We sought to determine whether there are defects in numbers, phenotype and/or function of professional APC in the peripheral blood of sOP infants. APC phenotypic counts, MHC II expression and intracellular cytokine levels were determined in response to TLR7/8 (R848) stimulation by flow cytometry. Innate immune mRNA expression was measured using RT-PCR and cytokines were measured using Luminex technology. Significant (P < 0.05) increases in the phenotypic counts of monocytes and conventional dendritic cells but not plasmacytoid DCs were observed in sOP compared with non-otitis-prone (NOP) age-matched infants. No significant differences in APC activation or function were observed. Expression of various TLRs, intracellular signaling molecules and downstream cytokines was also not found to be significantly different between sOP and NOP infants. Higher numbers of APCs in sOP infants suggest the possibility of a persistent mucosal inflammatory status. Transcriptional and cytokine profiles of PBMCs among sOP infants suggest their systemic innate responses are not different compared to NOP infants. © The Author(s) 2015.

  1. Use of alternative alkali chlorides in RT and PCR of polynucleotides containing G quadruplex structures.

    PubMed

    Ramos-Alemán, Fabiola; González-Jasso, Eva; Pless, Reynaldo C

    2018-02-15

    Several alkali chlorides were compared for their use in reverse transcription (RT) and PCR of different types of nucleic acid templates. On a test region of biological DNA incapable of forming G quadruplex (G4) structures, Taq DNA polymerase showed similar PCR performance with 50 mM KCl, CsCl, LiCl, and NaCl. In contrast, on a synthetic model polydeoxyribonucleotide prone to G4 formation, good PCR amplification was obtained with 50 mM CsCl, but little or none with LiCl or KCl. Similarly, in RT of a G4-prone model polyribonucleotide, MMLV reverse transcriptase produced a good yield with 50 mM CsCl, mediocre yields with LiCl or without added alkali chloride, and a poor yield with 50 mM KCl. The full RT-PCR assay starting from the G4-prone polyribonucleotide, showed good results with CsCl in both stages, poor results with LiCl, and no product formation with KCl. The model polynucleotides showed fast G quadruplex formation under PCR or RT conditions with 50 mM KCl, but not with CsCl or LiCl. The results argue for the use of CsCl instead of KCl for RT and PCR of G4-prone sequences. No advantage was observed when using the 7-deaza type nucleotide analog c 7 dGTP in PCR amplification of the G4-prone polydeoxyribonucleotide. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Error-prone bypass of O6-methylguanine by DNA polymerase of Pseudomonas aeruginosa phage PaP1.

    PubMed

    Gu, Shiling; Xiong, Jingyuan; Shi, Ying; You, Jia; Zou, Zhenyu; Liu, Xiaoying; Zhang, Huidong

    2017-09-01

    O 6 -Methylguanine (O 6 -MeG) is highly mutagenic and is commonly found in DNA exposed to methylating agents, generally leads to G:C to A:T mutagenesis. To study DNA replication encountering O 6 -MeG by the DNA polymerase (gp90) of P. aeruginosa phage PaP1, we analyzed steady-state and pre-steady-state kinetics of nucleotide incorporation opposite O 6 -MeG by gp90 exo - . O 6 -MeG partially inhibited full-length extension by gp90 exo - . O 6 -MeG greatly reduces dNTP incorporation efficiency, resulting in 67-fold preferential error-prone incorporation of dTTP than dCTP. Gp90 exo - extends beyond T:O 6 -MeG 2-fold more efficiently than C:O 6 -MeG. Incorporation of dCTP opposite G and incorporation of dCTP or dTTP opposite O 6 -MeG show fast burst phases. The pre-steady-state incorporation efficiency (k pol /K d,dNTP ) is decreased in the order of dCTP:G>dTTP:O 6 -MeG>dCTP:O 6 -MeG. The presence of O 6 -MeG at template does not affect the binding affinity of polymerase to DNA but it weakened their binding in the presence of dCTP and Mg 2+ . Misincorporation of dTTP opposite O 6 -MeG further weakens the binding affinity of polymerase to DNA. The priority of dTTP incorporation opposite O 6 -MeG is originated from the fact that dTTP can induce a faster conformational change step and a faster chemical step than dCTP. This study reveals that gp90 bypasses O 6 -MeG in an error-prone manner and provides further understanding in DNA replication encountering mutagenic alkylation DNA damage for P. aeruginosa phage PaP1. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A design of experiments approach to validation sampling for logistic regression modeling with error-prone medical records.

    PubMed

    Ouyang, Liwen; Apley, Daniel W; Mehrotra, Sanjay

    2016-04-01

    Electronic medical record (EMR) databases offer significant potential for developing clinical hypotheses and identifying disease risk associations by fitting statistical models that capture the relationship between a binary response variable and a set of predictor variables that represent clinical, phenotypical, and demographic data for the patient. However, EMR response data may be error prone for a variety of reasons. Performing a manual chart review to validate data accuracy is time consuming, which limits the number of chart reviews in a large database. The authors' objective is to develop a new design-of-experiments-based systematic chart validation and review (DSCVR) approach that is more powerful than the random validation sampling used in existing approaches. The DSCVR approach judiciously and efficiently selects the cases to validate (i.e., validate whether the response values are correct for those cases) for maximum information content, based only on their predictor variable values. The final predictive model will be fit using only the validation sample, ignoring the remainder of the unvalidated and unreliable error-prone data. A Fisher information based D-optimality criterion is used, and an algorithm for optimizing it is developed. The authors' method is tested in a simulation comparison that is based on a sudden cardiac arrest case study with 23 041 patients' records. This DSCVR approach, using the Fisher information based D-optimality criterion, results in a fitted model with much better predictive performance, as measured by the receiver operating characteristic curve and the accuracy in predicting whether a patient will experience the event, than a model fitted using a random validation sample. The simulation comparisons demonstrate that this DSCVR approach can produce predictive models that are significantly better than those produced from random validation sampling, especially when the event rate is low. © The Author 2015. Published by Oxford

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

    PubMed

    Smailes, David; Meins, Elizabeth; Fernyhough, Charles

    2015-01-01

    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. 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. 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. 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.

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

    PubMed

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

    2015-11-26

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

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

    PubMed Central

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

    2015-01-01

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

  7. Evidence that a burst of DNA depurination in SENCAR mouse skin induces error-prone repair and forms mutations in the H-ras gene.

    PubMed

    Chakravarti, D; Mailander, P C; Li, K M; Higginbotham, S; Zhang, H L; Gross, M L; Meza, J L; Cavalieri, E L; Rogan, E G

    2001-11-29

    Treatment of SENCAR mouse skin with dibenzo[a,l]pyrene results in abundant formation of abasic sites that undergo error-prone excision repair, forming oncogenic H-ras mutations in the early preneoplastic period. To examine whether the abundance of abasic sites causes repair infidelity, we treated SENCAR mouse skin with estradiol-3,4-quinone (E(2)-3,4-Q) and determined adduct levels 1 h after treatment, as well as mutation spectra in the H-ras gene between 6 h and 3 days after treatment. E(2)-3,4-Q formed predominantly (> or =99%) the rapidly-depurinating 4-hydroxy estradiol (4-OHE(2))-1-N3Ade adduct and the slower-depurinating 4-OHE(2)-1-N7Gua adduct. Between 6 h and 3 days, E(2)-3,4-Q induced abundant A to G mutations in H-ras DNA, frequently in the context of a 3'-G residue. Using a T.G-DNA glycosylase (TDG)-PCR assay, we determined that the early A to G mutations (6 and 12 h) were in the form of G.T heteroduplexes, suggesting misrepair at A-specific depurination sites. Since G-specific mutations were infrequent in the spectra, it appears that the slow rate of depurination of the N7Gua adducts during active repair may not generate a threshold level of G-specific abasic sites to affect repair fidelity. These results also suggest that E(2)-3,4-Q, a suspected endogenous carcinogen, is a genotoxic compound and could cause mutations.

  8. PSO4: a novel gene involved in error-prone repair in Saccharomyces cerevisiae.

    PubMed

    Henriques, J A; Vicente, E J; Leandro da Silva, K V; Schenberg, A C

    1989-09-01

    The haploid xs9 mutant, originally selected for on the basis of a slight sensitivity to the lethal effect of X-rays, was found to be extremely sensitive to inactivation by 8-methoxypsoralen (8MOP) photoaddition, especially when cells are treated in the G2 phase of the cell cycle. As the xs9 mutation showed no allelism with any of the 3 known pso mutations, it was now given the name of pso4-1. Regarding inactivation, the pso4-1 mutant is also sensitive to mono- (HN1) or bi-functional (HN2) nitrogen mustards, it is slightly sensitive to 254 nm UV radiation (UV), and shows nearly normal sensitivity to 3-carbethoxypsoralen (3-CPs) photoaddition or methyl methanesulfonate (MMS). Regarding mutagenesis, the pso4-1 mutation completely blocks reverse and forward mutations induced by either 8MOP or 3CPs photoaddition, or by gamma-rays. In the cases of UV, HN1, HN2 or MMS treatments, while reversion induction is still completely abolished, forward mutagenesis is only partially inhibited for UV, HN1, or MMS, and it is unaffected for HN2. Besides severely inhibiting induced mutagenesis, the pso4-1 mutation was found to be semi-dominant, to block sporulation, to abolish the diploid resistance effect, and to block induced mitotic recombination, which indicates that the PSO4 gene is involved in a recombinational pathway of error-prone repair, comparable to the E. coli SOS repair pathway.

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

    ERIC Educational Resources Information Center

    Saavedra, Pedro; Kuchak, JoAnn

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

  10. Effects of Shame and Guilt on Error Reporting Among Obstetric Clinicians.

    PubMed

    Zabari, Mara Lynne; Southern, Nancy L

    2018-04-17

    To understand how the experiences of shame and guilt, coupled with organizational factors, affect error reporting by obstetric clinicians. Descriptive cross-sectional. A sample of 84 obstetric clinicians from three maternity units in Washington State. In this quantitative inquiry, a variant of the Test of Self-Conscious Affect was used to measure proneness to guilt and shame. In addition, we developed questions to assess attitudes regarding concerns about damaging one's reputation if an error was reported and the choice to keep an error to oneself. Both assessments were analyzed separately and then correlated to identify relationships between constructs. Interviews were used to identify organizational factors that affect error reporting. As a group, mean scores indicated that obstetric clinicians would not choose to keep errors to themselves. However, bivariate correlations showed that proneness to shame was positively correlated to concerns about one's reputation if an error was reported, and proneness to guilt was negatively correlated with keeping errors to oneself. Interview data analysis showed that Past Experience with Responses to Errors, Management and Leadership Styles, Professional Hierarchy, and Relationships With Colleagues were influential factors in error reporting. Although obstetric clinicians want to report errors, their decisions to report are influenced by their proneness to guilt and shame and perceptions of the degree to which organizational factors facilitate or create barriers to restore their self-images. Findings underscore the influence of the organizational context on clinicians' decisions to report errors. Copyright © 2018 AWHONN, the Association of Women’s Health, Obstetric and Neonatal Nurses. Published by Elsevier Inc. All rights reserved.

  11. Overcoming the errors of in-house PCR used in the clinical laboratory for the diagnosis of extrapulmonary tuberculosis.

    PubMed

    Kunakorn, M; Raksakai, K; Pracharktam, R; Sattaudom, C

    1999-03-01

    Our experiences from 1993 to 1997 in the development and use of IS6110 base PCR for the diagnosis of extrapulmonary tuberculosis in a routine clinical setting revealed that error-correcting processes can improve existing diagnostic methodology. The reamplification method initially used had a sensitivity of 90.91% and a specificity of 93.75%. The concern was focused on the false positive results of this method caused by product-carryover contamination. This method was changed to single round PCR with carryover prevention by uracil DNA glycosylase (UDG), resulting in a 100% specificity but only 63% sensitivity. Dot blot hybridization was added after the single round PCR, increasing the sensitivity to 87.50%. However, false positivity resulted from the nonspecific dot blot hybridization signal, reducing the specificity to 89.47%. The hybridization of PCR was changed to a Southern blot with a new oligonucleotide probe giving the sensitivity of 85.71% and raising the specificity to 99.52%. We conclude that the PCR protocol for routine clinical use should include UDG for carryover prevention and hybridization with specific probes to optimize diagnostic sensitivity and specificity in extrapulmonary tuberculosis testing.

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

    PubMed

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

    2013-01-01

    The purpose of this study was to compare isometric strength of elbow extensors measured in supine- and prone-lying positions at elbow flexion angles of 45 and 90 degrees. Twenty-two male subjects under single-blind procedures participated in the study. Each subject participated in both supine-lying and prone-lying measuring protocols. Calibrated cable tensiometer was used to measure isometric strength of the right elbow extensors and a biofeedback electromyography was used to assure no substitution movements from shoulder girdle muscles. The mean values of isometric strength of elbow extensors measured from supine-lying position at elbow flexion angles of 45 and 90 degrees were 11.1  ±  4.2 kg and 13.1  ±  4.6 kg, while those measured from prone-lying position were 9.9  ±  3.6 kg and 12  ±  4.2 kg, respectively. There is statistical significant difference between the isometric strength of elbow extensors measured from supine-lying position at elbow flexion angles of 45 and 90 degrees compared to that measured from prone-lying position (p  <  0.05). The results suggest that in manual muscle testing starting position can affect the isometric strength of elbow extensors since supine-lying starting position is better than prone-lying starting position.

  13. Belief-bias reasoning in non-clinical delusion-prone individuals.

    PubMed

    Anandakumar, T; Connaughton, E; Coltheart, M; Langdon, R

    2017-03-01

    It has been proposed that people with delusions have difficulty inhibiting beliefs (i.e., "doxastic inhibition") so as to reason about them as if they might not be true. We used a continuity approach to test this proposal in non-clinical adults scoring high and low in psychometrically assessed delusion-proneness. High delusion-prone individuals were expected to show greater difficulty than low delusion-prone individuals on "conflict" items of a "belief-bias" reasoning task (i.e. when required to reason logically about statements that conflicted with reality), but not on "non-conflict" items. Twenty high delusion-prone and twenty low delusion-prone participants (according to the Peters et al. Delusions Inventory) completed a belief-bias reasoning task and tests of IQ, working memory and general inhibition (Excluded Letter Fluency, Stroop and Hayling Sentence Completion). High delusion-prone individuals showed greater difficulty than low delusion-prone individuals on the Stroop and Excluded Letter Fluency tests of inhibition, but no greater difficulty on the conflict versus non-conflict items of the belief-bias task. They did, however, make significantly more errors overall on the belief-bias task, despite controlling for IQ, working memory and general inhibitory control. The study had a relatively small sample size and used non-clinical participants to test a theory of cognitive processing in individuals with clinically diagnosed delusions. Results failed to support a role for doxastic inhibitory failure in non-clinical delusion-prone individuals. These individuals did, however, show difficulty with conditional reasoning about statements that may or may not conflict with reality, independent of any general cognitive or inhibitory deficits. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Belief-bias reasoning in non-clinical delusion-prone individuals.

    PubMed

    Anandakumar, T; Connaughton, E; Coltheart, M; Langdon, R

    2017-09-01

    It has been proposed that people with delusions have difficulty inhibiting beliefs (i.e., "doxastic inhibition") so as to reason about them as if they might not be true. We used a continuity approach to test this proposal in non-clinical adults scoring high and low in psychometrically assessed delusion-proneness. High delusion-prone individuals were expected to show greater difficulty than low delusion-prone individuals on "conflict" items of a "belief-bias" reasoning task (i.e. when required to reason logically about statements that conflicted with reality), but not on "non-conflict" items. Twenty high delusion-prone and twenty low delusion-prone participants (according to the Peters et al. Delusions Inventory) completed a belief-bias reasoning task and tests of IQ, working memory and general inhibition (Excluded Letter Fluency, Stroop and Hayling Sentence Completion). High delusion-prone individuals showed greater difficulty than low delusion-prone individuals on the Stroop and Excluded Letter Fluency tests of inhibition, but no greater difficulty on the conflict versus non-conflict items of the belief-bias task. They did, however, make significantly more errors overall on the belief-bias task, despite controlling for IQ, working memory and general inhibitory control. The study had a relatively small sample size and used non-clinical participants to test a theory of cognitive processing in individuals with clinically diagnosed delusions. Results failed to support a role for doxastic inhibitory failure in non-clinical delusion-prone individuals. These individuals did, however, show difficulty with conditional reasoning about statements that may or may not conflict with reality, independent of any general cognitive or inhibitory deficits. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

    PubMed

    Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan

    2016-01-01

    Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.

  16. Associations of hallucination proneness with free-recall intrusions and response bias in a nonclinical sample.

    PubMed

    Brébion, Gildas; Larøi, Frank; Van der Linden, Martial

    2010-10-01

    Hallucinations in patients with schizophrenia have been associated with a liberal response bias in signal detection and recognition tasks and with various types of source-memory error. We investigated the associations of hallucination proneness with free-recall intrusions and false recognitions of words in a nonclinical sample. A total of 81 healthy individuals were administered a verbal memory task involving free recall and recognition of one nonorganizable and one semantically organizable list of words. Hallucination proneness was assessed by means of a self-rating scale. Global hallucination proneness was associated with free-recall intrusions in the nonorganizable list and with a response bias reflecting tendency to make false recognitions of nontarget words in both types of list. The verbal hallucination score was associated with more intrusions and with a reduced tendency to make false recognitions of words. The associations between global hallucination proneness and two types of verbal memory error in a nonclinical sample corroborate those observed in patients with schizophrenia and suggest that common cognitive mechanisms underlie hallucinations in psychiatric and nonclinical individuals.

  17. A continuous quality improvement project to reduce medication error in the emergency department.

    PubMed

    Lee, Sara Bc; Lee, Larry Ly; Yeung, Richard Sd; Chan, Jimmy Ts

    2013-01-01

    Medication errors are a common source of adverse healthcare incidents particularly in the emergency department (ED) that has a number of factors that make it prone to medication errors. This project aims to reduce medication errors and improve the health and economic outcomes of clinical care in Hong Kong ED. In 2009, a task group was formed to identify problems that potentially endanger medication safety and developed strategies to eliminate these problems. Responsible officers were assigned to look after seven error-prone areas. Strategies were proposed, discussed, endorsed and promulgated to eliminate the problems identified. A reduction of medication incidents (MI) from 16 to 6 was achieved before and after the improvement work. This project successfully established a concrete organizational structure to safeguard error-prone areas of medication safety in a sustainable manner.

  18. WISC-R Examiner Errors: Cause for Concern.

    ERIC Educational Resources Information Center

    Slate, John R.; Chick, David

    1989-01-01

    Clinical psychology graduate students (N=14) administered Wechsler Intelligence Scale for Children-Revised. Found numerous scoring and mechanical errors that influenced full-scale intelligence quotient scores on two-thirds of protocols. Particularly prone to error were Verbal subtests of Vocabulary, Comprehension, and Similarities. Noted specific…

  19. Antigenic Variation in the Lyme Spirochete: Insights into Recombinational Switching with a Suggested Role for Error-Prone Repair.

    PubMed

    Verhey, Theodore B; Castellanos, Mildred; Chaconas, George

    2018-05-29

    The Lyme disease spirochete, Borrelia burgdorferi, uses antigenic variation as a strategy to evade the host's acquired immune response. New variants of surface-localized VlsE are generated efficiently by unidirectional recombination from 15 unexpressed vls cassettes into the vlsE locus. Using algorithms to analyze switching from vlsE sequencing data, we characterize a population of over 45,000 inferred recombination events generated during mouse infection. We present evidence for clustering of these recombination events within the population and along the vlsE gene, a role for the direct repeats flanking the variable region in vlsE, and the importance of sequence homology in determining the location of recombination, despite RecA's dispensability. Finally, we report that non-templated sequence variation is strongly associated with recombinational switching and occurs predominantly at the 5' end of conversion tracts. This likely results from an error-prone repair mechanism operational during recombinational switching that elevates the mutation rate > 5,000-fold in switched regions. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  20. Threat engagement, disengagement, and sensitivity bias in worry-prone individuals as measured by an emotional go/no-go task.

    PubMed

    Gole, Markus; Köchel, Angelika; Schäfer, Axel; Schienle, Anne

    2012-03-01

    The goal of the present study was to investigate a threat engagement, disengagement, and sensitivity bias in individuals suffering from pathological worry. Twenty participants high in worry proneness and 16 control participants low in worry proneness completed an emotional go/no-go task with worry-related threat words and neutral words. Shorter reaction times (i.e., threat engagement bias), smaller omission error rates (i.e., threat sensitivity bias), and larger commission error rates (i.e., threat disengagement bias) emerged only in the high worry group when worry-related words constituted the go-stimuli and neutral words the no-go stimuli. Also, smaller omission error rates as well as larger commission error rates were observed in the high worry group relative to the low worry group when worry-related go stimuli and neutral no-go stimuli were used. The obtained results await further replication within a generalized anxiety disorder sample. Also, further samples should include men as well. Our data suggest that worry-prone individuals are threat-sensitive, engage more rapidly with aversion, and disengage harder. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang Shijun; Yao Jianhua; Liu Jiamin

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

  2. An optimized one-tube, semi-nested PCR assay for Paracoccidioides brasiliensis detection.

    PubMed

    Pitz, Amanda de Faveri; Koishi, Andrea Cristine; Tavares, Eliandro Reis; Andrade, Fábio Goulart de; Loth, Eduardo Alexandre; Gandra, Rinaldo Ferreira; Venancio, Emerson José

    2013-01-01

    Herein, we report a one-tube, semi-nested-polymerase chain reaction (OTsn-PCR) assay for the detection of Paracoccidioides brasiliensis. We developed the OTsn-PCR assay for the detection of P. brasiliensis in clinical specimens and compared it with other PCR methods. The OTsn-PCR assay was positive for all clinical samples, and the detection limit was better or equivalent to the other nested or semi-nested PCR methods for P. brasiliensis detection. The OTsn-PCR assay described in this paper has a detection limit similar to other reactions for the molecular detection of P. brasiliensis, but this approach is faster and less prone to contamination than other conventional nested or semi-nested PCR assays.

  3. The PSO4 gene is responsible for an error-prone recombinational DNA repair pathway in Saccharomyces cerevisiae.

    PubMed

    de Andrade, H H; Marques, E K; Schenberg, A C; Henriques, J A

    1989-06-01

    The induction of mitotic gene conversion and crossing-over in Saccharomyces cerevisiae diploid cells homozygous for the pso4-1 mutation was examined in comparison to the corresponding wild-type strain. The pso4-1 mutant strain was found to be completely blocked in mitotic recombination induced by photoaddition of mono- and bifunctional psoralen derivatives as well as by mono- (HN1) and bifunctional (HN2) nitrogen mustards or 254 nm UV radiation in both stationary and exponential phases of growth. Concerning the lethal effect, diploids homozygous for the pso4-1 mutation are more sensitive to all agents tested in any growth phase. However, this effect is more pronounced in the G2 phase of the cell cycle. These results imply that the ploidy effect and the resistance of budding cells are under the control of the PSO4 gene. On the other hand, the pso4-1 mutant is mutationally defective for all agents used. Therefore, the pso4-1 mutant has a generalized block in both recombination and mutation ability. This indicates that the PSO4 gene is involved in an error-prone repair pathway which relies on a recombinational mechanism, strongly suggesting an analogy between the pso4-1 mutation and the RecA or LexA mutation of Escherichia coli.

  4. Simultaneous treatment of unspecified heteroskedastic model error distribution and mismeasured covariates for restricted moment models.

    PubMed

    Garcia, Tanya P; Ma, Yanyuan

    2017-10-01

    We develop consistent and efficient estimation of parameters in general regression models with mismeasured covariates. We assume the model error and covariate distributions are unspecified, and the measurement error distribution is a general parametric distribution with unknown variance-covariance. We construct root- n consistent, asymptotically normal and locally efficient estimators using the semiparametric efficient score. We do not estimate any unknown distribution or model error heteroskedasticity. Instead, we form the estimator under possibly incorrect working distribution models for the model error, error-prone covariate, or both. Empirical results demonstrate robustness to different incorrect working models in homoscedastic and heteroskedastic models with error-prone covariates.

  5. Operationalizing Proneness to Externalizing Psychopathology as a Multivariate Psychophysiological Phenotype

    PubMed Central

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

    2010-01-01

    The externalizing dimension is viewed as a broad dispositional factor underlying risk for numerous disinhibitory disorders. Prior work has documented deficits in event-related brain potential (ERP) responses in individuals prone to externalizing problems. Here, we constructed a direct physiological index of externalizing vulnerability from three ERP indicators and evaluated its validity in relation to criterion measures in two distinct domains: psychometric and physiological. The index was derived from three ERP measures that covaried in their relations with externalizing proneness the error-related negativity and two variants of the P3. Scores on this ERP composite predicted psychometric criterion variables and accounted for externalizing-related variance in P3 response from a separate task. These findings illustrate how a diagnostic construct can be operationalized as a composite (multivariate) psychophysiological variable (phenotype). PMID:20573054

  6. Comparing errors in ED computer-assisted vs conventional pediatric drug dosing and administration.

    PubMed

    Yamamoto, Loren; Kanemori, Joan

    2010-06-01

    Compared to fixed-dose single-vial drug administration in adults, pediatric drug dosing and administration requires a series of calculations, all of which are potentially error prone. The purpose of this study is to compare error rates and task completion times for common pediatric medication scenarios using computer program assistance vs conventional methods. Two versions of a 4-part paper-based test were developed. Each part consisted of a set of medication administration and/or dosing tasks. Emergency department and pediatric intensive care unit nurse volunteers completed these tasks using both methods (sequence assigned to start with a conventional or a computer-assisted approach). Completion times, errors, and the reason for the error were recorded. Thirty-eight nurses completed the study. Summing the completion of all 4 parts, the mean conventional total time was 1243 seconds vs the mean computer program total time of 879 seconds (P < .001). The conventional manual method had a mean of 1.8 errors vs the computer program with a mean of 0.7 errors (P < .001). Of the 97 total errors, 36 were due to misreading the drug concentration on the label, 34 were due to calculation errors, and 8 were due to misplaced decimals. Of the 36 label interpretation errors, 18 (50%) occurred with digoxin or insulin. Computerized assistance reduced errors and the time required for drug administration calculations. A pattern of errors emerged, noting that reading/interpreting certain drug labels were more error prone. Optimizing the layout of drug labels could reduce the error rate for error-prone labels. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  7. Proximal antecedents and correlates of adopted error approach: a self-regulatory perspective.

    PubMed

    Van Dyck, Cathy; Van Hooft, Edwin; De Gilder, Dick; Liesveld, Lillian

    2010-01-01

    The current study aims to further investigate earlier established advantages of an error mastery approach over an error aversion approach. The two main purposes of the study relate to (1) self-regulatory traits (i.e., goal orientation and action-state orientation) that may predict which error approach (mastery or aversion) is adopted, and (2) proximal, psychological processes (i.e., self-focused attention and failure attribution) that relate to adopted error approach. In the current study participants' goal orientation and action-state orientation were assessed, after which they worked on an error-prone task. Results show that learning goal orientation related to error mastery, while state orientation related to error aversion. Under a mastery approach, error occurrence did not result in cognitive resources "wasted" on self-consciousness. Rather, attention went to internal-unstable, thus controllable, improvement oriented causes of error. Participants that had adopted an aversion approach, in contrast, experienced heightened self-consciousness and attributed failure to internal-stable or external causes. These results imply that when working on an error-prone task, people should be stimulated to take on a mastery rather than an aversion approach towards errors.

  8. [A new method of processing quantitative PCR data].

    PubMed

    Ke, Bing-Shen; Li, Guang-Yun; Chen, Shi-Min; Huang, Xiang-Yan; Chen, Ying-Jian; Xu, Jun

    2003-05-01

    Today standard PCR can't satisfy the need of biotechnique development and clinical research any more. After numerous dynamic research, PE company found there is a linear relation between initial template number and cycling time when the accumulating fluorescent product is detectable.Therefore,they developed a quantitative PCR technique to be used in PE7700 and PE5700. But the error of this technique is too great to satisfy the need of biotechnique development and clinical research. A better quantitative PCR technique is needed. The mathematical model submitted here is combined with the achievement of relative science,and based on the PCR principle and careful analysis of molecular relationship of main members in PCR reaction system. This model describes the function relation between product quantity or fluorescence intensity and initial template number and other reaction conditions, and can reflect the accumulating rule of PCR product molecule accurately. Accurate quantitative PCR analysis can be made use this function relation. Accumulated PCR product quantity can be obtained from initial template number. Using this model to do quantitative PCR analysis,result error is only related to the accuracy of fluorescence intensity or the instrument used. For an example, when the fluorescence intensity is accurate to 6 digits and the template size is between 100 to 1,000,000, the quantitative result accuracy will be more than 99%. The difference of result error is distinct using same condition,same instrument but different analysis method. Moreover,if the PCR quantitative analysis system is used to process data, it will get result 80 times of accuracy than using CT method.

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

    DOE PAGES

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

    2014-01-01

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

  10. Reduced vision selectively impairs spatial updating in fall-prone older adults.

    PubMed

    Barrett, Maeve M; Doheny, Emer P; Setti, Annalisa; Maguinness, Corrina; Foran, Timothy G; Kenny, Rose Anne; Newell, Fiona N

    2013-01-01

    The current study examined the role of vision in spatial updating and its potential contribution to an increased risk of falls in older adults. Spatial updating was assessed using a path integration task in fall-prone and healthy older adults. Specifically, participants conducted a triangle completion task in which they were guided along two sides of a triangular route and were then required to return, unguided, to the starting point. During the task, participants could either clearly view their surroundings (full vision) or visuo-spatial information was reduced by means of translucent goggles (reduced vision). Path integration performance was measured by calculating the distance and angular deviation from the participant's return point relative to the starting point. Gait parameters for the unguided walk were also recorded. We found equivalent performance across groups on all measures in the full vision condition. In contrast, in the reduced vision condition, where participants had to rely on interoceptive cues to spatially update their position, fall-prone older adults made significantly larger distance errors relative to healthy older adults. However, there were no other performance differences between fall-prone and healthy older adults. These findings suggest that fall-prone older adults, compared to healthy older adults, have greater difficulty in reweighting other sensory cues for spatial updating when visual information is unreliable.

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

    PubMed Central

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

    2009-01-01

    Purpose: In computed tomographic colonography (CTC), a patient will be scanned twice—Once supine and once prone—to improve the sensitivity for polyp detection. To assist radiologists in CTC reading, in this paper we propose an automated method for colon registration from supine and prone CTC scans. Methods: We propose a new colon centerline registration method for prone and supine CTC scans using correlation optimized warping (COW) and canonical correlation analysis (CCA) based on the anatomical structure of the colon. Four anatomical salient points on the colon are first automatically distinguished. Then correlation optimized warping is applied to the segments defined by the anatomical landmarks to improve the global registration based on local correlation of segments. The COW method was modified by embedding canonical correlation analysis to allow multiple features along the colon centerline to be used in our implementation. Results: We tested the COW algorithm on a CTC data set of 39 patients with 39 polyps (19 training and 20 test cases) to verify the effectiveness of the proposed COW registration method. Experimental results on the test set show that the COW method significantly reduces the average estimation error in a polyp location between supine and prone scans by 67.6%, from 46.27±52.97 to 14.98 mm±11.41 mm, compared to the normalized distance along the colon centerline algorithm (p<0.01). Conclusions: The proposed COW algorithm is more accurate for the colon centerline registration compared to the normalized distance along the colon centerline method and the dynamic time warping method. Comparison results showed that the feature combination of z-coordinate and curvature achieved lowest registration error compared to the other feature combinations used by COW. The proposed method is tolerant to centerline errors because anatomical landmarks help prevent the propagation of errors across the entire colon centerline. PMID:20095272

  12. Single-Cell RT-PCR in Microfluidic Droplets with Integrated Chemical Lysis.

    PubMed

    Kim, Samuel C; Clark, Iain C; Shahi, Payam; Abate, Adam R

    2018-01-16

    Droplet microfluidics can identify and sort cells using digital reverse transcription polymerase chain reaction (RT-PCR) signals from individual cells. However, current methods require multiple microfabricated devices for enzymatic cell lysis and PCR reagent addition, making the process complex and prone to failure. Here, we describe a new approach that integrates all components into a single device. The method enables controlled exposure of isolated single cells to a high pH buffer, which lyses cells and inactivates reaction inhibitors but can be instantly neutralized with RT-PCR buffer. Using our chemical lysis approach, we distinguish individual cells' gene expression with data quality equivalent to more complex two-step workflows. Our system accepts cells and produces droplets ready for amplification, making single-cell droplet RT-PCR faster and more reliable.

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

    PubMed

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

    2013-01-01

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

  14. Treatment of ARDS With Prone Positioning.

    PubMed

    Scholten, Eric L; Beitler, Jeremy R; Prisk, G Kim; Malhotra, Atul

    2017-01-01

    Prone positioning was first proposed in the 1970s as a method to improve gas exchange in ARDS. Subsequent observations of dramatic improvement in oxygenation with simple patient rotation motivated the next several decades of research. This work elucidated the physiological mechanisms underlying changes in gas exchange and respiratory mechanics with prone ventilation. However, translating physiological improvements into a clinical benefit has proved challenging; several contemporary trials showed no major clinical benefits with prone positioning. By optimizing patient selection and treatment protocols, the recent Proning Severe ARDS Patients (PROSEVA) trial demonstrated a significant mortality benefit with prone ventilation. This trial, and subsequent meta-analyses, support the role of prone positioning as an effective therapy to reduce mortality in severe ARDS, particularly when applied early with other lung-protective strategies. This review discusses the physiological principles, clinical evidence, and practical application of prone ventilation in ARDS. Copyright © 2016 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

  15. Design and optimization of reverse-transcription quantitative PCR experiments.

    PubMed

    Tichopad, Ales; Kitchen, Rob; Riedmaier, Irmgard; Becker, Christiane; Ståhlberg, Anders; Kubista, Mikael

    2009-10-01

    Quantitative PCR (qPCR) is a valuable technique for accurately and reliably profiling and quantifying gene expression. Typically, samples obtained from the organism of study have to be processed via several preparative steps before qPCR. We estimated the errors of sample withdrawal and extraction, reverse transcription (RT), and qPCR that are introduced into measurements of mRNA concentrations. We performed hierarchically arranged experiments with 3 animals, 3 samples, 3 RT reactions, and 3 qPCRs and quantified the expression of several genes in solid tissue, blood, cell culture, and single cells. A nested ANOVA design was used to model the experiments, and relative and absolute errors were calculated with this model for each processing level in the hierarchical design. We found that intersubject differences became easily confounded by sample heterogeneity for single cells and solid tissue. In cell cultures and blood, the noise from the RT and qPCR steps contributed substantially to the overall error because the sampling noise was less pronounced. We recommend the use of sample replicates preferentially to any other replicates when working with solid tissue, cell cultures, and single cells, and we recommend the use of RT replicates when working with blood. We show how an optimal sampling plan can be calculated for a limited budget. .

  16. Skull registration for prone patient position using tracked ultrasound

    NASA Astrophysics Data System (ADS)

    Underwood, Grace; Ungi, Tamas; Baum, Zachary; Lasso, Andras; Kronreif, Gernot; Fichtinger, Gabor

    2017-03-01

    PURPOSE: Tracked navigation has become prevalent in neurosurgery. Problems with registration of a patient and a preoperative image arise when the patient is in a prone position. Surfaces accessible to optical tracking on the back of the head are unreliable for registration. We investigated the accuracy of surface-based registration using points accessible through tracked ultrasound. Using ultrasound allows access to bone surfaces that are not available through optical tracking. Tracked ultrasound could eliminate the need to work (i) under the table for registration and (ii) adjust the tracker between surgery and registration. In addition, tracked ultrasound could provide a non-invasive method in comparison to an alternative method of registration involving screw implantation. METHODS: A phantom study was performed to test the feasibility of tracked ultrasound for registration. An initial registration was performed to partially align the pre-operative computer tomography data and skull phantom. The initial registration was performed by an anatomical landmark registration. Surface points accessible by tracked ultrasound were collected and used to perform an Iterative Closest Point Algorithm. RESULTS: When the surface registration was compared to a ground truth landmark registration, the average TRE was found to be 1.6+/-0.1mm and the average distance of points off the skull surface was 0.6+/-0.1mm. CONCLUSION: The use of tracked ultrasound is feasible for registration of patients in prone position and eliminates the need to perform registration under the table. The translational component of error found was minimal. Therefore, the amount of TRE in registration is due to a rotational component of error.

  17. Multiple point mutations in a shuttle vector propagated in human cells: evidence for an error-prone DNA polymerase activity.

    PubMed

    Seidman, M M; Bredberg, A; Seetharam, S; Kraemer, K H

    1987-07-01

    Mutagenesis was studied at the DNA-sequence level in human fibroblast and lymphoid cells by use of a shuttle vector plasmid, pZ189, containing a suppressor tRNA marker gene. In a series of experiments, 62 plasmids were recovered that had two to six base substitutions in the 160-base-pair marker gene. Approximately 20-30% of the mutant plasmids that were recovered after passing ultraviolet-treated pZ189 through a repair-proficient human fibroblast line contained these multiple mutations. In contrast, passage of ultraviolet-treated pZ189 through an excision-repair-deficient (xeroderma pigmentosum) line yielded only 2% multiple base substitution mutants. Introducing a single-strand nick in otherwise unmodified pZ189 adjacent to the marker, followed by passage through the xeroderma pigmentosum cells, resulted in about 66% multiple base substitution mutants. The multiple mutations were found in a 160-base-pair region containing the marker gene but were rarely found in an adjacent 170-base-pair region. Passing ultraviolet-treated or nicked pZ189 through a repair-proficient human B-cell line also yielded multiple base substitution mutations in 20-33% of the mutant plasmids. An explanation for these multiple mutations is that they were generated by an error-prone polymerase while filling gaps. These mutations share many of the properties displayed by mutations in the immunoglobulin hypervariable regions.

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

    PubMed

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

    2015-06-07

    Difficulties with the ability to appreciate the perspective of others (mentalizing) is central to both autism and schizophrenia spectrum disorders. While the disorders are diagnostically independent, they can co-occur in the same individual. The effect of such co-morbidity is hypothesized to worsen mentalizing abilities. The recent influential 'diametric brain theory', however, suggests that the disorders are etiologically and phenotypically diametrical, predicting opposing effects on one's mentalizing abilities. To test these contrasting hypotheses, we evaluated the effect of psychosis and autism tendencies on the perspective-taking (PT) abilities of 201 neurotypical adults, on the assumption that autism tendencies and psychosis proneness are heritable dimensions of normal variation. We show that while both autism tendencies and psychosis proneness induce PT errors, their interaction reduced these errors. Our study is, to our knowledge, the first to observe that co-occurring autistic and psychotic traits can exert opposing influences on performance, producing a normalizing effect possibly by way of their diametrical effects on socio-cognitive abilities. This advances the notion that some individuals may, to some extent, be buffered against developing either illness or present fewer symptoms owing to a balanced expression of autistic and psychosis liability. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  19. Errors of Inference in Structural Equation Modeling

    ERIC Educational Resources Information Center

    McCoach, D. Betsy; Black, Anne C.; O'Connell, Ann A.

    2007-01-01

    Although structural equation modeling (SEM) is one of the most comprehensive and flexible approaches to data analysis currently available, it is nonetheless prone to researcher misuse and misconceptions. This article offers a brief overview of the unique capabilities of SEM and discusses common sources of user error in drawing conclusions from…

  20. Anticipating cognitive effort: roles of perceived error-likelihood and time demands.

    PubMed

    Dunn, Timothy L; Inzlicht, Michael; Risko, Evan F

    2017-11-13

    Why are some actions evaluated as effortful? In the present set of experiments we address this question by examining individuals' perception of effort when faced with a trade-off between two putative cognitive costs: how much time a task takes vs. how error-prone it is. Specifically, we were interested in whether individuals anticipate engaging in a small amount of hard work (i.e., low time requirement, but high error-likelihood) vs. a large amount of easy work (i.e., high time requirement, but low error-likelihood) as being more effortful. In between-subject designs, Experiments 1 through 3 demonstrated that individuals anticipate options that are high in perceived error-likelihood (yet less time consuming) as more effortful than options that are perceived to be more time consuming (yet low in error-likelihood). Further, when asked to evaluate which of the two tasks was (a) more effortful, (b) more error-prone, and (c) more time consuming, effort-based and error-based choices closely tracked one another, but this was not the case for time-based choices. Utilizing a within-subject design, Experiment 4 demonstrated overall similar pattern of judgments as Experiments 1 through 3. However, both judgments of error-likelihood and time demand similarly predicted effort judgments. Results are discussed within the context of extant accounts of cognitive control, with considerations of how error-likelihood and time demands may independently and conjunctively factor into judgments of cognitive effort.

  1. Empirical evaluation of humpback whale telomere length estimates; quality control and factors causing variability in the singleplex and multiplex qPCR methods.

    PubMed

    Olsen, Morten Tange; Bérubé, Martine; Robbins, Jooke; Palsbøll, Per J

    2012-09-06

    Telomeres, the protective cap of chromosomes, have emerged as powerful markers of biological age and life history in model and non-model species. The qPCR method for telomere length estimation is one of the most common methods for telomere length estimation, but has received recent critique for being too error-prone and yielding unreliable results. This critique coincides with an increasing awareness of the potentials and limitations of the qPCR technique in general and the proposal of a general set of guidelines (MIQE) for standardization of experimental, analytical, and reporting steps of qPCR. In order to evaluate the utility of the qPCR method for telomere length estimation in non-model species, we carried out four different qPCR assays directed at humpback whale telomeres, and subsequently performed a rigorous quality control to evaluate the performance of each assay. Performance differed substantially among assays and only one assay was found useful for telomere length estimation in humpback whales. The most notable factors causing these inter-assay differences were primer design and choice of using singleplex or multiplex assays. Inferred amplification efficiencies differed by up to 40% depending on assay and quantification method, however this variation only affected telomere length estimates in the worst performing assays. Our results suggest that seemingly well performing qPCR assays may contain biases that will only be detected by extensive quality control. Moreover, we show that the qPCR method for telomere length estimation can be highly precise and accurate, and thus suitable for telomere measurement in non-model species, if effort is devoted to optimization at all experimental and analytical steps. We conclude by highlighting a set of quality controls which may serve for further standardization of the qPCR method for telomere length estimation, and discuss some of the factors that may cause variation in qPCR experiments.

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

    PubMed Central

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

    2010-01-01

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

  3. The Prone Protected Posture

    DTIC Science & Technology

    1980-08-01

    5K 2. METHODOLOGY . . . . . . . . . . . . . . . . . . . . 5 3. RESULTS . . . . . . . . . . . . . . . . . . . . . . 23I 4...2. METHODOLOGY The first step required in this study was to characterize the prone protected posture. Basically, a man in the prone posture differs...reduction in the presented area of target personnel. Reference 6 contains a concise discussion of the methodology used to generate the shielding functions

  4. Quantitative Real-Time PCR using the Thermo Scientific Solaris qPCR Assay

    PubMed Central

    Ogrean, Christy; Jackson, Ben; Covino, James

    2010-01-01

    The Solaris qPCR Gene Expression Assay is a novel type of primer/probe set, designed to simplify the qPCR process while maintaining the sensitivity and accuracy of the assay. These primer/probe sets are pre-designed to >98% of the human and mouse genomes and feature significant improvements from previously available technologies. These improvements were made possible by virtue of a novel design algorithm, developed by Thermo Scientific bioinformatics experts. Several convenient features have been incorporated into the Solaris qPCR Assay to streamline the process of performing quantitative real-time PCR. First, the protocol is similar to commonly employed alternatives, so the methods used during qPCR are likely to be familiar. Second, the master mix is blue, which makes setting the qPCR reactions easier to track. Third, the thermal cycling conditions are the same for all assays (genes), making it possible to run many samples at a time and reducing the potential for error. Finally, the probe and primer sequence information are provided, simplifying the publication process. Here, we demonstrate how to obtain the appropriate Solaris reagents using the GENEius product search feature found on the ordering web site (www.thermo.com/solaris) and how to use the Solaris reagents for performing qPCR using the standard curve method. PMID:20567213

  5. Dual processing and diagnostic errors.

    PubMed

    Norman, Geoff

    2009-09-01

    In this paper, I review evidence from two theories in psychology relevant to diagnosis and diagnostic errors. "Dual Process" theories of thinking, frequently mentioned with respect to diagnostic error, propose that categorization decisions can be made with either a fast, unconscious, contextual process called System 1 or a slow, analytical, conscious, and conceptual process, called System 2. Exemplar theories of categorization propose that many category decisions in everyday life are made by unconscious matching to a particular example in memory, and these remain available and retrievable individually. I then review studies of clinical reasoning based on these theories, and show that the two processes are equally effective; System 1, despite its reliance in idiosyncratic, individual experience, is no more prone to cognitive bias or diagnostic error than System 2. Further, I review evidence that instructions directed at encouraging the clinician to explicitly use both strategies can lead to consistent reduction in error rates.

  6. Estimation of a cover-type change matrix from error-prone data

    Treesearch

    Steen Magnussen

    2009-01-01

    Coregistration and classification errors seriously compromise per-pixel estimates of land cover change. A more robust estimation of change is proposed in which adjacent pixels are grouped into 3x3 clusters and treated as a unit of observation. A complete change matrix is recovered in a two-step process. The diagonal elements of a change matrix are recovered from...

  7. First order error corrections in common introductory physics experiments

    NASA Astrophysics Data System (ADS)

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

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

  8. Boredom proneness in a psychiatric inpatient population.

    PubMed

    Newell, Susan E; Harries, Priscilla; Ayers, Susan

    2012-09-01

    Boredom has been reported as a common experience for service users of acute psychiatric wards. It has been associated with negative mental and physical health. Research has yet to show what factors are associated with boredom proneness within the acute psychiatric population. (1) To investigate the distribution of boredom proneness in a population of mentally ill inpatients according to age, gender, diagnosis, Mental Health Act status and length of stay in hospital. (2) To test the hypothesis that boredom proneness is negatively correlated with autonomous activity levels. Two self-report questionnaires were used with 55 inpatients of acute psychiatric wards: the Boredom Proneness Scale (Farmer & Sundberg, 1986) and the Hospital Anxiety and Depression Scale (Zigmond & Snaith, 1983). Questions were also asked about individuals' activity engagement during their current admission. Data on age, gender, diagnosis, ethnicity, Mental Health Act status and length of stay were collected from case notes. The highest incidence of boredom proneness was in participants with depression. Those detained under the Mental Health Act appeared less boredom prone than those admitted voluntarily. Boredom proneness was not associated with age, gender or length of stay. There was an association between engagement in more autonomous activities and lower boredom proneness.

  9. Serum Antibody Response to Five Streptococcus pneumoniae Proteins during Acute Otitis Media in Otitis Prone and Non-Otitis Prone Children

    PubMed Central

    Kaur, Ravinder; Casey, Janet R.; Pichichero, Michael E.

    2011-01-01

    Background Streptococcus pneumoniae (Spn) is one of the common bacteria responsible for episodic acute otitis media (AOM; non-otitis prone), recurrent AOM (otitis-prone) and AOM treatment failure (AOMTF) in children. Objective From a population of 268 children we sought to compare the serum IgG antibody titers to five different Spn proteins (PhtD, LytB, PcpA, PhtE and Ply) that are vaccine candidates in children with episodic AOM (n=34), who were otitis prone (n=35), and who had AOMTF (n=25) caused by Spn. Methods Antibody was quantitated by ELISA. Results At their acute AOM visit, anti-PhtD, -LytB, -PhtE and −Ply IgG antibody titers in otitis-prone children were significantly lower compared to non-otitis prone children (p <0.05) and children with AOMTF (p <0.05). Comparing acute to convalescent titers of antibody after AOM we found that otitis-prone, AOMTF and non-otitis prone children had no significant change in geometric mean IgG antibody titers against the five proteins (except for PhtE in children with AOMTF), but detailed analysis showed that about one-third of the children in each cohort had a 2-fold rise in antibody to the studied antigens. While non-otitis prone children had significant increases (p <0.001) between 6 and 24 months of age in anti-PhtD, PcpA, PhtE and Ply IgG antibody titers as a consequence of nasopharyngeal colonization and AOM, otitis-prone children either failed to show rises or the rises were significantly less than the non-otitis prone children. Conclusion Otitis-prone and AOMTF children mount less of an IgG serum antibody response than non-otitis prone children to Spn proteins following AOM and nasopharyngeal colonization. PMID:21487325

  10. Improving qPCR telomere length assays: Controlling for well position effects increases statistical power.

    PubMed

    Eisenberg, Dan T A; Kuzawa, Christopher W; Hayes, M Geoffrey

    2015-01-01

    Telomere length (TL) is commonly measured using quantitative PCR (qPCR). Although, easier than the southern blot of terminal restriction fragments (TRF) TL measurement method, one drawback of qPCR is that it introduces greater measurement error and thus reduces the statistical power of analyses. To address a potential source of measurement error, we consider the effect of well position on qPCR TL measurements. qPCR TL data from 3,638 people run on a Bio-Rad iCycler iQ are reanalyzed here. To evaluate measurement validity, correspondence with TRF, age, and between mother and offspring are examined. First, we present evidence for systematic variation in qPCR TL measurements in relation to thermocycler well position. Controlling for these well-position effects consistently improves measurement validity and yields estimated improvements in statistical power equivalent to increasing sample sizes by 16%. We additionally evaluated the linearity of the relationships between telomere and single copy gene control amplicons and between qPCR and TRF measures. We find that, unlike some previous reports, our data exhibit linear relationships. We introduce the standard error in percent, a superior method for quantifying measurement error as compared to the commonly used coefficient of variation. Using this measure, we find that excluding samples with high measurement error does not improve measurement validity in our study. Future studies using block-based thermocyclers should consider well position effects. Since additional information can be gleaned from well position corrections, rerunning analyses of previous results with well position correction could serve as an independent test of the validity of these results. © 2015 Wiley Periodicals, Inc.

  11. A comparative study of set up variations and bowel volumes in supine versus prone positions of patients treated with external beam radiation for carcinoma rectum.

    PubMed

    Rajeev, K R; Menon, Smrithy S; Beena, K; Holla, Raghavendra; Kumar, R Rajaneesh; Dinesh, M

    2014-01-01

    A prospective study was undertaken to evaluate the influence of patient positioning on the set up variations to determine the planning target volume (PTV) margins and to evaluate the clinical relevance volume assessment of the small bowel (SB) within the irradiated volume. During the period of months from December 2011 to April 2012, a computed tomography (CT) scan was done either in supine position or in prone position using a belly board (BB) for 20 consecutive patients. All the patients had histologically proven rectal cancer and received either post- or pre-operative pelvic irradiation. Using a three-dimensional planning system, the dose-volume histogram for SB was defined in each axial CT slice. Total dose was 46-50 Gy (2 Gy/fraction), delivered using the 4-field box technique. The set up variation of the study group was assessed from the data received from the electronic portal imaging device in the linear accelerator. The shift along X, Y, and Z directions were noted. Both systematic and random errors were calculated and using both these values the PTV margin was calculated. The systematic errors of patients treated in the supine position were 0.87 (X-mm), 0.66 (Y-mm), 1.6 (Z-mm) and in the prone position were 1.3 (X-mm), 0.59 (Y-mm), 1.17 (Z-mm). The random errors of patients treated in the supine positions were 1.81 (X-mm), 1.73 (Y-mm), 1.83 (Z-mm) and in prone position were 2.02 (X-mm), 1.21 (Y-mm), 3.05 (Z-mm). The calculated PTV margins in the supine position were 3.45 (X-mm), 2.87 (Y-mm), 5.31 (Z-mm) and in the prone position were 4.91 (X-mm), 2.32 (Y-mm), 5.08 (Z-mm). The mean volume of the peritoneal cavity was 648.65 cm 3 in the prone position and 1197.37 cm 3 in the supine position. The prone position using BB device was more effective in reducing irradiated SB volume in rectal cancer patients. There were no significant variations in the daily set up for patients treated in both supine and prone positions.

  12. Poster - 34: Clinical Implementation of Prone Breast Treatment

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jiang, Runqing; Fleming, Katrina; Kobeleva, Sofya

    2016-08-15

    Purpose: Prone breast treatment is used to reduce acute and late toxicities for large or pendulous breast patients. This study developed and implemented the clinical workflow of prone breast radiotherapy treatment. Methods: Varian kVue Access360™ Prone Breast Couchtop was used as prone breast board. The treatment planning (TP)is performed in Eclipse TP system. TP comparisons between supine deep inspiration breathing hold (DIBH) and prone breast; prone forward field-in-field (FinF) planning and inverse IMRT planning were performed and discussed. For the daily setup, breast coverage was assessed in the room using light field and MV imaging was used at day 1more » and weekly. Results: The first ten patients are CT scanned and planned both supine and prone. The coverage was all excellent for supine DIBH plan and prone breast plan. The plan in the prone position demonstrated improvements in lung sparing comparing to the DIBH plan. Both forward FinF plan and inverse IMRT plan achieved acceptable coverage of the breast, and heart dose is comparable. Considering the daily setup variations and MLC leakage, forward FinF plan was recommended for routine clinical use. The procedure has been tested in phantom and patients were treated clinically. Conclusions: Prone breast irradiation has been advocated for women with large pendulous breasts in order to decrease acute and late toxicities. The workflow for prone breast radiation therapy has been developed and the technique is ready to treat patients.« less

  13. Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions.

    PubMed

    Seo, Heewon; Park, Yoomi; Min, Byung Joo; Seo, Myung Eui; Kim, Ju Han

    2017-01-01

    The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58.2%, 18.7%, and 23.1% of the variants, respectively. We identified four distinct error patterns of variant calling that may be bioinformatically corrected when using different strategies: simplicity region, SNV cluster, peripheral sequence read, and base inversion. Local de novo assembly successfully corrected 201 (38.7%) of the 519 highly likely or likely false positives. We also demonstrate that the two sequencing kits from Thermo Fisher (the Ion PI Sequencing 200 kit V3 and the Ion PI Hi-Q kit) exhibit different error profiles across different error types. A refined calling algorithm with better polymerase may improve the performance of the Ion Proton sequencing platform.

  14. Software for Quantifying and Simulating Microsatellite Genotyping Error

    PubMed Central

    Johnson, Paul C.D.; Haydon, Daniel T.

    2007-01-01

    Microsatellite genetic marker data are exploited in a variety of fields, including forensics, gene mapping, kinship inference and population genetics. In all of these fields, inference can be thwarted by failure to quantify and account for data errors, and kinship inference in particular can benefit from separating errors into two distinct classes: allelic dropout and false alleles. Pedant is MS Windows software for estimating locus-specific maximum likelihood rates of these two classes of error. Estimation is based on comparison of duplicate error-prone genotypes: neither reference genotypes nor pedigree data are required. Other functions include: plotting of error rate estimates and confidence intervals; simulations for performing power analysis and for testing the robustness of error rate estimates to violation of the underlying assumptions; and estimation of expected heterozygosity, which is a required input. The program, documentation and source code are available from http://www.stats.gla.ac.uk/~paulj/pedant.html. PMID:20066126

  15. Keeping mammalian mutation load in check: regulation of the activity of error-prone DNA polymerases by p53 and p21.

    PubMed

    Livneh, Zvi

    2006-09-01

    To overcome DNA lesions that block replication the cell employs translesion DNA synthesis (TLS) polymerases, a group of low fidelity DNA polymerases that have the capacity to bypass a wide range of DNA lesions. This TLS process is also termed error-prone repair, due to its inherent mutagenic nature. We have recently shown that the tumor suppressor p53 and the cell cycle inhibitor p21 are global regulators of TLS. When these proteins are missing or nonfunctional, TLS gets out of control: its extent increases to very high levels, and its fidelity decreases, causing an overall increase in mutation load. This may be explained by the loss of selectivity in the bypass of specific DNA lesions by their cognate specialized polymerases, such that lesion bypass continues to a maximum, regardless of the price paid in increased mutations. The p53 and p21 proteins are also required for efficient UV light-induced monoubiquitination of PCNA, which is consistent with a model in which this modification of PCNA is necessary but not sufficient for the normal activity of TLS. This regulation suggests that TLS evolved in mammals as a system that balances gain in survival with a tolerable mutational cost, and that disturbing this balance causes a potentially harmful increase in mutations, which might play a role in carcinogenesis.

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

    PubMed Central

    Kebschull, Justus M.; Zador, Anthony M.

    2015-01-01

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

  17. Empirical evaluation of humpback whale telomere length estimates; quality control and factors causing variability in the singleplex and multiplex qPCR methods

    PubMed Central

    2012-01-01

    Background Telomeres, the protective cap of chromosomes, have emerged as powerful markers of biological age and life history in model and non-model species. The qPCR method for telomere length estimation is one of the most common methods for telomere length estimation, but has received recent critique for being too error-prone and yielding unreliable results. This critique coincides with an increasing awareness of the potentials and limitations of the qPCR technique in general and the proposal of a general set of guidelines (MIQE) for standardization of experimental, analytical, and reporting steps of qPCR. In order to evaluate the utility of the qPCR method for telomere length estimation in non-model species, we carried out four different qPCR assays directed at humpback whale telomeres, and subsequently performed a rigorous quality control to evaluate the performance of each assay. Results Performance differed substantially among assays and only one assay was found useful for telomere length estimation in humpback whales. The most notable factors causing these inter-assay differences were primer design and choice of using singleplex or multiplex assays. Inferred amplification efficiencies differed by up to 40% depending on assay and quantification method, however this variation only affected telomere length estimates in the worst performing assays. Conclusion Our results suggest that seemingly well performing qPCR assays may contain biases that will only be detected by extensive quality control. Moreover, we show that the qPCR method for telomere length estimation can be highly precise and accurate, and thus suitable for telomere measurement in non-model species, if effort is devoted to optimization at all experimental and analytical steps. We conclude by highlighting a set of quality controls which may serve for further standardization of the qPCR method for telomere length estimation, and discuss some of the factors that may cause variation in qPCR experiments

  18. Self-esteem and delusion proneness.

    PubMed

    Warman, Debbie M; Lysaker, Paul H; Luedtke, Brandi; Martin, Joel M

    2010-06-01

    The present study was an examination of global self-esteem and various types of unusual beliefs in a nonclinical population. Individuals with no history of psychotic disorder (N = 121) completed a measure of delusion-proneness and also a measure of self-esteem. Results indicated high delusion prone individuals had lower self-esteem than low delusion prone individuals (p = 0.044). In addition, higher levels of paranoid ideation and suspiciousness were associated with lower self-esteem (p < 0.001). Significant, yet smaller relationships also emerged between low self-esteem and higher levels of beliefs related to thought disturbances, catastrophic ideation/thought broadcasting, and ideation of reference/influence. The significance of these findings as they relate to theories of delusion formation is discussed.

  19. Boredom proneness in pathological gambling.

    PubMed

    Blaszczynski, A; McConaghy, N; Frankova, A

    1990-08-01

    To test the hypothesis that pathological gamblers seek stimulation as a means of reducing aversive under-aroused states of boredom and/or depression, the Beck Depression Inventory, Zuckerman's Sensation Seeking Scale and a Boredom Proneness Scale were administered to 48 diagnosed pathological gamblers and a control group of 40 family physician patients. Analyses of variance showed pathological gamblers obtained significantly higher boredom proneness and depression scores than those of controls. That the Boredom Proneness Scale failed to correlate with the Zuckerman Boredom Susceptibility subscale suggested the two measure differing dimensions. Results indicated the possible existence of three subtypes of pathological gamblers, one group characterized by boredom, another by depression, and a third by a mixture of both depression and boredom.

  20. Utility of PCR in diagnosing pulmonary tuberculosis.

    PubMed

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

    1996-06-01

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

  1. Efficient Variational Quantum Simulator Incorporating Active Error Minimization

    NASA Astrophysics Data System (ADS)

    Li, Ying; Benjamin, Simon C.

    2017-04-01

    One of the key applications for quantum computers will be the simulation of other quantum systems that arise in chemistry, materials science, etc., in order to accelerate the process of discovery. It is important to ask the following question: Can this simulation be achieved using near-future quantum processors, of modest size and under imperfect control, or must it await the more distant era of large-scale fault-tolerant quantum computing? Here, we propose a variational method involving closely integrated classical and quantum coprocessors. We presume that all operations in the quantum coprocessor are prone to error. The impact of such errors is minimized by boosting them artificially and then extrapolating to the zero-error case. In comparison to a more conventional optimized Trotterization technique, we find that our protocol is efficient and appears to be fundamentally more robust against error accumulation.

  2. Neglected children, shame-proneness, and depressive symptoms.

    PubMed

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

    2010-11-01

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

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

    PubMed

    Keller, Mark; Naue, Jana; Zengerle, Roland; von Stetten, Felix; Schmidt, Ulrike

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  5. Errors Affect Hypothetical Intertemporal Food Choice in Women

    PubMed Central

    Sellitto, Manuela; di Pellegrino, Giuseppe

    2014-01-01

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

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

    PubMed Central

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

    2012-01-01

    Current methodology in real-time Polymerase chain reaction (PCR) analysis performs well provided PCR efficiency remains constant over reactions. Yet, small changes in efficiency can lead to large quantification errors. Particularly in biological samples, the possible presence of inhibitors forms a challenge. We present a new approach to single reaction efficiency calculation, called Full Process Kinetics-PCR (FPK-PCR). It combines a kinetically more realistic model with flexible adaptation to the full range of data. By reconstructing the entire chain of cycle efficiencies, rather than restricting the focus on a ‘window of application’, one extracts additional information and loses a level of arbitrariness. The maximal efficiency estimates returned by the model are comparable in accuracy and precision to both the golden standard of serial dilution and other single reaction efficiency methods. The cycle-to-cycle changes in efficiency, as described by the FPK-PCR procedure, stay considerably closer to the data than those from other S-shaped models. The assessment of individual cycle efficiencies returns more information than other single efficiency methods. It allows in-depth interpretation of real-time PCR data and reconstruction of the fluorescence data, providing quality control. Finally, by implementing a global efficiency model, reproducibility is improved as the selection of a window of application is avoided. PMID:22102586

  7. Cognitive and affective predictors of boredom proneness.

    PubMed

    Isacescu, Julia; Struk, Andriy Anatolievich; Danckert, James

    2017-12-01

    Boredom proneness has been linked to various forms of cognitive and affective dysregulation including poor self-control and mind-wandering (MW), as well as depression and aggression. As such, understanding boredom and the associated cognitive and affective components of the experience, represents an important first step in combatting the consequences of boredom for psychological well-being. We surveyed 1928 undergraduate students on measures of boredom proneness, self-control, MW, depression and aggression to investigate how these constructs were related. Hierarchical regression analysis indicated that self-control operated as a strong negative predictor of boredom proneness. Finally, when controlling for age and self-control, we observed large decreases in the magnitudes of the relationships between boredom proneness and our other measures of interest. Together, these results imply a strong relationship between boredom proneness and cognitive and affective dysregulation, and show that individual levels of self-control can account for the lion's share of variance in the relationships between boredom, cognition, and affect.

  8. The application of Aronson's taxonomy to medication errors in nursing.

    PubMed

    Johnson, Maree; Young, Helen

    2011-01-01

    Medication administration is a frequent nursing activity that is prone to error. In this study of 318 self-reported medication incidents (including near misses), very few resulted in patient harm-7% required intervention or prolonged hospitalization or caused temporary harm. Aronson's classification system provided an excellent framework for analysis of the incidents with a close connection between the type of error and the change strategy to minimize medication incidents. Taking a behavioral approach to medication error classification has provided helpful strategies for nurses such as nurse-call cards on patient lockers when patients are absent and checking of medication sign-off by outgoing and incoming staff at handover.

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

    PubMed Central

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

    2014-01-01

    Human DNA polymerase kappa (hpol κ) 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 κ 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 κ 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 κ-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 κ were found to physically interact through the exo and RQC domains of WRN, and co-localization of WRN and hpol κ was observed in human cells treated with hydrogen peroxide. Thus, WRN limits the error-prone bypass of 8-oxo-dG by hpol κ, which could influence the sensitivity to oxidative damage that has previously been observed for Werner's syndrome cells. PMID:25294835

  10. Boredom proneness: its relationship to positive and negative affect.

    PubMed

    Vodanovich, S J; Verner, K M; Gilbride, T V

    1991-12-01

    170 undergraduate students completed the Boredom Proneness Scale by Farmer and Sundberg and the Multiple Affect Adjective Checklist by Zuckerman and Lubin. Significant negative relationships were found between boredom proneness and negative affect scores (i.e., Depression, Hostility, Anxiety). Significant positive correlations also obtained between boredom proneness and positive affect (i.e., Positive Affect, Sensation Seeking). The correlations between boredom proneness "subscales" and positive and negative affect were congruent with those obtained using total boredom proneness scores. Implications for counseling are discussed.

  11. Classification-Based Spatial Error Concealment for Visual Communications

    NASA Astrophysics Data System (ADS)

    Chen, Meng; Zheng, Yefeng; Wu, Min

    2006-12-01

    In an error-prone transmission environment, error concealment is an effective technique to reconstruct the damaged visual content. Due to large variations of image characteristics, different concealment approaches are necessary to accommodate the different nature of the lost image content. In this paper, we address this issue and propose using classification to integrate the state-of-the-art error concealment techniques. The proposed approach takes advantage of multiple concealment algorithms and adaptively selects the suitable algorithm for each damaged image area. With growing awareness that the design of sender and receiver systems should be jointly considered for efficient and reliable multimedia communications, we proposed a set of classification-based block concealment schemes, including receiver-side classification, sender-side attachment, and sender-side embedding. Our experimental results provide extensive performance comparisons and demonstrate that the proposed classification-based error concealment approaches outperform the conventional approaches.

  12. [Reduction of pressure sores during prone positioning of ventilated intensive care patients by the prone-head support system: a pilot study].

    PubMed

    Prebio, Michael; Katz-Papatheophilou, Elfriede; Heindl, Werner; Gelbmann, Herbert; Burghuber, Otto C

    2005-02-01

    Prone positioning in patients with adult respiratory distress syndrome is a well-known method to improve oxygenation. The aim of our study was to evaluate a new device for prone positioning, the prone-head support system (PHS system), with regard to reduction of cutaneous pressure sores. In a pilot study we randomized 8 patients with ARDS in two groups: 180 degrees standard prone positioning (group without mask) and prone positioning with the PHS system (group with mask). The PHS system consists of a facemask support, which is connected to an adapted air suspension bed. The patients of both groups were intermittently proned for several days. We evaluated the pressure sores on head and neck before turning the patients prone for the first time and after each period of prone positioning. We documented the quantity, the size, the type and the localization of the pressure sores. There was no significant difference in the mean duration of prone positioning (27.1+/-14.7 hours in the group with mask versus 24.5+/-18.7 h in the group without mask). In the group with mask there were 1.5+/-0.8 new pressure sores by each proning, whereas in the group without mask there were 2.37+/-1.6 new pressure sores, which was lower, but not significantly. The overall area of pressure sores (798 mm2 versus 3184 mm2, p=0.004), the area of pressure sores per patient (199.5+/-104.7 mm2 versus 796+/-478 mm2, p=0.03) and the increase of the area of pressure sores per proning (79.8+/-52.0 mm2 versus 398.0+/-214.3 mm2, p=0.004) were significantly lower in the group with mask in comparison to the group without mask. The lips were the most effected localization in both groups. The pressure sores in the group with mask were less severe and showed a homogenous distribution in comparison to the group without mask. Blisters dominated in the group with mask in comparison to erosions, necrosis and ulcers in the group without mask. The PHS system with its face mask is able to reduce the extent and the

  13. PCR Inhibition of a Quantitative PCR for Detection of Mycobacterium avium Subspecies Paratuberculosis DNA in Feces: Diagnostic Implications and Potential Solutions

    PubMed Central

    Acharya, Kamal R.; Dhand, Navneet K.; Whittington, Richard J.; Plain, Karren M.

    2017-01-01

    Molecular tests such as polymerase chain reaction (PCR) are increasingly being applied for the diagnosis of Johne’s disease, a chronic intestinal infection of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Feces, as the primary test sample, presents challenges in terms of effective DNA isolation, with potential for PCR inhibition and ultimately for reduced analytical and diagnostic sensitivity. However, limited evidence is available regarding the magnitude and diagnostic implications of PCR inhibition for the detection of MAP in feces. This study aimed to investigate the presence and diagnostic implications of PCR inhibition in a quantitative PCR assay for MAP (High-throughput Johne’s test) to investigate the characteristics of samples prone to inhibition and to identify measures that can be taken to overcome this. In a study of fecal samples derived from a high prevalence, endemically infected cattle herd, 19.94% of fecal DNA extracts showed some evidence of inhibition. Relief of inhibition by a five-fold dilution of the DNA extract led to an average increase in quantification of DNA by 3.3-fold that consequently increased test sensitivity of the qPCR from 55 to 80% compared to fecal culture. DNA extracts with higher DNA and protein content had 19.33 and 10.94 times higher odds of showing inhibition, respectively. The results suggest that the current test protocol is sensitive for herd level diagnosis of Johne’s disease but that test sensitivity and individual level diagnosis could be enhanced by relief of PCR inhibition, achieved by five-fold dilution of the DNA extract. Furthermore, qualitative and quantitative parameters derived from absorbance measures of DNA extracts could be useful for prediction of inhibitory fecal samples. PMID:28210245

  14. Error Covariance Penalized Regression: A novel multivariate model combining penalized regression with multivariate error structure.

    PubMed

    Allegrini, Franco; Braga, Jez W B; Moreira, Alessandro C O; Olivieri, Alejandro C

    2018-06-29

    A new multivariate regression model, named Error Covariance Penalized Regression (ECPR) is presented. Following a penalized regression strategy, the proposed model incorporates information about the measurement error structure of the system, using the error covariance matrix (ECM) as a penalization term. Results are reported from both simulations and experimental data based on replicate mid and near infrared (MIR and NIR) spectral measurements. The results for ECPR are better under non-iid conditions when compared with traditional first-order multivariate methods such as ridge regression (RR), principal component regression (PCR) and partial least-squares regression (PLS). Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Strongest Earthquake-Prone Areas in Kamchatka

    NASA Astrophysics Data System (ADS)

    Dzeboev, B. A.; Agayan, S. M.; Zharkikh, Yu. I.; Krasnoperov, R. I.; Barykina, Yu. V.

    2018-03-01

    The paper continues the series of our works on recognizing the areas prone to the strongest, strong, and significant earthquakes with the use of the Formalized Clustering And Zoning (FCAZ) intellectual clustering system. We recognized the zones prone to the probable emergence of epicenters of the strongest ( M ≥ 74/3) earthquakes on the Pacific Coast of Kamchatka. The FCAZ-zones are compared to the zones that were recognized in 1984 by the classical recognition method for Earthquake-Prone Areas (EPA) by transferring the criteria of high seismicity from the Andes mountain belt to the territory of Kamchatka. The FCAZ recognition was carried out with two-dimensional and three-dimensional objects of recognition.

  16. Medication errors reported to the National Medication Error Reporting System in Malaysia: a 4-year retrospective review (2009 to 2012).

    PubMed

    Samsiah, A; Othman, Noordin; Jamshed, Shazia; Hassali, Mohamed Azmi; Wan-Mohaina, W M

    2016-12-01

    Reporting and analysing the data on medication errors (MEs) is important and contributes to a better understanding of the error-prone environment. This study aims to examine the characteristics of errors submitted to the National Medication Error Reporting System (MERS) in Malaysia. A retrospective review of reports received from 1 January 2009 to 31 December 2012 was undertaken. Descriptive statistics method was applied. A total of 17,357 MEs reported were reviewed. The majority of errors were from public-funded hospitals. Near misses were classified in 86.3 % of the errors. The majority of errors (98.1 %) had no harmful effects on the patients. Prescribing contributed to more than three-quarters of the overall errors (76.1 %). Pharmacists detected and reported the majority of errors (92.1 %). Cases of erroneous dosage or strength of medicine (30.75 %) were the leading type of error, whilst cardiovascular (25.4 %) was the most common category of drug found. MERS provides rich information on the characteristics of reported MEs. Low contribution to reporting from healthcare facilities other than government hospitals and non-pharmacists requires further investigation. Thus, a feasible approach to promote MERS among healthcare providers in both public and private sectors needs to be formulated and strengthened. Preventive measures to minimise MEs should be directed to improve prescribing competency among the fallible prescribers identified.

  17. A prospective three-step intervention study to prevent medication errors in drug handling in paediatric care.

    PubMed

    Niemann, Dorothee; Bertsche, Astrid; Meyrath, David; Koepf, Ellen D; Traiser, Carolin; Seebald, Katja; Schmitt, Claus P; Hoffmann, Georg F; Haefeli, Walter E; Bertsche, Thilo

    2015-01-01

    To prevent medication errors in drug handling in a paediatric ward. One in five preventable adverse drug events in hospitalised children is caused by medication errors. Errors in drug prescription have been studied frequently, but data regarding drug handling, including drug preparation and administration, are scarce. A three-step intervention study including monitoring procedure was used to detect and prevent medication errors in drug handling. After approval by the ethics committee, pharmacists monitored drug handling by nurses on an 18-bed paediatric ward in a university hospital prior to and following each intervention step. They also conducted a questionnaire survey aimed at identifying knowledge deficits. Each intervention step targeted different causes of errors. The handout mainly addressed knowledge deficits, the training course addressed errors caused by rule violations and slips, and the reference book addressed knowledge-, memory- and rule-based errors. The number of patients who were subjected to at least one medication error in drug handling decreased from 38/43 (88%) to 25/51 (49%) following the third intervention, and the overall frequency of errors decreased from 527 errors in 581 processes (91%) to 116/441 (26%). The issue of the handout reduced medication errors caused by knowledge deficits regarding, for instance, the correct 'volume of solvent for IV drugs' from 49-25%. Paediatric drug handling is prone to errors. A three-step intervention effectively decreased the high frequency of medication errors by addressing the diversity of their causes. Worldwide, nurses are in charge of drug handling, which constitutes an error-prone but often-neglected step in drug therapy. Detection and prevention of errors in daily routine is necessary for a safe and effective drug therapy. Our three-step intervention reduced errors and is suitable to be tested in other wards and settings. © 2014 John Wiley & Sons Ltd.

  18. Random mutagenesis of BoNT/E Hc nanobody to construct a secondary phage-display library.

    PubMed

    Shahi, B; Mousavi Gargari, S L; Rasooli, I; Rajabi Bazl, M; Hoseinpoor, R

    2014-08-01

    To construct secondary mutant phage-display library of recombinant single variable domain (VHH) against botulinum neurotoxin E by error-prone PCR. The gene coding for specific VHH derived from the camel immunized with binding domain of botulinum neurotoxin E (BoNT/E) was amplified by error-prone PCR. Several biopanning rounds were used to screen the phage-displaying BoNT/E Hc nanobodies. The final nanobody, SHMR4, with increased affinity recognized BoNT/E toxin with no cross-reactivity with other antigens especially with related BoNT toxins. The constructed nanobody could be a suitable candidate for VHH-based biosensor production to detect the Clostridium botulinum type E. Diagnosis and treatment of botulinum neurotoxins are important. Generation of high-affinity antibodies based on the construction of secondary libraries using affinity maturation step leads to the development of reagents for precise diagnosis and therapy. © 2014 The Society for Applied Microbiology.

  19. Self-Interaction Error in Density Functional Theory: An Appraisal.

    PubMed

    Bao, Junwei Lucas; Gagliardi, Laura; Truhlar, Donald G

    2018-05-03

    Self-interaction error (SIE) is considered to be one of the major sources of error in most approximate exchange-correlation functionals for Kohn-Sham density-functional theory (KS-DFT), and it is large with all local exchange-correlation functionals and with some hybrid functionals. In this work, we consider systems conventionally considered to be dominated by SIE. For these systems, we demonstrate that by using multiconfiguration pair-density functional theory (MC-PDFT), the error of a translated local density-functional approximation is significantly reduced (by a factor of 3) when using an MCSCF density and on-top density, as compared to using KS-DFT with the parent functional; the error in MC-PDFT with local on-top functionals is even lower than the error in some popular KS-DFT hybrid functionals. Density-functional theory, either in MC-PDFT form with local on-top functionals or in KS-DFT form with some functionals having 50% or more nonlocal exchange, has smaller errors for SIE-prone systems than does CASSCF, which has no SIE.

  20. Beyond prone position in percutaneous nephrolithotomy: a comprehensive review.

    PubMed

    de la Rosette, Jean J M C H; Tsakiris, Peter; Ferrandino, Michael N; Elsakka, Ahmed M; Rioja, Jorge; Preminger, Glenn M

    2008-12-01

    Percutaneous nephrolithotomy (PNL) is traditionally performed with the patient in the prone position. To assess the efficacy and safety of the prone and supine positions, particularly in obese patients and in those with staghorn calculi. A Medline search was conducted for articles published during the last 10 yr related to PNL in the prone and supine positions. This search revealed 9 published studies for supine and 25 for prone PNL. None of the supine PNL studies reported visceral injuries, while transfusion rates were 0.0-9.4% and stone-free rates were 69.6-95.0%. One study of supine PNL evaluated a significant proportion of obese patients. Prone PNL studies in obese patients report transfusion rates of 3.2-8.8% and stone-free rates of 79.0-89.2%. In the only randomized study, excluding obese patients and staghorn calculi, operative time favors the supine position. A nonrandomized comparative study demonstrated similar complication rates with insignificant improvement in treatment success for supine PNL; however, when comparing series with similar proportions of staghorn calculi cases, there are slightly improved outcomes for prone PNL. Moreover, comparison of weighted means favors prone PNL. For obese patients and staghorn calculi, prone PNL appears to be associated with decreased operative times with similar bleeding rates and slightly better stone-free rates than supine PNL.

  1. The Diagnosis of Error in Histories of Science

    NASA Astrophysics Data System (ADS)

    Thomas, William

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

  2. An update on the prone position: Continuing Professional Development.

    PubMed

    Chui, Jason; Craen, Rosemary Ann

    2016-06-01

    The purpose of this Continuing Professional Development module is to provide information needed to prepare for and clinically manage a patient in the prone position. Prone positioning is required for surgical procedures that involve the posterior aspect of a patient. We searched MEDLINE(®) and EMBASE™ from January 2000 to January 2015 for literature related to the prone position and retrieved only original articles in English. We reviewed the advantages and disadvantages of various equipment used in prone positioning, the physiological changes associated with prone positioning, and the complications that can occur. We also reviewed strategies for the safe conduct and management of position-related complications. Increased age, elevated body mass index, the presence of comorbidities, and long duration of surgery appear to be the most important risk factors for complications associated with prone positioning. We recommend a structured team approach and careful selection of equipment tailored to the patient and surgery. The systematic use of checklists is recommended to guide operating room teams and to reduce prone position-related complications. Anesthesiologists should be prepared to manage major intraoperative emergencies (e.g., accidental extubation) and anticipate postoperative complications (e.g., airway edema and visual loss).

  3. Target Uncertainty Mediates Sensorimotor Error Correction.

    PubMed

    Acerbi, Luigi; Vijayakumar, Sethu; Wolpert, Daniel M

    2017-01-01

    Human movements are prone to errors that arise from inaccuracies in both our perceptual processing and execution of motor commands. We can reduce such errors by both improving our estimates of the state of the world and through online error correction of the ongoing action. Two prominent frameworks that explain how humans solve these problems are Bayesian estimation and stochastic optimal feedback control. Here we examine the interaction between estimation and control by asking if uncertainty in estimates affects how subjects correct for errors that may arise during the movement. Unbeknownst to participants, we randomly shifted the visual feedback of their finger position as they reached to indicate the center of mass of an object. Even though participants were given ample time to compensate for this perturbation, they only fully corrected for the induced error on trials with low uncertainty about center of mass, with correction only partial in trials involving more uncertainty. The analysis of subjects' scores revealed that participants corrected for errors just enough to avoid significant decrease in their overall scores, in agreement with the minimal intervention principle of optimal feedback control. We explain this behavior with a term in the loss function that accounts for the additional effort of adjusting one's response. By suggesting that subjects' decision uncertainty, as reflected in their posterior distribution, is a major factor in determining how their sensorimotor system responds to error, our findings support theoretical models in which the decision making and control processes are fully integrated.

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

    USGS Publications Warehouse

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

    2005-01-01

    Non-invasive genetic sampling (NGS) is becoming a popular tool for population estimation. However, multiple NGS studies have demonstrated that polymerase chain reaction (PCR) genotyping errors can bias demographic estimates. These errors can be detected by comprehensive data filters such as the multiple-tubes approach, but this approach is expensive and time consuming as it requires three to eight PCR replicates per locus. Thus, researchers have attempted to correct PCR errors in NGS datasets using non-comprehensive error checking methods, but these approaches have not been evaluated for reliability. We simulated NGS studies with and without PCR error and 'filtered' datasets using non-comprehensive approaches derived from published studies and calculated mark-recapture estimates using CAPTURE. In the absence of data-filtering, simulated error resulted in serious inflations in CAPTURE estimates; some estimates exceeded N by ??? 200%. When data filters were used, CAPTURE estimate reliability varied with per-locus error (E??). At E?? = 0.01, CAPTURE estimates from filtered data displayed < 5% deviance from error-free estimates. When E?? was 0.05 or 0.09, some CAPTURE estimates from filtered data displayed biases in excess of 10%. Biases were positive at high sampling intensities; negative biases were observed at low sampling intensities. We caution researchers against using non-comprehensive data filters in NGS studies, unless they can achieve baseline per-locus error rates below 0.05 and, ideally, near 0.01. However, we suggest that data filters can be combined with careful technique and thoughtful NGS study design to yield accurate demographic information. ?? 2005 The Zoological Society of London.

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

    NASA Technical Reports Server (NTRS)

    Hobbs, Alan; Williamson, Ann

    2002-01-01

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

  6. Systematic feasibility analysis of a quantitative elasticity estimation for breast anatomy using supine/prone patient postures.

    PubMed

    Hasse, Katelyn; Neylon, John; Sheng, Ke; Santhanam, Anand P

    2016-03-01

    Breast elastography is a critical tool for improving the targeted radiotherapy treatment of breast tumors. Current breast radiotherapy imaging protocols only involve prone and supine CT scans. There is a lack of knowledge on the quantitative accuracy with which breast elasticity can be systematically measured using only prone and supine CT datasets. The purpose of this paper is to describe a quantitative elasticity estimation technique for breast anatomy using only these supine/prone patient postures. Using biomechanical, high-resolution breast geometry obtained from CT scans, a systematic assessment was performed in order to determine the feasibility of this methodology for clinically relevant elasticity distributions. A model-guided inverse analysis approach is presented in this paper. A graphics processing unit (GPU)-based linear elastic biomechanical model was employed as a forward model for the inverse analysis with the breast geometry in a prone position. The elasticity estimation was performed using a gradient-based iterative optimization scheme and a fast-simulated annealing (FSA) algorithm. Numerical studies were conducted to systematically analyze the feasibility of elasticity estimation. For simulating gravity-induced breast deformation, the breast geometry was anchored at its base, resembling the chest-wall/breast tissue interface. Ground-truth elasticity distributions were assigned to the model, representing tumor presence within breast tissue. Model geometry resolution was varied to estimate its influence on convergence of the system. A priori information was approximated and utilized to record the effect on time and accuracy of convergence. The role of the FSA process was also recorded. A novel error metric that combined elasticity and displacement error was used to quantify the systematic feasibility study. For the authors' purposes, convergence was set to be obtained when each voxel of tissue was within 1 mm of ground-truth deformation. The authors

  7. Virtual PCR

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gardner, S N; Clague, D S; Vandersall, J A

    2006-02-23

    preliminary experiments were tainted by contaminated products received from the manufacturer. Much knowledge has been gained in the development of the code thus far, but without final debugging, increasing its robustness and verifying it against experimental results, the papers which we have drafted to share our findings still require the final data necessary for publication. The following sections summarize our final progress on VPCR as it stands after 1.5 years of effort on an ambitious project scoped for a 3 year period. We have additional details of the methods than are provided here, but would like to have legal protection in place before releasing them. The result of this project, a suite of programs that predict PCR products as a function of reaction conditions and sequences, will be used to address outstanding questions in pathogen detection and forensics at LLNL. VPCR should enable scientists to optimize PCR protocols in terms of time, temperature, ion concentration, and primer sequences and concentrations, and to estimate products and error rates in advance of performing experiments. Our proposed capabilities are well ahead of all currently available technologies, which do not model non-equilibrium kinetics, polymerase extension, or predict multiple or undesired PCR products. We are currently seeking DHS funding to complete the project, at which time licensing opportunities will be explored, an updated patent application will be prepared, and a publication will be submitted. A provisional and a full patent application have already been filed (1).« less

  8. Suggestibility and signal detection performance in hallucination-prone students.

    PubMed

    Alganami, Fatimah; Varese, Filippo; Wagstaff, Graham F; Bentall, Richard P

    2017-03-01

    Auditory hallucinations are associated with signal detection biases. We examine the extent to which suggestions influence performance on a signal detection task (SDT) in highly hallucination-prone and low hallucination-prone students. We also explore the relationship between trait suggestibility, dissociation and hallucination proneness. In two experiments, students completed on-line measures of hallucination proneness (the revised Launay-Slade Hallucination Scale; LSHS-R), trait suggestibility (Inventory of Suggestibility) and dissociation (Dissociative Experiences Scale-II). Students in the upper and lower tertiles of the LSHS-R performed an auditory SDT. Prior to the task, suggestions were made pertaining to the number of expected targets (Experiment 1, N = 60: high vs. low suggestions; Experiment 2, N = 62, no suggestion vs. high suggestion vs. no voice suggestion). Correlational and regression analyses indicated that trait suggestibility and dissociation predicted hallucination proneness. Highly hallucination-prone students showed a higher SDT bias in both studies. In Experiment 1, both bias scores were significantly affected by suggestions to the same degree. In Experiment 2, highly hallucination-prone students were more reactive to the high suggestion condition than the controls. Suggestions may affect source-monitoring judgments, and this effect may be greater in those who have a predisposition towards hallucinatory experiences.

  9. Boredom proneness: its relationship to psychological- and physical-health symptoms.

    PubMed

    Sommers, J; Vodanovich, S J

    2000-01-01

    The relationship between boredom proneness and health-symptom reporting was examined. Undergraduate students (N = 200) completed the Boredom Proneness Scale and the Hopkins Symptom Checklist. A multiple analysis of covariance indicated that individuals with high boredom-proneness total scores reported significantly higher ratings on all five subscales of the Hopkins Symptom Checklist (Obsessive-Compulsive, Somatization, Anxiety, Interpersonal Sensitivity, and Depression). The results suggest that boredom proneness may be an important element to consider when assessing symptom reporting. Implications for determining the effects of boredom proneness on psychological- and physical-health symptoms. as well as the application in clinical settings, are discussed.

  10. Prone position for the prevention of lung infection.

    PubMed

    Beuret, P

    2002-04-01

    Pulmonary infection is frequent in brain injured patients. It has been identified as an independent predictor of unfavorable neurological outcome, calling for attempts of prevention. We recently evaluated intermittent prone positioning for the prevention of ventilator-associated pneumonia (VAP) in comatose brain injured patients, in a randomized study. 25 patients were included in the prone position (PP) group: they were positioned on prone four hours once daily until they could get up to sit in an armchair; 26 patients were included in the supine position (SP) group. The main characteristics of the patients from the two groups were similar at randomization. The primary end-point was the incidence of lung worsening, defined by an increase in the Lung Injury Score by at least one point since the time of randomization. The incidence of lung worsening was lower in the PP group (12%) than in the SP group (50%) (p=0.003). The incidence of VAP was 38.4% in the SP group and 20% in the PP group (p=0.14). There was no serious complication attributable to prone positioning. In conclusion, the beneficial effect of prone positioning for prevention of lung infection in brain injured patients is not well established. However, in those patients, prone positioning is able to avoid the worsening of pulmonary function, especially in oxygenation.

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

    PubMed Central

    Ussowicz, Marek; Rybka, Blanka; Wendycz-Domalewska, Danuta; Ryczan, Renata; Gorczyńska, Ewa; Kałwak, Krzysztof; Woźniak, Mieczysław

    2010-01-01

    After stem cell transplantation, human patients are prone to life-threatening opportunistic infections with a plethora of microorganisms. We report a retrospective study on 116 patients (98 children, 18 adults) who were transplanted in a pediatric bone marrow transplantation unit. Blood, urine and stool samples were collected and monitored for adenovirus (AdV) DNA using polymerase chain reaction (PCR) and real-time PCR (RT-PCR) on a regular basis. AdV DNA was detected in 52 (44.8%) patients, with mortality reaching 19% in this subgroup. Variables associated with adenovirus infection were transplantations from matched unrelated donors and older age of the recipient. An increased seasonal occurrence of adenoviral infections was observed in autumn and winter. Analysis of immune reconstitution showed a higher incidence of AdV infections during periods of low T-lymphocyte count. This study also showed a strong interaction between co-infections of AdV and BK polyomavirus in patients undergoing hematopoietic stem cell transplantations. PMID:20848295

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    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.

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

    NASA Technical Reports Server (NTRS)

    Woolley, S. I.

    1993-01-01

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

  14. The Error-Prone DNA Polymerase κ Promotes Temozolomide Resistance in Glioblastoma through Rad17-Dependent Activation of ATR-Chk1 Signaling.

    PubMed

    Peng, Chenghao; Chen, Zhengxin; Wang, Shuai; Wang, Hong-Wei; Qiu, Wenjin; Zhao, Lin; Xu, Ran; Luo, Hui; Chen, Yuanyuan; Chen, Dan; You, Yongping; Liu, Ning; Wang, Huibo

    2016-04-15

    The acquisition of drug resistance is a persistent clinical problem limiting the successful treatment of human cancers, including glioblastoma (GBM). However, the molecular mechanisms by which initially chemoresponsive tumors develop therapeutic resistance remain poorly understood. In this study, we report that Pol κ, an error-prone polymerase that participates in translesion DNA synthesis, was significantly upregulated in GBM cell lines and tumor tissues following temozolomide treatment. Overexpression of Pol κ in temozolomide-sensitive GBM cells conferred resistance to temozolomide, whereas its inhibition markedly sensitized resistant cells to temozolomide in vitro and in orthotopic xenograft mouse models. Mechanistically, depletion of Pol κ disrupted homologous recombination (HR)-mediated repair and restart of stalled replication forks, impaired the activation of ATR-Chk1 signaling, and delayed cell-cycle re-entry and progression. Further investigation of the relationship between Pol κ and temozolomide revealed that Pol κ inactivation facilitated temozolomide-induced Rad17 ubiquitination and proteasomal degradation, subsequently silencing ATR-Chk1 signaling and leading to defective HR repair and the reversal of temozolomide resistance. Moreover, overexpression of Rad17 in Pol κ-depleted GBM cells restored HR efficiency, promoted the clearance of temozolomide-induced DNA breaks, and desensitized cells to the cytotoxic effects of temozolomide observed in the absence of Pol κ. Finally, we found that Pol κ overexpression correlated with poor prognosis in GBM patients undergoing temozolomide therapy. Collectively, our findings identify a potential mechanism by which GBM cells develop resistance to temozolomide and suggest that targeting the DNA damage tolerance pathway may be beneficial for overcoming resistance. Cancer Res; 76(8); 2340-53. ©2016 AACR. ©2016 American Association for Cancer Research.

  15. Ethnic and gender differences in boredom proneness

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gibson, G.S.; Morales,

    1996-02-01

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

  16. Portable and Error-Free DNA-Based Data Storage.

    PubMed

    Yazdi, S M Hossein Tabatabaei; Gabrys, Ryan; Milenkovic, Olgica

    2017-07-10

    DNA-based data storage is an emerging nonvolatile memory technology of potentially unprecedented density, durability, and replication efficiency. The basic system implementation steps include synthesizing DNA strings that contain user information and subsequently retrieving them via high-throughput sequencing technologies. Existing architectures enable reading and writing but do not offer random-access and error-free data recovery from low-cost, portable devices, which is crucial for making the storage technology competitive with classical recorders. Here we show for the first time that a portable, random-access platform may be implemented in practice using nanopore sequencers. The novelty of our approach is to design an integrated processing pipeline that encodes data to avoid costly synthesis and sequencing errors, enables random access through addressing, and leverages efficient portable sequencing via new iterative alignment and deletion error-correcting codes. Our work represents the only known random access DNA-based data storage system that uses error-prone nanopore sequencers, while still producing error-free readouts with the highest reported information rate/density. As such, it represents a crucial step towards practical employment of DNA molecules as storage media.

  17. Target Uncertainty Mediates Sensorimotor Error Correction

    PubMed Central

    Vijayakumar, Sethu; Wolpert, Daniel M.

    2017-01-01

    Human movements are prone to errors that arise from inaccuracies in both our perceptual processing and execution of motor commands. We can reduce such errors by both improving our estimates of the state of the world and through online error correction of the ongoing action. Two prominent frameworks that explain how humans solve these problems are Bayesian estimation and stochastic optimal feedback control. Here we examine the interaction between estimation and control by asking if uncertainty in estimates affects how subjects correct for errors that may arise during the movement. Unbeknownst to participants, we randomly shifted the visual feedback of their finger position as they reached to indicate the center of mass of an object. Even though participants were given ample time to compensate for this perturbation, they only fully corrected for the induced error on trials with low uncertainty about center of mass, with correction only partial in trials involving more uncertainty. The analysis of subjects’ scores revealed that participants corrected for errors just enough to avoid significant decrease in their overall scores, in agreement with the minimal intervention principle of optimal feedback control. We explain this behavior with a term in the loss function that accounts for the additional effort of adjusting one’s response. By suggesting that subjects’ decision uncertainty, as reflected in their posterior distribution, is a major factor in determining how their sensorimotor system responds to error, our findings support theoretical models in which the decision making and control processes are fully integrated. PMID:28129323

  18. Calibration-free assays on standard real-time PCR devices

    PubMed Central

    Debski, Pawel R.; Gewartowski, Kamil; Bajer, Seweryn; Garstecki, Piotr

    2017-01-01

    Quantitative Polymerase Chain Reaction (qPCR) is one of central techniques in molecular biology and important tool in medical diagnostics. While being a golden standard qPCR techniques depend on reference measurements and are susceptible to large errors caused by even small changes of reaction efficiency or conditions that are typically not marked by decreased precision. Digital PCR (dPCR) technologies should alleviate the need for calibration by providing absolute quantitation using binary (yes/no) signals from partitions provided that the basic assumption of amplification a single target molecule into a positive signal is met. Still, the access to digital techniques is limited because they require new instruments. We show an analog-digital method that can be executed on standard (real-time) qPCR devices. It benefits from real-time readout, providing calibration-free assessment. The method combines advantages of qPCR and dPCR and bypasses their drawbacks. The protocols provide for small simplified partitioning that can be fitted within standard well plate format. We demonstrate that with the use of synergistic assay design standard qPCR devices are capable of absolute quantitation when normal qPCR protocols fail to provide accurate estimates. We list practical recipes how to design assays for required parameters, and how to analyze signals to estimate concentration. PMID:28327545

  19. Calibration-free assays on standard real-time PCR devices

    NASA Astrophysics Data System (ADS)

    Debski, Pawel R.; Gewartowski, Kamil; Bajer, Seweryn; Garstecki, Piotr

    2017-03-01

    Quantitative Polymerase Chain Reaction (qPCR) is one of central techniques in molecular biology and important tool in medical diagnostics. While being a golden standard qPCR techniques depend on reference measurements and are susceptible to large errors caused by even small changes of reaction efficiency or conditions that are typically not marked by decreased precision. Digital PCR (dPCR) technologies should alleviate the need for calibration by providing absolute quantitation using binary (yes/no) signals from partitions provided that the basic assumption of amplification a single target molecule into a positive signal is met. Still, the access to digital techniques is limited because they require new instruments. We show an analog-digital method that can be executed on standard (real-time) qPCR devices. It benefits from real-time readout, providing calibration-free assessment. The method combines advantages of qPCR and dPCR and bypasses their drawbacks. The protocols provide for small simplified partitioning that can be fitted within standard well plate format. We demonstrate that with the use of synergistic assay design standard qPCR devices are capable of absolute quantitation when normal qPCR protocols fail to provide accurate estimates. We list practical recipes how to design assays for required parameters, and how to analyze signals to estimate concentration.

  20. Generalized Structured Component Analysis with Uniqueness Terms for Accommodating Measurement Error

    PubMed Central

    Hwang, Heungsun; Takane, Yoshio; Jung, Kwanghee

    2017-01-01

    Generalized structured component analysis (GSCA) is a component-based approach to structural equation modeling (SEM), where latent variables are approximated by weighted composites of indicators. It has no formal mechanism to incorporate errors in indicators, which in turn renders components prone to the errors as well. We propose to extend GSCA to account for errors in indicators explicitly. This extension, called GSCAM, considers both common and unique parts of indicators, as postulated in common factor analysis, and estimates a weighted composite of indicators with their unique parts removed. Adding such unique parts or uniqueness terms serves to account for measurement errors in indicators in a manner similar to common factor analysis. Simulation studies are conducted to compare parameter recovery of GSCAM and existing methods. These methods are also applied to fit a substantively well-established model to real data. PMID:29270146

  1. Delusion proneness and 'jumping to conclusions': relative and absolute effects.

    PubMed

    van der Leer, L; Hartig, B; Goldmanis, M; McKay, R

    2015-04-01

    That delusional and delusion-prone individuals 'jump to conclusions' is one of the most robust and important findings in the literature on delusions. However, although the notion of 'jumping to conclusions' (JTC) implies gathering insufficient evidence and reaching premature decisions, previous studies have not investigated whether the evidence gathering of delusion-prone individuals is, in fact, suboptimal. The standard JTC effect is a relative effect but using relative comparisons to substantiate absolute claims is problematic. In this study we investigated whether delusion-prone participants jump to conclusions in both a relative and an absolute sense. Healthy participants (n = 112) completed an incentivized probabilistic reasoning task in which correct decisions were rewarded and additional information could be requested for a small price. This combination of rewards and costs generated optimal decision points. Participants also completed measures of delusion proneness, intelligence and risk aversion. Replicating the standard relative finding, we found that delusion proneness significantly predicted task decisions, such that the more delusion prone the participants were, the earlier they decided. This finding was robust when accounting for the effects of risk aversion and intelligence. Importantly, high-delusion-prone participants also decided in advance of an objective rational optimum, gathering fewer data than would have maximized their expected payoff. Surprisingly, we found that even low-delusion-prone participants jumped to conclusions in this absolute sense. Our findings support and clarify the claim that delusion formation is associated with a tendency to 'jump to conclusions'. In short, most people jump to conclusions, but more delusion-prone individuals 'jump further'.

  2. Effect of lethality on the extinction and on the error threshold of quasispecies.

    PubMed

    Tejero, Hector; Marín, Arturo; Montero, Francisco

    2010-02-21

    In this paper the effect of lethality on error threshold and extinction has been studied in a population of error-prone self-replicating molecules. For given lethality and a simple fitness landscape, three dynamic regimes can be obtained: quasispecies, error catastrophe, and extinction. Using a simple model in which molecules are classified as master, lethal and non-lethal mutants, it is possible to obtain the mutation rates of the transitions between the three regimes analytically. The numerical resolution of the extended model, in which molecules are classified depending on their Hamming distance to the master sequence, confirms the results obtained in the simple model and shows how an error catastrophe regime changes when lethality is taken in account. (c) 2009 Elsevier Ltd. All rights reserved.

  3. Comparing errors in Medicaid reporting across surveys: evidence to date.

    PubMed

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

    2013-04-01

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

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

    ERIC Educational Resources Information Center

    System Development Corp., Falls Church, VA.

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

  5. Vocational interests and career indecision among psychosis-prone college students.

    PubMed

    Poreh, A M; Schullen, C

    1998-10-01

    This study investigated the relationship between scores on scales that purport to measure psychosis-proneness and scores on vocational interests, identity, and differentiation scales in a sample of 233 college students who completed the Perceptual Aberration and Magical Ideation scales, the Strong Campbell Interest Inventory, and the Career Decision Scale. The present findings are consistent with prior work indicating a sex-related association of scores on measures of psychosis-proneness and vocational interests. A positive correlation between scores on vocational indecision and measures of psychosis-proneness was also found, suggesting that both men and women who score high on psychosis-proneness find it difficult to formulate long-term career goals. Finally, there was no significant correlation between scores on measures of psychosis-proneness and Holland's Vocational Differentiation Index. Present results are discussed in light of previously reported sex differences among psychosis-prone adults and diagnosed schizophrenics. The implications of the findings for vocational counselors are also addressed.

  6. Digital Assays Part I: Partitioning Statistics and Digital PCR.

    PubMed

    Basu, Amar S

    2017-08-01

    A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error. The remainder focuses on digital PCR (dPCR) for quantification of nucleic acids. We discuss five commercial instruments that partition samples into physically isolated chambers (cdPCR) or droplet emulsions (ddPCR). We compare the strengths of dPCR (absolute quantitation, precision, and ability to detect rare or mutant targets) with those of its predecessor, quantitative real-time PCR (dynamic range, larger sample volumes, and throughput). Lastly, we describe several promising applications of dPCR, including copy number variation, quantitation of circulating tumor DNA and viral load, RNA/miRNA quantitation with reverse transcription dPCR, and library preparation for next-generation sequencing. This review is intended to give a broad perspective to scientists interested in adopting digital assays into their workflows. Part II focuses on digital protein and cell assays.

  7. Ketosis-Onset Diabetes and Ketosis-Prone Diabetes: Same or Not?

    PubMed Central

    Liu, Beiyan; Yu, Changhua; Li, Qiang; Li, Lin

    2013-01-01

    Objective. To compare clinical characteristics, immunological markers, and β-cell functions of 4 subgroups (“Aβ” classification system) of ketosis-onset diabetes and ketosis prone diabetes patients without known diabetes, presenting with ketosis or diabetic ketoacidosis (DKA) and admitted to our department from March 2011 to December 2011 in China, with 50 healthy persons as control group. Results. β-cell functional reserve was preserved in 63.52% of patients. In almost each subgroup (except A−  β− subgroup of ketosis prone group), male patients were more than female ones. The age of the majority of patients in ketosis prone group was older than that of ketosis-onset group, except A−  β− subgroup of ketosis prone group. The durations from the patient first time ketosis or DKA onset to admitting to the hospital have significant difference, which were much longer for the ketosis prone group except the A+ β+ subgroup. BMI has no significant difference among subgroups. FPG of ketosis prone group was lower than that of A−  β+ subgroup and A+ β+ subgroup in ketosis-onset group. A−  β− subgroup and A+ β+ subgroup of ketosis prone group have lower HbA1c than ketosis-onset group. Conclusions. Ketosis-onset diabetes and ketosis prone diabetes do not absolutely have the same clinical characteristics. Each subgroup shows different specialty. PMID:23710177

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

    ERIC Educational Resources Information Center

    Langhinrichsen-Rohling, Jennifer; Lamis, Dorian A.

    2008-01-01

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

  9. "Jumping to conclusions" in delusion-prone participants: an experimental economics approach.

    PubMed

    van der Leer, Leslie; McKay, Ryan

    2014-01-01

    That delusional and delusion-prone individuals "jump to conclusions" on probabilistic reasoning tasks is a key finding in cognitive neuropsychiatry. Here we focused on a less frequently investigated aspect of "jumping to conclusions" (JTC): certainty judgments. We incorporated rigorous procedures from experimental economics to eliminate potential confounds of miscomprehension and motivation and systematically investigated the effect of incentives on task performance. Low- and high-delusion-prone participants (n = 109) completed a series of computerised trials; on each trial, they were shown a black or a white fish, caught from one of the two lakes containing fish of both colours in complementary ratios. In the betting condition, participants were given £4 to distribute over the two lakes as they wished; in the control condition, participants simply provided an estimate of how probable each lake was. Deviations from Bayesian probabilities were investigated. Whereas high-delusion-prone participants in both the control and betting conditions underestimated the Bayesian probabilities (i.e. were conservative), low-delusion-prone participants in the control condition underestimated but those in the betting condition provided accurate estimates. In the control condition, there was a trend for high-delusion-prone participants to give higher estimates than low-delusion-prone participants, which is consistent with previous reports of "jumping to conclusions" in delusion-prone participants. However, our findings in the betting condition, where high-delusion-prone participants provided lower estimates than low-delusion-prone participants (who were accurate), are inconsistent with the jumping-to-conclusions effect in both a relative and an absolute sense. Our findings highlight the key role of task incentives and underscore the importance of comparing the responses of delusion-prone participants to an objective rational standard as well as to the responses of non-delusion-prone

  10. SU-F-T-404: Dosimetric Advantages of Flattening Free Beams to Prone Accelerated Partial Breast Irradiation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Galavis, P; Barbee, D; Jozsef, G

    2016-06-15

    Purpose: Prone accelerated partial breast irradiation (APBI) results in dose reduction to the heart and lung. Flattening filter free beams (FFF) reduce out of field dose due to the reduced scatter from the removal of the flattening filter and reduce the buildup region. The aim of this work is to evaluate the dosimetric advantages of FFF beams to prone APBI target coverage and reduction in dose to organs at risk. Methods: Fifteen clinical prone APBI cases using flattened photon beams were retrospectively re-planned in Eclipse-TPS using FFF beams. FFF plans were designed to provide equivalent target coverage with similar hotspotsmore » using the same field arrangements, resulting in comparable target DVHs. Both plans were transferred to a prone breast phantom and delivered on Varian-Edge-Linac. GafChromic-film was placed in the coronal plane of the phantom, partially overlapping the treatment field and extending into OARs to compare dose profiles from both plans. Results: FFF plans were comparable to the clinical plans with maximum doses of (108.3±2.3)% and (109.2±2.4)% and mean doses of (104.5±1.0)% and (104.6±1.2)%, respectively. Similar mean dose doses to the heart and contralateral lungs were observed from both plans, whereas the mean dose to the contra-lateral breast was (2.79±1.18) cGy and (2.86±1.40) cGy for FFF and clinical plans respectively. However for both plans the error between calculated and measured doses at 4 cm from the field edge was 10%. Conclusion: The results showed that FFF beams in prone APBI provide dosimetrically equivalent target coverage and improved coverage in superficial target due to softer energy spectra. Film analysis showed that the TPS underestimates dose outside field edges for both cases. The FFF measured plans showed less dose outside the beam that might reduce the probability of secondary cancers in the contralateral breast.« less

  11. Comprehensive analysis of a medication dosing error related to CPOE.

    PubMed

    Horsky, Jan; Kuperman, Gilad J; Patel, Vimla L

    2005-01-01

    This case study of a serious medication error demonstrates the necessity of a comprehensive methodology for the analysis of failures in interaction between humans and information systems. The authors used a novel approach to analyze a dosing error related to computer-based ordering of potassium chloride (KCl). The method included a chronological reconstruction of events and their interdependencies from provider order entry usage logs, semistructured interviews with involved clinicians, and interface usability inspection of the ordering system. Information collected from all sources was compared and evaluated to understand how the error evolved and propagated through the system. In this case, the error was the product of faults in interaction among human and system agents that methods limited in scope to their distinct analytical domains would not identify. The authors characterized errors in several converging aspects of the drug ordering process: confusing on-screen laboratory results review, system usability difficulties, user training problems, and suboptimal clinical system safeguards that all contributed to a serious dosing error. The results of the authors' analysis were used to formulate specific recommendations for interface layout and functionality modifications, suggest new user alerts, propose changes to user training, and address error-prone steps of the KCl ordering process to reduce the risk of future medication dosing errors.

  12. Delusion proneness and emotion appraisal in individuals with high psychosis vulnerability.

    PubMed

    Szily, Erika; Kéri, Szabolcs

    2013-01-01

    Evidence suggests that emotional processes play an important role in the development of delusions. The aim of the present study was to investigate emotion appraisal in individuals with high and low psychosis proneness. We compared 30 individuals who experienced a transient psychotic episode followed by a complete remission with 30 healthy control volunteers. The participants received the Peters et al. Delusion Inventory (PDI) and the Scherer's Emotion Appraisal Questionnaire. We also assessed the IQ and the severity of depressive and anxiety symptoms. Results revealed that individuals with high psychosis proneness displayed increased PDI scores and more pronounced anxiety compared with individuals with low psychosis proneness. There was a specific pattern of emotion appraisal in individuals with high psychosis proneness. In the case of fear, they achieved higher scores for external causality and immorality, and lower scores for coping ability and self-esteem compared with individuals with low proneness. The PDI scores were weakly related to external causality (r = 0.41) and self-esteem (r = -0.37). In the case of sadness and joy, no emotion appraisal differences were found between participants with low and high proneness. These results suggest that individuals who had a history of psychotic breakdown and therefore exhibit high psychosis proneness display an altered appraisal of fear, emphasizing external circumstances, feeling less power to cope and experience low self-esteem. Patients remitted from a transient psychotic episode still exhibit milder forms of delusion proneness. Emotion appraisal for fear is related to delusion proneness. Clinicians should pay a special attention to self-esteem and attribution biases in psychosis-prone individuals. Copyright © 2011 John Wiley & Sons, Ltd.

  13. [Comparative studies of serological typing and HLA-A, B antigen genotyping with PCR using sequence-specific primers].

    PubMed

    Wu, Da-lin; Ling, Han-xin; Tang, Hao

    2004-11-01

    To evaluate the accuracy of PCR with sequence-specific primers (PCR-SSP) for HLA-I genotyping and analyze the causes of the errors occurring in the genotyping. DNA samples and were obtained from 34 clinical patients, and serological typing with monoclonal antibody (mAb) and HLA-A and, B antigen genotyping with PCR-SSP were performed. HLA-A and, B alleles were successfully typed in 34 clinical samples by mAb and PCR-SSP. No false positive or false negative results were found, and the erroneous and missed diagnosis rates were obviously higher in serological detection, being 23.5% for HLA-A and 26.5% for HLA-B. Error or confusion was more likely to occur in the antigens of A2 and A68, A32 and A33, B5, B60 and B61. DNA typing for HLA-I class (A, B antigens) by PCR-SSP has high resolution, high specificity, and good reproducibility, which is more suitable for clinical application than serological typing. PCR-SSP may accurately detect the alleles that are easily missed or mistaken in serological typing.

  14. Comparing Errors in Medicaid Reporting across Surveys: Evidence to Date

    PubMed Central

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

    2013-01-01

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

  15. Experimental investigation of observation error in anuran call surveys

    USGS Publications Warehouse

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

    2010-01-01

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

  16. IPTV multicast with peer-assisted lossy error control

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

  17. Droplet-based micro oscillating-flow PCR chip

    NASA Astrophysics Data System (ADS)

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

    2005-08-01

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

  18. The role of a prone setup in breast radiation therapy.

    PubMed

    Huppert, Nelly; Jozsef, Gabor; Dewyngaert, Keith; Formenti, Silvia Chiara

    2011-01-01

    Most patients undergoing breast conservation therapy receive radiotherapy in the supine position. Historically, prone breast irradiation has been advocated for women with large pendulous breasts in order to decrease acute and late toxicities. With the advent of CT planning, the prone technique has become both feasible and reproducible. It was shown to be advantageous not only for women with larger breasts but in most patients since it consistently reduces, if not eliminates, the inclusion of heart and lung within the field. The prone setup has been accepted as the best localizing position for both MRI and stereotactic biopsy, but its adoption has been delayed in radiotherapy. New technological advances including image-modulated radiation therapy and image-guided radiation therapy have made possible the exploration of accelerated fractionation schemes with a concomitant boost to the tumor bed in the prone position, along with better imaging and verification of reproducibility of patient setup. This review describes some of the available techniques for prone breast radiotherapy and the available experience in their application. The NYU prone breast radiotherapy approach is discussed, including a summary of the results from several prospective trials.

  19. Medication errors as malpractice-a qualitative content analysis of 585 medication errors by nurses in Sweden.

    PubMed

    Björkstén, Karin Sparring; Bergqvist, Monica; Andersén-Karlsson, Eva; Benson, Lina; Ulfvarson, Johanna

    2016-08-24

    Many studies address the prevalence of medication errors but few address medication errors serious enough to be regarded as malpractice. Other studies have analyzed the individual and system contributory factor leading to a medication error. Nurses have a key role in medication administration, and there are contradictory reports on the nurses' work experience in relation to the risk and type for medication errors. All medication errors where a nurse was held responsible for malpractice (n = 585) during 11 years in Sweden were included. A qualitative content analysis and classification according to the type and the individual and system contributory factors was made. In order to test for possible differences between nurses' work experience and associations within and between the errors and contributory factors, Fisher's exact test was used, and Cohen's kappa (k) was performed to estimate the magnitude and direction of the associations. There were a total of 613 medication errors in the 585 cases, the most common being "Wrong dose" (41 %), "Wrong patient" (13 %) and "Omission of drug" (12 %). In 95 % of the cases, an average of 1.4 individual contributory factors was found; the most common being "Negligence, forgetfulness or lack of attentiveness" (68 %), "Proper protocol not followed" (25 %), "Lack of knowledge" (13 %) and "Practice beyond scope" (12 %). In 78 % of the cases, an average of 1.7 system contributory factors was found; the most common being "Role overload" (36 %), "Unclear communication or orders" (30 %) and "Lack of adequate access to guidelines or unclear organisational routines" (30 %). The errors "Wrong patient due to mix-up of patients" and "Wrong route" and the contributory factors "Lack of knowledge" and "Negligence, forgetfulness or lack of attentiveness" were more common in less experienced nurses. The experienced nurses were more prone to "Practice beyond scope of practice" and to make errors in spite of "Lack of adequate

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

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kreuer, Dieter; Quernheim, Ulrich

    1991-10-01

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

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

    PubMed

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

    2015-06-01

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

  3. Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay.

    PubMed

    Heredia, Nicholas J

    2018-01-01

    Digital PCR is a valuable tool to quantify next-generation sequencing (NGS) libraries precisely and accurately. Accurately quantifying NGS libraries enable accurate loading of the libraries on to the sequencer and thus improve sequencing performance by reducing under and overloading error. Accurate quantification also benefits users by enabling uniform loading of indexed/barcoded libraries which in turn greatly improves sequencing uniformity of the indexed/barcoded samples. The advantages gained by employing the Droplet Digital PCR (ddPCR™) library QC assay includes the precise and accurate quantification in addition to size quality assessment, enabling users to QC their sequencing libraries with confidence.

  4. Commission errors of active intentions: the roles of aging, cognitive load, and practice.

    PubMed

    Boywitt, C Dennis; Rummel, Jan; Meiser, Thorsten

    2015-01-01

    Performing an intended action when it needs to be withheld, for example, when temporarily prescribed medication is incompatible with the other medication, is referred to as commission errors of prospective memory (PM). While recent research indicates that older adults are especially prone to commission errors for finished intentions, there is a lack of research on the effects of aging on commission errors for still active intentions. The present research investigates conditions which might contribute to older adults' propensity to perform planned intentions under inappropriate conditions. Specifically, disproportionally higher rates of commission errors for still active intentions were observed in older than in younger adults with both salient (Experiment 1) and non-salient (Experiment 2) target cues. Practicing the PM task in Experiment 2, however, helped execution of the intended action in terms of higher PM performance at faster ongoing-task response times but did not increase the rate of commission errors. The results have important implications for the understanding of older adults' PM commission errors and the processes involved in these errors.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    1995-08-28

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

  6. Accident proneness : a research review.

    DOT National Transportation Integrated Search

    1993-05-01

    Accident proneness is a concept that refers to an enduring or stable personality characteristic that predisposes an individual toward having accidents (Haddon, Suchman, and Klein, 1964). The concept is controversial and has sustained a lively debate ...

  7. Arousal from sleep pathways are affected by the prone sleeping position and preterm birth: preterm birth, prone sleeping and arousal from sleep.

    PubMed

    Richardson, Heidi L; Horne, Rosemary S C

    2013-09-01

    Preterm infants exhibit depressed arousability from sleep when compared with term infants. As the final cortical element of the arousal process may be the most critical for survival, we hypothesized that the increased vulnerability of preterm infants to the Sudden Infant Death Syndrome (SIDS) could be explained by depressed cortical arousal (CA) responses. We evaluated the effects of preterm birth on stimulus-induced arousal processes in both the prone and supine sleeping positions. 10 healthy preterm infants were studied with daytime polysomnography, in both supine and prone sleeping positions, at 36 weeks gestational age, 2-4 weeks, 2-3 months and 5-6 months post-term corrected age. Sub-cortical activations and cortical arousals (CA) were expressed as proportions of total arousal responses. Preterm data were compared with data from 13 healthy term infants studied at the same corrected ages. In preterm infants increased CAs were observed in the prone position at all ages studied. Compared to term infants, preterm infants had significantly fewer CAs in QS when prone at 2-3 months of age and more CAs when prone at 2-4 weeks in AS. There were no differences in either sleep state when infants slept supine. Prone sleeping promoted CA responses in healthy preterm infants throughout the first six months of post-term age. We have previously suggested that in term infants enhanced CA represents a critical protection against a potentially harmful situation; we speculate that for preterm-born infants the need for this protection is greater than in term infants. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

  8. Validated reverse transcription droplet digital PCR serves as a higher order method for absolute quantification of Potato virus Y strains.

    PubMed

    Mehle, Nataša; Dobnik, David; Ravnikar, Maja; Pompe Novak, Maruša

    2018-05-03

    RNA viruses have a great potential for high genetic variability and rapid evolution that is generated by mutation and recombination under selection pressure. This is also the case of Potato virus Y (PVY), which comprises a high diversity of different recombinant and non-recombinant strains. Consequently, it is hard to develop reverse transcription real-time quantitative PCR (RT-qPCR) with the same amplification efficiencies for all PVY strains which would enable their equilibrate quantification; this is specially needed in mixed infections and other studies of pathogenesis. To achieve this, we initially transferred the PVY universal RT-qPCR assay to a reverse transcription droplet digital PCR (RT-ddPCR) format. RT-ddPCR is an absolute quantification method, where a calibration curve is not needed, and it is less prone to inhibitors. The RT-ddPCR developed and validated in this study achieved a dynamic range of quantification over five orders of magnitude, and in terms of its sensitivity, it was comparable to, or even better than, RT-qPCR. RT-ddPCR showed lower measurement variability. We have shown that RT-ddPCR can be used as a reference tool for the evaluation of different RT-qPCR assays. In addition, it can be used for quantification of RNA based on in-house reference materials that can then be used as calibrators in diagnostic laboratories.

  9. Biochemical analysis of six genetic variants of error-prone human DNA polymerase ι involved in translesion DNA synthesis.

    PubMed

    Kim, Jinsook; Song, Insil; Jo, Ara; Shin, Joo-Ho; Cho, Hana; Eoff, Robert L; Guengerich, F Peter; Choi, Jeong-Yun

    2014-10-20

    DNA polymerase (pol) ι is the most error-prone among the Y-family polymerases that participate in translesion synthesis (TLS). Pol ι can bypass various DNA lesions, e.g., N(2)-ethyl(Et)G, O(6)-methyl(Me)G, 8-oxo-7,8-dihydroguanine (8-oxoG), and an abasic site, though frequently with low fidelity. We assessed the biochemical effects of six reported genetic variations of human pol ι on its TLS properties, using the recombinant pol ι (residues 1-445) proteins and DNA templates containing a G, N(2)-EtG, O(6)-MeG, 8-oxoG, or abasic site. The Δ1-25 variant, which is the N-terminal truncation of 25 residues resulting from an initiation codon variant (c.3G > A) and also is the formerly misassigned wild-type, exhibited considerably higher polymerase activity than wild-type with Mg(2+) (but not with Mn(2+)), coinciding with its steady-state kinetic data showing a ∼10-fold increase in kcat/Km for nucleotide incorporation opposite templates (only with Mg(2+)). The R96G variant, which lacks a R96 residue known to interact with the incoming nucleotide, lost much of its polymerase activity, consistent with the kinetic data displaying 5- to 72-fold decreases in kcat/Km for nucleotide incorporation opposite templates either with Mg(2+) or Mn(2+), except for that opposite N(2)-EtG with Mn(2+) (showing a 9-fold increase for dCTP incorporation). The Δ1-25 variant bound DNA 20- to 29-fold more tightly than wild-type (with Mg(2+)), but the R96G variant bound DNA 2-fold less tightly than wild-type. The DNA-binding affinity of wild-type, but not of the Δ1-25 variant, was ∼7-fold stronger with 0.15 mM Mn(2+) than with Mg(2+). The results indicate that the R96G variation severely impairs most of the Mg(2+)- and Mn(2+)-dependent TLS abilities of pol ι, whereas the Δ1-25 variation selectively and substantially enhances the Mg(2+)-dependent TLS capability of pol ι, emphasizing the potential translational importance of these pol ι genetic variations, e.g., individual differences

  10. Biochemical Analysis of Six Genetic Variants of Error-Prone Human DNA Polymerase ι Involved in Translesion DNA Synthesis

    PubMed Central

    2015-01-01

    DNA polymerase (pol) ι is the most error-prone among the Y-family polymerases that participate in translesion synthesis (TLS). Pol ι can bypass various DNA lesions, e.g., N2-ethyl(Et)G, O6-methyl(Me)G, 8-oxo-7,8-dihydroguanine (8-oxoG), and an abasic site, though frequently with low fidelity. We assessed the biochemical effects of six reported genetic variations of human pol ι on its TLS properties, using the recombinant pol ι (residues 1–445) proteins and DNA templates containing a G, N2-EtG, O6-MeG, 8-oxoG, or abasic site. The Δ1–25 variant, which is the N-terminal truncation of 25 residues resulting from an initiation codon variant (c.3G > A) and also is the formerly misassigned wild-type, exhibited considerably higher polymerase activity than wild-type with Mg2+ (but not with Mn2+), coinciding with its steady-state kinetic data showing a ∼10-fold increase in kcat/Km for nucleotide incorporation opposite templates (only with Mg2+). The R96G variant, which lacks a R96 residue known to interact with the incoming nucleotide, lost much of its polymerase activity, consistent with the kinetic data displaying 5- to 72-fold decreases in kcat/Km for nucleotide incorporation opposite templates either with Mg2+ or Mn2+, except for that opposite N2-EtG with Mn2+ (showing a 9-fold increase for dCTP incorporation). The Δ1–25 variant bound DNA 20- to 29-fold more tightly than wild-type (with Mg2+), but the R96G variant bound DNA 2-fold less tightly than wild-type. The DNA-binding affinity of wild-type, but not of the Δ1–25 variant, was ∼7-fold stronger with 0.15 mM Mn2+ than with Mg2+. The results indicate that the R96G variation severely impairs most of the Mg2+- and Mn2+-dependent TLS abilities of pol ι, whereas the Δ1–25 variation selectively and substantially enhances the Mg2+-dependent TLS capability of pol ι, emphasizing the potential translational importance of these pol ι genetic variations, e.g., individual differences in TLS, mutation, and

  11. Angiotensin-converting enzyme insertion/deletion polymorphism genotyping error: the cause and a possible solution to the problem.

    PubMed

    Saracevic, Andrea; Simundic, Ana-Maria; Celap, Ivana; Luzanic, Valentina

    2013-07-01

    Rigat and colleagues were the first ones to develop a rapid PCR-based assay for identifying the angiotensin converting enzyme insertion/deletion (I/D) polymorphism. Due to a big difference between the length of the wild-type and mute alleles the PCR method is prone to mistyping because of preferential amplification of the D allele causing depicting I/D heterozygotes as D/D homozygotes. The aim of this study was to investigate whether this preferential amplification can be repressed by amplifying a longer DNA fragment in a so called Long PCR protocol. We also aimed to compare the results of genotyping using five different PCR protocols and to estimate the mistyping rate. The study included 200 samples which were genotyped using standard method used in our laboratory, a stepdown PCR, PCR protocol with the inclusion of 4 % DMSO, PCR with the use of insertion specific primers and new Long PCR method. The results of this study have shown that accurate ACE I/D polymorphism genotyping can be accomplished with the standard and the Long PCR method. Also, as of our results, accurate ACE I/D polymorphism genotyping can be accomplished regardless of the method used. Therefore, if the standard method is optimized more cautiously, accurate results can be obtained by this simple, inexpensive and rapid PCR protocol.

  12. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

    PubMed Central

    2017-01-01

    Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalized. In particular, sequencing errors in the UMI sequence are often ignored or else resolved in an ad hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single-cell RNA-seq data sets. Reproducibility between iCLIP replicates and single-cell RNA-seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package. PMID:28100584

  13. DNA assembly with error correction on a droplet digital microfluidics platform.

    PubMed

    Khilko, Yuliya; Weyman, Philip D; Glass, John I; Adams, Mark D; McNeil, Melanie A; Griffin, Peter B

    2018-06-01

    Custom synthesized DNA is in high demand for synthetic biology applications. However, current technologies to produce these sequences using assembly from DNA oligonucleotides are costly and labor-intensive. The automation and reduced sample volumes afforded by microfluidic technologies could significantly decrease materials and labor costs associated with DNA synthesis. The purpose of this study was to develop a gene assembly protocol utilizing a digital microfluidic device. Toward this goal, we adapted bench-scale oligonucleotide assembly methods followed by enzymatic error correction to the Mondrian™ digital microfluidic platform. We optimized Gibson assembly, polymerase chain reaction (PCR), and enzymatic error correction reactions in a single protocol to assemble 12 oligonucleotides into a 339-bp double- stranded DNA sequence encoding part of the human influenza virus hemagglutinin (HA) gene. The reactions were scaled down to 0.6-1.2 μL. Initial microfluidic assembly methods were successful and had an error frequency of approximately 4 errors/kb with errors originating from the original oligonucleotide synthesis. Relative to conventional benchtop procedures, PCR optimization required additional amounts of MgCl 2 , Phusion polymerase, and PEG 8000 to achieve amplification of the assembly and error correction products. After one round of error correction, error frequency was reduced to an average of 1.8 errors kb - 1 . We demonstrated that DNA assembly from oligonucleotides and error correction could be completely automated on a digital microfluidic (DMF) platform. The results demonstrate that enzymatic reactions in droplets show a strong dependence on surface interactions, and successful on-chip implementation required supplementation with surfactants, molecular crowding agents, and an excess of enzyme. Enzymatic error correction of assembled fragments improved sequence fidelity by 2-fold, which was a significant improvement but somewhat lower than

  14. Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes.

    PubMed

    Lau, Billy T; Ji, Hanlee P

    2017-09-21

    RNA-Seq measures gene expression by counting sequence reads belonging to unique cDNA fragments. Molecular barcodes commonly in the form of random nucleotides were recently introduced to improve gene expression measures by detecting amplification duplicates, but are susceptible to errors generated during PCR and sequencing. This results in false positive counts, leading to inaccurate transcriptome quantification especially at low input and single-cell RNA amounts where the total number of molecules present is minuscule. To address this issue, we demonstrated the systematic identification of molecular species using transposable error-correcting barcodes that are exponentially expanded to tens of billions of unique labels. We experimentally showed random-mer molecular barcodes suffer from substantial and persistent errors that are difficult to resolve. To assess our method's performance, we applied it to the analysis of known reference RNA standards. By including an inline random-mer molecular barcode, we systematically characterized the presence of sequence errors in random-mer molecular barcodes. We observed that such errors are extensive and become more dominant at low input amounts. We described the first study to use transposable molecular barcodes and its use for studying random-mer molecular barcode errors. Extensive errors found in random-mer molecular barcodes may warrant the use of error correcting barcodes for transcriptome analysis as input amounts decrease.

  15. Predicted Errors In Children's Early Sentence Comprehension

    PubMed Central

    Gertner, Yael; Fisher, Cynthia

    2012-01-01

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

  16. SU-E-J-21: Setup Variability of Colorectal Cancer Patients Treated in the Prone Position and Dosimetric Comparison with the Supine Position

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, A; Foster, J; Chu, W

    2015-06-15

    Purpose: Many cancer centers treat colorectal patients in the prone position on a belly board to minimize dose to the small bowel. That may potentially Result in patient setup instability with corresponding impact on dose delivery accuracy for highly conformal techniques such as IMRT/VMAT. Two aims of this work are 1) to investigate setup accuracy of rectum patients treated in the prone position on a belly board using CBCT and 2) to evaluate dosimetric impact on bladder and small bowel of treating rectum patients in supine vs. prone position. Methods: For the setup accuracy study, 10 patients were selected. Weeklymore » CBCTs were acquired and matched to bone. The CBCT-determined shifts were recorded. For the dosimetric study, 7 prone-setup patients and 7 supine-setup patients were randomly selected from our clinical database. Various clinically relevant dose volume histogram values were recorded for the small bowel and bladder. Results: The CBCT-determined rotational shifts had a wide variation. For the dataset acquired at the time of this writing, the ranges of rotational setup errors for pitch, roll, and yaw were [−3.6° 4.7°], [−4.3° 3.2°], and [−1.4° 1.4°]. For the dosimetric study: the small bowel V(45Gy) and mean dose for the prone position was 5.6±12.1% and 18.4±6.2Gy (ranges indicate standard deviations); for the supine position the corresponding dose values were 12.9±15.8% and 24.7±8.8Gy. For the bladder, the V(30Gy) and mean dose for prone position were 68.7±12.7% and 38.4±3.3Gy; for supine position these dose values were 77.1±13.7% and 40.7±3.1Gy. Conclusion: There is evidence of significant rotational instability in the prone position. The OAR dosimetry study indicates that there are some patients that may still benefit from the prone position, though many patients can be safely treated supine.« less

  17. A water-vapor radiometer error model. [for ionosphere in geodetic microwave techniques

    NASA Technical Reports Server (NTRS)

    Beckman, B.

    1985-01-01

    The water-vapor radiometer (WVR) is used to calibrate unpredictable delays in the wet component of the troposphere in geodetic microwave techniques such as very-long-baseline interferometry (VLBI) and Global Positioning System (GPS) tracking. Based on experience with Jet Propulsion Laboratory (JPL) instruments, the current level of accuracy in wet-troposphere calibration limits the accuracy of local vertical measurements to 5-10 cm. The goal for the near future is 1-3 cm. Although the WVR is currently the best calibration method, many instruments are prone to systematic error. In this paper, a treatment of WVR data is proposed and evaluated. This treatment reduces the effect of WVR systematic errors by estimating parameters that specify an assumed functional form for the error. The assumed form of the treatment is evaluated by comparing the results of two similar WVR's operating near each other. Finally, the observability of the error parameters is estimated by covariance analysis.

  18. Error rates and resource overheads of encoded three-qubit gates

    NASA Astrophysics Data System (ADS)

    Takagi, Ryuji; Yoder, Theodore J.; Chuang, Isaac L.

    2017-10-01

    A non-Clifford gate is required for universal quantum computation, and, typically, this is the most error-prone and resource-intensive logical operation on an error-correcting code. Small, single-qubit rotations are popular choices for this non-Clifford gate, but certain three-qubit gates, such as Toffoli or controlled-controlled-Z (ccz), are equivalent options that are also more suited for implementing some quantum algorithms, for instance, those with coherent classical subroutines. Here, we calculate error rates and resource overheads for implementing logical ccz with pieceable fault tolerance, a nontransversal method for implementing logical gates. We provide a comparison with a nonlocal magic-state scheme on a concatenated code and a local magic-state scheme on the surface code. We find the pieceable fault-tolerance scheme particularly advantaged over magic states on concatenated codes and in certain regimes over magic states on the surface code. Our results suggest that pieceable fault tolerance is a promising candidate for fault tolerance in a near-future quantum computer.

  19. Decreasing scoring errors on Wechsler Scale Vocabulary, Comprehension, and Similarities subtests: a preliminary study.

    PubMed

    Linger, Michele L; Ray, Glen E; Zachar, Peter; Underhill, Andrea T; LoBello, Steven G

    2007-10-01

    Studies of graduate students learning to administer the Wechsler scales have generally shown that training is not associated with the development of scoring proficiency. Many studies report on the reduction of aggregated administration and scoring errors, a strategy that does not highlight the reduction of errors on subtests identified as most prone to error. This study evaluated the development of scoring proficiency specifically on the Wechsler (WISC-IV and WAIS-III) Vocabulary, Comprehension, and Similarities subtests during training by comparing a set of 'early test administrations' to 'later test administrations.' Twelve graduate students enrolled in an intelligence-testing course participated in the study. Scoring errors (e.g., incorrect point assignment) were evaluated on the students' actual practice administration test protocols. Errors on all three subtests declined significantly when scoring errors on 'early' sets of Wechsler scales were compared to those made on 'later' sets. However, correcting these subtest scoring errors did not cause significant changes in subtest scaled scores. Implications for clinical instruction and future research are discussed.

  20. Noise-induced errors in geophysical parameter estimation from retarding potential analyzers in low Earth orbit

    NASA Astrophysics Data System (ADS)

    Debchoudhury, Shantanab; Earle, Gregory

    2017-04-01

    Retarding Potential Analyzers (RPA) have a rich flight heritage. Standard curve-fitting analysis techniques exist that can infer state variables in the ionospheric plasma environment from RPA data, but the estimation process is prone to errors arising from a number of sources. Previous work has focused on the effects of grid geometry on uncertainties in estimation; however, no prior study has quantified the estimation errors due to additive noise. In this study, we characterize the errors in estimation of thermal plasma parameters by adding noise to the simulated data derived from the existing ionospheric models. We concentrate on low-altitude, mid-inclination orbits since a number of nano-satellite missions are focused on this region of the ionosphere. The errors are quantified and cross-correlated for varying geomagnetic conditions.

  1. Detection of adenoviruses in shellfish by means of conventional-PCR, nested-PCR, and integrated cell culture PCR (ICC/PCR).

    PubMed

    Rigotto, C; Sincero, T C M; Simões, C M O; Barardi, C R M

    2005-01-01

    We tested three PCR based methodologies to detect adenoviruses associated with cultivated oysters. Conventional-PCR, nested-PCR, and integrated cell culture-PCR (ICC/PCR) were first optimized using oysters seeded with know amounts of Adenovirus serotype 5 (Ad5). The maximum sensitivity for Ad5 detection was determined for each method, and then used to detect natural adenovirus contamination in oysters from three aquiculture farms in Florianopolis, Santa Catarina State, Brazil, over a period of 6 months. The results showed that the nested-PCR was more sensitive (limit of detection: 1.2 PFU/g of tissue) than conventional-PCR and ICC-PCR (limit of detection for both: 1.2 x 10(2)PFU/g of tissue) for detection of Ad5 in oyster extracts. Nested-PCR was able to detect 90% of Ad5 contamination in harvested oyster samples, while conventional-PCR was unable to detect Ad5 in any of the samples. The present work suggests that detection of human adenoviruses can be used as a tool to monitor the presence of human viruses in marine environments where shellfish grow, and that nested-PCR is the method of choice.

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

    PubMed

    Skums, Pavel; Dimitrova, Zoya; Campo, David S; Vaughan, Gilberto; Rossi, Livia; Forbi, Joseph C; Yokosawa, Jonny; Zelikovsky, Alex; Khudyakov, Yury

    2012-06-25

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

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

    PubMed

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

    2015-01-01

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

  4. Proneness to Self-Conscious Emotions in Adults With and Without Autism Traits.

    PubMed

    Davidson, Denise; Vanegas, Sandra B; Hilvert, Elizabeth

    2017-11-01

    Self-conscious emotions, such as shame, guilt and pride, facilitate our social interactions by motivating us to adhere to social norms and external standards. In this study, we examined proneness to shame, guilt, hubristic pride and authentic pride in adults with Autism Spectrum Disorder traits (ASD-T) and in neurotypical (NT) adults. Relations between proneness to self-conscious emotions and theory of mind (ToM), fear of negative evaluation, and social functioning were also assessed. Adults with ASD-T showed greater proneness to shame, and less proneness to guilt and pride than NT adults. Both ToM and fear of negative evaluation predicted proneness to self-conscious emotions in ASD-T. These findings are discussed in terms of understanding complex emotion processing in adults with ASD-T.

  5. Effect of prone positioning on cannula function and impaired oxygenation during extracorporeal circulation.

    PubMed

    Masuda, Yoshiki; Tatsumi, Hiroomi; Imaizumi, Hitoshi; Gotoh, Kyoko; Yoshida, Shinichiro; Chihara, Shinya; Takahashi, Kanako; Yamakage, Michiaki

    2014-03-01

    Prone ventilation is an effective method for improving oxygenation in patients with acute respiratory failure. However, in extracorporeal circulation, there is a risk of cannula-related complications when changing the position. In this study, we investigated cannula-related complications when changing position for prone ventilation and the effect of prone ventilation on impaired oxygenation in patients who underwent extracorporeal membrane oxygenation (ECMO). The study subjects were patients who underwent prone ventilation during ECMO in the period from 2004 to 2011. Indication for prone ventilation was the presence of dorsal infiltration shown by lung computed tomography. Factors investigated were cannula insertion site, dislodgement or obstruction of the cannula, malfunction of vascular access and unplanned dislodgement of the catheters when changing position. Mean arterial pressure, PaO2/FiO2, PEEP level, blood flow and rotation speed of the pump were also determined before and after position change. Five patients were selected as study subjects. The mean duration of prone positioning was 15.3 ± 0.5 h. Strict management during position changes prevented cannula-related complications in the patients who underwent extracorporeal circulation. There were no significant changes in mean arterial pressure, PEEP level, blood flow and rotation speed of the pump when changing position. Low PaO2/FiO2 prior to prone ventilation was significantly increased after supine to prone and then prone to supine position. Prone positioning to improve impaired oxygenation is a safe procedure and not a contraindication in patients receiving extracorporeal circulation.

  6. Using Audit Information to Adjust Parameter Estimates for Data Errors in Clinical Trials

    PubMed Central

    Shepherd, Bryan E.; Shaw, Pamela A.; Dodd, Lori E.

    2013-01-01

    Background Audits are often performed to assess the quality of clinical trial data, but beyond detecting fraud or sloppiness, the audit data is generally ignored. In earlier work using data from a non-randomized study, Shepherd and Yu (2011) developed statistical methods to incorporate audit results into study estimates, and demonstrated that audit data could be used to eliminate bias. Purpose In this manuscript we examine the usefulness of audit-based error-correction methods in clinical trial settings where a continuous outcome is of primary interest. Methods We demonstrate the bias of multiple linear regression estimates in general settings with an outcome that may have errors and a set of covariates for which some may have errors and others, including treatment assignment, are recorded correctly for all subjects. We study this bias under different assumptions including independence between treatment assignment, covariates, and data errors (conceivable in a double-blinded randomized trial) and independence between treatment assignment and covariates but not data errors (possible in an unblinded randomized trial). We review moment-based estimators to incorporate the audit data and propose new multiple imputation estimators. The performance of estimators is studied in simulations. Results When treatment is randomized and unrelated to data errors, estimates of the treatment effect using the original error-prone data (i.e., ignoring the audit results) are unbiased. In this setting, both moment and multiple imputation estimators incorporating audit data are more variable than standard analyses using the original data. In contrast, in settings where treatment is randomized but correlated with data errors and in settings where treatment is not randomized, standard treatment effect estimates will be biased. And in all settings, parameter estimates for the original, error-prone covariates will be biased. Treatment and covariate effect estimates can be corrected by

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

    PubMed Central

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

    2011-01-01

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

  8. Using Block-local Atomicity to Detect Stale-value Concurrency Errors

    NASA Technical Reports Server (NTRS)

    Artho, Cyrille; Havelund, Klaus; Biere, Armin

    2004-01-01

    Data races do not cover all kinds of concurrency errors. This paper presents a data-flow-based technique to find stale-value errors, which are not found by low-level and high-level data race algorithms. Stale values denote copies of shared data where the copy is no longer synchronized. The algorithm to detect such values works as a consistency check that does not require any assumptions or annotations of the program. It has been implemented as a static analysis in JNuke. The analysis is sound and requires only a single execution trace if implemented as a run-time checking algorithm. Being based on an analysis of Java bytecode, it encompasses the full program semantics, including arbitrarily complex expressions. Related techniques are more complex and more prone to over-reporting.

  9. Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations

    PubMed Central

    Zhou, Shuntai; Jones, Corbin; Mieczkowski, Piotr

    2015-01-01

    ABSTRACT Validating the sampling depth and reducing sequencing errors are critical for studies of viral populations using next-generation sequencing (NGS). We previously described the use of Primer ID to tag each viral RNA template with a block of degenerate nucleotides in the cDNA primer. We now show that low-abundance Primer IDs (offspring Primer IDs) are generated due to PCR/sequencing errors. These artifactual Primer IDs can be removed using a cutoff model for the number of reads required to make a template consensus sequence. We have modeled the fraction of sequences lost due to Primer ID resampling. For a typical sequencing run, less than 10% of the raw reads are lost to offspring Primer ID filtering and resampling. The remaining raw reads are used to correct for PCR resampling and sequencing errors. We also demonstrate that Primer ID reveals bias intrinsic to PCR, especially at low template input or utilization. cDNA synthesis and PCR convert ca. 20% of RNA templates into recoverable sequences, and 30-fold sequence coverage recovers most of these template sequences. We have directly measured the residual error rate to be around 1 in 10,000 nucleotides. We use this error rate and the Poisson distribution to define the cutoff to identify preexisting drug resistance mutations at low abundance in an HIV-infected subject. Collectively, these studies show that >90% of the raw sequence reads can be used to validate template sampling depth and to dramatically reduce the error rate in assessing a genetically diverse viral population using NGS. IMPORTANCE Although next-generation sequencing (NGS) has revolutionized sequencing strategies, it suffers from serious limitations in defining sequence heterogeneity in a genetically diverse population, such as HIV-1 due to PCR resampling and PCR/sequencing errors. The Primer ID approach reveals the true sampling depth and greatly reduces errors. Knowing the sampling depth allows the construction of a model of how to maximize

  10. quantGenius: implementation of a decision support system for qPCR-based gene quantification.

    PubMed

    Baebler, Špela; Svalina, Miha; Petek, Marko; Stare, Katja; Rotter, Ana; Pompe-Novak, Maruša; Gruden, Kristina

    2017-05-25

    Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. We have developed "quantGenius" ( http://quantgenius.nib.si ), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry-independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases. To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation.

  11. Prone positioning for head and neck reconstructive surgery.

    PubMed

    Mobley, Steven Ross; Miller, Brian Thomas; Astor, Frank C; Fine, Bradley; Halliday, N James

    2007-11-01

    Certain head and neck surgical cases require the patient to be positioned prone. Such positioning carries with it an attendant subset of risks and complications not otherwise encountered in more traditional supine positioning. Gaining awareness of these risks and complications, and developing proactive positioning strategies, will enable the surgical team to position the patient optimally for the procedure and provide for every consideration of patient safety. This article consists of a specific literature review of those issues directly related to the anatomical and physiological concerns arising from prone positioning. Particular attention is paid to the cardiopulmonary, renal, ophthalmologic, and neurological vulnerabilities unique to this position. Proper planning by the surgical team and utilization of the correct equipment are a necessity. A tailored approach to the needs of the individual patient and an intimate awareness of the potential pitfalls will contribute to better outcomes when using the prone position.

  12. The effect of prone position on respiratory mechanics during spinal surgery.

    PubMed

    Manna, Essam M; Ibraheim, Osama A; Samarkandi, Abdulhamid H; Alotaibi, Wadha M; Elwatidy, Sherif M

    2005-10-01

    To study the effect of prone position on respiratory mechanics during spine surgery. Prospective study. Elective spine surgery at a university hospital. 12 ASA physical I & II with no coexisting cardiorespiratory disease undergoing cervical or lumbar laminectomy under general anesthesia in prone position. Ten min after induction of general anesthesia and endotracheal intubation, while patients were in supine position, the following measurements were taken using anesthesia delivery unit (Datex Ohmeda type A_Elec, Promma, Sweden): peak airway pressure (Ppeak), peak plataeu pressure (Pplat), peak mean pressure (Pmean) and dynamic lung compliance (DLC). The same measurements were recorded 10 min after placing patients into prone position. At the end of surgery and 5 min after turning the patients supine and before tracheal extubation, the same measurements were again recorded. The results expressed as means +/- sd. One way ANOVA was used for analysis of differences in the data before, during prone position and after turning patients supine at the end of the procedure. For all comparisons p < 0.05 was considered significant. During prone position there was significant reduction in DLC and significant increase in airway pressures. We conclude that turning the patients form supine to prone position during anesthesia for spine surgery caused significant decrease of DLC and significant increase of airway pressure.

  13. Impairment in flexible emotion-based learning in hallucination- and delusion-prone individuals.

    PubMed

    Cella, Matteo; Dymond, Simon; Cooper, Andrew

    2009-11-30

    Deficits in emotion-based learning are implicated in many psychiatric disorders. Research conducted with patients with schizophrenia using one of the most popular tasks for the investigation of emotion-based learning, the Iowa Gambling Task (IGT), has largely been inconclusive. The present study employed a novel, contingency-shifting variant IGT with hallucination- and delusion-prone university students to determine whether previous findings were due merely to the presence of psychosis. Following initial screening of a sample of 253 students (mean age = 20.13 years, S.D. = 3.27), 28 high (10 male, 18 female) and 27 low (12 male, 15 female) hallucination-prone and 27 high (7 male, 20 female) and 26 low (11 male, 15 female) delusion-prone individuals completed the contingency-shifting variant IGT. Results showed no significant differences between the performances of high and low hallucination- and delusion-prone individuals during the original phase of the task. Differences only emerged following the onset of the contingency-shift phases, with individuals high in hallucination- and delusion-proneness having impaired performance compared with low hallucination- and delusion-prone individuals. Overall, the present findings demonstrate that impairments associated with hallucination- and delusion-proneness are specific to the shift phase of the contingency-shifting variant IGT, which supports previous findings with patients with schizophrenia.

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

    PubMed Central

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

    2007-01-01

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

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

    PubMed Central

    Berman, Jennifer R.; Postovit, Lynne-Marie

    2016-01-01

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Feng, Shihai; Lo, Chien-Chi; Li, Po-E

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

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

    DOE PAGES

    Feng, Shihai; Lo, Chien-Chi; Li, Po-E; ...

    2016-02-29

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

  18. Intraoperative visualization and assessment of electromagnetic tracking error

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  19. SHAME AND GUILT-PRONENESS AS MEDIATORS OF ASSOCIATIONS BETWEEN GENERAL CAUSALITY ORIENTATIONS AND DEPRESSIVE SYMPTOMS

    PubMed Central

    YOUNG, CHELSIE M.; NEIGHBORS, CLAYTON; DIBELLO, ANGELO M.; TRAYLOR, ZACHARY K.; TOMKINS, MARY

    2017-01-01

    The present study examined the roles of shame- and guilt-proneness as mediators of associations between general causality orientations and depressive symptoms. We expected autonomy would be associated with less depressive symptoms based on higher guilt-proneness and lower shame-proneness, whereas control would be associated with more depressive symptoms based on lower guilt-proneness and higher shame-proneness. Undergraduates (N = 354) completed assessments of general causality orientations, shame- and guilt-proneness, and depressive symptoms in exchange for extra credit. Results of mediation analyses were generally supportive of the framework indicating that shame- and guilt-proneness mediate associations between self-determination and depressive symptoms. Autonomy was indirectly associated with less depressive symptoms through positive associations with guilt-proneness, in spite of unexpected positive associations with shame-proneness. Control and impersonal orientation were indirectly associated with more depressive symptoms through positive associations with shame-proneness. Results extend previous research relating self-determination to mental health in providing preliminary support suggesting that individual differences in self-determination facilitate differential tendencies in experiencing guilt and shame. PMID:28344381

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

    PubMed Central

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  2. Empathy, Guilt Proneness, and Gender: Relative Contributions to Prosocial Behaviour

    PubMed Central

    Torstveit, Linda; Sütterlin, Stefan; Lugo, Ricardo Gregorio

    2016-01-01

    Guilt is a moral emotion that is often looked upon as a negative trait. However, studies show that some individuals are more predisposed to think, feel and act in a more ethical manner because of a lower threshold to experience guilt. Some theories of helping behaviour emphasize the evolutionary mechanisms, while other theories stress the importance of social variables. This study investigated whether guilt proneness as a dispositional trait can be associated with prosocial behaviour. Five hundred sixty-nine participants reported in an online survey their own levels of guilt proneness, frequency of prosocial behaviour, and related cognitions such as empathy. This study is among the first to demonstrate how guilt proneness combined with empathy can explain additional variance in prosocial behaviour. The findings also indicate gender differences in the precursors of prosocial behaviour, suggesting women are more influenced by the effects of guilt proneness on prosocial behaviour than men. PMID:27298635

  3. Error Estimation of Pathfinder Version 5.3 SST Level 3C Using Three-way Error Analysis

    NASA Astrophysics Data System (ADS)

    Saha, K.; Dash, P.; Zhao, X.; Zhang, H. M.

    2017-12-01

    One of the essential climate variables for monitoring as well as detecting and attributing climate change, is Sea Surface Temperature (SST). A long-term record of global SSTs are available with observations obtained from ships in the early days to the more modern observation based on in-situ as well as space-based sensors (satellite/aircraft). There are inaccuracies associated with satellite derived SSTs which can be attributed to the errors associated with spacecraft navigation, sensor calibrations, sensor noise, retrieval algorithms, and leakages due to residual clouds. Thus it is important to estimate accurate errors in satellite derived SST products to have desired results in its applications.Generally for validation purposes satellite derived SST products are compared against the in-situ SSTs which have inaccuracies due to spatio/temporal inhomogeneity between in-situ and satellite measurements. A standard deviation in their difference fields usually have contributions from both satellite as well as the in-situ measurements. A real validation of any geophysical variable must require the knowledge of the "true" value of the said variable. Therefore a one-to-one comparison of satellite based SST with in-situ data does not truly provide us the real error in the satellite SST and there will be ambiguity due to errors in the in-situ measurements and their collocation differences. A Triple collocation (TC) or three-way error analysis using 3 mutually independent error-prone measurements, can be used to estimate root-mean square error (RMSE) associated with each of the measurements with high level of accuracy without treating any one system a perfectly-observed "truth". In this study we are estimating the absolute random errors associated with Pathfinder Version 5.3 Level-3C SST product Climate Data record. Along with the in-situ SST data, the third source of dataset used for this analysis is the AATSR reprocessing of climate (ARC) dataset for the corresponding

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

    ERIC Educational Resources Information Center

    Calamari, Elena; Pini, Mauro

    2003-01-01

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

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

    PubMed Central

    2012-01-01

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

  6. SU-F-T-536: Contra-Lateral Breast Study for Prone Versus Supine Patients

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Marrero, M; Joseph, K; Klein, E

    Purpose: There are several advantages to utilizing the prone technique for intact breast cancer patients. However, as the topography changes, accompanied by the influence of a supporting breast board and patient treatment couch, the question that arises is to whether there is a concern for contralateral breast dose for intact breast cancer patients being treated with this technique. Methods: An anthropomorphic phantom with breast mounds to duplicate intact breast cancer treatment was planned in prone and supine position. Two tangential beams were executed in the similar manner for as the radiotherapy planning system. For the prone setup, a breast densemore » foam board was used to support the phantom. A grid of 24 OSL nanodots was placed at 6cm, 4cm, and 2cm apart from the medial border for both prone and supine setups. The phantom was set up using megavoltage imaging and treated as per plan. Additional, a similar study was performed on a patient treated in prone position. Results: Overall, the contralateral breast dose was generally higher for prone setups at all locations especially when close to the medial border. The average mean dose was found to be 1.8%, 2.5% of the prescribed dose for supine respectively prone position. The average of the standard deviation is 1.04%, 1.38% for supine respectively prone position. As for patient treated in prone position average mean dose was found to be 1.165% of the prescribed dose and average of the standard deviation is 9.456%. Conclusion: There is minimal influence of scatter from the breast board. It appears that the volatility of the setup could lead to higher doses than expected from the planning system to the contralateral breast when the patient is in the prone position.« less

  7. Cross-cultural differences and similarities in proneness to shame: an adaptationist and ecological approach.

    PubMed

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

    2012-06-29

    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.

  8. Right-frontal cortical asymmetry predicts increased proneness to nostalgia.

    PubMed

    Tullett, Alexa M; Wildschut, Tim; Sedikides, Constantine; Inzlicht, Michael

    2015-08-01

    Nostalgia is often triggered by feelings-such as sadness, loneliness, or meaninglessness-that are typically associated with withdrawal motivation. Here, we examined whether a trait tendency to experience withdrawal motivation is associated with nostalgia proneness. Past work indicates that baseline right-frontal cortical asymmetry is a neural correlate of withdrawal-related motivation. We therefore hypothesized that higher baseline levels of right-frontal asymmetry would predict increased proneness to nostalgia. We assessed participants' baseline levels of frontal cortical activity using EEG. Results supported the hypothesis and demonstrated that the association between relative right-frontal asymmetry and increased nostalgia remained significant when controlling for the Big Five personality traits. Overall, these findings indicate that individuals with a stronger dispositional tendency to experience withdrawal-related motivation are more prone to nostalgia. © 2015 Society for Psychophysiological Research.

  9. Comparison of Dose Decrement from Intrafraction Motion for Prone and Supine Prostate Radiotherapy

    PubMed Central

    Olsen, Jeffrey; Parikh, Parag J; Watts, Michael; Noel, Camille E; Baker, Kenneth W; Santanam, Lakshmi; Michalski, Jeff M

    2012-01-01

    Background and Purpose Dose effects of intrafraction motion during prone prostate radiotherapy are unknown. We compared prone and supine treatment using real-time tracking data to model dose coverage. Material and Methods Electromagnetic tracking data was analyzed for 10 patients treated prone, and 15 treated supine, with IMRT for localized prostate cancer. Plans were generated using 0, 3, and 5 mm PTV expansions. Manual beam-hold interventions were applied to reposition the patient when translations exceeded a predetermined threshold. A custom software application (SWIFTER) used intrafraction tracking data acquired during beam-on to model delivered prostate dose, by applying rigid body transformations to the prostate structure contoured at simulation within the planned dose cloud. The delivered minimum prostate dose as a percentage of planned dose (Dmin%), and prostate volume covered by the prescription dose as a percentage of the planned volume (VRx%) were compared for prone and supine treatment. Results Dmin% was reduced for prone treatment for 0 (p=0.02) and 3 mm (p=0.03) PTV margins. VRx% was reduced for prone treatment only for 0 mm margins (p=0.002). No significant differences were found using 5 mm margins. Conclusions Intrafraction motion has a greater impact on target coverage for prone compared to supine prostate radiotherapy. PTV margins of 3 mm or less correlate with a significant decrease in delivered dose for prone treatment. PMID:22809590

  10. Comparison of dose decrement from intrafraction motion for prone and supine prostate radiotherapy.

    PubMed

    Olsen, Jeffrey R; Parikh, Parag J; Watts, Michael; Noel, Camille E; Baker, Kenneth W; Santanam, Lakshmi; Michalski, Jeff M

    2012-08-01

    Dose effects of intrafraction motion during prone prostate radiotherapy are unknown. We compared prone and supine treatment using real-time tracking data to model dose coverage. Electromagnetic tracking data were analyzed for 10 patients treated prone, and 15 treated supine, with IMRT for localized prostate cancer. Plans were generated using 0 mm, 3 mm, and 5mm PTV expansions. Manual beam-hold interventions were applied to reposition the patient when translations exceeded a predetermined threshold. A custom software application (SWIFTER) used intrafraction tracking data acquired during beam-on model delivered prostate dose, by applying rigid body transformations to the prostate structure contoured at simulation within the planned dose cloud. The delivered minimum prostate dose as a percentage of planned dose (Dmin%), and prostate volume covered by the prescription dose as a percentage of the planned volume (VRx%) were compared for prone and supine treatment. Dmin% was reduced for prone treatment for 0 (p=0.02) and 3 mm (p=0.03) PTV margins. VRx% was reduced for prone treatment only for 0mm margins (p=0.002). No significant differences were found using 5 mm margins. Intrafraction motion has a greater impact on target coverage for prone compared to supine prostate radiotherapy. PTV margins of 3 mm or less correlate with a significant decrease in delivered dose for prone treatment. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  11. Guilt and Proneness to Shame: Unethical Behaviour in Vulnerable and Grandiose Narcissism

    PubMed Central

    Poless, Pauline Georgees; Torstveit, Linda; Lugo, Ricardo Gregorio; Andreassen, Marita; Sütterlin, Stefan

    2018-01-01

    Narcissists are described as individuals with dysfunctional personality traits such as lack of psychological awareness and empathy. Theories of ethical behaviour assume that unethical actions trigger moral emotions of guilt and shame. Currently, there is a lack of knowledge on moral emotions as dispositional traits and their potential influences on behaviour in individuals with narcissistic traits. The present study examined vulnerable and grandiose narcissism’s differences in the propensity to experience guilt and shame as a proneness, across a range of personal transgressions. Guilt proneness was measured by negative evaluation of unethical behaviour, and whether this evaluation could influence reparation of tendencies of unethical action in vulnerable and grandiose narcissism. Shame proneness was investigated by negative evaluation of the self, and then whether the previous tendency could affect unethical decision making and behaviour (e.g., hiding), in vulnerable and grandiose narcissism. Two hundred and sixteen participants responded to the Guilt and Shame Proneness Scale, the Narcissistic Personality Inventory Scale and the Hypersensitive Narcissism Scale in an online questionnaire. Findings indicate that grandiose narcissism was negatively associated with guilt proneness, and the relation between the vulnerable narcissism and guilt proneness was negative. Additionally, the results confirm a negative association between grandiose narcissism and shame proneness, especially related to the subscale ‘shame negative self-evaluation’. Furthermore, guilt and shame proneness explained 20% of the variance in vulnerable narcissism and 11% in grandiose narcissism. This research indicates that both vulnerable and grandiose narcissism have the tendency to make unethical decisions, and they are more likely to enact in unethical behaviour. These findings are relevant for the detection of narcissistic individual’s propensity to act unethically in social context. PMID

  12. Guilt and Proneness to Shame: Unethical Behaviour in Vulnerable and Grandiose Narcissism.

    PubMed

    Poless, Pauline Georgees; Torstveit, Linda; Lugo, Ricardo Gregorio; Andreassen, Marita; Sütterlin, Stefan

    2018-03-01

    Narcissists are described as individuals with dysfunctional personality traits such as lack of psychological awareness and empathy. Theories of ethical behaviour assume that unethical actions trigger moral emotions of guilt and shame. Currently, there is a lack of knowledge on moral emotions as dispositional traits and their potential influences on behaviour in individuals with narcissistic traits. The present study examined vulnerable and grandiose narcissism's differences in the propensity to experience guilt and shame as a proneness, across a range of personal transgressions. Guilt proneness was measured by negative evaluation of unethical behaviour, and whether this evaluation could influence reparation of tendencies of unethical action in vulnerable and grandiose narcissism. Shame proneness was investigated by negative evaluation of the self, and then whether the previous tendency could affect unethical decision making and behaviour (e.g., hiding), in vulnerable and grandiose narcissism. Two hundred and sixteen participants responded to the Guilt and Shame Proneness Scale, the Narcissistic Personality Inventory Scale and the Hypersensitive Narcissism Scale in an online questionnaire. Findings indicate that grandiose narcissism was negatively associated with guilt proneness, and the relation between the vulnerable narcissism and guilt proneness was negative. Additionally, the results confirm a negative association between grandiose narcissism and shame proneness, especially related to the subscale 'shame negative self-evaluation'. Furthermore, guilt and shame proneness explained 20% of the variance in vulnerable narcissism and 11% in grandiose narcissism. This research indicates that both vulnerable and grandiose narcissism have the tendency to make unethical decisions, and they are more likely to enact in unethical behaviour. These findings are relevant for the detection of narcissistic individual's propensity to act unethically in social context.

  13. Identification and correction of systematic error in high-throughput sequence data

    PubMed Central

    2011-01-01

    Background A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed "next-gen" sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of systematic error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations. Results We characterize and describe systematic errors using overlapping paired reads from high-coverage data. We show that such errors occur in approximately 1 in 1000 base pairs, and that they are highly replicable across experiments. We identify motifs that are frequent at systematic error sites, and describe a classifier that distinguishes heterozygous sites from systematic error. Our classifier is designed to accommodate data from experiments in which the allele frequencies at heterozygous sites are not necessarily 0.5 (such as in the case of RNA-Seq), and can be used with single-end datasets. Conclusions Systematic errors can easily be mistaken for heterozygous sites in individuals, or for SNPs in population analyses. Systematic errors are particularly problematic in low coverage experiments, or in estimates of allele-specific expression from RNA-Seq data. Our characterization of systematic error has allowed us to develop a program, called SysCall, for identifying and correcting such errors. We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments. PMID:22099972

  14. Comparison of three PCR-based assays for SNP genotyping in sugar beet

    USDA-ARS?s Scientific Manuscript database

    Background: PCR allelic discrimination technologies have broad applications in the detection of single nucleotide polymorphisms (SNPs) in genetics and genomics. The use of fluorescence-tagged probes is the leading method for targeted SNP detection, but assay costs and error rates could be improved t...

  15. Relationship and variation of qPCR and culturable enterococci estimates in ambient surface waters are predictable

    USGS Publications Warehouse

    Whitman, Richard L.; Ge, Zhongfu; Nevers, Meredith B.; Boehm, Alexandria B.; Chern, Eunice C.; Haugland, Richard A.; Lukasik, Ashley M.; Molina, Marirosa; Przybyla-Kelly, Kasia; Shively, Dawn A.; White, Emily M.; Zepp, Richard G.; Byappanahalli, Muruleedhara N.

    2010-01-01

    The quantitative polymerase chain reaction (qPCR) method provides rapid estimates of fecal indicator bacteria densities that have been indicated to be useful in the assessment of water quality. Primarily because this method provides faster results than standard culture-based methods, the U.S. Environmental Protection Agency is currently considering its use as a basis for revised ambient water quality criteria. In anticipation of this possibility, we sought to examine the relationship between qPCR-based and culture-based estimates of enterococci in surface waters. Using data from several research groups, we compared enterococci estimates by the two methods in water samples collected from 37 sites across the United States. A consistent linear pattern in the relationship between cell equivalents (CCE), based on the qPCR method, and colony-forming units (CFU), based on the traditional culturable method, was significant (P 10CFU > 2.0/100 mL) while uncertainty increases at lower CFU values. It was further noted that the relative error in replicated qPCR estimates was generally higher than that in replicated culture counts even at relatively high target levels, suggesting a greater need for replicated analyses in the qPCR method to reduce relative error. Further studies evaluating the relationship between culture and qPCR should take into account analytical uncertainty as well as potential differences in results of these methods that may arise from sample variability, different sources of pollution, and environmental factors.

  16. Prone versus supine position in mechanically ventilated children: a pilot study.

    PubMed

    Sawhney, Ashu; Kumar, Nirmal; Sreenivas, Vishnubhatla; Gupta, Sangeeta; Tyagi, Vineet; Puliyel, Jacob M

    2005-05-01

    It is known that mechanically ventilated patients in the prone position have improved oxygenation compared with those supine. We did a prospective, randomized, controlled trial to evaluate the effect of prone position during mechanical ventilation, on survival in critically ill children. Forty-two children needing mechanical ventilation for various illnesses were randomized to receive initial ventilation for four hours prone or supine by drawing lots. Initial severity of illness and blood gases in all children were noted. In a crossover design, after the initial four hours the children were turned over and ventilated in the alternate posture for an hour. Oxygenation parameters and mean airway pressures were noted at one hour, four hours, and five hours. Mortality, duration of ventilation, and the above parameters were compared in the two groups. Initial PRISM scores were similar in the two groups. Mortality in the prone group was less than in the supine group. The odds ratio of mortality was 0.20 (95% CI 0.05-0.75). Duration of ventilation was similar in the two groups. The oxygenation index was significantly lower in the prone group at one, four, and five hours after onset of ventilation. Prone position in the first few hours of ventilation significantly improves gas exchange and oxygenation, reduces the mean airway pressures required to ventilate children, and may cause significant improvement in survival. Our study protocol allowed ventilator settings to be changed as needed during ventilation.

  17. Face emotion recognition is related to individual differences in psychosis-proneness.

    PubMed

    Germine, L T; Hooker, C I

    2011-05-01

    Deficits in face emotion recognition (FER) in schizophrenia are well documented, and have been proposed as a potential intermediate phenotype for schizophrenia liability. However, research on the relationship between psychosis vulnerability and FER has mixed findings and methodological limitations. Moreover, no study has yet characterized the relationship between FER ability and level of psychosis-proneness. If FER ability varies continuously with psychosis-proneness, this suggests a relationship between FER and polygenic risk factors. We tested two large internet samples to see whether psychometric psychosis-proneness, as measured by the Schizotypal Personality Questionnaire-Brief (SPQ-B), is related to differences in face emotion identification and discrimination or other face processing abilities. Experiment 1 (n=2332) showed that psychosis-proneness predicts face emotion identification ability but not face gender identification ability. Experiment 2 (n=1514) demonstrated that psychosis-proneness also predicts performance on face emotion but not face identity discrimination. The tasks in Experiment 2 used identical stimuli and task parameters, differing only in emotion/identity judgment. Notably, the relationships demonstrated in Experiments 1 and 2 persisted even when individuals with the highest psychosis-proneness levels (the putative high-risk group) were excluded from analysis. Our data suggest that FER ability is related to individual differences in psychosis-like characteristics in the normal population, and that these differences cannot be accounted for by differences in face processing and/or visual perception. Our results suggest that FER may provide a useful candidate intermediate phenotype.

  18. Complications associated with prone positioning in elective spinal surgery.

    PubMed

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

    2015-04-18

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

  19. Complications associated with prone positioning in elective spinal surgery

    PubMed Central

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

    2015-01-01

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

  20. Computationally mapping sequence space to understand evolutionary protein engineering.

    PubMed

    Armstrong, Kathryn A; Tidor, Bruce

    2008-01-01

    Evolutionary protein engineering has been dramatically successful, producing a wide variety of new proteins with altered stability, binding affinity, and enzymatic activity. However, the success of such procedures is often unreliable, and the impact of the choice of protein, engineering goal, and evolutionary procedure is not well understood. We have created a framework for understanding aspects of the protein engineering process by computationally mapping regions of feasible sequence space for three small proteins using structure-based design protocols. We then tested the ability of different evolutionary search strategies to explore these sequence spaces. The results point to a non-intuitive relationship between the error-prone PCR mutation rate and the number of rounds of replication. The evolutionary relationships among feasible sequences reveal hub-like sequences that serve as particularly fruitful starting sequences for evolutionary search. Moreover, genetic recombination procedures were examined, and tradeoffs relating sequence diversity and search efficiency were identified. This framework allows us to consider the impact of protein structure on the allowed sequence space and therefore on the challenges that each protein presents to error-prone PCR and genetic recombination procedures.

  1. Error Recovery in the Time-Triggered Paradigm with FTT-CAN.

    PubMed

    Marques, Luis; Vasconcelos, Verónica; Pedreiras, Paulo; Almeida, Luís

    2018-01-11

    Data networks are naturally prone to interferences that can corrupt messages, leading to performance degradation or even to critical failure of the corresponding distributed system. To improve resilience of critical systems, time-triggered networks are frequently used, based on communication schedules defined at design-time. These networks offer prompt error detection, but slow error recovery that can only be compensated with bandwidth overprovisioning. On the contrary, the Flexible Time-Triggered (FTT) paradigm uses online traffic scheduling, which enables a compromise between error detection and recovery that can achieve timely recovery with a fraction of the needed bandwidth. This article presents a new method to recover transmission errors in a time-triggered Controller Area Network (CAN) network, based on the Flexible Time-Triggered paradigm, namely FTT-CAN. The method is based on using a server (traffic shaper) to regulate the retransmission of corrupted or omitted messages. We show how to design the server to simultaneously: (1) meet a predefined reliability goal, when considering worst case error recovery scenarios bounded probabilistically by a Poisson process that models the fault arrival rate; and, (2) limit the direct and indirect interference in the message set, preserving overall system schedulability. Extensive simulations with multiple scenarios, based on practical and randomly generated systems, show a reduction of two orders of magnitude in the average bandwidth taken by the proposed error recovery mechanism, when compared with traditional approaches available in the literature based on adding extra pre-defined transmission slots.

  2. Error Recovery in the Time-Triggered Paradigm with FTT-CAN

    PubMed Central

    Pedreiras, Paulo; Almeida, Luís

    2018-01-01

    Data networks are naturally prone to interferences that can corrupt messages, leading to performance degradation or even to critical failure of the corresponding distributed system. To improve resilience of critical systems, time-triggered networks are frequently used, based on communication schedules defined at design-time. These networks offer prompt error detection, but slow error recovery that can only be compensated with bandwidth overprovisioning. On the contrary, the Flexible Time-Triggered (FTT) paradigm uses online traffic scheduling, which enables a compromise between error detection and recovery that can achieve timely recovery with a fraction of the needed bandwidth. This article presents a new method to recover transmission errors in a time-triggered Controller Area Network (CAN) network, based on the Flexible Time-Triggered paradigm, namely FTT-CAN. The method is based on using a server (traffic shaper) to regulate the retransmission of corrupted or omitted messages. We show how to design the server to simultaneously: (1) meet a predefined reliability goal, when considering worst case error recovery scenarios bounded probabilistically by a Poisson process that models the fault arrival rate; and, (2) limit the direct and indirect interference in the message set, preserving overall system schedulability. Extensive simulations with multiple scenarios, based on practical and randomly generated systems, show a reduction of two orders of magnitude in the average bandwidth taken by the proposed error recovery mechanism, when compared with traditional approaches available in the literature based on adding extra pre-defined transmission slots. PMID:29324723

  3. Laterality, spatial abilities, and accident proneness.

    PubMed

    Voyer, Susan D; Voyer, Daniel

    2015-01-01

    Although handedness as a measure of cerebral specialization has been linked to accident proneness, more direct measures of laterality are rarely considered. The present study aimed to fill that gap in the existing research. In addition, individual difference factors in accident proneness were further examined with the inclusion of mental rotation and navigation abilities measures. One hundred and forty participants were asked to complete the Mental Rotations Test, the Santa Barbara Sense of Direction scale, the Greyscales task, the Fused Dichotic Word Test, the Waterloo Handedness Questionnaire, and a grip strength task before answering questions related to number of accidents in five areas. Results indicated that handedness scores, absolute visual laterality score, absolute response time on the auditory laterality index, and navigation ability were significant predictors of the total number of accidents. Results are discussed with respect to cerebral hemispheric specialization and risk-taking attitudes and behavior.

  4. SU-E-T-307: Dosimetric Comparison of Prone Versus Supine Positioning for Adjuvant Breast Radiation Therapy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pope, C; O’Connor, B; Hayes, L

    Purpose: The prone treatment position has been used to reduce ipsilateral lung and heart dose in left breast radiation. We conducted a retrospective study to evaluate the difference in the dosimetry between prone and supine treatment positions. Methods: Eight left breast cancer patients were simulated in both the supine and prone positions as a pretreatment evaluation for the optimal treatment position. Treatment plans were created for all patients in both the supine and prone positions using a field in field three dimensional planning technique. Prescribed dose was 45 Gy delivered by two tangential photon fields. Irradiated volume (IV) was evaluatedmore » by V50, V100, and dose to lung and heart by V5, V10, V20, and the mean dose were evaluated. Results: All dosimetry metrics for both the supine and prone plans met our internal normal structure guidelines which are based on Quantec data. The average IVs (50% and 100%) were 2223cc and 1361cc prone, 2315cc and 1315cc supine. The average ipsilateral lung Mean dose (0.83Gy prone vs 5.8Gy supine), V5 (1.6% prone vs 20.9% supine), V10 (0.78% prone vs 15% supine) and V20 (0.36% prone vs 11% supine) were significantly lower in prone position. Heart Mean dose (1.4Gy prone vs 2.9Gy supine), V10 (1.4% prone vs 5.0% supine) and V20 (0.4% prone vs 3.5% supine) were found improved for all patients except one where the mean dose was the same and all other values were improved. Conclusion: The prone position offer preferable dosimetry for all patients planned in our study. These patients were chosen based on the physician’s belief that they would benefit from prone treatment either because they had large pendulous breasts or due to the amount of heart seen in the field on CT simulation.« less

  5. Modeling the Error of the Medtronic Paradigm Veo Enlite Glucose Sensor.

    PubMed

    Biagi, Lyvia; Ramkissoon, Charrise M; Facchinetti, Andrea; Leal, Yenny; Vehi, Josep

    2017-06-12

    Continuous glucose monitors (CGMs) are prone to inaccuracy due to time lags, sensor drift, calibration errors, and measurement noise. The aim of this study is to derive the model of the error of the second generation Medtronic Paradigm Veo Enlite (ENL) sensor and compare it with the Dexcom SEVEN PLUS (7P), G4 PLATINUM (G4P), and advanced G4 for Artificial Pancreas studies (G4AP) systems. An enhanced methodology to a previously employed technique was utilized to dissect the sensor error into several components. The dataset used included 37 inpatient sessions in 10 subjects with type 1 diabetes (T1D), in which CGMs were worn in parallel and blood glucose (BG) samples were analyzed every 15 ± 5 min Calibration error and sensor drift of the ENL sensor was best described by a linear relationship related to the gain and offset. The mean time lag estimated by the model is 9.4 ± 6.5 min. The overall average mean absolute relative difference (MARD) of the ENL sensor was 11.68 ± 5.07% Calibration error had the highest contribution to total error in the ENL sensor. This was also reported in the 7P, G4P, and G4AP. The model of the ENL sensor error will be useful to test the in silico performance of CGM-based applications, i.e., the artificial pancreas, employing this kind of sensor.

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

    PubMed

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

    2016-07-01

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

  7. Boredom proneness--the development and correlates of a new scale.

    PubMed

    Farmer, R; Sundberg, N D

    1986-01-01

    This article reports the development, validation, and correlates of a self-report measure of boredom proneness. The 28-item Boredom Proneness (BP) Scale demonstrates satisfactory levels of internal consistency (coefficient alpha = .79) and test-retest reliability (r = .83) over a 1-week interval. Evidence of validity for the BP is supported by correlations with other boredom measures and from a set of studies evaluating interest and attention in the classroom. Other hypothesized relationships with boredom were tested, with significant positive associations found with depression, hopelessness, perceived effort, loneliness, and amotivational orientation. Additional findings indicate boredom proneness to be negatively related to life satisfaction and autonomy orientation. The relationship of boredom to other affective states is discussed, and directions for future research are outlined.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch; Gallati, Sabina, E-mail: sabina.gallati@insel.ch; Schaller, Andre, E-mail: andre.schaller@insel.ch

    2012-07-06

    Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serialmore » 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

  9. Clinical errors that can occur in the treatment decision-making process in psychotherapy.

    PubMed

    Park, Jake; Goode, Jonathan; Tompkins, Kelley A; Swift, Joshua K

    2016-09-01

    Clinical errors occur in the psychotherapy decision-making process whenever a less-than-optimal treatment or approach is chosen when working with clients. A less-than-optimal approach may be one that a client is unwilling to try or fully invest in based on his/her expectations and preferences, or one that may have little chance of success based on contraindications and/or limited research support. The doctor knows best and the independent choice models are two decision-making models that are frequently used within psychology, but both are associated with an increased likelihood of errors in the treatment decision-making process. In particular, these models fail to integrate all three components of the definition of evidence-based practice in psychology (American Psychological Association, 2006). In this article we describe both models and provide examples of clinical errors that can occur in each. We then introduce the shared decision-making model as an alternative that is less prone to clinical errors. PsycINFO Database Record (c) 2016 APA, all rights reserved

  10. A comparative study of digital PCR and real-time qPCR for the detection and quantification of HPV mRNA in sentinel lymph nodes of cervical cancer patients.

    PubMed

    Carow, Katrin; Read, Christina; Häfner, Norman; Runnebaum, Ingo B; Corner, Adam; Dürst, Matthias

    2017-10-30

    Qualitative analyses showed that the presence of HPV mRNA in sentinel lymph nodes of cervical cancer patients with pN0 status is associated with significantly decreased recurrence free survival. To further address the clinical potential of the strategy and to define prognostic threshold levels it is necessary to use a quantitative assay. Here, we compare two methods of quantification: digital PCR and standard quantitative PCR. Serial dilutions of 5 ng-5 pg RNA (≙ 500-0.5 cells) of the cervical cancer cell line SiHa were prepared in 5 µg RNA of the HPV-negative human keratinocyte cell line HaCaT. Clinical samples consisted of 10 sentinel lymph nodes with varying HPV transcript levels. Reverse transcription of total RNA (5 µg RNA each) was performed in 100 µl and cDNA aliquots were analyzed by qPCR and dPCR. Digital PCR was run in the RainDrop ® Digital PCR system (RainDance Technologies) using a probe-based detection of HPV E6/E7 cDNA PCR products with 11 µl template. qPCR was done using a Rotor Gene Q 5plex HRM (Qiagen) amplifying HPV E6/E7 cDNA in a SYBR Green format with 1 µl template. For the analysis of both, clinical samples and serial dilution samples, dPCR and qPCR showed comparable sensitivity. With regard to reproducibility, both methods differed considerably, especially for low template samples. Here, we found with qPCR a mean variation coefficient of 126% whereas dPCR enabled a significantly lower mean variation coefficient of 40% (p = 0.01). Generally, we saw with dPCR a substantial reduction of subsampling errors, which most likely reflects the large cDNA amounts available for analysis. Compared to real-time PCR, dPCR shows higher reliability. Thus, our HPV mRNA dPCR assay holds promise for the clinical evaluation of occult tumor cells in histologically tumor-free lymph nodes in future studies.

  11. Prone positioning in hypoxemic respiratory failure: meta-analysis of randomized controlled trials.

    PubMed

    Kopterides, Petros; Siempos, Ilias I; Armaganidis, Apostolos

    2009-03-01

    Prone positioning is used to improve oxygenation in patients with hypoxemic respiratory failure (HRF). However, its role in clinical practice is not yet clearly defined. The aim of this meta-analysis was to assess the effect of prone positioning on relevant clinical outcomes, such as intensive care unit (ICU) and hospital mortality, days of mechanical ventilation, length of stay, incidence of ventilator-associated pneumonia (VAP) and pneumothorax, and associated complications. We used literature search of MEDLINE, Current Contents, and Cochrane Central Register of Controlled Trials. We focused only on randomized controlled trials reporting clinical outcomes in adult patients with HRF. Four trials met our inclusion criteria, including 662 patients randomized to prone ventilation and 609 patients to supine ventilation. The pooled odds ratio (OR) for the ICU mortality in the intention-to-treat analysis was 0.97 (95% confidence interval [CI], 0.77-1.22), for the comparison between prone and supine ventilated patients. Interestingly, the pooled OR for the ICU mortality in the selected group of the more severely ill patients favored prone positioning (OR, 0.34; 95% CI, 0.18-0.66). The duration of mechanical ventilation and the incidence of pneumothorax were not different between the 2 groups. The incidence of VAP was lower but not statistically significant in patients treated with prone positioning (OR, 0.81; 95% CI, 0.61-1.10). However, prone positioning was associated with a higher risk of pressure sores (OR, 1.49; 95% CI, 1.17-1.89) and a trend for more complications related to the endotracheal tube (OR, 1.30; 95% CI, 0.94-1.80). Despite the inherent limitations of the meta-analytic approach, it seems that prone positioning has no discernible effect on mortality in patients with HRF. It may decrease the incidence of VAP at the expense of more pressure sores and complications related to the endotracheal tube. However, a subgroup of the most severely ill patients may

  12. Molecular diagnosis of bloodstream infections in onco-haematology patients with PCR/ESI-MS technology.

    PubMed

    Jordana-Lluch, Elena; Rivaya, Belén; Marcó, Clara; Giménez, Montserrat; Quesada, Mª Dolores; Escobedo, Agustín; Batlle, Montserrat; Martró, Elisa; Ausina, Vicente

    2017-02-01

    Onco-haematological patients are prone to develop infections, and antibiotic prophylaxis may lead to negative blood cultures. Thus, the microbiological diagnosis and subsequent administration of a targeted antimicrobial therapy is often difficult. The goal of this study was to evaluate the usefulness of IRIDICA (PCR/ESI-MS technology) for the molecular diagnosis of bloodstream infections in this patient group. A total of 463 whole blood specimens from different sepsis episodes in 429 patients were analysed using the PCR/ESI-MS platform, comparing the results with those of blood culture and other clinically relevant information. The sensitivity of PCR/ESI-MS by specimen (excluding polymicrobial infections, n = 25) in comparison with blood culture was 64.3% overall, 69.0% in oncological patients, and 59.3% in haematological patients. When comparing with a clinical infection criterion, overall sensitivity rose to 74.7%, being higher in oncological patients (80.0%) than in haematological patients (67.7%). Thirty-one microorganisms isolated by culture were not detected by IRIDICA, whereas 42 clinically relevant pathogens not isolated by culture were detected moleculary. PCR/ESI-MS offers a reliable identification of pathogens directly from whole blood. While additional studies are needed to confirm our findings, the system showed a lower sensitivity in onco-haematological patients in comparison with previously reported results in patients from the Intensive Care Unit. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  13. Children's proneness to shame and guilt predict risky and illegal behaviors in young adulthood.

    PubMed

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

    2015-04-01

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

  14. Otitis-Prone Children Produce Functional Antibodies to Pneumolysin and Pneumococcal Polysaccharides.

    PubMed

    Kirkham, Lea-Ann S; Wiertsema, Selma P; Corscadden, Karli J; Mateus, Tulia; Mullaney, Gemma L; Zhang, Guicheng; Richmond, Peter C; Thornton, Ruth B

    2017-03-01

    The pneumococcus is a major otitis media (OM) pathogen, but data are conflicting regarding whether otitis-prone children have impaired humoral immunity to pneumococcal antigens. We and others have shown that otitis-prone and healthy children have similar antibody titers to pneumococcal proteins and polysaccharides (vaccine and nonvaccine types); however, the quality of antibodies from otitis-prone children has not been investigated. Antibody function, rather than titer, is considered to be a better correlate of protection from pneumococcal disease. Therefore, we compared the capacities of antibodies from otitis-prone (cases) and healthy (controls) children to neutralize pneumolysin, the pneumococcal toxin currently in development as a vaccine antigen, and to opsonize pneumococcal vaccine and nonvaccine serotypes. A pneumolysin neutralization assay was conducted on cholesterol-depleted complement-inactivated sera from 165 cases and 61 controls. A multiplex opsonophagocytosis assay (MOPA) was conducted on sera from 20 cases and 20 controls. Neutralizing and opsonizing titers were calculated with antigen-specific IgG titers to determine antibody potency for pneumolysin, pneumococcal conjugate vaccine (PCV) polysaccharides, and non-PCV polysaccharides. There was no significant difference in antibody potencies between cases and controls for the antigens tested. Antipneumolysin neutralizing titers increased with the number of episodes of acute OM, but antibody potency did not. Pneumolysin antibody potency was lower in children colonized with pneumococci than in noncarriers, and this was significant for the otitis-prone group ( P < 0.05). The production of functional antipneumococcal antibodies in otitis-prone children demonstrates that they respond to the current PCV and are likely to respond to pneumolysin-based vaccines as effectively as healthy children. Copyright © 2017 Kirkham et al.

  15. Otitis-Prone Children Produce Functional Antibodies to Pneumolysin and Pneumococcal Polysaccharides

    PubMed Central

    Wiertsema, Selma P.; Corscadden, Karli J.; Mateus, Tulia; Mullaney, Gemma L.; Zhang, Guicheng; Richmond, Peter C.; Thornton, Ruth B.

    2016-01-01

    ABSTRACT The pneumococcus is a major otitis media (OM) pathogen, but data are conflicting regarding whether otitis-prone children have impaired humoral immunity to pneumococcal antigens. We and others have shown that otitis-prone and healthy children have similar antibody titers to pneumococcal proteins and polysaccharides (vaccine and nonvaccine types); however, the quality of antibodies from otitis-prone children has not been investigated. Antibody function, rather than titer, is considered to be a better correlate of protection from pneumococcal disease. Therefore, we compared the capacities of antibodies from otitis-prone (cases) and healthy (controls) children to neutralize pneumolysin, the pneumococcal toxin currently in development as a vaccine antigen, and to opsonize pneumococcal vaccine and nonvaccine serotypes. A pneumolysin neutralization assay was conducted on cholesterol-depleted complement-inactivated sera from 165 cases and 61 controls. A multiplex opsonophagocytosis assay (MOPA) was conducted on sera from 20 cases and 20 controls. Neutralizing and opsonizing titers were calculated with antigen-specific IgG titers to determine antibody potency for pneumolysin, pneumococcal conjugate vaccine (PCV) polysaccharides, and non-PCV polysaccharides. There was no significant difference in antibody potencies between cases and controls for the antigens tested. Antipneumolysin neutralizing titers increased with the number of episodes of acute OM, but antibody potency did not. Pneumolysin antibody potency was lower in children colonized with pneumococci than in noncarriers, and this was significant for the otitis-prone group (P < 0.05). The production of functional antipneumococcal antibodies in otitis-prone children demonstrates that they respond to the current PCV and are likely to respond to pneumolysin-based vaccines as effectively as healthy children. PMID:28031178

  16. Reward and Affective Regulation in Depression-Prone Smokers

    PubMed Central

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

    2014-01-01

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

  17. Reward and affective regulation in depression-prone smokers.

    PubMed

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

    2014-11-01

    There is a disproportionately high smoking prevalence among individuals who are prone to depression. While depression has been conceptualized as a disorder of dysregulated positive affect and disrupted reward processing, little research has been conducted to determine the role of smoking in these processes among depression-prone smokers. Depression-prone smokers (DP+; n = 34) and smokers not depression-prone (DP-; n = 49) underwent two laboratory sessions, one while smoking abstinent and one while smoking ad libitum, to assess the relative reinforcing value of smoking and reward sensitivity. Using experience sampling methods, participants completed self-report measures of subjective reward, positive affect, and negative affect across 3 days while smoking as usual and 3 days while smoking abstinent. DP+ were two times more likely to work for cigarette puffs versus money in a progressive ratio, choice task (odds ratio 2.05; 95% confidence interval 1.04 to 4.06, p = .039) compared with DP-. Reward sensitivity as measured by the signal detection task did not yield any significant findings. Mixed models regressions revealed a three-way interaction (depression group, smoking phase, and time) for subjective reward, negative affect, and positive affect. For all three of these outcomes, the slopes for DP- and DP+ differed significantly from each other (ps < .05) and the effect of smoking (versus abstinence) over time was greater for DP+ than DP- smokers (ps < .05). These findings indicate that the effects of smoking on reward and positive affect regulation are specific to DP+ smokers and highlight novel targets for smoking cessation treatment in this population. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  18. Depression proneness and reactions to a depressive stimulus.

    PubMed

    Wernicke, Rachel A; Pearlman, Michelle Y; Thorndike, Frances P; Haaga, David A F

    2006-01-01

    In the context of a project examining depression vulnerability and cigarette smoking, the authors tested whether depression-vulnerable people differed from less vulnerable people in their reactions to a depressive stimulus. Regular smokers with a history of depression but not currently depressed (n = 63) and never-depressed smokers (n = 64) listened to audiotapes of confederates reading depressive and nondepressive scripts and reported their reactions. Neither a history of depression nor self-reported depression proneness predicted reactions to depression. However, depression proneness was positively correlated with beliefs about depression contagion. Likewise, stronger depression-related contagion beliefs and lower levels of empathic responding predicted behavioral rejection of the depressive stimulus.

  19. Ketosis-prone atypical diabetes in Cameroonian people with hyperglycaemic crisis: frequency, clinical and metabolic phenotypes.

    PubMed

    Lontchi-Yimagou, E; Nguewa, J L; Assah, F; Noubiap, J J; Boudou, P; Djahmeni, E; Balti, E V; Atogho-Tiedeu, B; Gautier, J F; Mbanya, J C; Sobngwi, E

    2017-03-01

    It is unclear whether ketosis-prone diabetes is a specific type or a subtype of Type 2 diabetes. We aimed to describe the clinical and metabolic features of ketosis-prone diabetes in a sub-Saharan population. We consecutively enrolled and characterized 173 people with non-autoimmune diabetes admitted for hyperglycaemic crisis at the Yaoundé Central Hospital, Cameroon. Blood samples were collected for fasting glucose, HbA 1c , lipid profile and C-peptide assays with insulin resistance and secretion estimation by homeostasis model assessment. People were classified as having Type 2 diabetes (n = 124) or ketosis-prone diabetes (n = 49). Ketosis-prone diabetes was sub-classified as new-onset ketotic phase (n = 34) or non-ketotic phase (n = 15). Ketosis-prone diabetes was found in 28.3% of the hyperglycaemic crises. Age at diabetes diagnosis was comparable in Type 2 and ketosis-prone diabetes [48 ± 14 vs 47 ± 11 years; P = 0.13] with a similar sex distribution. Overall BMI was 27.7 ± 13.4 kg/m 2 and was ≥ 25 kg/m 2 in 55.8% of those taking part, however, 73.5% of those with ketosis-prone diabetes reported weight loss of > 5% at diagnosis. Blood pressure and lipid profile were comparable in both types. Ketosis-prone diabetes in the ketotic phase was characterized by lower insulin secretion and higher serum triglycerides compared with non-ketotic ketosis prone and Type 2 diabetes. Type 2 and ketosis prone diabetes in the non-ketotic phase were comparable in terms of lipid profile, blood pressure, waist-to-hip ratio, BMI and fat mass, insulin secretion and insulin resistance indices. Ketosis-prone diabetes is likely to be a subtype of Type 2 diabetes with the potential to develop acute insulinopenic episodes. © 2016 Diabetes UK.

  20. Residents' numeric inputting error in computerized physician order entry prescription.

    PubMed

    Wu, Xue; Wu, Changxu; Zhang, Kan; Wei, Dong

    2016-04-01

    Computerized physician order entry (CPOE) system with embedded clinical decision support (CDS) can significantly reduce certain types of prescription error. However, prescription errors still occur. Various factors such as the numeric inputting methods in human computer interaction (HCI) produce different error rates and types, but has received relatively little attention. This study aimed to examine the effects of numeric inputting methods and urgency levels on numeric inputting errors of prescription, as well as categorize the types of errors. Thirty residents participated in four prescribing tasks in which two factors were manipulated: numeric inputting methods (numeric row in the main keyboard vs. numeric keypad) and urgency levels (urgent situation vs. non-urgent situation). Multiple aspects of participants' prescribing behavior were measured in sober prescribing situations. The results revealed that in urgent situations, participants were prone to make mistakes when using the numeric row in the main keyboard. With control of performance in the sober prescribing situation, the effects of the input methods disappeared, and urgency was found to play a significant role in the generalized linear model. Most errors were either omission or substitution types, but the proportion of transposition and intrusion error types were significantly higher than that of the previous research. Among numbers 3, 8, and 9, which were the less common digits used in prescription, the error rate was higher, which was a great risk to patient safety. Urgency played a more important role in CPOE numeric typing error-making than typing skills and typing habits. It was recommended that inputting with the numeric keypad had lower error rates in urgent situation. An alternative design could consider increasing the sensitivity of the keys with lower frequency of occurrence and decimals. To improve the usability of CPOE, numeric keyboard design and error detection could benefit from spatial

  1. Comparison of supine and prone positions for percutaneous nephrolithotomy in treatment of staghorn stones.

    PubMed

    Gökce, Mehmet İlker; Ibiş, Arif; Sancı, Adem; Akıncı, Aykut; Bağcı, Uygar; Ağaoğlu, Eylül Asya; Süer, Evren; Gülpınar, Ömer

    2017-12-01

    Percutaneous nephrolithotomy (PNL) is the primary treatment modality for management of staghorn stones. PNL in supine position has important advantages over prone positon. However, studies comparing prone and supine positions for PNL in staghorn stone patients have conflicting results, and the aim of the current study was to compare prone and supine positions for PNL in staghorn stone cases. Data of patients underwent PNL for staghorn stones in supine or prone position by a single urologist were collected prospectively. The supine and prone position groups were compared for stone free rate (SFR) and complication rates. All patients were evaluated with NCCT for evaluation of SFR. Chi-square test was used to compare categorical variables and Student t test was applied for continuous variables of the treatment groups. The groups were similar for demographic and stone-related characteristics. Multi-caliceal and intercostal access was more common in prone position. Operation duration was significantly shorter and hemoglobin drop was significantly less in supine group. SFR was 64.1 and 60.4% in the supine and prone groups, respectively (p = 0.72). Complication rates were similar in the two groups but Clavien III complications were observed in two patients in the prone group. PNL in supine position is an effective treatment for management of staghorn stones. The need for multi-caliceal and intercostal puncture is less when combined with retrograde intrarenal surgery. PNL in supine position should be considered as primary treatment option in staghorn stone cases.

  2. Effects of systematic prone positioning in hypoxemic acute respiratory failure: a randomized controlled trial.

    PubMed

    Guerin, Claude; Gaillard, Sandrine; Lemasson, Stephane; Ayzac, Louis; Girard, Raphaele; Beuret, Pascal; Palmier, Bruno; Le, Quoc Viet; Sirodot, Michel; Rosselli, Sylvaine; Cadiergue, Vincent; Sainty, Jean-Marie; Barbe, Philippe; Combourieu, Emmanuel; Debatty, Daniel; Rouffineau, Jean; Ezingeard, Eric; Millet, Olivier; Guelon, Dominique; Rodriguez, Luc; Martin, Olivier; Renault, Anne; Sibille, Jean-Paul; Kaidomar, Michel

    2004-11-17

    A recent trial showed that placing patients with acute lung injury in the prone position did not increase survival; however, whether those results hold true for patients with hypoxemic acute respiratory failure (ARF) is unclear. To determine whether prone positioning improves mortality in ARF patients. Prospective, unblinded, multicenter controlled trial of 791 ARF patients in 21 general intensive care units in France using concealed randomization conducted from December 14, 1998, through December 31, 2002. To be included, patients had to be at least 18 years, hemodynamically stable, receiving mechanical ventilation, and intubated and had to have a partial pressure of arterial oxygen (PaO2) to fraction of inspired oxygen (FIO2) ratio of 300 or less and no contraindications to lying prone. Patients were randomly assigned to prone position placement (n = 413), applied as early as possible for at least 8 hours per day on standard beds, or to supine position placement (n = 378). The primary end point was 28-day mortality; secondary end points were 90-day mortality, duration of mechanical ventilation, incidence of ventilator-associated pneumonia (VAP), and oxygenation. The 2 groups were comparable at randomization. The 28-day mortality rate was 32.4% for the prone group and 31.5% for the supine group (relative risk [RR], 0.97; 95% confidence interval [CI], 0.79-1.19; P = .77). Ninety-day mortality for the prone group was 43.3% vs 42.2% for the supine group (RR, 0.98; 95% CI, 0.84-1.13; P = .74). The mean (SD) duration of mechanical ventilation was 13.7 (7.8) days for the prone group vs 14.1 (8.6) days for the supine group (P = .93) and the VAP incidence was 1.66 vs 2.14 episodes per 100-patients days of intubation, respectively (P = .045). The PaO2/FIO2 ratio was significantly higher in the prone group during the 28-day follow-up. However, pressure sores, selective intubation, and endotracheal tube obstruction incidences were higher in the prone group. This trial

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

    PubMed Central

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

    2003-01-01

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

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

    ERIC Educational Resources Information Center

    Cassel, Russell N.; Cassel, Susie L.

    1984-01-01

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

  5. Causal inference with measurement error in outcomes: Bias analysis and estimation methods.

    PubMed

    Shu, Di; Yi, Grace Y

    2017-01-01

    Inverse probability weighting estimation has been popularly used to consistently estimate the average treatment effect. Its validity, however, is challenged by the presence of error-prone variables. In this paper, we explore the inverse probability weighting estimation with mismeasured outcome variables. We study the impact of measurement error for both continuous and discrete outcome variables and reveal interesting consequences of the naive analysis which ignores measurement error. When a continuous outcome variable is mismeasured under an additive measurement error model, the naive analysis may still yield a consistent estimator; when the outcome is binary, we derive the asymptotic bias in a closed-form. Furthermore, we develop consistent estimation procedures for practical scenarios where either validation data or replicates are available. With validation data, we propose an efficient method for estimation of average treatment effect; the efficiency gain is substantial relative to usual methods of using validation data. To provide protection against model misspecification, we further propose a doubly robust estimator which is consistent even when either the treatment model or the outcome model is misspecified. Simulation studies are reported to assess the performance of the proposed methods. An application to a smoking cessation dataset is presented.

  6. Prone position in patients with acute respiratory distress syndrome

    PubMed Central

    Setten, Mariano; Plotnikow, Gustavo Adrián; Accoce, Matías

    2016-01-01

    Acute respiratory distress syndrome occupies a great deal of attention in intensive care units. Despite ample knowledge of the physiopathology of this syndrome, the focus in intensive care units consists mostly of life-supporting treatment and avoidance of the side effects of invasive treatments. Although great advances in mechanical ventilation have occurred in the past 20 years, with a significant impact on mortality, the incidence continues to be high. Patients with acute respiratory distress syndrome, especially the most severe cases, often present with refractory hypoxemia due to shunt, which can require additional treatments beyond mechanical ventilation, among which is mechanical ventilation in the prone position. This method, first recommended to improve oxygenation in 1974, can be easily implemented in any intensive care unit with trained personnel. Prone position has extremely robust bibliographic support. Various randomized clinical studies have demonstrated the effect of prone decubitus on the oxygenation of patients with acute respiratory distress syndrome measured in terms of the PaO2/FiO2 ratio, including its effects on increasing patient survival. The members of the Respiratory Therapists Committee of the Sociedad Argentina de Terapia Intensiva performed a narrative review with the objective of discovering the available evidence related to the implementation of prone position, changes produced in the respiratory system due to the application of this maneuver, and its impact on mortality. Finally, guidelines are suggested for decision-making. PMID:27925054

  7. Prone position for acute respiratory failure in adults.

    PubMed

    Bloomfield, Roxanna; Noble, David W; Sudlow, Alexis

    2015-11-13

    Acute hypoxaemia de novo or on a background of chronic hypoxaemia is a common reason for admission to intensive care and for provision of mechanical ventilation. Various refinements of mechanical ventilation or adjuncts are employed to improve patient outcomes. Mortality from acute respiratory distress syndrome, one of the main contributors to the need for mechanical ventilation for hypoxaemia, remains approximately 40%. Ventilation in the prone position may improve lung mechanics and gas exchange and could improve outcomes. The objectives of this review are (1) to ascertain whether prone ventilation offers a mortality advantage when compared with traditional supine or semi recumbent ventilation in patients with severe acute respiratory failure requiring conventional invasive artificial ventilation, and (2) to supplement previous systematic reviews on prone ventilation for hypoxaemic respiratory failure in an adult population. We searched the Cochrane Central Register of Controlled Trials (CENTRAL; 2014, Issue 1), Ovid MEDLINE (1950 to 31 January 2014), EMBASE (1980 to 31 January 2014), the Cumulative Index to Nursing and Allied Health Literature (CINAHL) (1982 to 31 January 2014) and Latin American Caribbean Health Sciences Literature (LILACS) (1992 to 31 January 2014) in Ovid MEDLINE for eligible randomized controlled trials. We also searched for studies by handsearching reference lists of relevant articles, by contacting colleagues and by handsearching published proceedings of relevant journals. We applied no language constraints, and we reran the searches in CENTRAL, MEDLINE, EMBASE, CINAHL and LILACS in June 2015. We added five new studies of potential interest to the list of "Studies awaiting classification" and will incorporate them into formal review findings during the review update. We included randomized controlled trials (RCTs) that examined the effects of prone position versus supine/semi recumbent position during conventional mechanical ventilation in

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

    PubMed Central

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

    2009-01-01

    This study examined the relationships among three risk factors – body investment, depression, and alcohol use – and suicide proneness as measured by the Life Attitudes Schedule – Short Form (LAS-SF) in college students (n = 318). Path analysis was used to construct a causal model of suicide proneness. The Body Investment Scale (BIS) subscales were assumed to be causally prior to depression, which was in turn modeled as occurring prior to alcohol use, which was in turn modeled as prior to suicide proneness. Results revealed that, as expected suicide proneness was positively predicted by alcohol use, alcohol use was positively predicted by depression, and depression was negatively predicted by the body image component of the BIS. Additionally, the body image-suicide proneness link was significantly mediated by depression and its direct effect on suicide proneness as well as by the two-mediator path of body image on depression on drinking on suicide proneness. Implications are offered for the improved identification and treatment of young adults at risk for suicidal and health-diminishing behaviors. PMID:20573605

  9. [Care plan for patients in prone decubitus. An experience from practice].

    PubMed

    Oliva Torras, E; Subirana Casacuberta, M; Sebastià, M P; Jover Sancho, C; Solà Solé, N

    1995-01-01

    Offering a specific integral attention to patients with SDRA in prone decubitus positions makes us establish a performance plan with the aim to know the problems derived from the change in position, the time staying in prone decubitus and to standardize a care plan. We review the clinic records of the patients admitted in our unit from March '93 to March '95 who were positioned in prone decubitus. Taking as a base the nursing care model of V. Henderson and the taxonomy of NANDA, we analyse the needs which have been altered, and determine the nursing diagnosis, complications and most frequent interdependent problems establishing the aim to accomplish, planning the performance and rationalization. Five patients were positioned in prone decubitus before planning the performance and four more afterwards. All the patients tolerated SNG diet keeping a correct bowel transit. One patient showed an ulcera at frontal level. There were neither comeal ulceras nor alterations in the oral mucossa. The vascular accesses remained permeable. DP caused facial and periorbital edema in all the patients. We did not observe any increase in the amount of bronchial secretions. The eight patients who tolerated the change in position stayed in prone decubitus for an average of 77 hours, with a range of 10 to 216 hours. Four patients were discharged from the hospital, two of whom showed movility alterations, independently of the time staying in prone decubitus. We state explicitly the nursing care, determine five nursing diagnosis, one problem and seven interdependent complications. Establishing the nursing care from the experience and review of the records has allowed us to be more specific and objective. Standardizing the specific care plans makes the nursing care easier when dealing with real problems as well as with the care of complications derived from this situation.

  10. Musculoskeletal disorders, personality traits, psychological distress, and accident proneness of Chinese coal miners.

    PubMed

    Deng, Mingming; Wu, Feng; Wang, Jun; Sun, Linyan

    2017-01-01

    Human factors comprise one of the important reasons leading to the casualty accidents in coal mines. The aim of this study was to analyze the relationships among musculoskeletal disorders (MSDs), personality traits, psychological distress, and accident proneness of coal miners. There were 1500 Chinese coal miners surveyed in this study. Among these miners, 992 valid samples were obtained. The study surveyed the MSDs, personality traits, psychological distress, and accident proneness of coal miners with MSDs Likert scale, Eysenck personality questionnaire, Symptom Checklist-90 (SCL-90) scale, and accident proneness questionnaire, respectively. The highest MSDs level was found in the waist. The increasing working age of the miners was connected with increased MSDs and psychological distress. Significant differences in MSDs and psychological distress of miners from different types of work were observed. Coal miners with higher MSDs had higher accident proneness. Coal miners with higher neuroticism dimension of Eysenck personality and more serious psychological distress had higher accident proneness. Phobic anxiety, paranoid ideation and psychoticism dimension of psychological distress were the three most important indicators that had significant positive relationships with accident proneness. The MSDs, neuroticism dimension, and psychological distress of the coal mine workers are important to work safety and require serious attention. Some implications concerning coal mine safety management in China were provided.

  11. Prone position craniotomy in pregnancy without fetal heart rate monitoring.

    PubMed

    Jacob, Jean; Alexander, Ashish; Philip, Shoba; Thomas, Anoop

    2016-09-01

    A pregnant patient in second trimester scheduled for posterior fossa craniotomy in prone position is a challenge for the anesthesiologist. Things to consider are physiological changes during pregnancy, non-obstetric surgery in pregnant patients, neuroanesthetic principles, effects of prone positioning, and need for fetal heart rate (FHR) monitoring. We have described the anesthetic management of this case and discussed intra-operative FHR monitoring including controversies about its role, indications, and various options available as per fetal gestational age. In our case we attempted intermittent intra-operative FHR monitoring to optimize maternal positioning and fetal oxygenation even though the fetus was pre-viable. However the attempt was abandoned due to practical difficulties with prone positioning. Patient made good neurological recovery following the procedure and delivered a healthy term baby 4 months later. Decisions regarding fetal monitoring should be individualized based on viability of the fetus and feasibility of emergency cesarean delivery. Good communication between a multidisciplinary team involving neurosurgeon, anesthesiologist, obstetrician, and neonatologist is important for a successful outcome for mother and fetus. We conclude that prone position neurosurgery can safely be carried out in a pregnant patient with pre-viable fetus without FHR monitoring. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    USDA-ARS?s Scientific Manuscript database

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

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

    PubMed

    Wiltermuth, Scott S; Cohen, Taya R

    2014-11-01

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

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

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... flood-related erosion-prone areas. 60.24 Section 60.24 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone...

  15. Error-free versus mutagenic processing of genomic uracil--relevance to cancer.

    PubMed

    Krokan, Hans E; Sætrom, Pål; Aas, Per Arne; Pettersen, Henrik Sahlin; Kavli, Bodil; Slupphaug, Geir

    2014-07-01

    Genomic uracil is normally processed essentially error-free by base excision repair (BER), with mismatch repair (MMR) as an apparent backup for U:G mismatches. Nuclear uracil-DNA glycosylase UNG2 is the major enzyme initiating BER of uracil of U:A pairs as well as U:G mismatches. Deficiency in UNG2 results in several-fold increases in genomic uracil in mammalian cells. Thus, the alternative uracil-removing glycosylases, SMUG1, TDG and MBD4 cannot efficiently complement UNG2-deficiency. A major function of SMUG1 is probably to remove 5-hydroxymethyluracil from DNA with general back-up for UNG2 as a minor function. TDG and MBD4 remove deamination products U or T mismatched to G in CpG/mCpG contexts, but may have equally or more important functions in development, epigenetics and gene regulation. Genomic uracil was previously thought to arise only from spontaneous cytosine deamination and incorporation of dUMP, generating U:G mismatches and U:A pairs, respectively. However, the identification of activation-induced cytidine deaminase (AID) and other APOBEC family members as DNA-cytosine deaminases has spurred renewed interest in the processing of genomic uracil. Importantly, AID triggers the adaptive immune response involving error-prone processing of U:G mismatches, but also contributes to B-cell lymphomagenesis. Furthermore, mutational signatures in a substantial fraction of other human cancers are consistent with APOBEC-induced mutagenesis, with U:G mismatches as prime suspects. Mutations can be caused by replicative polymerases copying uracil in U:G mismatches, or by translesion polymerases that insert incorrect bases opposite abasic sites after uracil-removal. In addition, kataegis, localized hypermutations in one strand in the vicinity of genomic rearrangements, requires APOBEC protein, UNG2 and translesion polymerase REV1. What mechanisms govern error-free versus error prone processing of uracil in DNA remains unclear. In conclusion, genomic uracil is an

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

    PubMed

    Flynn, Francis J; Schaumberg, Rebecca L

    2012-01-01

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

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

    PubMed

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

    2013-09-01

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

  18. Clarifying the link between job satisfaction and absenteeism: The role of guilt proneness.

    PubMed

    Schaumberg, Rebecca L; Flynn, Francis J

    2017-06-01

    We propose that the relationship between job satisfaction and absenteeism depends partly on guilt proneness. Drawing on withdrawal and process models of absenteeism, we argue that job satisfaction predicts absences for employees who are low (but not high) in guilt proneness because low guilt-prone people's behaviors are governed more by fulfilling their own egoistic desires than by fulfilling others' normative expectations. We find support for this prediction in a sample of customer service agents working for a major telecommunications company and a sample of working adults employed in a range of industries. In each study, we use measures of employees' guilt proneness and job satisfaction to predict their subsequent workplace absences. In Study 2, we extend our hypothesis tests to 2 traits that are conceptually comparable to guilt proneness (i.e., moral identity and agreeableness), showing that these traits similarly moderate the relationship between job satisfaction and absenteeism. We discuss the implications of these findings for extant models of absenteeism and research on moral affectivity in the workplace. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  19. Detection limits of quantitative and digital PCR assays and their influence in presence-absence surveys of environmental DNA

    USGS Publications Warehouse

    Hunter, Margaret; Dorazio, Robert M.; Butterfield, John S.; Meigs-Friend, Gaia; Nico, Leo; Ferrante, Jason A.

    2017-01-01

    A set of universal guidelines is needed to determine the limit of detection (LOD) in PCR-based analyses of low concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjective, possibly resulting in biased estimates of species’ presence. Here, a conservative LOD analysis grounded in analytical chemistry is proposed to correct for overestimated DNA concentrations predominantly caused by the concentration plateau, a nonlinear relationship between expected and measured DNA concentrations. We have used statistical criteria to establish formal mathematical models for both quantitative and droplet digital PCR. To assess the method, a new Grass Carp (Ctenopharyngodon idella) TaqMan assay was developed and tested on both PCR platforms using eDNA in water samples. The LOD adjustment reduced Grass Carp occupancy and detection estimates while increasing uncertainty – indicating that caution needs to be applied to eDNA data without LOD correction. Compared to quantitative PCR, digital PCR had higher occurrence estimates due to increased sensitivity and dilution of inhibitors at low concentrations. Without accurate LOD correction, species occurrence and detection probabilities based on eDNA estimates are prone to a source of bias that cannot be reduced by an increase in sample size or PCR replicates. Other applications also could benefit from a standardized LOD such as GMO food analysis, and forensic and clinical diagnostics.

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

    ERIC Educational Resources Information Center

    Shoham-Salomon, Varda; Jancourt, Annick

    1985-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  2. Neck motion due to the halo-vest in prone and supine positions.

    PubMed

    Ivancic, Paul C; Telles, Connor J

    2010-05-01

    An in vitro biomechanical study of the effectiveness of halo-vest fixation. The objective was to evaluate motion of the injured cervical spine with normal halo-vest application and vest loose in the prone and supine positions. Snaking motion of the neck is defined as rotation in opposing directions throughout the cervical spine. Previous clinical studies have suggested snaking neck motion due to the halo-vest may lead to inadequate healing or nonunion. The halo-vest was applied to a Human Model of the Neck, which consisted of a cervical spine specimen mounted to the torso of an anthropometric test dummy and carrying a surrogate head. The model was transitioned from prone, to upright, to supine with the halo-vest applied normally and with the vest loose. Average peak spinal motions were computed in the prone and supine positions and contrasted with the physiologic rotation range, obtained from the intact flexibility test, and statistically compared (P < 0.05) between normal halo-vest application and vest loose. Snaking motion of the neck was observed in the prone and supine positions, consisting of extension at head/C1 and C1/2 and flexion at the inferior spinal levels. The intervertebral rotation peaks generally exceeded the physiologic range throughout the cervical spine due to the loose vest in the prone position. Significant increases in the extension peaks at head/C1 (16.9 degrees vs. 5.7 degrees) and flexion peaks at C4/5 (6.9 degrees vs. 3.6 degrees) and C7-T1 (5.2 degrees vs. 0.7 degrees) were observed in the prone position due to the loose vest, as compared to normal halo-vest application. Axial neck separation was consistently observed in the prone and supine positions. The present results, which document snaking motion of the cervical spine due to the halo-vest, indicate that an inadequately fitting or loose vest may significantly diminish its immobilization capacity leading to delayed healing or nonunion.

  3. Vegetation fire proneness in Europe

    NASA Astrophysics Data System (ADS)

    Pereira, Mário; Aranha, José; Amraoui, Malik

    2015-04-01

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

  4. Association of cytokine gene polymorphisms and risk factors with otitis media proneness in children.

    PubMed

    Miljanović, Olivera; Cikota-Aleksić, Bojana; Likić, Dragan; Vojvodić, Danilo; Jovićević, Ognjen; Magić, Zvonko

    2016-06-01

    In order to assess the association between gene polymorphisms and otitis media (OM) proneness, tumor necrosis factor alpha (TNFA) -308, interleukin (IL) 10-1082 and -3575, IL6 -597, IL2 -330, and CD14 -159 genotyping was performed in 58 OM-prone children and 85 controls who were exposed to similar number and frequency of environmental and host risk factors. The frequencies of genotypes (wild type vs. genotypes containing at least one polymorphic allele) were not significantly different between groups, except for IL10 -1082. Polymorphic genotypes IL10 -1082 GA and GG were more frequent in OM-prone children than in control group (RR 1.145, 95 % CI 1.011-1.298; p = 0.047). However, logistic regression did not confirm IL10 -1082 polymorphic genotypes as an independent risk factor for OM proneness. The present study indicates that high-producing IL10 -1082 GA/GG genotypes may increase the risk for OM proneness in its carriers when exposed to other environmental/host risk factors (day care attendance, passive smoking, male sex, respiratory infections, and atopic manifestations). This study revealed no significant independent genetic association, but the lack of breastfeeding in infancy was found to be the only independent risk factor for development of OM-prone phenotype, implying that breastfeeding had a protective role in development of susceptibility to OM. • The pathogenesis of OM is of multifactorial nature, dependent on infection, environmental factors, and immune response of the child. • Cytokines and CD14 play an important role in the presentation and clinical course of otitis media, but a clear link with otitis media proneness was not established. What is new: • This is the first clinical and genetic study on Montenegrin children with the otitis media-prone phenotype. • The study revealed that high-producing IL10 -1082 genotypes may influence otitis media proneness in children exposed to other environmental/host risk factors.

  5. [Difference of three standard curves of real-time reverse-transcriptase PCR in viable Vibrio parahaemolyticus quantification].

    PubMed

    Jin, Mengtong; Sun, Wenshuo; Li, Qin; Sun, Xiaohong; Pan, Yingjie; Zhao, Yong

    2014-04-04

    We evaluated the difference of three standard curves in quantifying viable Vibrio parahaemolyticus in samples by real-time reverse-transcriptase PCR (Real-time RT-PCR). The standard curve A was established by 10-fold diluted cDNA. The cDNA was reverse transcripted after RNA synthesized in vitro. The standard curve B and C were established by 10-fold diluted cDNA. The cDNA was synthesized after RNA isolated from Vibrio parahaemolyticus in pure cultures (10(8) CFU/mL) and shrimp samples (10(6) CFU/g) (Standard curve A and C were proposed for the first time). Three standard curves were performed to quantitatively detect V. parahaemolyticus in six samples, respectively (Two pure cultured V. parahaemolyticus samples, two artificially contaminated cooked Litopenaeus vannamei samples and two artificially contaminated Litopenaeus vannamei samples). Then we evaluated the quantitative results of standard curve and the plate counting results and then analysed the differences. The three standard curves all show a strong linear relationship between the fractional cycle number and V. parahaemolyticus concentration (R2 > 0.99); The quantitative results of Real-time PCR were significantly (p < 0.05) lower than the results of plate counting. The relative errors compared with the results of plate counting ranked standard curve A (30.0%) > standard curve C (18.8%) > standard curve B (6.9%); The average differences between standard curve A and standard curve B and C were - 2.25 Lg CFU/mL and - 0.75 Lg CFU/mL, respectively, and the mean relative errors were 48.2% and 15.9%, respectively; The average difference between standard curve B and C was among (1.47 -1.53) Lg CFU/mL and the average relative errors were among 19.0% - 23.8%. Standard curve B could be applied to Real-time RT-PCR when quantify the number of viable microorganisms in samples.

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  7. Apparent polyploidization after gamma irradiation: pitfalls in the use of quantitative polymerase chain reaction (qPCR) for the estimation of mitochondrial and nuclear DNA gene copy numbers.

    PubMed

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

    2013-05-30

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

  8. The 'modified prone position': a new approach for treating pre-vesical stones with extracorporeal shock wave lithotripsy.

    PubMed

    Köse, A C; Demirbas, M

    2004-02-01

    To investigate the utility of a new 'modified-prone' position for treating pre-vesical stones with extracorporeal shock wave lithotripsy (ESWL), usually considered an acceptable and effective treatment for such stones, but for which many different body positions have been used in an attempt to increase its efficacy. The study included 268 consecutive patients with a solitary pre-vesical stone who underwent ESWL either prone (69) or in the modified-prone position (199) between May 1999 and August 2001. Only those with one stone between the ureteric orifice and 1 cm proximal to the vesico-ureteric junction were included. In each case the stone diameter, days to stone clearance, number of shock waves applied per treatment, and number of sessions required to become stone-free were recorded. If the treatment failed this was also noted. Success rates in the prone and modified-prone groups were compared and analysed to assess which of the variables influenced success with ESWL. After ESWL, 95.5% of the 268 patients were stone-free; the rates in the prone and modified-prone groups were 89.9% and 97.5%, respectively (P = 0.015). The probability of success with ESWL therapy for pre-vesical calculi in modified-prone position was about five times (odds ratio 4.56, 95% confidence interval 1.2-17.7) greater than that expected with when prone. The modified-prone position was an independent factor most significantly influencing success with ESWL in these patients. The modified-prone position for ESWL is a new and very effective way to treat patients with pre-vesical stones.

  9. Intravenous Chemotherapy Compounding Errors in a Follow-Up Pan-Canadian Observational Study.

    PubMed

    Gilbert, Rachel E; Kozak, Melissa C; Dobish, Roxanne B; Bourrier, Venetia C; Koke, Paul M; Kukreti, Vishal; Logan, Heather A; Easty, Anthony C; Trbovich, Patricia L

    2018-05-01

    Intravenous (IV) compounding safety has garnered recent attention as a result of high-profile incidents, awareness efforts from the safety community, and increasingly stringent practice standards. New research with more-sensitive error detection techniques continues to reinforce that error rates with manual IV compounding are unacceptably high. In 2014, our team published an observational study that described three types of previously unrecognized and potentially catastrophic latent chemotherapy preparation errors in Canadian oncology pharmacies that would otherwise be undetectable. We expand on this research and explore whether additional potential human failures are yet to be addressed by practice standards. Field observations were conducted in four cancer center pharmacies in four Canadian provinces from January 2013 to February 2015. Human factors specialists observed and interviewed pharmacy managers, oncology pharmacists, pharmacy technicians, and pharmacy assistants as they carried out their work. Emphasis was on latent errors (potential human failures) that could lead to outcomes such as wrong drug, dose, or diluent. Given the relatively short observational period, no active failures or actual errors were observed. However, 11 latent errors in chemotherapy compounding were identified. In terms of severity, all 11 errors create the potential for a patient to receive the wrong drug or dose, which in the context of cancer care, could lead to death or permanent loss of function. Three of the 11 practices were observed in our previous study, but eight were new. Applicable Canadian and international standards and guidelines do not explicitly address many of the potentially error-prone practices observed. We observed a significant degree of risk for error in manual mixing practice. These latent errors may exist in other regions where manual compounding of IV chemotherapy takes place. Continued efforts to advance standards, guidelines, technological innovation, and

  10. Proneness to guilt, shame, and pride in children with Autism Spectrum Disorders and neurotypical children.

    PubMed

    Davidson, Denise; Hilvert, Elizabeth; Misiunaite, Ieva; Giordano, Michael

    2018-06-01

    Self-conscious emotions (e.g., guilt, shame, and pride) are complex emotions that require self-reflection and self-evaluation, and are thought to facilitate the maintenance of societal norms and personal standards. Despite the importance of self-conscious emotions, most research has focused on basic emotion processing in children with Autism Spectrum Disorders (ASD). Therefore, in the present study, we used the Test of Self-Conscious Affect for Children (TOSCA-C) to assess proneness to, or propensity to experience, the self-conscious emotions guilt, shame, and pride in children with ASD and neurotypical children. The TOSCA-C is designed to capture a child's natural tendency to experience a given emotion across a range of everyday situations [Tangney, Stuewig, & Mashek, 2007]. We also assessed how individual characteristics contribute to the development of proneness to self-conscious emotions, including theory of mind (ToM) and ASD symptomatology. In comparison to neurotypical children, children with ASD showed less proneness to guilt, although all children showed relatively high levels of proneness to guilt. Greater ToM ability was related to more proneness to guilt and authentic pride in children with ASD. Additionally, we found that children with ASD with more severe symptomatology were more prone to hubristic pride. Our results provide evidence of differences in proneness to self-conscious emotions in children with ASD, as well as highlight important mechanisms contributing to how children with ASD may experience self-conscious emotions. Autism Res 2018,11:883-892. ©2017 International Society for Autism Research, Wiley Periodicals, Inc. This research examined proneness to guilt, shame, and pride in children with Autism Spectrum Disorders (ASD) and neurotypical children. We found that children with ASD showed less proneness to guilt than neurotypical children. Better understanding of theory of mind was related to greater proneness to guilt and pride, but only

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

    PubMed Central

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

    2012-01-01

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beriwal, Sushil; Jain, Sheena K.; Heron, Dwight E.

    2007-02-01

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

  13. The prone bridge test: Performance, validity, and reliability among older and younger adults.

    PubMed

    Bohannon, Richard W; Steffl, Michal; Glenney, Susan S; Green, Michelle; Cashwell, Leah; Prajerova, Kveta; Bunn, Jennifer

    2018-04-01

    The prone bridge maneuver, or plank, has been viewed as a potential alternative to curl-ups for assessing trunk muscle performance. The purpose of this study was to assess prone bridge test performance, validity, and reliability among younger and older adults. Sixty younger (20-35 years old) and 60 older (60-79 years old) participants completed this study. Groups were evenly divided by sex. Participants completed surveys regarding physical activity and abdominal exercise participation. Height, weight, body mass index (BMI), and waist circumference were measured. On two occasions, 5-9 days apart, participants held a prone bridge until volitional exhaustion or until repeated technique failure. Validity was examined using data from the first session: convergent validity by calculating correlations between survey responses, anthropometrics, and prone bridge time, known groups validity by using an ANOVA comparing bridge times of younger and older adults and of men and women. Test-retest reliability was examined by using a paired t-test to compare prone bridge times for Session1 and Session 2. Furthermore, an intraclass correlation coefficient (ICC) was used to characterize relative reliability and minimal detectable change (MDC 95% ) was used to describe absolute reliability. The mean prone bridge time was 145.3 ± 71.5 s, and was positively correlated with physical activity participation (p ≤ 0.001) and negatively correlated with BMI and waist circumference (p ≤ 0.003). Younger participants had significantly longer plank times than older participants (p = 0.003). The ICC between testing sessions was 0.915. The prone bridge test is a valid and reliable measure for evaluating abdominal performance in both younger and older adults. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Environmental Health Risk Assesement in Flood-prone Area in Tamangapa Sub-District Makassar

    NASA Astrophysics Data System (ADS)

    Haris, Ibrahim Abdul; Basir, Basir

    2018-05-01

    Environmental health in Indonesia is still caution to concern, poor sanitation in Indonesia is characterized by the high incidence of infectious diseases in society. The society in flood-prone area has a high-risk exposure on the disease based on the environment because they live in disaster-prone area. This research aimed to describe the condition of sanitary facilities and risky behavior on public health in flood-prone areas in Manggala district particularly in Tamangapa sub-district of Makassar. This reserach uses an observation method with a descriptive approach. The data is processed by using SPSS and Arc View GIS applications. Environmental risk category is determined by the approach of Environmental Health Risk Assessment (EHRA). The results showed that the flood-prone area in RT 04 RW 06 was included in very high-risk category at 229 with an index value of environmental health risks 212-229. Meanwhile, RT 04 RW 05 was in the category of low risk in the amount of 155 with an index of 155-173. Environmental health hazards identified in Tamangapa flood-prone areas sub-district includes domestic sources of clean water, domestic wastewater, and household garbage.

  15. Neurodevelopmental correlates of proneness to guilt and shame in adolescence and early adulthood.

    PubMed

    Whittle, Sarah; Liu, Kirra; Bastin, Coralie; Harrison, Ben J; Davey, Christopher G

    2016-06-01

    Investigating how brain development during adolescence and early adulthood underlies guilt- and shame-proneness may be important for understanding risk processes for mental disorders. The aim of this study was to investigate the neurodevelopmental correlates of interpersonal guilt- and shame-proneness in healthy adolescents and young adults using structural magnetic resonance imaging (sMRI). Sixty participants (age range: 15-25) completed sMRI and self-report measures of interpersonal guilt- and shame-proneness. Independent of interpersonal guilt, higher levels of shame-proneness were associated with thinner posterior cingulate cortex (PCC) thickness and smaller amygdala volume. Higher levels of shame-proneness were also associated with attenuated age-related reductions in thickness of lateral orbitofrontal cortex (lOFC). Our findings highlight the complexities in understanding brain-behavior relationships during the adolescent/young adult period. Results were consistent with growing evidence that accelerated cortical thinning during adolescence may be associated with superior socioemotional functioning. Further research is required to understand the implications of these findings for mental disorders characterized by higher levels of guilt and shame. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. Individual Differences in Emotion Regulation, Childhood Trauma and Proneness to Shame and Guilt in Adolescence.

    PubMed

    Szentágotai-Tătar, Aurora; Miu, Andrei C

    2016-01-01

    Dispositional shame and guilt have been associated with psychopathology and an increasing number of studies have traced this relation back to adolescence. This developmental period is thought to be characterized by maturational changes in emotion regulation, which also play an important role in vulnerability to psychopathology, but little is known about the links between emotion regulation and dispositional shame and guilt. The current study investigated the relations between individual differences in the habitual use of a wide range of emotion regulation strategies and proneness to shame and guilt in a large sample of adolescents (N = 706), aged 13 to 17 years. History of childhood trauma was also assessed. Our results showed that emotion regulation independently explained about 20% of the variance of shame-proneness and guilt-proneness. Higher use of maladaptive (e.g., Self-Blaming, Catastrophizing) and lower use of adaptive (e.g., Refocus on Planning, Positive Reappraisal) emotion regulation strategies were positively associated with shame-proneness. In contrast, lower use of maladaptive (e.g., Catastrophizing, Blaming Others) and higher use of adaptive (e.g., Refocus on Planning, Positive Reappraisal) emotion regulation strategies were associated with guilt-proneness, independent of the influence of childhood trauma, which also explained a relatively minor portion of guilt-proneness. Although there were age differences (i.e., rumination was used more by older adolescents) and sex differences (i.e., girls reported higher use of Putting into Perspective and lower use of Other Blaming compared to boys) in emotion regulation, age and sex were not significantly associated with proneness to shame and guilt. The positive relations with maladaptive emotion regulation underscore the dysfunctional nature of shame-proneness. Future studies could use longitudinal measures to establish that emotion regulation drives dispositional shame and guilt, and also investigate

  17. Study of the bacterial diversity of foods: PCR-DGGE versus LH-PCR.

    PubMed

    Garofalo, Cristiana; Bancalari, Elena; Milanović, Vesna; Cardinali, Federica; Osimani, Andrea; Sardaro, Maria Luisa Savo; Bottari, Benedetta; Bernini, Valentina; Aquilanti, Lucia; Clementi, Francesca; Neviani, Erasmo; Gatti, Monica

    2017-02-02

    The present study compared two culture-independent methods, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and length-heterogeneity polymerase chain reaction (LH-PCR), for their ability to reveal food bacterial microbiota. Total microbial DNA and RNA were extracted directly from fourteen fermented and unfermented foods, and domain A of the variable regions V1 and V2 of the 16S rRNA gene was analyzed through LH-PCR and PCR-DGGE. Finally, the outline of these analyses was compared with bacterial viable counts obtained after bacterial growth on suitable selective media. For the majority of the samples, RNA-based PCR-DGGE revealed species that the DNA-based PCR-DGGE was not able to highlight. When analyzing either DNA or RNA, LH-PCR identified several lactic acid bacteria (LAB) and coagulase negative cocci (CCN) species that were not identified by PCR-DGGE. This phenomenon was particularly evident in food samples with viable loads<5.0 Logcfug -1 . Furthermore, LH-PCR was able to detect a higher number of peaks in the analyzed food matrices relative to species identified by PCR-DGGE. In light of these findings, it may be suggested that LH-PCR shows greater sensitivity than PCR-DGGE. However, PCR-DGGE detected some other species (LAB included) that were not detected by LH-PCR. Therefore, certain LH-PCR peaks not attributed to known species within the LH-PCR database could be solved by comparing them with species identified by PCR-DGGE. Overall, this study also showed that LH-PCR is a promising method for use in the food microbiology field, indicating the necessity to expand the LH-PCR database, which is based, up to now, mainly on LAB isolates from dairy products. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Historical change in the link between adolescent deviance proneness and marijuana use, 1979-2004.

    PubMed

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

    2008-03-01

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

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

    PubMed

    Schipler, Agnes; Iliakis, George

    2013-09-01

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

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

    PubMed Central

    Schipler, Agnes; Iliakis, George

    2013-01-01

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

  1. Hypnotic responsiveness: expectancy, attitudes, fantasy proneness, absorption, and gender.

    PubMed

    Green, Joseph P; Lynn, Steven Jay

    2011-01-01

    This study examines the effect of providing information linking participants' attitudes toward hypnosis with later hypnotic performance. Using total scale scores from McConkey's Opinions About Hypnosis scale, as well as subscale scores, the authors found a weak association between attitudes and performance among 460 student participants; however, the correlation was unaffected by prehypnotic information specifically connecting attitudes and performance. A brief, 3-item measure of hypnotic expectancies generated the strongest correlation with hypnotic responsiveness. The authors also found that the association between fantasy proneness and hypnotizability was unaffected by the order of scale administration. Finally, the study highlighted gender differences across measures of fantasy proneness, absorption, expectancy, and hypnotizability.

  2. The Prevalence of Boredom Proneness and Depression among Profoundly Deaf Residential School Adolescents.

    ERIC Educational Resources Information Center

    Watt, John D.; Davis, Faith E.

    1991-01-01

    Fifty profoundly deaf residential school adolescents were administered the Boredom Proneness scale and a modified version of the Beck Depression Inventory. Deaf students had a significantly higher incidence of depression and were more boredom prone than were hearing subjects. (Author/JDD)

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

    PubMed Central

    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

    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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Catron, T; Rosu, M; Weiss, E

    2014-06-01

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

  5. Statistical Reporting Errors and Collaboration on Statistical Analyses in Psychological Science.

    PubMed

    Veldkamp, Coosje L S; Nuijten, Michèle B; Dominguez-Alvarez, Linda; van Assen, Marcel A L M; Wicherts, Jelte M

    2014-01-01

    Statistical analysis is error prone. A best practice for researchers using statistics would therefore be to share data among co-authors, allowing double-checking of executed tasks just as co-pilots do in aviation. To document the extent to which this 'co-piloting' currently occurs in psychology, we surveyed the authors of 697 articles published in six top psychology journals and asked them whether they had collaborated on four aspects of analyzing data and reporting results, and whether the described data had been shared between the authors. We acquired responses for 49.6% of the articles and found that co-piloting on statistical analysis and reporting results is quite uncommon among psychologists, while data sharing among co-authors seems reasonably but not completely standard. We then used an automated procedure to study the prevalence of statistical reporting errors in the articles in our sample and examined the relationship between reporting errors and co-piloting. Overall, 63% of the articles contained at least one p-value that was inconsistent with the reported test statistic and the accompanying degrees of freedom, and 20% of the articles contained at least one p-value that was inconsistent to such a degree that it may have affected decisions about statistical significance. Overall, the probability that a given p-value was inconsistent was over 10%. Co-piloting was not found to be associated with reporting errors.

  6. Impact of Standardized Communication Techniques on Errors during Simulated Neonatal Resuscitation.

    PubMed

    Yamada, Nicole K; Fuerch, Janene H; Halamek, Louis P

    2016-03-01

    Current patterns of communication in high-risk clinical situations, such as resuscitation, are imprecise and prone to error. We hypothesized that the use of standardized communication techniques would decrease the errors committed by resuscitation teams during neonatal resuscitation. In a prospective, single-blinded, matched pairs design with block randomization, 13 subjects performed as a lead resuscitator in two simulated complex neonatal resuscitations. Two nurses assisted each subject during the simulated resuscitation scenarios. In one scenario, the nurses used nonstandard communication; in the other, they used standardized communication techniques. The performance of the subjects was scored to determine errors committed (defined relative to the Neonatal Resuscitation Program algorithm), time to initiation of positive pressure ventilation (PPV), and time to initiation of chest compressions (CC). In scenarios in which subjects were exposed to standardized communication techniques, there was a trend toward decreased error rate, time to initiation of PPV, and time to initiation of CC. While not statistically significant, there was a 1.7-second improvement in time to initiation of PPV and a 7.9-second improvement in time to initiation of CC. Should these improvements in human performance be replicated in the care of real newborn infants, they could improve patient outcomes and enhance patient safety. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  7. Detection limits of quantitative and digital PCR assays and their influence in presence-absence surveys of environmental DNA.

    PubMed

    Hunter, Margaret E; Dorazio, Robert M; Butterfield, John S S; Meigs-Friend, Gaia; Nico, Leo G; Ferrante, Jason A

    2017-03-01

    A set of universal guidelines is needed to determine the limit of detection (LOD) in PCR-based analyses of low-concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjective, possibly resulting in biased estimates of species' presence. Here, a conservative LOD analysis grounded in analytical chemistry is proposed to correct for overestimated DNA concentrations predominantly caused by the concentration plateau, a nonlinear relationship between expected and measured DNA concentrations. We have used statistical criteria to establish formal mathematical models for both quantitative and droplet digital PCR. To assess the method, a new Grass Carp (Ctenopharyngodon idella) TaqMan assay was developed and tested on both PCR platforms using eDNA in water samples. The LOD adjustment reduced Grass Carp occupancy and detection estimates while increasing uncertainty-indicating that caution needs to be applied to eDNA data without LOD correction. Compared to quantitative PCR, digital PCR had higher occurrence estimates due to increased sensitivity and dilution of inhibitors at low concentrations. Without accurate LOD correction, species occurrence and detection probabilities based on eDNA estimates are prone to a source of bias that cannot be reduced by an increase in sample size or PCR replicates. Other applications also could benefit from a standardized LOD such as GMO food analysis and forensic and clinical diagnostics. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

  8. Design and Sampling Plan Optimization for RT-qPCR Experiments in Plants: A Case Study in Blueberry.

    PubMed

    Die, Jose V; Roman, Belen; Flores, Fernando; Rowland, Lisa J

    2016-01-01

    The qPCR assay has become a routine technology in plant biotechnology and agricultural research. It is unlikely to be technically improved, but there are still challenges which center around minimizing the variability in results and transparency when reporting technical data in support of the conclusions of a study. There are a number of aspects of the pre- and post-assay workflow that contribute to variability of results. Here, through the study of the introduction of error in qPCR measurements at different stages of the workflow, we describe the most important causes of technical variability in a case study using blueberry. In this study, we found that the stage for which increasing the number of replicates would be the most beneficial depends on the tissue used. For example, we would recommend the use of more RT replicates when working with leaf tissue, while the use of more sampling (RNA extraction) replicates would be recommended when working with stems or fruits to obtain the most optimal results. The use of more qPCR replicates provides the least benefit as it is the most reproducible step. By knowing the distribution of error over an entire experiment and the costs at each step, we have developed a script to identify the optimal sampling plan within the limits of a given budget. These findings should help plant scientists improve the design of qPCR experiments and refine their laboratory practices in order to conduct qPCR assays in a more reliable-manner to produce more consistent and reproducible data.

  9. Individual differences in posterior cortical volume correlate with proneness to pride and gratitude

    PubMed Central

    Zahn, Roland; Garrido, Griselda; Moll, Jorge

    2014-01-01

    Proneness to specific moral sentiments (e.g. pride, gratitude, guilt, indignation) has been linked with individual variations in functional MRI (fMRI) response within anterior brain regions whose lesion leads to inappropriate behaviour. However, the role of structural anatomical differences in rendering individuals prone to particular moral sentiments relative to others is unknown. Here, we investigated grey matter volumes (VBM8) and proneness to specific moral sentiments on a well-controlled experimental task in healthy individuals. Individuals with smaller cuneus, and precuneus volumes were more pride-prone, whereas those with larger right inferior temporal volumes experienced gratitude more readily. Although the primary analysis detected no associations with guilt- or indignation-proneness, subgenual cingulate fMRI responses to guilt were negatively correlated with grey matter volumes in the left superior temporal sulcus and anterior dorsolateral prefrontal cortices (right >left). This shows that individual variations in functional activations within critical areas for moral sentiments were not due to grey matter volume differences in the same areas. Grey matter volume differences between healthy individuals may nevertheless play an important role by affecting posterior cortical brain systems that are non-critical but supportive for the experience of specific moral sentiments. This may be of particular relevance when their experience depends on visuo-spatial elaboration. PMID:24106333

  10. Dropout Proneness in Appalachia. Research Series 3.

    ERIC Educational Resources Information Center

    Mink, Oscar G.; Barker, Laurence W.

    Two aids used in the identification of potential dropouts are examined. The Mink Scale (a teacher-rated scale) is based on classification of social, psychological, and educational forces related to dropout proneness: (1) academic ability and performance, (2) negative identification with education, (3) family and socioeconomic status, and (4)…

  11. RD Optimized, Adaptive, Error-Resilient Transmission of MJPEG2000-Coded Video over Multiple Time-Varying Channels

    NASA Astrophysics Data System (ADS)

    Bezan, Scott; Shirani, Shahram

    2006-12-01

    To reliably transmit video over error-prone channels, the data should be both source and channel coded. When multiple channels are available for transmission, the problem extends to that of partitioning the data across these channels. The condition of transmission channels, however, varies with time. Therefore, the error protection added to the data at one instant of time may not be optimal at the next. In this paper, we propose a method for adaptively adding error correction code in a rate-distortion (RD) optimized manner using rate-compatible punctured convolutional codes to an MJPEG2000 constant rate-coded frame of video. We perform an analysis on the rate-distortion tradeoff of each of the coding units (tiles and packets) in each frame and adapt the error correction code assigned to the unit taking into account the bandwidth and error characteristics of the channels. This method is applied to both single and multiple time-varying channel environments. We compare our method with a basic protection method in which data is either not transmitted, transmitted with no protection, or transmitted with a fixed amount of protection. Simulation results show promising performance for our proposed method.

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

    PubMed

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

    2009-04-01

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

  13. Cocaine Dependence Treatment Data: Methods for Measurement Error Problems With Predictors Derived From Stationary Stochastic Processes

    PubMed Central

    Guan, Yongtao; Li, Yehua; Sinha, Rajita

    2011-01-01

    In a cocaine dependence treatment study, we use linear and nonlinear regression models to model posttreatment cocaine craving scores and first cocaine relapse time. A subset of the covariates are summary statistics derived from baseline daily cocaine use trajectories, such as baseline cocaine use frequency and average daily use amount. These summary statistics are subject to estimation error and can therefore cause biased estimators for the regression coefficients. Unlike classical measurement error problems, the error we encounter here is heteroscedastic with an unknown distribution, and there are no replicates for the error-prone variables or instrumental variables. We propose two robust methods to correct for the bias: a computationally efficient method-of-moments-based method for linear regression models and a subsampling extrapolation method that is generally applicable to both linear and nonlinear regression models. Simulations and an application to the cocaine dependence treatment data are used to illustrate the efficacy of the proposed methods. Asymptotic theory and variance estimation for the proposed subsampling extrapolation method and some additional simulation results are described in the online supplementary material. PMID:21984854

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

    ERIC Educational Resources Information Center

    Marini, David C.

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

  15. Evidence of functional cell-mediated immune responses to nontypeable Haemophilus influenzae in otitis-prone children

    PubMed Central

    Seppanen, Elke; Tan, Dino; Corscadden, Karli J.; Currie, Andrew J.; Richmond, Peter C.; Thornton, Ruth B.

    2018-01-01

    Otitis media (OM) remains a common paediatric disease, despite advances in vaccinology. Susceptibility to recurrent acute OM (rAOM) has been postulated to involve defective cell-mediated immune responses to common otopathogenic bacteria. We compared the composition of peripheral blood mononuclear cells (PBMC) from 20 children with a history of rAOM (otitis-prone) and 20 healthy non-otitis-prone controls, and assessed innate and cell-mediated immune responses to the major otopathogen nontypeable Haemophilus influenzae (NTHi). NTHi was a potent stimulator of inflammatory cytokine secretion from PBMC within 4 hours, with no difference in cytokine levels produced between PBMC from cases or controls. In the absence of antigen stimulation, otitis-prone children had more circulating Natural Killer (NK) cells (p<0.01), particularly NKdim (CD56lo) cells (p<0.01), but fewer CD4+ T cells (p<0.01) than healthy controls. NTHi challenge significantly increased the proportion of activated (CD107a+) NK cells in otitis-prone and non-otitis-prone children (p<0.01), suggesting that NK cells from otitis-prone children are functional and respond to NTHi. CD8+ T cells and NK cells from both cases and controls produced IFNγ in response to polyclonal stimulus (Staphylococcal enterotoxin B; SEB), with more IFNγ+ CD8+ T cells present in cases than controls (p<0.05) but similar proportions of IFNγ+ NK cells. Otitis-prone children had more circulating IFNγ-producing NK cells (p<0.05) and more IFNγ-producing CD4+ (p<0.01) or CD8+ T-cells (p<0.05) than healthy controls. In response to SEB, more CD107a-expressing CD8+ T cells were present in cases than controls (p<0.01). Despite differences in PBMC composition, PBMC from otitis-prone children mounted innate and T cell-mediated responses to NTHi challenge that were comparable to healthy children. These data provide evidence that otitis-prone children do not have impaired functional cell mediated immunity. PMID:29621281

  16. Individual Differences in Emotion Regulation, Childhood Trauma and Proneness to Shame and Guilt in Adolescence

    PubMed Central

    2016-01-01

    Dispositional shame and guilt have been associated with psychopathology and an increasing number of studies have traced this relation back to adolescence. This developmental period is thought to be characterized by maturational changes in emotion regulation, which also play an important role in vulnerability to psychopathology, but little is known about the links between emotion regulation and dispositional shame and guilt. The current study investigated the relations between individual differences in the habitual use of a wide range of emotion regulation strategies and proneness to shame and guilt in a large sample of adolescents (N = 706), aged 13 to 17 years. History of childhood trauma was also assessed. Our results showed that emotion regulation independently explained about 20% of the variance of shame-proneness and guilt-proneness. Higher use of maladaptive (e.g., Self-Blaming, Catastrophizing) and lower use of adaptive (e.g., Refocus on Planning, Positive Reappraisal) emotion regulation strategies were positively associated with shame-proneness. In contrast, lower use of maladaptive (e.g., Catastrophizing, Blaming Others) and higher use of adaptive (e.g., Refocus on Planning, Positive Reappraisal) emotion regulation strategies were associated with guilt-proneness, independent of the influence of childhood trauma, which also explained a relatively minor portion of guilt-proneness. Although there were age differences (i.e., rumination was used more by older adolescents, and the influence of emotion regulation on depression and anxiety symptoms increased with age) and sex differences (i.e., girls reported higher use of Putting into Perspective and Other Blaming compared to boys) in emotion regulation, age and sex were not significantly associated with proneness to shame and guilt. The positive relations with maladaptive emotion regulation underscores the dysfunctional nature of shame-proneness. Future studies could use longitudinal measures to establish that

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

    ERIC Educational Resources Information Center

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

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

  18. Prone positioning reduces severe pushing behavior: three case studies

    PubMed Central

    Fujino, Yuji; Amimoto, Kazu; Sugimoto, Satoshi; Fukata, Kazuhiro; Inoue, Masahide; Takahashi, Hidetoshi; Makita, Shigeru

    2016-01-01

    [Purpose] Pushing behavior is classically described as a disorder of body orientation in the coronal plane. Most interventions for pushing behavior have focused on correcting the deviation in vertical perception. However, pushing behavior seems to involve erroneous movements associated with excessive motor output by the non-paretic limbs and trunk. The present study aimed to inhibit muscular hyper-activity by placing the non-paretic limbs and trunk in the prone position. [Subjects and Methods] The subjects of the present study were 3 acute stroke patients with severe pushing behavior. The study consisted of the following 3 phases: baseline, intervention, and follow-up. In addition to conventional therapy, patients received relaxation therapy in the prone position for 10 minutes a day over 2 days. The severity of pushing behavior was assessed using the scale for contraversive pushing, and truncal balance was evaluated using the trunk control test. These assessments were performed before and after the baseline phase, and after the intervention and follow-up phases. [Results] At the baseline phase, both scores were poor. Both scores improved after the intervention and follow-up phases, and all the patients could sit independently. [Conclusion] Relaxation therapy in the prone position might ameliorate pushing behavior and impaired truncal balance. PMID:27799722

  19. Prone positioning reduces severe pushing behavior: three case studies.

    PubMed

    Fujino, Yuji; Amimoto, Kazu; Sugimoto, Satoshi; Fukata, Kazuhiro; Inoue, Masahide; Takahashi, Hidetoshi; Makita, Shigeru

    2016-09-01

    [Purpose] Pushing behavior is classically described as a disorder of body orientation in the coronal plane. Most interventions for pushing behavior have focused on correcting the deviation in vertical perception. However, pushing behavior seems to involve erroneous movements associated with excessive motor output by the non-paretic limbs and trunk. The present study aimed to inhibit muscular hyper-activity by placing the non-paretic limbs and trunk in the prone position. [Subjects and Methods] The subjects of the present study were 3 acute stroke patients with severe pushing behavior. The study consisted of the following 3 phases: baseline, intervention, and follow-up. In addition to conventional therapy, patients received relaxation therapy in the prone position for 10 minutes a day over 2 days. The severity of pushing behavior was assessed using the scale for contraversive pushing, and truncal balance was evaluated using the trunk control test. These assessments were performed before and after the baseline phase, and after the intervention and follow-up phases. [Results] At the baseline phase, both scores were poor. Both scores improved after the intervention and follow-up phases, and all the patients could sit independently. [Conclusion] Relaxation therapy in the prone position might ameliorate pushing behavior and impaired truncal balance.

  20. Correcting for Measurement Error in Time-Varying Covariates in Marginal Structural Models.

    PubMed

    Kyle, Ryan P; Moodie, Erica E M; Klein, Marina B; Abrahamowicz, Michał

    2016-08-01

    Unbiased estimation of causal parameters from marginal structural models (MSMs) requires a fundamental assumption of no unmeasured confounding. Unfortunately, the time-varying covariates used to obtain inverse probability weights are often error-prone. Although substantial measurement error in important confounders is known to undermine control of confounders in conventional unweighted regression models, this issue has received comparatively limited attention in the MSM literature. Here we propose a novel application of the simulation-extrapolation (SIMEX) procedure to address measurement error in time-varying covariates, and we compare 2 approaches. The direct approach to SIMEX-based correction targets outcome model parameters, while the indirect approach corrects the weights estimated using the exposure model. We assess the performance of the proposed methods in simulations under different clinically plausible assumptions. The simulations demonstrate that measurement errors in time-dependent covariates may induce substantial bias in MSM estimators of causal effects of time-varying exposures, and that both proposed SIMEX approaches yield practically unbiased estimates in scenarios featuring low-to-moderate degrees of error. We illustrate the proposed approach in a simple analysis of the relationship between sustained virological response and liver fibrosis progression among persons infected with hepatitis C virus, while accounting for measurement error in γ-glutamyltransferase, using data collected in the Canadian Co-infection Cohort Study from 2003 to 2014. © The Author 2016. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results.

    PubMed

    Vierna, J; Doña, J; Vizcaíno, A; Serrano, D; Jovani, R

    2017-10-01

    High-throughput DNA barcoding has become essential in ecology and evolution, but some technical questions still remain. Increasing the number of PCR cycles above the routine 20-30 cycles is a common practice when working with old-type specimens, which provide little amounts of DNA, or when facing annealing issues with the primers. However, increasing the number of cycles can raise the number of artificial mutations due to polymerase errors. In this work, we sequenced 20 COI libraries in the Illumina MiSeq platform. Libraries were prepared with 40, 45, 50, 55, and 60 PCR cycles from four individuals belonging to four species of four genera of cephalopods. We found no relationship between the number of PCR cycles and the number of mutations despite using a nonproofreading polymerase. Moreover, even when using a high number of PCR cycles, the resulting number of mutations was low enough not to be an issue in the context of high-throughput DNA barcoding (but may still remain an issue in DNA metabarcoding due to chimera formation). We conclude that the common practice of increasing the number of PCR cycles should not negatively impact the outcome of a high-throughput DNA barcoding study in terms of the occurrence of point mutations.

  2. Supine or prone position for mini-PNL procedure: does it matter.

    PubMed

    Tokatlı, Zafer; Gokce, Mehmet Ilker; Süer, Evren; Sağlam, Remzi

    2015-06-01

    In this study it is aimed to compare the success and complication rates of mini-PNL procedure in supine and prone positions. In this retrospective study data of 180 patients treated with MPNL either in supine (n = 54) or prone (n = 126) positions between May 2009 and August 2014 was investigated. Success was defined as no visible stones >2 mm. Perioperative complications were classified using the modified Clavien system. Groups were compared with Chi square test or Student t test and for statistical significance p value of 0.05 was accepted. Mean age of the population was 42.5 ± 8.2 years and mean stone size was 23.9 ± 4.1 mm. The two groups were similar with regard to demographic characteristics and stone related characteristics except the ASA status. Success rates of the supine and prone groups were 85.1 and 87.3%, respectively (p = 0.701). No statistically significant differences in terms of complications were observed. Mean operative time was the only parameter different between the two groups (55 vs 82 min, p = 0.001). Supine position for PNL seems to be promising and the complication and success rates are shown to be similar to the prone position with MPNL technique. The only significant benefit of this technique is shorter operative time.

  3. The prevalence of boredom proneness and depression among profoundly deaf residential school adolescents.

    PubMed

    Watt, J D; Davis, F E

    1991-12-01

    We investigated boredom proneness and depression among 50 profoundly deaf residential school adolescents using the Boredom Proneness (BP) scale and a version of the Beck Depression Inventory (BDI) that has been modified for use with deaf subjects. Consistent with previous research, the deaf students had a significantly higher incidence of depression than the hearing students. In addition, the deaf students were found to be significantly more boredom prone than the hearing subjects. The results suggest that deafness not only increases a person's vulnerability to mild levels of depression, but also tends to augment one's tendency toward experiencing boredom. Implications for educational settings and areas for future research are discussed.

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

    PubMed

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

    2014-03-01

    In this short-term longitudinal study, we systematically examined the distinctiveness of guilt- and shame-proneness in early adolescents (N = 395, mean age = 11.8 years) in terms of differential relations with peer reported prosocial behavior, withdrawal, and aggression. Results from structural equation modeling indicated that guilt-proneness 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. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  5. The 3 faces of clinical reasoning: Epistemological explorations of disparate error reduction strategies.

    PubMed

    Monteiro, Sandra; Norman, Geoff; Sherbino, Jonathan

    2018-06-01

    There is general consensus that clinical reasoning involves 2 stages: a rapid stage where 1 or more diagnostic hypotheses are advanced and a slower stage where these hypotheses are tested or confirmed. The rapid hypothesis generation stage is considered inaccessible for analysis or observation. Consequently, recent research on clinical reasoning has focused specifically on improving the accuracy of the slower, hypothesis confirmation stage. Three perspectives have developed in this line of research, and each proposes different error reduction strategies for clinical reasoning. This paper considers these 3 perspectives and examines the underlying assumptions. Additionally, this paper reviews the evidence, or lack of, behind each class of error reduction strategies. The first perspective takes an epidemiological stance, appealing to the benefits of incorporating population data and evidence-based medicine in every day clinical reasoning. The second builds on the heuristic and bias research programme, appealing to a special class of dual process reasoning models that theorizes a rapid error prone cognitive process for problem solving with a slower more logical cognitive process capable of correcting those errors. Finally, the third perspective borrows from an exemplar model of categorization that explicitly relates clinical knowledge and experience to diagnostic accuracy. © 2018 John Wiley & Sons, Ltd.

  6. Medication administration errors in nursing homes using an automated medication dispensing system.

    PubMed

    van den Bemt, Patricia M L A; Idzinga, Jetske C; Robertz, Hans; Kormelink, Dennis Groot; Pels, Neske

    2009-01-01

    OBJECTIVE To identify the frequency of medication administration errors as well as their potential risk factors in nursing homes using a distribution robot. DESIGN The study was a prospective, observational study conducted within three nursing homes in the Netherlands caring for 180 individuals. MEASUREMENTS Medication errors were measured using the disguised observation technique. Types of medication errors were described. The correlation between several potential risk factors and the occurrence of medication errors was studied to identify potential causes for the errors. RESULTS In total 2,025 medication administrations to 127 clients were observed. In these administrations 428 errors were observed (21.2%). The most frequently occurring types of errors were use of wrong administration techniques (especially incorrect crushing of medication and not supervising the intake of medication) and wrong time errors (administering the medication at least 1 h early or late).The potential risk factors female gender (odds ratio (OR) 1.39; 95% confidence interval (CI) 1.05-1.83), ATC medication class antibiotics (OR 11.11; 95% CI 2.66-46.50), medication crushed (OR 7.83; 95% CI 5.40-11.36), number of dosages/day/client (OR 1.03; 95% CI 1.01-1.05), nursing home 2 (OR 3.97; 95% CI 2.86-5.50), medication not supplied by distribution robot (OR 2.92; 95% CI 2.04-4.18), time classes "7-10 am" (OR 2.28; 95% CI 1.50-3.47) and "10 am-2 pm" (OR 1.96; 1.18-3.27) and day of the week "Wednesday" (OR 1.46; 95% CI 1.03-2.07) are associated with a higher risk of administration errors. CONCLUSIONS Medication administration in nursing homes is prone to many errors. This study indicates that the handling of the medication after removing it from the robot packaging may contribute to this high error frequency, which may be reduced by training of nurse attendants, by automated clinical decision support and by measures to reduce workload.

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

    PubMed Central

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

    2016-01-01

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

  8. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology.

    PubMed

    Smith, Cindy J; Osborn, A Mark

    2009-01-01

    Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.

  9. Chip PCR. I. Surface passivation of microfabricated silicon-glass chips for PCR.

    PubMed Central

    Shoffner, M A; Cheng, J; Hvichia, G E; Kricka, L J; Wilding, P

    1996-01-01

    The microreaction volumes of PCR chips (a microfabricated silicon chip bonded to a piece of flat glass to form a PCR reaction chamber) create a relatively high surface to volume ratio that increases the significance of the surface chemistry in the polymerase chain reaction (PCR). We investigated several surface passivations in an attempt to identify 'PCR friendly' surfaces and used those surfaces to obtain amplifications comparable with those obtained in conventional PCR amplification systems using polyethylene tubes. Surface passivations by a silanization procedure followed by a coating of a selected protein or polynucleotide and the deposition of a nitride or oxide layer onto the silicon surface were investigated. Native silicon was found to be an inhibitor of PCR and amplification in an untreated PCR chip (i.e. native slicon) had a high failure rate. A silicon nitride (Si(3)N(4) reaction surface also resulted in consistent inhibition of PCR. Passivating the PCR chip using a silanizing agent followed by a polymer treatment resulted in good amplification. However, amplification yields were inconsistent and were not always comparable with PCR in a conventional tube. An oxidized silicon (SiO(2) surface gave consistent amplifications comparable with reactions performed in a conventional PCR tube. PMID:8628665

  10. Implementing parallel spreadsheet models for health policy decisions: The impact of unintentional errors on model projections.

    PubMed

    Bailey, Stephanie L; Bono, Rose S; Nash, Denis; Kimmel, April D

    2018-01-01

    Spreadsheet software is increasingly used to implement systems science models informing health policy decisions, both in academia and in practice where technical capacity may be limited. However, spreadsheet models are prone to unintentional errors that may not always be identified using standard error-checking techniques. Our objective was to illustrate, through a methodologic case study analysis, the impact of unintentional errors on model projections by implementing parallel model versions. We leveraged a real-world need to revise an existing spreadsheet model designed to inform HIV policy. We developed three parallel versions of a previously validated spreadsheet-based model; versions differed by the spreadsheet cell-referencing approach (named single cells; column/row references; named matrices). For each version, we implemented three model revisions (re-entry into care; guideline-concordant treatment initiation; immediate treatment initiation). After standard error-checking, we identified unintentional errors by comparing model output across the three versions. Concordant model output across all versions was considered error-free. We calculated the impact of unintentional errors as the percentage difference in model projections between model versions with and without unintentional errors, using +/-5% difference to define a material error. We identified 58 original and 4,331 propagated unintentional errors across all model versions and revisions. Over 40% (24/58) of original unintentional errors occurred in the column/row reference model version; most (23/24) were due to incorrect cell references. Overall, >20% of model spreadsheet cells had material unintentional errors. When examining error impact along the HIV care continuum, the percentage difference between versions with and without unintentional errors ranged from +3% to +16% (named single cells), +26% to +76% (column/row reference), and 0% (named matrices). Standard error-checking techniques may not

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

    PubMed

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

    2011-08-01

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

  12. Data entry errors and design for model-based tight glycemic control in critical care.

    PubMed

    Ward, Logan; Steel, James; Le Compte, Aaron; Evans, Alicia; Tan, Chia-Siong; Penning, Sophie; Shaw, Geoffrey M; Desaive, Thomas; Chase, J Geoffrey

    2012-01-01

    Tight glycemic control (TGC) has shown benefits but has been difficult to achieve consistently. Model-based methods and computerized protocols offer the opportunity to improve TGC quality but require human data entry, particularly of blood glucose (BG) values, which can be significantly prone to error. This study presents the design and optimization of data entry methods to minimize error for a computerized and model-based TGC method prior to pilot clinical trials. To minimize data entry error, two tests were carried out to optimize a method with errors less than the 5%-plus reported in other studies. Four initial methods were tested on 40 subjects in random order, and the best two were tested more rigorously on 34 subjects. The tests measured entry speed and accuracy. Errors were reported as corrected and uncorrected errors, with the sum comprising a total error rate. The first set of tests used randomly selected values, while the second set used the same values for all subjects to allow comparisons across users and direct assessment of the magnitude of errors. These research tests were approved by the University of Canterbury Ethics Committee. The final data entry method tested reduced errors to less than 1-2%, a 60-80% reduction from reported values. The magnitude of errors was clinically significant and was typically by 10.0 mmol/liter or an order of magnitude but only for extreme values of BG < 2.0 mmol/liter or BG > 15.0-20.0 mmol/liter, both of which could be easily corrected with automated checking of extreme values for safety. The data entry method selected significantly reduced data entry errors in the limited design tests presented, and is in use on a clinical pilot TGC study. The overall approach and testing methods are easily performed and generalizable to other applications and protocols. © 2012 Diabetes Technology Society.

  13. Alcohol Use, Depressive Symptoms, and Impulsivity as Risk Factors for Suicide Proneness among College Students

    PubMed Central

    Dvorak, Robert D.; Lamis, Dorian A.; Malone, Patrick S.

    2013-01-01

    BACKGROUND Alcohol use, depression, and suicide are significant public health problems, particularly among college students. Impulsivity is associated with all of these factors. Additionally, impulsivity increases the effects of negative mood and alcohol use on maladaptive behavior. METHODS The current cross-sectional study examined the association between the four-factor model of impulsivity (urgency, (lack of) perseverance, (lack of) premeditation, and sensation seeking), depressive symptoms, and alcohol use as predictors of suicide proneness among college students. Participants (n =1100) completed online assessments of demographics, impulsivity, depressive symptoms, and suicide proneness. RESULTS All predictors were positively related to suicide proneness. The relation between depressive symptoms and suicide proneness was moderated by (lack of) perseverance, alcohol use, and joint interactions of urgency × alcohol use and sensation seeking × alcohol use. Despite some paradoxical findings regarding the depressive symptoms-suicide proneness relation when only one risk factor was elevated, the average level of suicide proneness increased as risk factors increased. LIMITATIONS This cross-sectional self-report data comes from a non-clinical sample of college students from a homogeneous background, limiting generalizability and causal predictions. CONCLUSIONS Overall, these findings indicate that the association between depressive symptoms and suicide proneness varies considerably by different facets of impulsivity and alcohol use. The results suggest that clinical risk-assessments should weigh two forms of impulsivity (urgency and sensation seeking) as particularly vital in the presence of heavy alcohol use. These findings highlight the importance of considering and exploring moderators of the mood-suicide relationship. PMID:23474093

  14. Alcohol use, depressive symptoms, and impulsivity as risk factors for suicide proneness among college students.

    PubMed

    Dvorak, Robert D; Lamis, Dorian A; Malone, Patrick S

    2013-07-01

    Alcohol use, depression, and suicide are significant public health problems, particularly among college students. Impulsivity is associated with all of these factors. Additionally, impulsivity increases the effects of negative mood and alcohol use on maladaptive behavior. The current cross-sectional study examined the association between the four-factor model of impulsivity (urgency, (lack of) perseverance, (lack of) premeditation, and sensation seeking), depressive symptoms, and alcohol use as predictors of suicide proneness among college students. Participants (n=1100) completed online assessments of demographics, impulsivity, depressive symptoms, and suicide proneness. All predictors were positively related to suicide proneness. The relation between depressive symptoms and suicide proneness was moderated by (lack of) perseverance, alcohol use, and joint interactions of urgency×alcohol use and sensation seeking×alcohol use. Despite some paradoxical findings regarding the depressive symptoms-suicide proneness relation when only one risk factor was elevated, the average level of suicide proneness increased as risk factors increased. This cross-sectional self-report data comes from a non-clinical sample of college students from a homogeneous background, limiting generalizability and causal predictions. Overall, these findings indicate that the association between depressive symptoms and suicide proneness varies considerably by different facets of impulsivity and alcohol use. The results suggest that clinical risk-assessments should weigh two forms of impulsivity (urgency and sensation seeking) as particularly vital in the presence of heavy alcohol use. These findings highlight the importance of considering and exploring moderators of the mood-suicide relationship. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Propensity Score Weighting with Error-Prone Covariates

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  16. Prone positioning in the patient who has acute respiratory distress syndrome: the art and science.

    PubMed

    Vollman, Kathleen M

    2004-09-01

    Acute respiratory distress syndrome (ARDS) remains a significant contributor to the morbidity and mortality of patients in the ICU. A variety of treatments are used to support the lung of the patient who has ARDS and improve gas exchange during the acute injury phase. It seems, however, that the simple, safe, and noninvasive act of prone positioning of the critically ill patient who has ARDS may improve gas exchange while preventing potential complications of high positive end-expiratory pressure, volutrauma, and oxygen toxicity. This article provides the critical care nurse with the physiologic rationale for use of the prone position, indications and contraindications for use, safe strategies for prone positioning, and care techniques and monitoring methods of the patient who is in the prone position.

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

    PubMed Central

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

    2016-01-01

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

  18. Improving specialist drug prescribing in primary care using task and error analysis: an observational study.

    PubMed

    Chana, Narinder; Porat, Talya; Whittlesea, Cate; Delaney, Brendan

    2017-03-01

    Electronic prescribing has benefited from computerised clinical decision support systems (CDSSs); however, no published studies have evaluated the potential for a CDSS to support GPs in prescribing specialist drugs. To identify potential weaknesses and errors in the existing process of prescribing specialist drugs that could be addressed in the development of a CDSS. Semi-structured interviews with key informants followed by an observational study involving GPs in the UK. Twelve key informants were interviewed to investigate the use of CDSSs in the UK. Nine GPs were observed while performing case scenarios depicting requests from hospitals or patients to prescribe a specialist drug. Activity diagrams, hierarchical task analysis, and systematic human error reduction and prediction approach analyses were performed. The current process of prescribing specialist drugs by GPs is prone to error. Errors of omission due to lack of information were the most common errors, which could potentially result in a GP prescribing a specialist drug that should only be prescribed in hospitals, or prescribing a specialist drug without reference to a shared care protocol. Half of all possible errors in the prescribing process had a high probability of occurrence. A CDSS supporting GPs during the process of prescribing specialist drugs is needed. This could, first, support the decision making of whether or not to undertake prescribing, and, second, provide drug-specific parameters linked to shared care protocols, which could reduce the errors identified and increase patient safety. © British Journal of General Practice 2017.

  19. A possible alternative to the error prone modified Hodge test to correctly identify the carbapenemase producing Gram-negative bacteria.

    PubMed

    Jeremiah, S S; Balaji, V; Anandan, S; Sahni, R D

    2014-01-01

    The modified Hodge test (MHT) is widely used as a screening test for the detection of carbapenemases in Gram-negative bacteria. This test has several pitfalls in terms of validity and interpretation. Also the test has a very low sensitivity in detecting the New Delhi metallo-β-lactamase (NDM). Considering the degree of dissemination of the NDM and the growing pandemic of carbapenem resistance, a more accurate alternative test is needed at the earliest. The study intends to compare the performance of the MHT with the commercially available Neo-Sensitabs - Carbapenemases/Metallo-β-Lactamase (MBL) Confirmative Identification pack to find out whether the latter could be an efficient alternative to the former. A total of 105 isolates of Klebsiella pneumoniae resistant to imipenem and meropenem, collected prospectively over a period of 2 years were included in the study. The study isolates were tested with the MHT, the Neo-Sensitabs - Carbapenemases/MBL Confirmative Identification pack and polymerase chain reaction (PCR) for detecting the blaNDM-1 gene. Among the 105 isolates, the MHT identified 100 isolates as carbapenemase producers. In the five isolates negative for the MHT, four were found to produce MBLs by the Neo-Sensitabs. The Neo-Sensitabs did not have any false negatives when compared against the PCR. The MHT can give false negative results, which lead to failure in detecting the carbapenemase producers. Also considering the other pitfalls of the MHT, the Neo-Sensitabs--Carbapenemases/MBL Confirmative Identification pack could be a more efficient alternative for detection of carbapenemase production in Gram-negative bacteria.

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

    PubMed Central

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

    2014-01-01

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

  1. Clinical Meaning of Early Oxygenation Improvement in Severe Acute Respiratory Distress Syndrome under Prolonged Prone Positioning

    PubMed Central

    Lee, Kwangha; Kim, Mi-Young; Yoo, Jung-Wan; Hong, Sang-Bum; Lim, Chae-Man

    2010-01-01

    Background/Aims Ventilating patients with acute respiratory distress syndrome (ARDS) in the prone position has been shown to improve arterial oxygenation, but prolonged prone positioning frequently requires continuous deep sedation, which may be harmful to patients. We evaluated the meaning of early gas exchange in patients with severe ARDS under prolonged (≥ 12 hours) prone positioning. Methods We retrospectively studied 96 patients (mean age, 60.1 ± 15.6 years; 75% men) with severe ARDS (PaO2/FiO2 ≤ 150 mmHg) admitted to a medical intensive care unit (MICU). The terms "PaO2 response" and "PaCO2 response" represented responses that resulted in increases in the PaO2/FiO2 ratio of ≥ 20 mmHg and decreases in PaCO2 of ≥ 1 mmHg, respectively, 8 to 12 hours after first placement in the prone position. Results The mean duration of prone positioning was 78.5 ± 61.2 hours, and the 28-day mortality rate after MICU admission was 56.3%. No significant difference in clinical characteristics was observed between PaO2 and PaCO2 responders and non-responders. The PaO2 responders after prone positioning showed an improved 28-day outcome, compared with non-responders by Kaplan-Meier survival estimates (p < 0.05 by the log-rank test), but the PaCO2 responders did not. Conclusions Our results suggest that the early oxygenation improvement after prone positioning might be associated with an improved 28-day outcome and may be an indicator to maintain prolonged prone positioning in patients with severe ARDS. PMID:20195404

  2. Statistical Reporting Errors and Collaboration on Statistical Analyses in Psychological Science

    PubMed Central

    Veldkamp, Coosje L. S.; Nuijten, Michèle B.; Dominguez-Alvarez, Linda; van Assen, Marcel A. L. M.; Wicherts, Jelte M.

    2014-01-01

    Statistical analysis is error prone. A best practice for researchers using statistics would therefore be to share data among co-authors, allowing double-checking of executed tasks just as co-pilots do in aviation. To document the extent to which this ‘co-piloting’ currently occurs in psychology, we surveyed the authors of 697 articles published in six top psychology journals and asked them whether they had collaborated on four aspects of analyzing data and reporting results, and whether the described data had been shared between the authors. We acquired responses for 49.6% of the articles and found that co-piloting on statistical analysis and reporting results is quite uncommon among psychologists, while data sharing among co-authors seems reasonably but not completely standard. We then used an automated procedure to study the prevalence of statistical reporting errors in the articles in our sample and examined the relationship between reporting errors and co-piloting. Overall, 63% of the articles contained at least one p-value that was inconsistent with the reported test statistic and the accompanying degrees of freedom, and 20% of the articles contained at least one p-value that was inconsistent to such a degree that it may have affected decisions about statistical significance. Overall, the probability that a given p-value was inconsistent was over 10%. Co-piloting was not found to be associated with reporting errors. PMID:25493918

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

    PubMed Central

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

    2015-01-01

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

  4. Individual differences in posterior cortical volume correlate with proneness to pride and gratitude.

    PubMed

    Zahn, Roland; Garrido, Griselda; Moll, Jorge; Grafman, Jordan

    2014-11-01

    Proneness to specific moral sentiments (e.g. pride, gratitude, guilt, indignation) has been linked with individual variations in functional MRI (fMRI) response within anterior brain regions whose lesion leads to inappropriate behaviour. However, the role of structural anatomical differences in rendering individuals prone to particular moral sentiments relative to others is unknown. Here, we investigated grey matter volumes (VBM8) and proneness to specific moral sentiments on a well-controlled experimental task in healthy individuals. Individuals with smaller cuneus, and precuneus volumes were more pride-prone, whereas those with larger right inferior temporal volumes experienced gratitude more readily. Although the primary analysis detected no associations with guilt- or indignation-proneness, subgenual cingulate fMRI responses to guilt were negatively correlated with grey matter volumes in the left superior temporal sulcus and anterior dorsolateral prefrontal cortices (right >left). This shows that individual variations in functional activations within critical areas for moral sentiments were not due to grey matter volume differences in the same areas. Grey matter volume differences between healthy individuals may nevertheless play an important role by affecting posterior cortical brain systems that are non-critical but supportive for the experience of specific moral sentiments. This may be of particular relevance when their experience depends on visuo-spatial elaboration. Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.

  5. Real-time PCR (qPCR) primer design using free online software.

    PubMed

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

    Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most commonly used fluorescent chemistries are SYBR® Green dyes and TaqMan®, Molecular Beacon or Scorpion probes. SYBR® Green is very simple to use and cost efficient. As SYBR® Green dye binds to any double-stranded DNA product, its success depends greatly on proper primer design. Many types of online primer design software are available, which can be used free of charge to design desirable SYBR® Green-based qPCR primers. This laboratory exercise is intended for those who have a fundamental background in PCR. It addresses the basic fluorescent chemistries of real-time PCR, the basic rules and pitfalls of primer design, and provides a step-by-step protocol for designing SYBR® Green-based primers with free, online software. Copyright © 2010 Wiley Periodicals, Inc.

  6. Recognition of strong earthquake-prone areas with a single learning class

    NASA Astrophysics Data System (ADS)

    Gvishiani, A. D.; Agayan, S. M.; Dzeboev, B. A.; Belov, I. O.

    2017-05-01

    This article presents a new Barrier recognition algorithm with learning, designed for recognition of earthquake-prone areas. In comparison to the Crust (Kora) algorithm, used by the classical EPA approach, the Barrier algorithm proceeds with learning just on one "pure" high-seismic class. The new algorithm operates in the space of absolute values of the geological-geophysical parameters of the objects. The algorithm is used for recognition of earthquake-prone areas with M ≥ 6.0 in the Caucasus region. Comparative analysis of the Crust and Barrier algorithms justifies their productive coherence.

  7. Mannitol dosing error during interfacility transfer for intracranial emergencies.

    PubMed

    Elliott, Cameron A; MacKenzie, Mark; O'Kelly, Cian J

    2015-11-01

    Mannitol is commonly used to treat elevated intracranial pressure (ICP). The authors analyzed mannitol dosing errors at peripheral hospitals prior to or during transport to tertiary care facilities for intracranial emergencies. They also investigated the appropriateness of mannitol use based on the 2007 Brain Trauma Foundation guidelines for severe traumatic brain injury. The authors conducted a retrospective review of the Shock Trauma Air Rescue Society (STARS) electronic patient database of helicopter medical evacuations in Alberta, Canada, between 2004 and 2012, limited to patients receiving mannitol before transfer. They extracted data on mannitol administration and patient characteristics, including diagnosis, mechanism, Glasgow Coma Scale score, weight, age, and pupil status. A total of 120 patients with an intracranial emergency received a mannitol infusion initiated at a peripheral hospital (median Glasgow Coma Scale score 6; range 3-13). Overall, there was a 22% dosing error rate, which comprised an underdosing rate (<0.25 g/kg) of 8.3% (10 of 120 patients), an overdosing rate (>1.5 g/kg) of 7.5% (9 of 120), and a nonbolus administration rate (>1 hour) of 6.7% (8 of 120). Overall, 72% of patients had a clear indication to receive mannitol as defined by meeting at least one of the following criteria based on Brain Trauma Foundation guidelines: neurological deterioration (11%), severe traumatic brain injury (69%), or pupillary abnormality (25%). Mannitol administration at peripheral hospitals is prone to dosing error. Strategies such as a pretransport checklist may mitigate this risk.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ramella, Sara, E-mail: s.ramella@unicampus.it; Trodella, Lucio; Ippolito, Edy

    2012-07-01

    To select among breast cancer patients and according to breast volume size those who may benefit from 3D conformal radiotherapy after conservative surgery applied with prone-position technique. Thirty-eight patients with early-stage breast cancer were grouped according to the target volume (TV) measured in the supine position: small ({<=}400 mL), medium (400-700 mL), and large ({>=}700 ml). An ad-hoc designed and built device was used for prone set-up to displace the contralateral breast away from the tangential field borders. All patients underwent treatment planning computed tomography in both the supine and prone positions. Dosimetric data to explore dose distribution and volumemore » 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.« less

  9. Considerations for analysis of time-to-event outcomes measured with error: Bias and correction with SIMEX.

    PubMed

    Oh, Eric J; Shepherd, Bryan E; Lumley, Thomas; Shaw, Pamela A

    2018-04-15

    For time-to-event outcomes, a rich literature exists on the bias introduced by covariate measurement error in regression models, such as the Cox model, and methods of analysis to address this bias. By comparison, less attention has been given to understanding the impact or addressing errors in the failure time outcome. For many diseases, the timing of an event of interest (such as progression-free survival or time to AIDS progression) can be difficult to assess or reliant on self-report and therefore prone to measurement error. For linear models, it is well known that random errors in the outcome variable do not bias regression estimates. With nonlinear models, however, even random error or misclassification can introduce bias into estimated parameters. We compare the performance of 2 common regression models, the Cox and Weibull models, in the setting of measurement error in the failure time outcome. We introduce an extension of the SIMEX method to correct for bias in hazard ratio estimates from the Cox model and discuss other analysis options to address measurement error in the response. A formula to estimate the bias induced into the hazard ratio by classical measurement error in the event time for a log-linear survival model is presented. Detailed numerical studies are presented to examine the performance of the proposed SIMEX method under varying levels and parametric forms of the error in the outcome. We further illustrate the method with observational data on HIV outcomes from the Vanderbilt Comprehensive Care Clinic. Copyright © 2017 John Wiley & Sons, Ltd.

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

    PubMed Central

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

    2011-01-01

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

  11. Bacterial adherence to periurethral epithelial cells in girls prone to urinary-tract infections.

    PubMed

    Källenius, G; Winberg, J

    1978-09-09

    Bacterial adherence to epithelial cells from the periurethral region of 48 healthy girls aged over 2 years and of 76 girls with repeated urinary-tract infections was investigated. The infection-prone girls had a significantly higher mean number of adhering bacteria than the healthy controls ( P less than 0.01). This difference was valid irrespective of whether or not the infection-prone girls had urinary-tract infections at the time of investigation. Furthermore, statistically significantly higher numbers of a pyelonephritic strain of Escherichia coli (075:H-:K-non-typable) were found to adhere to washed periurethral cells from infection-prone girls than to cells from healthy controls. These characteristics of the periurethral epithelial cells may facilitate the primary periurethral colonisation which precedes infection of the urinary tract.

  12. Description of a Simple Method of Stoma Protection During Prone Positioning.

    PubMed

    Mackert, Gina A; Reid, Christopher M; Dobke, Marek K; Tenenhaus, Mayer

    2016-06-01

    Surgeries conducted with the patient in the prone position are frequent and can be lengthy. Abdominal stomas and su- prapubic catheters require protection for the complete duration of the procedure to avoid complications such as stomal ischemia, bleeding, or mucocutaneous separation. Standard protection strategies such as pillows and wedges can eas- ily fail. In the course of managing several patients who had sustained ostomy complications following surgery in a prone position, a simple method of stoma protection was devised. Instead of discarding the foam headrest typically used dur- ing induction by anesthesia staff, this device is placed with its central recess over the stoma and secured to the patient's abdominal wall with gentle tape just before turning the patient into a prone position. This method, used in more than 80 patients, has been found to effectively relieve pressure, and no complications have been observed. The foam shape also enables unobstructed drainage of fluids, facilitating collection and preventing leakage and contamination of the surgical field. Because the device is widely used by anesthesia, it is readily available and does not add any extra cost.

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

    PubMed Central

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

    2012-01-01

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

  14. Using the prone position for ventilated patients with respiratory failure: a review.

    PubMed

    Wright, Angie D; Flynn, Maria

    2011-01-01

    this review explored the evidence relating to prone positioning in ventilated patients diagnosed with respiratory failure, including acute lung injury (ALI) or adult respiratory distress syndrome (ARDS). mortality rates for ventilated patients with ALI or ARDS are high, and there is a growing body of evidence suggesting that the position these patients are nursed in may influence clinical outcomes. However, there are no guidelines to inform nursing practice in positioning these patients. Medline, Scopus, Cinahl and the Cochrane Library databases were searched for original research reports or systematic reviews of evidence between 2000 and 2009. Reference lists of retrieved papers were hand searched and included studies were analysed using the Critical Appraisal and Skills Programme framework. A narrative data synthesis considered the strengths and limitations of studies, and findings were collated and interpreted. Application of the search strategy identified a systematic review, currently underway, which has not yet reported and 14 relevant studies eligible for inclusion in this review. Analysis showed considerable variation in study design, but suggests that PaO(2) /FiO(2) ratio, incidence of VAP and mortality may be positively affected by prone positioning. evidence of the clinical benefits associated with prone positioning is inconclusive and provides little guidance for nursing practice. There is a need for further research into the clinical outcomes of prone positioning, and greater understanding of the practicalities of prone positioning critically ill patients is required. nurses have a central role to play in the continual assessment and management of this patient group, including the position they are nursed in, not only to ensure the best clinical outcomes but also to provide care and comfort to the patient and their family. It is therefore important that their nursing practice and interventions are informed by the best available evidence.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    Physically based models provide insights into key hydrologic processes but are associated with uncertainties due to deficiencies in forcing data, model parameters, and model structure. Forcing uncertainty is enhanced in snow-affected catchments, where weather stations are scarce and prone to measurement errors, and meteorological variables exhibit high variability. Hence, there is limited understanding of how forcing error characteristics affect simulations of cold region hydrology and which error characteristics are most important. Here we employ global sensitivity analysis to explore how (1) different error types (i.e., bias, random errors), (2) different error probability distributions, and (3) different error magnitudes influence physically based simulations of four snow variables (snow water equivalent, ablation rates, snow disappearance, and sublimation). We use the Sobol' global sensitivity analysis, which is typically used for model parameters but adapted here for testing model sensitivity to coexisting errors in all forcings. We quantify the Utah Energy Balance model's sensitivity to forcing errors with 1 840 000 Monte Carlo simulations across four sites and five different scenarios. Model outputs were (1) consistently more sensitive to forcing biases than random errors, (2) generally less sensitive to forcing error distributions, and (3) critically sensitive to different forcings depending on the relative magnitude of errors. For typical error magnitudes found in areas with drifting snow, precipitation bias was the most important factor for snow water equivalent, ablation rates, and snow disappearance timing, but other forcings had a more dominant impact when precipitation uncertainty was due solely to gauge undercatch. Additionally, the relative importance of forcing errors depended on the model output of interest. Sensitivity analysis can reveal which forcing error characteristics matter most for hydrologic modeling.

  16. Health departments do it better: prenatal care site and prone infant sleep position.

    PubMed

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

    2005-06-01

    Reduction of prone infant sleep position has been the main public health effort to reduce the incidence of Sudden Infant Death Syndrome (SIDS). Oregon Pregnancy Risk Assessment Monitoring System (PRAMS) surveys a stratified random sample of women after a live birth. In 1998-1999, 1867 women completed the survey (64.0% unweighted response; 73.5% weighted response). Overall, 9.2% of all women "usually" chose prone infant sleep position, while 24.2% chose side and 66.5% chose supine position. Women receiving care from private physicians or HMOs more often chose prone position (10.6%) than women receiving prenatal care from health department clinics (2.5%), hospital clinics (6.1%) or other sites (8.3%). Compared to health department prenatal clinic patients, private prenatal patients were more likely to choose prone infant sleep position, adjusted odds ratio = 4.78 (95% confidence interval [CI] 1.64-13.92). Health Department clinics have done a better job than private physicians in educating mothers about putting infants to sleep on their backs. Providers-especially private providers-should continue to stress the importance of supine sleep position for infants.

  17. Does prone repositioning before posterior fixation produce greater lordosis in lateral lumbar interbody fusion (LLIF)?

    PubMed

    Yson, Sharon C; Sembrano, Jonathan N; Santos, Edward R G; Luna, Jeffrey T P; Polly, David W

    2014-10-01

    Retrospective comparative radiographic review. To determine if lateral to prone repositioning before posterior fixation confers additional operative level lordosis in lateral lumbar interbody fusion (LLIF) procedures. In a review of 56 consecutive patients who underwent LLIF, there was no statistically significant change in segmental lordosis from lateral to prone once a cage is in place. The greatest lordosis increase was observed after cage insertion. We reviewed 56 consecutive patients who underwent LLIF in the lateral position followed by posterior fixation in the prone position. Eighty-eight levels were fused. Disk space angle was measured on intraoperative C-arm images, and change in operative level segmental lordosis brought about by each of the following was determined: (1) cage insertion, (2) prone repositioning, and (3) posterior instrumentation. Paired t test was used to determine significance (α=0.05). Mean lordosis improvement brought about by cage insertion was 2.6 degrees (P=0.00005). There was a 0.1 degree mean lordosis change brought about by lateral to prone positioning (P=0.47). Mean lordosis improvement brought about by posterior fixation, including rod compression, was 1.0 degree (P=0.03). In LLIF procedures, the largest increase in operative level segmental lordosis is brought about by cage insertion. Further lordosis may be gained by placing posterior fixation, including compressive maneuvers. Prone repositioning after cage placement does not produce any incremental lordosis change. Therefore, posterior fixation may be performed in the lateral position without compromising operative level sagittal alignment.

  18. Spatial and temporal variability of the overall error of National Atmospheric Deposition Program measurements determined by the USGS collocated-sampler program, water years 1989-2001

    USGS Publications Warehouse

    Wetherbee, G.A.; Latysh, N.E.; Gordon, J.D.

    2005-01-01

    Data from the U.S. Geological Survey (USGS) collocated-sampler program for the National Atmospheric Deposition Program/National Trends Network (NADP/NTN) are used to estimate the overall error of NADP/NTN measurements. Absolute errors are estimated by comparison of paired measurements from collocated instruments. Spatial and temporal differences in absolute error were identified and are consistent with longitudinal distributions of NADP/NTN measurements and spatial differences in precipitation characteristics. The magnitude of error for calcium, magnesium, ammonium, nitrate, and sulfate concentrations, specific conductance, and sample volume is of minor environmental significance to data users. Data collected after a 1994 sample-handling protocol change are prone to less absolute error than data collected prior to 1994. Absolute errors are smaller during non-winter months than during winter months for selected constituents at sites where frozen precipitation is common. Minimum resolvable differences are estimated for different regions of the USA to aid spatial and temporal watershed analyses.

  19. Error-related brain activity and error awareness in an error classification paradigm.

    PubMed

    Di Gregorio, Francesco; Steinhauser, Marco; Maier, Martin E

    2016-10-01

    Error-related brain activity has been linked to error detection enabling adaptive behavioral adjustments. However, it is still unclear which role error awareness plays in this process. Here, we show that the error-related negativity (Ne/ERN), an event-related potential reflecting early error monitoring, is dissociable from the degree of error awareness. Participants responded to a target while ignoring two different incongruent distractors. After responding, they indicated whether they had committed an error, and if so, whether they had responded to one or to the other distractor. This error classification paradigm allowed distinguishing partially aware errors, (i.e., errors that were noticed but misclassified) and fully aware errors (i.e., errors that were correctly classified). The Ne/ERN was larger for partially aware errors than for fully aware errors. Whereas this speaks against the idea that the Ne/ERN foreshadows the degree of error awareness, it confirms the prediction of a computational model, which relates the Ne/ERN to post-response conflict. This model predicts that stronger distractor processing - a prerequisite of error classification in our paradigm - leads to lower post-response conflict and thus a smaller Ne/ERN. This implies that the relationship between Ne/ERN and error awareness depends on how error awareness is related to response conflict in a specific task. Our results further indicate that the Ne/ERN but not the degree of error awareness determines adaptive performance adjustments. Taken together, we conclude that the Ne/ERN is dissociable from error awareness and foreshadows adaptive performance adjustments. Our results suggest that the relationship between the Ne/ERN and error awareness is correlative and mediated by response conflict. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Anger Proneness and Prognostic Pessimism in Men With Prostate Cancer.

    PubMed

    Gerhart, James; Schmidt, Eric; Lillis, Teresa; O'Mahony, Sean; Duberstein, Paul; Hoerger, Michael

    2017-07-01

    Anger is a common reaction to cancer diagnosis which may impact patients' perceptions of their prognosis and goals of care. This study tested the hypothesis that men with prostate cancer who are anger prone are pessimistic regarding their cancer prognosis. Two hundred and twelve men with a history of prostate cancer completed measures of personality traits, their prostate cancer prognosis, and their perception of their doctor's assessment of their prognosis. Anger proneness was operationally defined by the presence of high levels (ie, above the medians) of neuroticism and disagreeableness. One in 4 men with prostate cancer disagreed with their doctor about prognosis. Anger-prone participants endorsed more pessimistic perceptions of prognosis ( P = .041). This significant association was maintained after accounting for potential confounders. Greater attention paid to patient anger regulation style and pessimistic perceptions will improve discussions about prognosis and goals of care among men with prostate cancer. Given recent calls for wider distress screening and earlier palliative care intervention in cancer settings, providers have an unprecedented opportunity to assess and respond to anger in the clinical setting. Communication could be improved through empathic statements that convey realistic optimism when appropriate, a commitment to the patient-provider relationship and a willingness to explore and address patient needs.

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

    PubMed

    Verona, Edelyn; Bresin, Konrad

    2015-11-01

    Aggressive behavior is observed in persons with various mental health problems and has been studied from the perspectives of neuroscience and psychophysiology. The present research reviews some of the extant experimental literature to help clarify the interplay between domains of functioning implicated in aggression proneness. We then convey a process-oriented model that elucidates how the interplay of the Negative Valence and Cognitive System domains of NIMH's Research Domain Criteria (RDoC) helps explain aggression proneness, particularly reactive aggression. Finally, we report on a study involving event-related potential (ERP) indices of emotional and inhibitory control processing during an emotional-linguistic go/no-go task among 67 individuals with histories of violence and criminal offending (30% female, 44% African-American) who reported on their aggressive tendencies using the Buss-Perry Aggression Questionnaire. Results provide evidence that tendencies toward angry and aggressive behavior relate to reduced inhibitory control processing (no-go P3) specifically during relevant threat-word blocks, suggesting deterioration of cognitive control by acute or sustained threat sensitivity. These findings highlight the value of ERP methodologies for clarifying the interplay of Negative Valence and Cognitive System processes in aggression proneness. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Coherent errors in quantum error correction

    NASA Astrophysics Data System (ADS)

    Greenbaum, Daniel; Dutton, Zachary

    Analysis of quantum error correcting (QEC) codes is typically done using a stochastic, Pauli channel error model for describing the noise on physical qubits. However, it was recently found that coherent errors (systematic rotations) on physical data qubits result in both physical and logical error rates that differ significantly from those predicted by a Pauli model. We present analytic results for the logical error as a function of concatenation level and code distance for coherent errors under the repetition code. For data-only coherent errors, we find that the logical error is partially coherent and therefore non-Pauli. However, the coherent part of the error is negligible after two or more concatenation levels or at fewer than ɛ - (d - 1) error correction cycles. Here ɛ << 1 is the rotation angle error per cycle for a single physical qubit and d is the code distance. These results support the validity of modeling coherent errors using a Pauli channel under some minimum requirements for code distance and/or concatenation. We discuss extensions to imperfect syndrome extraction and implications for general QEC.

  3. Child anger proneness moderates associations between child-mother attachment security and child behavior with mothers at 33 months.

    PubMed

    McElwain, Nancy L; Holland, Ashley S; Engle, Jennifer M; Wong, Maria S

    2012-02-01

    Child-mother attachment security, assessed via a modified Strange Situation procedure (Cassidy & Marvin, with the MacArthur Attachment Working Group, 1992), and parent-reported child proneness to anger were examined as correlates of observed child behavior toward mothers during a series of interactive tasks (N = 120, 60 girls). Controlling for maternal sensitivity and child gender and expressive language ability, greater attachment security, and lower levels of anger proneness were related to more child responsiveness to maternal requests and suggestions during play and snack sessions. As hypothesized, anger proneness also moderated several security-behavior associations. Greater attachment security was related to (a) more committed compliance during clean-up and snack-delay tasks for children high on anger proneness, (b) more self-assertiveness during play and snack for children moderate or high on anger proneness, and (c) more help-seeking during play and snack for children moderate or low on anger proneness. Findings further our understanding of the behavioral correlates of child-mother attachment security assessed during late toddlerhood via the Cassidy-Marvin system and underscore child anger proneness as a moderator of attachment-related differences in child behavior during this developmental period.

  4. Factors in Early Adolescence Associated With a Mole-Prone Phenotype in Late Adolescence.

    PubMed

    Xu, Haoming; Marchetti, Michael A; Dusza, Stephen W; Chung, Esther; Fonseca, Maira; Scope, Alon; Geller, Alan C; Bishop, Marilyn; Marghoob, Ashfaq A; Halpern, Allan C

    2017-10-01

    Nevi are important phenotypic risk factors for melanoma in adults. Few studies have examined the constitutional and behavioral factors associated with a mole-prone phenotype in adolescents. To identify host, behavioral, and dermoscopic factors in early adolescence (age, 14 years) that are associated with a mole-prone phenotype in late adolescence (age, 17 years). A prospective observational cohort study from the Study of Nevi in Children was conducted from January 1, 2009, to December 31, 2014, with a 2- to 3-year follow-up. A total of 569 students from the school system in Framingham, Massachusetts, were enrolled in the 8th or 9th grade (baseline; mean [SD] age, 14.4 [0.7] years). The overall retention rate was 73.3%, and 417 students were reassessed in the 11th grade. Mole-prone phenotype in the 11th grade, defined as total nevus count of the back and 1 randomly selected leg in the top decile of the cohort or having any nevi greater than 5 mm in diameter. Of the 417 students assessed at follow-up in the 11th grade (166 females and 251 males; mean [SD] age, 17.0 [0.4] years), 111 participants (26.6%) demonstrated a mole-prone phenotype: 69 students (62.2%) with 1 nevus greater than 5 mm in diameter, 23 students (20.7%) with total nevus count in the top decile, and 19 students (17.1%) with both characteristics. On multivariate analysis, baseline total nevus count (adjusted odds ratio, 9.08; 95% CI, 4.0-23.7; P < .001) and increased variability of nevus dermoscopic pattern (adjusted odds ratio, 4.24; 95% CI, 1.36-13.25; P = .01) were associated with a mole-prone phenotype. This study found clinically recognizable factors associated with a mole-prone phenotype that may facilitate the identification of individuals at risk for melanoma. These findings could have implications for primary prevention strategies and help target at-risk adolescents for higher-intensity counseling about sun protection and skin self-examination.

  5. Evaluation of a PCR assay on overgrown environmental samples cultured for Mycobacterium avium subsp. paratuberculosis.

    PubMed

    Arango-Sabogal, Juan C; Labrecque, Olivia; Paré, Julie; Fairbrother, Julie-Hélène; Roy, Jean-Philippe; Wellemans, Vincent; Fecteau, Gilles

    2016-11-01

    Culture of Mycobacterium avium subsp. paratuberculosis (MAP) is the definitive antemortem test method for paratuberculosis. Microbial overgrowth is a challenge for MAP culture, as it complicates, delays, and increases the cost of the process. Additionally, herd status determination is impeded when noninterpretable (NI) results are obtained. The performance of PCR is comparable to fecal culture, thus it may be a complementary detection tool to classify NI samples. Our study aimed to determine if MAP DNA can be identified by PCR performed on NI environmental samples and to evaluate the performance of PCR before and after the culture of these samples in liquid media. A total of 154 environmental samples (62 NI, 62 negative, and 30 positive) were analyzed by PCR before being incubated in an automated system. Growth was confirmed by acid-fast bacilli stain and then the same PCR method was again applied on incubated samples, regardless of culture and stain results. Change in MAP DNA after incubation was assessed by converting the PCR quantification cycle (Cq) values into fold change using the 2 -ΔCq method (ΔCq = Cq after culture - Cq before culture). A total of 1.6% (standard error [SE] = 1.6) of the NI environmental samples had detectable MAP DNA. The PCR had a significantly better performance when applied after culture than before culture (p = 0.004). After culture, a 66-fold change (SE = 17.1) in MAP DNA was observed on average. Performing a PCR on NI samples improves MAP culturing. The PCR method used in our study is a reliable and consistent method to classify NI environmental samples. © 2016 The Author(s).

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

    PubMed

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

    2016-02-01

    Quantitative polymerase chain reaction (qPCR) is a powerful technique for quantification of gene expression, especially genes involved in immune responses. Although qPCR is a very efficient and sensitive tool, variations in the enzymatic efficiency, quality of RNA and the presence of inhibitors can lead to errors. Therefore, qPCR needs to be normalised to obtain reliable results and allow comparison. The most common approach is to use reference genes as internal controls in qPCR analyses. In this study, expression of seven genes, including β-actin (ACTB), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-glucuronidase (GUSB), TATA box binding protein (TBP), α-tubulin (TUBAT) and 28S ribosomal RNA (r28S), was determined in cells isolated from chicken lymphoid tissues and stimulated with three different mitogens. The stability of the genes was measured using geNorm, NormFinder and BestKeeper software. The results from both geNorm and NormFinder were that the three most stably expressed genes in this panel were TBP, GAPDH and r28S. BestKeeper did not generate clear answers because of the highly heterogeneous sample set. Based on these data we will include TBP in future qPCR normalisation. The study shows the importance of appropriate reference gene normalisation in other tissues before qPCR analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Detection of canine distemper virus (CDV) through one step RT-PCR combined with nested PCR.

    PubMed

    Kim, Y H; Cho, K W; Youn, H Y; Yoo, H S; Han, H R

    2001-04-01

    A one step reverse transcription PCR (RT-PCR) combined nested PCR was set up to increase efficiency in the diagnosis of canine distemper virus (CDV) infection after developement of nested PCR. Two PCR primer sets were designed based on the sequence of nucleocapsid gene of CDV Onderstepoort strain. One-step RT-PCR with the outer primer pair was revealed to detect 10(2) PFU/ml. The sensitivity was increased hundredfold using the one-step RT-PCR combined with the nested PCR. Specificity of the PCR was also confirmed using other related canine virus and peripheral blood mononuclear cells (PBMC) and body secretes of healthy dogs. Of the 51 blood samples from dogs clinically suspected of CD, 45 samples were revealed as positive by one-step RT-PCR combined with nested PCR. However, only 15 samples were identified as positive with a single one step RT-PCR. Therefore approximately 60% increase in the efficiency of the diagnosis was observed by the combined method. These results suggested that one step RT-PCR combined with nested PCR could be a sensitive, specific, and practical method for diagnosis of CDV infection.

  8. dPCR: A Technology Review

    PubMed Central

    Quan, Phenix-Lan; Sauzade, Martin

    2018-01-01

    Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson distribution. Each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence. The proportion of PCR-positive partitions suffices to determine the concentration of the target sequence without a need for calibration. Advances in microfluidics enabled the current revolution of digital quantification by providing efficient partitioning methods. In this review, we compare the fundamental concepts behind the quantification of nucleic acids by dPCR and quantitative real-time PCR (qPCR). We detail the underlying statistics of dPCR and explain how it defines its precision and performance metrics. We review the different microfluidic digital PCR formats, present their underlying physical principles, and analyze the technological evolution of dPCR platforms. We present the novel multiplexing strategies enabled by dPCR and examine how isothermal amplification could be an alternative to PCR in digital assays. Finally, we determine whether the theoretical advantages of dPCR over qPCR hold true by perusing studies that directly compare assays implemented with both methods. PMID:29677144

  9. Sex Determination Using PCR

    ERIC Educational Resources Information Center

    Kima, Peter E.; Rasche, Madeline E.

    2004-01-01

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

  10. Anthropometric Renal Anatomic Alterations Between Supine and Prone Positions in Percutaneous Renal Ablation for Renal Cortical Neoplasms.

    PubMed

    Lusch, Achim; Fujimoto, Scott; Findeiss, Laura K; Okhunov, Zhamshid; McDougall, Elspeth M; Landman, Jaime

    2016-02-01

    To establish patterns of anatomic changes relevant to the kidney and colon during positional change between the supine and prone positions as noted on CT scans performed during percutaneous cryoablation for renal cortical neoplasms (RCN). Nineteen patients undergoing percutaneous cryoablation for RCN with abdominal CT scan in both the supine and prone positions were included in the study. We documented the anterior/posterior, medial/lateral, and cranial/caudal anatomic changes of the kidney, kidney rotation, and the proportion of the kidney whose access was limited by the liver, spleen, and lung. We also calculated the length of the percutaneous access tract and the distance between the colon and kidney in hilar position as well as the anterior/posterior location of the colon relative to the kidney. In the prone position, the kidney lies significantly more anteriorly on both sides: 4.7 cm vs 4.3 cm (L) and 4.4 cm vs 4.1 cm (R) (p = 0.02 and p = 0.03, respectively). On prone CT images, both kidneys are more cranial when compared with the supine position: 80.4 mm vs 60.8 mm (L) and 87.2 mm vs 57.4 mm (R) (p = 0.002 and p < 0.001, respectively). The skin to tumor distance is significantly shorter in the prone position (p < 0.0001 [L], p = 0.005 [R]). The colon lies closer to the hilum of the kidney and is more posteriorly located in the prone position: 1.21 cm vs 1.04 cm (L) and 0.80 cm vs 0.70 cm (R) (p = 0.005 and p = 0.005, respectively). In the prone position, the lung covers a significantly larger proportion of the right kidney (27.3 mm vs 6.05 mm, p = 0.0001). We documented clinically significant anatomic alterations between supine and prone CT imaging. The changes associated with the prone position modify percutaneous access, particularly for right upper pole tumors. Prone imaging before surgery may be helpful in selected cases.

  11. Medication Administration Errors in Nursing Homes Using an Automated Medication Dispensing System

    PubMed Central

    van den Bemt, Patricia M.L.A.; Idzinga, Jetske C.; Robertz, Hans; Kormelink, Dennis Groot; Pels, Neske

    2009-01-01

    Objective To identify the frequency of medication administration errors as well as their potential risk factors in nursing homes using a distribution robot. Design The study was a prospective, observational study conducted within three nursing homes in the Netherlands caring for 180 individuals. Measurements Medication errors were measured using the disguised observation technique. Types of medication errors were described. The correlation between several potential risk factors and the occurrence of medication errors was studied to identify potential causes for the errors. Results In total 2,025 medication administrations to 127 clients were observed. In these administrations 428 errors were observed (21.2%). The most frequently occurring types of errors were use of wrong administration techniques (especially incorrect crushing of medication and not supervising the intake of medication) and wrong time errors (administering the medication at least 1 h early or late).The potential risk factors female gender (odds ratio (OR) 1.39; 95% confidence interval (CI) 1.05–1.83), ATC medication class antibiotics (OR 11.11; 95% CI 2.66–46.50), medication crushed (OR 7.83; 95% CI 5.40–11.36), number of dosages/day/client (OR 1.03; 95% CI 1.01–1.05), nursing home 2 (OR 3.97; 95% CI 2.86–5.50), medication not supplied by distribution robot (OR 2.92; 95% CI 2.04–4.18), time classes “7–10 am” (OR 2.28; 95% CI 1.50–3.47) and “10 am-2 pm” (OR 1.96; 1.18–3.27) and day of the week “Wednesday” (OR 1.46; 95% CI 1.03–2.07) are associated with a higher risk of administration errors. Conclusions Medication administration in nursing homes is prone to many errors. This study indicates that the handling of the medication after removing it from the robot packaging may contribute to this high error frequency, which may be reduced by training of nurse attendants, by automated clinical decision support and by measures to reduce workload. PMID:19390109

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

    PubMed

    Mancusi, Rocco; Trevisani, Marcello

    2014-08-01

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

  13. [Error prevention through management of complications in urology: standard operating procedures from commercial aviation as a model].

    PubMed

    Kranz, J; Sommer, K-J; Steffens, J

    2014-05-01

    Patient safety and risk/complication management rank among the current megatrends in modern medicine, which has undoubtedly become more complex. In time-critical, error-prone and difficult situations, which often occur repeatedly in everyday clinical practice, guidelines are inappropriate for acting rapidly and intelligently. With the establishment and consistent use of standard operating procedures like in commercial aviation, a possible strategic approach is available. These medical aids to decision-making - quick reference cards - are short, optimized instructions that enable a standardized procedure in case of medical claims.

  14. Implementing parallel spreadsheet models for health policy decisions: The impact of unintentional errors on model projections

    PubMed Central

    Bailey, Stephanie L.; Bono, Rose S.; Nash, Denis; Kimmel, April D.

    2018-01-01

    Background Spreadsheet software is increasingly used to implement systems science models informing health policy decisions, both in academia and in practice where technical capacity may be limited. However, spreadsheet models are prone to unintentional errors that may not always be identified using standard error-checking techniques. Our objective was to illustrate, through a methodologic case study analysis, the impact of unintentional errors on model projections by implementing parallel model versions. Methods We leveraged a real-world need to revise an existing spreadsheet model designed to inform HIV policy. We developed three parallel versions of a previously validated spreadsheet-based model; versions differed by the spreadsheet cell-referencing approach (named single cells; column/row references; named matrices). For each version, we implemented three model revisions (re-entry into care; guideline-concordant treatment initiation; immediate treatment initiation). After standard error-checking, we identified unintentional errors by comparing model output across the three versions. Concordant model output across all versions was considered error-free. We calculated the impact of unintentional errors as the percentage difference in model projections between model versions with and without unintentional errors, using +/-5% difference to define a material error. Results We identified 58 original and 4,331 propagated unintentional errors across all model versions and revisions. Over 40% (24/58) of original unintentional errors occurred in the column/row reference model version; most (23/24) were due to incorrect cell references. Overall, >20% of model spreadsheet cells had material unintentional errors. When examining error impact along the HIV care continuum, the percentage difference between versions with and without unintentional errors ranged from +3% to +16% (named single cells), +26% to +76% (column/row reference), and 0% (named matrices). Conclusions

  15. Detecting medication errors in the New Zealand pharmacovigilance database: a retrospective analysis.

    PubMed

    Kunac, Desireé L; Tatley, Michael V

    2011-01-01

    administration stages of the medication use process, with the majority of errors 82.0% (50/61) deemed to have originated in the community setting. The CARM pharmacovigilance database includes medication errors, many of which were found to originate in the community setting and reported as ADRs. Error-prone situations were able to be identified, providing greater opportunity to improve patient safety. However, to enhance detection of medication errors by pharmacovigilance centres, reports should be prospectively reviewed for preventability and the reporting form revised to facilitate capture of important information that will provide meaningful insight into the nature of the underlying systems defects that caused the error.

  16. SU-E-J-227: Breathing Pattern Consistency and Reproducibility: Comparative Analysis for Supine and Prone Body Positioning

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Laugeman, E; Weiss, E; Chen, S

    2014-06-01

    Purpose: Evaluate and compare the cycle-to-cycle consistency of breathing patterns and their reproducibility over the course of treatment, for supine and prone positioning. Methods: Respiratory traces from 25 patients were recorded for sequential supine/prone 4DCT scans acquired prior to treatment, and during the course of the treatment (weekly or bi-weekly). For each breathing cycle, the average(AVE), end-of-exhale(EoE) and end-of-inhale( EoI) locations were identified using in-house developed software. In addition, the mean values and variations for the above quantities were computed for each breathing trace. F-tests were used to compare the cycle-to-cycle consistency of all pairs of sequential supine and pronemore » scans. Analysis of variances was also performed using population means for AVE, EoE and EoI to quantify differences between the reproducibility of prone and supine respiration traces over the treatment course. Results: Consistency: Cycle-to-cycle variations are less in prone than supine in the pre-treatment and during-treatment scans for AVE, EoE and EoI points, for the majority of patients (differences significant at p<0.05). The few cases where the respiratory pattern had more variability in prone appeared to be random events. Reproducibility: The reproducibility of breathing patterns (supine and prone) improved as treatment progressed, perhaps due to patients becoming more comfortable with the procedure. However, variability in supine position continued to remain significantly larger than in prone (p<0.05), as indicated by the variance analysis of population means for the pretreatment and subsequent during-treatment scans. Conclusions: Prone positioning stabilizes breathing patterns in most subjects investigated in this study. Importantly, a parallel analysis of the same group of patients revealed a tendency towards increasing motion amplitude of tumor targets in prone position regardless of their size or location; thus, the choice for body

  17. Contact high: Mania proneness and positive perception of emotional touches.

    PubMed

    Piff, Paul K; Purcell, Amanda; Gruber, June; Hertenstein, Matthew J; Keltner, Dacher

    2012-01-01

    How do extreme degrees of positive emotion-such as those characteristic of mania-influence emotion perception? The present study investigated how mania proneness, assessed using the Hypomanic Personality Scale, influences the perception of emotion via touch. Using a validated dyadic interaction paradigm for communicating emotion through touch (Hertenstein, Keltner, App, Bulleit, & Jaskolka, 2006), participants (N=53) received eight different touches to their forearm from a stranger and then identified the emotion via forced-choice methodology. Mania proneness predicted increased overall accuracy in touch perception, particularly for positive emotion touches, as well as the over-attribution of positive and under-attribution of negative emotions across all touches. These findings highlight the effects of positive emotion extremes on the perception of emotion in social interactions.

  18. [Reactance proneness, collectivism, uniqueness, and resistance to persuasion].

    PubMed

    Imajo, Shuzo

    2002-10-01

    This study examined the reliability and validity of Japanese psychological reactance scales. A total of 167 undergraduates completed a questionnaire of Therapeutic Reactance Scale (TRS), the Hong Reactance Scale (HRS), the Uniqueness Scale, and the Collectivism Scale. They also received messages involving three persuasion situations that were either high or low in terms of threat, and were asked to describe their reactions to them. The author categorized the reactions into three: acceptance, indirect resistance, and direct resistance. Reliabilities of the reactance scales were satisfactory. Their scores positively correlated with uniqueness scores, and negatively with collectivism scores. Those high on reactance proneness were less persuaded in two of the three situations. But in the third, an HRS by threat interaction was observed, indicating that only those who were high on reactance proneness under the high-threat condition showed resistance to persuasion. These results suggest that the Japanese versions of reactance scale were reliable and valid. However, the assertiveness aspect of TRS may not be appropriate for the definition of reactance. The influence of culture on psychological reactance was also discussed.

  19. A self-regulatory approach to understanding boredom proneness.

    PubMed

    Struk, A A; Scholer, A A; Danckert, J

    2015-07-29

    We investigated the relationship between self-regulation and two types of boredom proneness (perceived lack of internal stimulation, perceived lack of external stimulation) using a variety of measures of self-regulation. These included a general measure of self-control, measures of both regulatory focus (i.e., promotion or a sensitivity to gains/non-gains vs. prevention or a sensitivity to losses/non-losses) and regulatory mode (i.e., assessment or the tendency to compare means and goals vs. locomotion or the tendency to initiate and maintain commitment to action), and measures of cognitive flexibility (i.e., a perceived sense of control and the tendency to seek alternative solutions). Results identified a unique set of factors related to each boredom proneness component. Trait self-control and prevention focus were associated with lower boredom propensity due to a lack of external stimulation. Locomotion and the tendency to seek alternatives were associated with lower boredom propensity due to a lack of internal stimulation. These findings suggest that effective goal pursuit is associated with reduced likelihood of experiencing boredom.

  20. Inability of infants to push up in the prone position and subsequent development.

    PubMed

    Senju, Ayako; Shimono, Masayuki; Tsuji, Mayumi; Suga, Reiko; Shibata, Eiji; Fujino, Yoshihisa; Kawamoto, Toshihiro; Kusuhara, Koichi

    2018-06-14

    During routine health screenings, pediatricians may note that some infants cannot maintain the prone position with an extended arm support at 6 months. However, little is known regarding the development of full-term infants with this developmental deviation. We investigated the developmental course of infants exhibiting this characteristic. We included 2020 full-term infants from a regional center for the Japan Environment and Children's Study. Their development was measured using the Ages and Stages Questionnaire, Third Edition, at 0.5, 1, 1.5, 2, 2.5, and 3 years. The children were grouped according to their ability to stay prone on extended arms at 6 months, and their development was compared. The questionnaire revealed that 1625 infants could stay prone on extended arms and 179 could not. We excluded 212 infants who could stay prone on extended arms only sometimes, and four did not respond. In the Gross Motor domain, significant difference in questionnaire scores was observed between the "could" and "could-not" groups at 6 months (Hedges' g 1.83) and persisted until 3 years (Hedges' g 0.33). Significant differences were also observed in the Communication, Fine Motor, Problem Solving, and Personal-Social domains at 6 months (Hedges' g 0.20-0.58) and persisted until 1, 2, 2, and 1.5 years, respectively (Hedges' g 0.21-0.25). Infants who cannot maintain the prone position on extended arms lag behind those who can, although the effect sizes become relatively small after 1.5 years of age. Early interventions may be considered if delays are problematic or persistent. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  1. Error baseline rates of five sample preparation methods used to characterize RNA virus populations.

    PubMed

    Kugelman, Jeffrey R; Wiley, Michael R; Nagle, Elyse R; Reyes, Daniel; Pfeffer, Brad P; Kuhn, Jens H; Sanchez-Lockhart, Mariano; Palacios, Gustavo F

    2017-01-01

    Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses. However, both steps may lead to the introduction of artificial mutations, thereby skewing the data. To better understand how such errors are introduced during sample preparation, we determined and compared error baseline rates of five different sample preparation methods by analyzing in vitro transcribed Ebola virus RNA from an artificial plasmid-based system. These methods included: shotgun sequencing from plasmid DNA or in vitro transcribed RNA as a basic "no amplification" method, amplicon sequencing from the plasmid DNA or in vitro transcribed RNA as a "targeted" amplification method, sequence-independent single-primer amplification (SISPA) as a "random" amplification method, rolling circle reverse transcription sequencing (CirSeq) as an advanced "no amplification" method, and Illumina TruSeq RNA Access as a "targeted" enrichment method. The measured error frequencies indicate that RNA Access offers the best tradeoff between sensitivity and sample preparation error (1.4-5) of all compared methods.

  2. Error baseline rates of five sample preparation methods used to characterize RNA virus populations

    PubMed Central

    Kugelman, Jeffrey R.; Wiley, Michael R.; Nagle, Elyse R.; Reyes, Daniel; Pfeffer, Brad P.; Kuhn, Jens H.; Sanchez-Lockhart, Mariano; Palacios, Gustavo F.

    2017-01-01

    Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses. However, both steps may lead to the introduction of artificial mutations, thereby skewing the data. To better understand how such errors are introduced during sample preparation, we determined and compared error baseline rates of five different sample preparation methods by analyzing in vitro transcribed Ebola virus RNA from an artificial plasmid-based system. These methods included: shotgun sequencing from plasmid DNA or in vitro transcribed RNA as a basic “no amplification” method, amplicon sequencing from the plasmid DNA or in vitro transcribed RNA as a “targeted” amplification method, sequence-independent single-primer amplification (SISPA) as a “random” amplification method, rolling circle reverse transcription sequencing (CirSeq) as an advanced “no amplification” method, and Illumina TruSeq RNA Access as a “targeted” enrichment method. The measured error frequencies indicate that RNA Access offers the best tradeoff between sensitivity and sample preparation error (1.4−5) of all compared methods. PMID:28182717

  3. Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation.

    PubMed

    Whale, Alexandra S; Huggett, Jim F; Cowen, Simon; Speirs, Valerie; Shaw, Jacqui; Ellison, Stephen; Foy, Carole A; Scott, Daniel J

    2012-06-01

    One of the benefits of Digital PCR (dPCR) is the potential for unparalleled precision enabling smaller fold change measurements. An example of an assessment that could benefit from such improved precision is the measurement of tumour-associated copy number variation (CNV) in the cell free DNA (cfDNA) fraction of patient blood plasma. To investigate the potential precision of dPCR and compare it with the established technique of quantitative PCR (qPCR), we used breast cancer cell lines to investigate HER2 gene amplification and modelled a range of different CNVs. We showed that, with equal experimental replication, dPCR could measure a smaller CNV than qPCR. As dPCR precision is directly dependent upon both the number of replicate measurements and the template concentration, we also developed a method to assist the design of dPCR experiments for measuring CNV. Using an existing model (based on Poisson and binomial distributions) to derive an expression for the variance inherent in dPCR, we produced a power calculation to define the experimental size required to reliably detect a given fold change at a given template concentration. This work will facilitate any future translation of dPCR to key diagnostic applications, such as cancer diagnostics and analysis of cfDNA.

  4. Real-Time PCR (RT-PCR) Assays for Burkholderia mallei and B. pseudomallei

    DTIC Science & Technology

    2005-10-01

    1 Real-time PCR (RT-PCR) Assays for Burkholderia mallei and B. pseudomallei Vipin K. Rastogi1, Tu-chen Cheng1, Lisa Collins1 and Jennifer Bagley2 1...A 3. DATES COVERED - 4. TITLE AND SUBTITLE Real-time PCR (RT-PCR) Assays for Burkholderia mallei and B.pseudomallei 5a. CONTRACT NUMBER 5b...pseudomallei and B. mallei , respectively are the causative agents of meliodosis and glanders , primarily in animals (both pathogens), and in humans

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

    PubMed Central

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

    2014-01-01

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

  6. Individual differences in flow proneness are linked to a dopamine D2 receptor gene variant.

    PubMed

    Gyurkovics, Mate; Kotyuk, Eszter; Katonai, Eniko Rozsa; Horvath, Erzsebet Zsofia; Vereczkei, Andrea; Szekely, Anna

    2016-05-01

    Flow is a special mental state characterized by deep concentration that occurs during the performance of optimally challenging tasks. In prior studies, proneness to experience flow has been found to be moderately heritable. In the present study, we investigated whether individual differences in flow proneness are related to a polymorphism of the dopamine D2 receptor coding gene (DRD2 C957T rs6277). This polymorphism affects striatal D2 receptor availability, a factor that has been shown to be related to flow proneness. To our knowledge, this is the first study to investigate the association between this trait and a specific gene variant. In a sample of 236 healthy Hungarian adults, we found that CC homozygotes report higher flow proneness than do T allele carriers, but only during mandatory activities (i.e., studying and working), not during leisure time. We discuss implications of this result, e.g., the potential mediators of the relationship. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. RGB-to-RGBG conversion algorithm with adaptive weighting factors based on edge detection and minimal square error.

    PubMed

    Huang, Chengqiang; Yang, Youchang; Wu, Bo; Yu, Weize

    2018-06-01

    The sub-pixel arrangement of the RGBG panel and the image with RGB format are different and the algorithm that converts RGB to RGBG is urgently needed to display an image with RGB arrangement on the RGBG panel. However, the information loss is still large although color fringing artifacts are weakened in the published papers that study this conversion. In this paper, an RGB-to-RGBG conversion algorithm with adaptive weighting factors based on edge detection and minimal square error (EDMSE) is proposed. The main points of innovation include the following: (1) the edge detection is first proposed to distinguish image details with serious color fringing artifacts and image details which are prone to be lost in the process of RGB-RGBG conversion; (2) for image details with serious color fringing artifacts, the weighting factor 0.5 is applied to weaken the color fringing artifacts; and (3) for image details that are prone to be lost in the process of RGB-RGBG conversion, a special mechanism to minimize square error is proposed. The experiment shows that the color fringing artifacts are slightly improved by EDMSE, and the values of MSE of the image processed are 19.6% and 7% smaller than those of the image processed by the direct assignment and weighting factor algorithm, respectively. The proposed algorithm is implemented on a field programmable gate array to enable the image display on the RGBG panel.

  8. Prone to feel guilty: Self-evaluative emotions in alcohol-dependence.

    PubMed

    Grynberg, Delphine; de Timary, Philippe; Van Heuverswijn, Aude; Maurage, Pierre

    2017-10-01

    Prior research has repeatedly shown that alcohol-dependence is associated with interpersonal difficulties. However, guilt and shame, two crucial self-evaluative emotions triggered by the transgression of social norms, have not been explored among alcohol-dependent individuals despite their important role in psychiatric disorders. The present study thus aimed to investigate whether alcohol-dependence is associated with greater proneness to negatively evaluate one's own behaviors (guilt) or the entire self (shame). 25 alcohol-dependent individuals (ADI) and 25 matched healthy individuals completed a scenario-based inventory (TOSCA-3), requiring from participants to rate the extent they will react to each scenario in terms of (contextualized) guilt and shame. Participants also completed a list of adjectives related to the frequency at which they generally experience (uncontextualized) guilt and shame (PFQ-2). When controlling for possible confounds (i.e., depression and anxiety), ADI reported greater proneness to experience guilt at the TOSCA-3 (η 2 =.22) compared to healthy individuals. This study is the first to show that alcohol-dependence is associated with greater contextualized guilt-proneness, i.e., negative evaluation of one's own behaviors that transgress social norms. Therefore, these results reinforce the relevance of social disorders in alcohol-dependence and indicate that ADI may benefit of therapeutic programs to avoid a generalization of guilt towards shame. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Evaluation of an Improved U.S. Food and Drug Administration Method for the Detection of Cyclospora cayetanensis in Produce Using Real-Time PCR.

    PubMed

    Murphy, Helen R; Lee, Seulgi; da Silva, Alexandre J

    2017-07-01

    Cyclospora cayetanensis is a protozoan parasite that causes human diarrheal disease associated with the consumption of fresh produce or water contaminated with C. cayetanensis oocysts. In the United States, foodborne outbreaks of cyclosporiasis have been linked to various types of imported fresh produce, including cilantro and raspberries. An improved method was developed for identification of C. cayetanensis in produce at the U.S. Food and Drug Administration. The method relies on a 0.1% Alconox produce wash solution for efficient recovery of oocysts, a commercial kit for DNA template preparation, and an optimized TaqMan real-time PCR assay with an internal amplification control for molecular detection of the parasite. A single laboratory validation study was performed to assess the method's performance and compare the optimized TaqMan real-time PCR assay and a reference nested PCR assay by examining 128 samples. The samples consisted of 25 g of cilantro or 50 g of raspberries seeded with 0, 5, 10, or 200 C. cayetanensis oocysts. Detection rates for cilantro seeded with 5 and 10 oocysts were 50.0 and 87.5%, respectively, with the real-time PCR assay and 43.7 and 94.8%, respectively, with the nested PCR assay. Detection rates for raspberries seeded with 5 and 10 oocysts were 25.0 and 75.0%, respectively, with the real-time PCR assay and 18.8 and 68.8%, respectively, with the nested PCR assay. All unseeded samples were negative, and all samples seeded with 200 oocysts were positive. Detection rates using the two PCR methods were statistically similar, but the real-time PCR assay is less laborious and less prone to amplicon contamination and allows monitoring of amplification and analysis of results, making it more attractive to diagnostic testing laboratories. The improved sample preparation steps and the TaqMan real-time PCR assay provide a robust, streamlined, and rapid analytical procedure for surveillance, outbreak response, and regulatory testing of foods for

  10. Digital stereo photogrammetry for grain-scale monitoring of fluvial surfaces: Error evaluation and workflow optimisation

    NASA Astrophysics Data System (ADS)

    Bertin, Stephane; Friedrich, Heide; Delmas, Patrice; Chan, Edwin; Gimel'farb, Georgy

    2015-03-01

    Grain-scale monitoring of fluvial morphology is important for the evaluation of river system dynamics. Significant progress in remote sensing and computer performance allows rapid high-resolution data acquisition, however, applications in fluvial environments remain challenging. Even in a controlled environment, such as a laboratory, the extensive acquisition workflow is prone to the propagation of errors in digital elevation models (DEMs). This is valid for both of the common surface recording techniques: digital stereo photogrammetry and terrestrial laser scanning (TLS). The optimisation of the acquisition process, an effective way to reduce the occurrence of errors, is generally limited by the use of commercial software. Therefore, the removal of evident blunders during post processing is regarded as standard practice, although this may introduce new errors. This paper presents a detailed evaluation of a digital stereo-photogrammetric workflow developed for fluvial hydraulic applications. The introduced workflow is user-friendly and can be adapted to various close-range measurements: imagery is acquired with two Nikon D5100 cameras and processed using non-proprietary "on-the-job" calibration and dense scanline-based stereo matching algorithms. Novel ground truth evaluation studies were designed to identify the DEM errors, which resulted from a combination of calibration errors, inaccurate image rectifications and stereo-matching errors. To ensure optimum DEM quality, we show that systematic DEM errors must be minimised by ensuring a good distribution of control points throughout the image format during calibration. DEM quality is then largely dependent on the imagery utilised. We evaluated the open access multi-scale Retinex algorithm to facilitate the stereo matching, and quantified its influence on DEM quality. Occlusions, inherent to any roughness element, are still a major limiting factor to DEM accuracy. We show that a careful selection of the camera

  11. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... community shall consider— (1) Preservation of the flood-prone areas for open space purposes; (2) Relocation... debris, to provide an added margin of safety against floods having a magnitude greater than the base...

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

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... community shall consider— (1) Preservation of the flood-prone areas for open space purposes; (2) Relocation... debris, to provide an added margin of safety against floods having a magnitude greater than the base...

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... community shall consider— (1) Preservation of the flood-prone areas for open space purposes; (2) Relocation... debris, to provide an added margin of safety against floods having a magnitude greater than the base...

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goyal, Uma, E-mail: uma.goyal@gmail.com; Locke, Angela; Smith-Raymond, Lexie

    Our goal was to design a prone breast shield for the contralateral breast and study its efficacy in decreasing scatter radiation to the contralateral breast in a prone breast phantom setup receiving radiation therapy designed for breast cancer. We constructed a prone breast phantom setup consisting of (1) A thermoplastic mask with a left-sided depression created by a water balloon for a breast shape; (2) 2 plastic bags to hold water in the thermoplastic mask depression; (3) 2000 mL of water to fill the thermoplastic mask depression to create a water-based false breast; (4) 1-cm thick bolus placed in themore » contralateral breast holder; (5) 2 lead (Pb) sheets, each 0.1-cm thick for blocking scatter radiation in the contralateral bolus-based false breast; (6) a prone breast board to hold the thermoplastic mask, water, bolus, and lead; (7) 9 cm solid water on top of the breast board to simulate body; (8) a diode was used to verify dose for each treatment field of the treated water-based breast; (9) metal–oxide–semiconductor-field effect transistor (MOSFET) dosimeters to measure dose to the contralateral bolus-based breast. The phantom prone breast setup was CT simulated and treatment was designed with 95% isodose line covering the treated breast. The maximum dose was 107.1%. Megavoltage (MV) port images ensured accurate setup. Measurements were done using diodes on the treated water-based breast and MOSFET dosimeters at the medial and lateral sides of the contralateral bolus-based breast without and with the Pb shield. Five treatments were done for each of the 3 data sets and recorded individually for statistical purposes. All treatments were completed with 6 MV photons at 200 cGy per treatment. The dose contributions from each of the 3 data sets including 15 treatments total without and with the prone lead shield to the medial and lateral portions of contralateral bolus-based breast were averaged individually. Unshielded dose means were 37.11 and 2.94 c

  15. Can Perspective-Taking Reduce Crime? Examining a Pathway Through Empathic-Concern and Guilt-Proneness

    PubMed Central

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

    2015-01-01

    We describe and test 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 then ultimately inhibits criminal behavior (perspective-taking → empathic-concern → guilt-proneness → crime desistance). Data from two sources were analyzed: (1) a cross-sectional college sample and (2) a longitudinal sample of jail inmates. Overall, results lend credence to this model. Perspective-taking propensities ultimately “put the brakes” on criminal behavior via an affective pathway of empathic-concern and guilt-proneness. Discussion focuses on the nature of perspective-taking, its generative role in moral emotions, as well as potential applications for crime prevention. PMID:25324328

  16. Immuno-PCR: Achievements and Perspectives.

    PubMed

    Ryazantsev, D Y; Voronina, D V; Zavriev, S K

    2016-12-01

    The immuno-PCR (iPCR) method combines advantages of enzyme-linked immunosorbent assay and polymerase chain reaction, which is used in iPCR as a method of "visualization" of antigen-antibody interaction. The use of iPCR provides classical PCR sensitivity to objects traditionally detected by ELISA. This method could be very sensitive and allow for detection of quantities of femtograms/ml order. However, iPCR is still not widely used. The aim of this review is to highlight the special features of the iPCR method and to show the main aspects of its development and application in recent years.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  18. Disgust proneness predicts obsessive-compulsive disorder symptom severity in a clinical sample of youth: Distinctions from negative affect.

    PubMed

    Olatunji, Bunmi O; Ebesutani, Chad; Kim, Jingu; Riemann, Bradley C; Jacobi, David M

    2017-04-15

    Although studies have linked disgust proneness to the etiology and maintenance of obsessive-compulsive disorder (OCD) in adults, there remains a paucity of research examining the specificity of this association among youth. The present study employed structural equation modeling to examine the association between disgust proneness, negative affect, and OCD symptom severity in a clinical sample of youth admitted to a residential treatment facility (N =471). Results indicate that disgust proneness and negative affect latent factors independently predicted an OCD symptom severity latent factor. However, when both variables were modeled as predictors simultaneously, latent disgust proneness remained significantly associated with OCD symptom severity, whereas the association between latent negative affect and OCD symptom severity became nonsignificant. Tests of mediation converged in support of disgust proneness as a significant intervening variable between negative affect and OCD symptom severity. Subsequent analysis showed that the path from disgust proneness to OCD symptom severity in the structural model was significantly stronger among those without a primary diagnosis of OCD compared to those with a primary diagnosis of OCD. Given the cross-sectional design, the causal inferences that can be made are limited. The present study is also limited by the exclusive reliance on self-report measures. Disgust proneness may play a uniquely important role in OCD among youth. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Prone positioning ventilation for treatment of acute lung injury and acute respiratory distress syndrome.

    PubMed

    Lan, Mei-juan; He, Xiao-di

    2009-08-01

    Patients who are diagnosed with acute lung injury/acute respiratory distress syndrome (ALI/ARDS) usually have ventilation-perfusion mismatch, severe decrease in lung capacity, and gas exchange abnormalities. Health care workers have implemented various strategies in an attempt to compensate for these pathological alterations. By rotating patients with ALI/ARDS between the supine and prone position, it is possible to achieve a significant improvement in PaO2/FiO2, decrease shunting and therefore improve oxygenation without use of expensive, invasive and experimental procedures. Prone positioning is a safe and effective way to improve ventilation when conventional strategies fail to initiate a patient response. Because a specific cure for ARDS is not available, the goal is to support the patients with therapies that cause the least amount of injury while the lungs have an opportunity to heal. Based on current data, a trial of prone positioning ventilation should be offered to the patients who have ALI/ARDS in the early course of the disease. Published studies exhibit substantial heterogeneity in clinical results, suggesting that an adequately sized study optimizing the duration of proning ventilation strategy is warranted to enable definitive conclusions to be drawn.

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

    PubMed Central

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

    2015-01-01

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

  1. Advances in PCR technology.

    PubMed

    Lauerman, Lloyd H

    2004-12-01

    Since the discovery of the polymerase chain reaction (PCR) 20 years ago, an avalanche of scientific publications have reported major developments and changes in specialized equipment, reagents, sample preparation, computer programs and techniques, generated through business, government and university research. The requirement for genetic sequences for primer selection and validation has been greatly facilitated by the development of new sequencing techniques, machines and computer programs. Genetic libraries, such as GenBank, EMBL and DDBJ continue to accumulate a wealth of genetic sequence information for the development and validation of molecular-based diagnostic procedures concerning human and veterinary disease agents. The mechanization of various aspects of the PCR assay, such as robotics, microfluidics and nanotechnology, has made it possible for the rapid advancement of new procedures. Real-time PCR, DNA microarray and DNA chips utilize these newer techniques in conjunction with computer and computer programs. Instruments for hand-held PCR assays are being developed. The PCR and reverse transcription-PCR (RT-PCR) assays have greatly accelerated the speed and accuracy of diagnoses of human and animal disease, especially of the infectious agents that are difficult to isolate or demonstrate. The PCR has made it possible to genetically characterize a microbial isolate inexpensively and rapidly for identification, typing and epidemiological comparison.

  2. [Prospective assessment of medication errors in critically ill patients in a university hospital].

    PubMed

    Salazar L, Nicole; Jirón A, Marcela; Escobar O, Leslie; Tobar, Eduardo; Romero, Carlos

    2011-11-01

    Critically ill patients are especially vulnerable to medication errors (ME) due to their severe clinical situation and the complexities of their management. To determine the frequency and characteristics of ME and identify shortcomings in the processes of medication management in an Intensive Care Unit. During a 3 months period, an observational prospective and randomized study was carried out in the ICU of a university hospital. Every step of patient's medication management (prescription, transcription, dispensation, preparation and administration) was evaluated by an external trained professional. Steps with higher frequency of ME and their therapeutic groups involved were identified. Medications errors were classified according to the National Coordinating Council for Medication Error Reporting and Prevention. In 52 of 124 patients evaluated, 66 ME were found in 194 drugs prescribed. In 34% of prescribed drugs, there was at least 1 ME during its use. Half of ME occurred during medication administration, mainly due to problems in infusion rates and schedule times. Antibacterial drugs had the highest rate of ME. We found a 34% rate of ME per drug prescribed, which is in concordance with international reports. The identification of those steps more prone to ME in the ICU, will allow the implementation of an intervention program to improve the quality and security of medication management.

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

    PubMed

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

    2008-07-23

    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.

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

    PubMed Central

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

    2009-01-01

    We examined historical change in the association between adolescent deviance proneness and marijuana use using 26 years (from 1979 through 2004) of national 12th grade data from the Monitoring the Future (MTF) study. “Deviance proneness” was measured using a latent factor model of behavioral and personality characteristics that underlie both substance use and antisocial disorders. Marijuana use outcomes were measured in terms of youths’ annual frequency of use, and youths’ degree of involvement with marijuana. Separate within-gender structural equation models were used to determine whether links between deviance proneness and marijuana use were consistently significant and invariant in magnitude across 13 2-year historical cohorts. Overall results affirmed the established association between adolescent deviance proneness and both the frequency of marijuana use as well as regular use. Among male youth, the size of the association between deviance proneness and marijuana use was significantly smaller at the cohort of lowest population prevalence (1991/92) compared to cohorts marking peaks in marijuana use prevalence, thus suggesting a “softening” historical trend. By contrast, the prediction of female marijuana use from deviance proneness was not consistently related to historical shifts in population prevalence of marijuana use. Study findings point to the utility of risk-focused prevention programming that targets early precursors of both antisocial and substance use disorders. PMID:18317927

  5. Medical errors and uncertainty in primary healthcare: A comparative study of coping strategies among young and experienced GPs

    PubMed Central

    Kuikka, Liisa; Pitkälä, Kaisu

    2014-01-01

    Abstract Objective. To study coping differences between young and experienced GPs in primary care who experience medical errors and uncertainty. Design. Questionnaire-based survey (self-assessment) conducted in 2011. Setting. Finnish primary practice offices in Southern Finland. Subjects. Finnish GPs engaged in primary health care from two different respondent groups: young (working experience ≤ 5years, n = 85) and experienced (working experience > 5 years, n = 80). Main outcome measures. Outcome measures included experiences and attitudes expressed by the included participants towards medical errors and tolerance of uncertainty, their coping strategies, and factors that may influence (positively or negatively) sources of errors. Results. In total, 165/244 GPs responded (response rate: 68%). Young GPs expressed significantly more often fear of committing a medical error (70.2% vs. 48.1%, p = 0.004) and admitted more often than experienced GPs that they had committed a medical error during the past year (83.5% vs. 68.8%, p = 0.026). Young GPs were less prone to apologize to a patient for an error (44.7% vs. 65.0%, p = 0.009) and found, more often than their more experienced colleagues, on-site consultations and electronic databases useful for avoiding mistakes. Conclusion. Experienced GPs seem to better tolerate uncertainty and also seem to fear medical errors less than their young colleagues. Young and more experienced GPs use different coping strategies for dealing with medical errors. Implications. When GPs become more experienced, they seem to get better at coping with medical errors. Means to support these skills should be studied in future research. PMID:24914458

  6. Use of Bacteriophage MS2 as an Internal Control in Viral Reverse Transcription-PCR Assays

    PubMed Central

    Dreier, Jens; Störmer, Melanie; Kleesiek, Knut

    2005-01-01

    Diagnostic systems based on reverse transcription (RT)-PCR are widely used for the detection of viral genomes in different human specimens. The application of internal controls (IC) to monitor each step of nucleic acid amplification is necessary to prevent false-negative results due to inhibition or human error. In this study, we designed various real-time RT-PCRs utilizing the coliphage MS2 replicase gene, which differ in detection format, amplicon size, and efficiency of amplification. These noncompetitive IC assays, using TaqMan, hybridization probe, or duplex scorpion probe techniques, were tested on the LightCycler and Rotorgene systems. In our approach, clinical specimens were spiked with the control virus to monitor the efficiency of extraction, reverse transcription, and amplification steps. The MS2 RT-PCR assays were applied for internal control when using a second target hepatitis C virus RNA in duplex PCR in blood donor screening. The 95% detection limit was calculated by probit analysis to 44.9 copies per PCR (range, 38.4 to 73.4). As demonstrated routinely, application of MS2 IC assays exhibits low variability and can be applied in various RT-PCR assays. MS2 phage lysates were obtained under standard laboratory conditions. The quantification of phage and template RNA was performed by plating assays to determine PFU or via real-time RT-PCR. High stability of the MS2 phage preparations stored at −20°C, 4°C, and room temperature was demonstrated. PMID:16145106

  7. Lactobacillus johnsonii N6.2 stimulates the innate immune response through Toll-like receptor 9 in Caco-2 cells and increases intestinal crypt Paneth cell number in biobreeding diabetes-prone rats.

    PubMed

    Kingma, Sandra D K; Li, Nan; Sun, Frank; Valladares, Ricardo B; Neu, Joe; Lorca, Graciela L

    2011-06-01

    Lactobacillus johnsonii (Ljo) N6.2 has been shown to mitigate the development of type 1 diabetes when administered to diabetes-prone rats. The specific mechanisms underlying this observed response remain under investigation. The objective of this study was to assess the effect of Ljo N6.2 on mucosal inflammatory response using differentiated Caco-2 monolayers. The mRNA expression levels of CCL20, CXCL8, and CXCL10 chemokines were determined by qRT-PCR. Ljo at 10(11) CFU/L induced a strong response in all chemokines examined. To assess the specific host-signaling pathways involved, we performed RT-PCR amplification of Toll-like receptors (TLR) and nucleotide-binding oligomerization domain-like receptors. TLR7 and TLR9 expression levels were induced 4.2- and 9-fold, respectively, whereas other TLR and nucleotide-binding oligomerization domain receptors were not modified. A similar effect was observed in Caco-2 monolayers treated with Ljo cell-free extract or purified nucleic acids (NA). Increased levels of IFN type 1 and IFN regulators Stat1 and IRF7 followed the upregulation of TLR9. Activation of TLR9 was also evidenced by increased Frizzled 5 expression in Ljo-treated Caco-2 cells and an increase in the number of Paneth cells in Ljo-fed, diabetes-prone rats. These results are in agreement with the polarizing-tolerizing mechanism recently described in which the apical stimulation of TLR9 in intestinal epithelial cells leads to a higher state of immunologic alertness. Furthermore, these results suggest that live probiotics could be, in the future, replaced with select cellular components.

  8. Action errors, error management, and learning in organizations.

    PubMed

    Frese, Michael; Keith, Nina

    2015-01-03

    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.

  9. Modeling coherent errors in quantum error correction

    NASA Astrophysics Data System (ADS)

    Greenbaum, Daniel; Dutton, Zachary

    2018-01-01

    Analysis of quantum error correcting codes is typically done using a stochastic, Pauli channel error model for describing the noise on physical qubits. However, it was recently found that coherent errors (systematic rotations) on physical data qubits result in both physical and logical error rates that differ significantly from those predicted by a Pauli model. Here we examine the accuracy of the Pauli approximation for noise containing coherent errors (characterized by a rotation angle ɛ) under the repetition code. We derive an analytic expression for the logical error channel as a function of arbitrary code distance d and concatenation level n, in the small error limit. We find that coherent physical errors result in logical errors that are partially coherent and therefore non-Pauli. However, the coherent part of the logical error is negligible at fewer than {ε }-({dn-1)} error correction cycles when the decoder is optimized for independent Pauli errors, thus providing a regime of validity for the Pauli approximation. Above this number of correction cycles, the persistent coherent logical error will cause logical failure more quickly than the Pauli model would predict, and this may need to be combated with coherent suppression methods at the physical level or larger codes.

  10. Introduction to digital PCR.

    PubMed

    Bizouarn, Francisco

    2014-01-01

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

  11. The Next-Generation PCR-Based Quantification Method for Ambient Waters: Digital PCR.

    PubMed

    Cao, Yiping; Griffith, John F; Weisberg, Stephen B

    2016-01-01

    Real-time quantitative PCR (qPCR) is increasingly being used for ambient water monitoring, but development of digital polymerase chain reaction (digital PCR) has the potential to further advance the use of molecular techniques in such applications. Digital PCR refines qPCR by partitioning the sample into thousands to millions of miniature reactions that are examined individually for binary endpoint results, with DNA density calculated from the fraction of positives using Poisson statistics. This direct quantification removes the need for standard curves, eliminating the labor and materials associated with creating and running standards with each batch, and removing biases associated with standard variability and mismatching amplification efficiency between standards and samples. Confining reactions and binary endpoint measurements to small partitions also leads to other performance advantages, including reduced susceptibility to inhibition, increased repeatability and reproducibility, and increased capacity to measure multiple targets in one analysis. As such, digital PCR is well suited for ambient water monitoring applications and is particularly advantageous as molecular methods move toward autonomous field application.

  12. Detection of Rare Mutations in EGFR-ARMS-PCR-Negative Lung Adenocarcinoma by Sanger Sequencing.

    PubMed

    Liang, Chaoyue; Wu, Zhuolin; Gan, Xiaohong; Liu, Yuanbin; You, You; Liu, Chenxian; Zhou, Chengzhi; Liang, Ying; Mo, Haiyun; Chen, Allen M; Zhang, Jiexia

    2018-01-01

    This study aimed to identify potential epidermal growth factor receptor (EGFR) gene mutations in non-small cell lung cancer that went undetected by amplification refractory mutation system-Scorpion real-time PCR (ARMS-PCR). A total of 200 specimens were obtained from the First Affiliated Hospital of Guangzhou Medical University from August 2014 to August 2015. In total, 100 ARMS-negative and 100 ARMS-positive specimens were evaluated for EGFR gene mutations by Sanger sequencing. The methodology and sensitivity of each method and the outcomes of EGFR-tyrosine kinase inhibitor (TKI) therapy were analyzed. Among the 100 ARMS-PCR-positive samples, 90 were positive by Sanger sequencing, while 10 cases were considered negative, because the mutation abundance was less than 10%. Among the 100 negative cases, three were positive for a rare EGFR mutation by Sanger sequencing. In the curative effect analysis of EGFR-TKIs, the progression-free survival (PFS) analysis based on ARMS and Sanger sequencing results showed no difference. However, the PFS of patients with a high abundance of EGFR mutation was 12.4 months [95% confidence interval (CI), 11.6-12.4 months], which was significantly higher than that of patients with a low abundance of mutations detected by Sanger sequencing (95% CI, 10.7-11.3 months) (p<0.001). The ARMS method demonstrated higher sensitivity than Sanger sequencing, but was prone to missing mutations due to primer design. Sanger sequencing was able to detect rare EGFR mutations and deemed applicable for confirming EGFR status. A clinical trial evaluating the efficacy of EGFR-TKIs in patients with rare EGFR mutations is needed. © Copyright: Yonsei University College of Medicine 2018

  13. Effects of Prone Position and Positive End-Expiratory Pressure on Noninvasive Estimators of ICP: A Pilot Study.

    PubMed

    Robba, Chiara; Bragazzi, Nicola Luigi; Bertuccio, Alessandro; Cardim, Danilo; Donnelly, Joseph; Sekhon, Mypinder; Lavinio, Andrea; Duane, Derek; Burnstein, Rowan; Matta, Basil; Bacigaluppi, Susanna; Lattuada, Marco; Czosnyka, Marek

    2017-07-01

    Prone positioning and positive end-expiratory pressure can improve pulmonary gas exchange and respiratory mechanics. However, they may be associated with the development of intracranial hypertension. Intracranial pressure (ICP) can be noninvasively estimated from the sonographic measurement of the optic nerve sheath diameter (ONSD) and from the transcranial Doppler analysis of the pulsatility (ICPPI) and the diastolic component (ICPFVd) of the velocity waveform. The effect of the prone positioning and positive end-expiratory pressure on ONSD, ICPFVd, and ICPPI was assessed in a prospective study of 30 patients undergoing spine surgery. One-way repeated measures analysis of variance, fixed-effect multivariate regression models, and receiver operating characteristic analyses were used to analyze numerical data. The mean values of ONSD, ICPFVd, and ICPPI significantly increased after change from supine to prone position. Receiver operating characteristic analyses demonstrated that, among the noninvasive methods, the mean ONSD measure had the greatest area under the curve signifying it is the most effective in distinguishing a hypothetical change in ICP between supine and prone positioning (0.86±0.034 [0.79 to 0.92]). A cutoff of 0.43 cm was found to be a best separator of ONSD value between supine and prone with a specificity of 75.0 and a sensitivity of 86.7. Noninvasive ICP estimation may be useful in patients at risk of developing intracranial hypertension who require prone positioning.

  14. Errors in causal inference: an organizational schema for systematic error and random error.

    PubMed

    Suzuki, Etsuji; Tsuda, Toshihide; Mitsuhashi, Toshiharu; Mansournia, Mohammad Ali; Yamamoto, Eiji

    2016-11-01

    To provide an organizational schema for systematic error and random error in estimating causal measures, aimed at clarifying the concept of errors from the perspective of causal inference. We propose to divide systematic error into structural error and analytic error. With regard to random error, our schema shows its four major sources: nondeterministic counterfactuals, sampling variability, a mechanism that generates exposure events and measurement variability. Structural error is defined from the perspective of counterfactual reasoning and divided into nonexchangeability bias (which comprises confounding bias and selection bias) and measurement bias. Directed acyclic graphs are useful to illustrate this kind of error. Nonexchangeability bias implies a lack of "exchangeability" between the selected exposed and unexposed groups. A lack of exchangeability is not a primary concern of measurement bias, justifying its separation from confounding bias and selection bias. Many forms of analytic errors result from the small-sample properties of the estimator used and vanish asymptotically. Analytic error also results from wrong (misspecified) statistical models and inappropriate statistical methods. Our organizational schema is helpful for understanding the relationship between systematic error and random error from a previously less investigated aspect, enabling us to better understand the relationship between accuracy, validity, and precision. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. No Control Genes Required: Bayesian Analysis of qRT-PCR Data

    PubMed Central

    Matz, Mikhail V.; Wright, Rachel M.; Scott, James G.

    2013-01-01

    Background Model-based analysis of data from quantitative reverse-transcription PCR (qRT-PCR) is potentially more powerful and versatile than traditional methods. Yet existing model-based approaches cannot properly deal with the higher sampling variances associated with low-abundant targets, nor do they provide a natural way to incorporate assumptions about the stability of control genes directly into the model-fitting process. Results In our method, raw qPCR data are represented as molecule counts, and described using generalized linear mixed models under Poisson-lognormal error. A Markov Chain Monte Carlo (MCMC) algorithm is used to sample from the joint posterior distribution over all model parameters, thereby estimating the effects of all experimental factors on the expression of every gene. The Poisson-based model allows for the correct specification of the mean-variance relationship of the PCR amplification process, and can also glean information from instances of no amplification (zero counts). Our method is very flexible with respect to control genes: any prior knowledge about the expected degree of their stability can be directly incorporated into the model. Yet the method provides sensible answers without such assumptions, or even in the complete absence of control genes. We also present a natural Bayesian analogue of the “classic” analysis, which uses standard data pre-processing steps (logarithmic transformation and multi-gene normalization) but estimates all gene expression changes jointly within a single model. The new methods are considerably more flexible and powerful than the standard delta-delta Ct analysis based on pairwise t-tests. Conclusions Our methodology expands the applicability of the relative-quantification analysis protocol all the way to the lowest-abundance targets, and provides a novel opportunity to analyze qRT-PCR data without making any assumptions concerning target stability. These procedures have been implemented as the MCMC

  16. No control genes required: Bayesian analysis of qRT-PCR data.

    PubMed

    Matz, Mikhail V; Wright, Rachel M; Scott, James G

    2013-01-01

    Model-based analysis of data from quantitative reverse-transcription PCR (qRT-PCR) is potentially more powerful and versatile than traditional methods. Yet existing model-based approaches cannot properly deal with the higher sampling variances associated with low-abundant targets, nor do they provide a natural way to incorporate assumptions about the stability of control genes directly into the model-fitting process. In our method, raw qPCR data are represented as molecule counts, and described using generalized linear mixed models under Poisson-lognormal error. A Markov Chain Monte Carlo (MCMC) algorithm is used to sample from the joint posterior distribution over all model parameters, thereby estimating the effects of all experimental factors on the expression of every gene. The Poisson-based model allows for the correct specification of the mean-variance relationship of the PCR amplification process, and can also glean information from instances of no amplification (zero counts). Our method is very flexible with respect to control genes: any prior knowledge about the expected degree of their stability can be directly incorporated into the model. Yet the method provides sensible answers without such assumptions, or even in the complete absence of control genes. We also present a natural Bayesian analogue of the "classic" analysis, which uses standard data pre-processing steps (logarithmic transformation and multi-gene normalization) but estimates all gene expression changes jointly within a single model. The new methods are considerably more flexible and powerful than the standard delta-delta Ct analysis based on pairwise t-tests. Our methodology expands the applicability of the relative-quantification analysis protocol all the way to the lowest-abundance targets, and provides a novel opportunity to analyze qRT-PCR data without making any assumptions concerning target stability. These procedures have been implemented as the MCMC.qpcr package in R.

  17. Trust and the Compliance-Reliance Paradigm: The Effects of Risk, Error Bias, and Reliability on Trust and Dependence.

    PubMed

    Chancey, Eric T; Bliss, James P; Yamani, Yusuke; Handley, Holly A H

    2017-05-01

    This study provides a theoretical link between trust and the compliance-reliance paradigm. We propose that for trust mediation to occur, the operator must be presented with a salient choice, and there must be an element of risk for dependence. Research suggests that false alarms and misses affect dependence via two independent processes, hypothesized as trust in signals and trust in nonsignals. These two trust types manifest in categorically different behaviors: compliance and reliance. Eighty-eight participants completed a primary flight task and a secondary signaling system task. Participants evaluated their trust according to the informational bases of trust: performance, process, and purpose. Participants were in a high- or low-risk group. Signaling systems varied by reliability (90%, 60%) within subjects and error bias (false alarm prone, miss prone) between subjects. False-alarm rate affected compliance but not reliance. Miss rate affected reliance but not compliance. Mediation analyses indicated that trust mediated the relationship between false-alarm rate and compliance. Bayesian mediation analyses favored evidence indicating trust did not mediate miss rate and reliance. Conditional indirect effects indicated that factors of trust mediated the relationship between false-alarm rate and compliance (i.e., purpose) and reliance (i.e., process) but only in the high-risk group. The compliance-reliance paradigm is not the reflection of two types of trust. This research could be used to update training and design recommendations that are based upon the assumption that trust causes operator responses regardless of error bias.

  18. Prone Positioning Improves Oxygenation in Adult Burn Patients with Severe Acute Respiratory Distress Syndrome

    DTIC Science & Technology

    2012-01-01

    Prone positioning improves oxygenation in adult burn patients with severe acute respiratory distress syndrome Diane F. Hale, MD, Jeremy W. Cannon, MD...Kevin K. Chung, MD, San Antonio, Texas BACKGROUND: Prone positioning (PP) improves oxygenation and may provide a benefit in patients with acute... positioning improves oxygenation in adult burn patients with severe acute respiratory distress syndrome 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM

  19. The Social Antecedents of Anger Proneness in Young Adulthood

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  20. Prone breast forward intensity-modulated radiotherapy for Asian women with early left breast cancer: factors for cardiac sparing and clinical outcomes

    PubMed Central

    Chen, Jenny Ling-Yu; Cheng, Jason Chia-Hsien; Kuo, Sung-Hsin; Chan, Hsing-Min; Huang, Yu-Sen; Chen, Yu-Hsuan

    2013-01-01

    Since December 2009, after breast-conserving surgery for Stage 0–I cancer of the left breast, 21 women with relatively pendulous breasts underwent computed tomography prone and supine simulations. The adjuvant radiotherapy was 50 Gy in 25 fractions to the left breast alone. Four plans—conventional wedged tangents and forward intensity-modulated radiotherapy (fIMRT) in supine and prone positions—were generated. fIMRT generated better homogeneity in both positions. Prone position centralized the breast tissue by gravity and also shortened the breast width which led to better conformity in both planning techniques. Prone fIMRT significantly reduced doses to left lung, Level I and Level II axilla. The mean cardiac doses did not differ between positions. Among the four plans, prone fIMRT produced the best target dosimetry and normal organ sparing. In subgroup analysis, patients with absolute breast depth > 7 cm in the prone position or breast depth difference > 3 cm between positions had significant cardiac sparing with prone fIMRT. Sixteen patients with significant cardiac sparing in prone position were treated using prone fIMRT and the others using supine fIMRT. All patients received a supine electron tumor bed boost of 10 Gy in 5 fractions. No patients developed Grade 2 or worse acute or late toxicities. There was no difference in the number of segments or beams, monitor units, treatment time, or positioning reproducibility between prone and supine positions. At a median follow-up time of 26.8 months, no locoregional or distant recurrence or death was noted. PMID:23504450

  1. A modified MS-PCR approach to diagnose patients with Prader-Willi and Angelman syndrome.

    PubMed

    Dos Santos, Jéssica Fernandes; Mota, Laís R; Rocha, Pedro Henrique Silva Andrade; Ferreira de Lima, Renata Lúcia L

    2016-11-01

    Prader-Willi (PWS) and Angelman (AS) syndromes are clinically distinct neurodevelopmental genetic diseases with multiple phenotypic manifestations. They are one of the most common genetic syndromes caused by non-Mendelian inheritance in the form of genomic imprinting, and can be attributable to the loss of gene expression due to imprinting within the chromosomal region 15q11-q13. Clinical diagnosis of PWS and AS is challenging, and the use of molecular and cytomolecular studies is recommended to help in determining the diagnosis of these conditions. The methylation analysis is a sensible approach; however there are several techniques for this purpose, such as the methylation-sensitive polymerase chain reaction (MS-PCR). This study aims to optimize the MS-PCR assay for the diagnosis of potential PWS and AS patients using DNA modified by sodium bisulfite. We used the MS-PCR technique of PCR described by Kosaki et al. (1997) adapted with betaine. All different concentrations of betaine used to amplify the methylated and unmethylated chromosomal region 15q11-q13 on the gene SNRPN showed amplification results, which increased proportionally to the concentration of betaine. The methylation analysis is a technically robust and reproducible screening method for PWS and AS. The MS-PCR assures a faster, cheaper and more efficient method for the primary diagnosis of the SNRPN gene in cases with PWS and AS, and may detect all of the three associated genetic abnormalities: deletion, uniparental disomy or imprinting errors.

  2. Evaluation of Altona Diagnostics RealStar Zika Virus Reverse Transcription-PCR Test Kit for Zika Virus PCR Testing

    PubMed Central

    Lombos, Ernesto; Tang, Elaine; Perusini, Stephen; Eshaghi, Alireza; Nagra, Sandeep; Frantz, Christine; Olsha, Romy; Kristjanson, Erik; Dimitrova, Kristina; Safronetz, David; Drebot, Mike

    2017-01-01

    ABSTRACT With the emerging Zika virus (ZIKV) epidemic, accessible real-time reverse transcription-PCR (rRT-PCR) assays are needed to streamline testing. The commercial Altona Diagnostics RealStar ZIKV rRT-PCR test kit (Altona PCR) has been approved for emergency use authorization by the U.S. FDA. Our aim was to verify the Altona PCR by comparing it to the CDC-designed dual-target ZIKV rRT-PCR reference assay (reference PCR) and describe the demographics of patients tested for ZIKV by rRT-PCR in Ontario, Canada. A large set of clinical specimens was tested for ZIKV by the Altona PCR and the reference PCR. Positive or equivocal specimens underwent PCR and Sanger sequencing targeting the ZIKV NS5 gene. A total of 671 serum specimens were tested by the reference PCR: 58 (8.6%) were positive, 193 (28.8%) were equivocal, and 420 (62.6%) were negative. Ninety percent of the reference PCR-positive patients were tested in the first 5 days after symptom onset. The Altona PCR was performed on 284/671 specimens tested by the reference PCR. The Altona PCR was positive for 53/58 (91%) reference PCR-positive specimens and 16/193 (8%) reference PCR-equivocal specimens; the ZIKV NS5 PCR was positive for all 68 Altona PCR-positive specimens and negative for all 181 Altona PCR-negative specimens that underwent the NS5 PCR. The Altona PCR has very good sensitivity (91%) and specificity (97%) compared to the reference PCR. The Altona PCR can be used for ZIKV diagnostic testing and has less extensive verification requirements than a laboratory-developed test. PMID:28298448

  3. Profound Obstructive Hypotension From Prone Positioning Documented by Transesophageal Echocardiography in a Patient With Scoliosis: A Case Report.

    PubMed

    Abcejo, Arnoley S; Diaz Soto, Juan; Castoro, Courtney; Armour, Sarah; Long, Timothy R

    2017-08-01

    In a healthy 12-year-old female with scoliosis, prone positioning resulted in pressor-refractory cardiovascular collapse. Resumption of supine position immediately improved hemodynamics. Intraoperative transesophageal echocardiography (TEE) revealed a collapsed left atrium and biventricular failure. Repeat prone positioning resulted in a recurrence of hypotension. However, hemodynamic stabilization was restored and maintained by repositioning chest pads caudally. The patient successfully underwent a 6-hour scoliosis repair without perioperative morbidity. With this case, we aim to: (1) reintroduce awareness of this mechanical obstructive cause of reversible hypotension; (2) highlight the use of intraoperative TEE during prone hemodynamic collapse; and (3) suggest an alternative prone positioning technique if chest compression results in hemodynamic instability.

  4. ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.

    PubMed

    Perkins, James R; Dawes, John M; McMahon, Steve B; Bennett, David L H; Orengo, Christine; Kohl, Matthias

    2012-07-02

    Measuring gene transcription using real-time reverse transcription polymerase chain reaction (RT-qPCR) technology is a mainstay of molecular biology. Technologies now exist to measure the abundance of many transcripts in parallel. The selection of the optimal reference gene for the normalisation of this data is a recurring problem, and several algorithms have been developed in order to solve it. So far nothing in R exists to unite these methods, together with other functions to read in and normalise the data using the chosen reference gene(s). We have developed two R/Bioconductor packages, ReadqPCR and NormqPCR, intended for a user with some experience with high-throughput data analysis using R, who wishes to use R to analyse RT-qPCR data. We illustrate their potential use in a workflow analysing a generic RT-qPCR experiment, and apply this to a real dataset. Packages are available from http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.htmland http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html These packages increase the repetoire of RT-qPCR analysis tools available to the R user and allow them to (amongst other things) read their data into R, hold it in an ExpressionSet compatible R object, choose appropriate reference genes, normalise the data and look for differential expression between samples.

  5. ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data

    PubMed Central

    2012-01-01

    Background Measuring gene transcription using real-time reverse transcription polymerase chain reaction (RT-qPCR) technology is a mainstay of molecular biology. Technologies now exist to measure the abundance of many transcripts in parallel. The selection of the optimal reference gene for the normalisation of this data is a recurring problem, and several algorithms have been developed in order to solve it. So far nothing in R exists to unite these methods, together with other functions to read in and normalise the data using the chosen reference gene(s). Results We have developed two R/Bioconductor packages, ReadqPCR and NormqPCR, intended for a user with some experience with high-throughput data analysis using R, who wishes to use R to analyse RT-qPCR data. We illustrate their potential use in a workflow analysing a generic RT-qPCR experiment, and apply this to a real dataset. Packages are available from http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.htmland http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html Conclusions These packages increase the repetoire of RT-qPCR analysis tools available to the R user and allow them to (amongst other things) read their data into R, hold it in an ExpressionSet compatible R object, choose appropriate reference genes, normalise the data and look for differential expression between samples. PMID:22748112

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

    PubMed

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

    2015-07-01

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

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

    PubMed

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

    2014-12-01

    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. © 2014 by the Society for Personality and Social Psychology, Inc.

  8. Direct PCR amplification of forensic touch and other challenging DNA samples: A review.

    PubMed

    Cavanaugh, Sarah E; Bathrick, Abigail S

    2018-01-01

    DNA evidence sample processing typically involves DNA extraction, quantification, and STR amplification; however, DNA loss can occur at both the DNA extraction and quantification steps, which is not ideal for forensic evidence containing low levels of DNA. Direct PCR amplification of forensic unknown samples has been suggested as a means to circumvent extraction and quantification, thereby retaining the DNA typically lost during those procedures. Direct PCR amplification is a method in which a sample is added directly to an amplification reaction without being subjected to prior DNA extraction, purification, or quantification. It allows for maximum quantities of DNA to be targeted, minimizes opportunities for error and contamination, and reduces the time and monetary resources required to process samples, although data analysis may take longer as the increased DNA detection sensitivity of direct PCR may lead to more instances of complex mixtures. ISO 17025 accredited laboratories have successfully implemented direct PCR for limited purposes (e.g., high-throughput databanking analysis), and recent studies indicate that direct PCR can be an effective method for processing low-yield evidence samples. Despite its benefits, direct PCR has yet to be widely implemented across laboratories for the processing of evidentiary items. While forensic DNA laboratories are always interested in new methods that will maximize the quantity and quality of genetic information obtained from evidentiary items, there is often a lag between the advent of useful methodologies and their integration into laboratories. Delayed implementation of direct PCR of evidentiary items can be attributed to a variety of factors, including regulatory guidelines that prevent laboratories from omitting the quantification step when processing forensic unknown samples, as is the case in the United States, and, more broadly, a reluctance to validate a technique that is not widely used for evidence samples. The

  9. Diastereoselective synthesis of L: -threo-3,4-dihydroxyphenylserine by low-specific L: -threonine aldolase mutants.

    PubMed

    Gwon, Hui-Jeong; Baik, Sang-Ho

    2010-01-01

    Diastereoselectivity-enhanced mutants of L: -threonine aldolase (L: -TA) for L: -threo-3,4-dihydroxyphenylserine (L: -threo-DOPS) synthesis were isolated by error-prone PCR followed by a high-throughput screening. The most improved mutant was achieved from the mutant T3-3mm2, showing a 4-fold increase over the wild-type L: -TA. When aldol condensation activity was examined using whole cells of T3-3mm2, its de was constantly maintained at 55% during the batch reactions for 80 h, yielding 3.8 mg L: -threo-DOPS/ml.

  10. B cells regulate thymic CD8+T cell differentiation in lupus-prone mice.

    PubMed

    Xing, Chen; Zhu, Gaizhi; Xiao, He; Fang, Ying; Liu, Xiaoling; Han, Gencheng; Chen, Guojiang; Hou, Chunmei; Shen, Beifen; Li, Yan; Ma, Ning; Wang, Renxi

    2017-10-27

    Previous studies have shown that under normal physiological conditions thymic B cells play a critical function in T cell negative selection. We tested the effect of thymic B cells on thymic T-cell differentiation in autoimmune diseases including systemic lupus erythematosus (SLE). We found that thymic B cells and CD8 - CD4 + and CD4 - CD8 + T cells increased, whereas CD4 + CD8 + T cells decreased in lupus-prone mice. Once B cells were reduced, the change was reversed. Furthermore, we found that B cells blocked thymic immature single positive (ISP) CD4 - CD8 + CD3 lo/- RORγt - T cells progression into CD4 + CD8 + T cells. Interestingly, we found a novel population of thymic immature T cells (CD4 - CD8 + CD3 lo RORγt + ) that were induced into mature CD4 - CD8 + CD3 + RORγt + T cells by B cells in lupus-prone mice. Importantly, we found that IgG, produced by thymic B cells, played a critical role in the differentiation of thymic CD8 + ISP and mature RORγt + CD8 + T cells in lupus-prone mice. In conclusion, B cells blocked the differentiation from thymic CD8 + ISP and induced the differentiation of a novel immature CD4 - CD8 + CD3 lo RORγt + T cells into mature RORγt + CD8 + T cells by secreting IgG antibody in lupus-prone mice.

  11. Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR.

    PubMed

    Zhong, Qun; Bhattacharya, Smiti; Kotsopoulos, Steven; Olson, Jeff; Taly, Valérie; Griffiths, Andrew D; Link, Darren R; Larson, Jonathan W

    2011-07-07

    Quantitative polymerase chain reactions (qPCR) based on real-time PCR constitute a powerful and sensitive method for the analysis of nucleic acids. However, in qPCR, the ability to multiplex targets using differently colored fluorescent probes is typically limited to 4-fold by the spectral overlap of the fluorophores. Furthermore, multiplexing qPCR assays requires expensive instrumentation and most often lengthy assay development cycles. Digital PCR (dPCR), which is based on the amplification of single target DNA molecules in many separate reactions, is an attractive alternative to qPCR. Here we report a novel and easy method for multiplexing dPCR in picolitre droplets within emulsions-generated and read out in microfluidic devices-that takes advantage of both the very high numbers of reactions possible within emulsions (>10(6)) as well as the high likelihood that the amplification of only a single target DNA molecule will initiate within each droplet. By varying the concentration of different fluorogenic probes of the same color, it is possible to identify the different probes on the basis of fluorescence intensity. Adding multiple colors increases the number of possible reactions geometrically, rather than linearly as with qPCR. Accurate and precise copy numbers of up to sixteen per cell were measured using a model system. A 5-plex assay for spinal muscular atrophy was demonstrated with just two fluorophores to simultaneously measure the copy number of two genes (SMN1 and SMN2) and to genotype a single nucleotide polymorphism (c.815A>G, SMN1). Results of a pilot study with SMA patients are presented. This journal is © The Royal Society of Chemistry 2011

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Williams, Jason M.; Rani, Sudheer D.; Li, Xia

    2015-07-15

    Purpose: Previous studies have demonstrated how imaging of the breast with patients lying prone using a supportive positioning device markedly facilitates longitudinal and/or multimodal image registration. In this contribution, the authors’ primary objective was to determine if there are differences in the standardized uptake value (SUV) derived from [{sup 18}F]fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) in breast tumors imaged in the standard supine position and in the prone position using a specialized positioning device. Methods: A custom positioning device was constructed to allow for breast scanning in the prone position. Rigid and nonrigid phantom studies evaluated differences in prone andmore » supine PET. Clinical studies comprised 18F-FDG-PET of 34 patients with locally advanced breast cancer imaged in the prone position (with the custom support) followed by imaging in the supine position (without the support). Mean and maximum values (SUV{sub peak} and SUV{sub max}, respectively) were obtained from tumor regions-of-interest for both positions. Prone and supine SUV were linearly corrected to account for the differences in 18F-FDG uptake time. Correlation, Bland–Altman, and nonparametric analyses were performed on uptake time-corrected and uncorrected data. Results: SUV from the rigid PET breast phantom imaged in the prone position with the support device was 1.9% lower than without the support device. In the nonrigid PET breast phantom, prone SUV with the support device was 5.0% lower than supine SUV without the support device. In patients, the median (range) difference in uptake time between prone and supine scans was 16.4 min (13.4–30.9 min), which was significantly—but not completely—reduced by the linear correction method. SUV{sub peak} and SUV{sub max} from prone versus supine scans were highly correlated, with concordance correlation coefficients of 0.91 and 0.90, respectively. Prone SUV{sub peak} and SUV{sub max} were

  13. MicroRNA markers for forensic body fluid identification obtained from microarray screening and quantitative RT-PCR confirmation

    PubMed Central

    Zubakov, Dmitry; Boersma, Anton W. M.; Choi, Ying; van Kuijk, Patricia F.; Wiemer, Erik A. C.

    2010-01-01

    MicroRNAs (miRNAs) are non-protein coding molecules with important regulatory functions; many have tissue-specific expression patterns. Their very small size in principle makes them less prone to degradation processes, unlike messenger RNAs (mRNAs), which were previously proposed as molecular tools for forensic body fluid identification. To identify suitable miRNA markers for forensic body fluid identification, we first screened total RNA samples derived from saliva, semen, vaginal secretion, and venous and menstrual blood for the expression of 718 human miRNAs using a microarray platform. All body fluids could be easily distinguished from each other on the basis of complete array-based miRNA expression profiles. Results from quantitative reverse transcription PCR (RT-PCR; TaqMan) assays for microarray candidate markers confirmed strong over-expression in the targeting body fluid of several miRNAs for venous blood and several others for semen. However, no candidate markers from array experiments for other body fluids such as saliva, vaginal secretion, or menstrual blood could be confirmed by RT-PCR. Time-wise degradation of venous blood and semen stains for at least 1 year under lab conditions did not significantly affect the detection sensitivity of the identified miRNA markers. The detection limit of the TaqMan assays tested for selected venous blood and semen miRNA markers required only subpicogram amounts of total RNA per single RT-PCR test, which is considerably less than usually needed for reliable mRNA RT-PCR detection. We therefore propose the application of several stable miRNA markers for the forensic identification of blood stains and several others for semen stain identification, using commercially available TaqMan assays. Additional work remains necessary in search for suitable miRNA markers for other forensically relevant body fluids. Electronic supplementary material The online version of this article (doi:10.1007/s00414-009-0402-3) contains

  14. Evaluating abdominal core muscle fatigue: Assessment of the validity and reliability of the prone bridging test.

    PubMed

    De Blaiser, C; De Ridder, R; Willems, T; Danneels, L; Vanden Bossche, L; Palmans, T; Roosen, P

    2018-02-01

    The aims of this study were to research the amplitude and median frequency characteristics of selected abdominal, back, and hip muscles of healthy subjects during a prone bridging endurance test, based on surface electromyography (sEMG), (a) to determine if the prone bridging test is a valid field test to measure abdominal muscle fatigue, and (b) to evaluate if the current method of administrating the prone bridging test is reliable. Thirty healthy subjects participated in this experiment. The sEMG activity of seven abdominal, back, and hip muscles was bilaterally measured. Normalized median frequencies were computed from the EMG power spectra. The prone bridging tests were repeated on separate days to evaluate inter and intratester reliability. Significant differences in normalized median frequency slope (NMF slope ) values between several abdominal, back, and hip muscles could be demonstrated. Moderate-to-high correlation coefficients were shown between NMF slope values and endurance time. Multiple backward linear regression revealed that the test endurance time could only be significantly predicted by the NMF slope of the rectus abdominis. Statistical analysis showed excellent reliability (ICC=0.87-0.89). The findings of this study support the validity and reliability of the prone bridging test for evaluating abdominal muscle fatigue. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  15. Spinal Stiffness in Prone and Upright Postures During 0-1.8 g Induced by Parabolic Flight.

    PubMed

    Swanenburg, Jaap; Meier, Michael L; Langenfeld, Anke; Schweinhardt, Petra; Humphreys, B Kim

    2018-06-01

    The purpose of this study was to analyze posterior-to-anterior spinal stiffness in Earth, hyper-, and microgravity conditions during both prone and upright postures. During parabolic flight, the spinal stiffness of the L3 vertebra of a healthy 37-yr-old man was measured in normal Earth gravity (1.0 g), hypergravity (1.8 g), and microgravity (0.0 g) conditions induced in the prone and upright positions. Differences in spinal stiffness were significant across all three gravity conditions in the prone and upright positions. Most effect sizes were large; however, in the upright posture, the effect size between Earth gravity and microgravity was medium. Significant differences in spinal stiffness between the prone and upright positions were found during Earth gravity and hypergravity conditions. No difference was found between the two postures during microgravity conditions. Based on repeated measurements of a single individual, our results showed detectable changes in posterior-to-anterior spinal stiffness. Spinal stiffness increased during microgravity and decreased during hypergravity conditions. In microgravity conditions, posture did not impact spinal stiffness. More data on spinal stiffness in variable gravitational conditions is needed to confirm these results.Swanenburg J, Meier ML, Langenfeld A, Schweinhardt P, Humphreys BK. Spinal stiffness in prone and upright postures during 0-1.8 g induced by parabolic flight. Aerosp Med Hum Perform. 2018; 89(6):563-567.

  16. pcr: an R package for quality assessment, analysis and testing of qPCR data

    PubMed Central

    Ahmed, Mahmoud

    2018-01-01

    Background Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions. Methods We developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest. Results Using two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable. Conclusion The pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way. PMID:29576953

  17. Fantasy Proneness Correlates With the Intensity of Near-Death Experience.

    PubMed

    Martial, Charlotte; Cassol, Héléna; Charland-Verville, Vanessa; Merckelbach, Harald; Laureys, Steven

    2018-01-01

    Little is known about the personality characteristics of those who have experienced a "Near-Death Experience" (NDE). One interesting candidate is fantasy proneness. We studied this trait in individuals who developed NDEs in the presence (i.e., classical NDEs) or absence (i.e., NDEs-like) of a life-threatening situation. We surveyed a total of 228 individuals. From those, 108 qualified as NDE experiencers (i.e., Greyson NDE scale total score ≥7): 51 had their NDEs in the context of a life-threatening situation; 57 had their NDEs not related to a life-threatening situation. From those who did not meet the criteria to be considered "experiencers," 20 had their NDE in the absence of a life-threatening situation; 50 had faced death but did not recall a NDE and finally, 50 were healthy people without a history of life threat and/or NDE. All participants completed a measure of NDE intensity (the Greyson NDE scale) and a measure of fantasy proneness (the Creative Experiences Questionnaire). People reporting NDEs-like scored higher on fantasy proneness than those reporting classical NDEs, individuals whose experiences did not meet the NDE criteria and matched controls. By contrast, individuals reporting classical NDEs did not show different engagement in fantasy as matched controls. The reported intensity of the experiences was positively correlated with engagement in fantasy. Our findings support the view that strong engagement in fantasy by individuals recalling NDEs-like might make these persons more likely to report such subjective experiences when exposed to suitable physiological and/or psychological conditions (e.g., meditation, syncope).

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

    PubMed

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

    2002-05-01

    Comatose patients frequently exhibit pulmonary function worsening, especially in cases of pulmonary infection. It appears to have a deleterious effect on neurologic outcome. We therefore conducted a randomized trial to determine whether daily prone positioning would prevent lung worsening in these patients. Prospective, randomized, controlled study. Sixteen-bed intensive care unit. Fifty-one patients who required invasive mechanical ventilation because of coma with Glascow coma scores of 9 or less. In the prone position (PP) group: prone positioning for 4 h once daily until the patients could get up to sit in an armchair; in the supine position (SP) group: supine positioning. The primary end point was the incidence of lung worsening defined by an increase in the Lung Injury Score of at least 1 point since the time of randomization. The secondary end point was the incidence of ventilator-associated pneumonia (VAP). A total of 25 patients were randomly assigned to the PP group and 26 patients to the SP group. The characteristics of the patients from the two groups were similar at randomization. The incidence of lung worsening was lower in the PP group (12%) than in the SP group (50%) ( p=0.003). The incidence of VAP was 20% in the PP group and 38.4% in the SP group ( p=0.14). There was no serious complication attributable to prone positioning, however, there was a significant increase of intracranial pressure in the PP. In a selected population of comatose ventilated patients, daily prone positioning reduced the incidence of lung worsening.

  19. Error begat error: design error analysis and prevention in social infrastructure projects.

    PubMed

    Love, Peter E D; Lopez, Robert; Edwards, David J; Goh, Yang M

    2012-09-01

    Design errors contribute significantly to cost and schedule growth in social infrastructure projects and to engineering failures, which can result in accidents and loss of life. Despite considerable research that has addressed their error causation in construction projects they still remain prevalent. This paper identifies the underlying conditions that contribute to design errors in social infrastructure projects (e.g. hospitals, education, law and order type buildings). A systemic model of error causation is propagated and subsequently used to develop a learning framework for design error prevention. The research suggests that a multitude of strategies should be adopted in congruence to prevent design errors from occurring and so ensure that safety and project performance are ameliorated. Copyright © 2011. Published by Elsevier Ltd.

  20. Pneumocystis PCR: It Is Time to Make PCR the Test of Choice.

    PubMed

    Doyle, Laura; Vogel, Sherilynn; Procop, Gary W

    2017-01-01

    The testing strategy for Pneumocystis at the Cleveland Clinic changed from toluidine blue staining to polymerase chain reaction (PCR). We studied the differences in positivity rates for these assays and compared each with the detection of Pneumocystis in companion specimens by cytology and surgical pathology. We reviewed the results of all Pneumocystis test orders 1 year before and 1 year after the implementation of a Pneumocystis -specific PCR. We also reviewed the corresponding cytology and surgical pathology results, if performed. Finally, we reviewed the medical records of patients with rare Pneumocystis detected by PCR in an effort to differentiate colonization vs true disease. Toluidine blue staining and surgical pathology had similar sensitivities and negative predictive values, both of which were superior to cytology. There was a >4-fold increase in the annual detection of Pneumocystis by PCR compared with toluidine blue staining (toluidine blue staining: 11/1583 [0.69%] vs PCR: 44/1457 [3.0%]; chi-square P < .001). PCR detected 1 more case than surgical pathology and was far more sensitive than cytology. Chart review demonstrated that the vast majority of patients with rare Pneumocystis detected were immunosuppressed, had radiologic findings supportive of this infection, had no other pathogens detected, and were treated for pneumocystosis by the clinical team. PCR was the most sensitive method for the detection of Pneumocystis and should be considered the diagnostic test of choice. Correlation with clinical and radiologic findings affords discrimination of early true disease from the far rarer instances of colonization.

  1. Pneumocystis PCR: It Is Time to Make PCR the Test of Choice

    PubMed Central

    Doyle, Laura; Vogel, Sherilynn

    2017-01-01

    Abstract Background The testing strategy for Pneumocystis at the Cleveland Clinic changed from toluidine blue staining to polymerase chain reaction (PCR). We studied the differences in positivity rates for these assays and compared each with the detection of Pneumocystis in companion specimens by cytology and surgical pathology. Methods We reviewed the results of all Pneumocystis test orders 1 year before and 1 year after the implementation of a Pneumocystis-specific PCR. We also reviewed the corresponding cytology and surgical pathology results, if performed. Finally, we reviewed the medical records of patients with rare Pneumocystis detected by PCR in an effort to differentiate colonization vs true disease. Results Toluidine blue staining and surgical pathology had similar sensitivities and negative predictive values, both of which were superior to cytology. There was a >4-fold increase in the annual detection of Pneumocystis by PCR compared with toluidine blue staining (toluidine blue staining: 11/1583 [0.69%] vs PCR: 44/1457 [3.0%]; chi-square P < .001). PCR detected 1 more case than surgical pathology and was far more sensitive than cytology. Chart review demonstrated that the vast majority of patients with rare Pneumocystis detected were immunosuppressed, had radiologic findings supportive of this infection, had no other pathogens detected, and were treated for pneumocystosis by the clinical team. Conclusion PCR was the most sensitive method for the detection of Pneumocystis and should be considered the diagnostic test of choice. Correlation with clinical and radiologic findings affords discrimination of early true disease from the far rarer instances of colonization. PMID:29062861

  2. Digital PCR: A brief history.

    PubMed

    Morley, Alexander A

    2014-09-01

    Digital PCR for quantification of a target of interest has been independently developed several times, being described in 1990 and 1991 using the term "limiting dilution PCR" and in 1999 using the term "digital PCR". It came into use in the decade following its first development but its use was cut short by the description of real-time PCR in 1996. However digital PCR has now had a renaissance due to the recent development of new instruments and chemistry which have made it a much simpler and more practical technique.

  3. Comparison of allele-specific PCR, created restriction-site PCR, and PCR with primer-introduced restriction analysis methods used for screening complex vertebral malformation carriers in Holstein cattle

    PubMed Central

    Altınel, Ahmet

    2017-01-01

    Complex vertebral malformation (CVM) is an inherited, autosomal recessive disorder of Holstein cattle. The aim of this study was to compare sensitivity, specificity, positive and negative predictive values, accuracy, and rapidity of allele-specific polymerase chain reaction (AS-PCR), created restriction-site PCR (CRS-PCR), and PCR with primer-introduced restriction analysis (PCR-PIRA), three methods used in identification of CVM carriers in a Holstein cattle population. In order to screen for the G>T mutation in the solute carrier family 35 member A3 (SLC35A3) gene, DNA sequencing as the gold standard method was used. The prevalence of carriers and the mutant allele frequency were 3.2% and 0.016, respectively, among Holstein cattle in the Thrace region of Turkey. Among the three methods, the fastest but least accurate was AS-PCR. Although the rapidity of CRS-PCR and PCR-PIRA were nearly equal, the accuracy of PCR-PIRA was higher than that of CRS-PCR. Therefore, among the three methods, PCR-PIRA appears to be the most efficacious for screening of mutant alleles when identifying CVM carriers in a Holstein cattle population. PMID:28927256

  4. Analytical Performance of Four Polymerase Chain Reaction (PCR) and Real Time PCR (qPCR) Assays for the Detection of Six Leishmania Species DNA in Colombia.

    PubMed

    León, Cielo M; Muñoz, Marina; Hernández, Carolina; Ayala, Martha S; Flórez, Carolina; Teherán, Aníbal; Cubides, Juan R; Ramírez, Juan D

    2017-01-01

    Leishmaniasis comprises a spectrum of parasitic diseases caused by protozoans of the genus Leishmania . Molecular tools have been widely employed for the detection of Leishmania due to its high sensitivity and specificity. However, the analytical performance of molecular platforms as PCR and real time PCR (qPCR) including a wide variety of molecular markers has never been evaluated. Herein, the aim was to evaluate the analytical performance of 4 PCR-based assays (designed on four different targets) and applied on conventional and real-time PCR platforms. We evaluated the analytical performance of conventional PCR and real time PCR, determining exclusivity and inclusivity, Anticipated Reportable Range (ARR), limit of detection (LoD) and accuracy using primers directed to kDNA, HSP70, 18S and ITS-1 targets. We observed that the kDNA was the most sensitive but does not meet the criterion of exclusivity. The HSP70 presented a higher LoD in conventional PCR and qPCR in comparison with the other markers (1 × 10 1 and 1 × 10 -1 equivalent parasites/mL respectively) and had a higher coefficient of variation in qPCR. No statistically significant differences were found between the days of the test with the four molecular markers. The present study revealed that the 18S marker presented the best performance in terms of analytical sensitivity and specificity for the qPCR in the species tested (species circulating in Colombia). Therefore, we recommend to explore the analytical and diagnostic performance in future studies using a broader number of species across America.

  5. Analytical Performance of Four Polymerase Chain Reaction (PCR) and Real Time PCR (qPCR) Assays for the Detection of Six Leishmania Species DNA in Colombia

    PubMed Central

    León, Cielo M.; Muñoz, Marina; Hernández, Carolina; Ayala, Martha S.; Flórez, Carolina; Teherán, Aníbal; Cubides, Juan R.; Ramírez, Juan D.

    2017-01-01

    Leishmaniasis comprises a spectrum of parasitic diseases caused by protozoans of the genus Leishmania. Molecular tools have been widely employed for the detection of Leishmania due to its high sensitivity and specificity. However, the analytical performance of molecular platforms as PCR and real time PCR (qPCR) including a wide variety of molecular markers has never been evaluated. Herein, the aim was to evaluate the analytical performance of 4 PCR-based assays (designed on four different targets) and applied on conventional and real-time PCR platforms. We evaluated the analytical performance of conventional PCR and real time PCR, determining exclusivity and inclusivity, Anticipated Reportable Range (ARR), limit of detection (LoD) and accuracy using primers directed to kDNA, HSP70, 18S and ITS-1 targets. We observed that the kDNA was the most sensitive but does not meet the criterion of exclusivity. The HSP70 presented a higher LoD in conventional PCR and qPCR in comparison with the other markers (1 × 101 and 1 × 10-1 equivalent parasites/mL respectively) and had a higher coefficient of variation in qPCR. No statistically significant differences were found between the days of the test with the four molecular markers. The present study revealed that the 18S marker presented the best performance in terms of analytical sensitivity and specificity for the qPCR in the species tested (species circulating in Colombia). Therefore, we recommend to explore the analytical and diagnostic performance in future studies using a broader number of species across America. PMID:29046670

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

    PubMed Central

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

    2014-01-01

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

  7. Should diabetic ketosis without acidosis be included in ketosis-prone type 2 diabetes mellitus?

    PubMed

    Xie, Xiao-Jing; Hu, Yun; Cheng, Cheng; Feng, Tian-Tian; He, Ke; Mao, Xiao-Ming

    2014-01-01

    The incidence of ketosis-prone type 2 diabetes is very low except for people of sub-Saharan African origin and African Americans. However, there also are some type 2 diabetes patients with diabetic ketosis without acidosis (DKWA). We question whether DKWA should be included as a subtype of ketosis-prone type 2 diabetes mellitus and compared the clinical characteristics of DKWA and diabetic ketoacidosis (DKA) patients. The study population consisted of 594 consecutive unrelated Chinese inpatients with newly diagnosed type 2 diabetes. Demographic and clinical characteristics (age, gender, family history of diabetes, body mass index, blood pressure and plasma lipid parameters) were recorded. The patients were divided into ketosis-resistant diabetes (KRD), DKWA and DKA groups on the basis of urinary ketones, blood pH and bicarbonate levels. The blood glucose and c-peptide levels of the patients were also evaluated. The prevalence of KRD, DKWA and DKA were 78.33%, 19.72% and 1.95%, respectively, in the study population. The clinical characteristics of patients with DKWA group patients were similar to those with DKA, except that DKA patients had higher blood glucose and deteriorated β cell function. Diabetic ketosis without acidosis and DKA patients share similar clinical characteristics; DKWA should be considered ketosis-prone type 2 diabetes. Therefore, the prevalence of ketosis-prone type 2 diabetes might be underestimated. Copyright © 2013 John Wiley & Sons, Ltd.

  8. Genotype identification of Math1/LacZ knockout mice based on real-time PCR with SYBR Green I dye.

    PubMed

    Krizhanovsky, Valery; Golenser, Esther; Ben-Arie, Nissim

    2004-07-30

    Knockout mice are widely used in all fields of biomedical research. Determining the genotype of every newborn mouse is a tedious task, usually performed by Southern blot hybridization or Polymerase Chain Reaction (PCR). We describe here a quick and simple genotype identification assay based on real-time PCR and SYBR Green I dye, without using fluorescent primers. The discrimination between the wild type and targeted alleles is based on a PCR design that leads to a different melting temperature for each product. The identification of the genotype is obvious immediately after amplification, and no post-PCR manipulations are needed, reducing cost and time. Therefore, while the real-time PCR amplification increases the sensitivity, the fact that the reactions tubes are never opened after amplification, reduces the risk of contamination and eliminates errors, which are common during the repeated handling of dozens of samples from the same mouse line. The protocol we provide was tested on Math1 knockout mice, but is general, and may be utilized for any knockout line and real-time thermocycler, without any further modification, accessories or special reagents. Copyright 2004 Elsevier B.V.

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

    PubMed Central

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

    2016-01-01

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

  10. Real-time PCR in virology.

    PubMed

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

    2002-03-15

    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 laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of PCR product during real-time PCR. These are the DNA binding fluorophores, the 5' endonuclease, adjacent linear and hairpin oligoprobes and the self-fluorescing amplicons, which are described in detail. We also discuss factors that have restricted the development of multiplex real-time PCR as well as the role of real-time PCR in quantitating nucleic acids. Both amplification hardware and the fluorogenic detection chemistries have evolved rapidly as the understanding of real-time PCR has developed and this review aims to update the scientist on the current state of the art. We describe the background, advantages and limitations of real-time PCR and we review the literature as it applies to virus detection in the routine and research laboratory in order to focus on one of the many areas in which the application of real-time PCR has provided significant methodological benefits and improved patient outcomes. However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease.

  11. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... land in relation to the hazards involved, and (iii) does not increase the danger to human life; (2) Prohibit nonessential or improper installation of public utilities and public facilities in flood-prone... public purposes consistent with a policy of minimization of future property losses; (4) Acquisition of...

  12. Comparison of nested PCR and qPCR for the detection and quantitation of BoHV6 DNA.

    PubMed

    Kubiś, Piotr; Materniak, Magdalena; Kuźmak, Jacek

    2013-12-01

    Nested PCR and qPCR (quantitative PCR) tests based on glycoprotein B (gB) gene were designed for detecting Bovine herpesvirus 6 (BoHV6) in bovine whole blood samples and wild ruminant blood clots (deer and roe-deer). This virus, commonly known as BLHV (bovine lymphotropic herpesvirus) belongs to the Herpesviridae family, subfamily Gammaherpesvirinae and Macavirus genus. DNA isolated from 92 dairy cow blood samples and 69 wild ruminant clots were examined for the presence of BoHV6 using nested PCR and qPCR tests. Viral DNA was detected by using nested PCR in 59 out of 92 bovine blood samples (64.1%), and by qPCR in 68 out of 92 bovine blood samples (73.9%), but none out of 69 DNA samples isolated from wild ruminant blood clots, was positive in both assays. The specificity of nested PCR and qPCR was confirmed by using BoHV1, BoHV4, BoHV6, BFV, BIV, and BLV DNA. The sensitivity of nested PCR and qPCR was determined using a serially 10-fold diluted vector pCR2.1HgB (2 × 10(0)-2 × 10(6)copies/reaction). In this testing, qPCR was more sensitive than the nested PCR, detecting two copies of BoHV6 whilst the limit of detection for nested PCR was 20 copies. In all qPCR assays, the coefficients of determination (R(2)) ranged between 0.990 and 0.999, and the calculated amplification efficiencies (Eff%) within the range of 89.7-106.9. The intra- and inter-assay CV (coefficient of variation) values did not exceed 4%. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Terrorism and dispelling the myth of a panic prone public.

    PubMed

    Sheppard, Ben; Rubin, G James; Wardman, Jamie K; Wessely, Simon

    2006-01-01

    Governments and commentators perceive the public to be prone to panic in response to terrorist attacks--conventional or involving chemical, biological or radiological weapons. Evidence from five such incidents suggests that the public is not prone to panic, although people can change their behaviours and attitudes to reduce the risk of themselves being exposed to a terrorist incident. Behavioural responses may be divided into acts of omission, such as not making unnecessary journeys, and acts of commission, such as taking prophylactic medication despite the inherent risk of side effects. Evidence suggests that the public are aware of these differences, and tend to adopt responses proportionate to the risk. Drawing upon the literature in the social and natural sciences, our discussion encompasses differing risk perceptions of terrorist threats and consequences of attacks. How do fear and anxiety interact with behavioural responses to amplify or attenuate perceptions that can be modified through risk communication undertaken by authorities?

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

    PubMed

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

    2016-06-30

    Body image concerns are common in the general population and in some mental illnesses reach pathological levels. We investigated whether dysmorphic concern with appearance (a preoccupation with minor or imagined defects in appearance) is explained by psychotic processes in a community sample. In a cross-sectional design, two hundred and twenty six participants completed an online survey battery including: The Dysmorphic Concern Questionnaire; the Peters Delusional inventory; the Aberrant Salience Inventory; and the Depression, Anxiety, Stress Scale. Participants were native English speakers residing in Australia. Dysmorphic concern was positively correlated with delusional proneness, aberrant salience and negative emotion. Regression established that negative emotion and delusional proneness predicted dysmorphic concern, whereas, aberrant salience did not. Although delusional proneness was related to body dysmorphia, there was no evidence that it was related to aberrant salience. Understanding the contribution of other psychosis processes, and other health related variables to the severity of dysmorphic concern will be a focus of future research. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  15. The association of family functioning and psychosis proneness in five countries that differ in cultural values and family structures.

    PubMed

    Wüsten, Caroline; Lincoln, Tania M

    2017-07-01

    For decades, researchers have attributed the better prognosis of psychosis in developing countries to a host of socio-cultural factors, including family functioning. Nevertheless, it is unknown whether family functioning and its association with symptoms differ across countries. This study assessed family functioning (support, satisfaction with family relations, and criticism) and psychosis proneness in community samples from Chile (n =399), Colombia (n=486), Indonesia (n=115), Germany (n=174) and the USA (n=143). Family functioning was compared between prototypical developing countries (Chile, Columbia, Indonesia) and highly industrialized countries (Germany, USA). Hierarchical regression analysis was used to test for the moderating effect of country on the associations between family functioning and psychosis proneness. Participants from developing countries perceived more support and felt more satisfied. However, they also perceived more criticism than participants from highly industrialized countries. Criticism and family satisfaction were significantly associated with psychosis proneness. Moreover, the relationship between criticism and psychosis proneness was significantly stronger in developing countries compared to highly industrialized countries. Generally, family satisfaction and criticism appear to be more relevant to psychosis proneness than the quantity of family support. Moreover, criticism seems to be more closely related to psychosis proneness in developing countries. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

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

    PubMed

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

    2006-12-01

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

  17. Complex monitoring performance and the coronary-prone Type A behavior pattern.

    DOT National Transportation Integrated Search

    1986-03-01

    The present study examined the possible relationship of the coronary-prone Type A behavior pattern to performance of a complex monitoring task. The task was designed to functionally simulate the general task characteristics of future, highly automate...

  18. Reduced Serum IgG Responses to Pneumococcal Antigens in Otitis-Prone Children May Be Due to Poor Memory B-Cell Generation

    PubMed Central

    Sharma, Sharad K.; Casey, Janet R.

    2012-01-01

    A low level of serum antibody to antigens expressed by Streptococcus pneumoniae has been proposed to explain the susceptibility of children to recurrent episodes of acute otitis media (hereafter, “otitis-prone children”). By use of enzyme-linked immunospot assays, the percentages of memory B cells to pneumococcal protein antigens PhtD, LytB, PcpA, PhtE, and Ply were compared between otitis-prone and non–otitis-prone children at the time of acute otitis media or nasopharyngeal colonization with S. pneumoniae. We found significantly lower percentages of memory B cells to 3 pneumococcal protein antigens (PhtD, PhtE, and Ply) and reduced antigen-specific immunoglobulin G concentrations in otitis-prone children, compared with non–otitis-prone children. PMID:22383675

  19. Multiplex enrichment quantitative PCR (ME-qPCR): a high-throughput, highly sensitive detection method for GMO identification.

    PubMed

    Fu, Wei; Zhu, Pengyu; Wei, Shuang; Zhixin, Du; Wang, Chenguang; Wu, Xiyang; Li, Feiwu; Zhu, Shuifang

    2017-04-01

    Among all of the high-throughput detection methods, PCR-based methodologies are regarded as the most cost-efficient and feasible methodologies compared with the next-generation sequencing or ChIP-based methods. However, the PCR-based methods can only achieve multiplex detection up to 15-plex due to limitations imposed by the multiplex primer interactions. The detection throughput cannot meet the demands of high-throughput detection, such as SNP or gene expression analysis. Therefore, in our study, we have developed a new high-throughput PCR-based detection method, multiplex enrichment quantitative PCR (ME-qPCR), which is a combination of qPCR and nested PCR. The GMO content detection results in our study showed that ME-qPCR could achieve high-throughput detection up to 26-plex. Compared to the original qPCR, the Ct values of ME-qPCR were lower for the same group, which showed that ME-qPCR sensitivity is higher than the original qPCR. The absolute limit of detection for ME-qPCR could achieve levels as low as a single copy of the plant genome. Moreover, the specificity results showed that no cross-amplification occurred for irrelevant GMO events. After evaluation of all of the parameters, a practical evaluation was performed with different foods. The more stable amplification results, compared to qPCR, showed that ME-qPCR was suitable for GMO detection in foods. In conclusion, ME-qPCR achieved sensitive, high-throughput GMO detection in complex substrates, such as crops or food samples. In the future, ME-qPCR-based GMO content identification may positively impact SNP analysis or multiplex gene expression of food or agricultural samples. Graphical abstract For the first-step amplification, four primers (A, B, C, and D) have been added into the reaction volume. In this manner, four kinds of amplicons have been generated. All of these four amplicons could be regarded as the target of second-step PCR. For the second-step amplification, three parallels have been taken for

  20. A survey of tools for the analysis of quantitative PCR (qPCR) data.

    PubMed

    Pabinger, Stephan; Rödiger, Stefan; Kriegner, Albert; Vierlinger, Klemens; Weinhäusel, Andreas

    2014-09-01

    Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

  1. Positioning of patients with acute respiratory distress syndrome: combining prone and upright makes sense.

    PubMed

    Richard, Jean-Christophe M; Lefebvre, Jean-Claude

    2011-01-01

    Positional strategies have been proposed for mechanically ventilated patients with acute respiratory distress syndrome. Despite different physiological mechanisms involved, oxygenation improvement has been demonstrated with both prone and upright positions. In the previous issue of Critical Care, Robak and colleagues reported the first study evaluating the short-term effects of combining prone and upright positioning. The combined positioning enhanced the response rate in terms of oxygenation. Other benefits, such as a reduction in ventilator-associated pneumonia and better enteral feeding tolerance, can potentially be expected.

  2. Assessing individual differences in proneness to shame and guilt: development of the Self-Conscious Affect and Attribution Inventory.

    PubMed

    Tangney, J P

    1990-07-01

    Individual differences in proneness to shame and proneness to guilt are thought to play an important role in the development of both adaptive and maladaptive interpersonal and intrapersonal processes. But little empirical research has addressed these issues, largely because no reliable, valid measure has been available to researchers interested in differentiating proneness to shame from proneness to guilt. The Self-Conscious Affect and Attribution Inventory (SCAAI) was developed to assess characteristic affective, cognitive, and behavioral responses associated with shame and guilt among a young adult population. The SCAAI also includes indices of externalization of cause or blame, detachment/unconcern, pride in self, and pride in behavior. Data from 3 independent studies of college students and 1 study of noncollege adults provide support for the reliability of the main SCAAI subscales. Moreover, the pattern of relations among the SCAAI subscales and the relation of SCAAI subscales to 2 extant measures of shame and guilt support the validity of this new measure. The SCAAI appears to provide related but functionally distinct indices of proneness to shame and guilt in a way that these previous measures have not.

  3. Influence of Errors in Tactile Sensors on Some High Level Parameters Used for Manipulation with Robotic Hands.

    PubMed

    Sánchez-Durán, José A; Hidalgo-López, José A; Castellanos-Ramos, Julián; Oballe-Peinado, Óscar; Vidal-Verdú, Fernando

    2015-08-19

    Tactile sensors suffer from many types of interference and errors like crosstalk, non-linearity, drift or hysteresis, therefore calibration should be carried out to compensate for these deviations. However, this procedure is difficult in sensors mounted on artificial hands for robots or prosthetics for instance, where the sensor usually bends to cover a curved surface. Moreover, the calibration procedure should be repeated often because the correction parameters are easily altered by time and surrounding conditions. Furthermore, this intensive and complex calibration could be less determinant, or at least simpler. This is because manipulation algorithms do not commonly use the whole data set from the tactile image, but only a few parameters such as the moments of the tactile image. These parameters could be changed less by common errors and interferences, or at least their variations could be in the order of those caused by accepted limitations, like reduced spatial resolution. This paper shows results from experiments to support this idea. The experiments are carried out with a high performance commercial sensor as well as with a low-cost error-prone sensor built with a common procedure in robotics.

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

    PubMed

    MacKay, Donald G; Johnson, Laura W

    2013-11-01

    This review and perspective article outlines 15 observational constraints on theories of errors, error detection, and error correction, and their relation to hippocampal-region (HR) damage. The core observations come from 10 studies with H.M., an amnesic with cerebellar and HR damage but virtually no neocortical damage. Three studies examined the detection of errors planted in visual scenes (e.g., a bird flying in a fish bowl in a school classroom) and sentences (e.g., I helped themselves to the birthday cake). In all three experiments, H.M. detected reliably fewer errors than carefully matched memory-normal controls. Other studies examined the detection and correction of self-produced errors, with controls for comprehension of the instructions, impaired visual acuity, temporal factors, motoric slowing, forgetting, excessive memory load, lack of motivation, and deficits in visual scanning or attention. In these studies, H.M. corrected reliably fewer errors than memory-normal and cerebellar controls, and his uncorrected errors in speech, object naming, and reading aloud exhibited two consistent features: omission and anomaly. For example, in sentence production tasks, H.M. omitted one or more words in uncorrected encoding errors that rendered his sentences anomalous (incoherent, incomplete, or ungrammatical) reliably more often than controls. Besides explaining these core findings, the theoretical principles discussed here explain H.M.'s retrograde amnesia for once familiar episodic and semantic information; his anterograde amnesia for novel information; his deficits in visual cognition, sentence comprehension, sentence production, sentence reading, and object naming; and effects of aging on his ability to read isolated low frequency words aloud. These theoretical principles also explain a wide range of other data on error detection and correction and generate new predictions for future test. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.

    PubMed

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

    2011-08-01

    The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Design and use of mouse control DNA for DNA biomarker extraction and PCR detection from urine: Application for transrenal Mycobacterium tuberculosis DNA detection.

    PubMed

    Bordelon, Hali; Ricks, Keersten M; Pask, Megan E; Russ, Patricia K; Solinas, Francesca; Baglia, Mark L; Short, Philip A; Nel, Andrew; Blackburn, Jonathan; Dheda, Keertan; Zamudio, Carlos; Cáceres, Tatiana; Wright, David W; Haselton, Frederick R; Pettit, April C

    2017-05-01

    Urine samples are increasingly used for diagnosing infections including Escherichia coli, Ebola virus, and Zika virus. However, extraction and concentration of nucleic acid biomarkers from urine is necessary for many molecular detection strategies such as polymerase chain reaction (PCR). Since urine samples typically have large volumes with dilute biomarker concentrations making them prone to false negatives, another impediment for urine-based diagnostics is the establishment of appropriate controls particularly to rule out false negatives. In this study, a mouse glyceraldehyde 3-phosphate dehydrogenase (GAPDH) DNA target was added to retrospectively collected urine samples from tuberculosis (TB)-infected and TB-uninfected patients to indicate extraction of intact DNA and removal of PCR inhibitors from urine samples. We tested this design on surrogate urine samples, retrospective 1milliliter (mL) urine samples from patients in Lima, Peru and retrospective 5mL urine samples from patients in Cape Town, South Africa. Extraction/PCR control DNA was detectable in 97% of clinical samples with no statistically significant differences among groups. Despite the inclusion of this control, there was no difference in the amount of TB IS6110 Tr-DNA detected between TB-infected and TB-uninfected groups except for samples from known HIV-infected patients. We found an increase in TB IS6110 Tr-DNA between TB/HIV co-infected patients compared to TB-uninfected/HIV-infected patients (N=18, p=0.037). The inclusion of an extraction/PCR control DNA to indicate successful DNA extraction and removal of PCR inhibitors should be easily adaptable as a sample preparation control for other acellular sample types. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Design and use of mouse control DNA for DNA biomarker extraction and PCR detection from urine: application for transrenal Mycobacterium tuberculosis DNA detection

    PubMed Central

    Bordelon, Hali; Ricks, Keersten M.; Pask, Megan E.; Russ, Patricia K.; Solinas, Francesca; Baglia, Mark L.; Short, Philip A.; Nel, Andrew; Blackburn, Jonathan; Dheda, Keertan; Zamudio, Carlos; Cáceres, Tatiana; Wright, David W.; Haselton, Frederick R.; Pettit, April C.

    2017-01-01

    Urine samples are increasingly used for diagnosing infections including Escherichia coli, Ebola virus, and Zika virus. However, extraction and concentration of nucleic acid biomarkers from urine is necessary for many molecular detection strategies such as polymerase chain reaction (PCR). Since urine samples typically have large volumes with dilute biomarker concentrations making them prone to false negatives, another impediment for urine-based diagnostics is the establishment of appropriate controls particularly to rule out false negatives. In this study, a mouse glyceraldehyde 3-phosphate dehydrogenase (GAPDH) DNA target was added to retrospectively collected urine samples from tuberculosis (TB)-infected and TB-uninfected patients to indicate extraction of intact DNA and removal of PCR inhibitors from urine samples. We tested this design on surrogate urine samples, retrospective 1 milliliter (mL) urine samples from patients in Lima, Peru and retrospective 5 mL urine samples from patients in Cape Town, South Africa. Extraction/PCR control DNA was detectable in 97% of clinical samples with no statistically significant differences among groups. Despite the inclusion of this control, there was no difference in the amount of TB IS6110 Tr-DNA detected between TB-infected and TB-uninfected groups except for samples from known HIV-infected patients. We found a increase in TB IS6110 Tr-DNA between TB/HIV co-infected patients compared to TB-uninfected/HIV-infected patients (N=18, p=0.037). The inclusion of an extraction/PCR control DNA to indicate successful DNA extraction and removal of PCR inhibitors should be easily adaptable as a sample preparation control for other acellular sample types. PMID:28285168

  8. Real-time PCR detection chemistry.

    PubMed

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

    2015-01-15

    Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Real-time PCR evaluation of Strongylus vulgaris in horses on farms in Denmark and Central Kentucky.

    PubMed

    Nielsen, M K; Olsen, S N; Lyons, E T; Monrad, J; Thamsborg, S M

    2012-12-21

    Strongyle parasites are ubiquitous in grazing horses, and the large strongyle Strongylus vulgaris is considered the most pathogenic helminth parasite of horses. Recent investigations have suggested an association between occurrence of this parasite and usage of selective therapy based on regular fecal egg counts. The established diagnostic method for S. vulgaris involves larval culture and subsequent morphological identification of third stage larvae under the microscope. Recently, a real-time PCR assay was developed and validated for the detection and semi-quantification of S. vulgaris eggs in equine fecal samples. The purposes of the present study were (a) to determine the presence of S. vulgaris by real-time PCR in Danish and American horses on farms using vastly different anthelmintic treatment regimens and (b) to evaluate the association between larval culture results and the PCR. A total of 991 horses representing 53 different horse farms in Denmark and Central Kentucky were studied. Fresh fecal samples were collected from all horses, and strongyle eggs retrieved for DNA extraction and subsequent real-time PCR analysis. Individual larval cultures were performed on the Danish part of the data set (663 horses on 42 farms). On the Danish farms, the S. vulgaris PCR prevalence was found to be 9.2% on farms not basing parasite control on fecal egg counts, and 14.1% on farms using selective therapy. No horses were PCR positive in the American part of the study (328 horses on 11 farms). Kappa-values indicated a moderate agreement between PCR and larval culture results, while McNemar tests revealed no statistical difference between the paired proportions. Significant associations were found between PCR cycle of threshold (Ct) value groups and larval culture counts. Results indicate that both diagnostic methods can be useful for determining the occurrence of S. vulgaris on horse farms, but that they both are affected by potential sources of error. The PCR results

  10. Non-invasive ventilation in prone position for refractory hypoxemia after bilateral lung transplantation.

    PubMed

    Feltracco, Paolo; Serra, Eugenio; Barbieri, Stefania; Persona, Paolo; Rea, Federico; Loy, Monica; Ori, Carlo

    2009-01-01

    Temporary graft dysfunction with gas exchange abnormalities is a common finding during the postoperative course of a lung transplant and is often determined by the post-reimplantation syndrome. Supportive measures including oxygen by mask, inotropes, diuretics, and pulmonary vasodilators are usually effective in non-severe post-reimplantation syndromes. However, in less-responsive clinical pictures, tracheal intubation with positive pressure ventilation, or non-invasive positive pressure ventilation (NIV), is necessary. We report on the clinical course of two patients suffering from refractory hypoxemia due to post-reimplantation syndrome treated with NIV in the prone and Trendelenburg positions. NIV was well tolerated and led to resolution of atelectactic areas and dishomogeneous lung infiltrates. Repeated turning from supine to prone under non invasive ventilation determined a stable improvement of gas exchange and prevented a more invasive approach. Even though NIV in the prone position has not yet entered into clinical practice, it could be an interesting option to achieve a better match between ventilation and perfusion. This technique, which we successfully applied in lung transplantation, can be easily extended to other lung diseases with non-recruitable dorso-basal areas.

  11. Zonation of Landslide-Prone Using Microseismic Method and Slope Analysis in Margoyoso, Magelang

    NASA Astrophysics Data System (ADS)

    Aditya, Muchamad Reza; Fauqi Romadlon, Arriqo’; Agra Medika, Reymon; Alfontius, Yosua; Delva Jannet, Zukhruf; Hartantyo, Eddy

    2018-04-01

    Margoyoso Village, Salaman Sub-district, Magelang Regency, Central Java is one of the villages that were included in landslide prone areas. The steep slopes and land use in this village were quite apprehensive. There were fractures with 5 cm in width and a length of 50 m. Moreover, these fractures appeared in the home residents. Although the local government has established a disaster response organization, this village is still not getting adequate information about the landslide prone areas. Based on the description before, we conducted research with geophysical methods and geotechnical analysis to minimize the danger of landslides. The geophysical method used in this research was microseismic method and geotechnical analysis. The microseismic measurement and slope stability analysis at Margoyoso village was a step in analysing the landslide-prone zone boundary. The results of this research indicated that landslide potential areas had a low peak ground acceleration values with a range from 36 gal to 46 gal. Measurement of slope stability indicated that a slope angle values between 55°-78° are a potential landslide slope because the soil in this village has very loose properties so it is very easy to move.

  12. Prior caloric restriction increases survival of prepubertal obese- and PCOS-prone rats exposed to a challenge of time-limited feeding and physical activity.

    PubMed

    Diane, Abdoulaye; Vine, Donna F; Heth, C Donald; Russell, James C; Proctor, Spencer D; Pierce, W David

    2013-05-01

    We hypothesized that a polycystic ovary syndrome (PCOS) background associated with obese-prone genotype, coupled with preconditioning by caloric restriction, would confer a survival benefit in genetically prepubertal obese/PCOS (O/PCOS)-prone rats faced with an unpredictable challenge of food shortage. Female, juvenile JCR:LA-cp rats, O/PCOS- and lean-prone, were exposed to 1.5 h of daily meals and 22.5 h of voluntary wheel-running, a procedure that leads to activity anorexia (AA). One week before the AA challenge (AAC), O/PCOS-prone rats were freely fed (O/PCOS-FF) or pair fed (O/PCOS-FR) to lean-prone, free-feeding animals (Lean-FF). O/PCOS-FR and lean-prone, food-restricted (Lean-FR) groups were matched on relative average caloric intake. Animals were removed from protocol at 75% of initial body weight (starvation criterion) or after 14 days (survival criterion). The AAC induced weight loss in all rats, but there were significant effects of both genotype and feeding history on weight loss (lean-prone rats exhibited a higher rate of weight loss than O/PCOS-prone; P < 0.001), and rats with prior caloric restriction retained more weight than those free fed previously (90.68 ± 0.59% vs. 85.47 ± 0.46%; P < 0.001). The daily rate of running was higher in lean-prone rats compared with O/PCOS-prone. This difference in running rate correlated with differences in mean days of survival. All O/PCOS-FR rats survived at day 14. O/PCOS-FF rats survived longer (10.00 ± 0.97 days) than Lean-FR (6.17 ± 1.58 days) and Lean-FF (4.33 ± 0.42 days) rats (P < 0.05). Thus preconditioning by caloric restriction induces a substantial survival advantage, beyond genotype alone, in prepubertal O/PCOS-prone rats.

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

    PubMed

    Kong, Yong-Soo; Park, Seol; Kweon, Mi-Gyong; Park, Ji-Won

    2016-01-01

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

  14. A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples.

    PubMed

    Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Luo, Yunbo; Xu, Wentao

    2016-03-18

    Digital polymerase chain reaction (PCR) has developed rapidly since it was first reported in the 1990s. However, pretreatments are often required during preparation for digital PCR, which can increase operation error. The single-plex amplification of both the target and reference genes may cause uncertainties due to the different reaction volumes and the matrix effect. In the current study, a quantitative detection system based on the pretreatment-free duplex chamber digital PCR was developed. The dynamic range, limit of quantitation (LOQ), sensitivity and specificity were evaluated taking the GA21 event as the experimental object. Moreover, to determine the factors that may influence the stability of the duplex system, we evaluated whether the pretreatments, the primary and secondary structures of the probes and the SNP effect influence the detection. The results showed that the LOQ was 0.5% and the sensitivity was 0.1%. We also found that genome digestion and single nucleotide polymorphism (SNP) sites affect the detection results, whereas the unspecific hybridization within different probes had little side effect. This indicated that the detection system was suited for both chamber-based and droplet-based digital PCR. In conclusion, we have provided a simple and flexible way of achieving absolute quantitation for genetically modified organism (GMO) genome samples using commercial digital PCR detection systems.

  15. A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples

    PubMed Central

    Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Luo, Yunbo; Xu, Wentao

    2016-01-01

    Digital polymerase chain reaction (PCR) has developed rapidly since it was first reported in the 1990s. However, pretreatments are often required during preparation for digital PCR, which can increase operation error. The single-plex amplification of both the target and reference genes may cause uncertainties due to the different reaction volumes and the matrix effect. In the current study, a quantitative detection system based on the pretreatment-free duplex chamber digital PCR was developed. The dynamic range, limit of quantitation (LOQ), sensitivity and specificity were evaluated taking the GA21 event as the experimental object. Moreover, to determine the factors that may influence the stability of the duplex system, we evaluated whether the pretreatments, the primary and secondary structures of the probes and the SNP effect influence the detection. The results showed that the LOQ was 0.5% and the sensitivity was 0.1%. We also found that genome digestion and single nucleotide polymorphism (SNP) sites affect the detection results, whereas the unspecific hybridization within different probes had little side effect. This indicated that the detection system was suited for both chamber-based and droplet-based digital PCR. In conclusion, we have provided a simple and flexible way of achieving absolute quantitation for genetically modified organism (GMO) genome samples using commercial digital PCR detection systems. PMID:26999129

  16. Comparison between conventional protective mechanical ventilation and high-frequency oscillatory ventilation associated with the prone position.

    PubMed

    Fioretto, José Roberto; Klefens, Susiane Oliveira; Pires, Rafaelle Fernandes; Kurokawa, Cilmery Suemi; Carpi, Mario Ferreira; Bonatto, Rossano César; Moraes, Marcos Aurélio; Ronchi, Carlos Fernando

    2017-01-01

    To compare the effects of high-frequency oscillatory ventilation and conventional protective mechanical ventilation associated with the prone position on oxygenation, histology and pulmonary oxidative damage in an experimental model of acute lung injury. Forty-five rabbits with tracheostomy and vascular access were underwent mechanical ventilation. Acute lung injury was induced by tracheal infusion of warm saline. Three experimental groups were formed: healthy animals + conventional protective mechanical ventilation, supine position (Control Group; n = 15); animals with acute lung injury + conventional protective mechanical ventilation, prone position (CMVG; n = 15); and animals with acute lung injury + high-frequency oscillatory ventilation, prone position (HFOG; n = 15). Ten minutes after the beginning of the specific ventilation of each group, arterial gasometry was collected, with this timepoint being called time zero, after which the animal was placed in prone position and remained in this position for 4 hours. Oxidative stress was evaluated by the total antioxidant performance assay. Pulmonary tissue injury was determined by histopathological score. The level of significance was 5%. Both groups with acute lung injury showed worsening of oxygenation after induction of injury compared with the Control Group. After 4 hours, there was a significant improvement in oxygenation in the HFOG group compared with CMVG. Analysis of total antioxidant performance in plasma showed greater protection in HFOG. HFOG had a lower histopathological lesion score in lung tissue than CMVG. High-frequency oscillatory ventilation, associated with prone position, improves oxygenation and attenuates oxidative damage and histopathological lung injury compared with conventional protective mechanical ventilation.

  17. Comparison between conventional protective mechanical ventilation and high-frequency oscillatory ventilation associated with the prone position

    PubMed Central

    Fioretto, José Roberto; Klefens, Susiane Oliveira; Pires, Rafaelle Fernandes; Kurokawa, Cilmery Suemi; Carpi, Mario Ferreira; Bonatto, Rossano César; Moraes, Marcos Aurélio; Ronchi, Carlos Fernando

    2017-01-01

    Objective To compare the effects of high-frequency oscillatory ventilation and conventional protective mechanical ventilation associated with the prone position on oxygenation, histology and pulmonary oxidative damage in an experimental model of acute lung injury. Methods Forty-five rabbits with tracheostomy and vascular access were underwent mechanical ventilation. Acute lung injury was induced by tracheal infusion of warm saline. Three experimental groups were formed: healthy animals + conventional protective mechanical ventilation, supine position (Control Group; n = 15); animals with acute lung injury + conventional protective mechanical ventilation, prone position (CMVG; n = 15); and animals with acute lung injury + high-frequency oscillatory ventilation, prone position (HFOG; n = 15). Ten minutes after the beginning of the specific ventilation of each group, arterial gasometry was collected, with this timepoint being called time zero, after which the animal was placed in prone position and remained in this position for 4 hours. Oxidative stress was evaluated by the total antioxidant performance assay. Pulmonary tissue injury was determined by histopathological score. The level of significance was 5%. Results Both groups with acute lung injury showed worsening of oxygenation after induction of injury compared with the Control Group. After 4 hours, there was a significant improvement in oxygenation in the HFOG group compared with CMVG. Analysis of total antioxidant performance in plasma showed greater protection in HFOG. HFOG had a lower histopathological lesion score in lung tissue than CMVG. Conclusion High-frequency oscillatory ventilation, associated with prone position, improves oxygenation and attenuates oxidative damage and histopathological lung injury compared with conventional protective mechanical ventilation. PMID:29236845

  18. Gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of Japanese encephalitis virus

    NASA Astrophysics Data System (ADS)

    Huang, Su-Hua; Yang, Tsuey-Ching; Tsai, Ming-Hong; Tsai, I.-Shou; Lu, Huang-Chih; Chuang, Pei-Hsin; Wan, Lei; Lin, Ying-Ju; Lai, Chih-Ho; Lin, Cheng-Wen

    2008-10-01

    Virus isolation and antibody detection are routinely used for diagnosis of Japanese encephalitis virus (JEV) infection, but the low level of transient viremia in some JE patients makes JEV isolation from clinical and surveillance samples very difficult. We describe the use of gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of JEV from its RNA genome. We tested the effect of gold nanoparticles on four different PCR systems, including conventional PCR, reverse-transcription PCR (RT-PCR), and SYBR green real-time PCR and RT-PCR assays for diagnosis in the acute phase of JEV infection. Gold nanoparticles increased the amplification yield of the PCR product and shortened the PCR time compared to the conventional reaction. In addition, nanogold-based real-time RT-PCR showed a linear relationship between Ct and template amount using ten-fold dilutions of JEV. The nanogold-based RT-PCR and real-time quantitative RT-PCR assays were able to detect low levels (1-10 000 copies) of the JEV RNA genomes extracted from culture medium or whole blood, providing early diagnostic tools for the detection of low-level viremia in the acute-phase infection. The assays described here were simple, sensitive, and rapid approaches for detection and quantitation of JEV in tissue cultured samples as well as clinical samples.

  19. Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water

    PubMed Central

    Santísima-Trinidad, Ana Belén; Bornay-Llinares, Fernando Jorge; Martín González, Marcos; Pascual Valero, José Antonio; Ros Muñoz, Margarita

    2017-01-01

    The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation. We present two new protocols of DNA extraction from large volumes of reclaimed water. Quantitative PCR (qPCR) and digital PCR (dPCR) were able to detect low amounts of A. lumbricoides eggs. By using the first extraction protocol, which processes 500 mL of reclaimed water, qPCR can detect DNA concentrations as low as one A. lumbricoides egg equivalent, while dPCR can detect DNA concentrations as low as five A. lumbricoides egg equivalents. By using the second protocol, which processes 10 L of reclaimed water, qPCR was able to detect DNA concentrations equivalent to 20 A. lumbricoides eggs. This fact indicated the importance of developing new methodologies to detect helminth eggs with higher sensitivity and precision avoiding possible human infection risks. PMID:28377928

  20. Comparison of droplet digital PCR with quantitative real-time PCR for determination of zygosity in transgenic maize.

    PubMed

    Xu, Xiaoli; Peng, Cheng; Wang, Xiaofu; Chen, Xiaoyun; Wang, Qiang; Xu, Junfeng

    2016-12-01

    This study evaluated the applicability of droplet digital PCR (ddPCR) as a tool for maize zygosity determination using quantitative real-time PCR (qPCR) as a reference technology. Quantitative real-time PCR is commonly used to determine transgene copy number or GMO zygosity characterization. However, its effectiveness is based on identical reaction efficiencies for the transgene and the endogenous reference gene. Additionally, a calibrator sample should be utilized for accuracy. Droplet digital PCR is a DNA molecule counting technique that directly counts the absolute number of target and reference DNA molecules in a sample, independent of assay efficiency or external calibrators. The zygosity of the transgene can be easily determined using the ratio of the quantity of the target gene to the reference single copy endogenous gene. In this study, both the qPCR and ddPCR methods were used to determine insect-resistant transgenic maize IE034 zygosity. Both methods performed well, but the ddPCR method was more convenient because of its absolute quantification property.

  1. Learning time-dependent noise to reduce logical errors: real time error rate estimation in quantum error correction

    NASA Astrophysics Data System (ADS)

    Huo, Ming-Xia; Li, Ying

    2017-12-01

    Quantum error correction is important to quantum information processing, which allows us to reliably process information encoded in quantum error correction codes. Efficient quantum error correction benefits from the knowledge of error rates. We propose a protocol for monitoring error rates in real time without interrupting the quantum error correction. Any adaptation of the quantum error correction code or its implementation circuit is not required. The protocol can be directly applied to the most advanced quantum error correction techniques, e.g. surface code. A Gaussian processes algorithm is used to estimate and predict error rates based on error correction data in the past. We find that using these estimated error rates, the probability of error correction failures can be significantly reduced by a factor increasing with the code distance.

  2. PALATAL DYSMORPHOGENESIS: QUANTITATIVE RT-PCR

    EPA Science Inventory

    ABSTRACT

    Palatal Dysmorphogenesis : Quantitative RT-PCR

    Gary A. Held and Barbara D. Abbott

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

  3. Controlling false-negative errors in microarray differential expression analysis: a PRIM approach.

    PubMed

    Cole, Steve W; Galic, Zoran; Zack, Jerome A

    2003-09-22

    Theoretical considerations suggest that current microarray screening algorithms may fail to detect many true differences in gene expression (Type II analytic errors). We assessed 'false negative' error rates in differential expression analyses by conventional linear statistical models (e.g. t-test), microarray-adapted variants (e.g. SAM, Cyber-T), and a novel strategy based on hold-out cross-validation. The latter approach employs the machine-learning algorithm Patient Rule Induction Method (PRIM) to infer minimum thresholds for reliable change in gene expression from Boolean conjunctions of fold-induction and raw fluorescence measurements. Monte Carlo analyses based on four empirical data sets show that conventional statistical models and their microarray-adapted variants overlook more than 50% of genes showing significant up-regulation. Conjoint PRIM prediction rules recover approximately twice as many differentially expressed transcripts while maintaining strong control over false-positive (Type I) errors. As a result, experimental replication rates increase and total analytic error rates decline. RT-PCR studies confirm that gene inductions detected by PRIM but overlooked by other methods represent true changes in mRNA levels. PRIM-based conjoint inference rules thus represent an improved strategy for high-sensitivity screening of DNA microarrays. Freestanding JAVA application at http://microarray.crump.ucla.edu/focus

  4. Pre-existing differences in motivation for food and sensitivity to cocaine-induced locomotion in obesity-prone rats.

    PubMed

    Vollbrecht, Peter J; Nobile, Cameron W; Chadderdon, Aaron M; Jutkiewicz, Emily M; Ferrario, Carrie R

    2015-12-01

    Obesity is a significant problem in the United States, with roughly one third of adults having a body mass index (BMI) over thirty. Recent evidence from human studies suggests that pre-existing differences in the function of mesolimbic circuits that mediate motivational processes may promote obesity and hamper weight loss. However, few preclinical studies have examined pre-existing neurobehavioral differences related to the function of mesolimbic systems in models of individual susceptibility to obesity. Here, we used selectively bred obesity-prone and obesity-resistant rats to examine 1) the effect of a novel "junk-food" diet on the development of obesity and metabolic dysfunction, 2) over-consumption of "junk-food" in a free access procedure, 3) motivation for food using instrumental procedures, and 4) cocaine-induced locomotor activity as an index of general mesolimbic function. As expected, eating a sugary, fatty, "junk-food" diet exacerbated weight gain and increased fasted insulin levels only in obesity-prone rats. In addition, obesity-prone rats continued to over-consume junk-food during discrete access testing, even when this same food was freely available in the home cage. Furthermore, when asked to press a lever to obtain food in an instrumental task, rates of responding were enhanced in obesity-prone versus obesity-resistant rats. Finally, obesity-prone rats showed a stronger locomotor response to 15 mg/kg cocaine compared to obesity-resistant rats prior to any diet manipulation. This enhanced sensitivity to this dose of cocaine is indicative of basal differences in the function of mesolimbic circuits in obesity-prone rats. We speculate that pre-existing differences in motivational systems may contribute to over-consumption and enhanced motivation in susceptible individuals. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Pre-existing differences in motivation for food and sensitivity to cocaine-induced locomotion in obesity-prone rats

    PubMed Central

    Vollbrecht, Peter J.; Nobile, Cameron W.; Chadderdon, Aaron M.; Jutkiewicz, Emily M.; Ferrario, Carrie R.

    2015-01-01

    Obesity is a significant problem in the United States, with roughly one third of adults having a body mass index (BMI) over thirty. Recent evidence from human studies suggests that pre-existing differences in the function of mesolimbic circuits that mediate motivational processes may promote obesity and hamper weight loss. However, few preclinical studies have examined pre-existing neurobehavioral differences related to the function of mesolimbic systems in models of individual susceptibility to obesity. Here, we used selectively bred obesity-prone and obesity-resistant rats to examine 1) the effect of a novel “junk-food” diet on the development of obesity and metabolic dysfunction, 2) over-consumption of “junk-food” in a free access procedure, 3) motivation for food using instrumental procedures, and 4) cocaine-induced locomotor activity as an index of general mesolimbic function. As expected, eating a sugary, fatty, “junk-food” diet exacerbated weight gain and increased fasted insulin levels only in obesity-prone rats. In addition, obesity-prone rats continued to over-consume junk-food during discrete access testing, even when this same food was freely available in the home cage. Furthermore, when asked to press a lever to obtain food in an instrumental task, rates of responding were enhanced in obesity-prone versus obesity-resistant rats. Finally, obesity-prone rats showed a stronger locomotor response to 15 mg/kg cocaine compared to obesity-resistant rats prior to any diet manipulation. This enhanced sensitivity to this dose of cocaine is indicative of basal differences in the function of mesolimbic circuits in obesity-prone rats. We speculate that pre-existing differences in motivational systems may contribute to over-consumption and enhanced motivation in susceptible individuals. PMID:26423787

  6. Error and Error Mitigation in Low-Coverage Genome Assemblies

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2014-09-01

    Epidemic-prone diseases have traditionally been uncommon among nomadic pastoralists as mobility allows already dispersed populations to migrate away from epidemic threats. In the Karamoja region of Uganda, nomadic pastoralists are transitioning to an increasingly settled lifestyle due to cattle raiding and associated civil insecurity. In attempts to reduce conflict in the region, the Ugandan government has instituted disarmament campaigns and encouraged sedentism in place of mobility. In Karamoja, this transition to sedentism has contributed to the emergence and reemergence of epidemic-prone diseases such as cholera, hepatitis E, yellow fever, and meningococcal meningitis. The incidence of these diseases remains difficult to measure and several challenges exist to their control. Challenges to communicable disease surveillance and control among settling nomadic pastoralists are related to nomadic mobility, remote geography, vaccination and immunity, and poor sanitation and safe water access. In addition to improving gaps in infrastructure, attracting well-trained government health workers to Karamoja and similar areas with longstanding human resource limitations is critical to address the challenges to epidemic-prone disease surveillance and control among settling nomadic pastoralists. In conjunction with government health workers, community health teams provide a sustainable method by which public health programs can be improved in the austere environments inhabited by mobile and settling pastoralists. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Human Factors Risk Analyses of a Doffing Protocol for Ebola-Level Personal Protective Equipment: Mapping Errors to Contamination.

    PubMed

    Mumma, Joel M; Durso, Francis T; Ferguson, Ashley N; Gipson, Christina L; Casanova, Lisa; Erukunuakpor, Kimberly; Kraft, Colleen S; Walsh, Victoria L; Zimring, Craig; DuBose, Jennifer; Jacob, Jesse T

    2018-03-05

    Doffing protocols for personal protective equipment (PPE) are critical for keeping healthcare workers (HCWs) safe during care of patients with Ebola virus disease. We assessed the relationship between errors and self-contamination during doffing. Eleven HCWs experienced with doffing Ebola-level PPE participated in simulations in which HCWs donned PPE marked with surrogate viruses (ɸ6 and MS2), completed a clinical task, and were assessed for contamination after doffing. Simulations were video recorded, and a failure modes and effects analysis and fault tree analyses were performed to identify errors during doffing, quantify their risk (risk index), and predict contamination data. Fifty-one types of errors were identified, many having the potential to spread contamination. Hand hygiene and removing the powered air purifying respirator (PAPR) hood had the highest total risk indexes (111 and 70, respectively) and number of types of errors (9 and 13, respectively). ɸ6 was detected on 10% of scrubs and the fault tree predicted a 10.4% contamination rate, likely occurring when the PAPR hood inadvertently contacted scrubs during removal. MS2 was detected on 10% of hands, 20% of scrubs, and 70% of inner gloves and the predicted rates were 7.3%, 19.4%, 73.4%, respectively. Fault trees for MS2 and ɸ6 contamination suggested similar pathways. Ebola-level PPE can both protect and put HCWs at risk for self-contamination throughout the doffing process, even among experienced HCWs doffing with a trained observer. Human factors methodologies can identify error-prone steps, delineate the relationship between errors and self-contamination, and suggest remediation strategies.

  9. The effects of supine and prone positions on oxygenation in premature infants undergoing mechanical ventilation

    PubMed Central

    Abdeyazdan, Zahra; Nematollahi, Monirosadat; Ghazavi, Zohreh; Mohhamadizadeh, Majid

    2010-01-01

    BACKGROUND: Since the use of high concentrations of oxygen in infants may lead to chronic lung problems, using proper methods of care in infants under mechanical ventilation is one of the most important measures in NICU. This study aimed to investigate the effects of prone and supine positions on oxygenation (SPO2) in premature infants under mechanical ventilation and comparing infants’ oxygenation in the two positions. METHODS: In across over non randomized clinical trial study, 32 preterm infants under mechanical ventilation who had inclusion criteria were enrolled in simple convenient method. Firstly, they were placed in supine position for 120 minutes and further in prone position for 120 minutes .Their SPO2 were monitored by pulse oximeter continuously and was recorded every minute. Data analysis was done using Software SPSS15 by ANOVA test and post hoc test. RESULTS: The data showed that during 120 minutes of exposure of infants in each position there were no significant changes in SPO2. In addition, the SPO2 levels in the prone position were significantly higher than the SPO2 levels in the supine position from 15th minute to 120th minute (to the end). CONCLUSIONS: Neonatal positioning in prone position is a simple, non-invasive, and free of charge method that could lead to improve oxygenation in infants undergoing mechanical ventilation. PMID:22049286

  10. Pre-existing differences and diet-induced alterations in striatal dopamine systems of obesity-prone rats.

    PubMed

    Vollbrecht, Peter J; Mabrouk, Omar S; Nelson, Andrew D; Kennedy, Robert T; Ferrario, Carrie R

    2016-03-01

    Interactions between pre-existing differences in mesolimbic function and neuroadaptations induced by consumption of fatty, sugary foods are thought to contribute to human obesity. This study examined basal and cocaine-induced changes in striatal neurotransmitter levels without diet manipulation and D2 /D3 dopamine receptor-mediated transmission prior to and after consumption of "junk-foods" in obesity-prone and obesity-resistant rats. Microdialysis and liquid chromatography-mass spectrometry were used to determine basal and cocaine-induced changes in neurotransmitter levels in real time with cocaine-induced locomotor activity. Sensitivity to the D2 /D3 dopamine receptor agonist quinpirole was examined before and after restricted junk-food exposure. Selectively bred obesity-prone and obesity-resistant rats were used. Cocaine-induced locomotion was greater in obesity-prone rats versus obesity-resistant rats prior to diet manipulation. Basal and cocaine-induced increases in dopamine and serotonin levels did not differ. Obesity-prone rats were more sensitive to the D2 receptor-mediated effects of quinpirole, and junk-food produced modest alterations in quinpirole sensitivity in obesity-resistant rats. These data show that mesolimbic systems differ prior to diet manipulation in susceptible versus resistant rats, and that consumption of fatty, sugary foods produce different neuroadaptations in these populations. These differences may contribute to enhanced food craving and an inability to limit food intake in susceptible individuals. © 2016 The Obesity Society.

  11. Practical utilization of recombinant AAV vector reference standards: focus on vector genomes titration by free ITR qPCR.

    PubMed

    D'Costa, Susan; Blouin, Veronique; Broucque, Frederic; Penaud-Budloo, Magalie; François, Achille; Perez, Irene C; Le Bec, Christine; Moullier, Philippe; Snyder, Richard O; Ayuso, Eduard

    2016-01-01

    Clinical trials using recombinant adeno-associated virus (rAAV) vectors have demonstrated efficacy and a good safety profile. Although the field is advancing quickly, vector analytics and harmonization of dosage units are still a limitation for commercialization. AAV reference standard materials (RSMs) can help ensure product safety by controlling the consistency of assays used to characterize rAAV stocks. The most widely utilized unit of vector dosing is based on the encapsidated vector genome. Quantitative polymerase chain reaction (qPCR) is now the most common method to titer vector genomes (vg); however, significant inter- and intralaboratory variations have been documented using this technique. Here, RSMs and rAAV stocks were titered on the basis of an inverted terminal repeats (ITRs) sequence-specific qPCR and we found an artificial increase in vg titers using a widely utilized approach. The PCR error was introduced by using single-cut linearized plasmid as the standard curve. This bias was eliminated using plasmid standards linearized just outside the ITR region on each end to facilitate the melting of the palindromic ITR sequences during PCR. This new "Free-ITR" qPCR delivers vg titers that are consistent with titers obtained with transgene-specific qPCR and could be used to normalize in-house product-specific AAV vector standards and controls to the rAAV RSMs. The free-ITR method, including well-characterized controls, will help to calibrate doses to compare preclinical and clinical data in the field.

  12. Clinical Characteristics of Exacerbation-Prone Adult Asthmatics Identified by Cluster Analysis.

    PubMed

    Kim, Mi Ae; Shin, Seung Woo; Park, Jong Sook; Uh, Soo Taek; Chang, Hun Soo; Bae, Da Jeong; Cho, You Sook; Park, Hae Sim; Yoon, Ho Joo; Choi, Byoung Whui; Kim, Yong Hoon; Park, Choon Sik

    2017-11-01

    Asthma is a heterogeneous disease characterized by various types of airway inflammation and obstruction. Therefore, it is classified into several subphenotypes, such as early-onset atopic, obese non-eosinophilic, benign, and eosinophilic asthma, using cluster analysis. A number of asthmatics frequently experience exacerbation over a long-term follow-up period, but the exacerbation-prone subphenotype has rarely been evaluated by cluster analysis. This prompted us to identify clusters reflecting asthma exacerbation. A uniform cluster analysis method was applied to 259 adult asthmatics who were regularly followed-up for over 1 year using 12 variables, selected on the basis of their contribution to asthma phenotypes. After clustering, clinical profiles and exacerbation rates during follow-up were compared among the clusters. Four subphenotypes were identified: cluster 1 was comprised of patients with early-onset atopic asthma with preserved lung function, cluster 2 late-onset non-atopic asthma with impaired lung function, cluster 3 early-onset atopic asthma with severely impaired lung function, and cluster 4 late-onset non-atopic asthma with well-preserved lung function. The patients in clusters 2 and 3 were identified as exacerbation-prone asthmatics, showing a higher risk of asthma exacerbation. Two different phenotypes of exacerbation-prone asthma were identified among Korean asthmatics using cluster analysis; both were characterized by impaired lung function, but the age at asthma onset and atopic status were different between the two. Copyright © 2017 The Korean Academy of Asthma, Allergy and Clinical Immunology · The Korean Academy of Pediatric Allergy and Respiratory Disease

  13. Negative social comparisons and psychosis proneness in a healthy adolescent population.

    PubMed

    Cotier, F A; Toulopoulou, T

    2017-10-01

    There is growing evidence of an association between negative social comparisons (NSC) and both psychosis, and psychosis proneness. The majority of the work thus far, however, has focused largely on one type of NSC, namely, social rank. Whilst social rank is clearly an important factor, an individual's perception of belonging is likely also of importance; particularly, when considering individuals from collectivistic cultures such as China, where greater emphasis is placed on fitting into the group. There is also limited research investigating what factors may contribute towards the relationship between NSC and psychosis proneness, and to what extent this relationship may be due to common familial factors. To address these issues, we examined whether (1) Social rank and perceived belonging predict negative, positive and depressive psychotic experiences in a Chinese, adolescent, twin and sibling population, (2) coping styles moderate the impact of these relationships and (3), there is a familial association between NSC and psychosis proneness. Both social rank and perceived belonging were found to predict the negative and depressive dimensions of psychosis. These relationships were moderated by problem-focused coping styles. Interestingly, the association between perception of belonging, and negative psychotic experiences was familial-and stronger in Monozygotic twins-indicating perhaps shared aetiology due to common genes. Our findings highlight NSC as potential vulnerability markers for negative and depressive psychotic experiences, and suggest potentially different aetiological pathways amongst different NSC and different psychotic experiences. On a clinical level, our findings emphasize the need to consider coping styles when treating at-risk individuals. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  14. Unforced errors and error reduction in tennis

    PubMed Central

    Brody, H

    2006-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  16. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... minimize or eliminate infiltration of flood waters into the systems; and (6) Require within flood-prone... infiltration of flood waters into the systems and discharges from the systems into flood waters and (ii) onsite...

  17. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... minimize or eliminate infiltration of flood waters into the systems; and (6) Require within flood-prone... infiltration of flood waters into the systems and discharges from the systems into flood waters and (ii) onsite...

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

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... minimize or eliminate infiltration of flood waters into the systems; and (6) Require within flood-prone... infiltration of flood waters into the systems and discharges from the systems into flood waters and (ii) onsite...

  19. Comparison of Magnetic Resonance Imaging and Computed Tomography for Breast Target Volume Delineation in Prone and Supine Positions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pogson, Elise M.; Liverpool and Macarthur Cancer Therapy Centres, Liverpool; Ingham Institute for Applied Medical Research, Liverpool

    2016-11-15

    Purpose: To determine whether T2-weighted MRI improves seroma cavity (SC) and whole breast (WB) interobserver conformity for radiation therapy purposes, compared with the gold standard of CT, both in the prone and supine positions. Methods and Materials: Eleven observers (2 radiologists and 9 radiation oncologists) delineated SC and WB clinical target volumes (CTVs) on T2-weighted MRI and CT supine and prone scans (4 scans per patient) for 33 patient datasets. Individual observer's volumes were compared using the Dice similarity coefficient, volume overlap index, center of mass shift, and Hausdorff distances. An average cavity visualization score was also determined. Results: Imaging modalitymore » did not affect interobserver variation for WB CTVs. Prone WB CTVs were larger in volume and more conformal than supine CTVs (on both MRI and CT). Seroma cavity volumes were larger on CT than on MRI. Seroma cavity volumes proved to be comparable in interobserver conformity in both modalities (volume overlap index of 0.57 (95% Confidence Interval (CI) 0.54-0.60) for CT supine and 0.52 (95% CI 0.48-0.56) for MRI supine, 0.56 (95% CI 0.53-0.59) for CT prone and 0.55 (95% CI 0.51-0.59) for MRI prone); however, after registering modalities together the intermodality variation (Dice similarity coefficient of 0.41 (95% CI 0.36-0.46) for supine and 0.38 (0.34-0.42) for prone) was larger than the interobserver variability for SC, despite the location typically remaining constant. Conclusions: Magnetic resonance imaging interobserver variation was comparable to CT for the WB CTV and SC delineation, in both prone and supine positions. Although the cavity visualization score and interobserver concordance was not significantly higher for MRI than for CT, the SCs were smaller on MRI, potentially owing to clearer SC definition, especially on T2-weighted MR images.« less

  20. How Informative are the Vertical Buoyancy and the Prone Gliding Tests to Assess Young Swimmers’ Hydrostatic and Hydrodynamic Profiles?

    PubMed Central

    Barbosa, Tiago M.; Costa, Mário J.; Morais, Jorge E; Moreira, Marc; Silva, António J.; Marinho, Daniel A.

    2012-01-01

    The aim of this research was to develop a path-flow analysis model to highlight the relationships between buoyancy and prone gliding tests and some selected anthropometrical and biomechanical variables. Thirty-eight young male swimmers (12.97 ± 1.05 years old) with several competitive levels were evaluated. It were assessed the body mass, height, fat mass, body surface area, vertical buoyancy, prone gliding after wall push-off, stroke length, stroke frequency and velocity after a maximal 25 [m] swim. The confirmatory model included the body mass, height, fat mass, prone gliding test, stroke length, stroke frequency and velocity. All theoretical paths were verified except for the vertical buoyancy test that did not present any relationship with anthropometrical and biomechanical variables nor with the prone gliding test. The good-of-fit from the confirmatory path-flow model, assessed with the standardized root mean square residuals (SRMR), is considered as being close to the cut-off value, but even so not suitable of the theory (SRMR = 0.11). As a conclusion, vertical buoyancy and prone gliding tests are not the best techniques to assess the swimmer’s hydrostatic and hydrodynamic profile, respectively. PMID:23486528

  1. The gravitational distribution of ventilation-perfusion ratio is more uniform in prone than supine posture in the normal human lung

    PubMed Central

    Sá, Rui Carlos; Theilmann, Rebecca J.; Buxton, Richard B.; Prisk, G. Kim; Hopkins, Susan R.

    2013-01-01

    The gravitational gradient of intrapleural pressure is suggested to be less in prone posture than supine. Thus the gravitational distribution of ventilation is expected to be more uniform prone, potentially affecting regional ventilation-perfusion (V̇a/Q̇) ratio. Using a novel functional lung magnetic resonance imaging technique to measure regional V̇a/Q̇ ratio, the gravitational gradients in proton density, ventilation, perfusion, and V̇a/Q̇ ratio were measured in prone and supine posture. Data were acquired in seven healthy subjects in a single sagittal slice of the right lung at functional residual capacity. Regional specific ventilation images quantified using specific ventilation imaging and proton density images obtained using a fast gradient-echo sequence were registered and smoothed to calculate regional alveolar ventilation. Perfusion was measured using arterial spin labeling. Ventilation (ml·min−1·ml−1) images were combined on a voxel-by-voxel basis with smoothed perfusion (ml·min−1·ml−1) images to obtain regional V̇a/Q̇ ratio. Data were averaged for voxels within 1-cm gravitational planes, starting from the most gravitationally dependent lung. The slope of the relationship between alveolar ventilation and vertical height was less prone than supine (−0.17 ± 0.10 ml·min−1·ml−1·cm−1 supine, −0.040 ± 0.03 prone ml·min−1·ml−1·cm−1, P = 0.02) as was the slope of the perfusion-height relationship (−0.14 ± 0.05 ml·min−1·ml−1·cm−1 supine, −0.08 ± 0.09 prone ml·min−1·ml−1·cm−1, P = 0.02). There was a significant gravitational gradient in V̇a/Q̇ ratio in both postures (P < 0.05) that was less in prone (0.09 ± 0.08 cm−1 supine, 0.04 ± 0.03 cm−1 prone, P = 0.04). The gravitational gradients in ventilation, perfusion, and regional V̇a/Q̇ ratio were greater supine than prone, suggesting an interplay between thoracic cavity configuration, airway and vascular tree anatomy, and the effects of

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

    PubMed

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

    2014-01-01

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

  3. Droplet digital polymerase chain reaction (PCR) outperforms real-time PCR in the detection of environmental DNA from an invasive fish species.

    PubMed

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

    2015-05-05

    Environmental DNA (eDNA) has been used to investigate species distributions in aquatic ecosystems. Most of these studies use real-time polymerase chain reaction (PCR) to detect eDNA in water; however, PCR amplification is often inhibited by the presence of organic and inorganic matter. In droplet digital PCR (ddPCR), the sample is partitioned into thousands of nanoliter droplets, and PCR inhibition may be reduced by the detection of the end-point of PCR amplification in each droplet, independent of the amplification efficiency. In addition, real-time PCR reagents can affect PCR amplification and consequently alter detection rates. We compared the effectiveness of ddPCR and real-time PCR using two different PCR reagents for the detection of the eDNA from invasive bluegill sunfish, Lepomis macrochirus, in ponds. We found that ddPCR had higher detection rates of bluegill eDNA in pond water than real-time PCR with either of the PCR reagents, especially at low DNA concentrations. Limits of DNA detection, which were tested by spiking the bluegill DNA to DNA extracts from the ponds containing natural inhibitors, found that ddPCR had higher detection rate than real-time PCR. Our results suggest that ddPCR is more resistant to the presence of PCR inhibitors in field samples than real-time PCR. Thus, ddPCR outperforms real-time PCR methods for detecting eDNA to document species distributions in natural habitats, especially in habitats with high concentrations of PCR inhibitors.

  4. Genetic relationships among strains of Xanthomonas fragariae based on random amplified polymorphic DNA PCR, repetitive extragenic palindromic PCR, and enterobacterial repetitive intergenic consensus PCR data and generation of multiplexed PCR primers useful for the identification of this phytopathogen.

    PubMed Central

    Pooler, M R; Ritchie, D F; Hartung, J S

    1996-01-01

    Genetic relationships among 25 isolates of Xanthomonas fragariae from diverse geographic regions were determined by three PCR methods that rely on different amplification priming strategies: random amplified polymorphic DNA (RAPD) PCR, repetitive extragenic palindromic (REP) PCR, and enterobacterial repetitive intergenic consensus (ERIC) PCR. The results of these assays are mutually consistent and indicate that pathogenic strains are very closely related to each other. RAPD, ERIC, and REP PCR assays identified nine, four, and two genotypes, respectively, within X. fragariae isolates. A single nonpathogenic isolate of X. fragariae was not distinguishable by these methods. The results of the PCR assays were also fully confirmed by physiological tests. There was no correlation between DNA amplification product patterns and geographic sites of isolation, suggesting that this bacterium has spread largely through exchange of infected plant germ plasm. Sequences identified through the RAPD assays were used to develop three primer pairs for standard PCR assays to identify X. fragariae. In addition, we developed a stringent multiplexed PCR assay to identify X. fragariae by simultaneously using the three independently derived sets of primers specific for pathogenic strains of the bacteria. PMID:8795198

  5. Comparison of droplet digital PCR and quantitative real-time PCR for examining population dynamics of bacteria in soil.

    PubMed

    Kim, Tae Gwan; Jeong, So-Yeon; Cho, Kyung-Suk

    2014-07-01

    The newly developed droplet digital PCR (DD-PCR) has shown promise as a DNA quantification technology in medical diagnostic fields. This study evaluated the applicability of DD-PCR as a quantitative tool for soil DNA using quantitative real-time PCR (qRT-PCR) as a reference technology. Cupriavidus sp. MBT14 and Sphingopyxis sp. MD2 were used, and a primer/TaqMan probe set was designed for each (CupMBT and SphMD2, respectively). Standard curve analyses on tenfold dilution series showed that both qRT-PCR and DD-PCR exhibited excellent linearity (R (2) = 1.00) and PCR efficiency (≥92 %) across their detectable ranges. However, DD-PCR showed a tenfold greater sensitivity than qRT-PCR. MBT14 and MD2 were added to non-sterile soil at 0 ~ 5 × 10(8) and 0 ~ 5 × 10(7) cells per gram of soil, respectively (n = 5). This bacterial load test indicated that DD-PCR was more sensitive and discriminating than qRT-PCR. For instance, DD-PCR showed a gradual DNA increase from 14 to 141,160 MBT14 rDNA copies μL DNA extract(-1) as the bacterial load increased, while qRT-PCR could quantify the DNA (6,432 copies μL DNA(-1)) at ≥5 × 10(5) MBT14 per gram of soil. When temporal DNA changes were monitored for 3 weeks in the amended soils, the two technologies exhibited nearly identical changes over time. Linearity tests (y = a · x) revealed excellent quantitative agreement between the two technologies (a = 0.98, R (2) = 0.97 in the CupMBT set and a = 0.90, R (2) = 0.94 in the SphMD2 set). These results suggest that DD-PCR is a promising tool to examine temporal dynamics of microorganisms in complex environments.

  6. Droplet digital PCR (ddPCR) vs quantitative real-time PCR (qPCR) approach for detection and quantification of Merkel cell polyomavirus (MCPyV) DNA in formalin fixed paraffin embedded (FFPE) cutaneous biopsies.

    PubMed

    Arvia, Rosaria; Sollai, Mauro; Pierucci, Federica; Urso, Carmelo; Massi, Daniela; Zakrzewska, Krystyna

    2017-08-01

    Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma and high viral load in the skin was proposed as a risk factor for the occurrence of this tumour. MCPyV DNA was detected, with lower frequency, in different skin cancers but since the viral load was usually low, the real prevalence of viral DNA could be underestimated. To evaluate the performance of two assays (qPCR and ddPCR) for MCPyV detection and quantification in formalin fixed paraffin embedded (FFPE) tissue samples. Both assays were designed to simultaneous detection and quantification of both MCPyV as well as house-keeping DNA in clinical samples. The performance of MCPyV quantification was investigated using serial dilutions of cloned target DNA. We also evaluated the applicability of both tests for the analysis of 76 FFPE cutaneous biopsies. The two approaches resulted equivalent with regard to the reproducibility and repeatability and showed a high degree of linearity in the dynamic range tested in the present study. Moreover, qPCR was able to quantify ≥10 5 copies per reaction, while the upper limit of ddPCR was 10 4 copies. There was not significant difference between viral load measured by the two methods The detection limit of both tests was 0,15 copies per reaction, however, the number of positive samples obtained by ddPCR was higher than that obtained by qPCR (45% and 37% respectively). The ddPCR represents a better method for detection of MCPyV in FFPE biopsies, mostly these containing low copies number of viral genome. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Application of Reverse Transcriptase -PCR (RT-PCR) for rapid detection of viable Escherichia coli in drinking water samples.

    PubMed

    Molaee, Neda; Abtahi, Hamid; Ghannadzadeh, Mohammad Javad; Karimi, Masoude; Ghaznavi-Rad, Ehsanollah

    2015-01-01

    Polymerase chain reaction (PCR) is preferred to other methods for detecting Escherichia coli (E. coli) in water in terms of speed, accuracy and efficiency. False positive result is considered as the major disadvantages of PCR. For this reason, reverse transcriptase-polymerase chain reaction (RT-PCR) can be used to solve this problem. The aim of present study was to determine the efficiency of RT-PCR for rapid detection of viable Escherichia coli in drinking water samples and enhance its sensitivity through application of different filter membranes. Specific primers were designed for 16S rRNA and elongation Factor II genes. Different concentrations of bacteria were passed through FHLP and HAWP filters. Then, RT-PCR was performed using 16srRNA and EF -Tu primers. Contamination of 10 wells was determined by RT-PCR in Arak city. To evaluate RT-PCR efficiency, the results were compared with most probable number (MPN) method. RT-PCR is able to detect bacteria in different concentrations. Application of EF II primers reduced false positive results compared to 16S rRNA primers. The FHLP hydrophobic filters have higher ability to absorb bacteria compared with HAWB hydrophilic filters. So the use of hydrophobic filters will increase the sensitivity of RT-PCR. RT-PCR shows a higher sensitivity compared to conventional water contamination detection method. Unlike PCR, RT-PCR does not lead to false positive results. The use of EF-Tu primers can reduce the incidence of false positive results. Furthermore, hydrophobic filters have a higher ability to absorb bacteria compared to hydrophilic filters.

  8. [Effects of recruitment maneuver in prone position on hemodynamics in patients with severe pulmonary infection].

    PubMed

    Fan, Yuan-hua; Liu, Yuan-fei; Zhu, Hua-yong; Zhang, Min

    2012-02-01

    To evaluate effects of recruitment maneuver in prone position on hemodynamics in patients with severe pulmonary infection, based on the protective pulmonary ventilation strategy. Ninety-seven cases with severe pulmonary infection admitted to intensive care unit (ICU) of Ganzhou City People's Hospital undergoing mechanical ventilation were involved. Volume controlled ventilation mode with small tidal volume (8 ml/kg) and positive end-expiratory pressure (PEEP) of 6 cm H(2)O [1 cm H(2)O = 0.098 kPa] was conducted. Each patient underwent recruitment maneuver in supine position and then in prone position [PEEP 20 cm H(2)O+pressure control (PC) 20 cm H(2)O]. Heart rate (HR), mean arterial pressure (MAP), pulse oxygen saturation [SpO(2)] and blood gas analysis data were recorded before and after recruitment maneuver in either position. A double-lumen venous catheter was inserted into internal jugular vein or subclavian vein, and a pulse index contour cardiac output (PiCCO) catheter was introduced into femoral artery. Cardiac index (CI), stroke volume index (SVI), systemic vascular resistance index (SVRI), intra-thoracic blood volume index (ITBVI), extra vascular lung water index (EVLWI), global end-diastolic volume index (GEDVI), global ejection fraction (GEF), stroke volume variation (SVV) and central vein pressure (CVP) were monitored. (1) Compared with data before recruitment maneuver, there were no significant differences in HR and MAP after supine position and prone position recruitment maneuver, but significant differences in SpO(2) were found between before and after recruitment maneuver when patients' position was changed (supine position: 0.954 ± 0.032 vs. 0.917 ± 0.025, P < 0.05; prone position: 0.982 ± 0.028 vs. 0.936 ± 0.039, P < 0.05). SpO(2) was higher in prone position recruitment maneuver (P < 0.05). (2) Compared with data before recruitment maneuver, CI [L×min(-1)×m(-2)], SVI (ml/m(2)), GEDVI (ml/m(2)) and GEF were decreased significantly during

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

    EPA Science Inventory

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

  10. Childhood memories of threatening experiences and submissiveness and its relationship to hallucination proneness and ideas of reference: The mediating role of dissociation.

    PubMed

    Bellido-Zanin, Gloria; Perona-Garcelán, Salvador; Senín-Calderón, Cristina; López-Jiménez, Ana María; Ruiz-Veguilla, Miguel; Rodríguez-Testal, Juan Francisco

    2018-05-29

    Recent studies have emphasized the importance of childhood memories of threatening experiences and submissiveness in a diversity of psychological disorders. The purpose of this work was to study their specific relationship with hallucination proneness and ideas of reference in healthy subjects. The ELES scale for measuring memory of adverse childhood experiences, the DES-II scale for measuring dissociation, the LSHS-R scale for measuring hallucination proneness, and the REF for ideas of reference were applied to a sample of 472 subjects. A positive association was found between childhood memories of adverse experiences and hallucination proneness and ideas of reference, on one hand, and dissociation on the other. A mediation analysis showed that dissociation was a mediator between the memory of adverse childhood experiences and hallucination proneness on one hand, and ideas of reference on the other. When the role of mediator of the types of dissociative experiences was studied, it was found that absorption and depersonalization mediated between adverse experiences and hallucination proneness. However, this mediating effect was not found between adverse experiences and ideas of reference. The relationship between these last two variables was direct. The results suggest that childhood memories of adverse experiences are a relevant factor in understanding hallucination proneness and ideas of reference. Similarly, dissociation is a specific mediator between adverse childhood experiences and hallucination proneness. © 2018 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

  11. Is Disgust Proneness Associated With Anxiety and Related Disorders? A Qualitative Review and Meta-Analysis of Group Comparison and Correlational Studies.

    PubMed

    Olatunji, Bunmi O; Armstrong, Thomas; Elwood, Lisa

    2017-07-01

    Research suggests that disgust may be linked to the etiology of some anxiety-related disorders. The present investigation reviews this literature and employs separate meta-analyses of clinical group comparison and correlational studies to examine the association between disgust proneness and anxiety-related disorder symptoms. Meta-analysis of 43 group comparison studies revealed those high in anxiety disorder symptoms reported significantly more disgust proneness than those low in anxiety symptoms. Although this effect was not moderated by clinical versus analogue studies or type of disorder, larger group differences were observed for those high in anxiety symptoms associated with contagion concerns compared to those high in anxiety symptoms not associated with contagion concerns. Similarly, meta-analysis of correlational data across 83 samples revealed moderate associations between disgust proneness and anxiety-related disorder symptoms. Moderator analysis revealed that the association between disgust proneness and anxiety-related disorder symptoms was especially robust for anxiety symptoms associated with contagion concerns. After controlling for measures of negative affect, disgust proneness continued to be moderately correlated with anxiety-related disorder symptoms. However, negative affect was no longer significantly associated with symptoms of anxiety-related disorders when controlling for disgust proneness. The implications of these findings are discussed in the context of a novel transdiagnostic model.

  12. Facilitation of Hoffmann reflexes of ankle muscles in prone but not standing positions by focal ankle-joint cooling.

    PubMed

    Kim, Kyung-Min; Ingersoll, Christopher D; Hertel, Jay

    2015-05-01

    Focal ankle-joint cooling (FAJC) has been shown to increase Hoffmann (H) reflex amplitudes of select leg muscles while subjects lie prone, but it is unknown whether the neurophysiological cooling effects persist in standing. To assess the effects of FAJC on H-reflexes of the soleus and fibularis longus during 3 body positions (prone, bipedal, and unipedal stances) in individuals with and without chronic ankle instability (CAI). Crossover. Laboratory. 15 young adults with CAI (9 male, 6 female) and 15 healthy controls. All subjects received both FAJC and sham treatments on separate days in a randomized order. FAJC was accomplished by applying a 1.5-L plastic bag filled with crushed ice to the ankle for 20 min. Sham treatment involved room-temperature candy corn. Maximum amplitudes of H-reflexes and motor (M) waves were recorded while subjects lay prone and then stood in quiet bipedal and unipedal stances before and immediately after each treatment. Primary outcome measures were H(max):M(max) ratios for the soleus and fibularis longus. Three-factor (group × treatment condition × time) repeated-measures ANOVAs and Fisher LSD tests were performed for statistical analyses. Significant interactions of treatment condition by time for prone H(max):M(max) ratios were found in the soleus (P = .001) and fibularis longus (P = .003). In both muscles, prone H(max):M(max) ratios moderately increased after FAJC but not after sham treatment. The CAI and healthy groups responded similarly to FAJC. In contrast, there were no significant interactions or main effects in the bipedal and unipedal stances in either muscle (P > .05). FAJC moderately increased H-reflex amplitudes of the soleus and fibularis longus while subjects were prone but not during bipedal or unipedal standing. These results were not different between groups with and without CAI.

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  14. Using an agent-based model to examine forest management outcomes in a fire-prone landscape in Oregon, USA

    Treesearch

    Thomas A. Spies; Eric White; Alan Ager; Jeffrey D. Kline; John P. Bolte; Emily K. Platt; Keith A. Olsen; Robert J. Pabst; Ana M. G. Barros; John D. Bailey; Susan Charnley; Anita T. Morzillo; Jennifer Koch; Michelle M. Steen-Adams; Peter H. Singleton; James Sulzman; Cynthia Schwartz; Blair Csuti

    2017-01-01

    Fire-prone landscapes present many challenges for both managers and policy makers in developing adaptive behaviors and institutions. We used a coupled human and natural systems framework and an agent-based landscape model to examine how alternative management scenarios affect fire and ecosystem services metrics in a fire-prone multiownership landscape in the eastern...

  15. SU-E-T-292: Dosimetric Advantage of Prone Breast Radiotherapy for Korean Left-Sided Breast Cancer Patients

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chung, Y; Shin, J; Yu, J

    Purpose: To evaluate the dosimetric benefit of prone breast radiotherapy for Korean left-sided early-stage breast cancer patients who have relatively small breast Methods: From April to June, 2014, 10 left-sided breast cancer patients received the whole breast irradiation in prone position after partial mastectomy with sentinel lymph node biopsy or axillary lymph node dissection. All patients were pTmi-2N0-1mi. Each patient underwent two computed tomoradiography (CT) simulations in supine and prone positions. The whole breast, ipsilateral lung, heart, and left anterior descending coronary artery (LAD) were contoured on each simulation CT images, and then tangential-fields treatment plan in each position wasmore » designed for the whole breast irradiation with the total dose of 50 Gy in 2 Gy fractions. Dose-volume histograms of two setups were compared for target coverage and radiation dose to normal organs with Wilcoxon signed rank tests. Results: The median age of patients was 47 years (range, 37 to 53). The median chest size was 82.5 cm (range, 75 to 90) and bra cup size was A in 4, B in 4, and C in 2 patients. The radiation dose to the whole breast was similar when comparing mean dose (Dmean) and dose covering 95% of the breast volume, but maximum dose (Dmax) of breast was higher in supine (median 52.3 vs. 52.7 Gy, p=0.013). Prone position reduced significantly the radiation dose in ipsilateral lung, heart, and LAD by median 5.7, 1.1, and 6.9 Gy of Dmean (p=0.005, 0.007, and 0.005) and 28.2, 18.8, and 35.0 Gy of Dmax (p=0.005, 0.005, and 0.007), respectively. Conclusion: Prone breast radiotherapy could be beneficial for Korean breast cancer patients since it substantially spared normal organs while achieving adequate coverage of the breast tissue. Further prospective study is required to validate the potential benefit of prone breast radiotherapy.« less

  16. Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples

    PubMed Central

    2010-01-01

    Background Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Results Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. Conclusions We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system. PMID:20492695

  17. Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples.

    PubMed

    Mehta, Rohini; Birerdinc, Aybike; Hossain, Noreen; Afendy, Arian; Chandhoke, Vikas; Younossi, Zobair; Baranova, Ancha

    2010-05-21

    Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system.

  18. DNA analysis using an integrated microchip for multiplex PCR amplification and electrophoresis for reference samples.

    PubMed

    Le Roux, Delphine; Root, Brian E; Reedy, Carmen R; Hickey, Jeffrey A; Scott, Orion N; Bienvenue, Joan M; Landers, James P; Chassagne, Luc; de Mazancourt, Philippe

    2014-08-19

    A system that automatically performs the PCR amplification and microchip electrophoretic (ME) separation for rapid forensic short tandem repeat (STR) forensic profiling in a single disposable plastic chip is demonstrated. The microchip subassays were optimized to deliver results comparable to conventional benchtop methods. The microchip process was accomplished in sub-90 min compared with >2.5 h for the conventional approach. An infrared laser with a noncontact temperature sensing system was optimized for a 45 min PCR compared with the conventional 90 min amplification time. The separation conditions were optimized using LPA-co-dihexylacrylamide block copolymers specifically designed for microchip separations to achieve accurate DNA size calling in an effective length of 7 cm in a plastic microchip. This effective separation length is less than half of other reports for integrated STR analysis and allows a compact, inexpensive microchip design. This separation quality was maintained when integrated with microchip PCR. Thirty samples were analyzed conventionally and then compared with data generated by the microfluidic chip system. The microfluidic system allele calling was 100% concordant with the conventional process. This study also investigated allelic ladder consistency over time. The PCR-ME genetic profiles were analyzed using binning palettes generated from two sets of allelic ladders run three and six months apart. Using these binning palettes, no allele calling errors were detected in the 30 samples demonstrating that a microfluidic platform can be highly consistent over long periods of time.

  19. Comparison of CTAC and prone imaging for the detection of coronary artery disease using CZT SPECT.

    PubMed

    Ito, Shimpei; Endo, Akihiro; Okada, Taiji; Nakamura, Taku; Sugamori, Takashi; Takahashi, Nobuyuki; Yoshitomi, Hiroyuki; Tanabe, Kazuaki

    2017-10-01

    Cadmium-zinc-telluride (CZT) cameras have improved the evaluation of patients with chest pain. However, inferior/inferolateral attenuation artifacts similar to those seen with conventional Anger cameras persist. We added prone acquisitions and CT attenuation correction (CTAC) to the standard supine image acquisition and analyzed the resulting examinations. Seventy-two patients referred for invasive coronary angiography (CAG), and who also underwent rest/stress myocardial perfusion imaging (MPI) on a CZT camera in the supine and prone positions plus CTAC imaging, to examine known or suspected CAD between April 2013 and March 2014 were included. A sixteen-slice CT scan acquired on a SPECT/CT scanner between rest and stress imaging provided data for iterative reconstruction. Sensitivity, specificity, accuracy, and positive and negative likelihood ratios (LRs) were calculated to compare MPI with CAG on a per-patient basis. Per-patient sensitivity, specificity, and accuracy of supine images to predict coronary abnormalities on CAG were 35% [95% confidence interval (CI) 19-52], 86% (95% CI 80-92), and 74% (95% CI 66-82); those of prone imaging were 65% (95% CI 45-81), 82% (95% CI 76-87), and 78% (95% CI 68-85); and those of CTAC were 59% (95% CI 41-71), 93% (95% CI 87-97), and 85% (95% CI 76-91), respectively. Prone acquisition and CTAC images improve the ability to assess the inferior/inferolateral area.

  20. Impaired Gal-9 Dysregulates the PBMC-Induced Th1/Th2 Imbalance in Abortion-Prone Matings

    PubMed Central

    He, Mengzhou; Jiang, Ming; Zhou, Yuan; Li, Fanfan; Yang, Meitao; Fan, Yao; Xie, Yin; Beejadhursing, Rajluxmee; Feng, Ling

    2018-01-01

    Recurrent miscarriage is defined as the loss of 3 or more consecutive pregnancies; however, the underlying immunologic mechanisms that trigger pregnancy loss remain largely unelucidated. Galectin-9 (Gal-9) may modulate a variety of biologic functions and play an important role in Th1/Th2 immune deviation. To analyze the mechanism of Gal-9 in abortion, we used the classical abortion-prone mouse model (DBA/2-mated CBA/J mice) to detect the expression of Gal-9 at the maternal-fetal interface. We also mimicked the immune environment of pregnancy by culturing trophoblast cells with peripheral blood mononuclear cells (PBMCs) to explore how Gal-9 might be involved in the pathogenesis of abortion. We found that the expression levels of Gal-9 in abortion-prone matings were lower than that for controls. Using a coculture system, we detected a Th1 preponderance in the coculture from abortion-prone matings. Furthermore, Gal-9 blockade augmented the imbalance of Th1/Th2 immunity in abortion-prone matings by promoting the secretion of Th1-derived cytokines in coculture, while there was a Th2 preponderance when we administered recombinant Gal-9. In conclusion, our results suggest that the Gal-9 signal is important for the regulation of PBMC function toward a Th2 bias at the maternal-fetal interface, which is beneficial for the maintenance of a normal pregnancy. PMID:29651447