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Sample records for error prone pcr

  1. Error-prone PCR and effective generation of gene variant libraries for directed evolution.

    PubMed

    Copp, Janine N; Hanson-Manful, Paulina; Ackerley, David F; Patrick, Wayne M

    2014-01-01

    Any single-enzyme directed evolution strategy has two fundamental requirements: the need to efficiently introduce variation into a gene of interest and the need to create an effective library from those variants. Generation of a maximally diverse gene library is particularly important when employing nontargeted mutagenesis strategies such as error-prone PCR (epPCR), which seek to explore very large areas of sequence space. Here we present comprehensive protocols and tips for using epPCR to generate gene variants that exhibit a relatively balanced spectrum of mutations and for capturing as much diversity as possible through effective cloning of those variants. The detailed library preparation methods that we describe are generally applicable to any directed evolution strategy that uses restriction enzymes to clone gene variants into an expression plasmid. PMID:25055767

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

    PubMed

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

    2011-07-01

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

  3. Error-prone PCR of Vitreoscilla hemoglobin (VHb) to support the growth of microaerobic Escherichia coli.

    PubMed

    Andersson, C I; Holmberg, N; Farrés, J; Bailey, J E; Bülow, L; Kallio, P T

    2000-11-20

    Expression of the gene encoding bacterial hemoglobin (VHb) from Vitreoscilla has been previously used to improve recombinant cell growth and enhance product formation under microaerobic conditions. It is very likely that the properties of VHb are not optimized for foreign hosts; therefore, we used error-prone PCR to generate a number of randomly mutated vhb genes to be expressed and studied in Escherichia coli. In addition, the mutated VHb proteins also contained an extension of eight residues (MTMITPSF) at the amino terminus. VHb mutants were screened for improved growth properties under microaerobic conditions and 15 clones expressing mutated hemoglobin protein were selected for further characterization and cultivated in a microaerobic bioreactor to analyze the physiological effects of novel VHb proteins on cell growth. The expression of four VHb mutants, carried by pVM20, pVM50, pVM104, and pVM134, were able to enhance microaerobic growth of E. coli by approximately 22%, 155%, 50%, and 90%, respectively, with a concomitant decrease of acetate excretion into the culture medium. The vhb gene in pVM20 contains two mutations substituting residues Glu19(A17) and Glu137(H23) to Gly. pVM50 expresses a VHb protein carrying two mutations: His36(C1) to Arg36 and Gln66(E20) to Arg66. pVM104 and pVM134 express VHb proteins carrying the mutations Ala56(E10) to Gly and Ile24(B5) to Thr, respectively. Our experiments also indicate that the positive effects elicited by mutant VHb-expression from pVM20 and pVM50 are linked to the peptide tail. Removal of the N-terminal sequence reduced cell growth approximately 23% and 53%, respectively, relative to wild-type controls. These results clearly demonstrate that it is possible to obtain mutated VHb proteins with improved characteristics for improving microaerobic growth of E. coli by using combined mutation techniques, addition of a peptide tail, and random error-prone PCR. PMID:11005927

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

    PubMed Central

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

    2015-01-01

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

  5. Stepwise error-prone PCR and DNA shuffling changed the pH activity range and product specificity of the cyclodextrin glucanotransferase from an alkaliphilic Bacillus sp.

    PubMed Central

    Melzer, Susanne; Sonnendecker, Christian; Föllner, Christina; Zimmermann, Wolfgang

    2015-01-01

    Cyclodextrin glucanotransferase (EC 2.4.1.19) from the alkaliphilic Bacillus sp. G-825-6 converts starch mainly to ?-cyclodextrin (CD8). A combination of error-prone PCR and DNA shuffling was used to obtain variants of this enzyme with higher product specificity for CD8 and a broad pH activity range. The variant S54 with seven amino acid substitutions showed a 1.2-fold increase in CD8-synthesizing activity and the product ratio of CD7:CD8 was shifted to 1:7 compared to 1:3 of the wild-type enzyme. Nine amino acid substitutions of the cyclodextrin glucanotransferase were performed to generate the variant S35 active in a pH range 4.0–10.0. Compared to the wild-type enzyme which is inactive below pH 6.0, S35 retained 70% of its CD8-synthesizing activity at pH 4.0. PMID:26155461

  6. 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 ?3, ?4, ?5, ?6, ?F. Increased local flexibility of variant F19L explains molecular basis of its psychrophilic nature. PMID:26456196

  7. Optimal Audio Transmission over Error-Prone Wireless Links

    E-print Network

    Yousefi'zadeh, Homayoun

    for transmitting high quality audio sequences over error-prone wireless links. Our framework introduces apparatus due to an ever increasing de- mand. In that context, delivering high quality audio over error1 Optimal Audio Transmission over Error-Prone Wireless Links Ala' Khalifeh, Student Member IEEE

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

    PubMed Central

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

    2015-01-01

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

  9. Mutagenesis of Neisseria gonorrhoeae: absence of error-prone repair

    SciTech Connect

    Campbell, L.A.; Yasbin, R.E.

    1984-10-01

    The lethal and mutagenic effects of various mutagens on Neisseria gonorrhoeae were investigated. Lethality studies demonstrated that N. gonorrhoeae was relatively sensitive to ethyl methanesulfonate, UV light, and methyl methanesulfonate. Although N. gonorrhoeae was readily mutated by ethyl methanesulfonate and N-methyl-n'-nitro-N-nitrosoguanidine for the three genetic markers assayed, no increase in the mutation frequency was observed for any of the selective markers after UV irradiation of methyl methanesulfonate treatment. These results suggest than N. gonorrhoeae lacks an error-prone repair mechanism.

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

    PubMed

    Rodgers, Kasey; McVey, Mitch

    2016-01-01

    Preserving the integrity of the DNA double helix is crucial for the maintenance of genomic stability. Therefore, DNA double-strand breaks represent a serious threat to cells. In this review, we describe the two major strategies used to repair double strand breaks: non-homologous end joining and homologous recombination, emphasizing the mutagenic aspects of each. We focus on emerging evidence that homologous recombination, long thought to be an error-free repair process, can in fact be highly mutagenic, particularly in contexts requiring large amounts of DNA synthesis. Recent investigations have begun to illuminate the molecular mechanisms by which error-prone double-strand break repair can create major genomic changes, such as translocations and complex chromosome rearrangements. We highlight these studies and discuss proposed models that may explain some of the more extreme genetic changes observed in human cancers and congenital disorders. J. Cell. Physiol. 230: 15-24, 2016. © 2015 Wiley Periodicals, Inc. PMID:26033759

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

    NASA Astrophysics Data System (ADS)

    Nagy, George

    2013-01-01

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

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

    PubMed Central

    Pal, Doyel; Chen, Tingting; Khethavath, Praveen

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Yasbin, R. E.

    1981-06-01

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

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

    PubMed

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

    2012-08-01

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

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

    ERIC Educational Resources Information Center

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

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

  17. 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

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

    SciTech Connect

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

    2008-09-01

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

  19. 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…

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    2012-10-25

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2014-06-27

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

  5. Error-prone Replication Bypass of the Primary Aflatoxin B1 DNA Adduct, AFB1-N7-Gua*

    PubMed Central

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

    2014-01-01

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

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

    E-print Network

    Fox, George

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Kirouac, Kevin N.; Ling, Hong

    2009-06-30

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

  9. Unique Plasmids Generated via pUC Replicon Mutagenesis in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426.

    PubMed

    Kobayashi, Jyumpei; Tanabiki, Misaki; Doi, Shohei; Kondo, Akihiko; Ohshiro, Takashi; Suzuki, Hirokazu

    2015-11-01

    The plasmid pGKE75-catA138T, which comprises pUC18 and the catA138T gene encoding thermostable chloramphenicol acetyltransferase with an A138T amino acid replacement (CATA138T), serves as an Escherichia coli-Geobacillus kaustophilus shuttle plasmid that confers moderate chloramphenicol resistance on G. kaustophilus HTA426. The present study examined the thermoadaptation-directed mutagenesis of pGKE75-catA138T in an error-prone thermophile, generating the mutant plasmid pGKE75(??)-catA138T responsible for substantial chloramphenicol resistance at 65°C. pGKE75(??)-catA138T contained no mutation in the catA138T gene but had two mutations in the pUC replicon, even though the replicon has no apparent role in G. kaustophilus. Biochemical characterization suggested that the efficient chloramphenicol resistance conferred by pGKE75(??)-catA138T is attributable to increases in intracellular CATA138T and acetyl-coenzyme A following a decrease in incomplete forms of pGKE75(??)-catA138T. The decrease in incomplete plasmids may be due to optimization of plasmid replication by RNA species transcribed from the mutant pUC replicon, which were actually produced in G. kaustophilus. It is noteworthy that G. kaustophilus was transformed with pGKE75(??)-catA138T using chloramphenicol selection at 60°C. In addition, a pUC18 derivative with the two mutations propagated in E. coli at a high copy number independently of the culture temperature and high plasmid stability. Since these properties have not been observed in known plasmids, the outcomes extend the genetic toolboxes for G. kaustophilus and E. coli. PMID:26319877

  10. 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

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

    PubMed

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

    2008-09-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  13. 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?prone (NOP) age-matched infants. No significant differences in APC activation or function were observed. Expression of various TLRs, intracellular signaling molecules and downstream cytokines was also not found to be significantly different between sOP and NOP infants. Higher numbers of APCs in sOP infants suggest the possibility of a persistent mucosal inflammatory status. Transcriptional and cytokine profiles of PBMCs among sOP infants suggest their systemic innate responses are not different compared to NOP infants. PMID:26566651

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

    PubMed

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

    2014-08-19

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

  15. Error-prone translesion synthesis mediates acquired chemoresistance

    E-print Network

    Xie, Kun

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

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

    MedlinePLUS

    ... is misinterpreted as “K”) HCT hydrocortisone Mistaken as hydrochlorothiazide Use complete drug name Use complete drug name ... of a drug Use complete drug name HCTZ hydrochlorothiazide Mistaken as hydrocortisone (seen as HCT250 mg) Use ...

  17. 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,…

  18. Vegetation fire proneness in Europe

    NASA Astrophysics Data System (ADS)

    Pereira, Mário; Aranha, José; Amraoui, Malik

    2015-04-01

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

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

    PubMed

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

    2016-01-01

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

  20. PCR thermocycler

    DOEpatents

    Benett, William J.; Richards, James B.

    2005-05-17

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

  1. PCR thermocycler

    DOEpatents

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

    2003-01-01

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

  2. Ethnic and gender differences in boredom proneness

    SciTech Connect

    Gibson, G.S.; Morales,

    1996-02-01

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

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

    SciTech Connect

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

    2012-04-01

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

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

    E-print Network

    Abowd, Gregory D.

    the benefit of their context (Schomaker, 1994). Human accuracy increases to 88% for cursive handwriting of system designers is to try to eliminate them, for example by improving recogni­ tion accuracy (humans) can have a recogni­ tion accuracy as low as 54% when looking at word frag­ ments without

  5. Interfraction and Intrafraction Setup Variability for Prone Breast Radiation Therapy

    SciTech Connect

    Mitchell, James; Formenti, Silvia C.; DeWyngaert, J. Keith

    2010-04-15

    Purpose: To report the interfraction and intrafraction setup variation for prone breast radiotherapy and to determine an appropriate clinical tumor volume (CTV) to planning target volume (PTV) margin to account for motion and positional uncertainties. Methods and Materials: Ten consecutive patients were prospectively enrolled in a protocol of accelerated, hypofractionated prone breast irradiation. Portal images were acquired using an electronic portal imaging device in cine mode. Interfraction setup error was determined by comparing the first image from each fraction with the digitally reconstructed radiograph. The intrafraction motion was determined by evaluating every image acquired during each fraction and measuring the maximum displacement of an external fiducial and the breast surface. Mean values and 95% confidence intervals (CI) were calculated. Based on these results, a CTV to PTV expansion was derived using the equation M = 2.5SIGMA{sub tot} + 0.7sigma{sub tot.} Results: The mean interfraction setup variability for the fiducial was 0.08 cm (CI: 0.02-0.14) in the anterior to posterior (AP) direction and -0.04 cm (CI: -0.07-0.00) in the superior to inferior (SI) direction. The mean interfraction variability of the breast surface was -0.14 cm (CI: -0.24 to -0.04) in the AP direction. The mean intrafraction displacements of the fiducial and the breast surface were 0.13 cm (CI: 0.12-0.15) and 0.15 cm (CI: 0.14-0.17), respectively. Using the systematic and random errors for the external fiducial, the calculated CTV to PTV expansion was 1.4 cm. Conclusions: Acceptable interfraction and intrafraction variability were demonstrated. The findings resulted in a CTV to PTV expansion of 1.4 cm.

  6. Psychosis-proneness and socially relevant reasoning.

    PubMed

    Young, Eliane; Mason, Oliver

    2007-03-30

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

  7. Supine versus prone position for percutaneous nephrolithotomy.

    PubMed

    Salvadó, J A; Mendez, C E

    2015-12-01

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

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

    PubMed

    Concha L, Luciana; Durruty A, Pilar; García de Los Ríos A, Manuel

    2015-09-01

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

  11. Extralevator abdominoperineal resection in the prone position.

    PubMed

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

    2014-03-01

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

  12. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  13. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  14. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.23 Planning considerations for mudslide (i.e., mudflow)-prone areas. The planning...

  15. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.23 Planning considerations for mudslide (i.e., mudflow)-prone areas. The planning...

  16. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  17. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

  18. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  19. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  20. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

  1. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...AND USE Additional Considerations in Managing Flood-Prone, Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.23 Planning considerations for mudslide (i.e., mudflow)-prone areas. The planning...

  2. 44 CFR 60.22 - Planning considerations for flood-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  3. Psychosocial characteristics of coronary prone personality.

    PubMed

    Marquand, C J; Hughes, R N

    1982-06-01

    In a study of the psychosocial characteristics of the coronary prone personality, a semi-structured questionnaire and Type A/B, anxiety and depression scales were sent to residents of Rolleston registered on the Rakaia electoral district roll. Amongst the 256 respondents who replied there were no significant differences between proportions of Type A and B individuals found in various age, sex, smoking, drinking, CHD family history, exercise and recent stress categories. However, Type A men (but not women) who had experienced a stressful crisis during the preceding 12 months obtained higher anxiety scores than nonstressed men. Recently stressed Type B women (but not men) obtained higher anxiety scores than nonstressed women. Likewise, recently stressed women (but not men) obtained higher depression scores than nonstressed women. There was also some evidence of less frequent alcohol consumption in respondents from families in which a parent or sibling had suffered from CHD. PMID:6955656

  4. Medication Errors

    MedlinePLUS

    ... broader product safety issues. Relevant FDA Drug Safety Communications for Drug Products Associated with Medication Errors FDA Drug Safety Communication: FDA cautions about dosing errors when switching between ...

  5. PCR und Real-Time PCR

    NASA Astrophysics Data System (ADS)

    Konrad, Regina; Busch, Ulrich

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

  6. FLOOD-PLAIN DELINEATION IN ICE JAM PRONE REGIONS

    E-print Network

    Vogel, Richard M.

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

  7. Piezoelectric control of structures prone to instabilities

    NASA Astrophysics Data System (ADS)

    Kim, Sunjung

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

  8. Digital PCR and Quantitation

    E-print Network

    PCR · Calibrant concentration is independently determined (e.g. UV spectrophotometer) · Prepare a dilution curve measurement if the calibrant is inaccurate the measurement will be inaccurate · Spectrophotometer measures

  9. Refractive Errors

    MedlinePLUS

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

  10. Error Gravity and Error Hierarchies.

    ERIC Educational Resources Information Center

    McCretton, Elena; Rider, Nigel

    1993-01-01

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

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

    E-print Network

    Fox, George

    PCR detection of nearly any dengue virus strain using a highly sensitive primer `cocktail' Charul to target effectively. This problem is espe- cially pronounced with the mutation-prone RNA viruses. Dengue an estimated 50 million people annually [1]. Dengue hemorrhagic fever is a severe form of dengue fever

  12. The Role of a Prone Setup in Breast Radiation Therapy

    PubMed Central

    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. PMID:22655240

  13. Error analysis

    SciTech Connect

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

    1981-01-01

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

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

    SciTech Connect

    Louisiana State University; Balman, Mehmet; Kosar, Tevfik

    2010-10-27

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  16. dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ? variants

    PubMed Central

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

    2015-01-01

    Mutator phenotypes create genetic diversity that fuels tumor evolution. DNA polymerase (Pol) ? mediates leading strand DNA replication. Proofreading defects in this enzyme drive a number of human malignancies. Here, using budding yeast, we show that mutator variants of Pol ? depend on damage uninducible (Dun)1, an S-phase checkpoint kinase that maintains dNTP levels during a normal cell cycle and up-regulates dNTP synthesis upon checkpoint activation. Deletion of DUN1 (dun1?) suppresses the mutator phenotype of pol2-4 (encoding Pol ? proofreading deficiency) and is synthetically lethal with pol2-M644G (encoding altered Pol ? base selectivity). Although pol2-4 cells cycle normally, pol2-M644G cells progress slowly through S-phase. The pol2-M644G cells tolerate deletions of mediator of the replication checkpoint (MRC) 1 (mrc1?) and radiation sensitive (Rad) 9 (rad9?), which encode mediators of checkpoint responses to replication stress and DNA damage, respectively. The pol2-M644G mutator phenotype is partially suppressed by mrc1? but not rad9?; neither deletion suppresses the pol2-4 mutator phenotype. Thus, checkpoint activation augments the Dun1 effect on replication fidelity but is not required for it. Deletions of genes encoding key Dun1 targets that negatively regulate dNTP synthesis, suppress the dun1? pol2-M644G synthetic lethality and restore the mutator phenotype of pol2-4 in dun1? cells. DUN1 pol2-M644G cells have constitutively high dNTP levels, consistent with checkpoint activation. In contrast, pol2-4 and POL2 cells have similar dNTP levels, which decline in the absence of Dun1 and rise in the absence of the negative regulators of dNTP synthesis. Thus, dNTP pool levels correlate with Pol ? mutator severity, suggesting that treatments targeting dNTP pools could modulate mutator phenotypes for therapy. PMID:25827226

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

    PubMed Central

    Zhu, Catherine; Hsu, Ellen

    2010-01-01

    Sharks are representatives of the earliest vertebrates that possess an immune system utilizing V(D)J recombination to generate antigen receptors. Their antibody repertoire diversity is based in part on a somatic hypermutation process that introduces adjacent nucleotide substitutions of 2-5 bp. We have isolated mutant nonfunctional immunoglobulin rearrangements and intronic flank sequences in order to characterize the non-selected, intrinsic properties of this phenomenon; changes unique to shark were observed. Duplications and deletions were associated with N additions, suggesting participation of a DNA polymerase with some degree of template independence during the repair of DNA breaks initiated by activation-induced cytidine deaminase (AID). Other mutations were consistent with some in vitro activities of mammalian translesion DNA polymerase eta: tandem base substitutions, strand slippage, small insertions/deletions. The nature of substitution patterns shows that DNA lesions at shark immunoglobulin genes recruit DNA repair factors with a species-specific repertoire of activities. We speculate that the tandem mutations are introduced by direct sequential misinsertions and that, in shark B cells, the mispairs tend to be extended rather than proofread. Despite extensive changes undergone by some mutants, the physical range of mutational activity remained restricted to VDJ and within the first 2 kb portion of the 6.8 kb J-C intron, perhaps a self-regulating aspect of AID action that is conserved in evolution. PMID:20921520

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  20. Medication Errors

    MedlinePLUS

    Medicines cure infectious diseases, prevent problems from chronic diseases, and ease pain. But medicines can also cause harmful reactions if not used ... You can help prevent errors by Knowing your medicines. Keep a list of the names of your ...

  1. Denoising PCR-amplified metagenome data

    PubMed Central

    2012-01-01

    Background PCR amplification and high-throughput sequencing theoretically enable the characterization of the finest-scale diversity in natural microbial and viral populations, but each of these methods introduces random errors that are difficult to distinguish from genuine biological diversity. Several approaches have been proposed to denoise these data but lack either speed or accuracy. Results We introduce a new denoising algorithm that we call DADA (Divisive Amplicon Denoising Algorithm). Without training data, DADA infers both the sample genotypes and error parameters that produced a metagenome data set. We demonstrate performance on control data sequenced on Roche’s 454 platform, and compare the results to the most accurate denoising software currently available, AmpliconNoise. Conclusions DADA is more accurate and over an order of magnitude faster than AmpliconNoise. It eliminates the need for training data to establish error parameters, fully utilizes sequence-abundance information, and enables inclusion of context-dependent PCR error rates. It should be readily extensible to other sequencing platforms such as Illumina. PMID:23113967

  2. Apta-PCR.

    PubMed

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

    2016-01-01

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

  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. PMID:26147196

  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. Pathogenesis of A-beta+ ketosis-prone diabetes

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. 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

  7. 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…

  8. QUALITY ASSURANCE FOR PCR

    EPA Science Inventory

    The U.S. Environmental Protection Agency (EPA) held a workshop in January 2003 on the detection of viruses in water using polymerase chain reaction (PCR)-based methods. Speakers were asked to address a series of specific questions, including whether a single standard method coul...

  9. QUALITY CONTROLS FOR PCR

    EPA Science Inventory

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

  10. [PCR in forensic medicine].

    PubMed

    Coquoz, R

    1994-05-17

    PCR has brought important progress to forensic medicine. It has provided access to various effective, rapid and simple analytic techniques. It has distinctly increased the range of analyzable samples and comparably improved chances to identify a criminal. This had consequences for laboratories as well as police departments and even physicians that occasionally cooperate with legal agencies. PMID:7911590

  11. Understanding and Confronting Our Mistakes: The Epidemiology of Error in Radiology and Strategies for Error Reduction.

    PubMed

    Bruno, Michael A; Walker, Eric A; Abujudeh, Hani H

    2015-10-01

    Arriving at a medical diagnosis is a highly complex process that is extremely error prone. Missed or delayed diagnoses often lead to patient harm and missed opportunities for treatment. Since medical imaging is a major contributor to the overall diagnostic process, it is also a major potential source of diagnostic error. Although some diagnoses may be missed because of the technical or physical limitations of the imaging modality, including image resolution, intrinsic or extrinsic contrast, and signal-to-noise ratio, most missed radiologic diagnoses are attributable to image interpretation errors by radiologists. Radiologic interpretation cannot be mechanized or automated; it is a human enterprise based on complex psychophysiologic and cognitive processes and is itself subject to a wide variety of error types, including perceptual errors (those in which an important abnormality is simply not seen on the images) and cognitive errors (those in which the abnormality is visually detected but the meaning or importance of the finding is not correctly understood or appreciated). The overall prevalence of radiologists' errors in practice does not appear to have changed since it was first estimated in the 1960s. The authors review the epidemiology of errors in diagnostic radiology, including a recently proposed taxonomy of radiologists' errors, as well as research findings, in an attempt to elucidate possible underlying causes of these errors. The authors also propose strategies for error reduction in radiology. On the basis of current understanding, specific suggestions are offered as to how radiologists can improve their performance in practice. (©)RSNA, 2015. PMID:26466178

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

    PubMed Central

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

    2014-01-01

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

  13. MAMMALIAN DNA IN PCR REAGENTS

    EPA Science Inventory

    Ancient DNA analysis is becoming widespread. These studies use polymerase chain reaction (PCR) to amplify minute quantities of heavily damaged template. Unusual steps are taken to achieve the sensitivity necessary to detect ancient DNA, including high- cycle PCR amplification t...

  14. Enhancing disaster management by mapping disaster proneness and preparedness.

    PubMed

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

    2012-07-01

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

  15. 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

  16. An evaluation of four CT–MRI co-registration techniques for radiotherapy treatment planning of prone rectal cancer patients

    PubMed Central

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

    2012-01-01

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

  17. Hemispheric asymmetries in the activation and monitoring of memory errors.

    PubMed

    Giammattei, Jeannette; Arndt, Jason

    2012-10-01

    Previous research on the lateralization of memory errors suggests that the right hemisphere's tendency to produce more memory errors than the left hemisphere reflects hemispheric differences in semantic activation. However, all prior research that has examined the lateralization of memory errors has used self-paced recognition judgments. Because activation occurs early in memory retrieval, with more time to make a decision, other memory processes, like strategic monitoring processes, may affect memory errors. By manipulating the time subjects were given to make memory decisions, this study separated the influence of automatic memory processes (activation) from strategic memory processes (monitoring) on the production of false memories. The results indicated that when retrieval was fast, the right hemisphere produced more memory errors than the left hemisphere. However, when retrieval was slow, the left hemisphere's error-proneness increased compared to the fast retrieval condition, while the right hemisphere's error-proneness remained the same. These results suggest that the right hemisphere's errors are largely due to activation, while the left hemisphere's errors are influenced by both activation and monitoring. PMID:22626917

  18. Hemispheric Asymmetries in the Activation and Monitoring of Memory Errors

    PubMed Central

    Giammattei, Jeannette; Arndt, Jason

    2012-01-01

    Previous research on the lateralization of memory errors suggests that the right hemisphere’s tendency to produce more memory errors than the left hemisphere reflects hemispheric differences in semantic activation. However, all prior research that has examined the lateralization of memory errors has used self-paced recognition judgments. Because activation occurs early in memory retrieval, with more time to make a decision, other memory processes, like strategic monitoring processes, may affect memory errors. By manipulating the time subjects were given to make memory decisions, this study separated the influence of automatic memory processes (activation) from strategic memory processes (monitoring) on the production of false memories. The results indicated that when retrieval was fast, the right hemisphere produced more memory errors than the left hemisphere. However, when retrieval was slow, the left hemisphere’s error-proneness increased compared to the fast retrieval condition, while the right hemisphere’s error-proneness remained the same. These results suggest that the right hemisphere’s errors are largely due to activation, while the left hemisphere’s errors are influenced by both activation and monitoring. PMID:22626917

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

    PubMed

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

    2015-01-01

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

  20. Hare's Error

    E-print Network

    Gale, Dawn M.

    stream_size 32743 stream_content_type text/plain stream_name auslegung.v27.n01.001-015.pdf.txt stream_source_info auslegung.v27.n01.001-015.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 Hare...'s Error Dawn M. Gale University of Kansas A large portion of the work of moral philosopher R. M. Hare presents his attempt to ground normative ethics on mctaethics— the logic of moral reasoning and the meanings of the moral words. According to Hare...

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

    DOE PAGESBeta

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

    2014-01-01

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

  2. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Planning considerations for..., Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning process for communities identified under part 65 of...

  3. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Planning considerations for..., Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning process for communities identified under part 65 of...

  4. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 44 Emergency Management and Assistance 1 2014-10-01 2014-10-01 false Planning considerations for..., Mudslide (i.e., Mudflow)-Prone and Flood-Related Erosion-Prone Areas § 60.24 Planning considerations for flood-related erosion-prone areas. The planning process for communities identified under part 65 of...

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

    SciTech Connect

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

    1995-08-28

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

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

    PubMed

    Kebschull, Justus M; Zador, Anthony M

    2015-12-01

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

  7. 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

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

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

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

    2014-07-15

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

  10. Boredom proneness and emotion regulation predict emotional eating.

    PubMed

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

    2015-05-01

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

  11. Phacovitrectomy without prone posture for full thickness macular holes

    PubMed Central

    Simcock, P.; Scalia, S.

    2001-01-01

    AIMS—To investigate the role of phacovitrectomy surgery without prone posture for stage 2 and 3 macular holes.?METHODS—A pilot study was performed on 20 patients (20 eyes) having phacoemulsification lens removal and vitrectomy surgery with 20% C2F6 tamponade. Patients were advised to avoid lying on their backs for 10 days following surgery but no other posturing instructions were given. Closure rates and improvement in visual acuity were compared with a group of historical controls in whom phacovitrectomy with gas tamponade and face down posturing was performed.?RESULTS—Anatomical hole closure was noted in 18 of the 20 eyes (90%). 19 eyes (95%) showed an improvement of at least 0.3 logMAR units. This compares favourably with the postured group in which anatomical hole closure was noted in 11 of 13 eyes (85%) and nine of 13 eyes (69%) showed an improvement of at least 0.3 logMAR units.?CONCLUSION—Combined surgery facilitates the use of a large gas bubble. Sufficient tamponade of the hole occurs for closure without prone posturing. Combined surgery prevents patients posturing and returning for cataract surgery.?? PMID:11673297

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

    PubMed Central

    Neumann, Peter M.

    2008-01-01

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

  13. Errors in multidetector row computed tomography.

    PubMed

    Mazzei, M A; Volterrani, L

    2015-09-01

    Multidetector row computed tomography (MDCT) represents the technique of choice for the majority of pathologies today and is responsible for the majority of diagnoses. However, despite the low number of studies dedicated to errors in MDCT, CT reporting seems especially prone to generating errors and errors are an inevitable part of MDCT practice. Most of these arise during image interpretation but, differently from other radiological techniques, the awareness of radiologists regarding technical CT aspects and pathologies substantially contribute in generating errors, in particular because CT technology expands rapidly and radiologists do not routinely receive specific and appropriate training for its use and because CT examinations are not the same for each patient and each pathology and the choice of the most appropriate CT examination (including the dose exposure to the patient) presumes a very large awareness from radiologists. This review is aimed at increasing awareness regarding the type of errors in MDCT and in particular to also highlight technical and procedural errors. PMID:26108153

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-07-25

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

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

    PubMed

    Maier, Martin E; Steinhauser, Marco

    2016-01-15

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

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

    SciTech Connect

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

    1998-12-01

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

  18. 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…

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  20. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 2010-10-01 false Planning considerations for flood-related...Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional...Erosion-Prone Areas § 60.24 Planning considerations for flood-related...erosion-prone areas. The planning process for communities...

  1. 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…

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

    ERIC Educational Resources Information Center

    Gerdes, Eugenia Proctor; Sidler, John P.

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

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

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide...

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

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide...

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide...

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide...

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

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... flood-prone areas. 60.22 Section 60.22 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Additional Considerations in Managing Flood-Prone, Mudslide...

  8. 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…

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

    E-print Network

    Jacob, Eshel Ben

    Index Cohesive Force Analysis Reveals That the US Market Became Prone to Systemic Collapses Since/Principal Findings: The S&P500 dynamics during 4/1999­4/2010 is investigated in terms of the index cohesive force, Gur-Gershgoren G, et al. (2011) Index Cohesive Force Analysis Reveals That the US Market Became Prone

  10. Highly reproducible absolute quantification of Mycobacterium tuberculosis complex by digital PCR.

    PubMed

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

    2015-04-01

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

  11. Development of Korean Smartphone Addiction Proneness Scale for Youth

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  13. Male predominance in ketosis-prone diabetes mellitus

    PubMed Central

    WANG, XIAOHAO; TAN, HUIWEN

    2015-01-01

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

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

    PubMed

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

    2015-12-01

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

  15. Shame proneness in symptom dimensions of obsessive-compulsive disorder.

    PubMed

    Wetterneck, Chad T; Singh, Sonia; Hart, John

    2014-01-01

    Although one study has noted that shame may play a significant role in anxiety disorders (Fergus, Valentiner, McGratch, & Jencius, 2010), the literature does not address the appearance of shame within specific dimensions of obsessive-compulsive disorder (OCD). In this study, shame is assessed within four common symptom dimensions of OCD: contamination, harm, unacceptable thoughts, and symmetry. The authors hypothesized that shame would be significantly related to unacceptable thoughts and harm, but not other dimensions. Ninety-one individuals with OCD completed the Dimensional Obsessive-Compulsive Scale (measuring severity of OCD symptom dimensions) and the Test of Self-Conscious Affect (assessing shame proneness). Results indicated a positive significant relationship between shame and harm, but not unacceptable thoughts. Additionally, a significant correlation was found between shame and symmetry. This is possibly due to a relationship between perfectionism and symmetry (Wu & Cortesi, 2009). These findings suggest that shame is related to certain dimensions of OCD and may deserve consideration in relation to treatment. PMID:24870849

  16. 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.

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

    ERIC Educational Resources Information Center

    Shang, Yi

    2012-01-01

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

  18. 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.

  19. A Comprehensive Review of Prone Position in ARDS.

    PubMed

    Kallet, Richard H

    2015-11-01

    Prone position (PP) has been used since the 1970s to treat severe hypoxemia in patients with ARDS because of its effectiveness at improving gas exchange. Compared with the supine position (SP), placing patients in PP effects a more even tidal volume distribution, in part, by reversing the vertical pleural pressure gradient, which becomes more negative in the dorsal regions. PP also improves resting lung volume in the dorsocaudal regions by reducing the superimposed pressure of both the heart and the abdomen. In contrast, pulmonary perfusion remains preferentially distributed to the dorsal lung regions, thus improving overall alveolar ventilation/perfusion relationships. Moreover, the larger tissue mass suspended from a wider dorsal chest wall effects a more homogeneous distribution of pleural pressures throughout the lung that reduces abnormal strain and stress development. This is believed to ameliorate the severity or development of ventilator-induced lung injury and may partly explain why PP reduces mortality in severe ARDS. Over 40 years of clinical trials have consistently reported improved oxygenation in approximately 70% of subjects with ARDS. Early initiation of PP is more likely to improve oxygenation than initiation during the subacute phase. Maximal oxygenation improvement occurs over a wide time frame ranging from several hours to several days. Meta-analyses of randomized controlled trials suggest that PP provides a survival advantage only in patients with relatively severe ARDS (PaO2 /FIO2 <150 mm Hg). Moreover, survival is enhanced when patients are managed with a smaller tidal volume (?8 mL/kg), higher PEEP (10-13 cm H2O), and longer duration of PP sessions (>10-12 h/session). Combining adjunctive therapies (high PEEP, recruitment maneuvers, and inhaled vasodilators) with PP has an additive effect in improving oxygenation and may be particularly helpful in stabilizing gas exchange in very severe ARDS. PMID:26493592

  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. 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

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

    SciTech Connect

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

    2009-09-01

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

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

    PubMed

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

    2014-12-01

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

  4. Mapping radon-prone areas using ?-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 ?-radiation and geological maps. The advantage of the proposed approach is that it lessens the requirement for a high density of measurements by making use of commonly available information. It can be applied for an initial definition of radon-prone areas in countries committed to introducing a national radon policy or to improving existing radon maps in low population regions. PMID:23803560

  5. Error-prone repair and translesion synthesis III: the activation of UmuD (or less is more).

    PubMed

    Bridges, Bryn A

    2005-08-15

    Following DNA damage to Escherichia coli bacteria, RecA protein is activated by binding to single stranded DNA and cleaves its own gene repressor (LexA protein). Two papers from Graham Walker's laboratory showed that several bacterial genes in addition to RecA are repressed by the LexA repressor and are inducible following DNA damage [C.J. Keyon, G.C. Walker, DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli, in: Proceedings of the National Academy of Sciences of the United States of America 77, 1980, pp. 2819--2823] and predicted that one of them (UmuD) might itself be subject to activation by a further cleavage reaction involving activated RecA protein [K.L. Perry, S.J. Elledge, B.B. Mitchell, L. Marsh, G.C. Walker, umuD,C and mucA,B operans whose products are required for UV light- and chemical-induced mutagenesis: UmuD, MucA, and LexA proteins share homology, in: Proceedings of the National Academy of Sciences of the United States of America 82, 1985, pp. 4331--4335]. The processed form of UmuD, termed UmuD', later proved to be a subunit of DNA polymerase V, a key enzyme involved in translesion synthesis. PMID:15985388

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

    PubMed Central

    Goodman, Myron F.

    2014-01-01

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

  7. De novo DNA synthesis using single molecule PCR

    PubMed Central

    Yehezkel, Tuval Ben; Linshiz, Gregory; Buaron, Hen; Kaplan, Shai; Shabi, Uri; Shapiro, Ehud

    2008-01-01

    The throughput of DNA reading (sequencing) has dramatically increased recently due to the incorporation of in vitro clonal amplification. The throughput of DNA writing (synthesis) is trailing behind, with cloning and sequencing constituting the main bottleneck. To overcome this bottleneck, an in vitro alternative for in vivo DNA cloning must be integrated into DNA synthesis methods. Here we show how a new single molecule PCR (smPCR)-based procedure can be employed as a general substitute to in vivo cloning thereby allowing for the first time in vitro DNA synthesis. We integrated this rapid and high fidelity in vitro procedure into our earlier recursive DNA synthesis and error correction procedure and used it to efficiently construct and error-correct a 1.8-kb DNA molecule from synthetic unpurified oligos completely in vitro. Although we demonstrate incorporating smPCR in a particular method, the approach is general and can be used in principle in conjunction with other DNA synthesis methods as well. PMID:18667587

  8. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  9. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

  10. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  11. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  12. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  13. IEEE TRANSACTIONS ON VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS, VOL. 14, NO. 7, JULY 2006 763 Extraction Error Modeling and Automated Model

    E-print Network

    Veneris, Andreas

    Extraction Error Modeling and Automated Model Debugging in High-Performance Custom Designs Yu-Shen Yang the transistor-level representation. This is a semi-automated process which is error-prone. Once a test model model representations of the pipelines in high-performance designs today. It also develops an automated

  14. Field error lottery

    SciTech Connect

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

    1990-01-01

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

  15. Predicting failure-proneness in an evolving software product line Sandeep Krishnan a,

    E-print Network

    Goseva-Popstojanova, Katerina

    Predicting failure-proneness in an evolving software product line Sandeep Krishnan a, , Chris online 12 December 2012 Keywords: Software product lines Change metrics Reuse Prediction Post been used previously by researchers to study characteristics of product line software. Objective

  16. 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...

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

    MedlinePLUS

    ... html The Physically Active Less Prone to Post-Heart Attack Depression Research underscores link between physical activity and ... 6, 2015 FRIDAY, Nov. 6, 2015 (HealthDay News) -- Heart attack survivors who exercised for years prior to the ...

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

    PubMed

    Padrao, Gonçalo; Mallorquí, Aida; Cucurell, David; Rodriguez-Fornells, Antoni

    2015-12-01

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

  19. Secure Programming Common Errors

    E-print Network

    Roma "La Sapienza", Università di

    Practical demonstrations of some vulnerable Real World web applications (my totally independent security, May 4, 2009 #12;CWE-209: Error Message Information Leak Chatty or debug error messages could disclose

  20. Error correction of microchip synthesized genes using Surveyor nuclease

    PubMed Central

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

    2012-01-01

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

  1. Grammatical Errors Communication Breakdown.

    ERIC Educational Resources Information Center

    Tomiyana, Machiko

    1980-01-01

    Investigates to what extent ESL learners' syntactic errors in written communication cause comprehension breakdown. The variables considered are the omission, insertion, and wrong choice of articles and connectors. Results indicated that errors concerning connectors cause communication breakdown more often than do errors in article usage. (PMJ)

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

    PubMed

    Flannery, Alexander H; Parli, Sara E

    2016-01-01

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

  4. 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…

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

    E-print Network

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

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

    SciTech Connect

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

    2012-07-01

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

  7. Motion in the Unstable Cervical Spine When Transferring a Patient Positioned Prone to a Spine Board

    PubMed Central

    Conrad, Bryan P.; Marchese, Diana L.; Rechtine, Glenn R.; Prasarn, Mark; Del Rossi, Gianluca; Horodyski, MaryBeth H.

    2013-01-01

    Context: Two methods have been proposed to transfer an individual in the prone position to a spine board. Researchers do not know which method provides the best immobilization. Objective: To determine if motion produced in the unstable cervical spine differs between 2 prone logrolling techniques and to evaluate the effect of equipment on the motion produced during prone logrolling. Design: Crossover study. Setting: Laboratory. Patients or Other Participants: Tests were performed on 5 fresh cadavers (3 men, 2 women; age = 83 ± 8 years, mass = 61.2 ± 14.1 kg). Main Outcome Measure(s): Three-dimensional motions were recorded during 2 prone logroll protocols (pull, push) in cadavers with an unstable cervical spine. Three equipment conditions were evaluated: football shoulder pads and helmet, rigid cervical collar, and no equipment. The mean range of motion was calculated for each test condition. Results: The pull technique produced 16% more motion than the push technique in the lateral-bending angulation direction (F1,4 = 19.922, P = .01, ?2 = 0.833). Whereas the collar-only condition and, to a lesser extent, the football-shoulder-pads-and-helmet condition demonstrated trends toward providing more stability than the no-equipment condition, we found no differences among equipment conditions. We noted an interaction between technique and equipment, with the pull maneuver performed without equipment producing more anteroposterior motion than the push maneuver in any of the equipment conditions. Conclusions: We saw a slight difference in the motion measured during the 2 prone logrolling techniques tested, with less lateral-bending and anteroposterior motion produced with the logroll push than the pull technique. Therefore, we recommend adopting the push technique as the preferred spine-boarding maneuver when a patient is found in the prone position. Researchers should continue to seek improved methods for performing prone spine-board transfers to further decrease the motion produced in the unstable spine. PMID:23952045

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

    PubMed Central

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

    2013-01-01

    Study Objectives: Sudden infant death syndrome (SIDS) is a leading cause of infant death, and prone sleeping is the major risk factor. Prone sleeping impairs arousal from sleep and cardiovascular control in infants at 2-3 months, coinciding with the highest risk period for SIDS. We hypothesized that prone sleeping would also alter cerebrovascular control, and aimed to test this hypothesis by examining responses of cerebral oxygenation to head-up tilts (HUTs) over the first 6 months after birth. Study Design and Participants: Seventeen healthy full-term infants were studied at 2-4 weeks, 2-3 months, and 5-6 months of age using daytime polysomnography, with the additional measurements of blood pressure (BP, FinometerTM, Finometer Medical Systems, The Netherlands) and cerebral tissue oxygenation index (TOI, NIRO 200, Hamamatsu Photonics KK, Japan). HUTs were performed in active sleep (AS) and quiet sleep (QS) in both prone and supine positions. Results: When infants slept in the prone position, a sustained increase in TOI (P < 0.05) occurred following HUTs, except in QS at 2-3 months when TOI was unchanged. BP was either unchanged or fell below baseline during the sustained TOI increase, signifying cerebro-vasodilatation. In contrast, when infants slept supine, TOI did not change after HUTs, except in QS at 2-3 and 5-6 months when TOI dropped below baseline (P < 0.05). Conclusions: When infants slept in the prone position, cerebral arterial vasodilation and increased cerebral oxygenation occurred during head-up tilts, possibly as a protection against cerebral hypoxia. Absence of the vasodilatory response during quiet sleep at 2-3 months possibly underpins the decreased arousability from sleep and increased risk for sudden infant death syndrome at this age. Citation: Wong F; Yiallourou SR; Odoi A; Browne P; Walker AM; Horne RSC. Cerebrovascular control is altered in healthy term infants when they sleep prone. SLEEP 2013;36(12):1911-1918. PMID:24293766

  9. Aircraft system modeling error and control error

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

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

    PubMed

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

    2010-03-01

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

  11. Error detection method

    DOEpatents

    Olson, Eric J.

    2013-06-11

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

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

    SciTech Connect

    Catron, T; Rosu, M; Weiss, E

    2014-06-01

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

  13. 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

  14. 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

  15. COP Gage error budget

    SciTech Connect

    Thompson, D.C.

    1988-08-25

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

  16. Error coding simulations

    NASA Technical Reports Server (NTRS)

    Noble, Viveca K.

    1993-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2011-08-01

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

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

    PubMed

    Yamaguchi, Satoshi; Hirakawa, Kei; Kitamura, Jiro

    2013-01-01

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

  20. 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.

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

    PubMed

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

    2010-08-01

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

  2. [Considerations for normalisation of RT-qPCR in oncology].

    PubMed

    Ho-Pun-Cheung, A; Cellier, D; Lopez-Crapez, E

    2008-01-01

    Gene expression analysis has many applications in the management of cancer, including diagnosis, prognosis, and therapeutic care. In this context, the reverse transcription quantitative polymerase chain reaction (RT-qPCR) has become the "gold standard" for mRNA quantification. However, this technique involves several critical steps such as RNA extraction, cDNA synthesis, quantitative PCR, and analysis, which all can be source of variation. To obtain biologically meaningful results, data normalisation is required to correct sample-to-sample variations that may be introduced during this multistage process. Normalisation can be carried out against a housekeeping gene, total RNA mass, or cell number. Careful choice of the normalization method is crucial, as any variation in the reference will introduce errors in the quantification of mRNA transcripts. By reviewing the different methods available and their related problems, the aim of this article is to provide recommendations for the set up of an appropriate normalisation strategy for RT-qPCR data in oncology. PMID:18390422

  3. Carbohydrate intake improves cognitive performance of stress-prone individuals under controllable laboratory stress.

    PubMed

    Markus, C R; Panhuysen, G; Jonkman, L M; Bachman, M

    1999-12-01

    Cognitive performance has been found to decline after exposure to stress, particularly in stress-prone subjects. The present study investigated whether a carbohydrate-rich, protein-poor (CR/PP) diet, which may enhance cerebral serotonin function in stress-prone subjects due to increases in the available tryptophan, improves the performance of stress-prone subjects after exposure to acute laboratory stress. Twenty-two high-stress-prone (HS) subjects and twenty-one low-stress-prone (LS) subjects aged between 19 and 26 years performed a memory scanning task after controllable and uncontrollable stress, following either a CR/PP diet or a protein-rich, carbohydrate-poor (PR/CP) isoenergetic diet. Uncontrollable stress reduced feelings of control (F(1,38) 9.30; P = 0.004), whereas pulse rate and skin conductance increased after both stress tasks (F(1,38) 78.34; P = 0.0005 and F(1,37) 83.16; P = 0.0004). Diet, stress-proneness and stress-controllability interacted (F(1,36) 9.46; P = 0.004) in such a way that performance in HS subjects was better with the CR/PP diet than with the PR/CP diet, but only after controllable stress. As the CR/PP diet has been found to increase the plasma tryptophan:large neutral amino acids ratio, indicating an increased availability of cerebral tryptophan and, thus, higher serotonin levels, it appears that there may be an increased availability of brain serotonin in HS subjects after controllable laboratory stress. PMID:10690161

  4. Everyday Scale Errors

    ERIC Educational Resources Information Center

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

    2010-01-01

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

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

    USGS Publications Warehouse

    Meyer, Robert W.; Bowers, James C.

    2002-01-01

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

  6. Reverse lithotomy: modified prone position for simultaneous nephroscopic and ureteroscopic procedures in women.

    PubMed

    Lehman, T; Bagley, D H

    1988-12-01

    Occasionally there is need for nephroscopic and ureteroscopic access during the same surgical procedure. Patient positioning is problematic and usually the patient must be turned from supine to prone position or vice versa. Simultaneous access is possible by placing the patient in a prone position with the thighs and knees cradled laterally in a "boot" type stirrup. Thus access is afforded to a percutaneous nephrostomy tract and to the urethra for nephroscopic and ureteroscopic procedures, and at the same time adequate operator comfort is maintained. This approach has been used four times in 3 patients and has been a valuable factor in the endoscopic removal of massive renal and ureteral calculi. PMID:3201661

  7. Multiplex nested PCR for Brazilian Alphavirus diagnosis.

    PubMed

    Bronzoni, Roberta V M; Moreli, Marcos L; Cruz, Ana Cecília R; Figueiredo, Luiz Tadeu M

    2004-08-01

    A reverse-transcriptase PCR (RT-PCR) and a multiplex nested PCR were developed for the rapid detection and identification of 14 Brazilian alphaviruses. Using Alphavirus genus-specific primers in a RT-PCR, we obtained amplified products of 434 bp. Species-specific primers were selected and simultaneously tested in a multiplex nested PCR. The nested PCR increased the test sensitivity 1000-fold and was capable of identifying Brazilian Alphavirus showing the expected bands with diagnostic sizes for Venezuelan (400 bp), Eastern (124 bp), and Western (208 bp) equine encephalitis, Aura (86 bp), and Mayaro (270 bp) viruses. This strategy for diagnosis is fast, sensitive, specific and it can be used as a reliable alternative for routine Brazilian Alphavirus diagnosis. PMID:15186933

  8. Hybrid PCR sequencing: sequencing of PCR products using a universal primer.

    PubMed

    Berg, E S; Olaisen, B

    1994-11-01

    We describe a general method for making template DNA for sequencing of PCR products. The procedure may be particularly useful for PCR products where minimal sequence information is known or as an alternative to primer walking when sequencing long PCR products. A cassette containing the hybridization site for the M13 sequencing primer is ligated to a sample PCR product. Using one phosphorylated primer specific for the cassette together with one primer specific for the sample PCR product, subsequent PCR amplifies one hybrid construct directionally. This allows utilization of the universal M13 primer when sequencing of one strand after the removal of the complementary strand using lambda-exonuclease. PMID:7840970

  9. Multiplexed Primer Prediction for PCR

    Energy Science and Technology Software Center (ESTSC)

    2007-07-23

    MPP predicts sets of multiplex-compatible primers for Polymerase Chain Reaction (PCR), finding a near minimal set of primers such that at least one amplicon will be generated from every target sequence in the input file. The code finds highly conserved oligos that are suitable as primers, according to user-specified desired primer characteristics such as length, melting temperature, and amplicon length. The primers are predicted not to form unwanted dimer or hairpin structures. The target sequencesmore »used as input can be diverse, since no multiple sequence alighment is required. The code is scalable, taking up to tens of thousands of sequences as input, and works, for example, to find a "universal primer set" for all viral genomes provided as a single input file. The code generates a periodic check-point file, thus in the event of premature execution termination, the application can be restarted from the last check-point file.« less

  10. The Benefits of Prone SPECT Myocardial Perfusion Imaging in Reducing Both Artifact Defects and Patient Radiation Exposure

    PubMed Central

    Stathaki, Maria; Koukouraki, Sophia; Papadaki, Emmanouela; Tsaroucha, Angeliki; Karkavitsas, Nikolaos

    2015-01-01

    Background Prone imaging has been demonstrated to minimize diaphragmatic and breast tissue attenuation. Objectives To determine the role of prone imaging on the reduction of unnecessary rest perfusion studies and coronary angiographies performed, thus decreasing investigation time and radiation exposure. Methods We examined 139 patients, 120 with an inferior wall and 19 with an anterior wall perfusion defect that might represented attenuation artifact. Post-stress images were acquired in both the supine and prone position. Coronary angiography was used as the “gold standard” for evaluating coronary artery patency. The study was terminated and rest imaging was obviated in the presence of complete improvement of the defect in the prone position. Quantitative interpretation was performed. Results were compared with clinical data and coronary angiographic findings. Results Prone acquisition correctly revealed defect improvement in 89 patients (89/120) with inferior wall and 12 patients (12/19) with anterior wall attenuation artifact. Quantitative analysis demonstrated statistically significant difference in the mean summed stress scores (SSS) of supine and mean SSS of prone studies in patients with disappearing inferior wall defect in the prone position and patent right coronary artery (true negative results). The mean difference between SSS in supine and in prone position was higher with disappearing than with remaining defects. Conclusion Technetium-99m (Tc-99m) tetrofosmin myocardial perfusion imaging with the patient in the prone position overcomes soft tissue attenuation; moreover it provides an inexpensive, accurate approach to limit the number of unnecessary rest perfusion studies and coronary angiographies performed. PMID:26559981

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

    PubMed

    Adamo, Stephen; Cain, Matthew; Mitroff, Stephen

    2015-09-01

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

  12. Real-time PCR in microfluidic devices

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  13. Simple Fool's Guide GUIDE TO PCR

    E-print Network

    Palumbi, Stephen

    ......................................................................17 Solid phase stripping with biotinylated primers.F.G.........................................................................3 DNA Extraction For PCR ....................................................................4 General Extraction Protocol for Total DNA..........................................................4

  14. Propidium monoazide reverse transcriptase PCR and RT-qPCR for detecting infectious enterovirus and norovirus.

    PubMed

    Karim, Mohammad R; Fout, G Shay; Johnson, Clifford H; White, Karen M; Parshionikar, Sandhya U

    2015-07-01

    Presently there is no established cell line or small animal model that allows for the detection of infectious human norovirus. Current methods based on RT-PCR and RT-qPCR detect both infectious and non-infectious virus and thus the conclusions that may be drawn regarding the public health significance of positive findings are limited. In this study, PMA RT-PCR and RT-qPCR assays were evaluated for selective detection of infectious poliovirus, murine norovirus (MNV-1), and Norwalk virus. Viruses were inactivated using heat, chlorine, and ultraviolet light (UV). Infectious and non-infectious viruses were treated with PMA before RT-PCR and RT-qPCR. PMA RT-PCR was able to differentiate selectively between infectious and heat and chlorine inactivated poliovirus. PMA RT-PCR was able to differentiate selectively between infectious and noninfectious murine norovirus only when inactivated by chlorine. However, PMA RT-PCR could not differentiate infectious Norwalk virus from virus particles rendered non-infectious by any treatment. PMA RT-PCR assay was not able to differentiate between infectious and UV inactivated viruses suggesting that viral capsid damage may be necessary for PMA to enter and bind to the viral genome. PMA RT-PCR on naked MNV-1 and Norwalk virus RNA suggest that PMA RT-PCR can be used to detect intact, potentially infectious MNV-1 and Norwalk viruses and can be used to exclude the detection of free viral RNA by PCR assay. PMID:25796356

  15. Errors in neuroradiology.

    PubMed

    Caranci, Ferdinando; Tedeschi, Enrico; Leone, Giuseppe; Reginelli, Alfonso; Gatta, Gianluca; Pinto, Antonio; Squillaci, Ettore; Briganti, Francesco; Brunese, Luca

    2015-09-01

    Approximately 4 % of radiologic interpretation in daily practice contains errors and discrepancies that should occur in 2-20 % of reports. Fortunately, most of them are minor degree errors, or if serious, are found and corrected with sufficient promptness; obviously, diagnostic errors become critical when misinterpretation or misidentification should significantly delay medical or surgical treatments. Errors can be summarized into four main categories: observer errors, errors in interpretation, failure to suggest the next appropriate procedure, failure to communicate in a timely and a clinically appropriate manner. Misdiagnosis/misinterpretation percentage should rise up in emergency setting and in the first moments of the learning curve, as in residency. Para-physiological and pathological pitfalls in neuroradiology include calcification and brain stones, pseudofractures, and enlargement of subarachnoid or epidural spaces, ventricular system abnormalities, vascular system abnormalities, intracranial lesions or pseudolesions, and finally neuroradiological emergencies. In order to minimize the possibility of error, it is important to be aware of various presentations of pathology, obtain clinical information, know current practice guidelines, review after interpreting a diagnostic study, suggest follow-up studies when appropriate, communicate significant abnormal findings appropriately and in a timely fashion directly with the treatment team. PMID:26183038

  16. Uncorrected refractive errors

    PubMed Central

    Naidoo, Kovin S; Jaggernath, Jyoti

    2012-01-01

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

  17. Uncorrected refractive errors.

    PubMed

    Naidoo, Kovin S; Jaggernath, Jyoti

    2012-01-01

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

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

    PubMed Central

    Szentágotai-T?tar, Aurora; Chi?, 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

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

    USGS Publications Warehouse

    Lamke, Robert D.; Jones, Stanley H.

    1980-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 44 Emergency Management and Assistance 1 2013-10-01 2013-10-01 false Planning considerations for 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...

  2. 44 CFR 60.24 - Planning considerations for flood-related erosion-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 44 Emergency Management and Assistance 1 2012-10-01 2011-10-01 true Planning considerations for 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...

  3. An Empirical Study of the Fault-Proneness of Clone Mutation and Clone Migration

    E-print Network

    Zou, Ying

    An Empirical Study of the Fault-Proneness of Clone Mutation and Clone Migration Shuai Xie1, Foutse of code to reuse some existing code segments. This action creates code clones in the software system. The literature has documented different types of code clone (e.g., Type-1, Type-2, and Type-3). Once created

  4. An Empirical Study on the Fault-Proneness of Clone Migration in Clone Genealogies

    E-print Network

    Zou, Ying

    An Empirical Study on the Fault-Proneness of Clone Migration in Clone Genealogies Shuai Xie1, Canada. foutse.khomh@polymtl.ca Abstract--Copy and paste activities create clone groups in software systems. The evolution of a clone group across the history of a software system is termed as clone

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  6. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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

  7. 44 CFR 60.23 - Planning considerations for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 44 Emergency Management and Assistance 1 2012-10-01 2011-10-01 true Planning considerations for mudslide (i.e., mudflow)-prone areas. 60.23 Section 60.23 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY, DEPARTMENT OF HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program CRITERIA FOR...

  8. Reduced attention-driven auditory sensitivity in hallucination-prone individuals.

    PubMed

    Rayner, Louise H; Lee, Kwang-Hyuk; Woodruff, Peter W R

    2015-11-01

    BackgroundEvidence suggests that auditory hallucinations may result from abnormally enhanced auditory sensitivity.AimsTo investigate whether there is an auditory processing bias in healthy individuals who are prone to experiencing auditory hallucinations.MethodTwo hundred healthy volunteers performed a temporal order judgement task in which they determined whether an auditory or a visual stimulus came first under conditions of directed attention ('attend-auditory' and 'attend-visual' conditions). The Launay-Slade Hallucination Scale was used to divide the sample into high and low hallucination-proneness groups.ResultsThe high hallucination-proneness group exhibited a reduced sensitivity to auditory stimuli under the attend-auditory condition. By contrast, attention-directed visual sensitivity did not differ significantly between groups.ConclusionsHealthy individuals prone to hallucinatory experiences may possess a bias in attention towards internal auditory stimuli at the expense of external sounds. Interventions involving the redistribution of attentional resources would have therapeutic benefit in patients experiencing auditory hallucinations. PMID:26382950

  9. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., see the List of CFR Sections Affected, which appears in the Finding Aids section of the printed volume... 44 Emergency Management and Assistance 1 2012-10-01 2011-10-01 true Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency Management and Assistance FEDERAL...

  10. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., see the List of CFR Sections Affected, which appears in the Finding Aids section of the printed volume... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency Management and Assistance FEDERAL...

  11. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., see the List of CFR Sections Affected, which appears in the Finding Aids section of the printed volume... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency Management and Assistance FEDERAL...

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., see the List of CFR Sections Affected, which appears in the Finding Aids section of the printed volume... 44 Emergency Management and Assistance 1 2014-10-01 2014-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency Management and Assistance FEDERAL...

  13. 44 CFR 60.3 - Flood plain management criteria for flood-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., see the List of CFR Sections Affected, which appears in the Finding Aids section of the printed volume... 44 Emergency Management and Assistance 1 2013-10-01 2013-10-01 false Flood plain management criteria for flood-prone areas. 60.3 Section 60.3 Emergency Management and Assistance FEDERAL...

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

    PubMed Central

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

    2015-01-01

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

  15. Design Patterns and Change Proneness: An Examination of Five Evolving Systems.

    E-print Network

    Bieman, James M.

    Design Patterns and Change Proneness: An Examination of Five Evolving Systems. James M. Bieman wmunger@southern.edu Abstract Design patterns are recognized, named solutions to com- mon design problems. The use of the most commonly referenced design patterns should promote adaptable and reusable program code

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  17. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets.

    PubMed

    Pinto, Ameet J; Raskin, Lutgarde

    2012-01-01

    As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of sequencing and chimeric PCR artifacts through rigorous quality control measures. However, there has been little effort towards understanding the effect of multi-template PCR biases on microbial community structure. In this study, we used three bacterial and three archaeal mock communities consisting of, respectively, 33 bacterial and 24 archaeal 16S rRNA gene sequences combined in different proportions to compare the influences of (1) sequencing depth, (2) sequencing artifacts (sequencing errors and chimeric PCR artifacts), and (3) biases in multi-template PCR, towards the interpretation of community structure in pyrosequencing datasets. We also assessed the influence of each of these three variables on ?- and ?-diversity metrics that rely on the number of OTUs alone (richness) and those that include both membership and the relative abundance of detected OTUs (diversity). As part of this study, we redesigned bacterial and archaeal primer sets that target the V3-V5 region of the 16S rRNA gene, along with multiplexing barcodes, to permit simultaneous sequencing of PCR products from the two domains. We conclude that the benefits of deeper sequencing efforts extend beyond greater OTU detection and result in higher precision in ?-diversity analyses by reducing the variability between replicate libraries, despite the presence of more sequencing artifacts. Additionally, spurious OTUs resulting from sequencing errors have a significant impact on richness or shared-richness based ?- and ?-diversity metrics, whereas metrics that utilize community structure (including both richness and relative abundance of OTUs) are minimally affected by spurious OTUs. However, the greatest obstacle towards accurately evaluating community structure are the errors in estimated mean relative abundance of each detected OTU due to biases associated with multi-template PCR reactions. PMID:22905208

  18. Enhanced Named Entity Extraction via Error-Driven Aggregation

    SciTech Connect

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

    2010-02-22

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

  19. Facts about Refractive Errors

    MedlinePLUS

    ... the lens can cause refractive errors. What is refraction? Refraction is the bending of light as it passes ... rays entering the eye, causing a more precise refraction or focus. In many cases, contact lenses provide ...

  20. Measurement Error Webinar Series

    Cancer.gov

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

  1. Error mode prediction.

    PubMed

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

    1999-11-01

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

  2. Human error in aviation operations

    NASA Technical Reports Server (NTRS)

    Nagel, David C.

    1988-01-01

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

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

    PubMed Central

    Nilsson, Michael; Attia, John; Ejnell, Hasse

    2015-01-01

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

  4. Motion in the unstable thoracolumbar spine when spine boarding a prone patient

    PubMed Central

    Conrad, Bryan P.; Marchese, Diana L.; Rechtine, Glenn R.; Horodyski, MaryBeth

    2012-01-01

    Introduction Previous research has found that the log roll (LR) technique produces significant motion in the spinal column while transferring a supine patient onto a spine board. The purpose of this project was to determine whether log rolling a patient with an unstable spine from prone to supine with a pulling motion provides better thoracolumbar immobilization compared to log rolling with a push technique. Methods A global instability was surgically created at the L1 level in five cadavers. Two spine-boarding protocols were tested (LR Push and LR Pull). Both techniques entailed performing a 180° LR rotation of the prone patient from the ground to the supine position on the spine board. An electromagnetic tracking device registered motion between the T12 and L2 vertebral segments. Six motion parameters were tracked. Repeated-measures statistical analysis was performed to evaluate angular and translational motion. Results Less motion was produced during the LR Push compared to the LR Pull for all six motion parameters. The difference was statistically significant for three of the six parameters (flexion–extension, axial translation, and anterior–posterior (A–P) translation). Conclusions Both the LR Push and LR Pull generated significant motion in the thoracolumbar spine during the prone to supine LR. The LR Push technique produced statistically less motion than the LR Pull, and should be considered when a prone patient with a suspected thoracolumbar injury needs to be transferred to a long spine board. More research is needed to identify techniques to further reduce the motion in the unstable spine during prone to supine LR. PMID:22330191

  5. Perceived threat mediates the relationship between psychosis proneness and aggressive behavior

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

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

    2010-05-01

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

  7. Thermodynamics of error correction

    E-print Network

    Pablo Sartori; Simone Pigolotti

    2015-04-24

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

  8. 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.

  9. Testing for Genetically Modified Foods Using PCR

    ERIC Educational Resources Information Center

    Taylor, Ann; Sajan, Samin

    2005-01-01

    The polymerase chain reaction (PCR) is a Nobel Prize-winning technique that amplifies a specific segment of DNA and is commonly used to test for the presence of genetic modifications. Students use PCR to test corn meal and corn-muffin mixes for the presence of a promoter commonly used in genetically modified foods, the cauliflower mosaic virus 35S…

  10. Directed Evolution of Cyanide Degrading Enzymes 

    E-print Network

    Abou Nader, Mary 1983-

    2012-11-12

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

  11. GPS Satellite Multipath Range Errors

    NASA Technical Reports Server (NTRS)

    Young, Lawrence E.

    1988-01-01

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

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

    PubMed

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

    2014-07-01

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

  13. Online exercise for the design and simulation of PCR and PCR-RFLP experiments

    PubMed Central

    2013-01-01

    Background Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes, compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions The exercise is freely available at http://insilico.ehu.es/edu. PMID:24314313

  14. Compact disk error measurements

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  15. 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

  16. 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. PMID:25451956

  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. Differential expression of candidate virus receptors in human T lymphocytes prone or resistant to infection with patient-derived hepatitis C virus.

    PubMed

    Sarhan, Mohammed A; Chen, Annie Y; Michalak, Tomasz I

    2013-01-01

    Accumulated evidence implies that hepatitis C virus (HCV) infects not only the liver but also the immune system. A lymphocyte-specific CD5 molecule was recently identified as essential for infection of T cells with native, patient-derived HCV. To assess whether the proposed hepatocyte receptors may also contribute to HCV lymphotropism, expression of scavenger receptor-class B type 1 (SR-B1), claudin-1 (CLDN-1), claudin-6 (CLDN-6), occludin (OCLN), CD5 and CD81 was examined by real-time RT-PCR and the respective proteins quantified by immunoblotting in HCV-prone and resistant T cell lines, peripheral blood mononuclear cells (PBMC), primary T cells and their subsets, and compared to hepatoma Huh7.5 and HepG2 cells. SR-B1 protein was found in T and hepatoma cell lines but not in PBMC or primary T lymphocytes, CLDN-1 in HCV-resistant PM1 T cell line and hepatoma cells only, while CLDN-6 equally in the cells investigated. OCLN protein occurred in HCV-susceptible Molt4 and Jurkat T cells and its traces in primary T cells, but not in PBMC. CD5 was displayed by HCV-prone T cell lines, primary T cells and PBMC, but not by non-susceptible T and hepatoma cell lines, while CD81 in all cell types except HepG2. Knocking-down OCLN in virus-prone T cell line inhibited HCV infection, while de novo infection downregulated OCLN and CD81, and upregulated CD5 without modifying SR-B1 expression. Overall, while no association between SR-B1, CLDN-1 or CLDN-6 and the susceptibility to HCV was found, CD5 and CD81 expression coincided with virus lymphotropism and that of OCLN with permissiveness of T cell lines but unlikely primary T cells. This study narrowed the range of factors potentially utilized by HCV to infect T lymphocytes amongst those uncovered using laboratory HCV and Huh7.5 cells. Together with the demonstrated role for CD5 in HCV lymphotropism, the findings indicate that virus utilizes different molecules to enter hepatocytes and lymphocytes. PMID:23626783

  19. Differential Expression of Candidate Virus Receptors in Human T Lymphocytes Prone or Resistant to Infection with Patient-Derived Hepatitis C Virus

    PubMed Central

    Sarhan, Mohammed A.; Chen, Annie Y.; Michalak, Tomasz I.

    2013-01-01

    Accumulated evidence implies that hepatitis C virus (HCV) infects not only the liver but also the immune system. A lymphocyte-specific CD5 molecule was recently identified as essential for infection of T cells with native, patient-derived HCV. To assess whether the proposed hepatocyte receptors may also contribute to HCV lymphotropism, expression of scavenger receptor-class B type 1 (SR-B1), claudin-1 (CLDN-1), claudin-6 (CLDN-6), occludin (OCLN), CD5 and CD81 was examined by real-time RT-PCR and the respective proteins quantified by immunoblotting in HCV-prone and resistant T cell lines, peripheral blood mononuclear cells (PBMC), primary T cells and their subsets, and compared to hepatoma Huh7.5 and HepG2 cells. SR-B1 protein was found in T and hepatoma cell lines but not in PBMC or primary T lymphocytes, CLDN-1 in HCV-resistant PM1 T cell line and hepatoma cells only, while CLDN-6 equally in the cells investigated. OCLN protein occurred in HCV-susceptible Molt4 and Jurkat T cells and its traces in primary T cells, but not in PBMC. CD5 was displayed by HCV-prone T cell lines, primary T cells and PBMC, but not by non-susceptible T and hepatoma cell lines, while CD81 in all cell types except HepG2. Knocking-down OCLN in virus-prone T cell line inhibited HCV infection, while de novo infection downregulated OCLN and CD81, and upregulated CD5 without modifying SR-B1 expression. Overall, while no association between SR-B1, CLDN-1 or CLDN-6 and the susceptibility to HCV was found, CD5 and CD81 expression coincided with virus lymphotropism and that of OCLN with permissiveness of T cell lines but unlikely primary T cells. This study narrowed the range of factors potentially utilized by HCV to infect T lymphocytes amongst those uncovered using laboratory HCV and Huh7.5 cells. Together with the demonstrated role for CD5 in HCV lymphotropism, the findings indicate that virus utilizes different molecules to enter hepatocytes and lymphocytes. PMID:23626783

  20. 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…

  1. Error Free Software

    NASA Technical Reports Server (NTRS)

    1985-01-01

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

  2. Quantum error control codes 

    E-print Network

    Abdelhamid Awad Aly Ahmed, Sala

    2008-10-10

    stream_source_info 3-aly319.pdf.txt stream_content_type text/plain stream_size 344719 Content-Encoding UTF-8 stream_name 3-aly319.pdf.txt Content-Type text/plain; charset=UTF-8 QUANTUM ERROR CONTROL CODES A Dissertation... by SALAH ABDELHAMID AWAD ALY AHMED Submitted to the O–ce of Graduate Studies of Texas A&M University in partial fulflllment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2008 Major Subject: Computer Science QUANTUM ERROR CONTROL CODES A...

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

    SciTech Connect

    Jackson, Christopher B.; Gallati, Sabina; Schaller, Andre

    2012-07-06

    Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two genomes is demonstrated and which evaluates systematically the impact of DNA degradation on quantification of mtDNA copy number.

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

    NASA Astrophysics Data System (ADS)

    Materna, K.; Herring, T.

    2014-12-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

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

    SciTech Connect

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

    1989-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

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

    PubMed

    Hernando, D; Sörnmo, L; Sandberg, F; Laguna, P; Llamedo, M; Bailón, R

    2015-12-01

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

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

    SciTech Connect

    Bittner, Nathan; Wallner, Kent E.; Merrick, Gregory S.

    2010-06-01

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

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

    SciTech Connect

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

    2007-05-01

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

  11. 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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2014-01-01

    In order to reduce the risk of dengue outbreak recurrence in a dengue outbreak prone area, the members of the community need to sustain certain behavior to prevent mosquito from breeding. Our study aims to identify the factors associated with larval control practices in this particular community. A cross-sectional study involves 322 respondents living in a dengue outbreak prone area who were interviewed using a pretested questionnaire. The level of knowledge about Aedes mosquitoes, dengue transmission, its symptoms, and personal preventive measures ranges from fair to good. The level of attitude towards preventive measures was high. However, reported level of personal larval control practices was low (33.2%). Our multiple logistic regression analysis showed that only those with a good level of attitude towards personal preventive measure and frequent attendance to health campaigns were significantly associated with the good larval control practices. We conclude that, in a dengue outbreak prone area, having a good attitude towards preventive measures and frequent participation in health campaigns are important factors to sustain practices on larval control. PMID:25309602

  14. Real time PCR measurement by fluorescence anisotropy

    E-print Network

    Crane, Bryan Lee, 1976-

    2005-01-01

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

  15. Automatic Error Analysis Using Intervals

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  16. Control by model error estimation

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

  17. Imagery of Errors in Typing

    ERIC Educational Resources Information Center

    Rieger, Martina; Martinez, Fanny; Wenke, Dorit

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

  19. 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.

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

    PubMed Central

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

    2014-01-01

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

  1. Transgene detection by digital droplet PCR.

    PubMed

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

    2014-01-01

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

  2. Period, epoch and prediction errors of ephemeris from continuous sets of timing measurements

    E-print Network

    Deeg, Hans J

    2015-01-01

    Space missions such as Kepler and CoRoT have led to large numbers of eclipse or transit measurements in nearly continuous time series. This paper shows how to obtain the period error in such measurements from a basic linear least-squares fit, and how to correctly derive the timing error in the prediction of future transit or eclipse events. Assuming strict periodicity, a formula for the period error of such time series is derived: sigma_P = sigma_T (12/( N^3-N))^0.5, where sigma_P is the period error; sigma_T the timing error of a single measurement and N the number of measurements. Relative to the iterative method for period error estimation by Mighell & Plavchan (2013), this much simpler formula leads to smaller period errors, whose correctness has been verified through simulations. For the prediction of times of future periodic events, the usual linear ephemeris where epoch errors are quoted for the first time measurement, are prone to overestimation of the error of that prediction. This may be avoided...

  3. Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously

    PubMed Central

    Shevchuk, Nikolai A.; Bryksin, Anton V.; Nusinovich, Yevgeniya A.; Cabello, Felipe C.; Sutherland, Margaret; Ladisch, Stephan

    2004-01-01

    A procedure for precise assembly of linear DNA constructs as long as 20 kb is proposed. The method, which we call long multiple fusion, has been used to assemble up to four fragments simultaneously (for a 10.8 kb final product), offering an additional improvement on the combination of long PCR and overlap extension PCR. The method is based on Pfu polymerase mix, which has a proofreading activity. We successfully assembled (and confirmed by sequencing) seven different linear constructs ranging from 3 to 20 kb, including two 20 kb products (from fragments of 11, 1.7 and 7.5 kb), two 10.8 kb constructs, and two constructs of 6.1 and 6.2 kb, respectively. Accuracy of the PCR fusion is greater than or equal to one error per 6.6 kb, which is consistent with the expected error rate of the PCR mix. The method is expected to facilitate various kinds of complex genetic engineering projects that require precise in-frame assembly of multiple fragments, such as somatic cell knockout in human cells or creation of whole genomes of viruses for vaccine research. PMID:14739232

  4. A web server for performing electronic PCR

    PubMed Central

    Rotmistrovsky, Kirill; Jang, Wonhee; Schuler, Gregory D.

    2004-01-01

    ‘Electronic PCR’ (e-PCR) refers to a computational procedure that is used to search DNA sequences for sequence tagged sites (STSs), each of which is defined by a pair of primer sequences and an expected PCR product size. To gain speed, our implementation extracts short ‘words’ from the 3? end of each primer and stores them in a sorted hash table that can be accessed efficiently during the search. One recent improvement is the use of overlapping discontinuous words to allow matches to be found despite the presence of a mismatch. Moreover, it is possible to allow gaps in the alignment between the primer and the sequence. The effect of these changes is to improve sensitivity without significantly affecting specificity. The new software provides a search mode using a query STS against a sequence database to augment the previously available mode using a query sequence against an STS database. Finally, e-PCR may now be used through a web service, with search results linked to other web resources such as the UniSTS database and the MapViewer genome browser. The e-PCR web server may be found at www.ncbi.nlm.nih.gov/sutils/e-pcr. PMID:15215361

  5. Increased B Cell ADAM10 in Allergic Patients and Th2 Prone Mice

    PubMed Central

    Cooley, Lauren Folgosa; Martin, Rebecca K.; Zellner, Hannah B.; Irani, Anne-Marie; Uram-Tuculescu, Cora; El Shikh, Mohey Eldin; Conrad, Daniel H.

    2015-01-01

    ADAM10, as the sheddase of the low affinity IgE receptor (CD23), promotes IgE production and thus is a unique target for attenuating allergic disease. Herein, we describe that B cell levels of ADAM10, specifically, are increased in allergic patients and Th2 prone WT mouse strains (Balb/c and A/J). While T cell help augments ADAM10 expression, Balb WT B cells exhibit increased ADAM10 in the naïve state and even more dramatically increased ADAM10 after anti-CD40/IL4 stimulation compared C57 (Th1 prone) WT B cells. Furthermore, ADAM17 and TNF are reduced in allergic patients and Th2 prone mouse strains (Balb/c and A/J) compared to Th1 prone controls. To further understand this regulation, ADAM17 and TNF were studied in C57Bl/6 and Balb/c mice deficient in ADAM10. C57-ADAM10B-/- were more adept at increasing ADAM17 levels and thus TNF cleavage resulting in excess follicular TNF levels and abnormal secondary lymphoid tissue architecture not noted in Balb-ADAM10B-/-. Moreover, the level of B cell ADAM10 as well as Th context is critical for determining IgE production potential. Using a murine house dust mite airway hypersensitivity model, we describe that high B cell ADAM10 level in a Th2 context (Balb/c WT) is optimal for disease induction including bronchoconstriction, goblet cell metaplasia, mucus, inflammatory cellular infiltration, and IgE production. Balb/c mice deficient in B cell ADAM10 have attenuated lung and airway symptoms compared to Balb WT and are actually most similar to C57 WT (Th1 prone). C57-ADAM10B-/- have even further reduced symptomology. Taken together, it is critical to consider both innate B cell levels of ADAM10 and ADAM17 as well as Th context when determining host susceptibility to allergic disease. High B cell ADAM10 and low ADAM17 levels would help diagnostically in predicting Th2 disease susceptibility; and, we provide support for the use ADAM10 inhibitors in treating Th2 disease. PMID:25933166

  6. Human Error In Complex Systems

    NASA Technical Reports Server (NTRS)

    Morris, Nancy M.; Rouse, William B.

    1991-01-01

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

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

    PubMed

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

    2015-02-01

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

  8. Modular error embedding

    DOEpatents

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

    1999-01-01

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

  9. Error-Free Software

    NASA Technical Reports Server (NTRS)

    1989-01-01

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

  10. Development of qualitative and quantitative PCR analysis for meat adulteration from RNA samples.

    PubMed

    Cheng, Jai-Hong; Chou, Hsiao-Ting; Lee, Meng-Shiou; Sheu, Shyang-Chwen

    2016-02-01

    Total RNA samples were used to establish qualitative and quantitative PCR-based methods for assessing meat adulteration. The primers were designed based on the mRNA sequences of troponin I (TnI), mitochondrial ribosomal protein (MRP) and tropomodulin genes to distinguish chicken, pork, goat, beef and ostrich. There was no cross reaction between the primers, and the detection limit of the cDNA template was 0.01 and 20 ng in simplex PCR and multiplex PCR, respectively. In the low temperature storage test, the detection limits of cDNA template with 10 and 1 ng were determined at 4 °C and -80 °C. In quantitative assay, the precision of real-time PCR analysis expressed as a coefficient of variation (CV) ranged from 0.25% to 5.24% and the trueness, expressed as an error, ranged from 0.28% to 6.98% for adulteration. Thus, herein, we provided alternative tools for the assessment of meat adulteration using mRNA-based PCR methods. PMID:26304356

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

    PubMed

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

    2016-01-01

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

  12. Development of an automatic evaluation method for patient positioning error.

    PubMed

    Kubota, Yoshiki; Tashiro, Mutsumi; Shinohara, Ayaka; Abe, Satoshi; Souda, Saki; Okada, Ryosuke; Ishii, Takayoshi; Kanai, Tatsuaki; Ohno, Tatsuya; Nakano, Takashi

    2015-01-01

    Highly accurate radiotherapy needs highly accurate patient positioning. At our facility, patient positioning is manually performed by radiology technicians. After the positioning, positioning error is measured by manually comparing some positions on a digital radiography image (DR) to the corresponding positions on a digitally reconstructed radiography image (DRR). This method is prone to error and can be time-consuming because of its manual nature. Therefore, we propose an automated measuring method for positioning error to improve patient throughput and achieve higher reliability. The error between a position on the DR and a position on the DRR was calculated to determine the best matched position using the block-matching method. The zero-mean normalized cross correlation was used as our evaluation function, and the Gaussian weight function was used to increase importance as the pixel position approached the isocenter. The accuracy of the calculation method was evaluated using pelvic phantom images, and the method's effectiveness was evaluated on images of prostate cancer patients before the positioning, comparing them with the results of radiology technicians' measurements. The root mean square error (RMSE) of the calculation method for the pelvic phantom was 0.23 ± 0.05 mm. The coefficients between the calculation method and the measurement results of the technicians were 0.989 for the phantom images and 0.980 for the patient images. The RMSE of the total evaluation results of positioning for prostate cancer patients using the calculation method was 0.32 ± 0.18 mm. Using the proposed method, we successfully measured residual positioning errors. The accuracy and effectiveness of the method was evaluated for pelvic phantom images and images of prostate cancer patients. In the future, positioning for cancer patients at other sites will be evaluated using the calculation method. Consequently, we expect an improvement in treatment throughput for these other sites. PMID:26219004

  13. Inborn errors of metabolism.

    PubMed

    El-Hattab, Ayman W

    2015-06-01

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

  14. Error-correction coding

    NASA Technical Reports Server (NTRS)

    Hinds, Erold W. (Principal Investigator)

    1996-01-01

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

  15. 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. PMID:18570432

  16. Gender differences in depression and anxiety among victims of intimate partner violence: the moderating effect of shame proneness.

    PubMed

    Shorey, Ryan C; Sherman, Amanda E; Kivisto, Aaron J; Elkins, Sara R; Rhatigan, Deborah L; Moore, Todd M

    2011-06-01

    The current study examined the moderating role of shame proneness on the association between physical, psychological, and sexual intimate partner violence victimization and depressive and anxious symptoms among male and female college students (N = 967). Students completed self-report measures of dating violence, depression, anxiety, and shame proneness. Results showed that shame proneness moderated the association between all forms of victimization and mental health symptoms. A three-way interaction revealed that sexual victimization predicted symptoms of anxiety to a greater extent for men than for women at high levels of shame proneness. Furthermore, results showed that gender moderated the association between physical and psychological victimization and health outcomes, such that victimization was related to increased depressive and anxious symptoms for men but not for women. Interpretations of these findings are discussed in relation to violence interventions, including primary prevention, and men's health. PMID:20587460

  17. Dysfunctional meta-cognitive beliefs mediate the relation between temperament traits and hallucination-proneness in non-clinical population.

    PubMed

    Gaw?da, ?ukasz; Cicho?, Ewelina; Szczepanowski, Remigiusz

    2015-10-30

    We investigated whether dysfunctional metacognitive beliefs (negative beliefs about uncontrollability and danger of thoughts) mediate the relationship between temperamental characteristics of behavior and hallucinatory-like experiences in healthy subjects (n=137). Our analyses showed that four temperamental traits (emotional reactivity, perseveration, endurance and briskness) were mediated by negative beliefs about uncontrollability and danger of thoughts in relation to hallucination proneness. Our research tentatively suggests that temperament affects hallucination proneness via metacognition. PMID:26296753

  18. Propidium monoazide reverse transcription PCR and RT-qPCR for detecting infectious enterovirus and norovirus

    EPA Science Inventory

    Presently there is no established cell line or small animal model that allows for the detection of infectious human norovirus. Current methods based on RT-PCR and RT-qPCR detect both infectious and non-infectious virus and thus the conclusions that may be drawn regarding the publ...

  19. Nanomaterial Containing Wall Paints Can Increase Radon Concentration in Houses Located in Radon Prone Areas

    PubMed Central

    Haghani, M.; Mortazavi, S. M. J.; Faghihi, R.; Mehdizadeh, S.; Moradgholi, J.; Darvish, L.; Fathi-Pour, E.; Ansari, L.; Ghanbar-pour, M. R.

    2013-01-01

    Background: Nowadays, extensive technological advancements have made it possible to use nanopaints which show exciting properties. In IR Iran excessive radon levels (up to 3700 Bq m–3) have been reported in homes located in radon prone areas. Over the past decades, concerns have been raised about the risk posed by residential radon exposure. Objective: This study aims at investigating the effect of using nanomaterial containing wall paints on radon concentration in homes. Methods: Two wooden model houses were used in this study. Soil samples from Ramsar high background radiation areas were used for simulating the situation of a typical house in radon-prone areas. Conventional water-soluble wall paint was used for painting the walls of the 1st house model; while the 2nd house model was painted with the same wall paint with montmorillonitenanoclay. Results: Three days after sealing the house models, radon level was measured by using a portable radon survey meter. The mean radon level inside the 1st house model (conventional paint) was 515.3 ± 17.8 Bq/m3 while the mean radon concentration in the 2nd house model (nano-painted house model) was 570.8 ± 18.5 Bq/m3. The difference between these means was statistically significant (P<0.001). Conclusion: To the best of our knowledge, this study is the first investigation on the effect of nano-material containing wall paints on indoor radon concentrations.  It can be concluded that nano-material-containing wall paints should not be used in houses with wooden walls located in radon prone areas. Although the mechanism of this effect is not clearly known, decreased porosity in nano-paints might be a key factor in increasing the radon concentration in homes. PMID:25505754

  20. Quick Analysis Method for Estimating Debris Flow Prone Area Caused by Overflow from Landslide dam

    NASA Astrophysics Data System (ADS)

    Shimizu, T.; Uchida, T.; Yamakoshi, T.; Yoshino, K.; Kisa, H.; Ishizuka, T.; Kaji, A.

    2012-04-01

    When earthquake or torrential rainfall cause deep catastrophic landslides, landslide dams can be formed in mountainous region. If water overflows from the landslide dams, large scale debris flow can occurs and possibly causes serious disasters in the downward region. Debris flow caused by the overflow from landslide dam is possible to affect the larger area than normal debris flow and flash flood. It is important for both a decision maker and resident in the area to recognize the disaster prone area as early as possible. For that reason, it is important to establish a quick analysis method for estimating debris flow prone area caused by overflow from landslide dams under the emergency situation. This situation requires the method to have both accuracy and speed for release. Nonetheless these two factors have trade-off relationship. We recently developed the quick analysis method to estimate debris flow disaster prone area caused by overflow from landslide dams. The method including the ways of efficient survey and numerical simulation programs called QUAD-L (QUick Analysis system for Debris flow caused by Landslide dam overflow). Our quick analysis system was actually applied to show the area for evacuation against debris flow caused by overflow from landslide dam formed by the 2011 Typhoon Talas which hit mainly the central region of Japan on September 2-4th, 2011. In addition to background of this application, since May 1st, 2011, Erosion and Sediment Control (SABO) Department of the Ministry of Land, Infrastructure, Transport and Tourism, Japan (MLIT) launched a new scheme using above-mentioned quick analysis method.

  1. Altered activation and functional connectivity of neural systems supporting cognitive control of emotion in psychosis proneness.

    PubMed

    Modinos, Gemma; Ormel, Johan; Aleman, André

    2010-05-01

    Emotion regulation processes, such as reappraisal, are thought to operate through interactions between prefrontal emotion-control regions and subcortical emotion-generation regions such as the amygdala. Impairments in emotional processing and regulation have been reported in schizophrenia and at-risk populations. Psychometric measures may be used to detect vulnerability to schizophrenia in non-clinical samples, or psychosis proneness (PP). It has been shown that individuals with PP have a more than tenfold increased risk of developing a schizophrenia-spectrum disorder. In the present study, we used fMRI to examine the neural dynamics underlying reappraisal in such a sample. 600 undergraduate students completed the Community Assessment of Psychic Experiences Questionnaire (CAPE), positive subscale. Two groups were subsequently formed from the extremes of the distribution (total N=34). Blood-oxygenated-level-dependent activity elicited with a task involving 3 conditions was analyzed: viewing neutral pictures, viewing negative pictures, and reappraising negative pictures. Subjects reported the strength of experienced negative affect after each trial. Functional connectivity between prefrontal control regions and amygdala was investigated. At the behavioral level, both groups reported successful diminishment of experienced negative emotion. However, high psychosis-prone subjects showed stronger activation than low subjects in a number of prefrontal regions during reappraisal, relative to attending to negative pictures. The amygdala response to negative stimuli was decreased through reappraisal only in the low group. Functional connectivity analysis revealed less prefrontal-amygdala coupling in high psychosis-prone subjects. Thus, reduced cognitive control of emotion at a neural level appeared to be associated with PP. These findings extend the hypothesis of emotion dysregulation in schizophrenia to PP, and suggest that emotion regulation difficulties may be at the core of a vulnerability to psychosis. PMID:20188516

  2. Comparison of prone versus supine 18F-FDG-PET of locally advanced breast cancer: Phantom and preliminary clinical studies

    SciTech Connect

    Williams, Jason M.; Rani, Sudheer D.; Li, Xia; Whisenant, Jennifer G.; Abramson, Richard G.; Arlinghaus, Lori R.; Lee, Tzu-Cheng; MacDonald, Lawrence R.; Partridge, Savannah C.; Kang, Hakmook; Linden, Hannah M.; Kinahan, Paul E.; Yankeelov, Thomas E.

    2015-07-15

    Purpose: Previous studies have demonstrated how imaging of the breast with patients lying prone using a supportive positioning device markedly facilitates longitudinal and/or multimodal image registration. In this contribution, the authors’ primary objective was to determine if there are differences in the standardized uptake value (SUV) derived from [{sup 18}F]fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) in breast tumors imaged in the standard supine position and in the prone position using a specialized positioning device. Methods: A custom positioning device was constructed to allow for breast scanning in the prone position. Rigid and nonrigid phantom studies evaluated differences in prone and supine PET. Clinical studies comprised 18F-FDG-PET of 34 patients with locally advanced breast cancer imaged in the prone position (with the custom support) followed by imaging in the supine position (without the support). Mean and maximum values (SUV{sub peak} and SUV{sub max}, respectively) were obtained from tumor regions-of-interest for both positions. Prone and supine SUV were linearly corrected to account for the differences in 18F-FDG uptake time. Correlation, Bland–Altman, and nonparametric analyses were performed on uptake time-corrected and uncorrected data. Results: SUV from the rigid PET breast phantom imaged in the prone position with the support device was 1.9% lower than without the support device. In the nonrigid PET breast phantom, prone SUV with the support device was 5.0% lower than supine SUV without the support device. In patients, the median (range) difference in uptake time between prone and supine scans was 16.4 min (13.4–30.9 min), which was significantly—but not completely—reduced by the linear correction method. SUV{sub peak} and SUV{sub max} from prone versus supine scans were highly correlated, with concordance correlation coefficients of 0.91 and 0.90, respectively. Prone SUV{sub peak} and SUV{sub max} were significantly lower than supine in both original and uptake time-adjusted data across a range of index times (P < < 0.0001, Wilcoxon signed rank test). Before correcting for uptake time differences, Bland–Altman analyses revealed proportional bias between prone and supine measurements (SUV{sub peak} and SUV{sub max}) that increased with higher levels of FDG uptake. After uptake time correction, this bias was significantly reduced (P < 0.01). Significant prone-supine differences, with regard to the spatial distribution of lesions relative to isocenter, were observed between the two scan positions, but this was poorly correlated with the residual (uptake time-corrected) prone-supine SUV{sub peak} difference (P = 0.78). Conclusions: Quantitative 18F-FDG-PET/CT of the breast in the prone position is not deleteriously affected by the support device but yields SUV that is consistently lower than those obtained in the standard supine position. SUV differences between scans arising from FDG uptake time differences can be substantially reduced, but not removed entirely, with the current correction method. SUV from the two scan orientations is quantitatively different and should not be assumed equivalent or interchangeable within the same subject. These findings have clinical relevance in that they underscore the importance of patient positioning while scanning as a clinical variable that must be accounted for with longitudinal PET measurement, for example, in the assessment of treatment response.

  3. Correlates of the multidimensional construct of hypnotizability: paranormal belief, fantasy proneness, magical ideation, and dissociation.

    PubMed

    Dasse, Michelle N; Elkins, Gary R; Weaver, Charles A

    2015-01-01

    Hypnotizability is a multifaceted construct that may relate to multiple aspects of personality and beliefs. This study sought to address 4 known correlates of hypnotizability to aid in its understanding. Eighty undergraduates completed the Magical Ideation Scale (MIS), the Creative Experiences Questionnaire (CEQ), the Australian Sheep-Goat Scale (ASGS), and the Dissociative Experiences Scale (DES) and then were administered the Creative Imagination Scale (CIS). All 5 scales were significantly correlated. Participants higher in hypnotizability scored higher on the CEQ and the MIS. The findings demonstrate the influence of fantasy proneness and magical thinking on hypnotizability and support the theory that hypnotizability is a complex interaction of multiple traits. PMID:25978081

  4. Depression is an early disease manifestation in lupus-prone MRL/lpr mice.

    PubMed

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

    2009-02-15

    Many lupus patients develop neuropsychiatric manifestations, including cognitive dysfunction, depression, and anxiety. However, it is not clear if neuropsychiatric lupus is a primary disease manifestation, or is secondary to non-CNS disease. We found that MRL/lpr lupus-prone mice exhibited significant depression-like behavior already at 8 weeks of age, despite normal visual working memory, locomotor coordination and social preference. Moreover, depression was significantly correlated with titers of autoantibodies against DNA, NMDA receptors and cardiolipin. Our results indicate that lupus mice develop depression and CNS dysfunction very early in the course of disease, in the absence of substantial pathology involving other target organs. PMID:19121871

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

    PubMed Central

    Froggatt, P.

    1970-01-01

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

  6. Skylab water balance error analysis

    NASA Technical Reports Server (NTRS)

    Leonard, J. I.

    1977-01-01

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

  7. SU-E-J-227: Breathing Pattern Consistency and Reproducibility: Comparative Analysis for Supine and Prone Body Positioning

    SciTech Connect

    Laugeman, E; Weiss, E; Chen, S; Hugo, G; Rosu, M

    2014-06-01

    Purpose: Evaluate and compare the cycle-to-cycle consistency of breathing patterns and their reproducibility over the course of treatment, for supine and prone positioning. Methods: Respiratory traces from 25 patients were recorded for sequential supine/prone 4DCT scans acquired prior to treatment, and during the course of the treatment (weekly or bi-weekly). For each breathing cycle, the average(AVE), end-of-exhale(EoE) and end-of-inhale( EoI) locations were identified using in-house developed software. In addition, the mean values and variations for the above quantities were computed for each breathing trace. F-tests were used to compare the cycle-to-cycle consistency of all pairs of sequential supine and prone scans. Analysis of variances was also performed using population means for AVE, EoE and EoI to quantify differences between the reproducibility of prone and supine respiration traces over the treatment course. Results: Consistency: Cycle-to-cycle variations are less in prone than supine in the pre-treatment and during-treatment scans for AVE, EoE and EoI points, for the majority of patients (differences significant at p<0.05). The few cases where the respiratory pattern had more variability in prone appeared to be random events. Reproducibility: The reproducibility of breathing patterns (supine and prone) improved as treatment progressed, perhaps due to patients becoming more comfortable with the procedure. However, variability in supine position continued to remain significantly larger than in prone (p<0.05), as indicated by the variance analysis of population means for the pretreatment and subsequent during-treatment scans. Conclusions: Prone positioning stabilizes breathing patterns in most subjects investigated in this study. Importantly, a parallel analysis of the same group of patients revealed a tendency towards increasing motion amplitude of tumor targets in prone position regardless of their size or location; thus, the choice for body positioning during radiation therapy will have to consider the clinical relevance of the two opposing trends - breathing consistency and motion amplitude.

  8. Direct detection of PCR products for HLA class II typing.

    PubMed

    Chia, D; Terasaki, P; Chan, H; Tonai, R; Siauw, P A

    1993-09-01

    Direct detection of the PCR, or DD-PCR is proposed as an efficient method for performing PCR assays. Following the PCR reaction, ethidium homodimer dye is added to the reaction mixture and read by fluorescence. The dye step circumvents the necessity of running reactions on agarose gel electrophoresis, which is the current standard. This simple modification should find wide application for assays utilizing the PCR reaction. Here we show the ready detection of HLA class II polymorphism. PMID:8284789

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. Uncertainty quantification and error analysis

    SciTech Connect

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

    2010-01-01

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

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

    PubMed

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

    2013-10-01

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

  12. Errors in CT colonography.

    PubMed

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

    2015-10-01

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

  13. Forward Error Correction

    NASA Astrophysics Data System (ADS)

    Mizuochi, Takashi

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

  14. Variability in DNA polymerase efficiency: effects of random error, DNA extraction method, and isolate type

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using computer-generated data calculated with known amounts of random error (E = 1, 5 & 10%) associated with calculated qPCR cycle number (C ) at four jth 1:10 dilutions, we found that the “efficiency” (eff) associated with each population distribution of n = 10,000 measurements varied from 0.95 to ...

  15. Clearance of senescent hepatocytes in a neoplastic-prone microenvironment delays the emergence of hepatocellular carcinoma

    PubMed Central

    Sini, Marcella; Angius, Fabrizio; Laconi, Ezio

    2014-01-01

    Increasing evidence indicates that carcinogenesis is dependent on the tissue context in which it occurs, implying that the latter can be a target for preventive or therapeutic strategies. We tested the possibility that re-normalizing a senescent, neoplastic-prone tissue microenvironment would exert a modulatory effect on the emergence of neoplastic disease. Rats were exposed to a protocol for the induction of hepatocellular carcinoma (HCC). Using an orthotopic and syngeneic system for cell transplantation, one group of animal was then delivered 8 million normal hepatocytes, via the portal circulation. Hepatocytes transplantation resulted in a prominent decrease in the incidence of both pre-neoplastic and neoplastic lesions. At the end of 1 year 50% of control animals presented with HCC, while no HCC were observed in the transplanted group. Extensive hepatocyte senescence was induced by the carcinogenic protocol in the host liver; however, senescent cells were largely cleared following infusion of normal hepatocytes. Furthermore, levels of Il-6 increased in rats exposed to the carcinogenic protocol, while they returned to near control values in the group receiving hepatocyte transplantation. These results support the concept that strategies aimed at normalizing a neoplastic-prone tissue landscape can modulate progression of neoplastic disease. PMID:24464501

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

    SciTech Connect

    Lee, Minjung; Shin, Jaekyoon

    2011-09-16

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

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

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

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

  18. The Validity of Psychosis Proneness Scales as Vulnerability Indicators in Recent-Onset Schizophrenia Patients

    PubMed Central

    Horan, William P.; Reise, Steven P.; Subotnik, Kenneth L.; Ventura, Joseph; Nuechterlein, Keith H.

    2008-01-01

    The Psychosis Proneness Scales developed by the Chapmans and colleagues (Chapman et al., 1995) are widely used to identify nonpatient individuals who are hypothesized to possess heightened vulnerability to schizophrenia and related psychopathology. Yet surprisingly little is known about whether schizophrenia patients themselves show abnormalities on these scales across different clinical states, as would be expected for vulnerability indicators. Scores on four of the Psychosis Proneness Scales were evaluated at three assessment points over a 15-month period in healthy controls (n = 54) and in recent-onset schizophrenia patients (n = 72) who experienced symptom fluctuations across assessments. Patients showed steady elevations on the Physical Anhedonia Scale across time and clinical state, consistent with a stable vulnerability indicator. Patients had higher scores on the Perceptual Aberration and Magical Ideation Scales than controls throughout the follow-up period but scores also changed across clinical states, consistent with a mediating vulnerability indicator. Patients had higher scores on the Impulsive Non-Conformity Scale than controls only during a psychotic state, reflecting an episode indicator. The longitudinal characteristics of these scales in people who are actually diagnosed with schizophrenia provide key evidence for the validity of three commonly used psychometric indicators of vulnerability to psychosis. PMID:18221857

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2014-09-01

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

  1. Functioning of neural systems supporting emotion regulation in anxiety-prone individuals.

    PubMed

    Campbell-Sills, Laura; Simmons, Alan N; Lovero, Kathryn L; Rochlin, Alexis A; Paulus, Martin P; Stein, Murray B

    2011-01-01

    Previous neuroimaging studies suggest that prefrontal cortex (PFC) modulation of the amygdala and related limbic structures is an underlying neural substrate of effortful emotion regulation. Anxiety-prone individuals experience excessive negative emotions, signaling potential dysfunction of systems supporting down-regulation of negative emotions. We examined the hypothesis that anxious individuals require increased recruitment of lateral and medial PFC to decrease negative emotions. An emotion regulation task that involved viewing moderately negative images was presented during functional magnetic resonance imaging (fMRI). Participants with elevated trait anxiety scores (n=13) and normal trait anxiety scores (n=13) were trained to reduce negative emotions using cognitive reappraisal. Blood oxygenation level-dependent (BOLD) changes were contrasted for periods when participants were reducing emotions versus when they were maintaining emotions. Compared to healthy controls, anxious participants showed greater activation of brain regions implicated in effortful (lateral PFC) and automatic (subgenual anterior cingulate cortex) control of emotions during down-regulation of negative emotions. Left ventrolateral PFC activity was associated with greater self-reported reduction of distress in anxious participants, but not in healthy controls. These findings provide evidence of altered functioning of neural substrates of emotion regulation in anxiety-prone individuals. Anxious participants required greater engagement of lateral and medial PFC in order to successfully reduce negative emotions. PMID:20673804

  2. Prone Positioning Causes the Heart To Be Displaced Anteriorly Within the Thorax: Implications for Breast Cancer Treatment

    SciTech Connect

    Chino, Junzo P. Marks, Lawrence B.

    2008-03-01

    Introduction: Prone positioning has been suggested as an alternative to the conventional supine position for patients receiving breast radiotherapy, but few data exist on how this may alter heart location. We herein quantitatively compare the intrathoracic location of the heart in the prone and supine positions in patients treated for breast cancer. Methods and Materials: In 16 patients treated with tangent photons for breast cancer, the computed tomography planning images (obtained in the supine position) and diagnostic magnetic resonance images (obtained in the prone position) were studied. For each case, the distance between the anterior pericardium and the anterior chest wall was measured at nine specific points; three points at each of three axial levels. The differences in the measurements between the prone and supine positions were compared with the Wilcoxon signed-rank test. Results: There is a systematic displacement of the lateral and superior aspect of the heart closer to the chest wall in the prone vs. supine position (mean displacement 19 mm (95% confidence interval 13.7-25.1 mm, p < 0.001); the medial and inferior aspects remain fixed. There was also a reduction in volume of lung interposed between the heart and chest wall when prone (mean decrease of 22 mL, p < 0.001 for difference). Conclusions: The superior and lateral aspects of the heart typically move anteriorly during prone positioning compared with the supine position. This may have negative consequences in situations in which the high-risk target tissues include the chest wall or deep breast.

  3. ASePCR: alternative splicing electronic RT–PCR in multiple tissues and organs

    PubMed Central

    Kim, Namshin; Lim, Dajeong; Lee, Sanghyuk; Kim, Heebal

    2005-01-01

    RT–PCR is one of the most powerful and direct methods to detect transcript variants due to alternative splicing (AS) that increase transcript diversity significantly in vertebrates. ASePCR is an efficient web-based application that emulates RT–PCR in various tissues. It estimates the amplicon size for a given primer pair based on the transcript models identified by the reverse e-PCR program of the NCBI. The tissue specificity of each PCR band is deduced from the tissue information of expressed sequence tag (EST) sequences compatible with each transcript structure. The output page shows PCR bands like a gel electrophoresis in various tissues. Each band in the output picture represents a putative isoform that could happen in a tissue-specific manner. It also shows the EST alignment and tissue information in the genome browser. Furthermore, the user can compare the AS patterns of orthologous genes in other species. The ASePCR, available at , supports the transcriptome models of the RefSeq, Ensembl, ECgene and AceView for human, mouse, rat and chicken genomes. It will be a valuable web resource to explore the transcriptome diversity associated with different tissues and organs in multiple species. PMID:15980562

  4. Register file soft error recovery

    DOEpatents

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

    2013-10-15

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

  5. Rapid mapping of volumetric errors

    SciTech Connect

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

    1995-09-13

    This paper describes a relatively inexpensive, fast, and easy to execute approach to mapping the volumetric errors of a machine tool, coordinate measuring machine, or robot. An error map is used to characterize a machine or to improve its accuracy by compensating for the systematic errors. The method consists of three steps: (1) modeling the relationship between the volumetric error and the current state of the machine; (2) acquiring error data based on length measurements throughout the work volume; and (3) optimizing the model to the particular machine.

  6. The Power of Real-Time PCR

    ERIC Educational Resources Information Center

    Valasek, Mark A.; Repa, Joyce J.

    2005-01-01

    In recent years, real-time polymerase chain reaction (PCR) has emerged as a robust and widely used methodology for biological investigation because it can detect and quantify very small amounts of specific nucleic acid sequences. As a research tool, a major application of this technology is the rapid and accurate assessment of changes in gene…

  7. PCR and recombinant DNA Cristiano V. Bizarro

    E-print Network

    Ritort, Felix

    Science. Nucleic Acids are created by joining together nucleotides with a phosphodiester linkage: #12;DNA;Modification enzymes in molecular biology II Major types: - Exonucleases: digest DNA from an end of a strand: Molecular Biology of the Cell. Alberts et al. Garland Science. 21 22 23Number of molecules: #12;PCR: basic

  8. [Mutation detection by PCR-TGGE].

    PubMed

    Shirakawa, T; Nishiyama, K; Matsuo, M

    1995-07-01

    The variants in enterotoxigenic Escherichia coli (ETEC) heat-labile toxin (LT) gene were detected by temperature gradient gel electrophoresis (TGGE). 15 clinical strains isolated from patients and a wild type strain (B2C) were analyzed after the conventional PCR. Although all PCR products (707bp) corresponded to A-subunit of LT, three strains were the different electrophoretic patterns after silver staining as compared to the wild type. For further electrophoretic analyses, the 707bp region was divided into 4 parts. The different ones were localized in the downstream part (183bp), but each those DNA bands was not so clear than DNA bands in 707bp. The clearer patterns were obtained by using a primer attached GC-clamp. The hetero-duplex assays in TGGE were proceeded by a series of procedures in mixing with the equal quantity of PCR products derived from a variant and a wild type, heat-denaturation and then annealing. TGGE of those mixed samples had 4 bands that were 2 front bands as homo-duplex and 2 slower migration bands as hetero-duplex. To Confirm the site of the mutations, the nucleotide sequences in each 183bp PCR products were decided by dideoxynucleotide-fluorescent dye method. Indeed, two variants were recognized four one-base substitutions without deletions and the one was five. Thus, the difference of migration in TGGE depended on the number and the localization in mutation sites. PMID:7674540

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

    SciTech Connect

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

    2010-03-24

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    The majority of quantum-error-detection and correction protocols assume that the population in a qubit does not leak outside of its computational subspace. For many existing approaches, however, the physical qubits do possess more than two energy levels and consequently are prone to such leakage events. Analyzing the effects of leakage is therefore essential to devise optimal protocols for quantum gates, measurement, and error correction. In this article, we present a detailed study of leakage in a two-qubit superconducting stabilizer measurement circuit. We simulate the repeated ancilla-assisted measurement of a single ?z operator for a data qubit, record the outcome at the end of each measurement cycle, and explore the signature of leakage events in the obtained readout statistics. An analytic model is also developed that closely approximates the results of our numerical simulations. We find that leakage leads to destructive features in the quantum-error-detection scheme, making additional hardware and software protocols necessary.

  11. Period, epoch, and prediction errors of ephemerides from continuous sets of timing measurements

    NASA Astrophysics Data System (ADS)

    Deeg, H. J.

    2015-06-01

    Space missions such as Kepler and CoRoT have led to large numbers of eclipse or transit measurements in nearly continuous time series. This paper shows how to obtain the period error in such measurements from a basic linear least-squares fit, and how to correctly derive the timing error in the prediction of future transit or eclipse events. Assuming strict periodicity, a formula for the period error of these time series is derived, ?P = ?T (12 / (N3-N))1 / 2, where ?P is the period error, ?T the timing error of a single measurement, and N the number of measurements. Compared to the iterative method for period error estimation by Mighell & Plavchan (2013), this much simpler formula leads to smaller period errors, whose correctness has been verified through simulations. For the prediction of times of future periodic events, usual linear ephemeris were epoch errors are quoted for the first time measurement, are prone to an overestimation of the error of that prediction. This may be avoided by a correction for the duration of the time series. An alternative is the derivation of ephemerides whose reference epoch and epoch error are given for the centre of the time series. For long continuous or near-continuous time series whose acquisition is completed, such central epochs should be the preferred way for the quotation of linear ephemerides. While this work was motivated from the analysis of eclipse timing measures in space-based light curves, it should be applicable to any other problem with an uninterrupted sequence of discrete timings for which the determination of a zero point, of a constant period and of the associated errors is needed.

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

    PubMed Central

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

    2013-01-01

    Objectives Some hospitals have implemented computerized physician order entry (CPOE) systems to reduce the medical error rates. However, research in this area has been very limited, especially regarding the impact of CPOE use on the reduction of prescribing errors. Moreover, the past studies have dealt with the overall impact of CPOE on the reduction of broadly termed "medical errors", and they have not specified which medical errors have been reduced by CPOE. Furthermore, the majority of the past research in this field has been either qualitative or has not used robust empirical techniques. This research examined the impacts of usability of CPOE systems on the reduction of doctors' prescribing errors. Methods One hundred and sixty-six questionnaires were used for quantitative data analyses. Since the data was not normally distributed, partial least square path modelling-as the second generation of multivariate data analyses-was applied to analyze data. Results It was found that the ease of use of the system and information quality can significantly reduce prescribing errors. Moreover, the user interface consistency and system error prevention have a significant positive impact on the perceived ease of use. More than 50% of the respondents believed that CPOE reduces the likelihood of drug allergy, drug interaction, and drug dosing errors thus improving patient safety. Conclusions Prescribing errors in terms of drug allergy, drug interaction, and drug dosing errors are reduced if the CPOE is not error-prone and easy to use, if the user interface is consistent, and if it provides quality information to doctors. PMID:23882414

  13. Errors inducing radiation overdoses.

    PubMed

    Grammaticos, Philip C

    2013-01-01

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

  14. [Diagnostic errors in angiomas].

    PubMed

    Kämpfer, R; Hundeiker, M

    1977-11-01

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

  15. Satellite Photometric Error Determination

    NASA Astrophysics Data System (ADS)

    Payne, T.; Castro, P.; Gregory, S.; Dao, P.

    In this paper, we present analysis of the errors associated with optical photometry used in non-resolved object characterization for the Space Situational Awareness (SSA) community. We begin with an overview of standard astronomical techniques used to measure the brightness of spatially unresolved objects (point source photometry) in deep space. After discussing the standard astronomical techniques, we present the application of astronomical photometry for the purposes of space object characterization. Examples of filter photometry of geosynchronous satellites processed using the current techniques are shown. Next we advocate the adoption of new techniques based on in-frame photometric calibrations enabled by newly available all-sky star catalogs that contain highly accurate photometry.

  16. 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.

  17. Real-time RT-PCR assays for the rapid and differential detection of dolphin and porpoise morbilliviruses.

    PubMed

    Grant, Rebecca J; Banyard, Ashley C; Barrett, Tom; Saliki, Jeremiah T; Romero, Carlos H

    2009-03-01

    Real-time RT-PCR (rtRT-PCR) assays for identifying and differentiating infections caused by dolphin morbillivirus (DMV) and porpoise morbillivirus (PMV) were developed by targeting the hypervariable C-terminal domain of the nucleocapsid (N) gene. Total DMV and PMV RNA extracted from infected Vero cells expressing the canine signaling lymphocyte-activation molecule (SLAM) produced positive cycle threshold (C(T)) values after the 17th and 25th cycles, respectively. The assays were then validated using infected cetacean tissue RNA. The assays were specific for either DMV or PMV and did not cross-react with canine distemper virus (CDV), phocid distemper virus (PDV), rinderpest virus (RPV), peste des petits ruminants virus (PPRV) and measles virus (MV). The glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene was targeted as control for RNA quality, and a consensus GAPDH probe that reacted with 11 different marine mammal species, generating positive C(T) values ranging from the 21st to the 37th cycle was used. The rtRT-PCR assays have advantages over conventional assays in that they are rapid, easier to scale up, and are less prone to cross-contamination and have improved the limit of detection and specificity. PMID:19084557

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

    PubMed

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

    2014-07-01

    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

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    PubMed Central

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

    2013-01-01

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

  3. What is a prescribing error?

    PubMed Central

    Dean, B; Barber, N; Schachter, M

    2000-01-01

    N Barber, professor of the practice of pharmacy M Schachter, senior lecturer and honorary consultant physician Objective—To develop a practitioner led definition of a prescribing error for use in quantitative studies of their incidence. Design—Two stage Delphi technique. Subjects—A panel of 34 UK judges, which included physicians, surgeons, pharmacists, nurses and risk managers. Main outcome measures—The extent to which judges agreed with a general definition of a prescribing error, and the extent to which they agreed that each of 42 scenarios represented a prescribing error. Results—Responses were obtained from 30 (88%) of 34 judges in the first Delphi round, and from 26 (87%) of 30 in the second round. The general definition of a prescribing error was accepted. The panel reached consensus that 24 of the 42 scenarios should be included as prescribing errors and that five should be excluded. In general, transcription errors, failure to communicate essential information, and the use of drugs or doses inappropriate for the individual patient were considered prescribing errors; deviations from policies or guidelines were not. Conclusions—Health care professionals are in broad agreement about the types of events that should be included and excluded as prescribing errors. A general definition of a prescribing error has been developed, together with more detailed guidance regarding the types of events that should be included. This definition allows the comparison of prescribing error rates among different prescribing systems and different hospitals, and is suitable for use in both research and clinical governance initiatives. (Quality in Health Care 2000;9:232–237) Key Words: prescribing errors; medication errors; definition of error PMID:11101708

  4. QPCR: Application for real-time PCR data management and analysis

    PubMed Central

    Pabinger, Stephan; Thallinger, Gerhard G; Snajder, René; Eichhorn, Heiko; Rader, Robert; Trajanoski, Zlatko

    2009-01-01

    Background Since its introduction quantitative real-time polymerase chain reaction (qPCR) has become the standard method for quantification of gene expression. Its high sensitivity, large dynamic range, and accuracy led to the development of numerous applications with an increasing number of samples to be analyzed. Data analysis consists of a number of steps, which have to be carried out in several different applications. Currently, no single tool is available which incorporates storage, management, and multiple methods covering the complete analysis pipeline. Results QPCR is a versatile web-based Java application that allows to store, manage, and analyze data from relative quantification qPCR experiments. It comprises a parser to import generated data from qPCR instruments and includes a variety of analysis methods to calculate cycle-threshold and amplification efficiency values. The analysis pipeline includes technical and biological replicate handling, incorporation of sample or gene specific efficiency, normalization using single or multiple reference genes, inter-run calibration, and fold change calculation. Moreover, the application supports assessment of error propagation throughout all analysis steps and allows conducting statistical tests on biological replicates. Results can be visualized in customizable charts and exported for further investigation. Conclusion We have developed a web-based system designed to enhance and facilitate the analysis of qPCR experiments. It covers the complete analysis workflow combining parsing, analysis, and generation of charts into one single application. The system is freely available at PMID:19712446

  5. Unexpected tracheal narrowing during general anesthesia in the prone position of Duchenne muscular dystrophy patient -A report of two cases-

    PubMed Central

    Lee, Dong Kyu; Lim, Byung Gun; Lee, Il-Ok; Oh, Hye-Ran; Lim, Sang Ho

    2013-01-01

    Unexpected tracheal narrowing was observed in a patient with Duchenne muscular dystrophy during a corrective operation for thoracolumbar scoliosis. As the operating time progressed, peak airway pressure and end-tidal CO2 increased gradually in the prone position. We found a floppy portion of the trachea using fiberoptic bronchoscopy (FB) in the prone position. We advanced a wire-reinforced tube toward the carina beyond the lesion. This allowed correction of the ventilatory abnormalities. We encountered another patient scheduled for the same operation. We performed FB in advance before the position change and observed a narrowed portion of trachea. We advanced the tracheal tube under FB beyond the pathologic portion and then moved the patient into the prone position. The operation was done successfully without any problems. PMID:23741571

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

    SciTech Connect

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

    2014-04-01

    Extreme wind load cases are one of the most important external conditions in the design of offshore wind turbines in hurricane prone regions. Furthermore, in these areas, the increase in load with storm return-period is higher than in extra-tropical regions. However, current standards have limited information on the appropriate models to simulate wind loads from hurricanes. This study investigates turbulent wind models for load analysis of offshore wind turbines subjected to hurricane conditions. Suggested extreme wind models in IEC 61400-3 and API/ABS (a widely-used standard in oil and gas industry) are investigated. The present study further examines the wind turbine response subjected to Hurricane wind loads. Three-dimensional wind simulator, TurbSim, is modified to include the API wind model. Wind fields simulated using IEC and API wind models are used for an offshore wind turbine model established in FAST to calculate turbine loads and response.

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

    PubMed

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

    2002-03-01

    The effects of aniracetam, a cognition enhancer, on extracellular levels of glutamate (Glu), gamma-aminobutyric acid (GABA) and nitric oxide metabolites (NOx) were examined in the prefrontal cortex (PFC) and the basolateral amygdala (AMG) in stroke-prone spontaneously hypertensive rats (SHRSP) using in vivo microdialysis. Basal release of Glu, was lower in the AMG of SHRSP than in normotensive Wistar Kyoto rats, whereas no difference in GABA and NOx was noted. Aniracetam (100 mg/kg, p.o.) significantly increased the area under the curve of Glu levels in the PFC, but not in the AMG, of SHRSP. Aniracetam failed to exert any remarkable effects on GABA or NOx levels in either brain region. Our findings suggest that aniracetam enhances cortical glutamatergic release, which may be the mechanism involved in the ameliorating effects of aniracetam on various neuronal dysfunctions. PMID:11852174

  8. Continual Gram-negative bacterial challenge accelerates stroke onset in stroke-prone spontaneously hypertensive rats.

    PubMed

    Kawato, Takayuki; Tanaka, Hideki; Tabuchi, Masaki; Ooshima, Kana; Nakai, Kumiko; Yamashita, Yoshihisa; Maeno, Masao

    2013-01-01

    This study examined the effects of continual Gram-negative bacterial challenge on stroke onset. Stroke onset occurred significantly earlier in stroke-prone spontaneously hypertensive rats (SHRSP) injected with a bacterial cell suspension of Gram-negative rods or lipopolysaccharides (LPSs) than in uninjected controls. Paralysis of the hindlimb, piloerection, hypokinesis, and hyperkinesis were observed in LPS-injected SHRSP but not in uninjected controls during stroke onset. The serum levels of NOx, thiobarbituric acid reactive substance, and 8-hydroxydeoxyguanosine increased in LPS-injected SHRSP. These results suggest that continual Gram-negative bacterial challenge induces accelerated stroke onset in SHRSP, probably caused by oxidative stress responses derived from LPSs. PMID:22630606

  9. InSAR imaging of volcanic deformation over cloud-prone areas - Aleutian islands

    USGS Publications Warehouse

    Lu, Zhong

    2007-01-01

    Interferometric synthetic aperture radar (INSAR) is capable of measuring ground-surface deformation with centimeter-tosubcentimeter precision and spatial resolution of tens-of meters over a relatively large region. With its global coverage and all-weather imaging capability, INSAR is an important technique for measuring ground-surface deformation of volcanoes over cloud-prone and rainy regions such as the Aleutian Islands, where only less than 5 percent of optical imagery is usable due to inclement weather conditions. The spatial distribution of surface deformation data, derived from INSAR images, enables the construction of detailed mechanical models to enhance the study of magmatic processes. This paper reviews the basics of INSAR for volcanic deformation mapping and the INSAR studies of ten Aleutian volcanoes associated with both eruptive and noneruptive activity. These studies demonstrate that all-weather INSAR imaging can improve our understanding of how the Aleutian volcanoes work and enhance our capability to predict future eruptions and associated hazards.

  10. Synthesis of oxidant prone nanosilver to develop H2O2 responsive drug delivery system.

    PubMed

    Muhammad, Faheem; Wang, Aifei; Miao, Lu; Wang, Pengyuan; Li, Qin; Liu, Jia; Du, Jianshi; Zhu, Guangshan

    2015-01-13

    Our immune system uses toxicity of hydrogen peroxide to kill off bacterial invaders. In this contribution, we intended to integrate ROS producing capability of immune system with oxidant-sensitive nature of antibacterial silver nanoparticles (Ag NPs) to develop an oxidant drug delivery system. Prior to execute this strategy, we have developed an efficient one-pot synthetic protocol to produce ultrasmall (5 nm), water-stable, and oxidant-prone Ag NPs. Notably, the yield of as-synthesized Ag NPs is 10-fold higher than standard citrate reduction route. The resulting therapeutically active and well-dispersed Ag NPs are used as nanolids to cap the drug loaded nanochannels of porous silica. Upon exposing to H2O2, dissolution-accompanied aggregation of Ag nanolids unleashes the encapsulated therapeutic entities from channels of nanocarrier. Combination of antibacterial and anti-inflammatory drugs in single nanocarriers can potentially augment the effectiveness of various therapies. PMID:25486873

  11. Random errors in egocentric networks

    PubMed Central

    Almquist, Zack W.

    2013-01-01

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

  12. Nested Quantum Error Correction Codes

    E-print Network

    Zhuo Wang; Kai Sun; Hen Fan; Vlatko Vedral

    2009-09-28

    The theory of quantum error correction was established more than a decade ago as the primary tool for fighting decoherence in quantum information processing. Although great progress has already been made in this field, limited methods are available in constructing new quantum error correction codes from old codes. Here we exhibit a simple and general method to construct new quantum error correction codes by nesting certain quantum codes together. The problem of finding long quantum error correction codes is reduced to that of searching several short length quantum codes with certain properties. Our method works for all length and all distance codes, and is quite efficient to construct optimal or near optimal codes. Two main known methods in constructing new codes from old codes in quantum error-correction theory, the concatenating and pasting, can be understood in the framework of nested quantum error correction codes.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  17. The lipoxygenase inhibitor phenidone protects against proteinuria and stroke in stroke-prone spontaneously hypertensive rats.

    PubMed

    Munsiff, A V; Chander, P N; Levine, S; Stier, C T

    1992-02-01

    The present study examined whether the dual cyclooxygenase/lipoxygenase inhibitor phenidone would protect stroke-prone spontaneously hypertensive rats (SHRSP) from stroke and hypertensive renal disease. Vehicle-treated SHRSP (N = 6), fed stroke-prone rodent diet and 1% saline, exhibited severe systolic blood pressure elevation (261 +/- 10 mm Hg, mean +/- SEM), marked proteinuria (90 +/- 12 mg/day), and stroke, with an average age at death of 14 +/- 1 weeks. In a second group of six saline-loaded SHRSP, treatment with phenidone (60 mg/kg/day) was started at 8.4 weeks of age. Despite establishment of severe hypertension in this group (274 +/- 10 mm Hg), proteinuria remained at basal levels (28 +/- 13 mg/day), and signs of stroke were absent (P less than .01 v vehicle) through at least 16 weeks of age. Phenidone treatment also prevented the declines in body weight and food intake observed in vehicle-treated SHRSP, and maintained urine volume and saline intake. Serum 12-hydroxy-eicosatetraenoic acid (12-HETE) generation was significantly inhibited greater than 50% in incubates of whole blood from phenidone-treated SHRSP. We have previously shown that agents which interfere with the renin-angiotensin system afford protection from renal and cerebrovascular injury in saline-loaded SHRSP; cyclooxygenase inhibition alone will hasten the onset of these pathologic changes. Whether phenidone, which has been reported to attenuate angiotensin II-mediated effects, affords vascular protection by interference with a lipoxygenase-mediated action of angiotensin II remains to be elucidated. PMID:1550666

  18. Galactic-orbit eccentricity errors

    NASA Astrophysics Data System (ADS)

    Kutuzov, S. A.

    1987-08-01

    Expressions for eccentricities in terms of the motion integrals are found for a model of the Galactic gravitational field. Exact formulas are used to ascertain the influence of errors in heliocentric distance, radial velocity, and proper motion on eccentricity errors. Due to the proper motion errors, there is a tendency to overestimate the values of small eccentricities (the higher they are, the greater the distance).

  19. 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 15mg/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

  20. Contour Error Map Algorithm

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  1. Replaceable Microfluidic Cartridges for a PCR Biosensor

    NASA Technical Reports Server (NTRS)

    Francis, Kevin; Sullivan, Ron

    2005-01-01

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

  2. Compensating For GPS Ephemeris Error

    NASA Technical Reports Server (NTRS)

    Wu, Jiun-Tsong

    1992-01-01

    Method of computing position of user station receiving signals from Global Positioning System (GPS) of navigational satellites compensates for most of GPS ephemeris error. Present method enables user station to reduce error in its computed position substantially. User station must have access to two or more reference stations at precisely known positions several hundred kilometers apart and must be in neighborhood of reference stations. Based on fact that when GPS data used to compute baseline between reference station and user station, vector error in computed baseline is proportional ephemeris error and length of baseline.

  3. Retransmission error control with memory

    NASA Technical Reports Server (NTRS)

    Sindhu, P. S.

    1977-01-01

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

  4. A theory of human error

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  6. ERROR CORRELATION AND ERROR REDUCTION IN ENSEMBLE CLASSIFIERS

    E-print Network

    Tumer, Kagan

    ERROR CORRELATION AND ERROR REDUCTION IN ENSEMBLE CLASSIFIERS Kagan Tumer and Joydeep Ghosh generalizations by realizing different decision boundaries (Ghosh and Tumer, 1994). For example, when values (Lincoln and Skrzypek, 1990; Perrone and Cooper, 1993b; Tumer and Ghosh, 1996). Weighted averaging

  7. Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy

    E-print Network

    Quake, Stephen R.

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

  8. TqPCR: A Touchdown qPCR Assay with Significantly Improved Detection Sensitivity and Amplification Efficiency of SYBR Green qPCR

    PubMed Central

    Zhang, Qian; Wang, Jing; Deng, Fang; Yan, Zhengjian; Xia, Yinglin; Wang, Zhongliang; Ye, Jixing; Deng, Youlin; Zhang, Zhonglin; Qiao, Min; Li, Ruifang; Denduluri, Sahitya K.; Wei, Qiang; Zhao, Lianggong; Lu, Shun; Wang, Xin; Tang, Shengli; Liu, Hao; Luu, Hue H.; Haydon, Rex C.; He, Tong-Chuan; Jiang, Li

    2015-01-01

    The advent of fluorescence-based quantitative real-time PCR (qPCR) has revolutionized the quantification of gene expression analysis in many fields, including life sciences, agriculture, forensic science, molecular diagnostics, and medicine. While SYBR Green-based qPCR is the most commonly-used platform due to its inexpensive nature and robust chemistry, quantifying the expression of genes with low abundance or RNA samples extracted from highly restricted or limited sources can be challenging because the detection sensitivity of SYBR Green-based qPCR is limited. Here, we develop a novel and effective touchdown qPCR (TqPCR) protocol by incorporating a 4-cycle touchdown stage prior to the quantification amplification stage. Using the same cDNA templates, we find that TqPCR can reduce the average Cq values for Gapdh, Rps13, and Hprt1 reference genes by 4.45, 5.47, and 4.94 cycles, respectively, when compared with conventional qPCR; the overall average Cq value reduction for the three reference genes together is 4.95. We further find that TqPCR can improve PCR amplification efficiency and thus increase detection sensitivity. When the quantification of Wnt3A-induced target gene expression in mesenchymal stem cells is analyzed, we find that, while both conventional qPCR and TqPCR can detect the up-regulation of the relatively abundant target Axin2, only TqPCR can detect the up-regulation of the lowly-expressed targets Oct4 and Gbx2. Finally, we demonstrate that the MRQ2 and MRQ3 primer pairs derived from mouse reference gene Tbp can be used to validate the RNA/cDNA integrity of qPCR samples. Taken together, our results strongly suggest that TqPCR may increase detection sensitivity and PCR amplification efficiency. Overall, TqPCR should be advantageous over conventional qPCR in expression quantification, especially when the transcripts of interest are lowly expressed, and/or the availability of total RNA is highly restricted or limited. PMID:26172450

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

    USGS Publications Warehouse

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

    2005-01-01

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

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

    E-print Network

    Tsai, Ming-Daw

    Virus Sandeep Kumar, Brandon J. Lamarche, and Ming-Daw Tsai* Departments of Chemistry and Biochemistry, The Biophysics Program, and The Ohio State Biochemistry Program, The Ohio State UniVersity, Columbus, Ohio 43210 a vaccine to prevent ASFV infection nor a treatment for infected pigs is currently available, ASFV outbreaks

  11. Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein

    PubMed Central

    Yuan, Ying; Britton, Sébastien; Delteil, Christine; Coates, Julia; Jackson, Stephen P.; Barboule, Nadia; Frit, Philippe; Calsou, Patrick

    2015-01-01

    In humans, DNA double-strand breaks (DSBs) are repaired by two mutually-exclusive mechanisms, homologous recombination or end-joining. Among end-joining mechanisms, the main process is classical non-homologous end-joining (C-NHEJ) which relies on Ku binding to DNA ends and DNA Ligase IV (Lig4)-mediated ligation. Mostly under Ku- or Lig4-defective conditions, an alternative end-joining process (A-EJ) can operate and exhibits a trend toward microhomology usage at the break junction. Homologous recombination relies on an initial MRN-dependent nucleolytic degradation of one strand at DNA ends. This process, named DNA resection generates 3? single-stranded tails necessary for homologous pairing with the sister chromatid. While it is believed from the current literature that the balance between joining and recombination processes at DSBs ends is mainly dependent on the initiation of resection, it has also been shown that MRN activity can generate short single-stranded DNA oligonucleotides (ssO) that may also be implicated in repair regulation. Here, we evaluate the effect of ssO on end-joining at DSB sites both in vitro and in cells. We report that under both conditions, ssO inhibit C-NHEJ through binding to Ku and favor repair by the Lig4-independent microhomology-mediated A-EJ process. PMID:26350212

  12. Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein.

    PubMed

    Yuan, Ying; Britton, Sébastien; Delteil, Christine; Coates, Julia; Jackson, Stephen P; Barboule, Nadia; Frit, Philippe; Calsou, Patrick

    2015-12-01

    In humans, DNA double-strand breaks (DSBs) are repaired by two mutually-exclusive mechanisms, homologous recombination or end-joining. Among end-joining mechanisms, the main process is classical non-homologous end-joining (C-NHEJ) which relies on Ku binding to DNA ends and DNA Ligase IV (Lig4)-mediated ligation. Mostly under Ku- or Lig4-defective conditions, an alternative end-joining process (A-EJ) can operate and exhibits a trend toward microhomology usage at the break junction. Homologous recombination relies on an initial MRN-dependent nucleolytic degradation of one strand at DNA ends. This process, named DNA resection generates 3' single-stranded tails necessary for homologous pairing with the sister chromatid. While it is believed from the current literature that the balance between joining and recombination processes at DSBs ends is mainly dependent on the initiation of resection, it has also been shown that MRN activity can generate short single-stranded DNA oligonucleotides (ssO) that may also be implicated in repair regulation. Here, we evaluate the effect of ssO on end-joining at DSB sites both in vitro and in cells. We report that under both conditions, ssO inhibit C-NHEJ through binding to Ku and favor repair by the Lig4-independent microhomology-mediated A-EJ process. PMID:26350212

  13. 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. PMID:22664673

  14. Error coding simulations in C

    NASA Technical Reports Server (NTRS)

    Noble, Viveca K.

    1994-01-01

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

  15. Error estimates of spaceborne passive microwave retrievals of cloud liquid water over land

    SciTech Connect

    Greenwald, T.J.; Combs, C.L.; Jones, A.S.; Randel, D.L.; Vonder Haar, T.H.

    1999-03-01

    Cloud liquid water path (LWP) retrievals from the Special Sensor Microwave/Imager (SSM/I) and surface microwave radiometers are compared over land to assess the errors in selected satellite methods. These techniques require surface emissivity composites created from SSM/I and infrared (IR) data. Two different physical methods are tested: a single-channel (SC) approach; and a normalized polarization difference (NPD) approach. Comparisons were made at four sites in Oklahoma and Kansas over an 1-month period. The 85.5-GHz NPD method was the most accurate and robust under most conditions. An error analysis shows that the method`s random errors are dominated by uncertainties in the surface emissivity and instrument noise. Since the SC method is more prone to systematic errors (such as surface emissivity errors caused by rain events), it initially compared poorly to the ground observations. After filtering for rain events, the comparisons improved. Overall, the root mean square (rms) errors ranged from 0.12 to 0.14 kg m{sup {minus}2}, suggesting these methods can provide, at best, three categories of cloud LWP. It is anticipated that the techniques and strategies developed in this study, and prior related studies, to analyze passive microwave data will be requisite for maximizing the information content of future instruments.

  16. Determining Fungi rRNA Copy Number by PCR

    EPA Science Inventory

    The goal of this project is to improve the quantification of indoor fungal pollutants via the specific application of quantitative PCR (qPCR). Improvement will be made in the controls used in current qPCR applications. This work focuses on the use of two separate controls within ...

  17. Preparation of Plasmid DNA Preparation of PCR DNA

    E-print Network

    Campbell, A. Malcolm

    Abstract Preparation of Plasmid DNA Preparation of PCR DNA Design of DNA Chip Methods: Oligonucleotide Addition Results Graph ­ PCR vs. Plasmid Conclusions Future Experiment Comparison of the Use of Plasmid and PCR DNA on Microarray Chips Biology Department, Davidson College, Davidson, NC 28035Dan Pierce

  18. Sex GENOTYPING PROTOCOL PCR PROTOCOL NAME: Sex1

    E-print Network

    Shoubridge, Eric

    Sex GENOTYPING PROTOCOL GENE NAME: PCR PROTOCOL NAME: Sex1 PCR REAGENTS: 10X NEB THERMOPOL PCR) PRIMERS: Sex1 Forward (20uM Standard Working Concentration) Sex1 Reverse (20uM Standard Working CONDITIONS: Sex (or Sex1) 95 C for 3 min 95 C for 30 sec 60 C for 1 min 35 cycles

  19. Quantum error correction for continuously detected errors with any number of error channels per qubit

    E-print Network

    Charlene Ahn; H. M. Wiseman; Kurt Jacobs

    2004-02-10

    It was shown by Ahn, Wiseman, and Milburn [PRA {\\bf 67}, 052310 (2003)] that feedback control could be used as a quantum error correction process for errors induced by weak continuous measurement, given one perfectly measured error channel per qubit. Here we point out that this method can be easily extended to an arbitrary number of error channels per qubit. We show that the feedback protocols generated by our method encode $n-2$ logical qubits in $n$ physical qubits, thus requiring just one more physical qubit than in the previous case.

  20. Explaining Errors in Children's Questions

    ERIC Educational Resources Information Center

    Rowland, Caroline F.

    2007-01-01

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

  1. Dual Processing and Diagnostic Errors

    ERIC Educational Resources Information Center

    Norman, Geoff

    2009-01-01

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

  2. Barriers to Medical Error Reporting

    PubMed Central

    Poorolajal, Jalal; Rezaie, Shirin; Aghighi, Negar

    2015-01-01

    Background: This study was conducted to explore the prevalence of medical error underreporting and associated barriers. Methods: This cross-sectional study was performed from September to December 2012. Five hospitals, affiliated with Hamadan University of Medical Sciences, in Hamedan, Iran were investigated. A self-administered questionnaire was used for data collection. Participants consisted of physicians, nurses, midwives, residents, interns, and staffs of radiology and laboratory departments. Results: Overall, 50.26% of subjects had committed but not reported medical errors. The main reasons mentioned for underreporting were lack of effective medical error reporting system (60.0%), lack of proper reporting form (51.8%), lack of peer supporting a person who has committed an error (56.0%), and lack of personal attention to the importance of medical errors (62.9%). The rate of committing medical errors was higher in men (71.4%), age of 50–40 years (67.6%), less-experienced personnel (58.7%), educational level of MSc (87.5%), and staff of radiology department (88.9%). Conclusions: This study outlined the main barriers to reporting medical errors and associated factors that may be helpful for healthcare organizations in improving medical error reporting as an essential component for patient safety enhancement. PMID:26605018

  3. Dyslexia and Oral Reading Errors

    ERIC Educational Resources Information Center

    Singleton, Chris

    2005-01-01

    Thomson was the first of very few researchers to have studied oral reading errors as a means of addressing the question: Are dyslexic readers different to other readers? Using the Neale Analysis of Reading Ability and Goodman's taxonomy of oral reading errors, Thomson concluded that dyslexic readers are different, but he found that they do not…

  4. Christopher Monckton Gore's 10 Errors

    E-print Network

    by Christopher Monckton Gore's 10 Errors Old and New Scientific mistakes and exaggerations anything upon insufficient evidence. W. K. Clifford #12;3 Gore's 10 errors old and new Scientific mistakes warming pollution" is Gore's favorite phrase for "carbon dioxide." However, CO2 is not a pollutant

  5. Children's Scale Errors with Tools

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  6. A theory of human error

    NASA Technical Reports Server (NTRS)

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

    1981-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  8. Borderline Personality Features and Implicit Shame-Prone Self-Concept in Middle Childhood and Early Adolescence

    ERIC Educational Resources Information Center

    Hawes, David J.; Helyer, Rebekah; Herlianto, Eugene C.; Willing, Jonah

    2013-01-01

    This study tested if children and adolescents with high levels of borderline personality features (BPF) exhibit the same shame-prone self-concept previously found to characterize adults with borderline personality disorder (Rusch et al., 2007). Self-concept was indexed using the Implicit Association Test, in a community sample of…

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

    EPA Science Inventory

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

  10. The management of fire-prone forests, especially within the national forests of the west, is one of the

    E-print Network

    California at Berkeley, University of

    The management of fire-prone forests, especially within the national forests of the west, is one for Conservation Biology convened a scientific panel to review issues related to the ecology and management of fire. 2006a). The vegetation of North America has been shaped by recurring fires over millions of years

  11. Early Identification of Delinquency Prone Youth. The Eau Claire County Youth Study, Phase IV, 1969-1972.

    ERIC Educational Resources Information Center

    Feldhusen, John F.; And Others

    Procedures for early identification of delinquency-prone youth in Eau Claire County, Wisconsin, are described in this report of a 1961-1972 study designed to delineate the problems of aggressive and disruptive classroom behavior as related to delinquency. Data collection began in 1961, when each 3rd-, 6th-, and 9th-grade teacher in Eau Claire…

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

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  13. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Requirements for Flood...

  14. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 44 Emergency Management and Assistance 1 2012-10-01 2011-10-01 true Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Requirements for Flood...

  15. 44 CFR 60.4 - Flood plain management criteria for mudslide (i.e., mudflow)-prone areas.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Flood plain management... National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Requirements for Flood Plain Management Regulations § 60.4 Flood plain management criteria for mudslide (i.e., mudflow)-prone areas....

  16. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 44 Emergency Management and Assistance 1 2014-10-01 2014-10-01 false Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Requirements for Flood...

  17. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Requirements for Flood...

  18. 44 CFR 60.5 - Flood plain management criteria for flood-related erosion-prone areas.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 44 Emergency Management and Assistance 1 2013-10-01 2013-10-01 false Flood plain management criteria for flood-related erosion-prone areas. 60.5 Section 60.5 Emergency Management and Assistance... National Flood Insurance Program CRITERIA FOR LAND MANAGEMENT AND USE Requirements for Flood...

  19. When Passive Feels Active - Delusion-Proneness Alters Self-Recognition in the Moving Rubber Hand Illusion

    PubMed Central

    Louzolo, Anaïs; Kalckert, Andreas; Petrovic, Predrag

    2015-01-01

    Psychotic patients have problems with bodily self-recognition such as the experience of self-produced actions (sense of agency) and the perception of the body as their own (sense of ownership). While it has been shown that such impairments in psychotic patients can be explained by hypersalient processing of external sensory input it has also been suggested that they lack normal efference copy in voluntary action. However, it is not known how problems with motor predictions like efference copy contribute to impaired sense of agency and ownership in psychosis or psychosis-related states. We used a rubber hand illusion based on finger movements and measured sense of agency and ownership to compute a bodily self-recognition score in delusion-proneness (indexed by Peters’ Delusion Inventory - PDI). A group of healthy subjects (n=71) experienced active movements (involving motor predictions) or passive movements (lacking motor predictions). We observed a highly significant correlation between delusion-proneness and self-recognition in the passive conditions, while no such effect was observed in the active conditions. This was seen for both ownership and agency scores. The result suggests that delusion-proneness is associated with hypersalient external input in passive conditions, resulting in an abnormal experience of the illusion. We hypothesize that this effect is not present in the active condition because deficient motor predictions counteract hypersalience in psychosis proneness. PMID:26090797

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

    ERIC Educational Resources Information Center

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

    2006-01-01

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

  1. Spatial and temporal variability of seismic noise records on landslide-prone slopes

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    The assessment of the influence of slope dynamic response on earthquake landslide triggering is hampered by the scarcity of accelerometric data acquired on slopes prone to seismic failures. Previous studies showed that the spectral analysis of 3-component recordings of seismic noise can represent a promising tool for the characterisation of slope dynamic response. In this case the main method of analysis is based on the calculation of horizontal-to-vertical spectral ratios of noise recordings (HVNR). However, this method was originally designed to investigate properties of litostratigraphic amplification of sites with simple setting as approximated by 1D layering; thus its application to hillslope sites affected by 2D-3D and anisotropic amplification effects requires further tests to verify which properties of seismic response can be reliably obtained. For a fruitful interpretation of seismic noise recordings the main problems that needs to be addressed are i) the extension of analysis to frequencies below 1 Hz and ii) the temporal consistency and spatial resolution of noise recordings. The extension of analysis from microtremor frequencies (>1 Hz), mainly of anthropic origin, to microseismic frequencies (< 1Hz) of natural origin is desirable, in that lower frequencies can be more relevant for triggering of large landslides. However the reliability of the results of low frequency noise analysis strongly depends on the adequate response of portable instruments at such frequencies and on the influence of changing environmental conditions. Regarding the problem of spatial-temporal variability of noise signal, we stress that directional properties of site response can be masked by polarisation properties of transient noise sources and that the spatial scale of geological and morphological features causing directivity is still unclear. Thus, the repeatability of noise analysis results, as well as their spatial resolution and representativeness need to be verified through comparisons of noise recordings suitably arranged in space and time. With this motivation a series of tests of seismic noise recordings and analyses are in progress on landslide-prone slopes at Caramanico Terme, in central Italy, where the results of noise analysis can be compared with those derived from a long term accelerometric monitoring. In particular repeated noise recordings are carried out both at the same site and at different sites using simultaneously seismic sensors having different frequency response. The first results indicate that directional properties of site response appear to characterise landslide prone slopes also at frequencies lower than 1 Hz, even though in this case ad hoc methods of analysis need to be used to reveal such effects. Furthermore, the tests of seismic noise recordings conducted at different times and with different sensors show that ground motion anisotropy due to site response directivity can be discriminated from that related to noise source polarisation by few repetitions of noise data acquisitions of proper duration.

  2. Digital stereo photogrammetry for grain-scale monitoring of fluvial surfaces: Error evaluation and workflow optimisation

    NASA Astrophysics Data System (ADS)

    Bertin, Stephane; Friedrich, Heide; Delmas, Patrice; Chan, Edwin; Gimel'farb, Georgy

    2015-03-01

    Grain-scale monitoring of fluvial morphology is important for the evaluation of river system dynamics. Significant progress in remote sensing and computer performance allows rapid high-resolution data acquisition, however, applications in fluvial environments remain challenging. Even in a controlled environment, such as a laboratory, the extensive acquisition workflow is prone to the propagation of errors in digital elevation models (DEMs). This is valid for both of the common surface recording techniques: digital stereo photogrammetry and terrestrial laser scanning (TLS). The optimisation of the acquisition process, an effective way to reduce the occurrence of errors, is generally limited by the use of commercial software. Therefore, the removal of evident blunders during post processing is regarded as standard practice, although this may introduce new errors. This paper presents a detailed evaluation of a digital stereo-photogrammetric workflow developed for fluvial hydraulic applications. The introduced workflow is user-friendly and can be adapted to various close-range measurements: imagery is acquired with two Nikon D5100 cameras and processed using non-proprietary "on-the-job" calibration and dense scanline-based stereo matching algorithms. Novel ground truth evaluation studies were designed to identify the DEM errors, which resulted from a combination of calibration errors, inaccurate image rectifications and stereo-matching errors. To ensure optimum DEM quality, we show that systematic DEM errors must be minimised by ensuring a good distribution of control points throughout the image format during calibration. DEM quality is then largely dependent on the imagery utilised. We evaluated the open access multi-scale Retinex algorithm to facilitate the stereo matching, and quantified its influence on DEM quality. Occlusions, inherent to any roughness element, are still a major limiting factor to DEM accuracy. We show that a careful selection of the camera-to-object and baseline distance reduces errors in occluded areas and that realistic ground truths help to quantify those errors.

  3. DNA fingerprinting of medically important microorganisms by use of PCR.

    PubMed Central

    van Belkum, A

    1994-01-01

    Selected segments of any DNA molecule can be amplified exponentially by PCR. This technique provides a powerful tool to detect and identify minimal numbers of microorganisms. PCR is applicable both in diagnosis and in epidemiology. By amplification of hypervariable DNA domains, differences can be detected even among closely related strains. PCR fingerprinting is a valuable tool for medical microbiologists, epidemiologists, and microbial taxonomists. The current state of PCR-mediated genotyping is reviewed, and a comparison with conventional molecular typing methods is included. Because of its speed and versatility, PCR fingerprinting will play an important role in microbial genetics, epidemiology, and systematics. Images PMID:8055466

  4. Quantitative Real-Time PCR (qPCR) Workflow for Analyzing Staphylococcus aureus Gene Expression.

    PubMed

    Lewis, April M; Rice, Kelly C

    2016-01-01

    Quantitative real-time polymerase chain reaction (qPCR) is a sensitive tool that can be used to quantify and compare the amount of specific RNA transcripts between different biological samples. This chapter describes the use of a "two-step" qPCR method to calculate the relative fold change of expression of genes of interest in S. aureus. Using this work-flow, cDNA is synthesized from RNA templates (previously checked for the absence of significant genomic DNA contamination) using a cocktail of random primers and reverse-transcriptase enzyme. The cDNA pools generated can then be assessed for expression of specific genes of interest using SYBR Green-based qPCR and quantification of relative fold-change expression. PMID:25646613

  5. An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

    PubMed Central

    Pruvost, Mélanie; Bennett, E. Andrew; Grange, Thierry; Geigl, Eva-Maria

    2010-01-01

    Background PCR amplification of minute quantities of degraded DNA for ancient DNA research, forensic analyses, wildlife studies and ultrasensitive diagnostics is often hampered by contamination problems. The extent of these problems is inversely related to DNA concentration and target fragment size and concern (i) sample contamination, (ii) laboratory surface contamination, (iii) carry-over contamination, and (iv) contamination of reagents. Methodology/Principal Findings Here we performed a quantitative evaluation of current decontamination methods for these last three sources of contamination, and developed a new procedure to eliminate contaminating DNA contained in PCR reagents. We observed that most current decontamination methods are either not efficient enough to degrade short contaminating DNA molecules, rendered inefficient by the reagents themselves, or interfere with the PCR when used at doses high enough to eliminate these molecules. We also show that efficient reagent decontamination can be achieved by using a combination of treatments adapted to different reagent categories. Our procedure involves ?- and UV-irradiation and treatment with a mutant recombinant heat-labile double-strand specific DNase from the Antarctic shrimp Pandalus borealis. Optimal performance of these treatments is achieved in narrow experimental conditions that have been precisely analyzed and defined herein. Conclusions/Significance There is not a single decontamination method valid for all possible contamination sources occurring in PCR reagents and in the molecular biology laboratory and most common decontamination methods are not efficient enough to decontaminate short DNA fragments of low concentration. We developed a versatile multistrategy decontamination procedure for PCR reagents. We demonstrate that this procedure allows efficient reagent decontamination while preserving the efficiency of PCR amplification of minute quantities of DNA. PMID:20927390

  6. Reorganization of the flood-prone atmospheric patterns at the onset of the 20th century?

    NASA Astrophysics Data System (ADS)

    Wilhelm, Bruno; Vogel, Hendrik; Anselmetti, Flavio

    2015-04-01

    Frequency and intensity of heavy rainfalls, triggering floods and causing human and large economic losses, are expected to increase in the context of the global warming, due to the larger water carrying capacity of warmer air masses. However, the relationship between such events and climatic changes remains still poorly understood. In particular, the stability of the flood-prone atmospheric circulations under future climate changes is a key question for projections of extreme precipitation. This study aims at exploring this issue using flood reconstructions from the NW Mediterranean domain. We compiled existing historical records from the Southern Massif Central and lake-sediment records from the Eastern Pyrenees and the Southern French Alps. We completed this West-East transect by studying new lake sequences in the SE French Alps and the Western Italian Alps. For both of the new lake sediment sequences (Lake Foréant, Queyras massif, France and Lago Inferiore di Laurès, Aosta valley, Italy), several short cores were retrieved to understand the sedimentary processes. In the laboratory, high-resolution pictures, bulk density, geochemistry and grain size were measured. Dating was undertaken by short-lived radionuclides (EAWAG, Zürich) and radiocarbon (University of Bern) measurements. Lago Inferiore sequence covers the last 250 years and Lake Foréant sequence the last millennium. 232 turbidites were identified; 11 of which seem to be related to mass movements, whereas the other 221 were triggered by flood events. The reconstructed flood regimes were then compared to local flood activity based on historical data. The good agreement between the datasets supports the quality and sensitivity of flood reconstructions. In the NW Mediterranean domain, floods and related heavy rainfalls are mostly triggered by autumn humid air masses coming from the Mediterranean Sea. In detail, distinct atmospheric pathways transport these air masses and trigger floods in the different studied regions. Comparing all the flood reconstructions over the last 250 years aims at tracking these atmospheric pathways and their possible changes over time. Strong similarities in flood frequency are observed from 1750 to 1900 for the western part (Cévennes, Southern French Alps), while no convincing correlation appears between the other records. Around 1900, a drastic change appears with strong similarities between records of the eastern part (Southern Alps, SE French Alps and NW Italian Alps). In particular, the flood frequency largely increased in the Cévennes during the first part of the 20th century, while this period is one of the most 'quiet' in all other records. Hence, these results suggest a reorganization of the flood-prone atmospheric patterns at the onset of the 20th century.

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

    NASA Technical Reports Server (NTRS)

    Barr, Yael; Fogarty, Jennifer

    2010-01-01

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

  8. Differential mesocorticolimbic responses to palatable food in binge eating prone and binge eating resistant female rats.

    PubMed

    Sinclair, Elaine B; Culbert, Kristen M; Gradl, Dana R; Richardson, Kimberlei A; Klump, Kelly L; Sisk, Cheryl L

    2015-12-01

    Binge eating is a key symptom of many eating disorders (e.g. binge eating disorder, bulimia nervosa, anorexia nervosa binge/purge type), yet the neurobiological underpinnings of binge eating are poorly understood. The mesocorticolimbic reward circuit, including the nucleus accumbens and the medial prefrontal cortex, is likely involved because this circuit mediates the hedonic value and incentive salience of palatable foods (PF). Here we tested the hypothesis that higher propensity for binge eating is associated with a heightened response (i.e., Fos induction) of the nucleus accumbens and medial prefrontal cortex to PF, using an animal model that identifies binge eating prone (BEP) and binge eating resistant (BER) rats. Forty adult female Sprague-Dawley rats were given intermittent access to PF (high fat pellets) 3×/week for 3weeks. Based on a pattern of either consistently high or consistently low PF consumption across these feeding tests, 8 rats met criteria for categorization as BEP, and 11 rats met criteria for categorization as BER. One week after the final feeding test, BEP and BER rats were either exposed to PF in their home cages or were given no PF in their home cages for 1h prior to perfusion, leading to three experimental groups for the Fos analysis: BEPs given PF, BERs given PF, and a No PF control group. The total number of Fos-immunoreactive (Fos-ir) cells in the nucleus accumbens core and shell, and the cingulate, prelimbic, and infralimbic regions of the medial prefrontal cortex was estimated by stereological analysis. PF induced higher Fos expression in the nucleus accumbens shell and core and in the prelimbic and infralimbic cortex of BEP rats compared to No PF controls. Throughout the nucleus accumbens and medial prefrontal cortex, PF induced higher Fos expression in BEP than in BER rats, even after adjusting for differences in PF intake. Differences in the neural activation pattern between BEP and BER rats were more robust in prefrontal cortex than in nucleus accumbens. These data confirm that PF activates brain regions responsible for encoding the incentive salience and hedonic properties of PF, and suggest that binge eating proneness is associated with enhanced responses to PF in brain regions that exert executive control over food reward. PMID:26459117

  9. Delineation of Flood Prone Areas using Digital Elevation Models: Scale Dependence

    NASA Astrophysics Data System (ADS)

    di Leo, M.; Manfreda, S.; Sole, A.; Fiorentino, M.

    2009-04-01

    The delineation of the areas subject to flood inundations raises complex problems regarding the definition of hydrological forcing and the parametrization of models for flood wave propagation (e.g., Horritt & Bates, 2000, 2002). The increasing availability of new technologies for the measurement of surface elevation (eg GPS, SAR interferometry, radar and laser altimetry) led to an increase in the attraction of DEM-based procedures for the delineation of floodplains. In recent years, much effort has gone into the identification of flood prone areas through the use of hydrological and hydraulic studies carried out by River Basin Authorities (public institutions dedicated to river basins management). These studies are generally based on topographic surveys and numerical modelling for the flood wave propagation providing an enormous database rarely used for post processing. Manfreda et al. (2006) have recently used the technical documentation, produced during the definition of Hydrogeological Management Plan by the River Basin Authorities, to define a synthetic procedure for the delineation of flood inundation exposure. The relevance of such techniques lies in the ability to characterize, at least at first approximation, portions of the territory where is not possible to run expensive hydrological-hydraulic simulations. The development of simplified methodologies is taken further in the present study to investigate the relationship between areas exposed to flood inundation and the geomorphologic characteristics of the terrain (contributing area, local slope of the surface, curvature, TOPMODEL topographic index) showing a strong correlation with the TOPMODEL topographic index. Manfreda et al. (2006) also defined a new expression of the topographical index more suited to the task of delineating flood exposure directly from a DEM analysis. This permitted the definition of a fast procedure for the calculation of flood inundation areas using a threshold level (ITms) to discriminate between areas exposed to flood inundation and non exposed areas. The objective of the study is to estimate the optimal threshold level for the identification of flood prone areas and the scale dependence of the methodology. This approach was applied over several Italian catchments and sub-catchments of different sizes and using DEMs at resolution changing from 2m up to 230m.

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

    NASA Astrophysics Data System (ADS)

    Rockström, Johan; Barron, Jennie; Fox, Patrick

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

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

    SciTech Connect

    Li Ping; Napel, Sandy; Acar, Burak; Paik, David S.; Jeffrey, R. Brooke Jr.; Beaulieu, Christopher F.

    2004-10-01

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

  12. Relationship between C-reactive protein concentration and cytokine responses to exercise in healthy and illness-prone runners.

    PubMed

    Cox, Amanda J; Pyne, David B; Gleeson, Maree; Callister, Robin

    2009-11-01

    Differences in the immune and inflammatory response to exercise between healthy and illness-prone athletes may be one explanation why some athletes experience a greater incidence of upper respiratory symptoms than others. The aim of this study was to compare the C-reactive protein (CRP) response to acute exercise between healthy and illness-prone trained distance runners. Runners were classified as healthy (< or =2 episodes of upper respiratory symptoms per year; n = 10) or illness-prone (> or =4 episodes per year; n = 8) and completed three treadmill running protocols. CRP concentrations were determined prior to and 24 h following each exercise protocol and responses compared between the two groups. Plasma concentrations of Interleukin (IL)-6, IL-8, IL-10 and the IL-1 receptor antagonist (IL-1ra) were also determined immediately, 1 h, 10 h and 24 h post-exercise. The CRP response at 24 h post-exercise was not substantially different between healthy and illness-prone athletes (approximately 2-10%). There were small to moderate correlations between resting CRP concentrations and the peak IL-6 (r = 0.28, P = 0.04), IL-8 (r = 0.31, P = 0.03), IL-10 (r = 0.28, P = 0.05) and IL-1ra (r = 0.30, P = 0.03) concentrations post-exercise. The CRP response to exercise was not useful in distinguishing between healthy and illness-prone athletes. The relationship between resting CRP concentrations and the peak pro- and anti-inflammatory responses to exercise supports the likely involvement of CRP in the complex network regulating exercise-induced inflammatory disturbance. PMID:19693532

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

    SciTech Connect

    Lymberis, Stella C.; Wyngaert, John Keith de; Parhar, Preeti; Chhabra, Arpit M.; Fenton-Kerimian, Maria; Chang Jengwha; Hochman, Tsivia; Department of Environmental Medicine, New York University School of Medicine and Langone Medical Center, New York, New York ; Guth, Amber; Roses, Daniel; Goldberg, Judith D.; Department of Environmental Medicine, New York University School of Medicine and Langone Medical Center, New York, New York ; Formenti, Silvia C.

    2012-11-15

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

  14. Photometric Redshifts and Photometry Errors

    E-print Network

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

    2007-09-21

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

  15. Errors, error detection, error correction and hippocampal-region damage: data and theories.

    PubMed

    MacKay, Donald G; Johnson, Laura W

    2013-11-01

    This review and perspective article outlines 15 observational constraints on theories of errors, error detection, and error correction, and their relation to hippocampal-region (HR) damage. The core observations come from 10 studies with H.M., an amnesic with cerebellar and HR damage but virtually no neocortical damage. Three studies examined the detection of errors planted in visual scenes (e.g., a bird flying in a fish bowl in a school classroom) and sentences (e.g., I helped themselves to the birthday cake). In all three experiments, H.M. detected reliably fewer errors than carefully matched memory-normal controls. Other studies examined the detection and correction of self-produced errors, with controls for comprehension of the instructions, impaired visual acuity, temporal factors, motoric slowing, forgetting, excessive memory load, lack of motivation, and deficits in visual scanning or attention. In these studies, H.M. corrected reliably fewer errors than memory-normal and cerebellar controls, and his uncorrected errors in speech, object naming, and reading aloud exhibited two consistent features: omission and anomaly. For example, in sentence production tasks, H.M. omitted one or more words in uncorrected encoding errors that rendered his sentences anomalous (incoherent, incomplete, or ungrammatical) reliably more often than controls. Besides explaining these core findings, the theoretical principles discussed here explain H.M.'s retrograde amnesia for once familiar episodic and semantic information; his anterograde amnesia for novel information; his deficits in visual cognition, sentence comprehension, sentence production, sentence reading, and object naming; and effects of aging on his ability to read isolated low frequency words aloud. These theoretical principles also explain a wide range of other data on error detection and correction and generate new predictions for future test. PMID:23999403

  16. see Type I decision error see Type II decision error

    E-print Network

    -1, 12, 22; 4-11; 5-46 to 51; 7-7; 8-1, 2, 15, 16, 22, 24, 27; A-5; N-16 areas 2-5 HSA/scoping 2 INDEX see Type I decision error see Type II decision error 91b material 3-5 Amin area-25; 8-11, 17 area evaluation & HSA 3-11 classification 2-4, 5, 17, 28; 4-11 contaminated 2-3 land

  17. Error compensation for thermally induced errors on a machine tool

    SciTech Connect

    Krulewich, D.A.

    1996-11-08

    Heat flow from internal and external sources and the environment create machine deformations, resulting in positioning errors between the tool and workpiece. There is no industrially accepted method for thermal error compensation. A simple model has been selected that linearly relates discrete temperature measurements to the deflection. The biggest problem is how to locate the temperature sensors and to determine the number of required temperature sensors. This research develops a method to determine the number and location of temperature measurements.

  18. Rapid micro-PCR system for hepatitis C virus amplification

    NASA Astrophysics Data System (ADS)

    Lin, Yu-Cheng; Huang, Ming-Yuan; Young, Kung-Chia; Chang, Ting-Tsung; Wu, Ching-Yi

    2000-08-01

    A rapid micro-polymerase chain reaction ((mu) -PCR) system was integrated to amplify the complementary DNA (cDNA) molecules of hepatitis C virus (HCV). This system consists of a rapid thermal cycling system and a (mu) PCR chip fabricated by MEMS fabrication techniques. This rapid (mu) PCR system is verified by using serum samples from patients with chronic hepatitis C. The HCV amplicon of the rapid (mu) PCR system was analyzed by slab gel electrophoresis with separation of DNA marker in parallel. The (mu) PCR chip was fabricated on silicon wafer and Pyrex glass using photolithography, wet etching, and anodic bonding methods. Using silicon material to fabricate the raction well improves the temperature uniformity of sample and helps to reach the desired temperature faster. The rapid close loop thermal cycling system comprises power supplies, a thermal generator, a computer control PID controller, and a data acquisition subsystem. The thermoelectric (T.E.) cooler is used to work as the thermal generator and a heat sink by controlling the polarity of supplied power. The (mu) PCR system was verified with traditional PCR equipment by loading the same PCR mixture with HCV cDNA and running the same cycle numbers, then comparing both HCV amplicon slab gel electrophoresis. The HCV amplicon from the (mu) PCR system shows a DNA fragment with an expected size of 145 base pairs. The background is lower with the (mu) PCR system than that with the tradional PCR equipment. Comparing the traditional PCR equipment which spends 5.5 hours for 30 cycles to gain the detectable amount of HCV amplicon in slab gel separation, this (mu) PCR system takes 30 minutes to finish the 30 thermal cycles. This work has demonstrated that this rapid (mu) PCR system can provide rapid heat generation and dissipation, improved temperature uniformity in DNA amplification.

  19. Stochastic Models of Human Errors

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

    Humans play an important role in the overall reliability of engineering systems. More often accidents and systems failure are traced to human errors. Therefore, in order to have meaningful system risk analysis, the reliability of the human element must be taken into consideration. Describing the human error process by mathematical models is a key to analyzing contributing factors. Therefore, the objective of this research effort is to establish stochastic models substantiated by sound theoretic foundation to address the occurrence of human errors in the processing of the space shuttle.

  20. Error bounds in cascading regressions

    USGS Publications Warehouse

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

    1985-01-01

    Cascading regressions is a technique for predicting a value of a dependent variable when no paired measurements exist to perform a standard regression analysis. Biases in coefficients of a cascaded-regression line as well as error variance of points about the line are functions of the correlation coefficient between dependent and independent variables. Although this correlation cannot be computed because of the lack of paired data, bounds can be placed on errors through the required properties of the correlation coefficient. The potential meansquared error of a cascaded-regression prediction can be large, as illustrated through an example using geomorphologic data. ?? 1985 Plenum Publishing Corporation.

  1. Mars gravitational field estimation error

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

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

  2. Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial

    PubMed Central

    Kapp, Joshua R; Diss, Tim; Spicer, James; Gandy, Michael; Schrijver, Iris; Jennings, Lawrence J; Li, Marilyn M; Tsongalis, Gregory J; de Castro, David Gonzalez; Bridge, Julia A; Wallace, Andrew; Deignan, Joshua L; Hing, Sandra; Butler, Rachel; Verghese, Eldo; Latham, Gary J; Hamoudi, Rifat A

    2015-01-01

    Aims Mutation detection accuracy has been described extensively; however, it is surprising that pre-PCR processing of formalin-fixed paraffin-embedded (FFPE) samples has not been systematically assessed in clinical context. We designed a RING trial to (i) investigate pre-PCR variability, (ii) correlate pre-PCR variation with EGFR/BRAF mutation testing accuracy and (iii) investigate causes for observed variation. Methods 13 molecular pathology laboratories were recruited. 104 blinded FFPE curls including engineered FFPE curls, cell-negative FFPE curls and control FFPE tissue samples were distributed to participants for pre-PCR processing and mutation detection. Follow-up analysis was performed to assess sample purity, DNA integrity and DNA quantitation. Results Rate of mutation detection failure was 11.9%. Of these failures, 80% were attributed to pre-PCR error. Significant differences in DNA yields across all samples were seen using analysis of variance (p<0.0001), and yield variation from engineered samples was not significant (p=0.3782). Two laboratories failed DNA extraction from samples that may be attributed to operator error. DNA extraction protocols themselves were not found to contribute significant variation. 10/13 labs reported yields averaging 235.8?ng (95% CI 90.7 to 380.9) from cell-negative samples, which was attributed to issues with spectrophotometry. DNA measurements using Qubit Fluorometry demonstrated a median fivefold overestimation of DNA quantity by Nanodrop Spectrophotometry. DNA integrity and PCR inhibition were factors not found to contribute significant variation. Conclusions In this study, we provide evidence demonstrating that variation in pre-PCR steps is prevalent and may detrimentally affect the patient's ability to receive critical therapy. We provide recommendations for preanalytical workflow optimisation that may reduce errors in down-stream sequencing and for next-generation sequencing library generation. PMID:25430497

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

    PubMed Central

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

    2015-01-01

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

  4. Telomerase protects cancer-prone human cells from chromosomal instability and spontaneous immortalization.

    PubMed

    Elmore, Lynne W; Turner, Kristi C; Gollahon, Lauren S; Landon, Melissa R; Jackson-Cook, Colleen K; Holt, Shawn E

    2002-01-01

    Studies were conducted to directly test whether the introduction of telomerase protects cancer-prone human mammary epithelial cells from chromosomal instability and spontaneous immortalization. Using a model for Li Fraumeni Syndrome (LFS), infection of human telomerase resulted in maintenance of telomere lengths, extension of in vitro lifespan, and prevention of spontaneous immortalization. In stark contrast to the spontaneously immortalized LFS cells, cells expressing ectopic telomerase displayed a remarkably stable karyotype and even after >150 population doublings, did not express endogenous telomerase. Since the hTERT-infected and spontaneously immortal LFS cells, like the parental cells, exhibit loss of p53 function, our data suggests that telomere shortening is the primary driving force for the genomic instability characteristic of LFS cells, while p53 inactivation is necessary for triggering the spontaneous immortalization event. Collectively, our data indicate that exogenous telomerase prevents chromosomal instability and spontaneous immortalization of LFS cells, suggesting a unique protective role for telomerase in the progression to immortalization. PMID:12432253

  5. Fermented barley extract supplementation ameliorates metabolic state in stroke-prone spontaneously hypertensive rats.

    PubMed

    Ardiansyah; Shirakawa, Hitoshi; Giriwono, Puspo E; Oguchi, Kazuki; Ueda, Kazuma; Hokazono, Hideki; Hiwatashi, Kazuyuki; Takahashi, Saori; Sato, Shoko; Komai, Michio

    2015-11-01

    We studied the effects of fermented barley extract P (FBEP) in stroke-prone spontaneously hypertensive rats (SHRSP). Male 10-week-old SHRSP were divided into three groups that were fed: an AIN-93M diet (control), a low dose of FBEP (4 g/kg; FBEP1), and a high dose of FBEP (20 g/kg; FBEP2) for three weeks. Hypertension was significantly improved by the use of FBEP supplementation. The FBEP diet improved plasma triglyceride, insulin sensitivity, enhanced plasma catalase, and superoxide dismutase activities, and decreased plasma 8-hydroxy-2'-deoxyguanosine levels. In addition, the FBEP diet upregulated hepatic antioxidative genes and modulated Nrf2 protein levels in the liver. Furthermore, a single oral dose of FBEP (2 g/kg body weight) was able to lower blood pressure in SHRSP. In conclusion, our data suggest that increased expression of hepatic antioxidative genes and modulation of Nrf2 may play a role in the regulation of metabolic diseases in SHRSP consuming a FBEP diet. PMID:26072687

  6. Ambient seismic noise monitoring of active landslides and rock columns prone to failure

    NASA Astrophysics Data System (ADS)

    Carrière, Simon; Valentin, Johann; Larose, Eric; Jongmans, Denis; Baillet, Laurent; Bottelin, Pierre; Franz, Martin; Michoud, Clément; Jaboyedoff, Michel

    2015-04-01

    Ambient seismic noise can be used to monitor the integrity of unstable slopes and rock columns prone to failure. To that end, we record continuously seismic waveforms in the fields using 1D or 3D short period seismic sensors together with autonomous and telemetered data loggers that can be operated in severe environmental conditions. When monitoring landslides made of unconsolidated materials (such as clay), we propose to monitor the relative seismic velocity changes using the Coda Wave Interferometry technique operated on the coda of daily ambient seismic noise correlations (Passive Image Interferometry). When monitoring the rupture of a rock column, we propose to track the evolution of the polarization and natural frequencies of the first resonant modes of the structures. In both cases, experimental results suggest potential precursory signals some days before the failure. We also observe a clear dependence of the seismic properties of the soil and environmental conditions such as temperature and hydrology. Bibliography : G. Mainsant, E. Larose, C. Brönnimann, D. Jongmans, C. Michoud, M. Jaboyedoff : Ambient seismic noise monitoring of a clay landslide : toward failure prediction, J. Geophys. Res. 117, F01030 (2012). P. Bottelin, C. Lévy, L. Baillet, D. Jongmans, P. Gueguen, Modal and thermal analysis of les arches unstable rock column (vercors massif, french alps), Geophys. J. Int. 194 (2013) 849-858.

  7. Breast Shape Change Associated with Aging: A Study Using Prone Breast Magnetic Resonance Imaging

    PubMed Central

    Nakadate, Masashi

    2015-01-01

    Background: Objective assessments of the shapes of various parts of the body can be made using images acquired with multidetector row computed tomography or magnetic resonance imaging. These images can be useful for understanding the changes in body shape that accompany aging. Methods: Data from our previous bilateral prone breast magnetic resonance imaging studies between March and August 2013 were analyzed. Breast size and volume were measured using these images. All the patients included in the study were divided into a younger group (54 years or younger) and an older group (55 years or older). The values were compared between the 2 groups using paired t tests. Regarding variables that were shown to have a significant difference between the 2 groups, the relationships between age and the values of the variables were evaluated using the Pearson correlation coefficient. Results: A total of 90 breasts, 45 breasts in the younger group and 45 breasts in the older group, were used for analysis. There was a significant correlation between age and craniocaudal nipple deviation (R = ?0.38; P < 0.001) and between age and the measured breast volume (R = 0.26; P < 0.05). There was also a significant correlation between the measured breast volume and the craniocaudal nipple deviation (R = ?0.48; P < 0.001). Conclusions: A caudal deviation of the nipple and an increase in volume were age-related changes in breast shape. These 2 variables were also correlated. PMID:26180714

  8. Free-flank modified supine vs. prone position in percutaneous nephrolithotomy: A prospective randomised trial

    PubMed Central

    Abdel-Mohsen, Essam; Kamel, Mostafa; Zayed, Abdel-Latif; Salem, Emad A.; Ebrahim, Ehab; Abdel Wahab, Khalid; Elaymen, Ahmed; Shaheen, Ashraf; Kamel, Hussien M.

    2012-01-01

    Objective To compare the technical aspects, operative time, safety and effectiveness of percutaneous nephrolithotomy (PCNL) in the free-flank modified supine position (FFMSP) vs. the standard prone position (SPP). Patients and methods Seventy-seven patients (47 men and 30 women) with renal stones were enrolled and systematically randomised into two groups, A (39 patients) treated using the FFMSP, and B (38 patients) in the SPP. The outcome was considered as a cure (successful procedure) if the patient became stone-free or had residual fragments of <4 mm in diameter. The operative time (from the induction of anaesthesia to the removal of the endotracheal tube) was measured and any operative complications or conflicts were recorded. The different variables were compared and analysed between the groups. Results Patients in both groups had comparable preoperative clinical data and there were no significant differences in the preoperative clinical characteristics. The procedure was successful in 84.6% and 84% of group A and B, respectively. The operative time was significantly longer in group B (SPP) than A (FFMSP). There was no significant difference between the groups in fluoroscopy time and patients’ outcome. Conclusions The FFMSP (with a cushion under the ipsilateral shoulder) has similar efficacy and safety as the SPP for PCNL and is associated with a significantly quicker operation.

  9. Matching 3D Prone and Supine CT Colonography Scans Using Graphs

    PubMed Central

    Wang, Shijun; Petrick, Nicholas; Van Uitert, Robert L.; Periaswamy, Senthil; Wei, Zhuoshi

    2012-01-01

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

  10. Individual Differences in Gambling Proneness among Rats and Common Marmosets: An Automated Choice Task

    PubMed Central

    Manciocco, Arianna; Vitale, Augusto; Laviola, Giovanni

    2014-01-01

    Interest is rising for animal modeling of pathological gambling. Using the operant probabilistic-delivery task (PDT), gambling proneness can be evaluated in laboratory animals. Drawing a comparison with rats, this study evaluated the common marmoset (Callithrix jacchus) using a PDT. By nose- or hand-poking, subjects learnt to prefer a large (LLL, 5-6 pellets) over a small (SS, 1-2 pellets) reward and, subsequently, the probability of occurrence of large-reward delivery was decreased progressively to very low levels (from 100% to 17% and 14%). As probability decreased, subjects showed a great versus little shift in preference from LLL to SS reinforcer. Hence, two distinct subpopulations (“non-gambler” versus “gambler”) were differentiated within each species. A proof of the model validity comes from marmosets' reaction to reward-delivery omission. Namely, depending on individual temperament (“gambler” versus “non-gambler”), they showed either persistence (i.e., inadequate pokes towards LLL) or restlessness (i.e., inadequate pokes towards SS), respectively. In conclusion, the marmoset could be a suitable model for preclinical gambling studies. Implementation of the PDT to species other than rats may be relevant for determining its external validity/generalizability and improving its face/construct validity. PMID:24971360

  11. Individual differences in gambling proneness among rats and common marmosets: an automated choice task.

    PubMed

    Zoratto, Francesca; Sinclair, Emma; Manciocco, Arianna; Vitale, Augusto; Laviola, Giovanni; Adriani, Walter

    2014-01-01

    Interest is rising for animal modeling of pathological gambling. Using the operant probabilistic-delivery task (PDT), gambling proneness can be evaluated in laboratory animals. Drawing a comparison with rats, this study evaluated the common marmoset (Callithrix jacchus) using a PDT. By nose- or hand-poking, subjects learnt to prefer a large (LLL, 5-6 pellets) over a small (SS, 1-2 pellets) reward and, subsequently, the probability of occurrence of large-reward delivery was decreased progressively to very low levels (from 100% to 17% and 14%). As probability decreased, subjects showed a great versus little shift in preference from LLL to SS reinforcer. Hence, two distinct subpopulations ("non-gambler" versus "gambler") were differentiated within each species. A proof of the model validity comes from marmosets' reaction to reward-delivery omission. Namely, depending on individual temperament ("gambler" versus "non-gambler"), they showed either persistence (i.e., inadequate pokes towards LLL) or restlessness (i.e., inadequate pokes towards SS), respectively. In conclusion, the marmoset could be a suitable model for preclinical gambling studies. Implementation of the PDT to species other than rats may be relevant for determining its external validity/generalizability and improving its face/construct validity. PMID:24971360

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

    PubMed

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

    2014-10-01

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

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

    PubMed

    Fredriksson, K; Kalimo, H; Nordborg, C; Johansson, B B; Olsson, Y

    1988-01-01

    The brain lesions in stroke-prone spontaneously hypertensive rats (SHRSP) are characterized by multifocal microvascular and spongy-cystic parenchymal alterations particularly in the gray matter. An essential feature of the lesions is the presence of edema with massive extravasation of plasma constituents as evidenced by specific gravity measurements, Evans blue technique and immunohistochemistry. The nerve cell injury occurring in the brain lesions in SHRSP is further characterized by light and electron microscopy in the present study. Two types of neuronal changes were seen within the blood-brain barrier (BBB) leakage sites. A small number of neurons with dark condensed nucleus and cytoplasm were found most often at the periphery of recent lesions. The majority of injured neurons were pale and showed intracellular edema confined to the dendrites and perikarya sparing axons and synapses. Their nuclei were well preserved with finely dispersed chromatin. The swollen and watery cell processes of neurons and astrocytes gave a spongy appearance to the neuropil. The intracellular edema seemed to result in cytolysis. The results suggest that primary anoxia-ischemia is not the major pathogenetic mechanism behind the nerve cell injury in severely hypertensive SHRSP, rather it is the massive BBB leakage and consequent brain edema that causes cytolytic destruction of neurons. Secondary focal ischemia as a consequence of occlusion in microvessels may, however, contribute to the nerve cell destruction. PMID:3213425

  14. Social Participation and Disaster Risk Reduction Behaviors in Tsunami Prone Areas.

    PubMed

    Witvorapong, Nopphol; Muttarak, Raya; Pothisiri, Wiraporn

    2015-01-01

    This paper examines the relationships between social participation and disaster risk reduction actions. A survey of 557 households in tsunami prone areas in Phang Nga, Thailand was conducted following the 2012 Indian Ocean earthquakes. We use a multivariate probit model to jointly estimate the likelihood of undertaking three responses to earthquake and tsunami hazards (namely, (1) following disaster-related news closely, (2) preparing emergency kits and/or having a family emergency plan, and (3) having an intention to migrate) and community participation. We find that those who experienced losses from the 2004 tsunami are more likely to participate in community activities and respond to earthquake hazards. Compared to men, women are more likely to prepare emergency kits and/or have an emergency plan and have a greater intention to migrate. Living in a community with a higher proportion of women with tertiary education increases the probability of engaging in community activities and carrying out disaster risk reduction measures. Individuals who participate in village-based activities are 5.2% more likely to undertake all three risk reduction actions compared to those not engaging in community activities. This implies that encouraging participation in community activities can have positive externalities in disaster mitigation. PMID:26153891

  15. Social Participation and Disaster Risk Reduction Behaviors in Tsunami Prone Areas

    PubMed Central

    Witvorapong, Nopphol; Muttarak, Raya; Pothisiri, Wiraporn

    2015-01-01

    This paper examines the relationships between social participation and disaster risk reduction actions. A survey of 557 households in tsunami prone areas in Phang Nga, Thailand was conducted following the 2012 Indian Ocean earthquakes. We use a multivariate probit model to jointly estimate the likelihood of undertaking three responses to earthquake and tsunami hazards (namely, (1) following disaster-related news closely, (2) preparing emergency kits and/or having a family emergency plan, and (3) having an intention to migrate) and community participation. We find that those who experienced losses from the 2004 tsunami are more likely to participate in community activities and respond to earthquake hazards. Compared to men, women are more likely to prepare emergency kits and/or have an emergency plan and have a greater intention to migrate. Living in a community with a higher proportion of women with tertiary education increases the probability of engaging in community activities and carrying out disaster risk reduction measures. Individuals who participate in village-based activities are 5.2% more likely to undertake all three risk reduction actions compared to those not engaging in community activities. This implies that encouraging participation in community activities can have positive externalities in disaster mitigation. PMID:26153891

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

    PubMed Central

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

    2014-01-01

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

  17. Toso regulates differentiation and activation of inflammatory dendritic cells during persistence-prone virus infection

    PubMed Central

    Lang, P A; Meryk, A; Pandyra, A A; Brenner, D; Brüstle, A; Xu, H C; Merches, K; Lang, F; Khairnar, V; Sharma, P; Funkner, P; Recher, M; Shaabani, N; Duncan, G S; Duhan, V; Homey, B; Ohashi, P S; Häussinger, D; Knolle, P A; Honke, N; Mak, T W; Lang, K S

    2015-01-01

    During virus infection and autoimmune disease, inflammatory dendritic cells (iDCs) differentiate from blood monocytes and infiltrate infected tissue. Following acute infection with hepatotropic viruses, iDCs are essential for re-stimulating virus-specific CD8+ T cells and therefore contribute to virus control. Here we used the lymphocytic choriomeningitis virus (LCMV) model system to identify novel signals, which influence the recruitment and activation of iDCs in the liver. We observed that intrinsic expression of Toso (Faim3, Fc?R) influenced the differentiation and activation of iDCs in vivo and DCs in vitro. Lack of iDCs in Toso-deficient (Toso–/–) mice reduced CD8+ T-cell function in the liver and resulted in virus persistence. Furthermore, Toso–/– DCs failed to induce autoimmune diabetes in the rat insulin promoter-glycoprotein (RIP-GP) autoimmune diabetes model. In conclusion, we found that Toso has an essential role in the differentiation and maturation of iDCs, a process that is required for the control of persistence-prone virus infection. PMID:25257173

  18. A novel approach to quantitating leukemia fusion transcripts by qRT-PCR without the need for standard curves.

    PubMed

    Schumacher, Jonathan A; Scott Reading, N; Szankasi, Philippe; Matynia, Anna P; Kelley, Todd W

    2015-08-01

    Acute myeloid leukemia patients with recurrent cytogenetic abnormalities including inv(16);CBFB-MYH11 and t(15;17);PML-RARA may be assessed by monitoring the levels of the corresponding abnormal fusion transcripts by quantitative reverse transcription-PCR (qRT-PCR). Such testing is important for evaluating the response to therapy and for the detection of early relapse. Existing qRT-PCR methods are well established and in widespread use in clinical laboratories but they are laborious and require the generation of standard curves. Here, we describe a new method to quantitate fusion transcripts in acute myeloid leukemia by qRT-PCR without the need for standard curves. Our approach uses a plasmid calibrator containing both a fusion transcript sequence and a reference gene sequence, representing a perfect normalized copy number (fusion transcript copy number/reference gene transcript copy number; NCN) of 1.0. The NCN of patient specimens can be calculated relative to that of the single plasmid calibrator using experimentally derived PCR efficiency values. We compared the data obtained using the plasmid calibrator method to commercially available assays using standard curves and found that the results obtained by both methods are comparable over a broad range of values with similar sensitivities. Our method has the advantage of simplicity and is therefore lower in cost and may be less subject to errors that may be introduced during the generation of standard curves. PMID:26079545

  19. Sensitivity of PCR and real-time PCR for the diagnosis of human visceral leishmaniasis using peripheral blood

    PubMed Central

    da Costa Lima, Manoel Sebastião; Zorzenon, Denielly Christina Rodrigues; Dorval, Maria Elizabeth Cavalheiros; Pontes, Elenir Rose Jardim Cury; Oshiro, Elisa Teruya; Cunha, Rodrigo; Andreotti, Renato; Matos, Maria de Fatima Cepa

    2013-01-01

    Objective To evaluate the effectiveness of PCR and real-time PCR for the diagnosis of human visceral leishmaniasis using peripheral blood samples. Methods DNA extraction was performed using Promega Wizard® Genomic kits. PCR employing RV1/RV2 primers yielded 145-bp amplicons. Real-time PCR was performed with the same primers and SYBR Green ROX Plus mix. These techniques were used to analyze 100 peripheral blood samples from patients with clinical signs of the disease. Results The sensitivity and specificity levels were 91,3%% and 29,6%, respectively, for real-time PCR and 97.78% and 61.82%, respectively, for PCR. Conclusions Real-time PCR proved to be a satisfactory method for the diagnosis of human visceral leishmaniasis.

  20. Heterozygote PCR product melting curve prediction.

    PubMed

    Dwight, Zachary L; Palais, Robert; Kent, Jana; Wittwer, Carl T

    2014-03-01

    Melting curve prediction of PCR products is limited to perfectly complementary strands. Multiple domains are calculated by recursive nearest neighbor thermodynamics. However, the melting curve of an amplicon containing a heterozygous single-nucleotide variant (SNV) after PCR is the composite of four duplexes: two matched homoduplexes and two mismatched heteroduplexes. To better predict the shape of composite heterozygote melting curves, 52 experimental curves were compared with brute force in silico predictions varying two parameters simultaneously: the relative contribution of heteroduplex products and an ionic scaling factor for mismatched tetrads. Heteroduplex products contributed 25.7 ± 6.7% to the composite melting curve, varying from 23%-28% for different SNV classes. The effect of ions on mismatch tetrads scaled to 76%-96% of normal (depending on SNV class) and averaged 88 ± 16.4%. Based on uMelt (www.dna.utah.edu/umelt/umelt.html) with an expanded nearest neighbor thermodynamic set that includes mismatched base pairs, uMelt HETS calculates helicity as a function of temperature for homoduplex and heteroduplex products, as well as the composite curve expected from heterozygotes. It is an interactive Web tool for efficient genotyping design, heterozygote melting curve prediction, and quality control of melting curve experiments. The application was developed in Actionscript and can be found online at http://www.dna.utah.edu/hets/. PMID:24375593

  1. [Mission oriented diagnostic real-time PCR].

    PubMed

    Tomaso, Herbert; Scholz, Holger C; Al Dahouk, Sascha; Splettstoesser, Wolf D; Neubauer, Heinrich; Pfeffer, Martin; Straube, Eberhard

    2007-01-01

    In out of area military missions soldiers are potentially exposed to bacteria that are endemic in tropical areas and can be used as biological agents. It can be difficult to culture these bacteria due to sample contamination, low number of bacteria or pretreatment with antibiotics. Commercial biochemical identification systems are not optimized for these agents which can result in misidentification. Immunological assays are often not commercially available or not specific. Real-time PCR assays are very specific and sensitive and can shorten the time required to establish a diagnosis markedly. Therefore, real-time PCRs for the identification of Bacillus anthracis, Brucella spp., Burkholderia mallei und Burkholderia pseudomallei, Francisella tularensis und Yersinia pestis have been developed. PCR results can be false negative due to inadequate clinical samples, low number of bacteria in samples, DNA degradation, inhibitory substances and inappropriate DNA preparation. Hence, it is crucial to cultivate the organisms as a prerequisite for adequate antibiotic therapy and typing of the agent. In a bioterrorist scenario samples have to be treated according to rules applied in forensic medicine and documentation has to be flawless. PMID:17987355

  2. An evaluation of direct PCR amplification

    PubMed Central

    Hall, Daniel E.; Roy, Reena

    2014-01-01

    Aim To generate complete DNA profiles from blood and saliva samples deposited on FTA® and non-FTA® paper substrates following a direct amplification protocol. Methods Saliva samples from living donors and blood samples from deceased individuals were deposited on ten different FTA® and non-FTA® substrates. These ten paper substrates containing body fluids were kept at room temperature for varying lengths of time ranging from one day to approximately one year. For all assays in this research, 1.2 mm punches were collected from each substrate containing one type of body fluid and amplified with reagents provided in the nine commercial polymerase chain reaction (PCR) amplification kits. The substrates were not subjected to purification reagent or extraction buffer prior to amplification. Results Success rates were calculated for all nine amplification kits and all ten substrates based on their ability to yield complete DNA profiles following a direct amplification protocol. Six out of the nine amplification kits, and four out of the ten paper substrates had the highest success rates overall. Conclusion The data show that it is possible to generate complete DNA profiles following a direct amplification protocol using both standard (non-direct) and direct PCR amplification kits. The generation of complete DNA profiles appears to depend more on the success of the amplification kit rather than the than the FTA®- or non-FTA®-based substrates. PMID:25559837

  3. 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.

  4. Static Detection of Disassembly Errors

    SciTech Connect

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

    2009-10-13

    Static disassembly is a crucial ?rst step in reverse engineering executable ?les, and there is a consider- able body of work in reverse-engineering of binaries, as well as areas such as semantics-based security anal- ysis, that assumes that the input executable has been correctly disassembled. However, disassembly errors, e.g., arising from binary obfuscations, can render this assumption invalid. This work describes a machine- learning-based approach, using decision trees, for stat- ically identifying possible errors in a static disassem- bly; such potential errors may then be examined more closely, e.g., using dynamic analyses. Experimental re- sults using a variety of input executables indicate that our approach performs well, correctly identifying most disassembly errors with relatively few false positives.

  5. NAND Flash Error Control Code

    E-print Network

    Song, Hong-Yeop

    flash cell1 (scaling down shrinking)[1] cell MLC(multi-level cell) [2] . , 2 syndrome , error locator , . , , Berlekamp-Massey Euclidean Peterson-Gorenstein-Zierler Chien Search [9]. (module) pipelining 3-stage decoding [10]. NAND flash decoder syndrome

  6. Human errors and measurement uncertainty

    NASA Astrophysics Data System (ADS)

    Kuselman, Ilya; Pennecchi, Francesca

    2015-04-01

    Evaluating the residual risk of human errors in a measurement and testing laboratory, remaining after the error reduction by the laboratory quality system, and quantifying the consequences of this risk for the quality of the measurement/test results are discussed based on expert judgments and Monte Carlo simulations. A procedure for evaluation of the contribution of the residual risk to the measurement uncertainty budget is proposed. Examples are provided using earlier published sets of expert judgments on human errors in pH measurement of groundwater, elemental analysis of geological samples by inductively coupled plasma mass spectrometry, and multi-residue analysis of pesticides in fruits and vegetables. The human error contribution to the measurement uncertainty budget in the examples was not negligible, yet also not dominant. This was assessed as a good risk management result.

  7. Asymmetrical Search Errors in Infancy

    ERIC Educational Resources Information Center

    Butterworth, George

    1976-01-01

    To establish the spatial generality of perseverative errors in infant manual search, a group of infants aged 8-11 months performed Piaget's Stage IV task with an object hidden at successive locations in the vertical plane. (Author/JMB)

  8. A quadruplex PCR (qxPCR) assay for adulteration in dairy products.

    PubMed

    Agrimonti, Caterina; Pirondini, Andrea; Marmiroli, Marta; Marmiroli, Nelson

    2015-11-15

    This study describes the development of a quadruplex quantitative Real Time PCR (qxPCR) based on SYBR®GreenER chemistry, for rapid identification of DNA of cow, goat, sheep and buffalo in dairy products, and for quantification of cow DNA in these products. The platform was applied to: (i) mixes of milks at fixed percentages; (ii) cheeses prepared with the same mixes; (iii) commercial dairy products. The methodology enabled the detection of DNA from cow in mixes of milk and cheeses with a limit of detection (LOD) of 0.1%. When applied to commercial dairy products the qxPCR gave results comparable with each single-plex Real Time PCR. A good correlation (R(2)>0.9) between peaks' area of derivative of melting curves of amplicons and percentages of cow milk in milk mixes and cheeses, allows for an estimation of cow DNA in a dynamic range varying from 0.1-5% to 1-25%. PMID:25976998

  9. The evolution of real-time PCR machines to real-time PCR chips.

    PubMed

    Lee, Dasheng; Chen, Pei-Jer; Lee, Gwo-Bin

    2010-03-15

    Development of Micro-Electro-Mechanical Systems (MEMS) technology has recently allowed the migration of real-time polymerase chain reaction (PCR) machines to lab-on-a-chip systems. The miniaturization of biological instruments has been studied extensively, with several prototypes constructed and tested. In this study, the lab-on-a-chip system is evaluated; its DNA quantification is estimated by theorems, and the specifications of proposed chip prototypes are compared with the original machines. The analysis results suggest five hypotheses. Using experiments and the data collected from published papers, these hypotheses were either verified or rejected, and the advantages and shortcomings of real-time PCR chips were identified. The proven advantages of the lab-on-a-chip system are its compact size, low sample volume to nano-liter, and short analysis time-less than 10s to complete one PCR cycle and 370 s for completing the whole quantification process. However, the detection limits, quantification uncertainties, and melting analysis ability of the chip prototypes are at best comparable to, and perhaps worse than, those of commercial instruments. Real-time PCR chips are not perfectly accurate diagnostic tools for a laboratory but they have advantages over traditional techniques for point-of-care testing. PMID:20022485

  10. Iatrogenic error and physician responsibility.

    PubMed

    Sandroni, S

    2001-03-01

    The recent report on iatrogenic errors highlighted the scope of the problem and suggested solutions including a national agency to oversee error reporting. This may or may not occur; in the meantime physicians are not relieved of their responsibility to respond to the issue of patient safety. Reasons for the slow response to date are discussed and suggestions for the future are offered. PMID:11291568

  11. Eliminating PCR contamination: is UV irradiation the answer?

    PubMed

    Fox, J C; Ait-Khaled, M; Webster, A; Emery, V C

    1991-08-01

    The sensitivity of the polymerase chain reaction (PCR) can mean that even very low levels of contamination with the target DNA will result in a positive signal. At present this aspect is a major limitation in the use of PCR as a routine diagnostic method. By exposing PCR reagents to UV light, contaminating DNA can be inactivated, thus providing an opportunity to eradicate false positive reactions. UV irradiation was applied to PCR systems used for the detection of human cytomegalovirus (CMV) and human immunodeficiency virus (HIV) and shown to be effective in eradicating both laboratory encountered contamination and plasmid DNA (below 100 pg) added to PCR systems prior to UV exposure. The sensitivity of a PCR system to amplify the long terminal repeat (LTR) sequence of HIV-1 was not affected by the irradiation procedure; however, the ultimate sensitivity of a PCR system for the amplification of an early gene promotor sequence of the CMV genome was reduced 1000-fold. UV irradiation did not affect the size of the PCR product as determined by strand separating polyacrylamide gel electrophoresis of a 32P-labelled amplimer. Thus, a simple pre-exposure to UV light would seem a worthwhile step to incorporate into PCR protocols provided that the effects on sensitivity have been determined empirically for each PCR system. PMID:1664435

  12. DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity

    PubMed Central

    Gonzalez-Huici, Victor; Szakal, Barnabas; Urulangodi, Madhusoodanan; Psakhye, Ivan; Castellucci, Federica; Menolfi, Demis; Rajakumara, Eerappa; Fumasoni, Marco; Bermejo, Rodrigo; Jentsch, Stefan; Branzei, Dana

    2014-01-01

    DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability. PMID:24473148

  13. Correction of errors in tandem mass spectrum extraction enhances phosphopeptide identification.

    PubMed

    Hao, Piliang; Ren, Yan; Tam, James P; Sze, Siu Kwan

    2013-12-01

    The tandem mass spectrum extraction of phosphopeptides is more difficult and error-prone than that of unmodified peptides due to their lower abundance, lower ionization efficiency, the cofragmentation with other high-abundance peptides, and the use of MS(3) on MS(2) fragments with neutral losses. However, there are still no established methods to evaluate its correctness. Here we propose to identify and correct these errors via the combinatorial use of multiple spectrum extraction tools. We evaluated five free and two commercial extraction tools using Mascot and phosphoproteomics raw data from LTQ FT Ultra, in which RawXtract 1.9.9.2 identified the highest number of unique phosphopeptides (peptide expectation value <0.05). Surprisingly, ProteoWizzard (v. 3.0.3476) extracted wrong precursor mass for most MS(3) spectra. Comparison of the top three free extraction tools showed that only 54% of the identified spectra were identified consistently from all three tools, indicating that some errors might happen during spectrum extraction. Manual check of 258 spectra not identified from all three tools revealed 405 errors of spectrum extraction with 7.4% in selecting wrong precursor charge, 50.6% in selecting wrong precursor mass, and 42.1% in exporting MS/MS fragments. We then corrected the errors by selecting the best extracted MGF file for each spectrum among the three tools for another database search. With the errors corrected, it results in the 22.4 and 12.2% increase in spectrum matches and unique peptide identification, respectively, compared with the best single method. Correction of errors in spectrum extraction improves both the sensitivity and confidence of phosphopeptide identification. Data analysis on nonphosphopeptide spectra indicates that this strategy applies to unmodified peptides as well. The identification of errors in spectrum extraction will promote the improvement of spectrum extraction tools in future. PMID:24147958

  14. A PCR-free fluorescence strategy for detecting telomerase activity via double amplification strategy.

    PubMed

    Zhang, Xiafei; Cheng, Rui; Shi, Zhilu; Jin, Yan

    2016-01-15

    As a universal tumor biomarker, research on the activity and inhibition of telomerase is of great importance for cancer diagnosis and therapy. Although the telomeric repeat amplification protocol (TRAP) has served as a powerful assay for detecting telomerase activity, its application has been significantly limited by amplification related errors and time-consuming procedure. To address the limitations of PCR-based protocol, a dual amplification fluorescence assay was developed for PCR-free detecting telomerase activity. Briefly, we designed an arch-structure DNA probe to specifically control strand displacement reaction and subsequent enzyme-aided amplification. Telomerase substrate (TS) primer was extended by telomerase to form long elongation products which contain several TTAGGG repeat units. So, one elongation product can release more than one trigger DNA (t-DNA) via strand displacement reaction to realize first amplification. Subsequently, t-DNA specifically opened molecular beacon (MB) to restore the fluorescence of MB. Meanwhile, t-DNA was recycled by the aid of nicking endonuclease to continuously open more and more MBs, leading to a second amplification. Owing to the double amplification strategy, the proposed method allowed the measurement of telomerase activity in crude cell extracts equivalent to 5 HeLa cells and 10 CCRF-CEM cells without PCR amplification. Besides, the influence of telomere-binding ligands on the telomerase activity demonstrated that the proposed method holds the potential to evaluate the inhibition efficiency of telomerase inhibitors. PMID:26299822

  15. Quantification of algal endosymbionts (Symbiodinium) in coral tissue using real-time PCR.

    PubMed

    Mieog, J C; VAN Oppen, M J H; Berkelmans, R; Stam, W T; Olsen, J L

    2009-01-01

    Understanding the flexibility of the endosymbioses between scleractinian corals and single-cell algae of the genus Symbiodinium will provide valuable insights into the future of coral reefs. Here, a real-time polymerase chain reaction (PCR) assay is presented to accurately determine the cell densities of Symbiodinium clades C and D in the scleractinian coral Acropora millepora, which can be extended to other coral-symbiont associations in the future. The assay targets single- to low-copy genes of the actin family of both the coral host and algal symbiont. Symbiont densities are expressed as the ratio of Symbiodinium cells to each host cell (S/H ratio, error within 30%), but can also be normalized to coral surface area. Greater accuracy in estimating ratios of associations involving multiple clades is achieved compared with previous real-time PCR assays based on high-copy ribosomal DNA loci (error within an order of magnitude). Healthy adult A. millepora containing ~1.4 × 10(6) zooxanthellae per cm(2) (as determined by haemocytometer counts) had S/H ratios of c. 0.15, i.e. ~15 symbiont cells per 100 host cells. In severely bleached colonies, this ratio decreased to less than 0.005. Because of its capacity to accurately determine both densities and ratios of multiple symbionts within one sample, the assay will open the door for novel research into the mechanisms of symbiont shuffling and switching. PMID:21564569

  16. The efficacy and safety of prone positioning in adults patients with acute respiratory distress syndrome: a meta-analysis of randomized controlled trials

    PubMed Central

    Park, So Young; Kim, Hyun Jung; Yoo, Kwan Ha; Park, Yong Bum; Kim, Seo Woo; Lee, Seok Jeong; Kim, Eun Kyung; Kim, Jung Hyun; Kim, Yee Hyung; Moon, Ji-yong; Min, Kyung Hoon; Park, Sung Soo; Lee, Jinwoo; Lee, Chang-Hoon; Park, Jinkyeong; Byun, Min Kwang; Lee, Sei Won; Rlee, ChinKook; Jung, Ji Ye

    2015-01-01

    Background Prone positioning for acute respiratory distress syndrome (ARDS) has no impact on mortality despite significant improvements in oxygenation. However, a recent trial demonstrated reduced mortality rates in the prone position for severe ARDS. We evaluated effects of prone position duration and protective lung strategies on mortality rates in ARDS. Methods We extensively searched MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials to identify randomized controlled trials (RCTs) reporting on prone positioning during acute respiratory failure in adults for inclusion in our meta-analysis. Results Eight trials met our inclusion criteria, Totals of 1,099 and 1,042 patients were randomized to the prone and supine ventilation positions. The mortality rates associated with the prone and supine positions were 41% and 47% [risk ratio (RR), 0.90; 95% confidence interval (CI), 0.82-0.98, P=0.02], but the heterogeneity was moderate (P=0.01, I2=61%). In a subgroup analysis, the mortality rates for lung protective ventilation (RR 0.73, 95% CI, 0.62-0.86, P=0.0002) and duration of prone positioning >12 h (RR 0.75, 95% CI, 0.65-0.87, P<0.0001) were reduced in the prone position. Prone positioning was not associated with an increased incidence of cardiac events (RR 1.01, 95% CI, 0.87-1.17) or ventilator associated pneumonia (RR 0.88, 95% CI, 0.71-1.09), but it was associated with an increased incidence of pressure sores (RR 1.23, 95% CI, 1.07-1.41) and endotracheal dislocation (RR 1.33, 95% CI, 1.02-1.74). Conclusions Prone positioning tends to reduce the mortality rates in ARDS patients, especially when used in conjunction with a lung protective strategy and longer prone position durations. Prone positioning for ARDS patients should be prioritized over other invasive procedures because related life-threatening complications are rare. However, further additional randomized controlled design to study are required for confirm benefit of prone position in ARDS. PMID:25922713

  17. Nitrogen Subsidies and Fire Prone Ecosystems: the Case of African Savannas

    NASA Astrophysics Data System (ADS)

    Prihodko, L.; Hanan, N. P.

    2008-12-01

    Savannas are the most frequently burned ecosystems on earth and fires are known to have significant effects on community composition and species interactions across all trophic levels. Fire also plays a significant role in the biogeochemical cycles of carbon and various nutrients in savannas as they are emitted or chemically transformed into more available, or more recalcitrant, forms during fires. In Africa, savanna fires occur more frequently in the unstable (mean annual precipitation (MAP) > 516mm), dystrophic (nutrient poor) savannas than they do in the relatively more stable (MAP < 516mm), eutrophic (nutrient rich) savannas. Are these dystrophic savannas dystrophic because they burn? Are the eutrophic savannas eutrophic because they are subsidized by nutrient inputs from spatially remote fires? Africa is an ideal location to study ecosystem sensitivity to atmospheric inputs of nitrogen from biomass burning for several reasons. A large proportion of the continent is very fire prone and approximately 40% of global emissions from biomass burning originate in Africa. In contrast, emissions from fossil fuel sources are low compared to highly industrialized regions in the Americas, Europe and Asia and agricultural input of nitrogen is limited in Africa. As a result, the ecosystem impacts of pyrogenic loss and gain of nitrogen are likely to be more important in Africa than elsewhere. We combine data from recent analyses of fire frequency (GFED) with an atmospheric transport model (HYSPLIT4) to simulate pyrogenic nitrogen deposition fields and analyze the fate of fire-related nitrogen in the atmosphere, gross and net N-deposition fields and thus the role fires may play in displacing nitrogen and depleting or enriching adjacent regions.

  18. Increased Skin Dose With the Use of a Custom Mattress for Prone Breast Radiotherapy

    SciTech Connect

    Becker, Stewart J. Patel, Rakesh R.; Mackie, Thomas R.

    2007-10-01

    The purpose of this study was to measure and compare the loss of buildup to the skin of the breast in the prone position due to 2 different positioning systems during tangential external beam irradiation. Two experiments were performed; one with a standard nylon-covered foam support and another with a novel helium-filled Mylar bag support. The choice of helium-filled Mylar was to reduce the contamination to as low as possible. The experiments were designed to allow a surface dose measurement and a depth dose profile with the pads placed in the path of the beam in front of the detector. All measurements were taken using a Capintec PS-033 thin-window parallel plate ionization chamber. The standard nylon-covered foam pad caused the surface dose to rise as it got closer to the skin. When the pad was directly touching the surface, the surface dose increased by 300% compared to the result when no pad was present. This loss of buildup to the surface was similar to that of a custom bolus material. The opposite effect occurred with the use of the helium-filled Mylar bag, namely the surface dose gradually decreased as the pad got closer to the phantom. When the Mylar pad was directly touching the phantom, the surface dose was decreased by 7% compared to when no pad was present. The use of a foam pad could potentially result in a significant higher dose to the skin, resulting in an enhanced acute skin reaction. Therefore, special care should be taken in this clinical scenario and further investigation of an air- or helium-based mylar support pad should be investigated in the context of definitive breast radiation treatment.

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

    PubMed

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

    2012-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  1. True colors - changing perceptions of hydrological processes at a hillslope prone to slide

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    This study investigated runoff formation processes of a pre-alpine hillslope prone to slide. The experimental pasture plot (40 m × 60 m) is located in the northern front range of the Swiss Alps on a 30° steep hillslope (1180 m a.s.l., 1500+ mm annual precipitation). A gleysol (H-Go-Gr) overlies weathered marlstone and conglomerate of subalpine molasse. We conducted sprinkling experiments on a subplot (10 m × 10 m) with variable rainfall intensities. During both experiments fluorescein line-tracer injections into the topsoil, and sodium chloride (NaCl) injections into the sprinkling water were used to monitor flow velocities in the soil. The observed flow velocities for fluorescein in the soil were 1.2 and 1.4 × 10-3 m s-1. The NaCl breakthrough occurred almost simultaneously in all monitored discharge levels (0.05, 0.25 and 1 m depth), indicating a high infiltration capacity and efficient drainage of the soil. These initial observations suggested "transmissivity feedback", a form of subsurface stormflow, as the dominant runoff process. However, the results of a brilliant blue dye tracer experiment completely changed our perceptions of the hillslope's hydrological processes. Excavation of the dye-stained soils highlighted the dominance of "organic layer interflow", a form of shallow subsurface stormflow. The dye stained the entire H horizon, vertical soil fractures, and macropores (mostly worm burrows) up to 50 cm depth. Lateral drainage in the subsoil or at the soil-bedrock interface was not observed, and thus was limited to the organic topsoil. In the context of shallow landslides, the subsoil (Go/Gr) acted as an infiltration and exfiltration barrier, which produced significant lateral saturated drainage in the topsoil (H) and possibly a confined aquifer in the bedrock.

  2. Hydrologic Simulation in Mediterranean flood prone Watersheds using high-resolution quality data

    NASA Astrophysics Data System (ADS)

    Eirini Vozinaki, Anthi; Alexakis, Dimitrios; Pappa, Polixeni; Tsanis, Ioannis

    2015-04-01

    Flooding is a significant threat causing lots of inconveniencies in several societies, worldwide. The fact that the climatic change is already happening, increases the flooding risk, which is no longer a substantial menace to several societies and their economies. The improvement of spatial-resolution and accuracy of the topography and land use data due to remote sensing techniques could provide integrated flood inundation simulations. In this work hydrological analysis of several historic flood events in Mediterranean flood prone watersheds (island of Crete/Greece) takes place. Satellite images of high resolution are elaborated. A very high resolution (VHR) digital elevation model (DEM) is produced from a GeoEye-1 0.5-m-resolution satellite stereo pair and is used for floodplain management and mapping applications such as watershed delineation and river cross-section extraction. Sophisticated classification algorithms are implemented for improving Land Use/ Land Cover maps accuracy. In addition, soil maps are updated with means of Radar satellite images. The above high-resolution data are innovatively used to simulate and validate several historical flood events in Mediterranean watersheds, which have experienced severe flooding in the past. The hydrologic/hydraulic models used for flood inundation simulation in this work are HEC-HMS and HEC-RAS. The Natural Resource Conservation Service (NRCS) curve number (CN) approach is implemented to account for the effect of LULC and soil on the hydrologic response of the catchment. The use of high resolution data provides detailed validation results and results of high precision, accordingly. Furthermore, the meteorological forecasting data, which are also combined to the simulation model results, manage the development of an integrated flood forecasting and early warning system tool, which is capable of confronting or even preventing this imminent risk. The research reported in this paper was fully supported by the "ARISTEIA II" Action ("REINFORCE" program) of the "Operational Education and Life Long Learning programme" and is co-funded by the European Social Fund (ESF) and National Resources.

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

    PubMed Central

    Taghizadeh, Bahareh; Gail, Alexander

    2014-01-01

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

  4. Rehabilitation of a debris-flow prone mountain stream in southwestern China - Strategies, effects and implications

    NASA Astrophysics Data System (ADS)

    Yu, Guo-an; Huang, He Qing; Wang, Zhaoyin; Brierley, Gary; Zhang, Kang

    2012-01-01

    SummaryRehabilitation of Shengou Creek, a small, steep mountain stream in southwestern China that is prone to debris flows, started more than 30 years ago through an integrated program of engineering applications (check dams and guiding dikes), biological measures (reforestation), and social measures (reducing human disturbance). Small and medium-sized check dams and guiding dikes were constructed on key upper and middle sections of the creek to stabilize hillslopes and channel bed. Meanwhile, Leucaena leucocephala, a drought-tolerant, fast-growing, and highly adaptive plant species, was introduced to promote vegetation recovery in the watershed. The collective community structure of tree, shrub, and herb assemblages in the artificial L. leucocephala forest, which developed after 7 years, enhanced soil structure and drastically reduced soil erosion on hillslopes. Cultivation of steep land was strictly controlled in the basin, and some inhabitants were encouraged to move from upstream areas to downstream towns to reduce disturbance. These integrated measures reduced sediment supply from both hillslopes and upstream channels, preventing sediment-related hazards. The development of natural streambed resistance structures (mainly step-pool systems) and luxuriant riparian vegetation aided channel stability, diversity of stream habitat, and ecological maintenance in the creek. These findings are compared with Jiangjia and Xiaobaini Ravines, two adjacent non-rehabilitated debris-flow streams which have climate and geomorphologic conditions similar to Shengou Creek. Habitat diversity indices, taxa richness, biodiversity, and bio-community indices are much higher in Shengou Creek relative to Jiangjia and Xiaobaini Ravines, attesting to the effectiveness of rehabilitation measures.

  5. Trafficking of dietary fat in obesity-prone and obesity-resistant rats.

    PubMed

    Jackman, Matthew R; Kramer, Robert E; MacLean, Paul S; Bessesen, Daniel H

    2006-11-01

    The trafficking of dietary fat was assessed in obesity-prone (OP) and obesity-resistant (OR) male and female rats. Test meals containing [1-(14)C]palmitate were delivered through gastric feeding tubes while rats consumed a high-carbohydrate diet (HCD) or after 5 days of a high-fat diet (HFD). Over the subsequent 24 h, the appearance of (14)C was followed in the GI tract, skeletal muscles (SM), liver, adipose tissues (AT), and expired CO(2). There was no difference in the production of (14)CO(2) between OP and OR rats consuming a HCD. However, after 5 days on HFD, OR rats produced significantly more (14)CO(2) after the test meal than OP rats (P < 0.001 females, P = 0.03 males). The differential oxidation of dietary fat between OP and OR rats on HFD was not due to differences in absorption but rather was associated with preferential disposition of tracer to AT in OP rats. Measurements of lipoprotein lipase in part explained increased tracer uptake by AT in OP rats but were not consistent with increased SM tracer uptake in OR rats. Surprisingly, female rats oxidized more tracer than male rats irrespective of phenotype or diet. These results are consistent with the notion that differences in the partitioning of dietary fat between storage in AT and oxidation in SM and liver that develop shortly after the introduction of a HFD may in part underlie the differential tendency for OR and OP rats to gain weight on this diet. PMID:16803858

  6. Lipidomic analysis of plasma lipoprotein fractions in myocardial infarction-prone rabbits.

    PubMed

    Takeda, Hiroaki; Koike, Tomonari; Izumi, Yoshihiro; Yamada, Takayuki; Yoshida, Masaru; Shiomi, Masashi; Fukusaki, Eiichiro; Bamba, Takeshi

    2015-10-01

    Lipids play important roles in the body and are transported to various tissues via lipoproteins. It is commonly assumed that alteration of lipid levels in lipoproteins leads to dyslipidemia and serious diseases such as coronary artery disease (CAD). However, lipid compositions in each lipoprotein fraction induced by lipoprotein metabolism are poorly understood. Lipidomics, which involves the comprehensive and quantitative analysis of lipids, is expected to provide valuable information regarding the pathogenic mechanism of CAD. Here, we performed a lipidomic analysis of plasma and its lipoprotein fractions in myocardial infarction-prone Watanabe heritable hyperlipidemic (WHHLMI) rabbits. In total, 172 lipids in plasma obtained from normal and WHHLMI rabbits were quantified with high throughput and accuracy using supercritical fluid chromatography hybrid quadrupole-Orbitrap mass spectrometry (SFC/Q-Orbitrap-MS). Plasma levels of each lipid class (i.e., phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, lysophosphatidylcholine, lysophosphatidylethanolamine, sphingomyelin, ceramide, triacylglycerol, diacylglycerol, and cholesterol ester, except for free fatty acids) in 21-month-old WHHLMI rabbits were significantly higher than those in normal rabbits. High levels of functional lipids, such as alkyl-phosphatidylcholines, phospholipids including ?-6 fatty acids, and plasmalogens, were also observed in WHHLMI rabbit plasma. In addition, high-resolution lipidomic analysis using very low density lipoprotein (VLDL) and low density lipoprotein (LDL) provided information on the specific molecular species of lipids in each lipoprotein fraction. In particular, higher levels of phosphatidylethanolamine plasmalogens were detected in LDL than in VLDL. Our lipidomics approach for plasma lipoprotein fractions will be useful for in-depth studies on the pathogenesis of CAD. PMID:26162515

  7. Alpha-tocopherol in the brain tissue preservation of stroke-prone spontaneously hypertensive rats.

    PubMed

    Murad, Leonardo Borges; Guimarães, Marcela Rodrigues Moreira; Paganelli, Aline; de Oliveira, Carlos Alberto Basílio; Vianna, Lucia Marques

    2014-03-01

    Oxidative stress has an important role in neuronal damage during cerebral ischemia and can lead to cognitive and behavioral impairment. Alpha-tocopherol, a powerful antioxidant, may be able to preserve neuronal tissue and circumvent neurological deficits. Thus, this study aimed to investigate the influence of alpha-tocopherol in the preservation of brain tissue and the maintenance of memory formation in stroke-prone spontaneously hypertensive rats (SHRSP). To achieve this aim, twenty-four 15-week-old male SHRSP rats were separated into the following four groups (n?=?6 each) that received different treatments over a 4-week period: the alpha-tocopherol group, the control group, the L-NAME group, and the L-NAME?+?alpha-tocopherol group. We evaluated the physiological parameters (body weight, diuresis, and food and water intake), an oxidative stress marker (malondialdehyde levels), and neurological responses (the Morris Water Maze and Novel Objects Recognition tests). Afterwards, the brains were removed for histopathological analysis and quantification of the number of cells in the hippocampus. Statistically, the alpha-tocopherol group demonstrated better results when compared to all groups. The data indicated a reduction in oxidative stress and the preservation of neurological responses in groups treated with alpha-tocopherol. In contrast, the L-NAME group exhibited increased malondialdehyde levels, impairment of neurological responses, and several hippocampus tissue injuries. The others groups exhibited nerve tissue changes that were restricted to the glial nodes. No significant alterations were observed in the physiologic parameters. Based on these findings, we suggest that alpha-tocopherol can prevent stroke, preserve the structure of the hippocampus, and maintain both memory and cognition functions. PMID:23949732

  8. Submissive hypercapnia: Why COPD patients are more prone to CO2 retention than heart failure patients.

    PubMed

    Poon, Chi-Sang; Tin, Chung; Song, Gang

    2015-09-15

    Patients with late-stage chronic obstructive pulmonary disease (COPD) are prone to CO2 retention, a condition which has been often attributed to increased ventilation-perfusion mismatch particularly during oxygen therapy. However, patients with mild-to-moderate COPD or chronic heart failure (CHF) also suffer similar ventilatory inefficiency but they remain near-normocapnic at rest and during exercise with an augmented respiratory effort to compensate for the wasted dead space ventilation. In severe COPD, the augmented exercise ventilation progressively reverses as the disease advances, resulting in hypercapnia at peak exercise as ventilatory limitation due to increasing expiratory flow limitation and dynamic lung hyperinflation sets in. Submissive hypercapnia is an emerging paradigm for understanding optimal ventilatory control and cost/benefit decision-making under prohibitive respiratory chemical-mechanical constraints, where the need to maintain normocapnia gives way to the mounting need to conserve the work of breathing. In severe/very severe COPD, submissive hypercapnia epitomizes the respiratory controller's 'can't breathe, so won't breathe' say-uncle policy when faced with insurmountable ventilatory limitation. Even in health, submissive hypercapnia ensues during CO2 breathing/rebreathing when the inhaled CO2 renders normocapnia difficult to restore even with maximal respiratory effort, hence the respiratory controller's 'ain't fresh, so won't breathe' modus operandi. This 'wisdom of the body' with a principled decision to tolerate hypercapnia when faced with prohibitive ventilatory or gas exchange limitations rather than striving for untenable normocapnia at all costs is analogous to the notion of permissive hypercapnia in critical care, a clinical strategy to minimize the risks of ventilator-induced lung injury in patients receiving mechanical ventilation. PMID:25891787

  9. Ultrafast rotary PCR system for multiple influenza viral RNA detection.

    PubMed

    Jung, Jae Hwan; Choi, Seok Jin; Park, Byung Hyun; Choi, Young Ki; Seo, Tae Seok

    2012-05-01

    We presented a novel platform for an ultrafast PCR system, called the Rotary PCR Genetic Analyzer, which incorporates a thermal block and resistive temperature detector (RTD) for thermal cycling control, a disposable PCR microchip, and a stepper motor. The influenza viral RNAs from H3N2, H5N1, and H1N1 were simultaneously identified with high sensitivity and speed. PMID:22437437

  10. Automatic-repeat-request error control schemes

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

    Error detection incorporated with automatic-repeat-request (ARQ) is widely used for error control in data communication systems. This method of error control is simple and provides high system reliability. If a properly chosen code is used for error detection, virtually error-free data transmission can be attained. Various types of ARQ and hybrid ARQ schemes, and error detection using linear block codes are surveyed.

  11. Error-associated behaviors and error rates for robotic geology

    NASA Technical Reports Server (NTRS)

    Anderson, Robert C.; Thomas, Geb; Wagner, Jacob; Glasgow, Justin

    2004-01-01

    This study explores human error as a function of the decision-making process. One of many models for human decision-making is Rasmussen's decision ladder [9]. The decision ladder identifies the multiple tasks and states of knowledge involved in decision-making. The tasks and states of knowledge can be classified by the level of cognitive effort required to make the decision, leading to the skill, rule, and knowledge taxonomy (Rasmussen, 1987). Skill based decisions require the least cognitive effort and knowledge based decisions require the greatest cognitive effort. Errors can occur at any of the cognitive levels.

  12. Comparison of three supraglottic airway devices for airway rescue in the prone position: A manikin-based study

    PubMed Central

    Gupta, Babita; Gupta, Surender; Hijam, Bijaya; Shende, Pallavi; Rewari, Vimi

    2015-01-01

    Background: Accidental extubation during surgery in prone position can be life-threatening. Supraglottic airway devices (SAD) have been used successfully in such situations to rescue the airway. However, which SAD would be most appropriate in this setting has not been described in the literature. Aims: The aim of our study was to determine the most appropriate SAD for securing airway in a prone position during accidental extubation. Materials and Methods: In the study, Airway Trainer (Laerdal) manikin was used for studying insertion of three SADs; I-gel, Laryngeal Mask Airway ProSeal™ (PLMA) and LMA Classic™ (CLMA) in the prone position. Forty anesthesia resident doctors participated in this study. The time taken for insertion; ease of insertion and ventilation; bronchoscopic view; and insertion score were compared among the three groups. Results: The time taken for I-gel insertion was significantly lesser (12.89 ± 3.94 seconds) as compared to CLMA (17.07 ± 3.5 seconds) and PLMA (25 + 4.78 seconds). Least resistance was encountered in the insertion of I-gel, while maximum resistance was experienced in PLMA group (22.5% vs. 90%). The maneuver required for optimal positioning was observed in 27.5% of PLMA insertion, 2.5% in CLMA while no maneuver was required in any of the I-gel insertion. Ease of ventilation was comparable in all three SADs. The bronchoscopic view and insertion score were significantly higher with I-gel as compared to CLMA and PLMA. Conclusion: All three SADs were successful as rescue devices during accidental extubation in the prone position. However, the ease of insertion was maximum with I-gel, followed by CLMA and PLMA.

  13. Altered soluble epoxide hydrolase gene expression and function and vascular disease risk in the stroke-prone spontaneously hypertensive rat.

    PubMed

    Corenblum, Mandi J; Wise, Vance E; Georgi, Katrin; Hammock, Bruce D; Doris, Peter A; Fornage, Myriam

    2008-02-01

    Soluble epoxide hydrolase (sEH) metabolizes epoxyeicosatrienoic acids and represents a novel therapeutic target in cardiovascular disease treatment. We investigated the relationship among sequence variation in the sEH gene (Ephx2), sEH function, and risk of end-organ injury in strains of spontaneously hypertensive rat (SHRs) differing in their susceptibility to develop brain vascular disease. Brain Ephx2 expression was significantly lower in stroke-prone (SHR/A3) than in stroke-resistant (SHR/N) SHRs (5-fold; P<0.0001). Resequencing of the Ephx2 promoter in the 2 strains identified 3 polymorphisms that significantly influenced promoter transcriptional activity in vitro. Measurements of brain sEH enzyme activity and plasma levels of arachidonate and linoleate metabolites of sEH further suggested significant differences between the 2 strains. Ratios of epoxyoctadecenoic acids to dihydroxyoctadecenoic acids were significantly higher, indicating a lower sEH activity in SHR/A3 than in SHR/N (P<0.0001). Plasma dihydroxyeicosatrienoic acid levels were lower in SHR/A3 than in SHR/N (P<0.0001), but plasma epoxyeicosatrienoic acids levels were similar in the 2 strains. Association analysis of Ephx2 polymorphism in the F2 progeny of an SHR/A3xSHR/N cross showed that animals carrying the SHR/A3 allele of Ephx2 had a greater risk of stroke and associated urinary proteinuria than animals that do not. Investigation of patterns of allelic similarities and differences among multiple stroke-prone and stroke-resistant SHR substrains showed that Ephx2 belongs to a haplotype block shared among all of the stroke-prone but no stroke-resistant substrains. These data support a role for Ephx2 polymorphism on sEH gene expression and function and risk of end-organ injury in the stroke-prone SHR. PMID:18086949

  14. Management of human error by design

    NASA Technical Reports Server (NTRS)

    Wiener, Earl

    1988-01-01

    Design-induced errors and error prevention as well as the concept of lines of defense against human error are discussed. The concept of human error prevention, whose main focus has been on hardware, is extended to other features of the human-machine interface vulnerable to design-induced errors. In particular, it is pointed out that human factors and human error prevention should be part of the process of transport certification. Also, the concept of error tolerant systems is considered as a last line of defense against error.

  15. Geochemical analysis of selected hydrocarbon samples in the Douala basin, Cameroon: Implications for an oil-prone source rock

    SciTech Connect

    Ackerman, W.C.; Boatwright, D.C. ); Burwood, R.; Mycke, B.; Van Lerberche, D. ); Bondjo, E.; Tamfu, S.; Ovono, D. )

    1993-09-01

    Several oil seeps from the onshore Douala basin in southwest Cameroon have been analyzed by GC/MS, PY/GC, and PY/GC/MS to determine the nature and quality of their source rocks. Geochemical data indicate oil-prone source rocks exist in the Upper Cretaceous to middle Tertiary passive margin sedimentary section. Paleoenvironmental indicators suggest these source rocks were deposited in paralic/deltaic to hypersaline marine settings. In conjunction with existing geological data, two geochemical models are proposed. (1) The oils were derived from a kerogen facies, which grades from a hypersaline marine environment in the Albian to a marine facies in the Cenomanian Maastrichtian. (2) The oils were derived from a hypersaline marine facies in the Albian and a second marine facies deposited during the Oligocene. Although previous work by other authors has shown the Upper Cretaceous/lower Tertiary source rocks from wells in the Logbaba gas field to be gas prone (type III), data from the present study provide evidence that at least one mature oil-prone source rock exists within this interval elsewhere in the basin.

  16. Error Field Correction in ITER

    SciTech Connect

    Park, Jong-kyu; Boozer, Allen H.; Menard, Jonathan E.; Schaffer, Michael J.

    2008-05-22

    A new method for correcting magnetic field errors in the ITER tokamak is developed using the Ideal Perturbed Equilibrium Code (IPEC). The dominant external magnetic field for driving islands is shown to be localized to the outboard midplane for three ITER equilibria that represent the projected range of operational scenarios. The coupling matrices between the poloidal harmonics of the external magnetic perturbations and the resonant fields on the rational surfaces that drive islands are combined for different equilibria and used to determine an ordered list of the dominant errors in the external magnetic field. It is found that efficient and robust error field correction is possible with a fixed setting of the correction currents relative to the currents in the main coils across the range of ITER operating scenarios that was considered.

  17. Real-time cdPCR opens a window into events occurring in the first few PCR amplification cycles.

    PubMed

    Duewer, David L; Kline, Margaret C; Romsos, Erica L

    2015-12-01

    Polymerase chain reaction (PCR) end-point limiting dilution techniques, collectively termed "digital PCR (dPCR)", have been proposed as providing a potentially primary method for DNA quantification. We are evaluating several commercially available dPCR systems for use in certifying mass concentration in human genomic DNA reference materials. To better understand observed anomalies among results from chamber- and droplet-dPCR (cdPCR and ddPCR) systems, we have developed a graphical tool for evaluating and documenting the performance of PCR assays in real-time cdPCR systems: the ogive plot, the cumulative distribution of crossing threshold values. The ogive structure appears to embed information about early amplification events. We have successfully simulated ogives observed with different assays and reaction conditions using a four-stage amplification model parameterized by the probability of creating an intact 1) first generation "long" amplicon of indeterminate length from an original DNA target, 2) second generation defined-length amplicon from a long amplicon, and 3) defined-length amplicon from another defined-length amplicon. We are using insights from this model to optimize dPCR assay design and reaction conditions and to help validate assays proposed for use in value-assigning DNA reference materials. Graphical Abstract Cumulative distributions of crossing threshold (Ct) values for the same human genomic DNA evaluated with eight assays with a real-time chamber digital PCR platform. The shape and location of the curves (ogives) embed information about the PCR amplification process. PMID:26438478

  18. Loop-linker PCR: an advanced PCR technique for genome walking.

    PubMed

    Trinh, Quoclinh; Shi, Hui; Xu, Wentao; Hao, Junran; Luo, Yunbo; Huang, Kunlun

    2012-10-01

    In this article, we developed a novel PCR method, termed loop-linker PCR, to isolate flanking sequences in transgenic crops. The novelty of this approach is its use of a stem-loop structure to design a loop-linker adapter. The adapter is designed to form a nick site when ligated with restricted DNA. This modification not only can prevent the self-ligation of adapters but also promotes the elongation of the 3' end of the loop-linker adapter to generate a stem-loop structure in the ligation products. Moreover, the suppressive effect of the stem-loop structure decreases nonspecific amplification and increases the success rate of the approach; all extension products will suppress exponential amplification except from the ligation product that contains the specific primer binding site. Using this method, 442, 1830, 107, and 512 bp left border flanking sequences were obtained from the transgenic maizes LY038, DAS-59122-7, Event 3272, and the transgenic soybean MON89788, respectively. The experimental results demonstrated that loop-linker PCR is an efficient, reliable, and cost-effective method for identifying flanking sequences in transgenic crops and could be applied for other genome walking applications. PMID:23008115

  19. Correcting Quantum Errors with Entanglement

    E-print Network

    Todd Brun; Igor Devetak; Min-Hsiu Hsieh

    2006-10-11

    We show how entanglement shared between encoder and decoder can simplify the theory of quantum error correction. The entanglement-assisted quantum codes we describe do not require the dual-containing constraint necessary for standard quantum error correcting codes, thus allowing us to ``quantize'' all of classical linear coding theory. In particular, efficient modern classical codes that attain the Shannon capacity can be made into entanglement-assisted quantum codes attaining the hashing bound (closely related to the quantum capacity). For systems without large amounts of shared entanglement, these codes can also be used as catalytic codes, in which a small amount of initial entanglement enables quantum communication.

  20. 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 supplementary material, which is available to authorized users. PMID:20145944

  1. Gender and neurogenin3 influence the pathogenesis of ketosis-prone diabetes.

    PubMed

    Louet, J-F; Smith, S B; Gautier, J-F; Molokhia, M; Virally, M-L; Kevorkian, J-P; Guillausseau, P-J; Vexiau, P; Charpentier, G; German, M S; Vaisse, C; Urbanek, M; Mauvais-Jarvis, F

    2008-09-01

    Ketosis-prone diabetes (KPD) is a phenotypically defined form of diabetes characterized by male predominance and severe insulin deficiency. Neurogenin3 (NGN3) is a proendocrine gene, which is essential for the fate of pancreatic beta cells. Mice lacking ngn3 develop early insulin-deficient diabetes. Thus, we hypothesized that gender and variants in NGN3 could predispose to KPD. We have studied clinical and metabolic parameters according to gender in patients with KPD (n = 152) and common type 2 diabetes (T2DM) (n = 167). We have sequenced NGN3 in KPD patients and screened gene variants in T2DM and controls (n = 232). In KPD, male gender was associated with a more pronounced decrease in beta-cell insulin secretory reserve, assessed by fasting C-peptide [mean (ng/ml) +/- s.d., M: 1.1 +/- 0.6, F: 1.5 +/- 0.9; p = 0.02] and glucagon-stimulated C-peptide [mean (ng/ml) +/- s.d., M: 2.2 +/- 1.1, F: 3.1 +/- 1.7; p = 0.03]. The rare affected females were in an anovulatory state. We found two new variants in the promoter [-3812T/C (af: 2%) and -3642T/C (af: 1%)], two new coding variants [S171T (af: 1%) and A185S (af: 1%)] and the variant already described [S199F (af: 69%)]. These variants were not associated with diabetes. Clinical investigation revealed an association between 199F and hyperglycaemia assessed by glycated haemoglobin [HbA1c (%, +/-s.d.) S199: 12.6 +/- 1.6, S199F: 12.4 +/- 1.4 and 199F: 14.1 +/- 2.2; p = 0.01]. In vitro, the P171T, A185S and S199F variants did not reveal major functional alteration in the activation of NGN3 target genes. In conclusion, male gender, anovulatory state in females and NGN3 variations may influence the pathogenesis of KPD in West Africans. This has therapeutic implications for potential tailored pharmacological intervention in this population. PMID:18093211

  2. Extreme value analysis in typhoon prone areas: case study of the Pearl River estuary

    NASA Astrophysics Data System (ADS)

    Moerman, E.; de Graaff, R.; Rego, J. L.

    2014-12-01

    Extreme events such as tropical storms and typhoons are often the determining factor for the extreme values of wind, wave and water level conditions. The storm track, its propagation speed, the air pressure drop and the wind speed intensity of a typhoon determine the maximum occurring wave heights, water levels and currents. The stochastic behaviour of typhoons and tropical storms, however, lead to uncertainty in the extreme value analysis, because a slight variation of the typhoon track, propagation speed or wind speed intensity can have a significant impact on these local extreme hydrodynamic conditions. To determine the significance of the stochastic behaviour of typhoons a model assessment is performed comparing standard extreme value analysis values of measured water levels (e.g. values of 1/10, 1/50, and 1/100 year return periods) against model results of artificial typhoons. In the model assessment, making use of Delft3D, various artificial typhoons are modelled in which the typhoon tracks, propagation speeds and wind speed intensities are varied within realistic ranges (based on observed historical typhoons). The study focusses on the Pearl River estuary (China) where typically about 5 to 10 tropical storms or typhoons are observed every year. Once every few years an extreme typhoon hits the area. By quantifying the potential impact of artificial typhoons the uncertainty in the extreme water level values in such a typhoon prone area are better assessed. The model is validated simulating several historic typhoons. Subsequently the typhoons tracks, their propagation speeds and wind speed intensities are varied. The extreme water level values (extreme surge height + mean high water value) that follow from the artificial typhoon modelling are compared against values from a standard extreme value analysis, making use of the central limit theorem for the extreme values in a sample. A Peaks over Threshold approach is applied and the extremes are fitted and extrapolated according to a Generalized Pareto Distribution. One of our main conclusions is that while the peak surge heights and related total water levels resulting from the historical and synthetic typhoon simulations can exceed the once per 100 year extreme total water level estimates, they are generally within the 95% confidence interval of the estimate.

  3. Predicting Salmonella enterica serotypes by repetitive sequence-based PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive extragenic palindromic sequence-based PCR (rep-PCR) utilizing a semi-automated system, was evaluated as a method to determine Salmonella serotypes. A group of 216 Salmonella isolates belonging to 13 frequently isolated serotypes and one rarer serotype from poultry were used to create a D...

  4. Identification of Mycobacterium bovis Isolates by a multiplex PCR

    PubMed Central

    de Souza Figueiredo, Eduardo Eustáquio; Silvestre, Flávia Galindo; Campos, Wilma Neres; Furlanetto, Leone Vinícius; Medeiros, Luciana; Lilenbaum, Walter; Fonseca, Leila Sousa; Silva, Joab Trajano; Paschoalin, Vânia Margaret Flosi

    2009-01-01

    Isolates from suggestive bovine tuberculosis lesions were tested by a multiplex polymerase chain reaction (m-PCR) targeting for RvD1Rv2031c and IS6110 sequences, specific for M. bovis and Mycobacterium tuberculosis complex respectively. The m-PCR successfully identified as M. bovis 88.24% of the isolates. PMID:24031349

  5. ANIMAL DNA IN PCR REAGENTS PLAGUES ANCIENT DNA RESEARCH

    EPA Science Inventory

    Ancient DNA analysis is becoming widespread. These studies use polymerase chain reaction (PCR) to amplify minute quantities of heavily damaged template. Unusual steps are taken to achieve the sensitivity necessary to detect ancient DNA, including high-cycle PCR amplification targ...

  6. In-gel technology for PCR genotyping and pathogen detection.

    PubMed

    Atrazhev, Alexey; Manage, Dammika P; Stickel, Alexander J; Crabtree, H John; Pilarski, Linda M; Acker, Jason P

    2010-10-01

    This work describes the use of polyacrylamide gel and PCR reagents photopolymerized in a mold to create an array of semisolid posts that serve as reaction vessels for parallel PCR amplification of an externally added template. DNA amplification occurred in a cylindrical, self-standing 9 × 9 array of gel posts each less than 1 ?L in volume. Photopolymerization of the gel with an intercalating dye added prior to polymerization permitted acquisition of real-time PCR data and melting curve analysis data without the need for any type of post-PCR staining procedures. PCR was equally efficient and reproducible when template DNA was polymerized within the gel or when exogenous template was added atop precast gel posts. PCR amplification occurred with template from purified DNA or from raw urine of patients with BK viruria. Multiple primer sets can be utilized per gel post array with no detectable cross contamination. As few as 34 BK virus templates were consistently detected by PCR in an individual gel post. Amplification of HPA1 and FGFR2 genes in human genomic DNA (gDNA) required as little as 2-5 ng of gDNA template/gel post. The device prototype includes a Peltier element for PCR thermal cycling and a CCD camera to capture fluorescence for product detection. Our technology is amenable to integration in point of care microdevices. PMID:20809605

  7. Interlaboratory Comparison of Quantitative PCR Test Results for Dehalococcoides

    EPA Science Inventory

    Quantitative PCR (qPCR) techniques have been widely used to measure Dehalococcoides (Dhc) DNA in the groundwater at field sites for several years. Interpretation of these data may be complicated when different laboratories using alternate methods conduct the analysis. An...

  8. Detection of Salmonella spp. in oysters by PCR.

    PubMed Central

    Bej, A K; Mahbubani, M H; Boyce, M J; Atlas, R M

    1994-01-01

    PCR DNA amplification of a region of the himA gene of Salmonella typhimurium specifically detected Salmonella spp. In oysters, 1 to 10 cells of Salmonella spp. were rapidly detected by the PCR following a pre-enrichment step to increase sensitivity and to ensure that detection was based on the presence of viable Salmonella spp. Images PMID:8117091

  9. REAL-TIME PCR ASSAY DEVELOPMENT FOR MULTIPLE MAIZE PATHOGENS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This talk presents updates on the development of real-time PCR assays for two seedborne pathogens of maize, Pantoea (Erwinia) stewartii, the causal agent of Stewart's bacterial wilt, and Stenocarpella (Diplodia) maydis, the causal agent of Diplodia ear rot. We developed primers and a real-time PCR p...

  10. Bose 4/2004 Cloning PCR fragments into TOPO vectors

    E-print Network

    Doering, Tamara

    Bose 4/2004 Cloning PCR fragments into TOPO vectors Overview: This is to facilitate the cloning cloning kit has enough for 20 reactions. Each kit contains the following reagents: 20 µl vector, 100 µl as fragments that have been stored for a week or more may not clone well.] 2. Purify the PCR fragment

  11. Quantitative RT-PCR for measuring gene expression.

    PubMed

    Riedy, M C; Timm, E A; Stewart, C C

    1995-01-01

    Classical Northern blot analysis for measuring mRNA requires too many cells to be practical for cell sorting. Yet, measurement of gene expression in small subsets within a heterogeneous population of cells is often desired. The PCR in combination with prior reverse transcription (RT-PCR) of the mRNA of interest provides a means for measuring gene expression using as few as one cell. When RT-PCR is performed, the reliability of the data can be highly subjective due to the efficiency of both RT and PCR steps. This subjectivity can be eliminated by a technique for quantitating specific RNA molecules using an internal RNA competitive reference standard (RNA-CRS), which is identical to the sequence of interest except for a deletion of 80 bases. Here we illustrate a strategy for quantitative PCR using a RNA-CRS, synthesized solely using nonplasmid-based PCR techniques. The competitive reaction consists of a constant quantity of wild-type mRNA (from 100-1000 cells) added individually to tubes containing a serially decreasing amount of RNA-CRS. The RT-PCR is performed on these samples, then the resulting product is analyzed by gel electrophoresis and densitometry. The procedure for preparing the RNA-CRS and subsequent RT-PCR steps are described in detail. PMID:7702857

  12. Having Fun with Error Analysis

    ERIC Educational Resources Information Center

    Siegel, Peter

    2007-01-01

    We present a fun activity that can be used to introduce students to error analysis: the M&M game. Students are told to estimate the number of individual candies plus uncertainty in a bag of M&M's. The winner is the group whose estimate brackets the actual number with the smallest uncertainty. The exercise produces enthusiastic discussions and…

  13. Theory of Test Translation Error

    ERIC Educational Resources Information Center

    Solano-Flores, Guillermo; Backhoff, Eduardo; Contreras-Nino, Luis Angel

    2009-01-01

    In this article, we present a theory of test translation whose intent is to provide the conceptual foundation for effective, systematic work in the process of test translation and test translation review. According to the theory, translation error is multidimensional; it is not simply the consequence of defective translation but an inevitable fact…

  14. Amplify Errors to Minimize Them

    ERIC Educational Resources Information Center

    Stewart, Maria Shine

    2009-01-01

    In this article, the author offers her experience of modeling mistakes and writing spontaneously in the computer classroom to get students' attention and elicit their editorial response. She describes how she taught her class about major sentence errors--comma splices, run-ons, and fragments--through her Sentence Meditation exercise, a rendition…

  15. Multichannel error correction code decoder

    NASA Technical Reports Server (NTRS)

    Wagner, Paul K.; Ivancic, William D.

    1993-01-01

    A brief overview of a processing satellite for a mesh very-small-aperture (VSAT) communications network is provided. The multichannel error correction code (ECC) decoder system, the uplink signal generation and link simulation equipment, and the time-shared decoder are described. The testing is discussed. Applications of the time-shared decoder are recommended.

  16. DIGITAL Visual Fortran Error Messages

    E-print Network

    DIGITAL Visual Fortran Error Messages Date: September, 1998 Software Version: DIGITAL Visual 98, or Windows NT® Version 4 Digital Equipment Corporation Maynard, Massachusetts 8/25/98 5:23 PM #12;Copyright Page Digital Equipment Corporation makes no representations that the use of its products

  17. Detecting Positioning Errors and Estimating Correct Positions by Moving Window

    PubMed Central

    Song, Ha Yoon; Lee, Jun Seok

    2015-01-01

    In recent times, improvements in smart mobile devices have led to new functionalities related to their embedded positioning abilities. Many related applications that use positioning data have been introduced and are widely being used. However, the positioning data acquired by such devices are prone to erroneous values caused by environmental factors. In this research, a detection algorithm is implemented to detect erroneous data over a continuous positioning data set with several options. Our algorithm is based on a moving window for speed values derived by consecutive positioning data. Both the moving average of the speed and standard deviation in a moving window compose a moving significant interval at a given time, which is utilized to detect erroneous positioning data along with other parameters by checking the newly obtained speed value. In order to fulfill the designated operation, we need to examine the physical parameters and also determine the parameters for the moving windows. Along with the detection of erroneous speed data, estimations of correct positioning are presented. The proposed algorithm first estimates the speed, and then the correct positions. In addition, it removes the effect of errors on the moving window statistics in order to maintain accuracy. Experimental verifications based on our algorithm are presented in various ways. We hope that our approach can help other researchers with regard to positioning applications and human mobility research. PMID:26624282

  18. Reducing Error in Mail Surveys. ERIC Digest.

    ERIC Educational Resources Information Center

    Cui, Weiwei

    This Digest describes four types of errors in mail surveys and summarizes the ways they can be reduced. Any one of these sources of error can make survey results unacceptable. Sampling error is examined through inferential statistics applied to sample survey results. In general, increasing sample size will decrease sampling error when simple…

  19. Statistical Characterization of GLONASS Broadcast Ephemeris Errors

    E-print Network

    Stanford University

    Statistical Characterization of GLONASS Broadcast Ephemeris Errors Liang Heng, Grace Xingxin Gao (without counting in clock errors) based on the data in the past three years. The ephemeris errors are com. Anomalous satel- lite behaviors and bad receiver data are excluded by an out- lier filter. Ephemeris errors

  20. Lessons to Be Learned from Past Errors

    MedlinePLUS

    Lessons to Be Learned from Past Errors The following advice, based on real errors that have happened, comes from ISMP’s ... medicines safely General Advice on Safe Medication Use Lessons to Be Learned from Past Errors Preventing Drug Errors in Children ...

  1. Problems in Contrastive Analysis and Error Analysis.

    ERIC Educational Resources Information Center

    Hughes, Arthur

    Recent years have seen the decline in popularity of contrastive analysis (CA) and the rise of error analysis (EA) as a method for explaining and predicting errors in second language learning. In CA, it is felt that by comparing the structure of a first language (L1) to that of one being learned (L2), errors can be predicted. These errors are…

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

    PubMed

    Guan, Yongtao; Li, Yehua; Sinha, Rajita

    2011-06-01

    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

  4. Determining relative error bounds for the CVBEM

    USGS Publications Warehouse

    Hromadka, T.V., II

    1985-01-01

    The Complex Variable Boundary Element Methods provides a measure of relative error which can be utilized to subsequently reduce the error or provide information for further modeling analysis. By maximizing the relative error norm on each boundary element, a bound on the total relative error for each boundary element can be evaluated. This bound can be utilized to test CVBEM convergence, to analyze the effects of additional boundary nodal points in reducing the modeling error, and to evaluate the sensitivity of resulting modeling error within a boundary element from the error produced in another boundary element as a function of geometric distance. ?? 1985.

  5. ERROR ANALYSIS OF COMPOSITE SHOCK INTERACTION PROBLEMS.

    SciTech Connect

    LEE,T.MU,Y.ZHAO,M.GLIMM,J.LI,X.YE,K.

    2004-07-26

    We propose statistical models of uncertainty and error in numerical solutions. To represent errors efficiently in shock physics simulations we propose a composition law. The law allows us to estimate errors in the solutions of composite problems in terms of the errors from simpler ones as discussed in a previous paper. In this paper, we conduct a detailed analysis of the errors. One of our goals is to understand the relative magnitude of the input uncertainty vs. the errors created within the numerical solution. In more detail, we wish to understand the contribution of each wave interaction to the errors observed at the end of the simulation.

  6. Restoration of impaired intestinal barrier function by the hydrolysed casein diet contributes to the prevention of type 1 diabetes in the diabetes-prone BioBreeding rat

    PubMed Central

    Lammers, K.; Hoogendijk, A.; Boer, M. W.; Brugman, S.; Beijer-Liefers, S.; Zandvoort, A.; Harmsen, H.; Welling, G.; Stellaard, F.; Bos, N. A.; Fasano, A.; Rozing, J.

    2010-01-01

    Aims/hypothesis Impaired intestinal barrier function is observed in type 1 diabetes patients and animal models of the disease. Exposure to diabetogenic antigens from the intestinal milieu due to a compromised intestinal barrier is considered essential for induction of the autoimmune process leading to type 1 diabetes. Since a hydrolysed casein (HC) diet prevents autoimmune diabetes onset in diabetes-prone (DP)-BioBreeding (BB) rats, we studied the role of the HC diet on intestinal barrier function and, therefore, prevention of autoimmune diabetes onset in this animal model. Methods DP-BB rats were fed the HC diet from weaning onwards and monitored for autoimmune diabetes development. Intestinal permeability was assessed in vivo by lactulose–mannitol test and ex vivo by measuring transepithelial electrical resistance (TEER). Levels of serum zonulin, a physiological tight junction modulator, were measured by ELISA. Ileal mRNA expression of Myo9b, Cldn1, Cldn2 and Ocln (which encode the tight junction-related proteins myosin IXb, claudin-1, claudin-2 and occludin) and Il-10, Tgf-ß (also known as Il10 and Tgfb, respectively, which encode regulatory cytokines) was analysed by quantitative PCR. Results The HC diet reduced autoimmune diabetes by 50% in DP-BB rats. In DP-BB rats, prediabetic gut permeability negatively correlated with the moment of autoimmune diabetes onset. The improved intestinal barrier function that was induced by HC diet in DP-BB rats was visualised by decreasing lactulose:mannitol ratio, decreasing serum zonulin levels and increasing ileal TEER. The HC diet modified ileal mRNA expression of Myo9b, and Cldn1 and Cldn2, but left Ocln expression unaltered. Conclusions/interpretation Improved intestinal barrier function might be an important intermediate in the prevention of autoimmune diabetes by the HC diet in DP-BB rats. Effects on tight junctions, ileal cytokines and zonulin production might be important mechanisms for this effect. Electronic supplementary material The online version of this article (doi:10.1007/s00125-010-1903-9) contains supplementary material, which is available to authorised users. PMID:20853098

  7. PCR detection of Babesia ovata from questing ticks in Japan.

    PubMed

    Sivakumar, Thillaiampalam; Tattiyapong, Muncharee; Okubo, Kazuhiro; Suganuma, Keisuke; Hayashida, Kyoko; Igarashi, Ikuo; Zakimi, Satoshi; Matsumoto, Kotaro; Inokuma, Hisashi; Yokoyama, Naoaki

    2014-04-01

    Babesia ovata is a tick-transmitted hemoprotozoan parasite of cattle. In the present study, we analyzed tick DNA samples (n=1459) prepared from questing ticks collected from various cattle pastures in Hokkaido (Shibecha, Taiki, Otofuke, Memuro, and Shin-Hidaka districts) and Okinawa (Yonaguni Island) prefectures of Japan for B. ovata. When all the tick DNA samples were screened by a previously described B. ovata-specific apical membrane antigen-1 (AMA-1) gene-based polymerase chain reaction (PCR) assay, none of the DNA samples was positive. Therefore, we developed a PCR assay based on the protozoan beta-tubulin (?-tubulin) gene to detect B. ovata from ticks in Japan. In the specificity test, the PCR assay amplified the expected 444-bp target gene fragment from B. ovata DNA. No PCR products were amplified from DNA samples from other blood pathogens, bovine blood, or ticks. In addition, the PCR assay detected 100 fg of B. ovata-genomic DNA extracted from an in vitro culture of the parasites. Subsequently, when all the tick DNA samples were screened by this new PCR assay, 18 were positive for B. ovata. Positive samples were found only in the Yonaguni and Memuro areas. In Okinawa, where all the ticks were identified as Haemaphysalis longicornis, 9.7% of the samples were PCR-positive, while a single tick (Ixodes ovatus) from Memuro was infected with B. ovata. When the nucleotide sequences of the PCR amplicons were phylogenetically analyzed, they formed a separate clade containing a previously described ?-tubulin gene sequence from B. ovata (Miyake strain), confirming that the PCR assay had detected only B. ovata from the tick DNA samples. This is the first report that describes the PCR detection of B. ovata in ticks. The findings warrant transmission experiments to evaluate I. ovatus as a potential vector of B. ovata. PMID:24572609

  8. Error control in the GCF: An information-theoretic model for error analysis and coding

    NASA Technical Reports Server (NTRS)

    Adeyemi, O.

    1974-01-01

    The structure of data-transmission errors within the Ground Communications Facility is analyzed in order to provide error control (both forward error correction and feedback retransmission) for improved communication. Emphasis is placed on constructing a theoretical model of errors and obtaining from it all the relevant statistics for error control. No specific coding strategy is analyzed, but references to the significance of certain error pattern distributions, as predicted by the model, to error correction are made.

  9. Chromatin Immunoprecipitation (ChIP): Revisiting the Efficacy of Sample Preparation, Sonication, Quantification of Sheared DNA, and Analysis via PCR

    PubMed Central

    Schoppee Bortz, Pamela D.; Wamhoff, Brian R.

    2011-01-01

    The “quantitative” ChIP, a tool commonly used to study protein-DNA interactions in cells and tissue, is a difficult assay often plagued with technical error. We present, herein, the process required to merge multiple protocols into a quick, reliable and easy method and an approach to accurately quantify ChIP DNA prior to performing PCR. We demonstrate that high intensity sonication for at least 30 min is required for full cellular disruption and maximum DNA recovery because ChIP lysis buffers fail to lyse formaldehyde-fixed cells. In addition, extracting ChIP DNA with chelex-100 yields samples that are too dilute for evaluation of shearing efficiency or quantification via nanospectrophotometry. However, DNA extracted from the Mock-ChIP supernatant via the phenol-chloroform-isoamyl alcohol (PCIA) method can be used to evaluate DNA shearing efficiency and used as the standard in a fluorescence-based microplate assay. This enabled accurate quantification of DNA in chelex-extracted ChIP samples and normalization to total DNA concentration prior to performing real-time PCR (rtPCR). Thus, a quick ChIP assay that can be completed in nine bench hours over two days has been validated along with a rapid, accurate and repeatable way to quantify ChIP DNA. The resulting rtPCR data more accurately depicts treatment effects on protein-DNA interactions of interest. PMID:22046253

  10. Comparison of the effect of robotic reinforced movement learning technology on the development of prone locomotion in infants with and without risk for cerebral

    E-print Network

    Fagg, Andrew H.

    of prone locomotion in infants with and without risk for cerebral palsy. Kolobe, Thubi H.A, PT, PhD1 , Fagg in infants with cerebral palsy (CP). Study Design: Repeated measures experimental design with 3 groups

  11. The Adaptive Response in p53 Cancer Prone Mice: Loss of heterozygosity and Genomic Instability

    SciTech Connect

    Josee, Lavoie; Dolling, Jo-Anna; Mitchel, Ron E.J.; Boreham, Douglas R.

    2004-09-28

    The Trp53 gene is clearly associated with increased cancer risk. This, coupled with the broad understanding of its mode of action at the molecular level, makes this gene a good candidate for investigating the relationship between genetic risk factors and spontaneous cancer occurring in a mouse model exposed to low dose radiation. We have shown that adaptive response to chronic low dose radiation could increase cancer latency, as well as overall lifespan. To better understand the molecular processes that influence cellular risk, modern tools in molecular biology were used to evaluate the loss of heterozigozity (LOH) at the Trp53 locus, and chromosomal instability in the cells from mice exposed to chronic low dose radiation. Female mice carrying a single defective copy of the Trp53 gene were irradiated with doses of gamma-radiation delivered at a low dose rate of about 0.7 mGy/hr. Groups of mice (5 irradiated and 5 unexposed) were exposed to 0.33 mGy per day for 15, 30, 45, 60, 67 and 75 weeks equaling total body doses of 2.4, 4.7, 7.2, 9.7, 10.9 and 12.1 cGy, respectively. The presence of a single defective copy of the Trp53 gene increases cancer risk in these mice. However, in vivo exposure to low dose radiation increased cancer latency. We hypothesized that: (1) These mice might have spontaneous chromosome instability, and (2) that this low dose adaptive exposure would reduce the chromosomal instability. This instability was investigated using spectral karyotyping (SKY). Bone marrow cells from 5 irradiated mice (doses of 10.9 and 12.1 cGy) and 5 control mice were collected for metaphase harvest. Briefly, the cells were incubated at 37 C for 4 hours in RPMI containing 25% heat-inactivated FBS and 0.1 mg/ml colcemid, and then given a hypotonic treatment of 0.075M KCl for 20 minutes at 37 C. An average of 100 metaphases per mouse were karyotyped. The Trp53 heterozygous mice do not show apparent structural chromosome instability. From both unexposed and irradiated mice, only numerical aberrations were observed in 5 to 20% of the cells. There seem to be an age related increase in numerical aberrations as mice grow old. The results indicate that the presence of a defective copy of the Trp53 gene does not seem to affect spontaneous chromosomal instability or in response to chronic low dose exposure to g-radiation. In previous studies it was speculated that low dose and low dose rate in vivo exposure to g-radiation induces an adaptive response, which reduces the risk of cancer death generated by subsequent DNA damage from either spontaneous or radiation induced events due to enhanced recombinational repair. Induced recombination could result from reversion to homozygosity at Trp53 gene locus (Trp53 +/- to +/+) or loss of heterozygosity in unexposed mice (Trp53 +/- to -/-). This hypothesis was investigated using the quantitative real-time Polymerase Chain Reaction (QRT-PCR) quantification method and the novel Rolling Circle Amplification technique (RCA). For these purposes, spleenocytes and bone marrow cells from all the mice were isolated for cell fixation and DNA extraction. The defective Trp53 allele is generated by integration of a portion of the cloning vector pKONEO DNA into the coding sequence. Therefore, the genotypic changes are monitored based on the detection of the NEO allele and the normal Trp53 allele in the cells. To evaluate loss of heterozygosity at the Trp53 gene locus in a cell, detection of the NEO allele and the normal Trp53 allele using the dual color RCA was utilized. In our hands, this protocol did not give the required sensitivity. The gene signal enumeration was inconsistent and not reproducible. The protocol was modified and could not be optimized. Therefore, the QRT-PCR method was selected to evaluate the loss of heterozygosity with greater sensitivity and efficiency. A set of 4 primers was designed to target the NEO allele and the normal Trp53 allele in a PCR experiment using the LightCycler instrument (Roche Diagnostics). Detection of the specific PCR amplicon using the SYBR Green fluorescent dye pr

  12. RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers

    PubMed Central

    2011-01-01

    Background The polymerase chain reaction (PCR) is commonly used to detect the presence of nucleic acid sequences both in research and diagnostic settings. While high specificity is often achieved, biological requirements sometimes necessitate that primers are placed in suboptimal locations which lead to problems with the formation of primer dimers and/or misamplification of homologous sequences. Results Pyrococcus abyssi (P.a.) RNase H2 was used to enable PCR to be performed using blocked primers containing a single ribonucleotide residue which are activated via cleavage by the enzyme (rhPCR). Cleavage occurs 5'-to the RNA base following primer hybridization to the target DNA. The requirement of the primer to first hybridize with the target sequence to gain activity eliminates the formation of primer-dimers and greatly reduces misamplification of closely related sequences. Mismatches near the scissile linkage decrease the efficiency of cleavage by RNase H2, further increasing the specificity of the assay. When applied to the detection of single nucleotide polymorphisms (SNPs), rhPCR was found to be far more sensitive than standard allele-specific PCR. In general, the best discrimination occurs when the mismatch is placed at the RNA:DNA base pair. Conclusion rhPCR eliminates the formation of primer dimers and markedly improves the specificity of PCR with respect to off-target amplification. These advantages of the assay should find utility in challenging qPCR applications such as genotyping, high level multiplex assays and rare allele detection. PMID:21831278

  13. Quantification of Listeria monocytogenes cells with digital PCR and their biofilm cells with real-time PCR.

    PubMed

    Klan?nik, Anja; Toplak, Nataša; Kova?, Minka; Marquis, Hélène; Jeršek, Barbara

    2015-11-01

    The purpose of this study was to develop a PCR-based method for quantification of Listeria monocytogenes adhesion in microtitre plates. We optimized isolation of DNA in the microtitre plates using cell lysis, ultrasound treatment, heating, and centrifugation of the lysate. Digital PCR was applied for quantification of L. monocytogenes DNA that was used for construction of the standard curve, and real-time PCR was used for quantification of the attached L. monocytogenes cells. This PCR-based method was applied to quantify different strains of L. monocytogenes at different times of biofilm formation, and to study the anti-adhesive actions of natural bioactive substances (epigallocatechin gallate, (-)-?-pinene). The results show that the PCR-based method developed here can be widely used as a novel approach for adhesion assays and biofilm research. PMID:26304835

  14. A drainage basin scale model for earthflow-prone landscapes over geomorphic timescales

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

    Landscape evolution models can be informative tools for understanding how sediment transport processes, regulated by tectonic and climatic forcing, interact to control fundamental landscape characteristics such as relief, channel network organization, and hillslope form. Many studies have proposed simple mathematical geomorphic transport laws for modeling hillslope and fluvial processes, and these models are capable of generating synthetic landscapes similar to many of those observed in nature. However, deep-seated mass movements dominate the topographic development of many tectonically active landscapes, yet few compelling transport laws exist for accurately describing these processes at the drainage basin scale. Specifically, several detailed field and theoretical studies describe the mechanics of deep-seated earthflows, such as those found throughout the northern California coast ranges, but these studies are often restricted to a single earthflow site. Here, we generalize earthflow behavior to larger spatial and geomorphically significant temporal scales using a mathematical model to determine how interactions between earthflow, weathering, hillslope, and fluvial processes control sediment flux and topographic form. The model couples the evolution of the land surface with the evolution of a weathered zone driven by fluctuations in the groundwater table. The lower boundary of this weathered zone sets the potential failure plane for earthflows, which occur once the shear stress on this plane exceeds a threshold value. Earthflows deform downslope with a non-Newtonian viscous rheology while gullying, modeled with a stream power equation, and soil creep, modeled with a diffusion equation, continuously act on the land surface. To compare the intensities of these different processes, we define a characteristic timescale for each modeled process, and demonstrate how the ratios of these timescales control the steady-state topographic characteristics of the simulated landscapes. As changes in earthflow rheological properties or thickening of the weathered zone increase the intensity of earthflow processes, relief decreases, hillslopes become more planar, and fluvial incision is inhibited at low drainage areas. The model also predicts that earthflows make their most significant contribution to long term lowering of the land surface at mid- and upper-slope locations. Fluvial processes dominate at high drainage area hillslope toes, and soil creep dominates at highly convex ridgelines. We find the predictions of our model in agreement with the following general observations of earthflow prone terrain, drawn from analysis of a 1m resolution LiDAR digital elevation model of terrain adjacent to the main stem of the Eel River, northern California: (1) hillslope profiles tend to be slightly convex at the foot, broadly concave through the mid-slope, and highly convex at the ridgeline, (2) gully incision of earthflow transport zones and toes may be important in delivering sediment from hillslopes to high order streams, and (3) as with shallow landsliding, magnitude-frequency distributions of active earthflows tend to be heavy tailed.

  15. Methods for delineating flood-prone areas in the Great Basin of Nevada and adjacent states

    USGS Publications Warehouse

    Burkham, D.E.

    1988-01-01

    The Great Basin is a region of about 210,000 square miles having no surface drainage to the ocean; it includes most of Nevada and parts of Utah, California, Oregon, Idaho, and Wyoming. The area is characterized by many parallel mountain ranges and valleys trending north-south. Stream channels usually are well defined and steep within the mountains, but on reaching the alluvial fan at the canyon mouth, they may diverge into numerous distributary channels, be discontinuous near the apex of the fan, or be deeply entrenched in the alluvial deposits. Larger rivers normally have well-defined channels to or across the valley floors, but all terminate at lakes or playas. Major floods occur in most parts of the Great Basin and result from snowmelt, frontal-storm rainfall, and localized convective rainfall. Snowmelt floods typically occur during April-June. Floods resulting from frontal rain and frontal rain on snow generally occur during November-March. Floods resulting from convective-type rainfall during localized thunderstorms occur most commonly during the summer months. Methods for delineating flood-prone areas are grouped into five general categories: Detailed, historical, analytical, physiographic, and reconnaissance. The detailed and historical methods are comprehensive methods; the analytical and physiographic are intermediate; and the reconnaissance method is only approximate. Other than the reconnaissance method, each method requires determination of a T-year discharge (the peak rate of flow during a flood with long-term average recurrence interval of T years) and T-year profile and the development of a flood-boundary map. The procedure is different, however, for each method. Appraisal of the applicability of each method included consideration of its technical soundness, limitations and uncertainties, ease of use, and costs in time and money. Of the five methods, the detailed method is probably the most accurate, though most expensive. It is applicable to hydraulic and topographic conditions found in many parts of the Great Basin. The historical method is also applicable over a wide range of conditions and is less expensive than the detailed method. However, it requires more historical flood data than are usually available, and experience and judgement are needed to obtain meaningful results. The analytical method is also less expensive than the detailed method and can be used over a wide range of conditions in which the T-year discharge can be determined directly. Experience, good judgement, and thorough knowledge of hydraulic principles are required to obtain adequate results, and the method has limited application in other than rigid-channel situations. The physiographic method is applicable to rigid-boundary channels and is less accurate than the detailed method. The reconnaissance method is relatively imprecise, but it may be the most rational method to use on alluvial fans or valley floors with discontinuous channels. In general, a comprehensive method is most suitable for use with rigid-bank streams in urban areas; only an approximate method seems justified in undeveloped areas.

  16. mtDNA and the origin of Caucasians: identification of ancient Caucasian-specific haplogroups, one of which is prone to a recurrent somatic duplication in the D-loop region.

    PubMed Central

    Torroni, A.; Lott, M. T.; Cabell, M. F.; Chen, Y. S.; Lavergne, L.; Wallace, D. C.

    1994-01-01

    mtDNA sequence variation was examined in 175 Caucasians from the United States and Canada by PCR amplification and high-resolution restriction-endonuclease analysis. The majority of the Caucasian mtDNAs were subsumed within four mtDNA lineages (haplogroups) defined by mutations that are rarely seen in Africans and Mongoloids. The sequence divergence of these haplogroups indicates that they arose early in Caucasian radiation and gave raise to modern European mtDNAs. Although ancient, none of these haplogroups is old enough to be compatible with a Neanderthal origin, suggesting that Homo sapiens sapiens displaced H. s. neanderthaliensis, rather than mixed with it. The mtDNAs of one of these haplogroups have a unique homoplasmic insertion between nucleotide pair (np) 573 and np 574, within the D-loop control region. This insertion makes these mtDNAs prone to a somatic mutation that duplicates a 270-bp portion of the D-loop region between np 309 and np 572. This finding suggests that certain nonpathogenic mtDNA mutations could predispose individuals to mtDNA rearrangements. Images Figure 3 Figure 4 PMID:7942855

  17. Robot learning and error correction

    NASA Technical Reports Server (NTRS)

    Friedman, L.

    1977-01-01

    A model of robot learning is described that associates previously unknown perceptions with the sensed known consequences of robot actions. For these actions, both the categories of outcomes and the corresponding sensory patterns are incorporated in a knowledge base by the system designer. Thus the robot is able to predict the outcome of an action and compare the expectation with the experience. New knowledge about what to expect in the world may then be incorporated by the robot in a pre-existing structure whether it detects accordance or discrepancy between a predicted consequence and experience. Errors committed during plan execution are detected by the same type of comparison process and learning may be applied to avoiding the errors.

  18. Managing human error in aviation.

    PubMed

    Helmreich, R L

    1997-05-01

    Crew resource management (CRM) programs were developed to address team and leadership aspects of piloting modern airplanes. The goal is to reduce errors through team work. Human factors research and social, cognitive, and organizational psychology are used to develop programs tailored for individual airlines. Flight crews study accident case histories, group dynamics, and human error. Simulators provide pilots with the opportunity to solve complex flight problems. CRM in the simulator is called line-oriented flight training (LOFT). In automated cockpits CRM promotes the idea of automation as a crew member. Cultural aspects of aviation include professional, business, and national culture. The aviation CRM model has been adapted for training surgeons and operating room staff in human factors. PMID:11536800

  19. Shift toward prior knowledge confers a perceptual advantage in early psychosis and psychosis-prone healthy individuals.

    PubMed

    Teufel, Christoph; Subramaniam, Naresh; Dobler, Veronika; Perez, Jesus; Finnemann, Johanna; Mehta, Puja R; Goodyer, Ian M; Fletcher, Paul C

    2015-10-27

    Many neuropsychiatric illnesses are associated with psychosis, i.e., hallucinations (perceptions in the absence of causative stimuli) and delusions (irrational, often bizarre beliefs). Current models of brain function view perception as a combination of two distinct sources of information: bottom-up sensory input and top-down influences from prior knowledge. This framework may explain hallucinations and delusions. Here, we characterized the balance between visual bottom-up and top-down processing in people with early psychosis (study 1) and in psychosis-prone, healthy individuals (study 2) to elucidate the mechanisms that might contribute to the emergence of psychotic experiences. Through a specialized mental-health service, we identified unmedicated individuals who experience early psychotic symptoms but fall below the threshold for a categorical diagnosis. We observed that, in early psychosis, there was a shift in information processing favoring prior knowledge over incoming sensory evidence. In the complementary study, we capitalized on subtle variations in perception and belief in the general population that exhibit graded similarity with psychotic experiences (schizotypy). We observed that the degree of psychosis proneness in healthy individuals, and, specifically, the presence of subtle perceptual alterations, is also associated with stronger reliance on prior knowledge. Although, in the current experimental studies, this shift conferred a performance benefit, under most natural viewing situations, it may provoke anomalous perceptual experiences. Overall, we show that early psychosis and psychosis proneness both entail a basic shift in visual information processing, favoring prior knowledge over incoming sensory evidence. The studies provide complementary insights to a mechanism by which psychotic symptoms may emerge. PMID:26460044

  20. Comparison of the short-term postoperative results of prone positioning and lateral decubitus positioning during thoracoscopic esophagectomy

    PubMed Central

    Peng, Wen-Ling; Liu, Chia-Chuan; Shih, Chih-Hsun

    2015-01-01

    Introduction The conventional approach during thoracoscopic esophagectomy was performed in the left lateral decubitus position (LLDP). Recently, thoracoscopic esophagectomy in the prone position (PP) has attracted the attention of surgeons. Aim To report institutional experience with thoracoscopic esophagectomy in PP and compare it with the conventional LLDP approach. Material and methods We reviewed 59 consecutive patients who had presented with esophageal cancer undergoing three-stage thoracoscopic/laparoscopic esophagectomy (TLE) from May 2011 to Dec 2013. The TLE was sequentially performed on enrolled patients in LLDP from May 2011 to Oct 2012 and in PP from Nov 2012 to Dec 2013. Immediate postoperative outcomes were collected and compared to determine differences between the 2 groups. Results Thirty-eight patients had their operations in LLDP and 21 in PP. No differences in blood loss, respiratory condition during surgery, or postoperative pain scores were observed between the 2 groups. The PP had a shorter thoracic stage duration (3.4 vs. 3.9 h; p = 0.03) and shorter intensive care unit (ICU) stay (1.0 vs. 1.5 days; p = 0.03) but yielded a similar number of lymph nodes. Incidence of complications was similar between the 2 groups, except significantly lower incidence of pneumonia in PP (0% vs. 21.1%; p = 0.04) and higher incidence of hoarseness in PP (52.4% vs. 23.7%; p = 0.03). The symptoms resolved within 3 months in all patients except in the 2 patients with vocal cord palsy. Conclusions It is feasible and safe to perform thoracoscopic esophagectomy by adopting the prone position. Thoracoscopic esophagectomy in the prone position is potentially associated with fewer major complications and shorter ICU stay. PMID:25960791