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Sample records for mph1 requires mismatch

  1. Differential regulation of the anti-crossover and replication fork regression activities of Mph1 by Mte1

    PubMed Central

    Xue, Xiaoyu; Papusha, Alma; Choi, Koyi; Bonner, Jaclyn N.; Kumar, Sandeep; Niu, Hengyao; Kaur, Hardeep; Zheng, Xiao-Feng; Donnianni, Roberto A.; Lu, Lucy; Lichten, Michael; Zhao, Xiaolan; Ira, Grzegorz; Sung, Patrick

    2016-01-01

    We identified Mte1 (Mph1-associated telomere maintenance protein 1) as a multifunctional regulator of Saccharomyces cerevisiae Mph1, a member of the FANCM family of DNA motor proteins important for DNA replication fork repair and crossover suppression during homologous recombination. We show that Mte1 interacts with Mph1 and DNA species that resemble a DNA replication fork and the D loop formed during recombination. Biochemically, Mte1 stimulates Mph1-mediated DNA replication fork regression and branch migration in a model substrate. Consistent with this activity, genetic analysis reveals that Mte1 functions with Mph1 and the associated MHF complex in replication fork repair. Surprisingly, Mte1 antagonizes the D-loop-dissociative activity of Mph1–MHF and exerts a procrossover role in mitotic recombination. We further show that the influence of Mte1 on Mph1 activities requires its binding to Mph1 and DNA. Thus, Mte1 differentially regulates Mph1 activities to achieve distinct outcomes in recombination and replication fork repair. PMID:26966246

  2. Trophic mismatch requires seasonal heterogeneity of warming.

    PubMed

    Straile, Dietmar; Kerimoglu, Onur; Peeters, Frank

    2015-10-01

    Climate warming has been shown to advance the phenology of species. Asynchronous changes in phenology between interacting species may disrupt feeding interactions (phenological mismatch), which could have tremendous consequences for ecosystem functioning. Long-term field observations have suggested asynchronous shifts in phenology with warming, whereas experimental studies have not been conclusive. Using proxy-based modeling of three trophic levels (algae, herbivores, and fish), we .show that asynchronous changes in phenology only occur if warming is seasonally heterogeneous, but not if warming is constant throughout the year. If warming is seasonally heterogeneous, the degree and even direction of asynchrony depends on the specific seasonality of the warming. Conclusions about phenological mismatches in food web interactions may therefore produce controversial results if the analyses do not distinguish between seasonally constant and seasonal specific warming. Furthermore, our results suggest that predicting asynchrony between interacting species requires reliable warming predictions that resolve sub-seasonal time scales.

  3. Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance

    PubMed Central

    Silva, Sonia; Altmannova, Veronika; Luke-Glaser, Sarah; Henriksen, Peter; Gallina, Irene; Yang, Xuejiao; Choudhary, Chunaram; Luke, Brian; Krejci, Lumir

    2016-01-01

    Mph1 is a member of the conserved FANCM family of DNA motor proteins that play key roles in genome maintenance processes underlying Fanconi anemia, a cancer predisposition syndrome in humans. Here, we identify Mte1 as a novel interactor of the Mph1 helicase in Saccharomyces cerevisiae. In vitro, Mte1 (Mph1-associated telomere maintenance protein 1) binds directly to DNA with a preference for branched molecules such as D loops and fork structures. In addition, Mte1 stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Deletion of MTE1 reduces crossover recombination and suppresses the sensitivity of mph1Δ mutant cells to replication stress. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres, and MTE1 deletion results in elongated telomeres. Taken together, our data indicate that Mte1 plays a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. PMID:26966248

  4. Binding of the Fkh1 Forkhead Associated Domain to a Phosphopeptide within the Mph1 DNA Helicase Regulates Mating-Type Switching in Budding Yeast

    PubMed Central

    Su, Zhangli; Cherney, Rachel; Choi, Koyi; Denu, John; Zhao, Xiaolan; Fox, Catherine A.

    2016-01-01

    The Saccharomyces cerevisiae Fkh1 protein has roles in cell-cycle regulated transcription as well as a transcription-independent role in recombination donor preference during mating-type switching. The conserved FHA domain of Fkh1 regulates donor preference by juxtaposing two distant regions on chromosome III to promote their recombination. A model posits that this Fkh1-mediated long-range chromosomal juxtaposition requires an interaction between the FHA domain and a partner protein(s), but to date no relevant partner has been described. In this study, we used structural modeling, 2-hybrid assays, and mutational analyses to show that the predicted phosphothreonine-binding FHA domain of Fkh1 interacted with multiple partner proteins. The Fkh1 FHA domain was important for its role in cell-cycle regulation, but no single interaction partner could account for this role. In contrast, Fkh1’s interaction with the Mph1 DNA repair helicase regulated donor preference during mating-type switching. Using 2-hybrid assays, co-immunoprecipitation, and fluorescence anisotropy, we mapped a discrete peptide within the regulatory Mph1 C-terminus required for this interaction and identified two threonines that were particularly important. In vitro binding experiments indicated that at least one of these threonines had to be phosphorylated for efficient Fkh1 binding. Substitution of these two threonines with alanines (mph1-2TA) specifically abolished the Fkh1-Mph1 interaction in vivo and altered donor preference during mating-type switching to the same degree as mph1Δ. Notably, the mph1-2TA allele maintained other functions of Mph1 in genome stability. Deletion of a second Fkh1-interacting protein encoded by YMR144W also resulted in a change in Fkh1-FHA-dependent donor preference. We have named this gene FDO1 for Forkhead one interacting protein involved in donor preference. We conclude that a phosphothreonine-mediated protein-protein interface between Fkh1-FHA and Mph1 contributes

  5. Processing of DNA structures via DNA unwinding and branch migration by the S. cerevisiae Mph1 protein.

    PubMed

    Zheng, Xiao-Feng; Prakash, Rohit; Saro, Dorina; Longerich, Simonne; Niu, Hengyao; Sung, Patrick

    2011-10-10

    The budding yeast Mph1 protein, the putative ortholog of human FANCM, possesses a 3' to 5' DNA helicase activity and is capable of disrupting the D-loop structure to suppress chromosome arm crossovers in mitotic homologous recombination. Similar to FANCM, genetic studies have implicated Mph1 in DNA replication fork repair. Consistent with this genetic finding, we show here that Mph1 is able to mediate replication fork reversal, and to process the Holliday junction via DNA branch migration. Moreover, Mph1 unwinds 3' and 5' DNA Flap structures that bear key features of the D-loop. These biochemical results not only provide validation for a role of Mph1 in the repair of damaged replication forks, but they also offer mechanistic insights as to its ability to efficiently disrupt the D-loop intermediate.

  6. MTE1 Functions with MPH1 in Double-Strand Break Repair.

    PubMed

    Yimit, Askar; Kim, TaeHyung; Anand, Ranjith P; Meister, Sarah; Ou, Jiongwen; Haber, James E; Zhang, Zhaolei; Brown, Grant W

    2016-05-01

    Double-strand DNA breaks occur upon exposure of cells to ionizing radiation and certain chemical agents or indirectly through replication fork collapse at DNA damage sites. If left unrepaired, double-strand breaks can cause genome instability and cell death, and their repair can result in loss of heterozygosity. In response to DNA damage, proteins involved in double-strand break repair by homologous recombination relocalize into discrete nuclear foci. We identified 29 proteins that colocalize with recombination repair protein Rad52 in response to DNA damage. Of particular interest, Ygr042w/Mte1, a protein of unknown function, showed robust colocalization with Rad52. Mte1 foci fail to form when the DNA helicase gene MPH1 is absent. Mte1 and Mph1 form a complex and are recruited to double-strand breaks in vivo in a mutually dependent manner. MTE1 is important for resolution of Rad52 foci during double-strand break repair and for suppressing break-induced replication. Together our data indicate that Mte1 functions with Mph1 in double-strand break repair.

  7. Rad5-dependent DNA repair functions of the Saccharomyces cerevisiae FANCM protein homolog Mph1.

    PubMed

    Daee, Danielle L; Ferrari, Elisa; Longerich, Simonne; Zheng, Xiao-feng; Xue, Xiaoyu; Branzei, Dana; Sung, Patrick; Myung, Kyungjae

    2012-08-03

    Interstrand cross-links (ICLs) covalently link complementary DNA strands, block DNA replication, and transcription and must be removed to allow cell survival. Several pathways, including the Fanconi anemia (FA) pathway, can faithfully repair ICLs and maintain genomic integrity; however, the precise mechanisms of most ICL repair processes remain enigmatic. In this study we genetically characterized a conserved yeast ICL repair pathway composed of the yeast homologs (Mph1, Chl1, Mhf1, Mhf2) of four FA proteins (FANCM, FANCJ, MHF1, MHF2). This pathway is epistatic with Rad5-mediated DNA damage bypass and distinct from the ICL repair pathways mediated by Rad18 and Pso2. In addition, consistent with the FANCM role in stabilizing ICL-stalled replication forks, we present evidence that Mph1 prevents ICL-stalled replication forks from collapsing into double-strand breaks. This unique repair function of Mph1 is specific for ICL damage and does not extend to other types of damage. These studies reveal the functional conservation of the FA pathway and validate the yeast model for future studies to further elucidate the mechanism of the FA pathway.

  8. Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination.

    PubMed

    Prakash, Rohit; Satory, Dominik; Dray, Eloïse; Papusha, Almas; Scheller, Jürgen; Kramer, Wilfried; Krejci, Lumir; Klein, Hannah; Haber, James E; Sung, Patrick; Ira, Grzegorz

    2009-01-01

    Eukaryotes possess mechanisms to limit crossing over during homologous recombination, thus avoiding possible chromosomal rearrangements. We show here that budding yeast Mph1, an ortholog of human FancM helicase, utilizes its helicase activity to suppress spontaneous unequal sister chromatid exchanges and DNA double-strand break-induced chromosome crossovers. Since the efficiency and kinetics of break repair are unaffected, Mph1 appears to channel repair intermediates into a noncrossover pathway. Importantly, Mph1 works independently of two other helicases-Srs2 and Sgs1-that also attenuate crossing over. By chromatin immunoprecipitation, we find targeting of Mph1 to double-strand breaks in cells. Purified Mph1 binds D-loop structures and is particularly adept at unwinding these structures. Importantly, Mph1, but not a helicase-defective variant, dissociates Rad51-made D-loops. Overall, the results from our analyses suggest a new role of Mph1 in promoting the noncrossover repair of DNA double-strand breaks.

  9. Wastewater treatment models in teaching and training: the mismatch between education and requirements for jobs.

    PubMed

    Hug, Thomas; Benedetti, Lorenzo; Hall, Eric R; Johnson, Bruce R; Morgenroth, Eberhard; Nopens, Ingmar; Rieger, Leiv; Shaw, Andrew; Vanrolleghem, Peter A

    2009-01-01

    As mathematical modeling of wastewater treatment plants has become more common in research and consultancy, a mismatch between education and requirements for model-related jobs has developed. There seems to be a shortage of skilled people, both in terms of quantity and in quality. In order to address this problem, this paper provides a framework to outline different types of model-related jobs, assess the required skills for these jobs and characterize different types of education that modelers obtain "in school" as well as "on the job". It is important to consider that education of modelers does not mainly happen in university courses and that the variety of model related jobs goes far beyond use for process design by consulting companies. To resolve the mismatch, the current connection between requirements for different jobs and the various types of education has to be assessed for different geographical regions and professional environments. This allows the evaluation and improvement of important educational paths, considering quality assurance and future developments. Moreover, conclusions from a workshop involving practitioners and academics from North America and Europe are presented. The participants stressed the importance of non-technical skills and recommended strengthening the role of realistic modeling experience in university training. However, this paper suggests that all providers of modeling education and support, not only universities, but also software suppliers, professional associations and companies performing modeling tasks are called to assess and strengthen their role in training and support of professional modelers.

  10. DNA mismatch repair proteins are required for efficient herpes simplex virus 1 replication.

    PubMed

    Mohni, Kareem N; Mastrocola, Adam S; Bai, Ping; Weller, Sandra K; Heinen, Christopher D

    2011-12-01

    Herpes simplex virus 1 (HSV-1) is a double-stranded DNA virus that replicates in the nucleus of its human host cell and is known to interact with many cellular DNA repair proteins. In this study, we examined the role of cellular mismatch repair (MMR) proteins in the virus life cycle. Both MSH2 and MLH1 are required for efficient replication of HSV-1 in normal human cells and are localized to viral replication compartments. In addition, a previously reported interaction between MSH6 and ICP8 was confirmed by coimmunoprecipitation and extended to show that UL12 is also present in this complex. We also report for the first time that MLH1 associates with ND10 nuclear bodies and that like other ND10 proteins, MLH1 is recruited to the incoming genome. Knockdown of MLH1 inhibits immediate-early viral gene expression. MSH2, on the other hand, which is generally thought to play a role in mismatch repair at a step prior to that of MLH1, is not recruited to incoming genomes and appears to act at a later step in the viral life cycle. Silencing of MSH2 appears to inhibit early gene expression. Thus, both MLH1 and MSH2 are required but appear to participate in distinct events in the virus life cycle. The observation that MLH1 plays an earlier role in HSV-1 infection than does MSH2 is surprising and may indicate a novel function for MLH1 distinct from its known MSH2-dependent role in mismatch repair.

  11. MPH1, a yeast gene encoding a DEAH protein, plays a role in protection of the genome from spontaneous and chemically induced damage.

    PubMed Central

    Scheller, J; Schürer, A; Rudolph, C; Hettwer, S; Kramer, W

    2000-01-01

    We have characterized the MPH1 gene from Saccharomyces cerevisiae. mph1 mutants display a spontaneous mutator phenotype. Homologs were found in archaea and in the EST libraries of Drosophila, mouse, and man. Mph1 carries the signature motifs of the DEAH family of helicases. Selected motifs were shown to be necessary for MPH1 function by introducing missense mutations. Possible indirect effects on translation and splicing were excluded by demonstrating nuclear localization of the protein and splicing proficiency of the mutant. A mutation spectrum did not show any conspicuous deviations from wild type except for an underrepresentation of frameshift mutations. The mutator phenotype was dependent on REV3 and RAD6. The mutant was sensitive to MMS, EMS, 4-NQO, and camptothecin, but not to UV light and X rays. Epistasis analyses were carried out with representative mutants from various repair pathways (msh6, mag1, apn1, rad14, rad52, rad6, mms2, and rev3). No epistatic interactions were found, either for the spontaneous mutator phenotype or for MMS, EMS, and 4-NQO sensitivity. mph1 slightly increased the UV sensitivity of mms2, rad6, and rad14 mutants, but no effect on X-ray sensitivity was observed. These data suggest that MPH1 is not part of a hitherto known repair pathway. Possible functions are discussed. PMID:10880470

  12. Differential requirement for proliferating cell nuclear antigen in 5' and 3' nick-directed excision in human mismatch repair.

    PubMed

    Guo, Shuangli; Presnell, Steven R; Yuan, Fenghua; Zhang, Yanbin; Gu, Liya; Li, Guo-Min

    2004-04-23

    Proliferating cell nuclear antigen (PCNA) is involved in mammalian mismatch repair at a step prior to or at mismatch excision, but the molecular mechanism of this process is not fully understood. To examine the role of PCNA in mismatch-provoked and nick-directed excision, orientation-specific mismatch removal of heteroduplexes with a pre-existing nick was monitored in human nuclear extracts supplemented with the PCNA inhibitor protein p21. We show here that, whereas 3' nick-directed mismatch excision was completely inhibited by low concentrations of p21 or a p21 C-terminal fusion protein, 5' nick-directed excision was only partially blocked under the same conditions. No further reduction of the 5' excision was detected when a much higher concentration of p21 C-terminal protein was used. These results suggest the following. (i) There is a differential requirement for PCNA in 3' and 5' nick-directed excision; and (ii) 5' nick-directed excision is conducted by a manner either dependent on or independent of PCNA. Our in vitro reconstitution experiments indeed identified a 5' nick-directed excision pathway that is dependent on PCNA, hMutSalpha, and a partially purified fraction from a HeLa nuclear extract.

  13. Sgs1 and Mph1 Helicases Enforce the Recombination Execution Checkpoint During DNA Double-Strand Break Repair in Saccharomyces cerevisiae.

    PubMed

    Jain, Suvi; Sugawara, Neal; Mehta, Anuja; Ryu, Taehyun; Haber, James E

    2016-06-01

    We have previously shown that a recombination execution checkpoint (REC) regulates the choice of the homologous recombination pathway used to repair a given DNA double-strand break (DSB) based on the homology status of the DSB ends. If the two DSB ends are synapsed with closely-positioned and correctly-oriented homologous donors, repair proceeds rapidly by the gene conversion (GC) pathway. If, however, homology to only one of the ends is present, or if homologies to the two ends are situated far away from each other or in the wrong orientation, REC blocks the rapid initiation of new DNA synthesis from the synapsed end(s) and repair is carried out by the break-induced replication (BIR) machinery after a long pause. Here we report that the simultaneous deletion of two 3'→5' helicases, Sgs1 and Mph1, largely abolishes the REC-mediated lag normally observed during the repair of large gaps and BIR substrates, which now get repaired nearly as rapidly and efficiently as GC substrates. Deletion of SGS1 and MPH1 also produces a nearly additive increase in the efficiency of both BIR and long gap repair; this increase is epistatic to that seen upon Rad51 overexpression. However, Rad51 overexpression fails to mimic the acceleration in repair kinetics that is produced by sgs1Δ mph1Δ double deletion.

  14. SPATIAL MISMATCH OR RACIAL MISMATCH?*

    PubMed Central

    Hellerstein, Judith K.; Neumark, David; McInerney, Melissa

    2008-01-01

    We contrast the spatial mismatch hypothesis with what we term the racial mismatch hypothesis – that the problem is not a lack of jobs, per se, where blacks live, but a lack of jobs where blacks live into which blacks are hired. We first report new evidence on the spatial mismatch hypothesis, using data from Census Long-Form respondents. We construct direct measures of the presence of jobs in detailed geographic areas, and find that these job density measures are related to employment of black male residents in ways that would be predicted by the spatial mismatch hypothesis – in particular that spatial mismatch is primarily an issue for low-skilled black male workers. We then look at mismatch along not only spatial lines but racial lines as well, by estimating the effects of job density measures that are disaggregated by race. We find that it is primarily black job density that influences black male employment, whereas white job density has little if any influence on their employment. The evidence implies that space alone plays a relatively minor role in low black male employment rates. PMID:19727422

  15. Mismatch repair.

    PubMed

    Fishel, Richard

    2015-10-30

    Highly conserved MutS homologs (MSH) and MutL homologs (MLH/PMS) are the fundamental components of mismatch repair (MMR). After decades of debate, it appears clear that the MSH proteins initiate MMR by recognizing a mismatch and forming multiple extremely stable ATP-bound sliding clamps that diffuse without hydrolysis along the adjacent DNA. The function(s) of MLH/PMS proteins is less clear, although they too bind ATP and are targeted to MMR by MSH sliding clamps. Structural analysis combined with recent real-time single molecule and cellular imaging technologies are providing new and detailed insight into the thermal-driven motions that animate the complete MMR mechanism.

  16. Mismatch Repair in Schizosaccharomyces Pombe Requires the Mutl Homologous Gene Pms1: Molecular Cloning and Functional Analysis

    PubMed Central

    Schar, P.; Baur, M.; Schneider, C.; Kohli, J.

    1997-01-01

    Homologues of the bacterial mutS and mutL genes involved in DNA mismatch repair have been found in organisms from bacteria to humans. Here, we describe the structure and function of a newly identified Schizosaccharomyces pombe gene that encodes a predicted amino acid sequence of 794 residues with a high degree of homology to MutL related proteins. On the basis of its closer relationship to the eukaryotic ``PMS'' genes than to the ``MLH'' genes, we have designated the S. pombe homologue pms1. Disruption of the pms1 gene causes a significant increase of spontaneous mutagenesis as documented by reversion rate measurements. Tetrad analyses of crosses homozygous for the pms1 mutation reveal a reduction of spore viability from >92% to 80% associated with a low proportion (~50%) of meioses producing four viable spores and a significant, allele-dependent increase of the level of post-meiotic segregation of genetic marker allele pairs. The mutant phenotypes are consistent with a general function of pms1 in correction of mismatched base pairs arising as a consequence of DNA polymerase errors during DNA synthesis, or of hybrid DNA formation between homologous but not perfectly complementary DNA strands during meiotic recombination. PMID:9258673

  17. The mismatched nucleotides in the 5'-terminal hairpin of minute virus of mice are required for efficient viral DNA replication.

    PubMed Central

    Costello, E; Sahli, R; Hirt, B; Beard, P

    1995-01-01

    The 5'-terminal sequence in the DNA of the parvovirus minute virus of mice (MVM) is a palindrome. It can form a hairpin, the stem of which is entirely base-paired except for three consecutive unpaired nucleotides which form a bubble. Since this structure is well conserved among different parvoviruses, we examined its importance for viral replication by generating MVM mutants with alterations in this region. A clone of MVMp DNA which contained the entire 3' end and more than half of the 5' palindrome was made. Although it lacked the sequence information to form a wild-type bubble, this DNA was infectious. On transfection into A9 fibroblasts, it gave rise to a virus (MVMs) which had a bubble in its 5' palindrome. The bubble consisted of four mismatched nucleotides in the same location as the unpaired nucleotides of the wild-type palindrome. Apparently, neighboring plasmid sequences were incorporated into the viral DNA, enabling formation of the mismatch. This observation suggested that a bubble is critical for growth of MVM but that its sequence is not. To find out whether MVM lacking a bubble in the 5' palindrome is viable, we made a second clone in which the plasmid sequences incorporated in MVMs were removed. Transfection of this DNA gave rise to a virus (MVMx) in which the nucleotides unpaired in the wild-type hairpin are now fully base-paired. Although MVMx can be propagated, it is defective in comparison with wild-type MVMp; it exhibited about a 50-fold-lower ratio of plaque-forming units to DNA content. In mixed infections, MVMp consistently outgrew the bubbleless MVMx. The rate of accumulation of DNA replication intermediates was lower for MVMx than for the wild-type virus. Quantitative analysis of the 5' termini of replicative form DNA suggested that the ability of MVMx to convert hairpin 5' termini to extended termini is impaired. In contrast, the virus with the altered bubble, MVMs, behaved like the wild-type MVMp in all the assays. We conclude that MVM

  18. A Mutation in a Saccharomyces Cerevisiae Gene (Rad3) Required for Nucleotide Excision Repair and Transcription Increases the Efficiency of Mismatch Correction

    PubMed Central

    Yang, Y.; Johnson, A. L.; Johnston, L. H.; Siede, W.; Friedberg, E. C.; Ramachandran, K.; Kunz, B. A.

    1996-01-01

    RAD3 functions in DNA repair and transcription in Saccharomyces cerevisiae and particular rad3 alleles confer a mutator phenotype, possibly as a consequence of defective mismatch correction. We assessed the potential involvement of the Rad3 protein in mismatch correction by comparing heteroduplex repair in isogenic rad3-1 and wild-type strains. The rad3-1 allele increased the spontaneous mutation rate but did not prevent heteroduplex repair or bias its directionality. Instead, the efficiency of mismatch correction was enhanced in the rad3-1 strain. This surprising result prompted us to examine expression of yeast mismatch repair genes. We determined that MSH2, but not MLH1, is transcriptionally regulated during the cell-cycle like PMS1, and that rad3-1 does not increase the transcript levels for these genes in log phase cells. These observations suggest that the rad3-1 mutation gives rise to an enhanced efficiency of mismatch correction via a process that does not involve transcriptional regulation of mismatch repair. Interestingly, mismatch repair also was more efficient when error-editing by yeast DNA polymerase δ was eliminated. We discuss our results in relation to possible mechanisms that may link the rad3-1 mutation to mismatch correction efficiency. PMID:8889512

  19. DNA Triplet Repeat Expansion and Mismatch Repair

    PubMed Central

    Iyer, Ravi R.; Pluciennik, Anna; Napierala, Marek; Wells, Robert D.

    2016-01-01

    DNA mismatch repair is a conserved antimutagenic pathway that maintains genomic stability through rectification of DNA replication errors and attenuation of chromosomal rearrangements. Paradoxically, mutagenic action of mismatch repair has been implicated as a cause of triplet repeat expansions that cause neurological diseases such as Huntington disease and myotonic dystrophy. This mutagenic process requires the mismatch recognition factor MutSβ and the MutLα (and/or possibly MutLγ) endonuclease, and is thought to be triggered by the transient formation of unusual DNA structures within the expanded triplet repeat element. This review summarizes the current knowledge of DNA mismatch repair involvement in triplet repeat expansion, which encompasses in vitro biochemical findings, cellular studies, and various in vivo transgenic animal model experiments. We present current mechanistic hypotheses regarding mismatch repair protein function in mediating triplet repeat expansions and discuss potential therapeutic approaches targeting the mismatch repair pathway. PMID:25580529

  20. Artificial mismatch hybridization

    DOEpatents

    Guo, Zhen; Smith, Lloyd M.

    1998-01-01

    An improved nucleic acid hybridization process is provided which employs a modified oligonucleotide and improves the ability to discriminate a control nucleic acid target from a variant nucleic acid target containing a sequence variation. The modified probe contains at least one artificial mismatch relative to the control nucleic acid target in addition to any mismatch(es) arising from the sequence variation. The invention has direct and advantageous application to numerous existing hybridization methods, including, applications that employ, for example, the Polymerase Chain Reaction, allele-specific nucleic acid sequencing methods, and diagnostic hybridization methods.

  1. Formal Education, Mismatch and Wages after Transition: Assessing the Impact of Unobserved Heterogeneity Using Matching Estimators

    ERIC Educational Resources Information Center

    Lamo, Ana; Messina, Julian

    2010-01-01

    This paper studies the incidence and consequences of the mismatch between formal education and the educational requirements of jobs in Estonia during the years 1997-2003. We find large wage penalties associated with the phenomenon of educational mismatch. Moreover, the incidence and wage penalty of mismatches increase with age. This suggests that…

  2. Mismatch repair proteins: key regulators of genetic recombination.

    PubMed

    Surtees, J A; Argueso, J L; Alani, E

    2004-01-01

    Mismatch repair (MMR) systems are central to maintaining genome stability in prokaryotes and eukaryotes. MMR proteins play a fundamental role in avoiding mutations, primarily by removing misincorporation errors that occur during DNA replication. MMR proteins also act during genetic recombination in steps that include repairing mismatches in heteroduplex DNA, modulating meiotic crossover control, removing 3' non-homologous tails during double-strand break repair, and preventing recombination between divergent sequences. In this review we will, first, discuss roles for MMR proteins in repairing mismatches that occur during recombination, particularly during meiosis. We will also explore how studying this process has helped to refine models of double-strand break repair, and particularly to our understanding of gene conversion gradients. Second, we will examine the role of MMR proteins in repressing homeologous recombination, i.e. recombination between divergent sequences. We will also compare the requirements for MMR proteins in preventing homeologous recombination to the requirements for these proteins in mismatch repair.

  3. Replication infidelity via a mismatch with Watson-Crick geometry.

    PubMed

    Bebenek, Katarzyna; Pedersen, Lars C; Kunkel, Thomas A

    2011-02-01

    In describing the DNA double helix, Watson and Crick suggested that "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." Indeed, among many mispairing possibilities, either tautomerization or ionization of bases might allow a DNA polymerase to insert a mismatch with correct Watson-Crick geometry. However, despite substantial progress in understanding the structural basis of error prevention during polymerization, no DNA polymerase has yet been shown to form a natural base-base mismatch with Watson-Crick-like geometry. Here we provide such evidence, in the form of a crystal structure of a human DNA polymerase λ variant poised to misinsert dGTP opposite a template T. All atoms needed for catalysis are present at the active site and in positions that overlay with those for a correct base pair. The mismatch has Watson-Crick geometry consistent with a tautomeric or ionized base pair, with the pH dependence of misinsertion consistent with the latter. The results support the original idea that a base substitution can originate from a mismatch having Watson-Crick geometry, and they suggest a common catalytic mechanism for inserting a correct and an incorrect nucleotide. A second structure indicates that after misinsertion, the now primer-terminal G • T mismatch is also poised for catalysis but in the wobble conformation seen in other studies, indicating the dynamic nature of the pathway required to create a mismatch in fully duplex DNA.

  4. Interaction between Mismatch Repair and Genetic Recombination in Saccharomyces Cerevisiae

    PubMed Central

    Alani, E.; Reenan, RAG.; Kolodner, R. D.

    1994-01-01

    The yeast Saccharomyces cerevisiae encodes a set of genes that show strong amino acid sequence similarity to MutS and MutL, proteins required for mismatch repair in Escherichia coli. We examined the role of MSH2 and PMS1, yeast homologs of mutS and mutL, respectively, in the repair of base pair mismatches formed during meiotic recombination. By using specifically marked HIS4 and ARG4 alleles, we showed that msh2 mutants displayed a severe defect in the repair of all base pair mismatches as well as 1-, 2- and 4-bp insertion/deletion mispairs. The msh2 and pms1 phenotypes were indistinguishable, suggesting that the wild-type gene products act in the same repair pathway. A comparison of gene conversion events in wild-type and msh2 mutants indicated that mismatch repair plays an important role in genetic recombination. (1) Tetrad analysis at five different loci revealed that, in msh2 mutants, the majority of aberrant segregants displayed a sectored phenotype, consistent with a failure to repair mismatches created during heteroduplex formation. In wild type, base pair mismatches were almost exclusively repaired toward conversion rather than restoration. (2) In msh2 strains 10-19% of the aberrant tetrads were Ab4:4. (3) Polarity gradients at HIS4 and ARG4 were nearly abolished in msh2 mutants. The frequency of gene conversion at the 3' end of these genes was increased and was nearly the frequency observed at the 5' end. (4) Co-conversion studies were consistent with mismatch repair acting to regulate heteroduplex DNA tract length. We favor a model proposing that recombination events occur through the formation and resolution of heteroduplex intermediates and that mismatch repair proteins specifically interact with recombination enzymes to regulate the length of symmetric heteroduplex DNA. PMID:8056309

  5. Dynamics of DNA Mismatch Repair

    NASA Astrophysics Data System (ADS)

    Coats, Julie; Lin, Yuyen; Rasnik, Ivan

    2009-11-01

    DNA mismatch repair protects the genome from spontaneous mutations by recognizing errors, excising damage, and re-synthesizing DNA in a pathway that is highly conserved. Mismatch recognition is accomplished by the MutS family of proteins which are weak ATPases that bind specifically to damaged DNA, but the specific molecular mechanisms by which these proteins recognize damage and initiate excision are not known. Previous structural investigations have implied that protein-induced conformational changes are central to mismatch recognition. Because damage detection is a highly dynamic process in which conformational changes of the protein-DNA complexes occur on a time scale of a few seconds, it is difficult to obtain meaningful kinetic information with traditional ensemble techniques. In this work, we use single molecule fluorescence resonance energy transfer (smFRET) to study the conformational dynamics of fluorescently labeled DNA substrates in the presence of the mismatch repair protein MutS from E. coli and its human homolog MSH2/MSH6. Our studies allow us to obtain quantitative kinetic information about the rates of binding and dissociation and to determine the conformational states for each protein-DNA complex.

  6. Educational Mismatch and Self-Employment

    ERIC Educational Resources Information Center

    Bender, Keith A.; Roche, Kristen

    2013-01-01

    Previous research on educational mismatch concentrates on estimating its labor market consequences but with a focus on wage and salary workers. This paper examines the far less studied influence of mismatch on the self-employed. Using a sample of workers in science and engineering fields, results show larger earnings penalties for mismatch among…

  7. The structural impact of DNA mismatches

    PubMed Central

    Rossetti, Giulia; Dans, Pablo D.; Gomez-Pinto, Irene; Ivani, Ivan; Gonzalez, Carlos; Orozco, Modesto

    2015-01-01

    The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We found that the presence of mismatches produced significant local structural alterations, especially in the case of purine transversions. Mismatched pairs often show promiscuous hydrogen bonding patterns, which interchange among each other in the nanosecond time scale. This therefore defines flexible base pairs, where breathing is frequent, and where distortions in helical parameters are strong, resulting in significant alterations in groove dimension. Even if the DNA structure is plastic enough to absorb the structural impact of the mismatch, local structural changes can be propagated far from the mismatch site, following the expected through-backbone and a previously unknown through-space mechanism. The structural changes related to the presence of mismatches help to understand the different susceptibility of mismatches to the action of repairing proteins. PMID:25820425

  8. Supply and Demand Mismatches in Training: Can Anything Be Done?

    ERIC Educational Resources Information Center

    Castro, Claudio de Moura; de Andrade, Antonio Cabral

    1990-01-01

    Vocational training often fails to provide what employers need and students want. To correct supply/demand mismatches requires improving feedback from employers, increasing the flow of information, bringing schools closer to businesses, rewarding institutions for successful employment of graduates, and providing incentives for entrepreneurs. (SK)

  9. Educational Mismatch between Graduates' Possessed Skills and Market Demands in Pakistan

    ERIC Educational Resources Information Center

    Uzair-ul-Hassan, Muhammad; Noreen, Zahida

    2013-01-01

    Educational mismatch in skills that graduates possess and market requires creates barriers for organizations as well as for job seekers. The study was conducted to find out the educational mismatch between graduates possessed skills and market demands. Convenient sampling was carried out and data were collected from 200 graduates of economics…

  10. [Cognitive evoked potentials. Perspectives for mismatch negativity].

    PubMed

    Gurtubay, I G

    2009-01-01

    The techniques of cognitive evoked potentials are considered long and technically complex, which is why their use in clinical practice is not very widespread in spite of their potential utility. Recent advances in registering and analysis, together with improvement of the software managing these signals, have appreciably reduced these problems. Mismatch negativity stands out as the most promising of all the cognitive potentials due to its special characteristics regarding its generation requisites and its proven clinical utility. The fact that it can be generated without care requirements makes it especially useful for evaluating subjects with a low level of consciousness; it serves for predicting when they will emerge from a coma, amongst other uses. The incorporation of this technique into the arsenal of neurophysiological techniques for evaluating the state of these subjects will bring a substantial improvement in the evaluation of cases whose management in clinical practice is extremely complex.

  11. Calculation of wind speeds required to damage or destroy buildings

    NASA Astrophysics Data System (ADS)

    Liu, Henry

    Determination of wind speeds required to damage or destroy a building is important not only for the improvement of building design and construction but also for the estimation of wind speeds in tornadoes and other damaging storms. For instance, since 1973 the U.S. National Weather Service has been using the well-known Fujita scale (F scale) to estimate the maximum wind speeds of tornadoes [Fujita, 1981]. The F scale classifies tornadoes into 13 numbers, F-0 through F-12. The wind speed (maximum gust speed) associated with each F number is given in Table 1. Note that F-6 through F-12 are for wind speeds between 319 mi/hr (mph) and the sonic velocity (approximately 760 mph; 1 mph = 1.6 km/kr). However, since no tornadoes have been classified to exceed F-5, the F-6 through F-12 categories have no practical meaning [Fujita, 1981].

  12. Valence band anticrossing in highly mismatched alloys

    NASA Astrophysics Data System (ADS)

    Alberi, Kirstin Mclean

    Semiconductor alloys offer the ability to tune certain material parameters such as the band gap or carrier effective mass through precise control of the alloy composition, allowing them to be optimized for specific device requirements. While many alloys demonstrate near linear composition dependencies in these properties, those containing isoelectronic anion species that are significantly mismatched in electronegativity or ionization energy, known as highly mismatched alloys (HMA), exhibit substantial deviation from this trend. Here, the optical and electrical properties of HMAs containing dilute concentrations of large metallic anions are investigated in the context of a valence band anticrossing (VBAC) theory. Minority species with low ionization energies often introduce localized p-states near the valence band edge of the host semiconductor. Hybridization of these localized states with the extended p-states of the host may be described by a 12 x 12 Hamiltonian and produces a splitting of the alloy valence band into E+ and E - states. Photomodulated reflectance studies coupled with the VBAC theory confirm that the band gap bowing observed in GaSbxAs1-x and GaBixAs1-x is caused by an upward movement of the valence band edge as a result of the anticrossing interaction between the E+ and E- states. The valence band restructuring also adversely affects hole transport in these alloys through an increase in the heavy hole effective mass and the addition of an alloy disorder scattering mechanism. Finally, the VBAC theory has been extended to group IV HMAs as well as to the dilute magnetic semiconductor Ga1-x MnxAs, both of which exhibit strong hole localization at the minority species sites.

  13. Entanglement verification with detection efficiency mismatch

    NASA Astrophysics Data System (ADS)

    Zhang, Yanbao; Lütkenhaus, Norbert

    Entanglement is a necessary condition for secure quantum key distribution (QKD). When there is an efficiency mismatch between various detectors used in the QKD system, it is still an open problem how to verify entanglement. Here we present a method to address this problem, given that the detection efficiency mismatch is characterized and known. The method works without assuming an upper bound on the number of photons going to each threshold detector. Our results suggest that the efficiency mismatch affects the ability to verify entanglement: the larger the efficiency mismatch is, the smaller the set of entangled states that can be verified becomes. When there is no mismatch, our method can verify entanglement even if the method based on squashing maps [PRL 101, 093601 (2008)] fails.

  14. Mismatch Receptive Fields in Mouse Visual Cortex.

    PubMed

    Zmarz, Pawel; Keller, Georg B

    2016-11-23

    In primary visual cortex, a subset of neurons responds when a particular stimulus is encountered in a certain location in visual space. This activity can be modeled using a visual receptive field. In addition to visually driven activity, there are neurons in visual cortex that integrate visual and motor-related input to signal a mismatch between actual and predicted visual flow. Here we show that these mismatch neurons have receptive fields and signal a local mismatch between actual and predicted visual flow in restricted regions of visual space. These mismatch receptive fields are aligned to the retinotopic map of visual cortex and are similar in size to visual receptive fields. Thus, neurons with mismatch receptive fields signal local deviations of actual visual flow from visual flow predicted based on self-motion and could therefore underlie the detection of objects moving relative to the visual flow caused by self-motion. VIDEO ABSTRACT.

  15. Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange.

    PubMed

    Borgogno, María V; Monti, Mariela R; Zhao, Weixing; Sung, Patrick; Argaraña, Carlos E; Pezza, Roberto J

    2016-03-04

    Recombination between homologous chromosomes is required for the faithful meiotic segregation of chromosomes and leads to the generation of genetic diversity. The conserved meiosis-specific Dmc1 recombinase catalyzes homologous recombination triggered by DNA double strand breaks through the exchange of parental DNA sequences. Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 must also guard against recombination between divergent sequences. How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood. We have used fluorescence resonance energy transfer to study the mechanism of Dmc1-mediated strand exchange between DNA oligonucleotides with different degrees of heterology. The efficiency of strand exchange is highly sensitive to the location, type, and distribution of mismatches. Mismatches near the 3' end of the initiating DNA strand have a small effect, whereas most mismatches near the 5' end impede strand exchange dramatically. The Hop2-Mnd1 protein complex stimulates Dmc1-catalyzed strand exchange on homologous DNA or containing a single mismatch. We observed that Dmc1 can reject divergent DNA sequences while bypassing a few mismatches in the DNA sequence. Our findings have important implications in understanding meiotic recombination. First, Dmc1 acts as an initial barrier for heterologous recombination, with the mismatch repair system providing a second level of proofreading, to ensure that ectopic sequences are not recombined. Second, Dmc1 stepping over infrequent mismatches is likely critical for allowing recombination between the polymorphic sequences of homologous chromosomes, thus contributing to gene conversion and genetic diversity.

  16. Osmium complexation of mismatched DNA: effect of the bases adjacent to mismatched 5-methylcytosine.

    PubMed

    Nomura, Akiko; Tainaka, Kazuki; Okamoto, Akimitsu

    2009-03-18

    The efficiency of osmium complex formation at 5-methylcytosine in mismatched DNA duplexes is a key point for the design of sequence-specific detection of DNA methylation. Osmium complexation was not observed in fully matched duplexes, whereas the complexation site and efficiency in mismatched duplexes changed depending on the type of 5'-neighboring base of the 5-methylcytosine forming a mismatched base pair. In particular, when the base adjacent to the 5' side of the mismatched base pair was thymine, a unique "side reaction" was observed. However, the nature of the mismatched base pairs in the reaction site did not influence the selectivity of osmium complex formation with methylated DNA.

  17. The Association Between Broad Antigen HLA Mismatches, Eplet HLA Mismatches and Acute Rejection After Kidney Transplantation

    PubMed Central

    Do Nguyen, Hung Thanh; Wong, Germaine; Chapman, Jeremy R.; McDonald, Stephen P.; Coates, Patrick T.; Watson, Narelle; Russ, Graeme R.; D'Orsogna, Lloyd; Lim, Wai Hon

    2016-01-01

    Background Epitope matching, which evaluates mismatched amino acids within antigen-antibody interaction sites (eplets), may better predict acute rejection than broad antigen matching alone. We aimed to determine the association between eplet mismatches and acute rejection in kidney transplant recipients. Methods The association between eplet mismatches, broad antigen mismatches and acute rejection was assessed using adjusted Cox proportional hazard regression. Model discrimination for acute rejection was evaluated using the area under receiver operating characteristic curves. Results Of the 3,499 kidney transplant recipients from 2006 to 2011, the average (SD) number of broad antigen and eplet mismatches were 3.4 (1.7) and 22.8 (12.2), respectively. Compared with 0 to 2 eplet mismatches, the adjusted hazard ratio (HR) for acute rejection among those with 20 or greater eplet mismatches was 2.16 (95% confidence interval [CI], 1.33-3.52; P = 0.001). The adjusted area under the curve for broad antigen mismatches was 0.58 (95% CI, 0.56-0.61), similar to that for eplet mismatches (HR, 0.59; 95% CI, 0.56-0.61; P = 0.365). In recipients who were considered as low immunological risk (0-2 broad antigen HLA-ABDR mismatch), those with 20 or greater eplet mismatches experienced an increased risk of rejection compared to those with less than 20 mismatches (adjusted HR, 1.85; 95% CI, 1.11-3.08; P = 0.019). Conclusions Increasing number of eplet mismatches is associated with acute rejection in kidney transplant recipients. Consideration of eplet HLA mismatches may improve risk stratification for acute rejection in a selected group of kidney transplant candidates. PMID:27990485

  18. A new acoustic mismatch theory for Kapitsa resistance

    NASA Astrophysics Data System (ADS)

    Budaev, Bair V.; Bogy, David B.

    2010-10-01

    This paper generalizes the well-known acoustic mismatch theory of Kapitsa interface thermal resistance by taking into consideration a broad class of thermal vibrations that were excluded from that theory by the imposition of the Sommerfeld radiation condition, which is required for the theory of sound but is not relevant for the analysis of heat transport. This extension preserves the main ideas of the acoustic mismatch theory but provides much more reasonable estimates for the interface resistance. The predictions of the new theory are compared with various published experimental results for the thermal resistance between liquid helium at low temperatures and several different metals (Ag, Au, Cu, Pb and Pt). The computations are straightforward and require only well-known material parameters. The predictions agree with the experiments to within their stated range of accuracy.

  19. Impact of ABO blood group mismatch in alemtuzumab-based reduced-intensity conditioned haematopoietic SCT.

    PubMed

    Brierley, C K; Littlewood, T J; Peniket, A J; Gregg, R; Ward, J; Clark, A; Parker, A; Malladi, R; Medd, P

    2015-07-01

    The impact of ABO incompatibility on clinical outcomes following haematopoietic SCT (HSCT) remains controversial. This retrospective study assessed the effect of ABO mismatch on transplant outcomes and transfusion requirements in 594 patients undergoing reduced-intensity conditioned (RIC) HSCT with alemtuzumab in three UK transplant centres. We found no significant effects of minor, major or bidirectional ABO mismatch on overall survival, relapse-free survival, nonrelapse mortality or relapse incidence. Although the rate of acute GVHD was unaffected by ABO mismatch, the incidence of extensive chronic GVHD was higher in patients with minor and major mismatch compared with those who were ABO matched (hazard ratio (HR) 1.74, P=0.032 for minor, HR 1.69 P=0.0036 for major mismatch). Red cell and platelet transfusion requirements in the first 100 days post transplant did not differ by ABO mismatch. In this large UK series, ABO mismatch in RIC HSCT has no clinically significant effect on survival outcomes but appears to modify susceptibility to extensive chronic GVHD.

  20. Lattice QCD with mismatched fermi surfaces.

    PubMed

    Yamamoto, Arata

    2014-04-25

    We study two flavor fermions with mismatched chemical potentials in quenched lattice QCD. We first consider a large isospin chemical potential, where a charged pion is condensed, and then introduce a small mismatch between the chemical potentials of the up quark and the down antiquark. We find that the homogeneous pion condensate is destroyed by the mismatch of the chemical potentials. We also find that the two-point correlation function shows spatial oscillation, which indicates an inhomogeneous ground state, although it is not massless but massive in the present simulation setup.

  1. Snowshoe hares display limited phenotypic plasticity to mismatch in seasonal camouflage

    PubMed Central

    Zimova, Marketa; Mills, L. Scott; Lukacs, Paul M.; Mitchell, Michael S.

    2014-01-01

    As duration of snow cover decreases owing to climate change, species undergoing seasonal colour moults can become colour mismatched with their background. The immediate adaptive solution to this mismatch is phenotypic plasticity, either in phenology of seasonal colour moults or in behaviours that reduce mismatch or its consequences. We observed nearly 200 snowshoe hares across a wide range of snow conditions and two study sites in Montana, USA, and found minimal plasticity in response to mismatch between coat colour and background. We found that moult phenology varied between study sites, likely due to differences in photoperiod and climate, but was largely fixed within study sites with only minimal plasticity to snow conditions during the spring white-to-brown moult. We also found no evidence that hares modify their behaviour in response to colour mismatch. Hiding and fleeing behaviours and resting spot preference of hares were more affected by variables related to season, site and concealment by vegetation, than by colour mismatch. We conclude that plasticity in moult phenology and behaviours in snowshoe hares is insufficient for adaptation to camouflage mismatch, suggesting that any future adaptation to climate change will require natural selection on moult phenology or behaviour. PMID:24619446

  2. Snowshoe hares display limited phenotypic plasticity to mismatch in seasonal camouflage

    USGS Publications Warehouse

    Zimova, Marketa; Mills, L. Scott; Lukacs, Paul M.; Mitchell, Michael S.

    2014-01-01

    As duration of snow cover decreases owing to climate change, species undergoing seasonal colour moults can become colour mismatched with their background. The immediate adaptive solution to this mismatch is phenotypic plasticity, either in phenology of seasonal colour moults or in behaviours that reduce mismatch or its consequences. We observed nearly 200 snowshoe hares across a wide range of snow conditions and two study sites in Montana, USA, and found minimal plasticity in response to mismatch between coat colour and background. We found that moult phenology varied between study sites, likely due to differences in photoperiod and climate, but was largely fixed within study sites with only minimal plasticity to snow conditions during the spring white-to-brown moult. We also found no evidence that hares modify their behaviour in response to colour mismatch. Hiding and fleeing behaviours and resting spot preference of hares were more affected by variables related to season, site and concealment by vegetation, than by colour mismatch. We conclude that plasticity in moult phenology and behaviours in snowshoe hares is insufficient for adaptation to camouflage mismatch, suggesting that any future adaptation to climate change will require natural selection on moult phenology or behaviour.

  3. Snowshoe hares display limited phenotypic plasticity to mismatch in seasonal camouflage.

    PubMed

    Zimova, Marketa; Mills, L Scott; Lukacs, Paul M; Mitchell, Michael S

    2014-05-07

    As duration of snow cover decreases owing to climate change, species undergoing seasonal colour moults can become colour mismatched with their background. The immediate adaptive solution to this mismatch is phenotypic plasticity, either in phenology of seasonal colour moults or in behaviours that reduce mismatch or its consequences. We observed nearly 200 snowshoe hares across a wide range of snow conditions and two study sites in Montana, USA, and found minimal plasticity in response to mismatch between coat colour and background. We found that moult phenology varied between study sites, likely due to differences in photoperiod and climate, but was largely fixed within study sites with only minimal plasticity to snow conditions during the spring white-to-brown moult. We also found no evidence that hares modify their behaviour in response to colour mismatch. Hiding and fleeing behaviours and resting spot preference of hares were more affected by variables related to season, site and concealment by vegetation, than by colour mismatch. We conclude that plasticity in moult phenology and behaviours in snowshoe hares is insufficient for adaptation to camouflage mismatch, suggesting that any future adaptation to climate change will require natural selection on moult phenology or behaviour.

  4. Infra-red parametric generation: Phase mismatch condition

    NASA Astrophysics Data System (ADS)

    Ghosh, S.; Dubey, Swati; Jain, Kamal

    2015-07-01

    An analytical investigation is made for the Infrared parametric generation in doped semiconductor plasma under phase mismatch condition. Theoretical formulations are undertaken to determine induced polarization and threshold pump field for the onset of parametric generation in semiconductor plasma medium. The origin of this nonlinear interaction lies in the second order optical susceptibility arising due to the induced nonlinear current density in piezoelectric medium. Numerical estimations are made for n- type InSb at 77 K duly irradiated by a pulsed 10.6µm CO2 laser. It is very difficult to attain exact phase matching in experimental frame so we have considered a tolerable small phase mismatch in order to attain a new result. Its effect on the Infrared parametric generation in compound semiconductor is examined through induced polarization. Transmitted intensity is determined to have an idea about conversion efficiency of the said process. Phase mismatch tends to raise the required pump field to stimulate the parametric generation. Transmitted intensity is found to decrease with coherence length lc and increase carrier concentration n0, which is favorable for improved conversion efficiency.

  5. Infra-red parametric generation: Phase mismatch condition

    SciTech Connect

    Ghosh, S.; Dubey, Swati; Jain, Kamal

    2015-07-31

    An analytical investigation is made for the Infrared parametric generation in doped semiconductor plasma under phase mismatch condition. Theoretical formulations are undertaken to determine induced polarization and threshold pump field for the onset of parametric generation in semiconductor plasma medium. The origin of this nonlinear interaction lies in the second order optical susceptibility arising due to the induced nonlinear current density in piezoelectric medium. Numerical estimations are made for n- type InSb at 77 K duly irradiated by a pulsed 10.6µm CO{sub 2} laser. It is very difficult to attain exact phase matching in experimental frame so we have considered a tolerable small phase mismatch in order to attain a new result. Its effect on the Infrared parametric generation in compound semiconductor is examined through induced polarization. Transmitted intensity is determined to have an idea about conversion efficiency of the said process. Phase mismatch tends to raise the required pump field to stimulate the parametric generation. Transmitted intensity is found to decrease with coherence length lc and increase carrier concentration n{sub 0}, which is favorable for improved conversion efficiency.

  6. Halo formation from mismatched beam-beam interactions

    SciTech Connect

    Qiang, Ji

    2003-05-23

    In this paper, we report on the halo formation and emittance growth driven by a parametric resonance during mismatched beam-beam collisions. In the regime of the weak-strong beam-beam interaction, if two beams have the same machine tunes, on-axis head-on collisions between a mismatched strong beam and a weak beam will not cause the formation of halo. However, if the two beams collide with an initial offset, the beam-beam force from the mismatched strong beam can cause halo formation and emittance growth in the weak beam. Meanwhile, if two beams have different machine tunes, for opposite charged colliding beams, when the machine tune of the weak beam is smaller than that of strong beam, there is emittance growth in the weak beam. When the machine tune of the weak beam is larger than that of the strong beam, there is little emittance growth. In the regime of strong-strong beam-beam interaction, halo is formed in both beams even when the two beams collide head-on on the axis with equal machine tunes. This puts a strong requirement for a good beam match during the injection to colliders in order to avoid the emittance growth.

  7. Non-canonical actions of mismatch repair

    PubMed Central

    Crouse, Gray F.

    2015-01-01

    At the heart of the mismatch repair (MMR) system are proteins that recognize mismatches in DNA. Such mismatches can be mispairs involving normal or damaged bases or insertion/deletion loops due to strand misalignment. When such mispairs are generated during replication or recombination, MMR will direct removal of an incorrectly paired base or block recombination between nonidentical sequences. However, when mispairs are recognized outside the context of replication, proper strand discrimination between old and new DNA is lost, and MMR can act randomly and mutagenically on mispaired DNA. Such non-canonical actions of MMR are important in somatic hypermutation and class switch recombination, expansion of triplet repeats, and potentially in mutations arising in nondividing cells. MMR involvement in damage recognition and signaling is complex, with the end result likely dependent on the amount of DNA damage in a cell. PMID:26698648

  8. Nonpermissive HLA-DPB1 mismatch increases mortality after myeloablative unrelated allogeneic hematopoietic cell transplantation

    PubMed Central

    Lee, Stephanie J.; Ahn, Kwang Woo; Spellman, Stephen; Wang, Hai-Lin; Aljurf, Mahmoud; Askar, Medhat; Dehn, Jason; Fernandez Viña, Marcelo; Gratwohl, Alois; Gupta, Vikas; Hanna, Rabi; Horowitz, Mary M.; Hurley, Carolyn K.; Inamoto, Yoshihiro; Kassim, Adetola A.; Nishihori, Taiga; Mueller, Carlheinz; Oudshoorn, Machteld; Petersdorf, Effie W.; Prasad, Vinod; Robinson, James; Saber, Wael; Schultz, Kirk R.; Shaw, Bronwen; Storek, Jan; Wood, William A.; Woolfrey, Ann E.; Anasetti, Claudio

    2014-01-01

    We examined current outcomes of unrelated donor allogeneic hematopoietic cell transplantation (HCT) to determine the clinical implications of donor-recipient HLA matching. Adult and pediatric patients who had first undergone myeloablative-unrelated bone marrow or peripheral blood HCT for acute myelogenous leukemia, acute lymphoblastic leukemia, chronic myelogenous leukemia, and myelodysplastic syndrome between 1999 and 2011 were included. All had high-resolution typing for HLA-A, -B, -C, and -DRB1. Of the total (n = 8003), cases were 8/8 (n = 5449), 7/8 (n = 2071), or 6/8 (n = 483) matched. HLA mismatch (6-7/8) conferred significantly increased risk for grades II to IV and III to IV acute graft vs host disease (GVHD), chronic GVHD, transplant-related mortality (TRM), and overall mortality compared with HLA-matched cases (8/8). Type (allele/antigen) and locus (HLA-A, -B, -C, and -DRB1) of mismatch were not associated with overall mortality. Among 8/8 matched cases, HLA-DPB1 and -DQB1 mismatch resulted in increased acute GVHD, and HLA-DPB1 mismatch had decreased relapse. Nonpermissive HLA-DPB1 allele mismatch was associated with higher TRM compared with permissive HLA-DPB1 mismatch or HLA-DPB1 match and increased overall mortality compared with permissive HLA-DPB1 mismatch in 8/8 (and 10/10) matched cases. Full matching at HLA-A, -B, -C, and -DRB1 is required for optimal unrelated donor HCT survival, and avoidance of nonpermissive HLA-DPB1 mismatches in otherwise HLA-matched pairs is indicated. PMID:25161269

  9. Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS.

    PubMed

    Monti, Maria Chiara; Cohen, Serge X; Fish, Alexander; Winterwerp, Herrie H K; Barendregt, Arjan; Friedhoff, Peter; Perrakis, Anastassis; Heck, Albert J R; Sixma, Titia K; van den Heuvel, Robert H H; Lebbink, Joyce H G

    2011-10-01

    The DNA mismatch repair protein MutS recognizes mispaired bases in DNA and initiates repair in an ATP-dependent manner. Understanding of the allosteric coupling between DNA mismatch recognition and two asymmetric nucleotide binding sites at opposing sides of the MutS dimer requires identification of the relevant MutS.mmDNA.nucleotide species. Here, we use native mass spectrometry to detect simultaneous DNA mismatch binding and asymmetric nucleotide binding to Escherichia coli MutS. To resolve the small differences between macromolecular species bound to different nucleotides, we developed a likelihood based algorithm capable to deconvolute the observed spectra into individual peaks. The obtained mass resolution resolves simultaneous binding of ADP and AMP.PNP to this ABC ATPase in the absence of DNA. Mismatched DNA regulates the asymmetry in the ATPase sites; we observe a stable DNA-bound state containing a single AMP.PNP cofactor. This is the first direct evidence for such a postulated mismatch repair intermediate, and showcases the potential of native MS analysis in detecting mechanistically relevant reaction intermediates.

  10. Mismatch repair during homologous and homeologous recombination.

    PubMed

    Spies, Maria; Fishel, Richard

    2015-03-02

    Homologous recombination (HR) and mismatch repair (MMR) are inextricably linked. HR pairs homologous chromosomes before meiosis I and is ultimately responsible for generating genetic diversity during sexual reproduction. HR is initiated in meiosis by numerous programmed DNA double-strand breaks (DSBs; several hundred in mammals). A characteristic feature of HR is the exchange of DNA strands, which results in the formation of heteroduplex DNA. Mismatched nucleotides arise in heteroduplex DNA because the participating parental chromosomes contain nonidentical sequences. These mismatched nucleotides may be processed by MMR, resulting in nonreciprocal exchange of genetic information (gene conversion). MMR and HR also play prominent roles in mitotic cells during genome duplication; MMR rectifies polymerase misincorporation errors, whereas HR contributes to replication fork maintenance, as well as the repair of spontaneous DSBs and genotoxic lesions that affect both DNA strands. MMR suppresses HR when the heteroduplex DNA contains excessive mismatched nucleotides, termed homeologous recombination. The regulation of homeologous recombination by MMR ensures the accuracy of DSB repair and significantly contributes to species barriers during sexual reproduction. This review discusses the history, genetics, biochemistry, biophysics, and the current state of studies on the role of MMR in homologous and homeologous recombination from bacteria to humans.

  11. Aortic mismatch in heart transplantation: readaptation.

    PubMed

    Miralles, A

    1997-10-01

    Great vessel mismatch between donor and recipient is very usual in heart transplantation. Different procedures have been used to manage this situation. A tailoring aortoplasty is described, as a technical alternative, in cases of considerable size incongruence between donor and recipient aortic diameters.

  12. Mismatch Repair during Homologous and Homeologous Recombination

    PubMed Central

    Spies, Maria; Fishel, Richard

    2015-01-01

    Homologous recombination (HR) and mismatch repair (MMR) are inextricably linked. HR pairs homologous chromosomes before meiosis I and is ultimately responsible for generating genetic diversity during sexual reproduction. HR is initiated in meiosis by numerous programmed DNA double-strand breaks (DSBs; several hundred in mammals). A characteristic feature of HR is the exchange of DNA strands, which results in the formation of heteroduplex DNA. Mismatched nucleotides arise in heteroduplex DNA because the participating parental chromosomes contain nonidentical sequences. These mismatched nucleotides may be processed by MMR, resulting in nonreciprocal exchange of genetic information (gene conversion). MMR and HR also play prominent roles in mitotic cells during genome duplication; MMR rectifies polymerase misincorporation errors, whereas HR contributes to replication fork maintenance, as well as the repair of spontaneous DSBs and genotoxic lesions that affect both DNA strands. MMR suppresses HR when the heteroduplex DNA contains excessive mismatched nucleotides, termed homeologous recombination. The regulation of homeologous recombination by MMR ensures the accuracy of DSB repair and significantly contributes to species barriers during sexual reproduction. This review discusses the history, genetics, biochemistry, biophysics, and the current state of studies on the role of MMR in homologous and homeologous recombination from bacteria to humans. PMID:25731766

  13. HLA Mismatching Strategies for Solid Organ Transplantation – A Balancing Act

    PubMed Central

    Zachary, Andrea A.; Leffell, Mary S.

    2016-01-01

    HLA matching provides numerous benefits in organ transplantation including better graft function, fewer rejection episodes, longer graft survival, and the possibility of reduced immunosuppression. Mismatches are attended by more frequent rejection episodes that require increased immunosuppression that, in turn, can increase the risk of infection and malignancy. HLA mismatches also incur the risk of sensitization, which can reduce the opportunity and increase waiting time for a subsequent transplant. However, other factors such as donor age, donor type, and immunosuppression protocol, can affect the benefit derived from matching. Furthermore, finding a well-matched donor may not be possible for all patients and usually prolongs waiting time. Strategies to optimize transplantation for patients without a well-matched donor should take into account the immunologic barrier represented by different mismatches: what are the least immunogenic mismatches considering the patient’s HLA phenotype; should repeated mismatches be avoided; is the patient sensitized to HLA and, if so, what are the strengths of the patient’s antibodies? This information can then be used to define the HLA type of an immunologically optimal donor and the probability of such a donor occurring. A probability that is considered to be too low may require expanding the donor population through paired donation or modifying what is acceptable, which may require employing treatment to overcome immunologic barriers such as increased immunosuppression or desensitization. Thus, transplantation must strike a balance between the risk associated with waiting for the optimal donor and the risk associated with a less than optimal donor. PMID:28003816

  14. Osmium complex binding to mismatched methylcytosine: effect of adjacent bases.

    PubMed

    Nomura, Akiko; Tainaka, Kazuki; Okamoto, Akimitsu

    2009-01-01

    We investigated the efficiency of osmium complex formation at 5-methylcytosine in mismatched DNA duplexes. Osmium complexation was not observed in fully matched duplexes, whereas the complexation site and efficiency in mismatched duplexes depended on the 5'-neighboring base of the 5-methylcytosine. In particular, when the base adjacent to the 5' side of the mismatched base pair was thymine, a unique side reaction was observed. However, the mismatched base pairs did not influence the selectivity of osmium complexation with methylated DNA.

  15. Mismatch Repair Balances Leading and Lagging Strand DNA Replication Fidelity

    DTIC Science & Technology

    2012-10-11

    the most deleterious mismatches (i.e., indel mismatches). Within classes of similar deleterious potential (base-base mismatches), evolution has...spontaneous mutation rates and the sequencing of URA3 mutants were as previously described [2,13,21], save that MSH2 was deleted from haploid pol2

  16. Dynamic control of strand excision during human DNA mismatch repair.

    PubMed

    Jeon, Yongmoon; Kim, Daehyung; Martín-López, Juana V; Lee, Ryanggeun; Oh, Jungsic; Hanne, Jeungphill; Fishel, Richard; Lee, Jong-Bong

    2016-03-22

    Mismatch repair (MMR) is activated by evolutionarily conserved MutS homologs (MSH) and MutL homologs (MLH/PMS). MSH recognizes mismatched nucleotides and form extremely stable sliding clamps that may be bound by MLH/PMS to ultimately authorize strand-specific excision starting at a distant 3'- or 5'-DNA scission. The mechanical processes associated with a complete MMR reaction remain enigmatic. The purified human (Homo sapien or Hs) 5'-MMR excision reaction requires the HsMSH2-HsMSH6 heterodimer, the 5' → 3' exonuclease HsEXOI, and the single-stranded binding heterotrimer HsRPA. The HsMLH1-HsPMS2 heterodimer substantially influences 5'-MMR excision in cell extracts but is not required in the purified system. Using real-time single-molecule imaging, we show that HsRPA or Escherichia coli EcSSB restricts HsEXOI excision activity on nicked or gapped DNA. HsMSH2-HsMSH6 activates HsEXOI by overcoming HsRPA/EcSSB inhibition and exploits multiple dynamic sliding clamps to increase tract length. Conversely, HsMLH1-HsPMS2 regulates tract length by controlling the number of excision complexes, providing a link to 5' MMR.

  17. Transfusion of ABO-mismatched platelets leads to early platelet refractoriness.

    PubMed

    Carr, R; Hutton, J L; Jenkins, J A; Lucas, G F; Amphlett, N W

    1990-07-01

    Forty-three consecutive patients previously unexposed to platelets and undergoing treatment for acute leukaemia or autografting for relapsed Hodgkin's lymphoma were randomized to receive transfused platelets of either their own ABO group (OG) or of a major mismatched group (MMG). The 26 evaluable patients were equally distributed between the two study groups. Nine of 13 (69%) MMG patients became refractory with a median onset at transfusion 7 (15 d), compared with only one of 13 (8%) OG patients (P = 0.001). Refractoriness was associated with the formation of high titre isoagglutinins, anti-HLA and platelet specific antibodies. In one patient refractoriness appeared to be due to high titre isoagglutinins alone. Six other patients developed an increase in isoagglutinin titre sufficient to adversely affect platelet increments. Patients receiving ABO-mismatched platelets had a higher incidence of anti-HLA antibodies (5 v. 1) and platelet specific antibodies (4 v. 1). ABO-mismatched platelets transfused prior to the onset of refractoriness resulted in increments similar to those achieved by ABO-matched platelets. The study demonstrates that ABO-mismatched platelets are as effective as matched platelets in patients with low titre isoagglutinins requiring only few transfusions. However, the greater incidence of early refractoriness induced in MMG patients indicates that ABO-mismatched platelets should not be given to patients with marrow failure requiring long-term support.

  18. Infrequent identity mismatches are frequently undetected

    PubMed Central

    Goldinger, Stephen D.

    2014-01-01

    The ability to quickly and accurately match faces to photographs bears critically on many domains, from controlling purchase of age-restricted goods to law enforcement and airport security. Despite its pervasiveness and importance, research has shown that face matching is surprisingly error prone. The majority of face-matching research is conducted under idealized conditions (e.g., using photographs of individuals taken on the same day) and with equal proportions of match and mismatch trials, a rate that is likely not observed in everyday face matching. In four experiments, we presented observers with photographs of faces taken an average of 1.5 years apart and tested whether face-matching performance is affected by the prevalence of identity mismatches, comparing conditions of low (10 %) and high (50 %) mismatch prevalence. Like the low-prevalence effect in visual search, we observed inflated miss rates under low-prevalence conditions. This effect persisted when participants were allowed to correct their initial responses (Experiment 2), when they had to verify every decision with a certainty judgment (Experiment 3) and when they were permitted “second looks” at face pairs (Experiment 4). These results suggest that, under realistic viewing conditions, the low-prevalence effect in face matching is a large, persistent source of errors. PMID:24500751

  19. Eukaryotic Mismatch Repair in Relation to DNA Replication.

    PubMed

    Kunkel, Thomas A; Erie, Dorothy A

    2015-01-01

    Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication. We consider differences in MMR efficiency in relation to mismatch recognition, signaling to direct MMR to the nascent strand, mismatch removal, and the timing of MMR. These studies are refining our understanding of relationships between generating and repairing replication errors to achieve accurate replication of both DNA strands of the nuclear genome.

  20. A non-canonical mismatch repair pathway in prokaryotes.

    PubMed

    Castañeda-García, A; Prieto, A I; Rodríguez-Beltrán, J; Alonso, N; Cantillon, D; Costas, C; Pérez-Lago, L; Zegeye, E D; Herranz, M; Plociński, P; Tonjum, T; García de Viedma, D; Paget, M; Waddell, S J; Rojas, A M; Doherty, A J; Blázquez, J

    2017-01-27

    Mismatch repair (MMR) is a near ubiquitous pathway, essential for the maintenance of genome stability. Members of the MutS and MutL protein families perform key steps in mismatch correction. Despite the major importance of this repair pathway, MutS-MutL are absent in almost all Actinobacteria and many Archaea. However, these organisms exhibit rates and spectra of spontaneous mutations similar to MMR-bearing species, suggesting the existence of an alternative to the canonical MutS-MutL-based MMR. Here we report that Mycobacterium smegmatis NucS/EndoMS, a putative endonuclease with no structural homology to known MMR factors, is required for mutation avoidance and anti-recombination, hallmarks of the canonical MMR. Furthermore, phenotypic analysis of naturally occurring polymorphic NucS in a M. smegmatis surrogate model, suggests the existence of M. tuberculosis mutator strains. The phylogenetic analysis of NucS indicates a complex evolutionary process leading to a disperse distribution pattern in prokaryotes. Together, these findings indicate that distinct pathways for MMR have evolved at least twice in nature.

  1. A non-canonical mismatch repair pathway in prokaryotes

    PubMed Central

    Castañeda-García, A.; Prieto, A. I.; Rodríguez-Beltrán, J.; Alonso, N.; Cantillon, D.; Costas, C.; Pérez-Lago, L.; Zegeye, E. D.; Herranz, M.; Plociński, P.; Tonjum, T.; García de Viedma, D.; Paget, M.; Waddell, S. J.; Rojas, A. M.; Doherty, A. J.; Blázquez, J.

    2017-01-01

    Mismatch repair (MMR) is a near ubiquitous pathway, essential for the maintenance of genome stability. Members of the MutS and MutL protein families perform key steps in mismatch correction. Despite the major importance of this repair pathway, MutS–MutL are absent in almost all Actinobacteria and many Archaea. However, these organisms exhibit rates and spectra of spontaneous mutations similar to MMR-bearing species, suggesting the existence of an alternative to the canonical MutS–MutL-based MMR. Here we report that Mycobacterium smegmatis NucS/EndoMS, a putative endonuclease with no structural homology to known MMR factors, is required for mutation avoidance and anti-recombination, hallmarks of the canonical MMR. Furthermore, phenotypic analysis of naturally occurring polymorphic NucS in a M. smegmatis surrogate model, suggests the existence of M. tuberculosis mutator strains. The phylogenetic analysis of NucS indicates a complex evolutionary process leading to a disperse distribution pattern in prokaryotes. Together, these findings indicate that distinct pathways for MMR have evolved at least twice in nature. PMID:28128207

  2. Mismatched DNTP Incorporation By DNA Polymerase Beta Does Not Proceed Via Globally Different Conformational Pathways

    SciTech Connect

    Tang, K.-H.; Niebuhr, M.; Tung, C.-S.; Chan, H.-c.; Chou, C.-C.; Tsai, M.-D.

    2009-05-26

    Understanding how DNA polymerases control fidelity requires elucidation of the mechanisms of matched and mismatched dNTP incorporations. Little is known about the latter because mismatched complexes do not crystallize readily. In this report, we employed small-angle X-ray scattering (SAXS) and structural modeling to probe the conformations of different intermediate states of mammalian DNA polymerase {beta} (Pol {beta}) in its wild-type and an error-prone variant, I260Q. Our structural results indicate that the mismatched ternary complex lies in-between the open and the closed forms, but more closely resembles the open form for WT and the closed form for I260Q. On the basis of molecular modeling, this over-stabilization of mismatched ternary complex of I260Q is likely caused by formation of a hydrogen bonding network between the side chains of Gln{sup 260}, Tyr{sup 296}, Glu{sup 295} and Arg{sup 258}, freeing up Asp{sup 192} to coordinate MgdNTP. These results argue against recent reports suggesting that mismatched dNTP incorporations follow a conformational path distinctly different from that of matched dNTP incorporation, or that its conformational closing is a major contributor to fidelity.

  3. Job Supply and Demand for University Graduates in Spain: A (Relative) Mismatch Perspective

    ERIC Educational Resources Information Center

    Parellada, Marti; Duch, Nestor; Alvarez, Montserrat

    2009-01-01

    This article provides an analysis of job supply by Spanish firms and the demand for work, and the mismatch that occurs between these two variables. Data are taken for the year 2006, with particular attention to jobs offered by firms that require people with university degrees or other higher education qualifications. Demand and supply are broken…

  4. Production and characterization of the celery mismatch endonuclease CEL II using baculovirus/silkworm expression system.

    PubMed

    Mon, Hiroaki; Lee, Jaeman; Fukushima, Mai; Nagata, Yudai; Fujii, Mie; Xu, Jian; Nishi, Oumi; Iiyama, Kazuhiro; Kusakabe, Takahiro

    2013-08-01

    Mutation and polymorphism detection by nucleases has become a more important tool in clinical and biological researches. There are several kinds of single-stranded nucleases for detecting mismatched DNAs. One of them, CEL II, was isolated from Apium graveolens and cleaves DNA with high specificity at sites of mismatch. High-throughput mutation scanning requires large quantity of CEL II endonuclease. Here, we demonstrate high-level expression of CEL II using silkworm-baculovirus system. The recombinant CEL II secreted in silkworm hemolymph was glycosylated and susceptible to N-glycosidase F. Additionally, larger metal ions such as Ca(2+) and Sr(2+) were able to replace Mg(2+) and enhanced mismatch cleavage activity of CEL II. These results indicate that the silkworm-baculovirus platform is a good alternative system to obtain the functional CEL II.

  5. An IQ mismatch calibration and compensation technique for wideband wireless transceivers

    NASA Astrophysics Data System (ADS)

    Jin, Peng; Liguo, Zhou; Heng, Yao; Fang, Yuan; Zhi, Fang; Yin, Shi

    2014-08-01

    An IQ mismatch calibration and compensation technique based on the digital baseband for wideband wireless communication transmitters is proposed. The digital baseband transmits the signal used for IQ mismatch calibration. The signal passes through the RF transmitter path, the calibration loop (which is composed of a square power detector and a band-pass filter in the RF transceiver) and the variable gain amplifier of the receiver. The digital baseband samples the signal for IQ mismatch estimation and compensates for it. Compared with the self-calibration technique in the RF chip, the proposed technique saves area and power consumption for the wireless local area network solution. This technique has been successfully used for the 802.11n system and satisfies the requirement of the standard by achieving over 50 dB image suppression.

  6. Mismatch binding, ADP-ATP exchange and intramolecular signaling during mismatch repair

    PubMed Central

    Hingorani, Manju M.

    2015-01-01

    The focus of this article is on the DNA binding and ATPase activities of the mismatch repair (MMR) protein, MutS—our current understanding of how this protein uses ATP to fuel its actions on DNA and initiate repair via interactions with MutL, the next protein in the pathway. Structure-function and kinetic studies have yielded detailed views of the MutS mechanism of action in MMR. How MutS and MutL work together after mismatch recognition to enable strand-specific nicking, which leads to strand excision and synthesis, is less clear and remains an active area of investigation. PMID:26704427

  7. Proteasome inhibition rescues clinically significant unstable variants of the mismatch repair protein Msh2

    PubMed Central

    Arlow, Tim; Scott, Kristan; Wagenseller, Aubrey; Gammie, Alison

    2013-01-01

    MSH2 is required for DNA mismatch repair recognition in eukaryotes. Deleterious mutations in human MSH2 account for approximately half of the alleles associated with a common hereditary cancer syndrome. Previously, we characterized clinically identified MSH2 missense mutations, using yeast as a model system, and found that the most common cause of defective DNA mismatch repair was low levels of the variant Msh2 proteins. Here, we show that increased protein turnover is responsible for the reduced cellular levels. Increasing gene dosage of more than half of the missense alleles fully restored function. A titration experiment revealed that raising the expression level of one variant to less than wild-type levels restored mismatch repair, suggesting that overexpression is not always required to regain function. We found that the ubiquitin-mediated proteasome degradation pathway is the major mechanism for increased turnover of the Msh2 variants and identified the primary ubiquitin ligase as San1. Deletion of San1 restored protein levels for all but one variant, but did not elevate wild-type Msh2 levels. The unstable variants interacted with San1, whereas wild-type Msh2 did not. Additionally, san1Δ suppressed the mismatch repair defect of unstable variants. Of medical significance, the clinically approved drug Bortezomib partially restored protein levels and mismatch repair function for low-level variants and reversed the resistance to cisplatin, a common chemotherapeutic. Our results provide the foundation for an innovative therapeutic regime for certain mismatch-repair-defective cancers that are refractory to conventional chemotherapies. PMID:23248292

  8. Visual mismatch negativity: a predictive coding view

    PubMed Central

    Stefanics, Gábor; Kremláček, Jan; Czigler, István

    2014-01-01

    An increasing number of studies investigate the visual mismatch negativity (vMMN) or use the vMMN as a tool to probe various aspects of human cognition. This paper reviews the theoretical underpinnings of vMMN in the light of methodological considerations and provides recommendations for measuring and interpreting the vMMN. The following key issues are discussed from the experimentalist's point of view in a predictive coding framework: (1) experimental protocols and procedures to control “refractoriness” effects; (2) methods to control attention; (3) vMMN and veridical perception. PMID:25278859

  9. Temperature-dependent spectral mismatch corrections

    DOE PAGES

    Osterwald, Carl R.; Campanelli, Mark; Moriarty, Tom; ...

    2015-11-01

    This study develops the mathematical foundation for a translation of solar cell short-circuit current from one thermal and spectral irradiance operating condition to another without the use of ill-defined and error-prone temperature coefficients typically employed in solar cell metrology. Using the partial derivative of quantum efficiency with respect to temperature, the conventional isothermal expression for spectral mismatch corrections is modified to account for changes of current due to temperature; this modification completely eliminates the need for short-circuit-current temperature coefficients. An example calculation is provided to demonstrate use of the new translation.

  10. Repair of mismatched basepairs in mammalian DNA

    SciTech Connect

    Taylor, J.H.; Hare, J.T.

    1991-08-01

    We have concentrated on three specific areas of our research plan. Our greatest emphasis is on the role of single strand nicks in influencing template strand selection in mismatch repair. We have found, that the ability of a nick in one strand to influence which strand is repaired is not a simple function of distance from the mismatched site but rather that an hot spot where a nick is more likely to have an influence can exist. The second line was production of single-genotype heteroduplexes in order to examine independently the repair of T/G and A/C mispairs within the same sequence context as in our mixed mispair preparations. We have shown preparations of supercoiled heteroduplex can be prepared that were exclusively T/G or exclusively A/C at the mispair site. The third effort has been to understand the difference in repair bias of different cell lines or different transfection conditions as it may relate to different repair systems in the cell. We have identified some of the sources of variation, including cell cycle position. We hope to continue this work to more precisely identify the phase of the cell cycle.

  11. Convergent Transmission of RNAi Guide-Target Mismatch Information across Argonaute Internal Allosteric Network

    PubMed Central

    Joseph, Thomas T.; Osman, Roman

    2012-01-01

    In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA) is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC) that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand “seed region” have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the cumulative

  12. ABO blood group mismatched hematopoietic stem cell transplantation.

    PubMed

    Tekgündüz, Sibel Akpınar; Özbek, Namık

    2016-02-01

    Apart from solid organ transplantations, use of ABO-blood group mismatched (ABO-mismatched) donors is acceptable in hematopoietic stem cell transplantation (HSCT) patients. About 20-40% of allogeneic HSCT recipients will receive grafts from ABO-mismatched donors. ABO incompatible HSCT procedures are associated with immediate and late consequences, including but not restricted to acute or delayed hemolytic reactions, delayed red blood cell recovery, pure red cell aplasia and graft-versus-host disease. This review summarizes the current knowledge about consequences of ABO-mismatched HSCT in terms of associated complications and will evaluate its impact on important outcome parameters of HSCT.

  13. Alignment to natural and imposed mismatches between the senses.

    PubMed

    van der Kooij, K; Brenner, E; van Beers, R J; Schot, W D; Smeets, J B J

    2013-04-01

    Does the nervous system continuously realign the senses so that objects are seen and felt in the same place? Conflicting answers to this question have been given. Research imposing a sensory mismatch has provided evidence that the nervous system realigns the senses to reduce the mismatch. Other studies have shown that when subjects point with the unseen hand to visual targets, their end points show visual-proprioceptive biases that do not disappear after episodes of visual feedback. These biases are indicative of intersensory mismatches that the nervous system does not align for. Here, we directly compare how the nervous system deals with natural and imposed mismatches. Subjects moved a hand-held cube to virtual cubes appearing at pseudorandom locations in three-dimensional space. We alternated blocks in which subjects moved without visual feedback of the hand with feedback blocks in which we rendered a cube representing the hand-held cube. In feedback blocks, we rotated the visual feedback by 5° relative to the subject's head, creating an imposed mismatch between vision and proprioception on top of any natural mismatches. Realignment occurred quickly but was incomplete. We found more realignment to imposed mismatches than to natural mismatches. We propose that this difference is related to the way in which the visual information changed when subjects entered the experiment: the imposed mismatches were different from the mismatch in daily life, so alignment started from scratch, whereas the natural mismatches were not imposed by the experimenter, so subjects are likely to have entered the experiment partly aligned.

  14. Phenological mismatch and the effectiveness of assisted gene flow.

    PubMed

    Wadgymar, Susana M; Weis, Arthur E

    2016-12-10

    The persistence of narrowly adapted species under climate change will depend on their ability to migrate apace with their historical climatic envelope or to adapt in place to maintain fitness. This second path to persistence can only occur if there is sufficient genetic variance for response to new selection regimes. Inadequate levels of genetic variation can be remedied through assisted gene flow (AGF), that is the intentional introduction of individuals genetically adapted to localities with historic climates similar to the current or future climate experienced by the resident population. However, the timing of reproduction is frequently adapted to local conditions. Phenological mismatch between residents and migrants can reduce resident × migrant mating frequencies, slowing the introgression of migrant alleles into the resident genetic background and impeding evolutionary rescue efforts. Focusing on plants, we devised a method to estimate the frequency of resident × migrant matings based on flowering schedules and applied it in an experiment that mimicked the first generation of an AGF program with Chamaecrista fasciculata, a prairie annual, under current and expected future temperature regimes. Phenological mismatch reduced the potential for resident × migrant matings by 40-90%, regardless of thermal treatment. The most successful migrant sires were the most resident like in their flowering time, further biasing the genetic admixture between resident and migrant populations. Other loci contributing to local adaptation-heat-tolerance genes, for instance-may be in linkage disequilibrium with phenology when residents and migrants are combined into a single mating pool. Thus, introgression of potentially adaptive migrant alleles into the resident genetic background is slowed when selection acts against migrant phenology. Successful AGF programs may require sustained high immigration rates or preliminary breeding programs when phenologically matched migrant

  15. Comparison of Arterial Spin Labeling and Bolus Perfusion-Weighted Imaging for Detecting Mismatch in Acute Stroke

    PubMed Central

    Zaharchuk, Greg; El Mogy, Ibraheem S.; Fischbein, Nancy J.; Albers, Gregory W.

    2012-01-01

    PURPOSE The perfusion-weighted imaging (PWI) – diffusion-weighted imaging (DWI) mismatch paradigm is widely used in stroke imaging studies. Arterial spin labeling (ASL) is an alternative perfusion method that does not require contrast. This study compares the agreement of ASL-DWI and PWI-DWI mismatch classification in stroke patients. MATERIALS AND METHODS This was a retrospective study drawn from all 1.5T MRI studies performed in 2010 at a single institution. Inclusion criteria were: symptom onset<5 days, DWI lesion>10 ml, acquisition of both PWI and ASL. DWI and PWI-Tmax>6 sec lesion volumes were determined using automated software. Patients were classified into reperfused, matched, or mismatch groups. Two radiologists classified ASL-DWI qualitatively into the same categories, blinded to DWI-PWI. Agreement between both individual readers and methods was assessed. RESULTS 51 studies met the inclusion criteria. Seven cases were excluded (1 due to PWI susceptibility artifact, 2 due to motion, and 4 due to severe ASL borderzone sign), resulting in 44 studies for comparison. Inter-rater agreement for ASL–DWI mismatch status was high (κ =0.92, 95% CI 0.80–1.00). ASL-DWI and PWI-DWI mismatch categories agreed in 25/44 cases (57%). In the 16 of 19 discrepant cases (84%), ASL overestimated the PWI lesion size. In 34/44 cases (77%), they agreed regarding the presence of mismatch versus no mismatch. CONCLUSION Mismatch classification based on ASL and PWI agree frequently but not perfectly. ASL tends to overestimate the PWI-Tmax lesion volume. Improved ASL methodologies and/or higher field strength are necessary before ASL can be recommended for routine use in acute stroke. PMID:22539548

  16. Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea

    PubMed Central

    Ishino, Sonoko; Nishi, Yuki; Oda, Soichiro; Uemori, Takashi; Sagara, Takehiro; Takatsu, Nariaki; Yamagami, Takeshi; Shirai, Tsuyoshi; Ishino, Yoshizumi

    2016-01-01

    The common mismatch repair system processed by MutS and MutL and their homologs was identified in Bacteria and Eukarya. However, no evidence of a functional MutS/L homolog has been reported for archaeal organisms, and it is not known whether the mismatch repair system is conserved in Archaea. Here, we describe an endonuclease that cleaves double-stranded DNA containing a mismatched base pair, from the hyperthermophilic archaeon Pyrococcus furiosus. The corresponding gene revealed that the activity originates from PF0012, and we named this enzyme Endonuclease MS (EndoMS) as the mismatch-specific Endonuclease. The sequence similarity suggested that EndoMS is the ortholog of NucS isolated from Pyrococcus abyssi, published previously. Biochemical characterizations of the EndoMS homolog from Thermococcus kodakarensis clearly showed that EndoMS specifically cleaves both strands of double-stranded DNA into 5′-protruding forms, with the mismatched base pair in the central position. EndoMS cleaves G/T, G/G, T/T, T/C and A/G mismatches, with a more preference for G/T, G/G and T/T, but has very little or no effect on C/C, A/C and A/A mismatches. The discovery of this endonuclease suggests the existence of a novel mismatch repair process, initiated by the double-strand break generated by the EndoMS endonuclease, in Archaea and some Bacteria. PMID:27001046

  17. Speaking Self-Assessment: Mismatches between Learners' and Teachers' Criteria

    ERIC Educational Resources Information Center

    Babaii, Esmat; Taghaddomi, Shahin; Pashmforoosh, Roya

    2016-01-01

    Perceptual (mis)matches between teachers and learners are said to affect learning success or failure. Self-assessment, as a formative assessment tool, may, inter alia, be considered a means to minimize such mismatches. Therefore, the present study investigated the extent to which learners' assessment of their own speaking performance, before and…

  18. Design and analysis of mismatch probes for long oligonucleotide microarrays

    SciTech Connect

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  19. Educational Mismatch of Graduates: A Multidimensional and Fuzzy Indicator

    ERIC Educational Resources Information Center

    Betti, Gianni; D'Agostino, Antonella; Neri, Laura

    2011-01-01

    In this paper we attempt to measure the educational mismatch, seen as a problem of overeducation, using a multidimensional and fuzzy methodology. Educational mismatch can be difficult to measure because many factors can converge to its definition and the traditional unidimensional indicators presented in literature can offer a restricted view of…

  20. PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

    PubMed Central

    Le, D.T.; Uram, J.N.; Wang, H.; Bartlett, B.R.; Kemberling, H.; Eyring, A.D.; Skora, A.D.; Luber, B.S.; Azad, N.S.; Laheru, D.; Biedrzycki, B.; Donehower, R.C.; Zaheer, A.; Fisher, G.A.; Crocenzi, T.S.; Lee, J.J.; Duffy, S.M.; Goldberg, R.M.; de la Chapelle, A.; Koshiji, M.; Bhaijee, F.; Huebner, T.; Hruban, R.H.; Wood, L.D.; Cuka, N.; Pardoll, D.M.; Papadopoulos, N.; Kinzler, K.W.; Zhou, S.; Cornish, T.C.; Taube, J.M.; Anders, R.A.; Eshleman, J.R.; Vogelstein, B.; Diaz, L.A.

    2015-01-01

    BACKGROUND Somatic mutations have the potential to encode “non-self” immunogenic antigens. We hypothesized that tumors with a large number of somatic mutations due to mismatch-repair defects may be susceptible to immune checkpoint blockade. METHODS We conducted a phase 2 study to evaluate the clinical activity of pembrolizumab, an anti–programmed death 1 immune checkpoint inhibitor, in 41 patients with progressive metastatic carcinoma with or without mismatch-repair deficiency. Pembrolizumab was administered intravenously at a dose of 10 mg per kilogram of body weight every 14 days in patients with mismatch repair–deficient colorectal cancers, patients with mismatch repair–proficient colorectal cancers, and patients with mismatch repair–deficient cancers that were not colorectal. The coprimary end points were the immune-related objective response rate and the 20-week immune-related progression-free survival rate. RESULTS The immune-related objective response rate and immune-related progression-free survival rate were 40% (4 of 10 patients) and 78% (7 of 9 patients), respectively, for mismatch repair–deficient colorectal cancers and 0% (0 of 18 patients) and 11% (2 of 18 patients) for mismatch repair–proficient colorectal cancers. The median progression-free survival and overall survival were not reached in the cohort with mismatch repair–deficient colorectal cancer but were 2.2 and 5.0 months, respectively, in the cohort with mismatch repair–proficient colorectal cancer (hazard ratio for disease progression or death, 0.10 [P<0.001], and hazard ratio for death, 0.22 [P = 0.05]). Patients with mismatch repair–deficient noncolorectal cancer had responses similar to those of patients with mismatch repair–deficient colorectal cancer (immune-related objective response rate, 71% [5 of 7 patients]; immune-related progression-free survival rate, 67% [4 of 6 patients]). Whole-exome sequencing revealed a mean of 1782 somatic mutations per tumor in

  1. A periodic table of symmetric tandem mismatches in RNA.

    PubMed

    Wu, M; McDowell, J A; Turner, D H

    1995-03-14

    The stabilities and structures of a series of RNA octamers containing symmetric tandem mismatches were studied by UV melting and imino proton NMR. The free energy increments for tandem mismatch formation are found to depend upon both mismatch sequence and adjacent base pairs. The observed sequence dependence of tandem mismatch stability is UGGU > GUUG > GAAG > or = AGGA > UUUU > CAAC > or = CUUC approximately UCCU approximately CCCC approximately ACCA approximately AAAA, and the closing base pair dependence is 5'G3'C > 5'C3'G > 5'U3'A approximately 5'A3'U. These results differ from expectations based on models used in RNA folding algorithms and from the sequence dependence observed for folding of RNA hairpins. Imino proton NMR results indicate the sequence dependence is partially due to hydrogen bonding within mismatches.

  2. The mismatch repair system reduces meiotic homeologous recombination and stimulates recombination-dependent chromosome loss.

    PubMed Central

    Chambers, S R; Hunter, N; Louis, E J; Borts, R H

    1996-01-01

    Efficient genetic recombination requires near-perfect homology between participating molecules. Sequence divergence reduces the frequency of recombination, a process that is dependent on the activity of the mismatch repair system. The effects of chromosomal divergence in diploids of Saccharomyces cerevisiae in which one copy of chromosome III is derived from a closely related species, Saccharomyces paradoxus, have been examined. Meiotic recombination between the diverged chromosomes is decreased by 25-fold. Spore viability is reduced with an observable increase in the number of tetrads with only two or three viable spores. Asci with only two viable spores are disomic for chromosome III, consistent with meiosis I nondisjunction of the homeologs. Asci with three viable spores are highly enriched for recombinants relative to tetrads with four viable spores. In 96% of the class with three viable spores, only one spore possesses a recombinant chromosome III, suggesting that the recombination process itself contributes to meiotic death. This phenomenon is dependent on the activities of the mismatch repair genes PMS1 and MSH2. A model of mismatch-stimulated chromosome loss is proposed to account for this observation. As expected, crossing over is increased in pms1 and msh2 mutants. Furthermore, genetic exchange in pms1 msh2 double mutants is affected to a greater extent than in either mutant alone, suggesting that the two proteins act independently to inhibit homeologous recombination. All mismatch repair-deficient strains exhibited reductions in the rate of chromosome III nondisjunction. PMID:8887641

  3. Novel Rx IQ mismatch compensation considering laser phase noise for CO-OFDM system

    NASA Astrophysics Data System (ADS)

    Ma, Xiurong; Ding, Zhaocai; Li, Kun; Wang, Xiao

    2015-08-01

    In this paper, a novel compensation scheme for receiver (Rx) in-phase/quadrature (IQ) mismatch is proposed in coherent optical orthogonal frequency division multiplexing (CO-OFDM) system in the presence of laser phase noise. In this scheme, laser phase noise and channel distortion were combined as a new channel transfer factor, the IQ mismatch factor and initial channel transfer factor can be estimated independently based on the relationship of IQ mismatch factors. And the channel transfer factor can be updated on a symbol-by-symbol basis which retrieves an estimation of the phase noise value by extracting and averaging the phase drift of all OFDM sub-channels. Numerical results indicate that when the phase and amplitude mismatch are 10° and 2 dB respectively, a 1.6 dB optical signal-to noise ratio is improved at laser linewidth of 60 kHz. Furthermore, the complexity of the proposed method is analyzed in terms of the number of required complex multiplications per bit.

  4. Mismatch Repair Proteins Are Activators of Toxic Responses to Chromium-DNA Damage

    PubMed Central

    Peterson-Roth, Elizabeth; Reynolds, Mindy; Quievryn, George; Zhitkovich, Anatoly

    2005-01-01

    Chromium(VI) is a toxic and carcinogenic metal that causes the formation of DNA phosphate-based adducts. Cr-DNA adducts are genotoxic in human cells, although they do not block replication in vitro. Here, we report that induction of cytotoxicity in Cr(VI)-treated human colon cells and mouse embryonic fibroblasts requires the presence of all major mismatch repair (MMR) proteins. Cr-DNA adducts lost their ability to block replication of Cr-modified plasmids in human colon cells lacking MLH1 protein. The presence of functional mismatch repair caused induction of p53-independent apoptosis associated with activation of caspases 2 and 7. Processing of Cr-DNA damage by mismatch repair resulted in the extensive formation of γ-H2AX foci in G2 phase, indicating generation of double-stranded breaks as secondary toxic lesions. Induction of γ-H2AX foci was observed at 6 to 12 h postexposure, which was followed by activation of apoptosis in the absence of significant G2 arrest. Our results demonstrate that mismatch repair system triggers toxic responses to Cr-DNA backbone modifications through stress mechanisms that are significantly different from those for other forms of DNA damage. Selection for Cr(VI) resistant, MMR-deficient cells may explain the very high frequency of lung cancers with microsatellite instability among chromate workers. PMID:15831465

  5. The effects of phenological mismatches on demography

    PubMed Central

    Miller-Rushing, Abraham J.; Høye, Toke Thomas; Inouye, David W.; Post, Eric

    2010-01-01

    Climate change is altering the phenology of species across the world, but what are the consequences of these phenological changes for the demography and population dynamics of species? Time-sensitive relationships, such as migration, breeding and predation, may be disrupted or altered, which may in turn alter the rates of reproduction and survival, leading some populations to decline and others to increase in abundance. However, finding evidence for disrupted relationships, or lack thereof, and their demographic effects, is difficult because the necessary detailed observational data are rare. Moreover, we do not know how sensitive species will generally be to phenological mismatches when they occur. Existing long-term studies provide preliminary data for analysing the phenology and demography of species in several locations. In many instances, though, observational protocols may need to be optimized to characterize timing-based multi-trophic interactions. As a basis for future research, we outline some of the key questions and approaches to improving our understanding of the relationships among phenology, demography and climate in a multi-trophic context. There are many challenges associated with this line of research, not the least of which is the need for detailed, long-term data on many organisms in a single system. However, we identify key questions that can be addressed with data that already exist and propose approaches that could guide future research. PMID:20819811

  6. Does ergonomic mismatch at school impact pain in school children?

    PubMed

    Brewer, J M; Davis, K G; Dunning, K K; Succop, P A

    2009-01-01

    Musculoskeletal pain in school-aged children is highly prevalent. While there are many potential factors relating to this discomfort, one unexplored factor is the ergonomic mismatch. The objective of this study was to determine whether the degree of mismatch between the body dimensions and the classroom furniture was associated with body discomfort. One hundred and thirty-nine children in a Midwestern U.S. school district participated in the study where demographic information, anthropometric measurements, self-reported regional body discomfort, and furniture measurements were collected. The results indicate an extremely high prevalence of ergonomic mismatch. Contrary to what was hypothesized, the ergonomic mismatch was not associated with body discomfort. The lack of association may have been a result of the extremely high prevalence of ergonomic mismatch as well as potential adaptations by the students. Although almost every student was found to not fit their desk and chairs, ergonomic mismatch had limited impact on the body discomfort. It appears that other factors such as backpack weight and time carrying may contribute more to the discomfort of students. However, caution is stress with regard to dismissing ergonomic mismatch factor as a potential risk factor since the extremely high prevalence may have washed out any effect.

  7. Mismatch repair genes in renal cortical neoplasms.

    PubMed

    Baiyee, Daniel; Banner, Barbara

    2006-02-01

    Mutation of human mutL homolog 1 (MLH-1) and human mutS homolog 2 (MSH-2) has been linked with the pathogenesis of colorectal carcinoma in hereditary nonpolyposis colorectal cancer syndrome and other carcinomas. Mutations of these genes in renal cell carcinomas were recently described. The aim of this study was to examine the expression of MLH-1 and MSH-2 in renal cortical neoplasms of various histological types by immunohistochemistry. Thirty-eight (n = 38) resected renal tumors were obtained from the surgical pathology files of the UMass Memorial Healthcare, including clear cell carcinomas (CLEARs, n = 20), papillary carcinomas (PAPs, n = 8), chromophobe carcinomas (CHRs, n = 4), and oncocytomas (ONCs, n = 6). Positive immunostaining for MLH-1 and MSH-2 was graded by the number of positive tumor cell nuclei, as follows: 0, negative; 1, up to one third of positive nuclei; 2, one to two thirds positive; and 3, greater than two thirds positive. Loss of MLH-1 or MSH-2 was defined as a tumor with grade 0 or 1, compared with the normal tubules. Normal tubules and intercalated ducts contained cells positive for MLH-1 and MSH-2 in all cases. For both antibodies, positive staining in tumors ranged from grade 1 to 3 in the CLEAR and PAP but was only grade 2 to 3 in the CHR and ONC. Loss of MLH-1 and/or MSH-2 occurred in malignant tumors but not in ONC. Loss of MLH-1 was present in 8 (40%) of 20 CLEARs and 4 (50%) of 8 PAPs, compared with loss of MSH-2 in 4 (20%) of 20 CLEARs and 1 (25%) of 4 CHRs. Our results suggest that loss of mismatch repair genes is involved in the malignant transformation in some renal carcinomas, particularly those derived from the proximal tubules.

  8. [Avoidance of patient-prosthesis mismatch].

    PubMed

    Sakamoto, Y; Hashimoto, K

    2006-04-01

    To minimize the incidence of patient-prosthesis mismatch (PPM), we have routinely adopted aortic root enlargement to avoid PPM for patients with small aortic annulus. The aim of this study was to review our strategy of avoiding PPM. The Carpentier-Edwards Perimount (CEP) valves were implanted in 53 patients who were mostly aged over 65 and the St. Jude Medical (SJM) mechanical valves were used in 128 patients aged under 65. A standard 21-mm SJM valve was used in only 3 patients and no 19-mm valves were employed. However, 19-mm CEP valves were used in 12 patients with a small body surface area (1.43 +/- 0.14 m2). Of these, 26 patients (14.4%) who had a small aortic annulus and 24 patients aged under 65 underwent aortic root enlargement. No patient receiving an SJM valve had an projected indexed effective orifice area (EOAI) < or = 0.85 cm2/m2 because of performing aortic valve replacement (AVR) with annular enlargement and only 2 (3.8%) out of 53 patients receiving CEP valves developed PPM. Consequently, the prevalence of PPM was 1.1% in this series. The prevalence of PPM was low in patients over 65 years old with a relatively small body size who received bioprosthetic valves. A pericardial bioprosthesis was considered to be an appropriate valve in older population with regard to avoiding PPM. In patients under 65 years old with a small annulus, the first choice for avoiding PPM is aortic annular enlargement, which may be avoided by high performance mechanical valves with larger EOA.

  9. Communication in the Home and Classroom: Match or Mismatch?

    ERIC Educational Resources Information Center

    Iglesias, Aquiles

    1985-01-01

    The article examines variations in communication of cultural-linguistic minority children at home and in school and describes a communicative match/mismatch model. Implications of educational policy and program development are noted. (CL)

  10. [Moving sound source discrimination in humans (mismatch negativity and psychophysics)].

    PubMed

    Vasilenko, Iu A; Shestopalova, L B

    2010-01-01

    Ability to discriminate the moving sound sources with different dynamic properties was studied in humans. The auditory motion was simulated by introducing variable interaural time differences into the deviant stimuli. The electrophysiological experiment explored mismatch negativity elicited by the abrupt sound shift taken as deviant against gradual sound motion taken as standard. The psychoacoustic procedure revealed that these stimuli were not differentiated behaviorally. Nevertheless, the significant mismatch negativities were obtained. It was also established that the mismatch negativity was not influenced by the direction of sound motion. The results obtained are discussed from the point of view of actual theories of moving sound localization. The findings are in line with the hypothesis that mismatch negativity should not be considered as a direct index of behavioral discrimination accuracy.

  11. Identifying Mismatches in Alignments of Large Anatomical Ontologies

    PubMed Central

    Zhang, Songmao; Bodenreider, Olivier

    2007-01-01

    Objective: The objective of this study is to propose a model of matching errors for identifying mismatches in alignments of large anatomical ontologies. Methods: Three approaches to identifying mismatches are utilized: 1) lexical, based on the presence of modifiers in the names of the concepts aligned; 2) structural, identifying conflicting relations resulting from the alignment; and 3) semantic, based on disjoint top-level categories across ontologies. Results: 83% of the potential mismatches identified by the HMatch system are identified by at least one of the approaches. Conclusions: Although not a substitute for a careful validation of the matches, these approaches significantly reduce the need for manual validation by effectively characterizing most mismatches. PMID:18693957

  12. Elastic-plastic fracture mechanics of strength-mismatching

    SciTech Connect

    Parks, D.M.; Ganti, S.; McClintock, F.A.

    1996-12-31

    Approximate solutions to stress-fields are provided for a strength-mismatched interface crack in small-scale yielding (SSY) for non-hardening and low hardening materials. Variations of local deformation intensities, characterized by a J-type contour integral, are proposed. The softer material experiences a higher deformation intensity level, J{sub S}, while the harder material sees a much lower deformation intensity level, J{sub H}, compared to that obtained from the applied J near the respective homogeneous crack-tips. For a low hardening material, the stress fields are obtained by scaling from an elastic/perfectly-plastic problem, based on an effective mismatch, M{sub eff}, which is a function of mismatch, M, and the hardening exponent, n. Triaxial stress build-up is discussed quantitatively in terms of M. The influence of strength-mismatch on cleavage fracture is discussed using Weibull statistics.

  13. Hemangioma of the tongue demonstrating a perfusion blood pool mismatch

    SciTech Connect

    Front, D.; Groshar, D.; Israel, O.; Robinson, E.

    1986-02-01

    Perfusion blood pool mismatch using Tc-99m labeled red blood cells (RBCs) in a hemangioma of the tongue is described. The method is useful in the evaluation of size of the residual blood pool after irradiation of the tumor.

  14. Heterodyne detection with mismatch correction based on array detector

    NASA Astrophysics Data System (ADS)

    Dong, Hongzhou; Li, Guoqiang; Yang, Ruofu; Yang, Chunping; Ao, Mingwu

    2016-07-01

    Based on an array detector, a new heterodyne detection system, which can correct the mismatches of amplitude and phase between signal and local oscillation (LO) beams, is presented in this paper. In the light of the fact that, for a heterodyne signal, there is a certain phase difference between the adjacent two samples of analog-to-digital converter (ADC), we propose to correct the spatial phase mismatch by use of the time-domain phase difference. The corrections can be realized by shifting the output sequences acquired from the detector elements in the array, and the steps of the shifting depend on the quantity of spatial phase mismatch. Numerical calculations of heterodyne efficiency are conducted to confirm the excellent performance of our system. Being different from previous works, our system needs not extra optical devices, so it provides probably an effective means to ease the problem resulted from the mismatches.

  15. Heterodyne detection with mismatch correction base on array detector

    NASA Astrophysics Data System (ADS)

    Hongzhou, Dong; Guoqiang, Li; Ruofu, Yang; Chunping, Yang; Mingwu, Ao

    2016-07-01

    Based on an array detector, a new heterodyne detection system, which can correct the mismatches of amplitude and phase between signal and local oscillation (LO) beams, is presented in this paper. In the light of the fact that, for a heterodyne signal, there is a certain phase difference between the adjacent two samples of analog-to-digital converter (ADC), we propose to correct the spatial phase mismatch by use of the time-domain phase difference. The corrections can be realized by shifting the output sequences acquired from the detector elements in the array, and the steps of the shifting depend on the quantity of spatial phase mismatch. Numerical calculations of heterodyne efficiency are conducted to confirm the excellent performance of our system. Being different from previous works, our system needs not extra optical devices, so it provides probably an effective means to ease the problem resulted from the mismatches.

  16. The Effect of Basepair Mismatch on DNA Strand Displacement.

    PubMed

    Broadwater, D W Bo; Kim, Harold D

    2016-04-12

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality.

  17. Deficient mismatch repair: Read all about it (Review)

    PubMed Central

    RICHMAN, SUSAN

    2015-01-01

    Defects in the DNA mismatch repair (MMR) proteins, result in a phenotype called microsatellite instability (MSI), occurring in up to 15% of sporadic colorectal cancers. Approximately one quarter of colon cancers with deficient MMR (dMMR) develop as a result of an inherited predisposition syndrome, Lynch syndrome (formerly known as HNPCC). It is essential to identify patients who potentially have Lynch syndrome, as not only they, but also family members, may require screening and monitoring. Diagnostic criteria have been developed, based primarily on Western populations, and several methodologies are available to identify dMMR tumours, including immunohistochemistry and microsatellite testing. These criteria have provided evidence supporting the introduction of reflex testing. Yet, it is becoming increasingly clear that tests have a limited sensitivity and specificity and may yet be superseded by next generation sequencing. In this review, the limitations of diagnostic criteria are discussed, and current and emerging screening technologies explained. There is now useful evidence supporting the prognostic and predictive value of dMMR status in colorectal tumours, but much less is known about their value in extracolonic tumours, that may also feature in Lynch syndrome. This review assesses current literature relating to dMMR in endometrial, ovarian, gastric and melanoma cancers, which it would seem, may benefit from large-scale clinical trials in order to further close the gap in knowledge between colorectal and extracolonic tumours. PMID:26315971

  18. Chimeric Proteins to Detect DNA Damage and Mismatches

    SciTech Connect

    McCutchen-Maloney, S; Malfatti, M; Robbins, K M

    2002-01-14

    The goal of this project was to develop chimeric proteins composed of a DNA mismatch or damage binding protein and a nuclease, as well as methods to detect DNA mismatches and damage. We accomplished this through protein engineering based on using polymerase chain reactions (PCRs) to create chimeras with novel functions for damage and mismatch detection. This project addressed fundamental questions relating to disease susceptibility and radiation-induced damage in cells. It also supported and enhanced LLNL's competency in the emerging field of proteomics. In nature, DNA is constantly being subjected to damaging agents such as exposure to ultraviolet (UV) radiation and various environmental and dietary carcinogens. If DNA damage is not repaired however, mutations in DNA result that can eventually manifest in cancer and other diseases. In addition to damage-induced DNA mutations, single nucleotide polymorphisms (SNPs), which are variations in the genetic sequence between individuals, may predispose some to disease. As a result of the Human Genome Project, the integrity of a person's DNA can now be monitored. Therefore, methods to detect DNA damage, mutations, and SNPs are useful not only in basic research but also in the health and biotechnology industries. Current methods of detection often use radioactive labeling and rely on expensive instrumentation that is not readily available in many research settings. Our methods to detect DNA damage and mismatches employ simple gel electrophoresis and flow cytometry, thereby alleviating the need for radioactive labeling and expensive equipment. In FY2001, we explored SNP detection by developing methods based on the ability of the chimeric proteins to detect mismatches. Using multiplex assays with flow cytometry and fluorescent beads to which the DNA substrates where attached, we showed that several of the chimeras possess greater affinity for damaged and mismatched DNA than for native DNA. This affinity was demonstrated in

  19. Mismatch repair balances leading and lagging strand DNA replication fidelity.

    PubMed

    Lujan, Scott A; Williams, Jessica S; Pursell, Zachary F; Abdulovic-Cui, Amy A; Clark, Alan B; Nick McElhinny, Stephanie A; Kunkel, Thomas A

    2012-01-01

    The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases, α, δ, and ε. Current evidence suggests that DNA polymerase ε (Pol ε) is the primary leading strand replicase, whereas Pols α and δ primarily perform lagging strand replication. The fact that these polymerases differ in fidelity and error specificity is interesting in light of the fact that the stability of the nuclear genome depends in part on the ability of mismatch repair (MMR) to correct different mismatches generated in different contexts during replication. Here we provide the first comparison, to our knowledge, of the efficiency of MMR of leading and lagging strand replication errors. We first use the strand-biased ribonucleotide incorporation propensity of a Pol ε mutator variant to confirm that Pol ε is the primary leading strand replicase in Saccharomyces cerevisiae. We then use polymerase-specific error signatures to show that MMR efficiency in vivo strongly depends on the polymerase, the mismatch composition, and the location of the mismatch. An extreme case of variation by location is a T-T mismatch that is refractory to MMR. This mismatch is flanked by an AT-rich triplet repeat sequence that, when interrupted, restores MMR to > 95% efficiency. Thus this natural DNA sequence suppresses MMR, placing a nearby base pair at high risk of mutation due to leading strand replication infidelity. We find that, overall, MMR most efficiently corrects the most potentially deleterious errors (indels) and then the most common substitution mismatches. In combination with earlier studies, the results suggest that significant differences exist in the generation and repair of Pol α, δ, and ε replication errors, but in a generally complementary manner that results in high-fidelity replication of both DNA strands of the yeast nuclear genome.

  20. Bubbles and mismatches in DNA melting

    NASA Astrophysics Data System (ADS)

    Zeng, Yan

    We obtained the first experimental measurements of the length of the denaturation bubble appearing in the DNA melting transition. This is achieved by working with short oligomers which can form only one bubble per molecule. We used sequences clamped at the ends with GC pairs (strong binding) and possessing AT rich (weaker binding) middle regions in order to have the bubble open in the middle, and sequences with GC pairs at one end and AT pairs at the other end in order to form the bubble at the end. Use a quenching technique to trap the bubble states, we could measure the length of the bubble and the relative weights of the bubble states as a function of temperature. We found that the average bubble size <ℓ> grows for increasing temperature, but reaches a plateau at a length of order B (the length of the AT region). After the plateau, the average bubble length jumps to 1. This jump of the order parameter is a signature of a discontinuous transition, one where the bubble size remains finite up to critical temperature of strand separation. When B increases, the extension of the plateau shrinks. This suggests a continuous transition for a homogenous sequence (e.g. all AT base pairs) in the thermodynamic limit. The presence of the bubble states decreases as B is reduced. By plotting the average statistical weight of the bubble states vs. B, we obtained the first direct measurement of the nucleation size of the bubble. For a bubble flanked by double-stranded regions, the nucleation size is ˜ 3 bases. For bubbles opening at the ends of the molecule there is no nucleation threshold. The measured statistical weights of the bubble states agree with the predictions of the widely used thermodynamic models in the case of unzipping from the ends; however, internal bubble states are not completely described by the model. For the first time we show experimentally that a single mismatch transforms a transition with many intermediates into a nearly two-state transition for

  1. Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.

    PubMed

    Nakae, Setsu; Hijikata, Atsushi; Tsuji, Toshiyuki; Yonezawa, Kouki; Kouyama, Ken-Ichi; Mayanagi, Kouta; Ishino, Sonoko; Ishino, Yoshizumi; Shirai, Tsuyoshi

    2016-11-01

    Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.

  2. The Effect of Codon Mismatch on the Protein Translation System.

    PubMed

    Zhang, Dinglin; Chen, Danfeng; Cao, Liaoran; Li, Guohui; Cheng, Hong

    2016-01-01

    Incorrect protein translation, caused by codon mismatch, is an important problem of living cells. In this work, a computational model was introduced to quantify the effects of codon mismatch and the model was used to study the protein translation of Saccharomyces cerevisiae. According to simulation results, the probability of codon mismatch will increase when the supply of amino acids is unbalanced, and the longer is the codon sequence, the larger is the probability for incorrect translation to occur, making the synthesis of long peptide chain difficult. By comparing to simulation results without codon mismatch effects taken into account, the fraction of mRNAs with bound ribosome decrease faster along the mRNAs, making the 5' ramp phenomenon more obvious. It was also found in our work that the premature mechanism resulted from codon mismatch can reduce the proportion of incorrect translation when the amino acid supply is extremely unbalanced, which is one possible source of high fidelity protein synthesis after peptidyl transfer.

  3. High fitness costs of climate change-induced camouflage mismatch.

    PubMed

    Zimova, Marketa; Mills, L Scott; Nowak, J Joshua

    2016-03-01

    Anthropogenic climate change has created myriad stressors that threaten to cause local extinctions if wild populations fail to adapt to novel conditions. We studied individual and population-level fitness costs of a climate change-induced stressor: camouflage mismatch in seasonally colour molting species confronting decreasing snow cover duration. Based on field measurements of radiocollared snowshoe hares, we found strong selection on coat colour molt phenology, such that animals mismatched with the colour of their background experienced weekly survival decreases up to 7%. In the absence of adaptive response, we show that these mortality costs would result in strong population-level declines by the end of the century. However, natural selection acting on wide individual variation in molt phenology might enable evolutionary adaptation to camouflage mismatch. We conclude that evolutionary rescue will be critical for hares and other colour molting species to keep up with climate change.

  4. Forecasting photovoltaic array power production subject to mismatch losses

    SciTech Connect

    Picault, D.; Raison, B.; Bacha, S.; de la Casa, J.; Aguilera, J.

    2010-07-15

    The development of photovoltaic (PV) energy throughout the world this last decade has brought to light the presence of module mismatch losses in most PV applications. Such power losses, mainly occasioned by partial shading of arrays and differences in PV modules, can be reduced by changing module interconnections of a solar array. This paper presents a novel method to forecast existing PV array production in diverse environmental conditions. In this approach, field measurement data is used to identify module parameters once and for all. The proposed method simulates PV arrays with adaptable module interconnection schemes in order to reduce mismatch losses. The model has been validated by experimental results taken on a 2.2 kW{sub p} plant, with three different interconnection schemes, which show reliable power production forecast precision in both partially shaded and normal operating conditions. Field measurements show interest in using alternative plant configurations in PV systems for decreasing module mismatch losses. (author)

  5. Mismatches in genetic markers in a large family study.

    PubMed Central

    Ashton, G C

    1980-01-01

    The Hawaii Family Study of Cognition provided an opportunity to investigate the frequency and implications of non-agreement, or mismatches, between observed and expected genetic marker phenotypes of husbands, wives, and children. Mismatch data from 68 families in which one or both spouses were known not to be a biological parent were used to determine the rate of undeclared nonparentage in 1,748 families in which conventional relationships were claimed. Two independent approaches gave consistent estimates, suggesting that approximately 2.3% of the 2,839 tested children from these families were probably the result of infidelity, concealed adoption, or another event. About two-thirds of the mismatches detected were probably due to properties of the techniques employed. PMID:6930820

  6. Highly Mismatched Alloys for Intermediate Band Solar Cells

    SciTech Connect

    Walukiewicz, W.; Yu, K.M.; Wu, J.; Ager III, J.W.; Shan, W.; Scrapulla, M.A.; Dubon, O.D.; Becla, P.

    2005-03-21

    It has long been recognized that the introduction of a narrow band of states in a semiconductor band gap could be used to achieve improved power conversion efficiency in semiconductor-based solar cells. The intermediate band would serve as a ''stepping stone'' for photons of different energy to excite electrons from the valence to the conduction band. An important advantage of this design is that it requires formation of only a single p-n junction, which is a crucial simplification in comparison to multijunction solar cells. A detailed balance analysis predicts a limiting efficiency of more than 50% for an optimized, single intermediate band solar cell. This is higher than the efficiency of an optimized two junction solar cell. Using ion beam implantation and pulsed laser melting we have synthesized Zn{sub 1-y}Mn{sub y}O{sub x}Te{sub 1-x} alloys with x<0.03. These highly mismatched alloys have a unique electronic structure with a narrow oxygen-derived intermediate band. The width and the location of the band is described by the Band Anticrossing model and can be varied by controlling the oxygen content. This provides a unique opportunity to optimize the absorption of solar photons for best solar cell performance. We have carried out systematic studies of the effects of the intermediate band on the optical and electrical properties of Zn{sub 1-y}Mn{sub y}O{sub x}Te{sub 1-x} alloys. We observe an extension of the photovoltaic response towards lower photon energies, which is a clear indication of optical transitions from the valence to the intermediate band.

  7. Teaching Counselling in Universities: Match or Mismatch?

    ERIC Educational Resources Information Center

    Berry, Mary; Woolfe, Ray

    1997-01-01

    Raises questions about the match between the culture of counseling and the culture of universities, with a particular emphasis on traditional university styles of pedagogy and the learning requirements of trainee counselors. Drawing on Kolb's model of experiential learning, examines issues relating to teaching methods and assessment procedures.…

  8. Roles for mismatch repair family proteins in promoting meiotic crossing over

    PubMed Central

    Manhart, Carol M.; Alani, Eric

    2015-01-01

    The mismatch repair (MMR) family complexes Msh4-Msh5 and Mlh1-Mlh3 act with Exo1 and Sgs1-Top3-Rmi1 in a meiotic double strand break repair pathway that results in the asymmetric cleavage of double Holliday junctions (dHJ) to form crossovers. This review discusses how meiotic roles for Msh4-Msh5 and Mlh1-Mlh3 do not fit paradigms established for post-replicative MMR. We also outline models used to explain how these factors promote the formation of meiotic crossovers required for the accurate segregation of chromosome homologs during the Meiosis I division. PMID:26686657

  9. Computing highly specific and mismatch tolerant oligomers efficiently.

    PubMed

    Yamada, Tomoyuki; Morishita, Shinichi

    2003-01-01

    The sequencing of the genomes of a variety of species and the growing databases containing expressed sequence tags (ESTs) and complementary DNAs (cDNAs) facilitate the design of highly specific oligomers for use as genomic markers, PCR primers, or DNA oligo microarrays. The first step in evaluating the specificity of short oligomers of about twenty units in length is to determine the frequencies at which the oligomers occur. However, for oligomers longer than about fifty units this is not efficient, as they usually have a frequency of only 1. A more suitable procedure is to consider the mismatch tolerance of an oligomer, that is, the minimum number of mismatches that allows a given oligomer to match a sub-sequence other than the target sequence anywhere in the genome or the EST database. However, calculating the exact value of mismatch tolerance is computationally costly and impractical. Therefore, we studied the problem of checking whether an oligomer meets the constraint that its mismatch tolerance is no less than a given threshold. Here, we present an efficient dynamic programming algorithm solution that utilizes suffix and height arrays. We demonstrated the effectiveness of this algorithm by efficiently computing a dense list of oligo-markers applicable to the human genome. Experimental results show that the algorithm runs faster than well-known Abrahamson's algorithm by orders of magnitude and is able to enumerate 63% to approximately 79% of qualified oligomers.

  10. Minority Students and Research Universities: How to Overcome the "Mismatch"

    ERIC Educational Resources Information Center

    Tapia, Richard A.

    2009-01-01

    A controversial theory much in the news lately claims that affirmative action is often unfair to the very students it is intended to help. Called the "mismatch" theory, it suggests that underrepresented minority students are more likely to leave science, math, and engineering when, because of affirmative action, they attend colleges for which they…

  11. Educational Mismatch and Spatial Flexibility in Italian Local Labour Markets

    ERIC Educational Resources Information Center

    Croce, Giuseppe; Ghignoni, Emanuela

    2015-01-01

    According to recent literature, this paper highlights the relevance of spatial mobility as an explanatory factor of the individual risk of job-education mismatch. To investigate this causal link, we use individual information about daily home-to-work commuting time and choices to relocate in a different local area to get a job. Our model takes…

  12. ABO-Mismatched Allogeneic Hematopoietic Stem Cell Transplantation

    PubMed Central

    Worel, Nina

    2016-01-01

    Summary Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative option for a variety of malignant and non-malignant hematological and congenital diseases. Due to the fact that the human leukocyte antigen system is inherited independently of the blood group system, approximately 40-50% of all HSCTs are performed across the ABO blood group barrier. The expected immune-hematological consequences after transplantation of an ABO-mismatched stem cell graft are immediate and delayed hemolytic complications due to presence of isohemagglutinins or passenger lymphocyte syndrome. The risks of these complications can partially be prevented by graft manipulation and appropriate transfusion support. Dependent on the kind of ABO mismatch, different effects on engraftment have been observed, e.g. delayed red blood cell recovery and pure red cell aplasia. Data on incidence of acute graft-versus-host disease (GVHD), non-relapse mortality, relapse, and overall survival are inconsistent as most studies include limited patient numbers, various graft sources, and different conditioning and GVHD prophylaxis regimens. This makes it difficult to detect a consistent effect of ABO-mismatched transplantation in the literature. However, knowledge of expectable complications and close monitoring of patients helps to detect problems early and to treat patients efficiently, thus reducing the number of fatal or life-threatening events caused by ABO-mismatched HSCT. PMID:27022317

  13. Avalanching mutations in biallelic mismatch repair deficiency syndrome.

    PubMed

    Waterfall, Joshua J; Meltzer, Paul S

    2015-03-01

    Tumors from pediatric patients generally contain relatively few somatic mutations. A new study reports a striking exception in individuals in whom biallelic germline deficiency for mismatch repair is compounded by somatic loss of function in DNA proofreading polymerases, resulting in 'ultra-hypermutated' malignant brain tumors.

  14. A mishmash of methods for mitigating the model mismatch mess

    NASA Astrophysics Data System (ADS)

    Ker, Andrew D.; Pevný, Tomáš

    2014-02-01

    The model mismatch problem occurs in steganalysis when a binary classifier is trained on objects from one cover source and tested on another: an example of domain adaptation. It is highly realistic because a steganalyst would rarely have access to much or any training data from their opponent, and its consequences can be devastating to classifier accuracy. This paper presents an in-depth study of one particular instance of model mismatch, in a set of images from Flickr using one fixed steganography and steganalysis method, attempting to separate different effects of mismatch in feature space and find methods of mitigation where possible. We also propose new benchmarks for accuracy, which are more appropriate than mean error rates when there are multiple actors and multiple images, and consider the case of 3-valued detectors which also output `don't know'. This pilot study demonstrates that some simple feature-centering and ensemble methods can reduce the mismatch penalty considerably, but not completely remove it.

  15. Job Sprawl, Spatial Mismatch, and Black Employment Disadvantage

    ERIC Educational Resources Information Center

    Stoll, Michael A.

    2006-01-01

    This paper examines the relationship between job sprawl and the spatial mismatch between blacks and jobs. Using data from a variety of sources, including the 1990 and 2000 U.S. Census and U.S. Department of Commerce's ZIP Code Business Patterns, I control extensively for metropolitan area characteristics and other factors. In addition, I use…

  16. Skills Mismatch among University Graduates in the Nigeria Labor Market

    ERIC Educational Resources Information Center

    Pitan, Oluyomi S.; Adedeji, S. O.

    2012-01-01

    University graduates in Nigeria have been reported to be poorly prepared for work in recent years. This has implications on the relevance of university education, the employability and productivity of university graduates. One of the reasons suggested for this condition by previous studies was skill mismatch--a situation where there is a disparity…

  17. Mismatch Negativity in Children with Autism and Typical Development

    ERIC Educational Resources Information Center

    Dunn, Michelle A.; Gomes, Hilary; Gravel, Judith

    2008-01-01

    Children with autism are often characterized as having abnormalities in auditory processing. This study examined automatic and active processing of simple auditory stimuli in children using a component of event related potentials, the mismatch negativity (MMN). Amplitude of MMN in children with autism was significantly smaller than in children…

  18. Mismatch of Vocational Graduates: What Penalty on French Labour Market?

    ERIC Educational Resources Information Center

    Beduwe, Catherine; Giret, Jean-Francois

    2011-01-01

    This study explores individual effects of educational mismatch on wages, job satisfaction and on-the-job-search on French labour market. We distinguish between horizontal matches (job matches with field of studies) and vertical matches (job matches the level of qualification) on the one hand and skills matches (worker's assessment) on the other…

  19. Alleles of the yeast Pms1 mismatch-repair gene that differentially affect recombination- and replication-related processes.

    PubMed Central

    Welz-Voegele, Caroline; Stone, Jana E; Tran, Phuoc T; Kearney, Hutton M; Liskay, R Michael; Petes, Thomas D; Jinks-Robertson, Sue

    2002-01-01

    Mismatch-repair (MMR) systems promote eukaryotic genome stability by removing errors introduced during DNA replication and by inhibiting recombination between nonidentical sequences (spellchecker and antirecombination activities, respectively). Following a common mismatch-recognition step effected by MutS-homologous Msh proteins, homologs of the bacterial MutL ATPase (predominantly the Mlh1p-Pms1p heterodimer in yeast) couple mismatch recognition to the appropriate downstream processing steps. To examine whether the processing steps in the spellchecker and antirecombination pathways might differ, we mutagenized the yeast PMS1 gene and screened for mitotic separation-of-function alleles. Two alleles affecting only the antirecombination function of Pms1p were identified, one of which changed an amino acid within the highly conserved ATPase domain. To more specifically address the role of ATP binding/hydrolysis in MMR-related processes, we examined mutations known to compromise the ATPase activity of Pms1p or Mlh1p with respect to the mitotic spellchecker and antirecombination activities and with respect to the repair of mismatches present in meiotic recombination intermediates. The results of these analyses confirm a differential requirement for the Pms1p ATPase activity in replication vs. recombination processes, while demonstrating that the Mlh1p ATPase activity is important for all examined MMR-related functions. PMID:12454061

  20. Unnatural substrates reveal the importance of 8-oxoguanine for in vivo mismatch repair by MutY

    PubMed Central

    Livingston, Alison L.; O’Shea, Valerie L.; Kim, Taewoo; Kool, Eric T.; David, Sheila S.

    2009-01-01

    Escherchia coli MutY plays an important role in preventing mutations associated with the oxidative lesion 7,8-dihydro-8-oxo-2′-deoxyguanosine (OG) in DNA by excising adenines from OG:A mismatches as the first step of base excision repair. To determine the importance of specific steps in the base pair recognition and base removal process of MutY, we have evaluated the effects of modifications of the OG:A substrate on the kinetics of base removal, mismatch affinity and repair to G:C in an Escherchia coli-based assay. Surprisingly, adenine modification was tolerated in the cellular assay, while modification of OG results in minimal cellular repair. High affinity for the mismatch and efficient base removal require the presence of OG. Taken together, these results suggest that the presence of OG is a critical feature for MutY to locate OG:A mismatches and select the appropriate adenines for excision to initiate repair in vivo prior to replication. PMID:18026095

  1. US protected lands mismatch biodiversity priorities

    PubMed Central

    Pimm, Stuart L.; Sexton, Joseph O.

    2015-01-01

    Because habitat loss is the main cause of extinction, where and how much society chooses to protect is vital for saving species. The United States is well positioned economically and politically to pursue habitat conservation should it be a societal goal. We assessed the US protected area portfolio with respect to biodiversity in the country. New synthesis maps for terrestrial vertebrates, freshwater fish, and trees permit comparison with protected areas to identify priorities for future conservation investment. Although the total area protected is substantial, its geographic configuration is nearly the opposite of patterns of endemism within the country. Most protected lands are in the West, whereas the vulnerable species are largely in the Southeast. Private land protections are significant, but they are not concentrated where the priorities are. To adequately protect the nation’s unique biodiversity, we recommend specific areas deserving additional protection, some of them including public lands, but many others requiring private investment. PMID:25847995

  2. Meniscus regeneration by syngeneic, minor mismatched, and major mismatched transplantation of synovial mesenchymal stem cells in a rat model.

    PubMed

    Okuno, Makiko; Muneta, Takeshi; Koga, Hideyuki; Ozeki, Nobutake; Nakagawa, Yusuke; Tsuji, Kunikazu; Yoshiya, Shinichi; Sekiya, Ichiro

    2014-07-01

    We compared the effect of syngeneic and allogeneic transplantation of synovial mesenchymal stem cells (MSCs) for meniscus regeneration in a rat model. Synovium was harvested from the knee joints of three strains of rats. The anterior half of the medial meniscus in both knees of F344 rats was removed and 5 million synovial MSCs derived from F344 (syngeneic transplantation), Lewis (minor mismatched transplantation), and ACI (major mismatched transplantation) were injected into the knee of the F344 rats. At 4 weeks, the area of the regenerated meniscus in the F344 group was significantly larger than that in the ACI group. Histological score was significantly better in the F344 and Lewis groups than in the ACI group at 8 weeks. DiI labeled cells could be observed in the knee joint in the F344 group, but were hardly detected in the ACI group at 1 week. The number of macrophages and CD8 T cells at synovium around the meniscus defect was significantly lower in the F344 group than in the ACI group at 1 week. Syngeneic and minor mismatched transplantation of synovial MSCs promoted meniscus regeneration better than major mismatched transplantation in a rat meniscectmized model.

  3. Thermodynamic properties of the specific binding between Ag+ ions and C:C mismatched base pairs in duplex DNA.

    PubMed

    Torigoe, Hidetaka; Miyakawa, Yukako; Ono, Akira; Kozasa, Tetsuo

    2011-02-01

    Metal-mediated base pairs formed by the interaction between metal ions and artificial bases in oligonucleotides have been developed for potential applications in nanotechnology. We recently found that a natural C:C mismatched base pair bound to an Ag(+) ion to generate a novel metal-mediated base pair in duplex DNA. Preparation of the novel C-Ag-C base pair involving natural bases is more convenient than that of metal-mediated base pairs involving artificial bases because time-consuming base synthesis is not required. Here, we examined the thermodynamic properties of the binding between the Ag(+) ion and each of single and double C:C mismatched base pair in duplex DNA by isothermal titration calorimetry. The Ag(+) ion specifically bound to the C:C mismatched base pair at a 1:1 molar ratio with 10(6) M(-1) binding constant, which was significantly larger than those for nonspecific metal ion-DNA interactions. The specific binding between the Ag(+) ion and the single C:C mismatched base pair was mainly driven by the positive dehydration entropy change and the negative binding enthalpy change. In the interaction between the Ag(+) ion and each of the consecutive and interrupted double C:C mismatched base pairs, stoichiometric binding at a 1:1 molar ratio was achieved in each step of the first and second Ag(+) binding. The binding affinity for the second Ag(+) binding was similar to that for the first Ag(+) binding. Stoichiometric binding without interference and negative cooperativity may be favorable for aligning multiple Ag(+) ions in duplex DNA for applications of the metal-mediated base pairs in nanotechnology.

  4. Mismatch Responses to Lexical Tone, Initial Consonant, and Vowel in Mandarin-Speaking Preschoolers

    ERIC Educational Resources Information Center

    Lee, Chia-Ying; Yen, Huei-ling; Yeh, Pei-wen; Lin, Wan-Hsuan; Cheng, Ying-Ying; Tzeng, Yu-Lin; Wu, Hsin-Chi

    2012-01-01

    The present study investigates how age, phonological saliency, and deviance size affect the presence of mismatch negativity (MMN) and positive mismatch response (P-MMR). This work measured the auditory mismatch responses to Mandarin lexical tones, initial consonants, and vowels in 4- to 6-year-old preschoolers using the multiple-deviant oddball…

  5. Mismatch repair genes identified using genetic screens in Blm-deficient embryonic stem cells.

    PubMed

    Guo, Ge; Wang, Wei; Bradley, Allan

    2004-06-24

    Phenotype-driven recessive genetic screens in diploid organisms require a strategy to render the mutation homozygous. Although homozygous mutant mice can be generated by breeding, a reliable method to make homozygous mutations in cultured cells has not been available, limiting recessive screens in culture. Cultured embryonic stem (ES) cells provide access to all of the genes required to elaborate the fundamental components and physiological systems of a mammalian cell. Here we have exploited the high rate of mitotic recombination in Bloom's syndrome protein (Blm)-deficient ES cells to generate a genome-wide library of homozygous mutant cells from heterozygous mutations induced with a revertible gene trap retrovirus. We have screened this library for cells with defects in DNA mismatch repair (MMR), a system that detects and repairs base-base mismatches. We demonstrate the recovery of cells with homozygous mutations in known and novel MMR genes. We identified Dnmt1(ref. 5) as a novel MMR gene and confirmed that Dnmt1-deficient ES cells exhibit micro-satellite instability, providing a mechanistic explanation for the role of Dnmt1 in cancer. The combination of insertional mutagenesis in Blm-deficient ES cells establishes a new approach for phenotype-based recessive genetic screens in ES cells.

  6. New insights into the mechanism of DNA mismatch repair

    PubMed Central

    Reyes, Gloria X.; Schmidt, Tobias T.; Kolodner, Richard D.; Hombauer, Hans

    2015-01-01

    The genome of all organisms is constantly being challenged by endogenous and exogenous sources of DNA damage. Errors like base:base mismatches or small insertions and deletions, primarily introduced by DNA polymerases during DNA replication are repaired by an evolutionary conserved DNA mismatch repair (MMR) system. The MMR system, together with the DNA replication machinery, promote repair by an excision and resynthesis mechanism during or after DNA replication, increasing replication fidelity by upto-three orders of magnitude. Consequently, inactivation of MMR genes results in elevated mutation rates that can lead to increased cancer susceptibility in humans. In this review, we summarize our current understanding of MMR with a focus on the different MMR protein complexes, their function and structure. We also discuss how recent findings have provided new insights in the spatio-temporal regulation and mechanism of MMR. PMID:25862369

  7. Mismatch repair system proteins in oral benign and malignant lesions.

    PubMed

    Amaral-Silva, Gleyson Kleber do; Martins, Manoela Domingues; Pontes, Hélder Antônio Rebelo; Fregnani, Eduardo Rodrigues; Lopes, Márcio Ajudarte; Fonseca, Felipe Paiva; Vargas, Pablo Agustin

    2017-04-01

    Different environmental agents may cause DNA mutations by disrupting its double-strand structure; however, even normal DNA polymerase function may synthesize mismatch nucleotide bases, occasionally demonstrating failure in its proofreading activity. To overcome this issue, mismatch repair (MMR) system, a group of proteins specialized in finding mispairing bases and small loops of insertion or deletion, works to avoid the occurrence of mutations that could ultimately lead to innumerous human diseases. In the last decades, the role of MMR proteins in oral carcinogenesis and in the development of other oral cavity neoplasms has grown, but their importance in the pathogenesis and their prognostic potential for patients affected by oral malignancies, especially oral squamous cell carcinoma (OSCC), remain unclear. Therefore, in this manuscript we aimed to review and critically discuss the currently available data on MMR proteins expression in oral potentially malignant lesions, in OSCC, and in other oral neoplasms to better understand their relevance in these lesions.

  8. Mismatch between classroom furniture and anthropometric measures in Chilean schools.

    PubMed

    Castellucci, H I; Arezes, P M; Viviani, C A

    2010-07-01

    Children spend about five hours per day sitting down while doing their school work. Considering this as well as the potential inadequate use of school furniture, it is likely that some anatomical-functional changes and problems in the learning process may occur. The aim of this study was to compare furniture sizes within three different schools with the anthropometric characteristics of Chilean students in the Valparaíso region, in order to evaluate the potential mismatch between them. The sample consisted of 195 volunteer students (94 male, 101 female) of the 8th grade, ranging from 12.5 to 14.5 years of age from 3 different schools. Regarding the methodology, 6 anthropometric measures (Stature, Popliteal height, Buttock-popliteal length, Elbow height while sitting, Hip width, Thigh thickness and Subscapular height) were gathered, as well as 8 dimensions from the school furniture. For the evaluation of classroom furniture a match criterion equation was defined. After considering the existing classroom furniture dimensions in each match criterion equation, the anthropometric characteristics of the considered population were compared in order to determine the mismatch between them. Results indicated that seat height, which should be considered as the starting point for the design of classroom furniture, was appropriate for students' popliteal height in only 14% of the 2 out of the 3 schools, and 28% in the third. Seat to desk height was too high and mismatched 99% of the students in one school and 100% in the others. Therefore, it was possible to conclude that the classroom's furniture was inadequate in almost all the analyzed cases and subjects. It is possible that the high mismatch percentage found between furniture and students' anthropometry can be associated to the fact that the acquisition and selection of the furniture was made without any ergonomic concern or criteria.

  9. Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks

    PubMed Central

    Bawono, Punto; van der Velde, Arjan; Abeln, Sanne; Heringa, Jaap

    2015-01-01

    Multiple Sequence Alignment (MSA) methods are typically benchmarked on sets of reference alignments. The quality of the alignment can then be represented by the sum-of-pairs (SP) or column (CS) scores, which measure the agreement between a reference and corresponding query alignment. Both the SP and CS scores treat mismatches between a query and reference alignment as equally bad, and do not take the separation into account between two amino acids in the query alignment, that should have been matched according to the reference alignment. This is significant since the magnitude of alignment shifts is often of relevance in biological analyses, including homology modeling and MSA refinement/manual alignment editing. In this study we develop a new alignment benchmark scoring scheme, SPdist, that takes the degree of discordance of mismatches into account by measuring the sequence distance between mismatched residue pairs in the query alignment. Using this new score along with the standard SP score, we investigate the discriminatory behavior of the new score by assessing how well six different MSA methods perform with respect to BAliBASE reference alignments. The SP score and the SPdist score yield very similar outcomes when the reference and query alignments are close. However, for more divergent reference alignments the SPdist score is able to distinguish between methods that keep alignments approximately close to the reference and those exhibiting larger shifts. We observed that by using SPdist together with SP scoring we were able to better delineate the alignment quality difference between alternative MSA methods. With a case study we exemplify why it is important, from a biological perspective, to consider the separation of mismatches. The SPdist scoring scheme has been implemented in the VerAlign web server (http://www.ibi.vu.nl/programs/veralignwww/). The code for calculating SPdist score is also available upon request. PMID:25993129

  10. Phenotypic Mismatches Reveal Escape from Arms-Race Coevolution

    PubMed Central

    Hanifin, Charles T; Brodie, Edmund D; Brodie, Edmund D

    2008-01-01

    Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts) and predator traits (tetrodotoxin resistance of snakes) to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were “ahead” of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race. PMID:18336073

  11. The developmental mismatch in structural brain maturation during adolescence.

    PubMed

    Mills, Kathryn L; Goddings, Anne-Lise; Clasen, Liv S; Giedd, Jay N; Blakemore, Sarah-Jayne

    2014-01-01

    Regions of the human brain develop at different rates across the first two decades of life, with some maturing before others. It has been hypothesized that a mismatch in the timing of maturation between subcortical regions (involved in affect and reward processing) and prefrontal regions (involved in cognitive control) underlies the increase in risk-taking and sensation-seeking behaviors observed during adolescence. Most support for this 'dual systems' hypothesis relies on cross-sectional data, and it is not known whether this pattern is present at an individual level. The current study utilizes longitudinal structural magnetic resonance imaging (MRI) data to describe the developmental trajectories of regions associated with risk-taking and sensation-seeking behaviors, namely, the amygdala, nucleus accumbens (NAcc) and prefrontal cortex (PFC). Structural trajectories of gray matter volumes were analyzed using FreeSurfer in 33 participants aged 7-30 years, each of whom had at least three high-quality MRI scans spanning three developmental periods: late childhood, adolescence and early adulthood (total 152 scans). The majority of individuals in our sample showed relatively earlier maturation in the amygdala and/or NAcc compared to the PFC, providing evidence for a mismatch in the timing of structural maturation between these structures. We then related individual developmental trajectories to retrospectively assessed self-reported risk-taking and sensation-seeking behaviors during adolescence in a subsample of 24 participants. Analysis of this smaller sample failed to find a relationship between the presence of a mismatch in brain maturation and risk-taking and sensation-seeking behaviors during adolescence. Taken together, it appears that the developmental mismatch in structural brain maturation is present in neurotypically developing individuals. This pattern of development did not directly relate to self-reported behaviors at an individual level in our sample

  12. Role of mismatch repair in the Escherichia coli UVM response.

    PubMed

    Murphy, H S; Palejwala, V A; Rahman, M S; Dunman, P M; Wang, G; Humayun, M Z

    1996-12-01

    Mutagenesis at 3,N4-ethenocytosine (epsilonC), a nonpairing mutagenic lesion, is significantly enhanced in Escherichia coli cells pretreated with UV, alkylating agents, or H2O2. This effect, termed UVM (for UV modulation of mutagenesis), is distinct from known DNA damage-inducible responses, such as the SOS response, the adaptive response to alkylating agents, or the oxyR-mediated response to oxidative agents. Here, we have addressed the hypothesis that UVM results from transient depletion of a mismatch repair activity that normally acts to reduce mutagenesis. To test whether the loss of mismatch repair activities results in the predicted constitutive UVM phenotype, E. coli cells defective for methyl-directed mismatch repair, for very-short-patch repair, or for the N-glycosylase activities MutY and MutM were treated with the UVM-inducing agent 1-methyl-3-nitro-1-nitrosoguanidine, with subsequent transfection of M13 viral single-stranded DNA bearing a site-specific epsilonC lesion. Survival of the M13 DNA was measured as transfection efficiency, and mutation fixation at the lesion was characterized by multiplex sequencing technology. The results showed normal UVM induction patterns in all the repair-defective strains tested. In addition, normal UVM induction was observed in cells overexpressing MutH, MutL, or MutS. All strains displayed UVM reactivation, the term used to describe the increased survival of epsilonC-containing DNA in UVM-induced cells. Taken together, these results indicate that the UVM response is independent of known mismatch repair systems in E. coli and may thus represent a previously unrecognized misrepair or misreplication pathway.

  13. Semiblind Hyperspectral Unmixing in the Presence of Spectral Library Mismatches

    NASA Astrophysics Data System (ADS)

    Fu, Xiao; Ma, Wing-Kin; Bioucas-Dias, Jose M.; Chan, Tsung-Han

    2016-09-01

    The dictionary-aided sparse regression (SR) approach has recently emerged as a promising alternative to hyperspectral unmixing (HU) in remote sensing. By using an available spectral library as a dictionary, the SR approach identifies the underlying materials in a given hyperspectral image by selecting a small subset of spectral samples in the dictionary to represent the whole image. A drawback with the current SR developments is that an actual spectral signature in the scene is often assumed to have zero mismatch with its corresponding dictionary sample, and such an assumption is considered too ideal in practice. In this paper, we tackle the spectral signature mismatch problem by proposing a dictionary-adjusted nonconvex sparsity-encouraging regression (DANSER) framework. The main idea is to incorporate dictionary correcting variables in an SR formulation. A simple and low per-iteration complexity algorithm is tailor-designed for practical realization of DANSER. Using the same dictionary correcting idea, we also propose a robust subspace solution for dictionary pruning. Extensive simulations and real-data experiments show that the proposed method is effective in mitigating the undesirable spectral signature mismatch effects.

  14. Current status of the Scandiatransplant acceptable mismatch program.

    PubMed

    Weinreich, I D; Pedersen, F; Grunnet, N

    2013-04-01

    This article describes the Scandiatransplant Acceptable Mismatch Program (STAMP), which was set into action in 2009. The aim of STAMP is to define human leukocyte antigens (HLA) toward which the potential kidney recipient has not developed antibodies, as "acceptable mismatches" in the Scandiatransplant database. In many cases this may improve the probability for a highly immunized recipient to receive a suitable kidney graft from a deceased donor. Using data extracted from the Scandiatransplant database on the outcomes of the program after the first 3 years, 31/115 recipients included in the program have undergone transplantation. From 2008 to 2011 the mean waiting time for highly immunized patients has decreased from 42 to 37 months. Continuous evaluation and follow-up of the program is essential to improve the procedures and outcomes. Calculation of transplantability based on a given set of acceptable mismatches was added to the program in 2011, based on the historical deceased donor pool providing the possibility of a specific patient to receive a kidney through STAMP. It is still a challenge for the tissue typing laboratories to determine which detected HLA antibodies are clinical relevant. We concluded that STAMP has had the intended effects, however adjustments and improvements is an ongoing process. As an improvment of the program HLA-C was added to the STAMP search algorithm in September 2012.

  15. Memory-based mismatch response to frequency changes in rats.

    PubMed

    Astikainen, Piia; Stefanics, Gabor; Nokia, Miriam; Lipponen, Arto; Cong, Fengyu; Penttonen, Markku; Ruusuvirta, Timo

    2011-01-01

    Any occasional changes in the acoustic environment are of potential importance for survival. In humans, the preattentive detection of such changes generates the mismatch negativity (MMN) component of event-related brain potentials. MMN is elicited to rare changes ('deviants') in a series of otherwise regularly repeating stimuli ('standards'). Deviant stimuli are detected on the basis of a neural comparison process between the input from the current stimulus and the sensory memory trace of the standard stimuli. It is, however, unclear to what extent animals show a similar comparison process in response to auditory changes. To resolve this issue, epidural potentials were recorded above the primary auditory cortex of urethane-anesthetized rats. In an oddball condition, tone frequency was used to differentiate deviants interspersed randomly among a standard tone. Mismatch responses were observed at 60-100 ms after stimulus onset for frequency increases of 5% and 12.5% but not for similarly descending deviants. The response diminished when the silent inter-stimulus interval was increased from 375 ms to 600 ms for +5% deviants and from 600 ms to 1000 ms for +12.5% deviants. In comparison to the oddball condition the response also diminished in a control condition in which no repetitive standards were presented (equiprobable condition). These findings suggest that the rat mismatch response is similar to the human MMN and indicate that anesthetized rats provide a valuable model for studies of central auditory processing.

  16. Investigating Interaural Frequency-Place Mismatches via Bimodal Vowel Integration

    PubMed Central

    Santurette, Sébastien; Chalupper, Josef; Dau, Torsten

    2014-01-01

    For patients having residual hearing in one ear and a cochlear implant (CI) in the opposite ear, interaural place-pitch mismatches might be partly responsible for the large variability in individual benefit. Behavioral pitch-matching between the two ears has been suggested as a way to individualize the fitting of the frequency-to-electrode map but is rather tedious and unreliable. Here, an alternative method using two-formant vowels was developed and tested. The interaural spectral shift was inferred by comparing vowel spaces, measured by presenting the first formant (F1) to the nonimplanted ear and the second (F2) on either side. The method was first evaluated with eight normal-hearing listeners and vocoder simulations, before being tested with 11 CI users. Average vowel distributions across subjects showed a similar pattern when presenting F2 on either side, suggesting acclimatization to the frequency map. However, individual vowel spaces with F2 presented to the implant did not allow a reliable estimation of the interaural mismatch. These results suggest that interaural frequency-place mismatches can be derived from such vowel spaces. However, the method remains limited by difficulties in bimodal fusion of the two formants. PMID:25421087

  17. Ultrafast and octave-spanning optical nonlinearities from strongly phase-mismatched quadratic interactions.

    PubMed

    Zhou, B B; Chong, A; Wise, F W; Bache, M

    2012-07-27

    Cascaded nonlinearities have attracted much interest, but ultrafast applications have been seriously hampered by the simultaneous requirements of being near phase matching and having ultrafast femtosecond response times. Here we show that in strongly phase-mismatched nonlinear frequency conversion crystals the pump pulse can experience a large and extremely broadband self-defocusing cascaded Kerr-like nonlinearity. The large cascaded nonlinearity is ensured through interaction with the largest quadratic tensor element in the crystal, and the strong phase mismatch ensures an ultrafast nonlinear response with an octave-spanning bandwidth. We verify this experimentally by showing few-cycle soliton compression with noncritical cascaded second-harmonic generation: Energetic 47 fs infrared pulses are compressed in a just 1-mm long bulk lithium niobate crystal to 17 fs (under 4 optical cycles) with 80% efficiency, and upon further propagation an octave-spanning supercontinuum is observed. Such ultrafast cascading is expected to occur for a broad range of pump wavelengths spanning the near- and mid-IR using standard nonlinear crystals.

  18. On compensation of mismatched recording conditions in the Bayesian approach for forensic automatic speaker recognition.

    PubMed

    Botti, F; Alexander, A; Drygajlo, A

    2004-12-02

    This paper deals with a procedure to compensate for mismatched recording conditions in forensic speaker recognition, using a statistical score normalization. Bayesian interpretation of the evidence in forensic automatic speaker recognition depends on three sets of recordings in order to perform forensic casework: reference (R) and control (C) recordings of the suspect, and a potential population database (P), as well as a questioned recording (QR) . The requirement of similar recording conditions between suspect control database (C) and the questioned recording (QR) is often not satisfied in real forensic cases. The aim of this paper is to investigate a procedure of normalization of scores, which is based on an adaptation of the Test-normalization (T-norm) [2] technique used in the speaker verification domain, to compensate for the mismatch. Polyphone IPSC-02 database and ASPIC (an automatic speaker recognition system developed by EPFL and IPS-UNIL in Lausanne, Switzerland) were used in order to test the normalization procedure. Experimental results for three different recording condition scenarios are presented using Tippett plots and the effect of the compensation on the evaluation of the strength of the evidence is discussed.

  19. Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity.

    PubMed

    Dillon, Laura W; Kumar, Pankaj; Shibata, Yoshiyuki; Wang, Yuh-Hwa; Willcox, Smaranda; Griffith, Jack D; Pommier, Yves; Takeda, Shunichi; Dutta, Anindya

    2015-06-23

    MicroDNAs are <400-base extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs have been found in all tissue types, including sperm. MicroDNAs arise preferentially from areas with high gene density, GC content, and exon density from promoters with activating chromatin modifications and in sperm from the 5'-UTR of full-length LINE-1 elements, but are depleted from lamin-associated heterochromatin. Analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cells defective in various DNA repair proteins reveals that homologous recombination and non-homologous end joining repair pathways are not required for microDNA production. Deletion of the MSH3 DNA mismatch repair protein results in a significant decrease in microDNA abundance, specifically from non-CpG genomic regions. Thus, microDNAs arise as part of normal cellular physiology—either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair.

  20. LNA modification of single-stranded DNA oligonucleotides allows subtle gene modification in mismatch-repair-proficient cells.

    PubMed

    van Ravesteyn, Thomas W; Dekker, Marleen; Fish, Alexander; Sixma, Titia K; Wolters, Astrid; Dekker, Rob J; Te Riele, Hein P J

    2016-04-12

    Synthetic single-stranded DNA oligonucleotides (ssODNs) can be used to generate subtle genetic modifications in eukaryotic and prokaryotic cells without the requirement for prior generation of DNA double-stranded breaks. However, DNA mismatch repair (MMR) suppresses the efficiency of gene modification by >100-fold. Here we present a commercially available ssODN design that evades MMR and enables subtle gene modification in MMR-proficient cells. The presence of locked nucleic acids (LNAs) in the ssODNs at mismatching bases, or also at directly adjacent bases, allowed 1-, 2-, or 3-bp substitutions in MMR-proficient mouse embryonic stem cells as effectively as in MMR-deficient cells. Additionally, in MMR-proficient Escherichia coli, LNA modification of the ssODNs enabled effective single-base-pair substitution. In vitro, LNA modification of mismatches precluded binding of purified E. coli MMR protein MutS. These findings make ssODN-directed gene modification particularly well suited for applications that require the evaluation of a large number of sequence variants with an easy selectable phenotype.

  1. LNA modification of single-stranded DNA oligonucleotides allows subtle gene modification in mismatch-repair-proficient cells

    PubMed Central

    van Ravesteyn, Thomas W.; Dekker, Marleen; Fish, Alexander; Sixma, Titia K.; Wolters, Astrid; Dekker, Rob J.; te Riele, Hein P. J.

    2016-01-01

    Synthetic single-stranded DNA oligonucleotides (ssODNs) can be used to generate subtle genetic modifications in eukaryotic and prokaryotic cells without the requirement for prior generation of DNA double-stranded breaks. However, DNA mismatch repair (MMR) suppresses the efficiency of gene modification by >100-fold. Here we present a commercially available ssODN design that evades MMR and enables subtle gene modification in MMR-proficient cells. The presence of locked nucleic acids (LNAs) in the ssODNs at mismatching bases, or also at directly adjacent bases, allowed 1-, 2-, or 3-bp substitutions in MMR-proficient mouse embryonic stem cells as effectively as in MMR-deficient cells. Additionally, in MMR-proficient Escherichia coli, LNA modification of the ssODNs enabled effective single-base-pair substitution. In vitro, LNA modification of mismatches precluded binding of purified E. coli MMR protein MutS. These findings make ssODN-directed gene modification particularly well suited for applications that require the evaluation of a large number of sequence variants with an easy selectable phenotype. PMID:26951689

  2. Climate change can cause spatial mismatch of trophically interacting species.

    PubMed

    Schweiger, Oliver; Settele, Josef; Kudrna, Otakar; Klotz, Stefan; Kühn, Ingolf

    2008-12-01

    Climate change is one of the most influential drivers of biodiversity. Species-specific differences in the reaction to climate change can become particularly important when interacting species are considered. Current studies have evidenced temporal mismatching of interacting species at single points in space, and recently two investigations showed that species interactions are relevant for their future ranges. However, so far we are not aware that the ranges of interacting species may become substantially spatially mismatched. We developed separate ecological-niche models for a monophagous butterfly (Boloria titania) and its larval host plant (Polygonum bistorta) based on monthly interpolated climate data, land-cover classes, and soil data at a 10'-grid resolution. We show that all of three chosen global-change scenarios, which cover a broad range of potential developments in demography, socio-economics, and technology during the 21st century from moderate to intermediate to maximum change, will result in a pronounced spatial mismatch between future niche spaces of these species. The butterfly may expand considerably its future range (by 124-258%) if the host plant has unlimited dispersal, but it could lose 52-75% of its current range if the host plant is not able to fill its projected ecological niche space, and 79-88% if the butterfly also is assumed to be highly dispersal limited. These findings strongly suggest that climate change has the potential to disrupt trophic interactions because co-occurring species do not necessarily react in a similar manner to global change, having important consequences at ecological and evolutionary time scales.

  3. Visual-Functional Mismatch Between Coronary Angiography, Fractional Flow Reserve, and Quantitative Coronary Angiography.

    PubMed

    Safi, Morteza; Eslami, Vahid; Namazi, Mohammad Hasan; Vakili, Hossain; Saadat, Habib; Alipourparsa, Saeid; Adibi, Ali; Movahed, Mohammad Reza

    2016-12-01

    Anatomical and functional mismatches are not uncommon in the assessment of coronary lesions. The aim of this study was to identify clinical and lesion-specific factors affecting angiographic, anatomical, and functional mismatch in intermediate coronary lesions. In patients who underwent coronary angiography for clinical reasons, fractional flow reserve (FFR), and quantitative coronary angiography (QCA) analyses for intermediate stenotic lesions were performed simultaneously. Mismatches between the measured values were analyzed. A total of 95 intermediate lesions were assessed simultaneously by visual angiography, FFR, and QCA. The visual-FFR mismatch was found in 40% of the lesions while reverse visual-FFR mismatch was determined in nearly 14% of the lesions. Mismatch and reverse mismatch between FFR and QCA parameters were observed in 10 and 23% of the lesions. FFR value was significant in 32% of the lesions while visually significant stenosis was shown in 61% of the lesions. Among the visual-FFR reverse mismatch group, the prevalence of culprit lesions within the left anterior descending (LAD) was significantly higher than other vessels (p value < 0.02). There were high frequencies of angiographic, QCA, and functional mismatches in analyses of intermediate coronary lesions. LAD lesions showed the highest mismatch. Angiographic or QCA estimation of lesion severity has consistently resulted in inappropriate stenting of functionally nonsignificant lesions or undertreatment of significant lesions based on FFR.

  4. Mismatch negativity, social cognition, and functional outcomes in patients after traumatic brain injury

    PubMed Central

    Sun, Hui-yan; Li, Qiang; Chen, Xi-ping; Tao, Lu-yang

    2015-01-01

    Mismatch negativity is generated automatically, and is an early monitoring indicator of neuronal integrity impairment and functional abnormality in patients with brain injury, leading to decline of cognitive function. Antipsychotic medication cannot affect mismatch negativity. The present study aimed to explore the relationships of mismatch negativity with neurocognition, daily life and social functional outcomes in patients after brain injury. Twelve patients with traumatic brain injury and 12 healthy controls were recruited in this study. We examined neurocognition with the Wechsler Adult Intelligence Scale-Revised China, and daily and social functional outcomes with the Activity of Daily Living Scale and Social Disability Screening Schedule, respectively. Mismatch negativity was analyzed from electroencephalogram recording. The results showed that mismatch negativity amplitudes decreased in patients with traumatic brain injury compared with healthy controls. Mismatch negativity amplitude was negatively correlated with measurements of neurocognition and positively correlated with functional outcomes in patients after traumatic brain injury. Further, the most significant positive correlations were found between mismatch negativity in the fronto-central region and measures of functional outcomes. The most significant positive correlations were also found between mismatch negativity at the FCz electrode and daily living function. Mismatch negativity amplitudes were extremely positively associated with Social Disability Screening Schedule scores at the Fz electrode in brain injury patients. These experimental findings suggest that mismatch negativity might efficiently reflect functional outcomes in patients after traumatic brain injury. PMID:26170824

  5. Fast damping in mismatched high intensity beam transportation

    NASA Astrophysics Data System (ADS)

    Variale, V.

    2001-08-01

    A very fast damping of beam envelope oscillation amplitudes was recently observed in simulations of high intensity beam transport, through periodic FODO cells, in mismatched conditions [V. Variale, Nuovo Cimento Soc. Ital. Fis. 112A, 1571-1582 (1999) and T. Clauser et al., in Proceedings of the Particle Accelerator Conference, New York, 1999 (IEEE, Piscataway, NJ, 1999), p. 1779]. A Landau damping mechanism was proposed at the origin of observed effect. In this paper, to further investigate the source of this fast damping, extensive simulations have been carried out. The results presented here support the interpretation of the mechanism at the origin of the fast damping as a Landau damping effect.

  6. Absolute gain measurement by the image method under mismatched condition

    NASA Technical Reports Server (NTRS)

    Lee, Richard Q.; Baddour, Maurice F.

    1987-01-01

    Purcell's image method for measuring the absolute gain of an antenna is particularly attractive for small test antennas. The method is simple to use and utilizes only one antenna with a reflecting plane to provide an image for the receiving antenna. However, the method provides accurate results only if the antenna is matched to its waveguide. In this paper, a waveguide junction analysis is developed to determine the gain of an antenna under mismatched condition. Absolute gain measurements for two standard gain horn antennas have been carried out. Experimental results agree closely with published data.

  7. Emotional intelligence and mismatching expressive and verbal messages: a contribution to detection of deception.

    PubMed

    Wojciechowski, Jerzy; Stolarski, Maciej; Matthews, Gerald

    2014-01-01

    Processing facial emotion, especially mismatches between facial and verbal messages, is believed to be important in the detection of deception. For example, emotional leakage may accompany lying. Individuals with superior emotion perception abilities may then be more adept in detecting deception by identifying mismatch between facial and verbal messages. Two personal factors that may predict such abilities are female gender and high emotional intelligence (EI). However, evidence on the role of gender and EI in detection of deception is mixed. A key issue is that the facial processing skills required to detect deception may not be the same as those required to identify facial emotion. To test this possibility, we developed a novel facial processing task, the FDT (Face Decoding Test) that requires detection of inconsistencies between facial and verbal cues to emotion. We hypothesized that gender and ability EI would be related to performance when cues were inconsistent. We also hypothesized that gender effects would be mediated by EI, because women tend to score as more emotionally intelligent on ability tests. Data were collected from 210 participants. Analyses of the FDT suggested that EI was correlated with superior face decoding in all conditions. We also confirmed the expected gender difference, the superiority of high EI individuals, and the mediation hypothesis. Also, EI was more strongly associated with facial decoding performance in women than in men, implying there may be gender differences in strategies for processing affective cues. It is concluded that integration of emotional and cognitive cues may be a core attribute of EI that contributes to the detection of deception.

  8. Emotional Intelligence and Mismatching Expressive and Verbal Messages: A Contribution to Detection of Deception

    PubMed Central

    Wojciechowski, Jerzy; Stolarski, Maciej; Matthews, Gerald

    2014-01-01

    Processing facial emotion, especially mismatches between facial and verbal messages, is believed to be important in the detection of deception. For example, emotional leakage may accompany lying. Individuals with superior emotion perception abilities may then be more adept in detecting deception by identifying mismatch between facial and verbal messages. Two personal factors that may predict such abilities are female gender and high emotional intelligence (EI). However, evidence on the role of gender and EI in detection of deception is mixed. A key issue is that the facial processing skills required to detect deception may not be the same as those required to identify facial emotion. To test this possibility, we developed a novel facial processing task, the FDT (Face Decoding Test) that requires detection of inconsistencies between facial and verbal cues to emotion. We hypothesized that gender and ability EI would be related to performance when cues were inconsistent. We also hypothesized that gender effects would be mediated by EI, because women tend to score as more emotionally intelligent on ability tests. Data were collected from 210 participants. Analyses of the FDT suggested that EI was correlated with superior face decoding in all conditions. We also confirmed the expected gender difference, the superiority of high EI individuals, and the mediation hypothesis. Also, EI was more strongly associated with facial decoding performance in women than in men, implying there may be gender differences in strategies for processing affective cues. It is concluded that integration of emotional and cognitive cues may be a core attribute of EI that contributes to the detection of deception. PMID:24658500

  9. Predictable patterns of trait mismatches between interacting plants and insects

    PubMed Central

    2010-01-01

    Background There are few predictions about the directionality or extent of morphological trait (mis)matches between interacting organisms. We review and analyse studies on morphological trait complementarity (e.g. floral tube length versus insect mouthpart length) at the population and species level. Results Plants have consistently more exaggerated morphological traits than insects at high trait magnitudes and in some cases less exaggerated traits than insects at smaller trait magnitudes. This result held at the population level, as well as for phylogenetically adjusted analyses at the species-level and for both pollination and host-parasite interactions, perhaps suggesting a general pattern. Across communities, the degree of trait mismatch between one specialist plant and its more generalized pollinator was related to the level of pollinator specialization at each site; the observed pattern supports the "life-dinner principle" of selection acting more strongly on species with more at stake in the interaction. Similarly, plant mating system also affected the degree of trait correspondence because selfing reduces the reliance on pollinators and is analogous to pollination generalization. Conclusions Our analyses suggest that there are predictable "winners" and "losers" of evolutionary arms races and the results of this study highlight the fact that breeding system and the degree of specialization can influence the outcome. PMID:20604973

  10. Case Report: Prothesis-patient mismatch after aortic valve replacement.

    PubMed

    Rodriguez-Ospina, Luis; Garcia-Morell, Juan; Rodriguez-Monserrate, Carla P; Valentin-Nieves, Julio

    2015-01-01

    Valve replacement is the standard surgical treatment of diseased valves that cannot be repaired. The main goal of replacement is to exchange the diseased valve with one that has the engineering and hemodynamics as close as possible to the disease free native valve. However due to mechanical and fluid dynamic constraints all prosthetic heart valves (PHVs) are smaller than normal and thus are inherently stenotic. This represents a challenge when it comes time to replace a valve. The correct valve with the correct and matching profile has to be selected before the procedure to avoid possible complications. It is well recognized that patients are also prone to patient-prosthesis mismatch at long term which could have consequences in the clinical outcomes (1). The evaluation of patient-prosthesis mismatch (PPM) has not been sufficiently emphasized in common practice. Failure to recognize this fact may lead to significant hemodynamic impairment and worsening of the clinical status over the time. Making efforts to identifying patients at risk may decrease the prevalence of PPM, the economic impact to our health system, the morbidity and mortality involved in these cases as well as creates efforts to standardized pre-operative protocols to minimized risk of PPM. We present a case of a 78 years old male patient who underwent aortic valve replacement due severe aortic stenosis, afterwards his clinical course got complicated with several admissions for shortness of breath and decompensated congestive heart failure (CHF).

  11. Predicting χ for polymers with stiffness mismatch from simulations

    NASA Astrophysics Data System (ADS)

    Kozuch, Daniel; Zhang, Wenlin; Gomez, Enrique; Milner, Scott

    The Flory-Huggins χ parameter describes the excess free energy of mixing and governs phase behavior for polymer blends and block copolymers. For chemically distinct polymers, the value of χ is dominated by the mismatch in cohesive energy densities of the monomers. For blends of chemically similar polymers, the entropic portion of χ, arising from non-ideal local packing, becomes more significant. Using polymer field theory, Fredrickson, Liu, and Bates predict that a difference in backbone stiffness can result in a positive χ for chains consisting of chemically identical monomers. To quantitatively investigate this phenomenon, we perform molecular dynamic (MD) simulations for bead-spring chains which differ only in stiffness. From the simulations, we apply a novel thermodynamic integration to extract χ as low as 10-3 per monomer for blends with mild stiffness mismatch. By introducing a standardized effective monomer, we map real polymers to our bead-spring chains and show that the predicted entropic portion of χ are consistent with experimental data.

  12. Mismatch Repair Proficiency and In Vitro Response to 5-Fluorouracil

    PubMed Central

    CARETHERS, JOHN M.; CHAUHAN, DHARAM P.; FINK, DANIEL; NEBEL, SIBYLLE; BRESALIER, ROBERT S.; HOWELL, STEPHEN B.; BOLAND, C. RICHARD

    2015-01-01

    Background & Aims The DNA mismatch repair (MMR) system recognizes certain DNA adducts caused by alkylation damage in addition to its role in recognizing and directing repair of interstrand nucleotide mismatches and slippage mistakes at microsatellite sequences. Because defects in the MMR system can confer tolerance to acquired DNA damage and, by inference, the toxic effects of certain chemotherapeutic agents, we investigated the effect of 5-fluorouracil (5-FU) on colon cancer cell lines. Methods We determined growth selection by cell enrichment assay and cloning efficiency after treatment with 5 μmol/L 5-FU, assayed nucleic 3H–5-FU incorporation, and analyzed the cell cycle by flow cytometry. Results 5-FU treatment provided a growth advantage for MMR-deficient cell lines, indicating a relative degree of tolerance to 5-FU by the MMR-deficient cell lines. Enhanced survival was statistically significant after 5 days of growth, and a 28-fold reduction in survival was noted in the MMR-proficient cells by clonagenic assays after 10 days of growth. Differences in nucleotide uptake of 5-FU did not account for the observed growth differences, and specific cell cycle checkpoint arrest was not detected. Conclusions Intact DNA MMR seems to recognize 5-FU incorporated into DNA but may do so in a different manner than other types of alkylation damage. Defective DNA MMR might be one mechanism for tumor resistance to 5-FU. PMID:10381918

  13. Toward a phenological mismatch in estuarine pelagic food web?

    PubMed Central

    Chevillot, Xavier; Drouineau, Hilaire; Lambert, Patrick; Carassou, Laure; Sautour, Benoit; Lobry, Jérémy

    2017-01-01

    Alterations of species phenology in response to climate change are now unquestionable. Until now, most studies have reported precocious occurrence of life cycle events as a major phenological response. Desynchronizations of biotic interactions, in particular predator-prey relationships, are however assumed to strongly impact ecosystems’ functioning, as formalized by the Match-Mismatch Hypothesis (MMH). Temporal synchronicity between juvenile fish and zooplankton in estuaries is therefore of essential interest since estuaries are major nursery grounds for many commercial fish species. The Gironde estuary (SW France) has suffered significant alterations over the last three decades, including two Abrupt Ecosystem Shifts (AES), and three contrasted intershift periods. The main objective of this study was to depict modifications in fish and zooplankton phenology among inter-shift periods and discuss the potential effects of the resulting mismatches at a community scale. A flexible Bayesian method was used to estimate and compare yearly patterns of species abundance in the estuary among the three pre-defined periods. Results highlighted (1) an earlier peak of zooplankton production and entrance of fish species in the estuary and (2) a decrease in residence time of both groups in the estuary. Such species-specific phenological changes led to changes in temporal overlap between juvenile fish and their zooplanktonic prey. This situation questions the efficiency and potentially the viability of nursery function of the Gironde estuary, with potential implications for coastal marine fisheries of the Bay of Biscay. PMID:28355281

  14. Toward a phenological mismatch in estuarine pelagic food web?

    PubMed

    Chevillot, Xavier; Drouineau, Hilaire; Lambert, Patrick; Carassou, Laure; Sautour, Benoit; Lobry, Jérémy

    2017-01-01

    Alterations of species phenology in response to climate change are now unquestionable. Until now, most studies have reported precocious occurrence of life cycle events as a major phenological response. Desynchronizations of biotic interactions, in particular predator-prey relationships, are however assumed to strongly impact ecosystems' functioning, as formalized by the Match-Mismatch Hypothesis (MMH). Temporal synchronicity between juvenile fish and zooplankton in estuaries is therefore of essential interest since estuaries are major nursery grounds for many commercial fish species. The Gironde estuary (SW France) has suffered significant alterations over the last three decades, including two Abrupt Ecosystem Shifts (AES), and three contrasted intershift periods. The main objective of this study was to depict modifications in fish and zooplankton phenology among inter-shift periods and discuss the potential effects of the resulting mismatches at a community scale. A flexible Bayesian method was used to estimate and compare yearly patterns of species abundance in the estuary among the three pre-defined periods. Results highlighted (1) an earlier peak of zooplankton production and entrance of fish species in the estuary and (2) a decrease in residence time of both groups in the estuary. Such species-specific phenological changes led to changes in temporal overlap between juvenile fish and their zooplanktonic prey. This situation questions the efficiency and potentially the viability of nursery function of the Gironde estuary, with potential implications for coastal marine fisheries of the Bay of Biscay.

  15. Disturbance observer based sliding mode control of nonlinear mismatched uncertain systems

    NASA Astrophysics Data System (ADS)

    Ginoya, Divyesh; Shendge, P. D.; Phadke, S. B.

    2015-09-01

    This paper presents a new design of multiple-surface sliding mode control for a class of nonlinear uncertain systems with mismatched uncertainties and disturbances. In the method of multiple-surface sliding mode control, it is required to compensate for the derivatives of the virtual inputs which gives rise to the so-called problem of 'explosion of terms'. In this paper a disturbance observer based multiple-surface sliding mode control is proposed to estimate the uncertainties as well as the derivative of the virtual inputs to overcome this problem. The practical stability of the overall system is proved. The effectiveness of the proposed control strategy is illustrated via simulation of a benchmark problem and comparison with other control strategies. The proposed scheme is validated by implementing it on a serial flexible joint manipulator in the laboratory.

  16. Unattentive speech processing is influenced by orthographic knowledge: evidence from mismatch negativity.

    PubMed

    Pattamadilok, Chotiga; Morais, José; Colin, Cécile; Kolinsky, Régine

    2014-10-01

    How far can acquired knowledge such as orthographic knowledge affect pre-existing abilities such as speech perception? This controversial issue was addressed by investigating the automaticity of the influence of orthographic knowledge on speech processing. Many studies demonstrated this influence in active, lexico-semantic speech processing tasks. However, it has never been observed when speech is unattended. Here, the Mismatch Negativity (MMN), an automatic index of experience-dependent auditory traces, was recorded in an unattended oddball paradigm manipulating the orthographic congruency between frequent and deviant spoken riming words. Both orthographically congruent and incongruent deviant words elicited a typical MMN over the fronto-central regions, with a stronger response in the incongruent condition. The finding showed that the orthographic dimension of spoken words influences a physiological marker of speech processing although participants were required not to attend to the auditory input. This provides evidence for an impact of acquiring a written code on speech processing.

  17. Strain analysis by mismatch moire method and grid method using Fourier transform

    NASA Astrophysics Data System (ADS)

    Morimoto, Y.; Seguchi, Y.; Higashi, T.

    1990-01-01

    We have formerly presented a new method of the moire analysis of strain using the Fourier transform. It uses the phase information of the moire fringe brightness. By shifting the Fourier spectrum of the image of deformed grating lines, we obtain the “complex moire pattern”. Strain distribution is given as the derivatives of the phases of the complex moire fringes. The analysis is completely automated by digital image processing. All of the laborious and subjective procedures required in the conventional analysis such as fringe sign determination, fringe ordering and fringe interpolation are thus eliminated, and objective, fast and accurate analysis can be made. In this paper, we develop the method to a mismatch method and a grid method. We show some applications for analyzing strain distribution by using this method.

  18. Mismatch repair status may predict response to adjuvant chemotherapy in resectable pancreatic ductal adenocarcinoma.

    PubMed

    Riazy, Maziar; Kalloger, Steve E; Sheffield, Brandon S; Peixoto, Renata D; Li-Chang, Hector H; Scudamore, Charles H; Renouf, Daniel J; Schaeffer, David F

    2015-10-01

    Deficiencies in DNA mismatch repair have been associated with inferior response to 5-FU in colorectal cancer. Pancreatic ductal adenocarcinoma is similarly treated with pyrimidine analogs, yet the predictive value of mismatch repair status for response to these agents has not been examined in this malignancy. A tissue microarray with associated clinical outcome, comprising 254 resected pancreatic ductal adenocarcinoma patients was stained for four mismatch repair proteins (MLH1, MSH2, MSH6 and PMS2). Mismatch repair deficiency and proficiency was determined by the absence or presence of uniform nuclear staining in tumor cells, respectively. Cases identified as mismatch repair deficient on the tissue microarray were confirmed by immunohistochemistry on whole slide sections. Of the 265 cases, 78 (29%) received adjuvant treatment with a pyrimidine analog and 41 (15%) showed a mismatch repair-deficient immunoprofile. Multivariable disease-specific survival in the mismatch repair-proficient cohort demonstrated that adjuvant chemotherapy, regional lymph-node status, gender, and the presence of tumor budding were significant independent prognostic variables (P≤0.04); however, none of the eight clinico-pathologic covariates examined in the mismatch repair-deficient cohort were of independent prognostic significance. Univariable assessment of disease-specific survival revealed an almost identical survival profile for both treated and untreated patients with a mismatch repair-deficient profile, while treatment in the mismatch repair-proficient cohort conferred a greater than 10-month median disease-specific survival advantage over their untreated counterparts (P=0.0018). In this cohort, adjuvant chemotherapy with a pyrimidine analog conferred no survival advantage to mismatch repair-deficient pancreatic ductal adenocarcinoma patients. Mismatch repair immunoprofiling is a feasible predictive marker in pancreatic ductal adenocarcinoma patients, and further prospective

  19. Effect of strength mismatch on fracture toughness of HSLA steel weld joints

    SciTech Connect

    Rak, I.; Gliha, V.; Gubeljak, N.; Praunseis, Z.; Kocak, M.

    1995-12-31

    The purpose of this experimental work is to present the results of measured toughness and strength on mismatched weld joints made on HSLA steel grade HT 80. In the determined over and undermatched weld joints the local mismatching in the through thickness direction was found by hardness measurement. It seems that local mismatch because of WM low toughness has controlled the fracture behavior of weld metal and HAZ in both cases instead of the global one. Direct local CTOD({delta}{sub 5}) technique is found to be particular useful for the determination of fracture toughness values on mismatched weld joints.

  20. Decentralized Adaptive Control of Systems with Uncertain Interconnections, Plant-Model Mismatch and Actuator Failures

    NASA Technical Reports Server (NTRS)

    Patre, Parag; Joshi, Suresh M.

    2011-01-01

    Decentralized adaptive control is considered for systems consisting of multiple interconnected subsystems. It is assumed that each subsystem s parameters are uncertain and the interconnection parameters are not known. In addition, mismatch can exist between each subsystem and its reference model. A strictly decentralized adaptive control scheme is developed, wherein each subsystem has access only to its own state but has the knowledge of all reference model states. The mismatch is estimated online for each subsystem and the mismatch estimates are used to adaptively modify the corresponding reference models. The adaptive control scheme is extended to the case with actuator failures in addition to mismatch.

  1. HLA-Mismatched Renal Transplantation without Maintenance Immunosuppression

    PubMed Central

    Kawai, Tatsuo; Cosimi, A. Benedict; Spitzer, Thomas R.; Tolkoff-Rubin, Nina; Suthanthiran, Manikkam; Saidman, Susan L.; Shaffer, Juanita; Preffer, Frederic I.; Ding, Ruchuang; Sharma, Vijay; Fishman, Jay A.; Dey, Bimalangshu; Ko, Dicken S.C.; Hertl, Martin; Goes, Nelson B.; Wong, Waichi; Williams, Winfred W.; Colvin, Robert B.; Sykes, Megan; Sachs, David H.

    2010-01-01

    Summary Five patients with end-stage renal disease received combined bone marrow and kidney transplants from HLA single-haplotype mismatched living related donors, with the use of a nonmyeloablative preparative regimen. Transient chimerism and reversible capillary leak syndrome developed in all recipients. Irreversible humoral rejection occurred in one patient. In the other four recipients, it was possible to discontinue all immunosuppressive therapy 9 to 14 months after the transplantation, and renal function has remained stable for 2.0 to 5.3 years since transplantation. The T cells from these four recipients, tested in vitro, showed donor-specific unresponsiveness and in specimens from allograft biopsies, obtained after withdrawal of immunosuppressive therapy, there were high levels of P3 (FOXP3) messenger RNA (mRNA) but not granzyme B mRNA. PMID:18216355

  2. Performance of mismatched Viterbi receiver on satellite channels

    NASA Technical Reports Server (NTRS)

    Divsalar, D.; Omura, J. K.

    1979-01-01

    This paper presents an analysis of a satellite communication system using a Viterbi receiver. Here we have a bandlimited nonlinear channel where both uplink and downlink are taken into account as well as the effect of Intersymbol Interference, phase and time synchronization errors. In order that ISI can be combatted effectively, we use a Viterbi demodulator which is designed for the satellite channel when there is no uplink noise. The Viterbi demodulator for the channels with large memory is too complex to be implemented. To reduce the complexity, a Viterbi demodulator with memory shorter than the true channel memory is used. The objective of this paper is to analyze the performance degradation of this 'Mismatched Viterbi Receiver' due to the uplink noise and memory truncation, and to understand how the time and phase synchronization errors influence the performance.

  3. DNA mismatch repair and the DNA damage response

    PubMed Central

    Li, Zhongdao; Pearlman, Alexander H.; Hsieh, Peggy

    2015-01-01

    This review discusses the role of DNA mismatch repair (MMR) in the DNA damage response (DDR) that triggers cell cycle arrest and, in some cases, apoptosis. Although the focus is on findings from mammalian cells, much has been learned from studies in other organisms including bacteria and yeast [1,2]. MMR promotes a DDR mediated by a key signaling kinase, ATM and Rad3-related (ATR), in response to various types of DNA damage including some encountered in widely used chemotherapy regimes. An introduction to the DDR mediated by ATR reveals its immense complexity and highlights the many biological and mechanistic questions that remain. Recent findings and future directions are highlighted. PMID:26704428

  4. Automated effective band structures for defective and mismatched supercells

    NASA Astrophysics Data System (ADS)

    Brommer, Peter; Quigley, David

    2014-12-01

    In plane-wave density functional theory codes, defects and incommensurate structures are usually represented in supercells. However, interpretation of E versus k band structures is most effective within the primitive cell, where comparison to ideal structures and spectroscopy experiments are most natural. Popescu and Zunger recently described a method to derive effective band structures (EBS) from supercell calculations in the context of random alloys. In this paper, we present bs_sc2pc, an implementation of this method in the CASTEP code, which generates an EBS using the structural data of the supercell and the underlying primitive cell with symmetry considerations handled automatically. We demonstrate the functionality of our implementation in three test cases illustrating the efficacy of this scheme for capturing the effect of vacancies, substitutions and lattice mismatch on effective primitive cell band structures.

  5. Automated effective band structures for defective and mismatched supercells.

    PubMed

    Brommer, Peter; Quigley, David

    2014-12-03

    In plane-wave density functional theory codes, defects and incommensurate structures are usually represented in supercells. However, interpretation of E versus k band structures is most effective within the primitive cell, where comparison to ideal structures and spectroscopy experiments are most natural. Popescu and Zunger recently described a method to derive effective band structures (EBS) from supercell calculations in the context of random alloys. In this paper, we present bs_sc2pc, an implementation of this method in the CASTEP code, which generates an EBS using the structural data of the supercell and the underlying primitive cell with symmetry considerations handled automatically. We demonstrate the functionality of our implementation in three test cases illustrating the efficacy of this scheme for capturing the effect of vacancies, substitutions and lattice mismatch on effective primitive cell band structures.

  6. Three perspectives on the mismatch between measures of material poverty.

    PubMed

    Hick, Rod

    2015-03-01

    The two most prominent measures of material poverty within contemporary European poverty analysis are low income and material deprivation. However, it is by now well-known that these measures identify substantially different people as being poor. In this research note, I seek to demonstrate that there are at least three ways to understand the mismatch between low income and material deprivation, relating to three different forms of identification: identifying poor households, identifying groups at risk of poverty and identifying trends in material poverty over time. Drawing on data from the British Household Panel Survey, I show that while low income and material deprivation identify very different households as being poor, and display distinct trends over time, in many cases they identify the same groups at being at risk of material poverty.

  7. Guanine- 5-carboxylcytosine base pairs mimic mismatches during DNA replication.

    PubMed

    Shibutani, Toshihiro; Ito, Shinsuke; Toda, Mariko; Kanao, Rie; Collins, Leonard B; Shibata, Marika; Urabe, Miho; Koseki, Haruhiko; Masuda, Yuji; Swenberg, James A; Masutani, Chikahide; Hanaoka, Fumio; Iwai, Shigenori; Kuraoka, Isao

    2014-06-09

    The genetic information encoded in genomes must be faithfully replicated and transmitted to daughter cells. The recent discovery of consecutive DNA conversions by TET family proteins of 5-methylcytosine into 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine (5caC) suggests these modified cytosines act as DNA lesions, which could threaten genome integrity. Here, we have shown that although 5caC pairs with guanine during DNA replication in vitro, G·5caC pairs stimulated DNA polymerase exonuclease activity and were recognized by the mismatch repair (MMR) proteins. Knockdown of thymine DNA glycosylase increased 5caC in genome, affected cell proliferation via MMR, indicating MMR is a novel reader for 5caC. These results suggest the epigenetic modification products of 5caC behave as DNA lesions.

  8. Is it time to move mismatch negativity into the clinic?

    PubMed

    Schall, Ulrich

    2016-04-01

    Since its inception in the 1970s, the mismatch negativity (MMN) event-related potential has improved our understanding of pre-attentive detection of rule violations, which is a fundamental cognitive process considered by some a form of "primitive intelligence". The body of research to date ranges from animal studies (i.e. when investigating the neural mechanisms and pharmacological properties of MMN generation) to researching the psychophysiological nature of human consciousness. MMN therefore offers the possibility to detect abnormal functioning in the neural system involved in MMN generation, such as it occurs in some neurodevelopmental disorders or patients in vegetative state. While the clinical research data holds considerable promise for translation into clinical practice, standardization and normative data of an optimized (i.e. disorder-specific) MMN recording algorithm is needed in order for MMN to become a valuable clinical investigation tool.

  9. Indexing a sequence for mapping reads with a single mismatch

    PubMed Central

    Crochemore, Maxime; Langiu, Alessio; Rahman, M. Sohel

    2014-01-01

    Mapping reads against a genome sequence is an interesting and useful problem in computational molecular biology and bioinformatics. In this paper, we focus on the problem of indexing a sequence for mapping reads with a single mismatch. We first focus on a simpler problem where the length of the pattern is given beforehand during the data structure construction. This version of the problem is interesting in its own right in the context of the next generation sequencing. In the sequel, we show how to solve the more general problem. In both cases, our algorithm can construct an efficient data structure in time and space and can answer subsequent queries in time. Here, n is the length of the sequence, m is the length of the read, 0<ε<1 and is the optimal output size. PMID:24751874

  10. Hip resurfacing arthroplasty complicated by mismatched implant components

    PubMed Central

    Calistri, Alessandro; Campbell, Patricia; Van Der Straeten, Catherine; De Smet, Koen Aimè

    2017-01-01

    Metal-on-metal hip resurfacing has gained popularity as a feasible treatment option for young and active patients with hip osteoarthritis and high functional expectations. This procedure should only be performed by surgeons who have trained specifically in this technique. Preoperative planning is essential for hip resurfacing in order to execute a successful operation and preview any technical problems. The authors present a case of a man who underwent a resurfacing arthroplasty for osteoarthritis of the left hip that was complicated by mismatched implant components that were revised three days afterwards for severe pain and leg length discrepancy. Such mistakes, although rare, can be prevented by educating operating room staff in the size and colour code tables provided by the companies on their prostheses or implant boxes. PMID:28361022

  11. Radiation of cylindrical duct acoustic modes with flow mismatch

    NASA Technical Reports Server (NTRS)

    Savkar, S. D.; Edelfelt, I. H.

    1975-01-01

    Calculations for the radiation of spinning acoustic modes, with or without a centerbody, and with or without flow temperature and velocity discontinuity, are presented. Solutions to the appropriate convected wave equations devised around Fourier transforms and Wiener-Hopf technique are presented. The decomposition of the asymmetric kernel, resulting from a flow and temperature mismatch, is carried out in part exactly and partially using the so-called Carrier-Koiter approximation procedure. The resulting solutions offer a good approximation to the radiation of both symmetric and asymmetric modes through a flow discontinuity represented as a plug flow jet issuing from a cylindrical duct. Besides the Koiter approximation, the major limitation on the calculation program is the difficulty of calculating the high order Bessel functions with sufficient accuracy.

  12. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses

    NASA Technical Reports Server (NTRS)

    Urakawa, Hidetoshi; Noble, Peter A.; El Fantroussi, Said; Kelly, John J.; Stahl, David A.

    2002-01-01

    The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

  13. Identification of a permissible HLA mismatch in hematopoietic stem cell transplantation

    PubMed Central

    Fernandez-Viña, Marcelo A.; Wang, Tao; Lee, Stephanie J.; Haagenson, Michael; Aljurf, Mahmoud; Askar, Medhat; Battiwalla, Minoo; Baxter-Lowe, Lee-Ann; Gajewski, James; Jakubowski, Ann A.; Marino, Susana; Oudshoorn, Machteld; Marsh, Steven G. E.; Petersdorf, Effie W.; Schultz, Kirk; Turner, E. Victoria; Waller, Edmund K.; Woolfrey, Ann; Umejiego, John; Spellman, Stephen R.; Setterholm, Michelle

    2014-01-01

    In subjects mismatched in the HLA alleles C*03:03/C*03:04 no allogeneic cytotoxic T-lymphocyte responses are detected in vitro. Hematopoietic stem cell transplantation (HSCT) with unrelated donors (UDs) showed no association between the HLA-C allele mismatches (CAMMs) and adverse outcomes; antigen mismatches at this and mismatches other HLA loci are deleterious. The absence of effect of the CAMM may have resulted from the predominance of the mismatch C*03:03/C*03:04. Patients with hematologic malignancies receiving UD HSCT matched in 8/8 and 7/8 HLA alleles were examined. Transplants mismatched in HLA-C antigens or mismatched in HLA-A, -B, or -DRB1 presented significant differences (P < .0001) in mortality (hazard ratio [HR] = 1.37, 1.30), disease-free survival (HR = 1.33, 1.27), treatment-related mortality (HR = 1.54, 1.54), and grade 3-4 acute graft-versus-host disease (HR = 1.49, 1.77) compared with the 8/8 group; transplants mismatched in other CAMMs had similar outcomes with HR ranging from 1.34 to 172 for these endpoints. The C*03:03/C*03:04 mismatched and the 8/8 matched groups had identical outcomes (HR ranging from 0.96-1.05). The previous finding that CAMMs do not associate with adverse outcomes is explained by the predominance (69%) of the mismatch C*03:03/03:04 in this group that is better tolerated than other HLA mismatches. PMID:24408320

  14. Role of frequency mismatch in neuronal communication through coherence.

    PubMed

    Sancristóbal, Belén; Vicente, Raul; Garcia-Ojalvo, Jordi

    2014-10-01

    Neuronal gamma oscillations have been described in local field potentials of different brain regions of multiple species. Gamma oscillations are thought to reflect rhythmic synaptic activity organized by inhibitory interneurons. While several aspects of gamma rhythmogenesis are relatively well understood, we have much less solid evidence about how gamma oscillations contribute to information processing in neuronal circuits. One popular hypothesis states that a flexible routing of information between distant populations occurs via the control of the phase or coherence between their respective oscillations. Here, we investigate how a mismatch between the frequencies of gamma oscillations from two populations affects their interaction. In particular, we explore a biophysical model of the reciprocal interaction between two cortical areas displaying gamma oscillations at different frequencies, and quantify their phase coherence and communication efficiency. We observed that a moderate excitatory coupling between the two areas leads to a decrease in their frequency detuning, up to ∼6 Hz, with no frequency locking arising between the gamma peaks. Importantly, for similar gamma peak frequencies a zero phase difference emerges for both LFP and MUA despite small axonal delays. For increasing frequency detunings we found a significant decrease in the phase coherence (at non-zero phase lag) between the MUAs but not the LFPs of the two areas. Such difference between LFPs and MUAs behavior is due to the misalignment between the arrival of afferent synaptic currents and the local excitability windows. To test the efficiency of communication we evaluated the success of transferring rate-modulations between the two areas. Our results indicate that once two populations lock their peak frequencies, an optimal phase relation for communication appears. However, the sensitivity of locking to frequency mismatch suggests that only a precise and active control of gamma frequency could

  15. Reducing measurement scale mismatch to improve surface energy flux estimation

    NASA Astrophysics Data System (ADS)

    Iwema, Joost; Rosolem, Rafael; Rahman, Mostaquimur; Blyth, Eleanor; Wagener, Thorsten

    2016-04-01

    Soil moisture importantly controls land surface processes such as energy and water partitioning. A good understanding of these controls is needed especially when recognizing the challenges in providing accurate hyper-resolution hydrometeorological simulations at sub-kilometre scales. Soil moisture controlling factors can, however, differ at distinct scales. In addition, some parameters in land surface models are still often prescribed based on observations obtained at another scale not necessarily employed by such models (e.g., soil properties obtained from lab samples used in regional simulations). To minimize such effects, parameters can be constrained with local data from Eddy-Covariance (EC) towers (i.e., latent and sensible heat fluxes) and Point Scale (PS) soil moisture observations (e.g., TDR). However, measurement scales represented by EC and PS still differ substantially. Here we use the fact that Cosmic-Ray Neutron Sensors (CRNS) estimate soil moisture at horizontal footprint similar to that of EC fluxes to help answer the following question: Does reduced observation scale mismatch yield better soil moisture - surface fluxes representation in land surface models? To answer this question we analysed soil moisture and surface fluxes measurements from twelve COSMOS-Ameriflux sites in the USA characterized by distinct climate, soils and vegetation types. We calibrated model parameters of the Joint UK Land Environment Simulator (JULES) against PS and CRNS soil moisture data, respectively. We analysed the improvement in soil moisture estimation compared to uncalibrated model simulations and then evaluated the degree of improvement in surface fluxes before and after calibration experiments. Preliminary results suggest that a more accurate representation of soil moisture dynamics is achieved when calibrating against observed soil moisture and further improvement obtained with CRNS relative to PS. However, our results also suggest that a more accurate

  16. Human MutL-complexes monitor homologous recombination independently of mismatch repair.

    PubMed

    Siehler, Simone Yasmin; Schrauder, Michael; Gerischer, Ulrike; Cantor, Sharon; Marra, Giancarlo; Wiesmüller, Lisa

    2009-02-01

    The role of mismatch repair proteins has been well studied in the context of DNA repair following DNA polymerase errors. Particularly in yeast, MSH2 and MSH6 have also been implicated in the regulation of genetic recombination, whereas MutL homologs appeared to be less important. So far, little is known about the role of the human MutL homolog hMLH1 in recombination, but recently described molecular interactions suggest an involvement. To identify activities of hMLH1 in this process, we applied an EGFP-based assay for the analysis of different mechanisms of DNA repair, initiated by a targeted double-stranded DNA break. We analysed 12 human cellular systems, differing in the hMLH1 and concomitantly in the hPMS1 and hPMS2 status via inducible protein expression, genetic reconstitution, or RNA interference. We demonstrate that hMLH1 and its complex partners hPMS1 and hPMS2 downregulate conservative homologous recombination (HR), particularly when involving DNA sequences with only short stretches of uninterrupted homology. Unexpectedly, hMSH2 is dispensable for this effect. Moreover, the damage-signaling kinase ATM and its substrates BLM and BACH1 are not strictly required, but the combined effect of ATM/ATR-signaling components may mediate the anti-recombinogenic effect. Our data indicate a protective role of hMutL-complexes in a process which may lead to detrimental genome rearrangements, in a manner which does not depend on mismatch repair.

  17. The effects of mismatch repair and RAD1 genes on interchromosomal crossover recombination in Saccharomyces cerevisiae.

    PubMed

    Nicholson, Ainsley; Fabbri, Rebecca M; Reeves, Jason W; Crouse, Gray F

    2006-06-01

    We have previously shown that recombination between 400-bp substrates containing only 4-bp differences, when present in an inverted repeat orientation, is suppressed by >20-fold in wild-type strains of S. cerevisiae. Among the genes involved in this suppression were three genes involved in mismatch repair--MSH2, MSH3, and MSH6--and one in nucleotide excision repair, RAD1. We now report the involvement of these genes in interchromosomal recombination occurring via crossovers using these same short substrates. In these experiments, recombination was stimulated by a double-strand break generated by the HO endonuclease and can occur between completely identical (homologous) substrates or between nonidentical (homeologous) substrates. In addition, a unique feature of this system is that recombining DNA strands can be given a choice of either type of substrate. We find that interchromosomal crossover recombination with these short substrates is severely inhibited in the absence of MSH2, MSH3, or RAD1 and is relatively insensitive to the presence of mismatches. We propose that crossover recombination with these short substrates requires the products of MSH2, MSH3, and RAD1 and that these proteins have functions in recombination in addition to the removal of terminal nonhomology. We further propose that the observed insensitivity to homeology is a result of the difference in recombinational mechanism and/or the timing of the observed recombination events. These results are in contrast with those obtained using longer substrates and may be particularly relevant to recombination events between the abundant short repeated sequences that characterize the genomes of higher eukaryotes.

  18. Luminescence of [Ru(bpy)2(dppz)]2+ bound to RNA mismatches.

    PubMed

    McConnell, Anna J; Song, Hang; Barton, Jacqueline K

    2013-09-03

    The luminescence of rac-[Ru(bpy)2(dppz)](2+) (bpy = 2,2'-bipyridine and dppz = dipyrido[3,2-a:2',3'-c]phenazine) was explored in the presence of RNA oligonucleotides containing a single RNA mismatch (CA and GG) in order to develop a probe for RNA mismatches. While there is minimal luminescence of [Ru(bpy)2(dppz)](2+) in the presence of matched RNA due to weak binding, the luminescence is significantly enhanced in the presence of a single CA mismatch. The luminescence differential between CA mismatched and matched RNA is substantially higher compared to the DNA analogue, and therefore, [Ru(bpy)2(dppz)](2+) appears to be also a sensitive light switch probe for a CA mismatch in duplex RNA. Although the luminescence intensity is lower in the presence of RNA than DNA, Förster resonance energy transfer (FRET) between the donor ruthenium complex and FRET acceptor SYTO 61 is successfully exploited to amplify the luminescence in the presence of the mismatch. Luminescence and quenching studies with sodium iodide suggest that [Ru(bpy)2(dppz)](2+) binds to these mismatches via metalloinsertion from the minor groove. This work provides further evidence that metalloinsertion is a general binding mode of octahedral metal complexes to thermodynamically destabilized mismatches not only in DNA but also in RNA.

  19. The Impact of Major-Job Mismatch on College Graduates' Early Career Earnings: Evidence from China

    ERIC Educational Resources Information Center

    Zhu, Rong

    2014-01-01

    This paper assesses the impact of the mismatch between a college major and job on college graduates' early career earnings using a sample from China. On average, a major-job mismatched college graduate is found to suffer from an income loss that is much lower than the penalty documented in previous studies. The income losses are also found to be…

  20. On the Mismatch between Multicultural Education and Its Subjects in the Field

    ERIC Educational Resources Information Center

    Mizrachi, Nissim

    2012-01-01

    This article draws attention to the growing evidence of a mismatch between sociological categorization and actors' worlds of meaning as expressed in the classroom. The mismatch is especially blatant in cases where students from disadvantaged groups are introduced to what educators and theorists presume to be the liberating discourse of…

  1. A mismatch characterization and simulation environment for weak-to-strong inversion CMOS transistors

    NASA Astrophysics Data System (ADS)

    Velarde-Ramirez, J.; Vicente-Sanchez, G.; Serrano-Gotarredona, T.; Linares-Barranco, B.

    2005-06-01

    Mismatch analysis and simulation is crucial for modern analog design with submicron technologies, where transistors tend to be biased in weak and moderate inversion regions because of the down shrinking of power supply voltage. For optimum analog design where speed, power consumption, area, noise, and accuracy need to be carefully traded off, it is crucial to have available a precise estimation of transistor mismatch in order to avoid overdesign and consequently sacrify unnecessarily speed, power consumption, and area. In this paper we will provide experimental mismatch measurements of different 0.35um CMOS technologies. Each technology has been characterized for a large number of transistor sizes (25-30), by sweeping different width and length values. A large number of transistor curves are measured ranging over different possible biasing conditions. A recent mismatch model will be used to fit the data, and extract electrical parameters. Some of those parameters will be used to adjust the measured mismatch. As a result, a set of standard deviations and correlation coefficients result for the statistical characterization of the mismatch responsible parameters. The resulting electrical parameters, and statistical mismatch parameters are then used in the Spectre simulator of Cadence design environment, to implement the mismatch models using the AHDL behavioral level Spectre description language. The paper shows good agreement between measured data, predicted data, and simulated data.

  2. Are Educational Mismatches Responsible for the "Inequality Increasing Effect" of Education?

    ERIC Educational Resources Information Center

    Budria, Santiago

    2011-01-01

    This paper asks whether educational mismatches can account for the positive association between education and wage inequality found in the data. We use two different data sources, the European Community Household Panel and the Portuguese Labour Force Survey, and consider several types of mismatch, including overqualification, underqualification…

  3. Novel DNA mismatch-repair activity involving YB-1 in human mitochondria.

    PubMed

    de Souza-Pinto, Nadja C; Mason, Penelope A; Hashiguchi, Kazunari; Weissman, Lior; Tian, Jingyan; Guay, David; Lebel, Michel; Stevnsner, Tinna V; Rasmussen, Lene Juel; Bohr, Vilhelm A

    2009-06-04

    Maintenance of the mitochondrial genome (mtDNA) is essential for proper cellular function. The accumulation of damage and mutations in the mtDNA leads to diseases, cancer, and aging. Mammalian mitochondria have proficient base excision repair, but the existence of other DNA repair pathways is still unclear. Deficiencies in DNA mismatch repair (MMR), which corrects base mismatches and small loops, are associated with DNA microsatellite instability, accumulation of mutations, and cancer. MMR proteins have been identified in yeast and coral mitochondria; however, MMR proteins and function have not yet been detected in human mitochondria. Here we show that human mitochondria have a robust mismatch-repair activity, which is distinct from nuclear MMR. Key nuclear MMR factors were not detected in mitochondria, and similar mismatch-binding activity was observed in mitochondrial extracts from cells lacking MSH2, suggesting distinctive pathways for nuclear and mitochondrial MMR. We identified the repair factor YB-1 as a key candidate for a mitochondrial mismatch-binding protein. This protein localizes to mitochondria in human cells, and contributes significantly to the mismatch-binding and mismatch-repair activity detected in HeLa mitochondrial extracts, which are significantly decreased when the intracellular levels of YB-1 are diminished. Moreover, YB-1 depletion in cells increases mitochondrial DNA mutagenesis. Our results show that human mitochondria contain a functional MMR repair pathway in which YB-1 participates, likely in the mismatch-binding and recognition steps.

  4. Bifunctional rhodium intercalator conjugates as mismatch-directing DNA alkylating agents.

    PubMed

    Schatzschneider, Ulrich; Barton, Jacqueline K

    2004-07-21

    A conjugate of a DNA mismatch-specific rhodium intercalator, containing the bulky chrysenediimine ligand, and an aniline mustard has been prepared, and targeting of mismatches in DNA by this conjugate has been examined. The preferential alkylation of mismatched over fully matched DNA is found by a mobility shift assay at concentrations where untethered organic mustards show little reaction. The binding site of the Rh intercalator was determined by DNA photocleavage, and the position of covalent modification was established on the basis of the enhanced depurination associated with N-alkylation. The site-selective alkylation at mismatched DNA renders these conjugates useful tools for the covalent tagging of DNA base pair mismatches and new chemotherapeutic design.

  5. The Shape Interaction Matrix-Based Affine Invariant Mismatch Removal for Partial-Duplicate Image Search.

    PubMed

    Lin, Yang; Lin, Zhouchen; Zha, Hongbin

    2017-02-01

    Mismatch removal is a key step in many computer vision problems. In this paper, we handle the mismatch removal problem by adopting shape interaction matrix (SIM). Given the homogeneous coordinates of the two corresponding point sets, we first compute the SIMs of the two point sets. Then, we detect the mismatches by picking out the most different entries between the two SIMs. Even under strong affine transformations, outliers, noises, and burstiness, our method can still work well. Actually, this paper is the first non-iterative mismatch removal method that achieves affine invariance. Extensive results on synthetic 2D points matching data sets and real image matching data sets verify the effectiveness, efficiency, and robustness of our method in removing mismatches. Moreover, when applied to partial-duplicate image search, our method reaches higher retrieval precisions with shorter time cost compared with the state-of-the-art geometric verification methods.

  6. A Modified Protocol with Improved Detection Rate for Mis-Matched Donor HLA from Low Quantities of DNA in Urine Samples from Kidney Graft Recipients

    PubMed Central

    Kwok, Janette; Choi, Leo C. W.; Ho, Jenny C. Y.; Chan, Gavin S. W.; Mok, Maggie M. Y.; Lam, Man-Fei; Chak, Wai-Leung; Cheuk, Au; Chau, Ka-Foon; Tong, Matthew; Chan, Kwok-Wah; Chan, Tak-Mao

    2016-01-01

    Background Urine from kidney transplant recipient has proven to be a viable source for donor DNA. However, an optimized protocol would be required to determine mis-matched donor HLA specificities in view of the scarcity of DNA obtained in some cases. Methods In this study, fresh early morning urine specimens were obtained from 155 kidney transplant recipients with known donor HLA phenotype. DNA was extracted and typing of HLA-A, B and DRB1 loci by polymerase chain reaction-specific sequence primers was performed using tailor-made condition according to the concentration of extracted DNA. Results HLA typing of DNA extracted from urine revealed both recipient and donor HLA phenotypes, allowing the deduction of the unknown donor HLA and hence the degree of HLA mis-match. By adopting the modified procedures, mis-matched donor HLA phenotypes were successfully deduced in all of 35 tested urine samples at DNA quantities spanning the range of 620–24,000 ng. Conclusions This urine-based method offers a promising and reliable non-invasive means for the identification of mis-matched donor HLA antigens in kidney transplant recipients with unknown donor HLA phenotype or otherwise inadequate donor information. PMID:27861530

  7. Single-molecule views of MutS on mismatched DNA

    PubMed Central

    Lee, Jong-Bong; Cho, Won-Ki; Park, Jonghyun; Jeon, Yongmoon; Kim, Daehyung; Lee, Seung Hwan; Fishel, Richard

    2014-01-01

    Base-pair mismatches that occur during DNA replication or recombination can reduce genetic stability or conversely increase genetic diversity. The genetics and biophysical mechanism of mismatch repair (MMR) has been extensively studied since its discovery nearly 50 years ago. MMR is a strand-specific excision-resynthesis reaction that is initiated by MutS homolog (MSH) binding to the mismatched nucleotides. The MSH mismatch-binding signal is then transmitted to the immediate downstream MutL homolog (MLH/PMS) MMR components and ultimately to a distant strand scission site where excision begins. The mechanism of signal transmission has been controversial for decades. We have utilized single molecule Forster Resonance Energy Transfer (smFRET), Fluorescence Tracking (smFT) and Polarization Total Internal Reflection Fluorescence (smP-TIRF) to examine the interactions and dynamic behaviors of single Thermus aquaticus MutS (TaqMutS) particles on mismatched DNA. We determined that Taq-MutS forms an incipient clamp to search for a mismatch in ∼1 s intervals by 1-dimensional (1D) thermal fluctuation-driven rotational diffusion while in continuous contact with the helical duplex DNA. When MutS encounters a mismatch it lingers for ∼3 s to exchange bound ADP for ATP (ADP → ATP exchange). ATP binding by TaqMutS induces an extremely stable clamp conformation (∼10 min) that slides off the mismatch and moves along the adjacent duplex DNA driven simply by 1D thermal diffusion. The ATP-bound sliding clamps rotate freely while in discontinuous contact with the DNA. The visualization of a train of MSH proteins suggests that dissociation of ATP-bound sliding clamps from the mismatch permits multiple mismatch-dependent loading events. These direct observations have provided critical clues into understanding the molecular mechanism of MSH proteins during MMR. PMID:24629484

  8. Emotion-Related Visual Mismatch Responses in Schizophrenia: Impairments and Correlations with Emotion Recognition

    PubMed Central

    Csukly, Gábor; Stefanics, Gábor; Komlósi, Sarolta; Czigler, István; Czobor, Pál

    2013-01-01

    Background and Objectives Mismatch negativity (MMN) is an event-related potential (ERP) measure of preattentional sensory processing. While deficits in the auditory MMN are robust electrophysiological findings in schizophrenia, little is known about visual mismatch response and its association with social cognitive functions such as emotion recognition in schizophrenia. Our aim was to study the potential deficit in the visual mismatch response to unexpected facial emotions in schizophrenia and its association with emotion recognition impairments, and to localize the sources of the mismatch signals. Experimental Design The sample comprised 24 patients with schizophrenia and 24 healthy control subjects. Controls were matched individually to patients by gender, age, and education. ERPs were recorded using a high-density 128-channel BioSemi amplifier. Mismatch responses to happy and fearful faces were determined in 2 time windows over six regions of interest (ROIs). Emotion recognition performance and its association with the mismatch response were also investigated. Principal Observations Mismatch signals to both emotional conditions were significantly attenuated in patients compared to controls in central and temporal ROIs. Controls recognized emotions significantly better than patients. The association between overall emotion recognition performance and mismatch response to the happy condition was significant in the 250–360 ms time window in the central ROI. The estimated sources of the mismatch responses for both emotional conditions were localized in frontal regions, where patients showed significantly lower activity. Conclusions Impaired generation of mismatch signals indicate insufficient automatic processing of emotions in patients with schizophrenia, which correlates strongly with decreased emotion recognition. PMID:24116046

  9. Computed MISTR Requirement Changes and Parts Support - Analysis of a Mismatch.

    DTIC Science & Technology

    1980-06-09

    gratitude to the "I" Division, Sacramento Air Logistics Center (ALC), for sponsoring this research. John Keith and other members of the ALC were of...5. Maintenance Inventory Control Records 6. Output generated by G062 for IMS 8 Research Hypothesis The pen or pencil adjusting of the Air Force Logis ...AFB OH, September 1976. 5. .manaement of Items Sub ject to Repair (MITR). AFLC Regulation 05-1z. Wright-PatEterson KFff OHT, 2 August, 1978. 6. Baird

  10. Employability of German Geography Graduates: The Mismatch between Knowledge Acquired and Competences Required

    ERIC Educational Resources Information Center

    Hennemann, Stefan; Liefner, Ingo

    2010-01-01

    The employability of university graduates is a concern in higher education as labour markets change more and more rapidly. This is of particular relevance for multi-faceted subjects such as geography. Studies on employability have to consider to what degree a university education helps graduates start a career. The results of a survey of 257…

  11. Effect of contralateral white noise masking on the mismatch negativity.

    PubMed

    Salo, S K; Lang, A H; Salmivalli, A J

    1995-01-01

    Mismatch negativity (MMN), an auditive event-related potential (ERP) component, evoked by deviant stimuli in a homogeneous stream of standard stimuli was studied in a unilateral stimulation and contralateral white noise masking condition. Eleven subjects (Ss) with normal hearing (aged 20-35 years) were examined using sine tone stimuli (70 dB HL, interstimulus interval 300 ms, duration 40 ms with 5 ms rise and fall times). Three blocks of standard (std)/deviant (dev) series of stimuli were used: std 500/dev 600 Hz, std 2000/dev 1900 Hz, and std 2000/dev 1600 Hz. The first block was repeated for another group of 11 Ss with normal hearing (aged 17-27 years). The MMN was analysed from the difference curves recorded at Fz, Cz and Pz. The stimuli were delivered unilaterally, either with or without 50 dB effective masking level white noise to the contralateral ear. The MMN amplitude attenuated significantly when contralateral masking was used. In addition, there was interaction between noise masking and the stimulated ear. The MMN latencies were not affected by white noise masking.

  12. Modeling cross-hatch surface morphology in growing mismatched layers

    NASA Astrophysics Data System (ADS)

    Andrews, A. M.; Speck, J. S.; Romanov, A. E.; Bobeth, M.; Pompe, W.

    2002-02-01

    We propose and investigate a model for the development of cross-hatch surface morphology in growing mismatched layers. The model incorporates two important elements: (i) strain relaxation due to dislocation glide in the layer (film) interior that is also associated with misfit dislocation formation at the film/substrate interface and (ii) lateral surface transport that eliminates surface steps that originated from dislocation glide. A combination of dislocation-assisted strain relaxation and surface step flow leads to the appearance of surface height undulations during layer growth. A Monte Carlo simulation technique was applied to model dislocation nucleation events in the course of strain relaxation. The simulation was used to model the influence of dislocations on film surface height profiles. The surface height displacement was calculated from the analytic elasticity solutions for edge dislocations near a free surface. The results of the modeling predict that the average amplitude of the surface undulations and their apparent wavelength both increase with increasing film relaxation and film thickness. The developed cross-hatch pattern is characterized by an atomically smooth but mesoscopically (lateral dimensions ˜0.1-10 μm) rough surface morphology. The conclusions of the model are in agreement with atomic force microscopy observations of cross-hatch surface relief in In0.25Ga0.75As/GaAs samples grown well beyond the critical thickness for misfit dislocation formation.

  13. Systematic misestimation in a vernier task arising from contrast mismatch.

    PubMed

    Sun, Hao; Lee, Barry B; Baraas, Rigmor C

    2008-01-01

    Luminance signals mediated by the magnocellular (MC) pathway play an important role in vernier tasks. MC ganglion cells show a phase advance in their responses to sinusoidal stimuli with increasing contrast due to contrast gain control mechanisms. If the phase information in MC ganglion cell responses were utilized by central mechanisms in vernier tasks, one might expect systematic errors caused by the phase advance. This systematic error may contribute to the contrast paradox phenomenon, where vernier performance deteriorates, rather than improves, when only one of the target pair increases in contrast. Vernier psychometric functions for a pair of gratings of mismatched contrast were measured to seek such misestimation. In associated electrophysiological experiments, MC and parvocellular (PC) ganglion cells' responses to similar stimuli were measured to provide a physiological reference. The psychophysical experiments show that a high-contrast grating is perceived as phase advanced in the drift direction compared to a low-contrast grating, especially at a high drift rate (8 Hz). The size of the phase advance was comparable to that seen in MC cells under similar stimulus conditions. These results are consistent with the MC pathway supporting vernier performance with achromatic gratings. The shifts in vernier psychometric functions were negligible for pairs of chromatic gratings under the conditions tested here, consistent with the lack of phase advance both in responses of PC ganglion cells and in frequency-doubled chromatic responses of MC ganglion cells.

  14. Modelling Trial-by-Trial Changes in the Mismatch Negativity

    PubMed Central

    Lieder, Falk; Daunizeau, Jean; Garrido, Marta I.; Friston, Karl J.; Stephan, Klaas E.

    2013-01-01

    The mismatch negativity (MMN) is a differential brain response to violations of learned regularities. It has been used to demonstrate that the brain learns the statistical structure of its environment and predicts future sensory inputs. However, the algorithmic nature of these computations and the underlying neurobiological implementation remain controversial. This article introduces a mathematical framework with which competing ideas about the computational quantities indexed by MMN responses can be formalized and tested against single-trial EEG data. This framework was applied to five major theories of the MMN, comparing their ability to explain trial-by-trial changes in MMN amplitude. Three of these theories (predictive coding, model adjustment, and novelty detection) were formalized by linking the MMN to different manifestations of the same computational mechanism: approximate Bayesian inference according to the free-energy principle. We thereby propose a unifying view on three distinct theories of the MMN. The relative plausibility of each theory was assessed against empirical single-trial MMN amplitudes acquired from eight healthy volunteers in a roving oddball experiment. Models based on the free-energy principle provided more plausible explanations of trial-by-trial changes in MMN amplitude than models representing the two more traditional theories (change detection and adaptation). Our results suggest that the MMN reflects approximate Bayesian learning of sensory regularities, and that the MMN-generating process adjusts a probabilistic model of the environment according to prediction errors. PMID:23436989

  15. Meniscus replacement: Influence of geometrical mismatches on chondroprotective capabilities.

    PubMed

    Párraga Quiroga, J M; Ito, K; van Donkelaar, C C

    2015-06-01

    The chondroprotective success of meniscal transplantation is variable. Poorly controlled factors such as a geometrical mismatch of the implant may be partly responsible. Clinical data, animal studies and cadaver experiments suggest that smaller transplants perform better than oversized, but clear evidence is lacking. The hypothesis of this study is that smaller menisci outperform larger ones because they distribute stresses more effectively at those particular locations that receive the highest loads. Consequently, collagen in the adjacent cartilage is protected from damage due to overstraining. Experimentally it is not possible to measure load distribution and collagen strain inside articular cartilage (AC). Therefore, a numerical model was used to determine the mechanical conditions throughout the depth of the AC. Meniscus implants with different sizes and mechanical properties were evaluated. These were compared with healthy and with meniscectomized joints. To account for the time-dependent behavior 600s of loading was simulated; results were visualized after 1s and 600s. Simulations showed that AC's strains strongly depended on implant size and loading duration. They depended less on the stiffness of the implant material. With an oversized implant, collagen strains were particularly large in the femoral AC initially and further increased upon sustained loading. The severest compressive strains occurred after sustained loading in the meniscectomized joint. Strains with an undersized meniscus were comparable to a perfectly sized implant. In conclusion, these results support the hypothesis that an undersized implant may outperform an oversized one because it distributes stresses better in the most intensely loaded joint area.

  16. Rubberband Effect in Temporal Control of Mismatch Negativity

    PubMed Central

    Wang, Lingyan; Lin, Xiaoxiong; Zhou, Bin; Pöppel, Ernst; Bao, Yan

    2016-01-01

    Mismatch negativity (MMN) is a difference event-related potential (ERP) wave reflecting the brain’s automatic reaction to deviant sensory stimuli, and it has been proven to be a useful tool in research on cognitive functions or clinical disorders. In most MMN studies, amplitude, peak latency, or the integral of the responses, in rare cases also the slopes of the responses, have been employed as parameters of the ERP responses for quantitative analyses. However, little is known about correlations between these parameters. To better understand the relations between different ERP parameters, we extracted and correlated several different parameters characterizing the MMN waves. We found an unexpected correlation which gives new insight into the temporal control of MMN: response amplitudes are positively correlated with downside slopes, whereas barely correlated with upside slopes. This result suggests an efficient feedback mechanism for the MMN to return to the baseline within a predefined time window, contradicting an exponential decay function as one might expect. As a metaphor we suggest a rubberband effect for the MMN responses, i.e., the larger the distance of the response from neural equilibrium, the stronger the return force to equilibrium. PMID:27642285

  17. Mammalian mismatches in nucleotide metabolism: implications for xenotransplantation.

    PubMed

    Khalpey, Zain; Yuen, Ada H Y; Lavitrano, Marialuisa; McGregor, Christopher G A; Kalsi, Kameljit K; Yacoub, Magdi H; Smolenski, Ryszard T

    2007-10-01

    Acute humoral rejection (AHR) limits the clinical application of animal organs for xenotransplantation. Mammalian disparities in nucleotide metabolism may contribute significantly to the microvascular component in AHR; these, however remain ill-defined. We evaluated the extent of species-specific differences in nucleotide metabolism. HPLC analysis was performed on venous blood samples (nucleotide metabolites) and heart biopsies (purine enzymes) from wild type mice, rats, pigs, baboons, and human donors.Ecto-5'-nucleotidase (E5'N) activities were 4-fold lower in pigs and baboon hearts compared to human and mice hearts while rat activity was highest. Similar differences between pigs and humans were also observed with kidneys and endothelial cells. More than 10-fold differences were observed with other purine enzymes. AMP deaminase (AMPD) activity was exceptionally high in mice but very low in pig and baboon hearts. Adenosine deaminase (ADA) activity was highest in baboons. Adenosine kinase (AK) activity was more consistent across different species. Pig blood had the highest levels of hypoxanthine, inosine and adenine. Human blood uric acid concentration was almost 100 times higher than in other species studied. We conclude that species-specific differences in nucleotide metabolism may affect compatibility of pig organs within a human metabolic environment. Furthermore, nucleotide metabolic mismatches may affect clinical relevance of animal organ transplant models. Supplementation of deficient precursors or application of inhibitors of nucleotide metabolism (e.g., allopurinol) or transgenic upregulation of E5'N may overcome some of these differences.

  18. Anterior insula coordinates hierarchical processing of tactile mismatch responses

    PubMed Central

    Allen, Micah; Fardo, Francesca; Dietz, Martin J.; Hillebrandt, Hauke; Friston, Karl J.; Rees, Geraint; Roepstorff, Andreas

    2016-01-01

    The body underlies our sense of self, emotion, and agency. Signals arising from the skin convey warmth, social touch, and the physical characteristics of external stimuli. Surprising or unexpected tactile sensations can herald events of motivational salience, including imminent threats (e.g., an insect bite) and hedonic rewards (e.g., a caressing touch). Awareness of such events is thought to depend upon the hierarchical integration of body-related mismatch responses by the anterior insula. To investigate this possibility, we measured brain activity using functional magnetic resonance imaging, while healthy participants performed a roving tactile oddball task. Mass-univariate analysis demonstrated robust activations in limbic, somatosensory, and prefrontal cortical areas previously implicated in tactile deviancy, body awareness, and cognitive control. Dynamic Causal Modelling revealed that unexpected stimuli increased the strength of forward connections along a caudal to rostral hierarchy—projecting from thalamic and somatosensory regions towards insula, cingulate and prefrontal cortices. Within this ascending flow of sensory information, the AIC was the only region to show increased backwards connectivity to the somatosensory cortex, augmenting a reciprocal exchange of neuronal signals. Further, participants who rated stimulus changes as easier to detect showed stronger modulation of descending PFC to AIC connections by deviance. These results suggest that the AIC coordinates hierarchical processing of tactile prediction error. They are interpreted in support of an embodied predictive coding model where AIC mediated body awareness is involved in anchoring a global neuronal workspace. PMID:26584870

  19. Mouse models of DNA mismatch repair in cancer research

    PubMed Central

    Lee, Kyeryoung; Tosti, Elena; Edelmann, Winfried

    2016-01-01

    Germline mutations in DNA mismatch repair (MMR) genes are the cause of hereditary non-polyposis colorectal cancer/Lynch syndrome (HNPCC/LS) one of the most common cancer predisposition syndromes, and defects in MMR are also prevalent in sporadic colorectal cancers. In the past, the generation and analysis of mouse lines with knockout mutations in all of the known MMR genes has provided insight into how loss of individual MMR genes affects genome stability and contributes to cancer susceptibility. These studies also revealed essential functions for some of the MMR genes in B cell maturation and fertility. In this review, we will provide a brief overview of the cancer predisposition phenotypes of recently developed mouse models with targeted mutations in MutS and MutL homologs (Msh and Mlh, respectively) and their utility as preclinical models. The focus will be on mouse lines with conditional MMR mutations that have allowed more accurate modeling of human cancer syndromes in mice and that together with new technologies in gene targeting, hold great promise for the analysis of MMR-deficient intestinal tumors and other cancers which will drive the development of preventive and therapeutic treatment strategies. PMID:26708047

  20. Mouse models of DNA mismatch repair in cancer research.

    PubMed

    Lee, Kyeryoung; Tosti, Elena; Edelmann, Winfried

    2016-02-01

    Germline mutations in DNA mismatch repair (MMR) genes are the cause of hereditary non-polyposis colorectal cancer/Lynch syndrome (HNPCC/LS) one of the most common cancer predisposition syndromes, and defects in MMR are also prevalent in sporadic colorectal cancers. In the past, the generation and analysis of mouse lines with knockout mutations in all of the known MMR genes has provided insight into how loss of individual MMR genes affects genome stability and contributes to cancer susceptibility. These studies also revealed essential functions for some of the MMR genes in B cell maturation and fertility. In this review, we will provide a brief overview of the cancer predisposition phenotypes of recently developed mouse models with targeted mutations in MutS and MutL homologs (Msh and Mlh, respectively) and their utility as preclinical models. The focus will be on mouse lines with conditional MMR mutations that have allowed more accurate modeling of human cancer syndromes in mice and that together with new technologies in gene targeting, hold great promise for the analysis of MMR-deficient intestinal tumors and other cancers which will drive the development of preventive and therapeutic treatment strategies.

  1. Repair of Single- and Multiple-Substitution Mismatches during Recombination in Streptococcus Pneumoniae

    PubMed Central

    Gasc, A. M.; Sicard, A. M.; Claverys, J. P.

    1989-01-01

    The use as genetic markers, during transformation of Streptococcus pneumoniae, of 19 sequences differing from wild type, located throughout the amiA locus, enabled us to examine the fate of 24 single- and 11 multiple-mismatches during recombination. Tentative mismatch ranking as a function of decreasing repair efficiency by the Hex mismatch repair system is G/T = A/C = G/G (maximum repair: 90-95%) > C/T (mostly 75 to 90% repair) > A/A (from 50 to 90% repair) > T/T (50-65% repair) > A/G (from 0 to 20% repair) > C/C. No indication of correction of the latter has been obtained. Over the limited number of samples examined, we observed no influence of the base composition of the surrounding sequence on correction efficiency for both transition mismatches and for G/G and C/C. Variations in the surrounding sequence affect repair of A/G and C/T, and, even more strongly, of A/A and T/T. No simple correlation to the G:C content of the surrounding sequence is apparent from our results, in contrast to the conclusion drawn for the Mut mismatch repair system of Escherichia coli. Examination of the fate of multiple mismatches suggests that C/C may sometimes impede recognition of otherwise corrected mismatches. PMID:2645195

  2. Ventromedial prefrontal cortex drives hippocampal theta oscillations induced by mismatch computations.

    PubMed

    Garrido, Marta I; Barnes, Gareth R; Kumaran, Dharshan; Maguire, Eleanor A; Dolan, Raymond J

    2015-10-15

    Detecting environmental change is fundamental for adaptive behavior in an uncertain world. Previous work indicates the hippocampus supports the generation of novelty signals via implementation of a match-mismatch detector that signals when an incoming sensory input violates expectations based on past experience. While existing work has emphasized the particular contribution of the hippocampus, here we ask which other brain structures also contribute to match-mismatch detection. Furthermore, we leverage the fine-grained temporal resolution of magnetoencephalography (MEG) to investigate whether mismatch computations are spectrally confined to the theta range, based on the prominence of this range of oscillations in models of hippocampal function. By recording MEG activity while human subjects perform a task that incorporates conditions of match-mismatch novelty we show that mismatch signals are confined to the theta band and are expressed in both the hippocampus and ventromedial prefrontal cortex (vmPFC). Effective connectivity analyses (dynamic causal modeling) show that the hippocampus and vmPFC work as a functional circuit during mismatch detection. Surprisingly, our results suggest that the vmPFC drives the hippocampus during the generation and processing of mismatch signals. Our findings provide new evidence that the hippocampal-vmPFC circuit is engaged during novelty processing, which has implications for emerging theories regarding the role of vmPFC in memory.

  3. Marrow Ablative and Immunosuppressive Effects of I-131-anti-CD45 Antibody in Congenic and H2-Mismatched Murine Transplant Models

    SciTech Connect

    Matthews, D. C.; Martin, P J.; Nourigat, C.; Appelbaum, F. R.; Fisher, Darrell R. ); Bernstein, I. D.

    1998-12-01

    Targeted hematopoietic irradiation delivered by I-131-anti-CD45 antibody has been combined with conventional marrow transplant preparative regimens in an effort to decrease relapse. Before increasing the proportion of therapy delivered by radiolabeled antibody, the myeloablative and immunosuppressive effects of such low dose rate irradiation must be quantitated. We have examined the ability of I-131-anti-CD45 antibody to facilitate engraftment in Ly5-congenic and H2-mismatched murine marrow transplant models. Recipient B6-Ly5-a mice were treated with 30F11 antibody labeled with 0.1 to 1.5 mCi I-131 and/or total body irradiation (TBI), followed by T-cell-depleted marrow from Ly5-b-congenic (C57BL/6) or H2-mismatched (BALB/c) donors. Engraftment was achieved readily in the Ly5-congenic setting, with greater than 80% donor granulocytes and T cells after 0.5 mCi I-131 (estimated 17 Gy to marrow) or 8 Gy TBI. A higher TBI dose (14 Gy) was required to achieve engraftment of H2-mismatched mar row, and engraftment occurred in only 3 of 11 mice receiving 1.5 mCi I-131 delivered by anti-CD45 antibody. Engraftment of H2-mismatched marrow was achieved in 22 of 23 animals receiving 0.75 mCi I-131 delivered by anti-CD45 antibody combined with 8 Gy TBI. Thus, targeted radiation delivered via I-131-anti-CD45 antibody can enable engraftment of congenic marrow and can partially replace TBI when transplanting T-cell-depleted H2-mismatched marrow.

  4. Negative effects of a disulfide bond mismatch in anti-rabies G protein single-chain antibody variable fragment FV57.

    PubMed

    Duan, Ye; Gu, Tiejun; Zhang, Xizhen; Jiang, Chunlai; Yuan, Ruosen; Li, Zhuang; Wang, Dandan; Chen, Xiaoxu; Wu, Chunlai; Chen, Yan; Wu, Yongge; Kong, Wei

    2014-06-01

    Rabies virus (RV) causes a fatal infectious disease requiring efficient post-exposure prophylaxis (PEP), which includes a rabies vaccine and rabies immunoglobulin (RIG). The single-chain antibody variable fragment (scFv), a small engineered antibody fragment derived from an antibody variable heavy chain and light chain, has the potential to replace the current application of RIG. In previous studies, we constructed and evaluated an anti-rabies virus G protein scFv (FV57) based on the monoclonal antibody CR57. Of the five cysteines in FV57, four are linked in intra-chain disulfide bonds (Cys-VH28/Cys-VH98 and Cys-VL16/Cys-VL84), and one is free (Cys-VL85). However, the thiol in Cys-VL85 neighboring Cys-VL84 in the CDR3 of the light chain is likely to mismatch with the thiol in Cys-VL16 during the renaturing process. In order to study effects of the mismatched disulfide bond, Cys-VL85 and Cys-VL84 of FV57 were mutated to serine to construct mutants FV57(VL85S) and FV57(VL84S). Furthermore, the disulfide bonds in the light chain of FV57, FV57(VL85S) and FV57(VL84S) were deleted by mutating Cys-VL16 to serine. All mutants were prepared and evaluated along with the original FV57. The results indicated that the mismatched disulfide bond of FV57 linking the light chain FR1 and CDR3 would confer deleterious negative effects on its activity against RV, likely due to spatial hindrance in the light chain CDR3. Moreover, avoidance of the disulfide bond mismatch provided an additional 30% protective efficacy against RV infection in the mouse RV challenge model. Thus, modifications of FV57 to eliminate the disulfide bond mismatch may provide a candidate therapeutic agent for effective PEP against rabies.

  5. Social, Spatial, and Skill Mismatch among Immigrants and Native-Born Workers in Los Angeles. Working Paper.

    ERIC Educational Resources Information Center

    Pastor, Manuel, Jr.; Marcelli, Enrico A.

    Racially different economic outcomes stem from multiple causes, including various "mismatches" between minority employees and available jobs. A skill mismatch occurs when individuals' education and job skills do not qualify them for existing jobs. A spatial mismatch means that people live far from the work for which they qualify. A…

  6. Economic thermoregulatory response explains mismatch between thermal physiology and behaviour in newts.

    PubMed

    Gvoždík, Lumír; Kristín, Peter

    2017-03-15

    Temperature is an important factor determining distribution and abundance of organisms. Predicting the impact of warming climate on ectotherm populations requires information about species' thermal requirements, i.e. their so-called 'thermal niche'. The characterization of thermal niche remains a complicated task. We compared the applicability of two indirect approaches, based on reaction norm (aerobic scope curve) and optimality (preferred body temperature) concepts, for indirect estimation of thermal niche while using newts, Ichthyosaura alpestris, as a study system. If the two approaches are linked, then digesting newts should keep their body temperatures close to values maximizing aerobic scope for digestion. After feeding, newts maintained their body temperatures within a narrower range than did hungry individuals. The range of preferred body temperatures was well below the temperature maximizing aerobic scope for digestion. Optimal temperatures for factorial aerobic scope fell within the preferred body temperature range of digesting individuals. We conclude that digesting newts prefer body temperatures that are optimal for the maximum aerobic performance but relative to the maintenance costs. What might be termed the 'economic' thermoregulatory response explains the mismatch between thermal physiology and behaviour in this system.

  7. Autofrettage to Counteract Coefficient of Thermal Expansion Mismatch in Cryogenic Pressurized Pipes with Metallic Liners

    NASA Technical Reports Server (NTRS)

    Wen, Ed; Barbero, Ever; Tygielski, Phlip; Turner, James E. (Technical Monitor)

    2001-01-01

    Composite feedlines with metal liners have the potential to reduce weight/cost while providing the same level of permeation resistance and material compatibility of all-metal feedlines carrying cryogenic propellants in spacecraft. The major technical challenges are the large difference in Coefficient of Thermal Expansion between the liner and the composite, and the manufacturing method required to make a very thin liner with the required strength and dimensional tolerance. This study investigates the use of autofrettage (compressive preload) to counteract Coefficient of Thermal Expansion when pre-pressurization procedures cannot be used to solve this problem. Promising materials (aluminum 2219, Inconel 718, nickel, nickel alloy) and manufacturing techniques (chemical milling, electroplating) are evaluated to determine the best liner candidates. Robust, autofrettaged feedlines with a low Coefficient of Thermal Expansion liner (Inconel 718 or nickel alloy) are shown to successfully counteract mismatch at LOX temperature. A new concept, autofrettage by temperature, is introduced for high Coefficient of Thermal Expansion materials (aluminum and pure nickel) where pressure cannot be used to add compressive preload.

  8. Re-Examining Risk of Repeated HLA Mismatch in Kidney Transplantation.

    PubMed

    Tinckam, Kathryn J; Rose, Caren; Hariharan, Sundaram; Gill, John

    2016-09-01

    Kidney retransplantation is a risk factor for decreased allograft survival. Repeated mismatched HLA antigens between first and second transplant may be a stimulus for immune memory responses and increased risk of alloimmune damage to the second allograft. Historical data identified a role of repeated HLA mismatches in allograft loss. However, evolution of HLA testing methods and a modern transplant era necessitate re-examination of this role to more accurately risk-stratify recipients. We conducted a contemporary registry analysis of data from 13,789 patients who received a second kidney transplant from 1995 to 2011, of which 3868 had one or more repeated mismatches. Multivariable Cox proportional hazards modeling revealed no effect of repeated mismatches on all-cause or death-censored graft loss. Analysis of predefined subgroups, however, showed that any class 2 repeated mismatch increased the hazard of death-censored graft loss, particularly in patients with detectable panel-reactive antibody before second transplant (hazard ratio [HR], 1.15; 95% confidence interval [95% CI], 1.02 to 1.29). Furthermore, in those who had nephrectomy of the first allograft, class 2 repeated mismatches specifically associated with all-cause (HR, 1.30; 95% CI, 1.07 to 1.58) and death-censored graft loss (HR, 1.41; 95% CI, 1.12 to 1.78). These updated data redefine the effect of repeated mismatches in retransplantation and challenge the paradigm that repeated mismatches in isolation confer increased immunologic risk. We also defined clear recipient categories for which repeated mismatches may be of greater concern in a contemporary cohort. Additional studies are needed to determine appropriate interventions for these recipients.

  9. Influence of sequence mismatches on the specificity of recombinase polymerase amplification technology.

    PubMed

    Daher, Rana K; Stewart, Gale; Boissinot, Maurice; Boudreau, Dominique K; Bergeron, Michel G

    2015-04-01

    Recombinase polymerase amplification (RPA) technology relies on three major proteins, recombinase proteins, single-strand binding proteins, and polymerases, to specifically amplify nucleic acid sequences in an isothermal format. The performance of RPA with respect to sequence mismatches of closely-related non-target molecules is not well documented and the influence of the number and distribution of mismatches in DNA sequences on RPA amplification reaction is not well understood. We investigated the specificity of RPA by testing closely-related species bearing naturally occurring mismatches for the tuf gene sequence of Pseudomonas aeruginosa and/or Mycobacterium tuberculosis and for the cfb gene sequence of Streptococcus agalactiae. In addition, the impact of the number and distribution of mismatches on RPA efficiency was assessed by synthetically generating 14 types of mismatched forward primers for detecting five bacterial species of high diagnostic relevance such as Clostridium difficile, Staphylococcus aureus, S. agalactiae, P. aeruginosa, and M. tuberculosis as well as Bacillus atropheus subsp. globigii for which we use the spores as internal control in diagnostic assays. A total of 87 mismatched primers were tested in this study. We observed that target specific RPA primers with mismatches (n > 1) at their 3'extrimity hampered RPA reaction. In addition, 3 mismatches covering both extremities and the center of the primer sequence negatively affected RPA yield. We demonstrated that the specificity of RPA was multifactorial. Therefore its application in clinical settings must be selected and validated a priori. We recommend that the selection of a target gene must consider the presence of closely-related non-target genes. It is advisable to choose target regions with a high number of mismatches (≥36%, relative to the size of amplicon) with respect to closely-related species and the best case scenario would be by choosing a unique target gene.

  10. Band anticrossing effects in highly mismatched semiconductor alloys

    SciTech Connect

    Wu, Junqiao

    2002-01-01

    The first five chapters of this thesis focus on studies of band anticrossing (BAC) effects in highly electronegativity- mismatched semiconductor alloys. The concept of bandgap bowing has been used to describe the deviation of the alloy bandgap from a linear interpolation. Bowing parameters as large as 2.5 eV (for ZnSTe) and close to zero (for AlGaAs and ZnSSe) have been observed experimentally. Recent advances in thin film deposition techniques have allowed the growth of semiconductor alloys composed of significantly different constituents with ever- improving crystalline quality (e.g., GaAs1-xNx and GaP1-xNx with x ~< 0.05). These alloys exhibit many novel and interesting properties including, in particular, a giant bandgap bowing (bowing parameters > 14 eV). A band anticrossing model has been developed to explain these properties. The model shows that the predominant bowing mechanism in these systems is driven by the anticrossing interaction between the localized level associated with the minority component and the band states of the host. In this thesis I discuss my studies of the BAC effects in these highly mismatched semiconductors. It will be shown that the results of the physically intuitive BAC model can be derived from the Hamiltonian of the many-impurity Anderson model. The band restructuring caused by the BAC interaction is responsible for a series of experimental observations such as a large bandgap reduction, an enhancement of the electron effective mass, and a decrease in the pressure coefficient of the fundamental gap energy. Results of further experimental investigations of the optical properties of quantum wells based on these materials will be also presented. It will be shown that the BAC interaction occurs not only between localized states and conduction band states at the Brillouin zone center, but also exists over all of k-space. Finally, taking ZnSTe and ZnSeTe as examples, I show that BAC also

  11. Band Anticrossing in Highly Mismatched Compound Semiconductor Alloys

    NASA Technical Reports Server (NTRS)

    Yu, Kin Man; Wu, J.; Walukiewicz, W.; Ager, J. W.; Haller, E. E.; Miotkowski, I.; Su, Ching-Hua; Curreri, Peter A. (Technical Monitor)

    2001-01-01

    Compound semiconductor alloys in which metallic anions are partially replaced with more electronegative isoelectronic atoms have recently attracted significant attention. Group IIIN(sub x)V(sub 1-x) alloys with a small amount of the electronegative N substituting more metallic column V elements has been the most extensively studied class of such Highly Mismatched Alloys (HMAs). We have shown that many of the unusual properties of the IIIN(sub x)V(sub 1-x) alloys can be well explained by the Band Anticrossing (BAC) model that describes the electronic structure in terms of an interaction between highly localized levels of substitutional N and the extended states of the host semiconductor matrix. Most recently the BAC model has been also used to explain similar modifications of the electronic band structure observed in Te-rich ZnS(sub x)Te(sub 1-x) and ZnSe(sub y)Te(sub 1-y) alloys. To date studies of HMAs have been limited to materials with relatively small concentrations of highly electronegative atoms. Here we report investigations of the electronic structure of ZnSe(sub y)Te(sub 1-y) alloys in the entire composition range, y between 0 and 1. The samples used in this study are bulk ZnSe(sub y)Te(sub 1-y) crystals grown by either a modified Bridgman method or by physical vapor transport. Photomodulated reflection (PR) spectroscopy was used to measure the composition dependence of optical transitions from the valence band edge and from the spin-orbit split off band to the conduction band. The pressure dependence of the band gap was measured using optical absorption in a diamond anvil cell. We find that the energy of the spin-orbit split off valence band edge does not depend on composition and is located at about 3 eV below the conduction band edge of ZnSe. On the Te-rich side the pressure and the composition dependence of the optical transitions are well explained by the BAC model which describes the downward shift of the conduction band edge in terms of the

  12. Band Anticrossing in Highly Mismatched Compound Semiconductor Alloys

    NASA Technical Reports Server (NTRS)

    Yu, Kin Man; Wu, J.; Walukiewicz, W.; Ager, J. W.; Haller, E. E.; Miotkowski, I.; Ramdas, A.; Su, Ching-Hua; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Compound semiconductor alloys in which metallic anions are partially replaced with more electronegative isoelectronic atoms have recently attracted significant attention. Group IIIN(x)V(1-x), alloys with a small amount of the electronegative N substituting more metallic column V elements has been the most extensively studied class of such Highly Mismatched Alloys (HMAs). We have shown that many of the unusual properties of the IIIN(x),V(1-x) alloys can be well explained by the Band Anticrossing (BAC) model that describes the electronic structure in terms of an interaction between highly localized levels of substitutional N and the extended states of the host semiconductor matrix. Most recently the BAC model has been also used to explain similar modifications of the electronic band structure observed in Te-rich ZnS(x)Te(l-x) and ZnSe(Y)Te(1-y) alloys. To date studies of HMAs have been limited to materials with relatively small concentrations of highly electronegative atoms. Here we report investigations of the electronic structure of ZnSe(y)Te(1-y) alloys in the entire composition range, 0 less than or equal to y less than or equal to 1. The samples used in this study are bulk ZnSe(y)Te(1-y) crystals grown by either a modified Bridgman method or by physical vapor transport. Photomodulated reflection (PR) spectroscopy was used to measure the composition dependence of optical transitions from the valence band edge and from the spin-orbit split off band to the conduction band. The pressure dependence of the band gap was measured using optical absorption in a diamond anvil cell. We find that the energy of the spin-orbit split off valence band edge does not depend on composition and is located at about 3 eV below the conduction band edge of ZnSe. On the Te-rich side the pressure and the composition dependence of the optical transitions are well explained by the BAC model which describes the downward shift of the conduction band edge in terms of the interaction between

  13. Bilayer Thickness Mismatch Controls Domain Size in Model Membranes

    SciTech Connect

    Heberle, Frederick A; Petruzielo, Robin S; Pan, Jianjun; Drazba, Paul; Kucerka, Norbert; Feigenson, Gerald; Katsaras, John

    2013-01-01

    The observation of lateral phase separation in lipid bilayers has received considerable attention, especially in connection to lipid raft phenomena in cells. It is widely accepted that rafts play a central role in cellular processes, notably signal transduction. While micrometer-sized domains are observed with some model membrane mixtures, rafts much smaller than 100 nm beyond the reach of optical microscopy are now thought to exist, both in vitro and in vivo. We have used small-angle neutron scattering, a probe free technique, to measure the size of nanoscopic membrane domains in unilamellar vesicles with unprecedented accuracy. These experiments were performed using a four-component model system containing fixed proportions of cholesterol and the saturated phospholipid 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), mixed with varying amounts of the unsaturated phospholipids 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dioleoylsn- glycero-3-phosphocholine (DOPC). We find that liquid domain size increases with the extent of acyl chain unsaturation (DOPC:POPC ratio). Furthermore, we find a direct correlation between domain size and the mismatch in bilayer thickness of the coexisting liquid-ordered and liquid-disordered phases, suggesting a dominant role for line tension in controlling domain size. While this result is expected from line tension theories, we provide the first experimental verification in free-floating bilayers. Importantly, we also find that changes in bilayer thickness, which accompany changes in the degree of lipid chain unsaturation, are entirely confined to the disordered phase. Together, these results suggest how the size of functional domains in homeothermic cells may be regulated through changes in lipid composition.

  14. Interictal lack of habituation of mismatch negativity in migraine.

    PubMed

    de Tommaso, M; Guido, M; Libro, G; Losito, L; Difruscolo, O; Sardaro, M; Puca, F M

    2004-08-01

    The aim was to study mismatch negativity features and habituation during the interictal phase of migraine. In migraine patients, a strong negative correlation has been found between the initial amplitude of long latency auditory-evoked potentials and their amplitude increase during subsequent averaging. We studied 12 outpatients with a diagnosis of migraine without aura recorded in a headache-free interval and 10 gender- and age-matched healthy volunteers not suffering from any recurrent headache. The experiment consisted of two sequential blocks of 2000 stimulations, during which 1800 (90%) recordings for standard tones and 200 (10%) for target tones were selected for averaging. The latency of the N1 component was significantly increased in migraine patients in respect of controls in both the first and second repetitions; the MMN latency was increased in the second repetition. In the control group the MMN amplitude decreased on average by 3.2 +/- 1.4 microV in the second trial, whereas in migraine patients it showed a slight increase of 0.21 +/- 0.11 microV in the second repetition. The MMN latency relieved in the second trial was significantly correlated with the duration of illness in the migraine patients (Spearman correlation coefficient: 0.69; P < 0.05). The increases in N1 latency and MMN latency and amplitude, the latter correlated with duration of illness, seemed to be due to a reduced anticipatory effect of stimulus repetition in migraine patients. This suggests that such hypo-activity of automatic cortical processes, subtending the discrimination of acoustic stimuli, may be a basic abnormality in migraine, developing in the course of the disease.

  15. MUTYH and the mismatch repair system: partners in crime?

    PubMed

    Niessen, Renée C; Sijmons, Rolf H; Ou, J; Olthof, Sandra G M; Osinga, Jan; Ligtenberg, Marjolijn J; Hogervorst, Frans B L; Weiss, Marjan M; Tops, Carli M J; Hes, Frederik J; de Bock, Geertruida H; Buys, Charles H C M; Kleibeuker, Jan H; Hofstra, Robert M W

    2006-03-01

    Biallelic germline mutations of MUTYH-a gene encoding a base excision repair protein-are associated with an increased susceptibility of colorectal cancer. Whether monoallelic MUTYH mutations also increase cancer risk is not yet clear, although there is some evidence suggesting a slight increase of risk. As the MUTYH protein interacts with the mismatch repair (MMR) system, we hypothesised that the combination of a monoallelic MUTYH mutation with an MMR gene mutation increases cancer risk. We therefore investigated the prevalence of monoallelic MUTYH mutations in carriers of a germline MMR mutation: 40 carriers of a truncating mutation (group I) and 36 of a missense mutation (group II). These patients had been diagnosed with either colorectal or endometrial cancer. We compared their MUTYH mutation frequencies with those observed in a group of 134 Dutch colorectal and endometrial cancer patients without an MMR gene mutation (0.7%) and those reported for Caucasian controls (1.5%). In group I one monoallelic MUTYH mutation was found (2.5%). In group II five monoallelic germline MUTYH mutations were found (14%), four of them in MSH6 missense mutation carriers (20%). Of all patients with an MMR gene mutation, only those with a missense mutation showed a significantly higher frequency of (monoallelic) MUTYH mutations than the Dutch cancer patients without MMR gene mutations (P = 0.002) and the published controls (P = 0.001). These results warrant further study to test the hypothesis of mutations in MMR genes (in particular MSH6) and MUTYH acting together to increase cancer risk.

  16. Mismatched racial identities, colourism, and health in Toronto and Vancouver.

    PubMed

    Veenstra, Gerry

    2011-10-01

    Using original telephone survey data collected from adult residents of Toronto (n = 685) and Vancouver (n = 814) in 2009, I investigate associations between mental and physical health and variously conceived racial identities. An 'expressed racial identity' is a self-identification with a racial grouping that a person will readily express to others when asked to fit into official racial classifications presented by Census forms, survey researchers, insurance forms, and the like. Distinguishing between Asian, Black, South Asian, and White expressed racial identities, I find that survey respondents expressing Black identity are the most likely to report high blood pressure or hypertension, a risk that is slightly attenuated by socioeconomic status, and that respondents expressing Asian identity are the most likely to report poorer self-rated mental health and self-rated overall health, risks that are not explained by socioeconomic status. I also find that darker-skinned Black respondents are more likely than lighter-skinned Black respondents to report poor health outcomes, indicating that colourism, processes of discrimination which privilege lighter-skinned people of colour over their darker-skinned counterparts, exists and has implications for well-being in Canada as it does in the United States. Finally, 'reflected racial identity' refers to the racial identity that a person believes that others tend to perceive him or her to be. I find that expressed and reflected racial identities differ from one another for large proportions of self-expressed Black and South Asian respondents and relatively few self-expressed White and Asian respondents. I also find that mismatched racial identities correspond with relatively high risks of various poor health outcomes, especially for respondents who consider themselves White but believe that others tend to think they are something else. I conclude by presenting a framework for conceptualizing multifaceted suites of racial

  17. Ventilation/perfusion mismatch during lung aeration at birth.

    PubMed

    Lang, Justin A R; Pearson, James T; te Pas, Arjan B; Wallace, Megan J; Siew, Melissa L; Kitchen, Marcus J; Fouras, Andreas; Lewis, Robert A; Wheeler, Kevin I; Polglase, Graeme R; Shirai, Mikiyasu; Sonobe, Takashi; Hooper, Stuart B

    2014-09-01

    At birth, the transition to newborn life is triggered by lung aeration, which stimulates a large increase in pulmonary blood flow (PBF). Current theories predict that the increase in PBF is spatially related to ventilated lung regions as they aerate after birth. Using simultaneous phase-contrast X-ray imaging and angiography we investigated the spatial relationships between lung aeration and the increase in PBF after birth. Six near-term (30-day gestation) rabbits were delivered by caesarean section, intubated and an intravenous catheter inserted, before they were positioned for X-ray imaging. During imaging, iodine was injected before ventilation onset, after ventilation of the right lung only, and after ventilation of both lungs. Unilateral ventilation increased iodine levels entering both left and right pulmonary arteries (PAs) and significantly increased heart rate, iodine ejection per beat, diameters of both left and right PAs, and number of visible vessels in both lungs. Within the 6th intercostal space, the mean gray level (relative measure of iodine level) increased from 68.3 ± 11.6 and 70.3 ± 7.5%·s to 136.3 ± 22.6 and 136.3 ± 23.7%·s in the left and right PAs, respectively. No differences were observed between vessels in the left and right lungs, despite the left lung not initially being ventilated. The increase in PBF at birth is not spatially related to lung aeration allowing a large ventilation/perfusion mismatch, or pulmonary shunting, to occur in the partially aerated lung at birth.

  18. Disease-associated repeat instability and mismatch repair.

    PubMed

    Schmidt, Monika H M; Pearson, Christopher E

    2016-02-01

    Expanded tandem repeat sequences in DNA are associated with at least 40 human genetic neurological, neurodegenerative, and neuromuscular diseases. Repeat expansion can occur during parent-to-offspring transmission, and arise at variable rates in specific tissues throughout the life of an affected individual. Since the ongoing somatic repeat expansions can affect disease age-of-onset, severity, and progression, targeting somatic expansion holds potential as a therapeutic target. Thus, understanding the factors that regulate this mutation is crucial. DNA repair, in particular mismatch repair (MMR), is the major driving force of disease-associated repeat expansions. In contrast to its anti-mutagenic roles, mammalian MMR curiously drives the expansion mutations of disease-associated (CAG)·(CTG) repeats. Recent advances have broadened our knowledge of both the MMR proteins involved in disease repeat expansions, including: MSH2, MSH3, MSH6, MLH1, PMS2, and MLH3, as well as the types of repeats affected by MMR, now including: (CAG)·(CTG), (CGG)·(CCG), and (GAA)·(TTC) repeats. Mutagenic slipped-DNA structures have been detected in patient tissues, and the size of the slip-out and their junction conformation can determine the involvement of MMR. Furthermore, the formation of other unusual DNA and R-loop structures is proposed to play a key role in MMR-mediated instability. A complex correlation is emerging between tissues showing varying amounts of repeat instability and MMR expression levels. Notably, naturally occurring polymorphic variants of DNA repair genes can have dramatic effects upon the levels of repeat instability, which may explain the variation in disease age-of-onset, progression and severity. An increasing grasp of these factors holds prognostic and therapeutic potential.

  19. Velocity synchronization of multi-agent systems with mismatched parameters via sampled position data.

    PubMed

    Sun, Wen; Huang, Chunli; Lü, Jinhu; Li, Xiong; Chen, Shihua

    2016-02-01

    Power systems are special multi-agent systems with nonlinear coupling function and symmetric structures. This paper extends these systems to a class of multi-agent systems with mismatched parameters, linear coupling function, and asymmetric structures and investigates their velocity synchronization via sampled position data. The dynamics of the agents is adopted as that of generators with mismatched parameters, while the system structures are supposed to be complex. Two distributed linear consensus protocols are designed, respectively, for multi-agent systems without or with communication delay. Necessary and sufficient conditions based on the sampling period, the mismatched parameters, the delay, and the nonzero eigenvalues of the Laplacian matrix are established. It is shown that velocity synchronization of multi-agent systems with mismatched parameters can be achieved if the sampled period is chosen appropriately. Simulations are given to illustrate the effectiveness of the theoretical results.

  20. A Direct Adaptive Control Approach in the Presence of Model Mismatch

    NASA Technical Reports Server (NTRS)

    Joshi, Suresh M.; Tao, Gang; Khong, Thuan

    2009-01-01

    This paper considers the problem of direct model reference adaptive control when the plant-model matching conditions are violated due to abnormal changes in the plant or incorrect knowledge of the plant's mathematical structure. The approach consists of direct adaptation of state feedback gains for state tracking, and simultaneous estimation of the plant-model mismatch. Because of the mismatch, the plant can no longer track the state of the original reference model, but may be able to track a new reference model that still provides satisfactory performance. The reference model is updated if the estimated plant-model mismatch exceeds a bound that is determined via robust stability and/or performance criteria. The resulting controller is a hybrid direct-indirect adaptive controller that offers asymptotic state tracking in the presence of plant-model mismatch as well as parameter deviations.

  1. Effects of electrode array length on frequency-place mismatch and speech perception with cochlear implants.

    PubMed

    Venail, Frederic; Mathiolon, Caroline; Menjot de Champfleur, Sophie; Piron, Jean Pierre; Sicard, Marielle; Villemus, Françoise; Vessigaud, Marie Aude; Sterkers-Artieres, Françoise; Mondain, Michel; Uziel, Alain

    2015-01-01

    Frequency-place mismatch often occurs after cochlear implantation, yet its effect on speech perception outcome remains unclear. In this article, we propose a method, based on cochlea imaging, to determine the cochlear place-frequency map. We evaluated the effect of frequency-place mismatch on speech perception outcome in subjects implanted with 3 different lengths of electrode arrays. A deeper insertion was responsible for a larger frequency-place mismatch and a decreased and delayed speech perception improvement by comparison with a shallower insertion, for which a similar but slighter effect was noticed. Our results support the notion that selecting an electrode array length adapted to each individual's cochlear anatomy may reduce frequency-place mismatch and thus improve speech perception outcome.

  2. New Spectral Method for Halo Particle Definition in Intense Mis-matched Beams

    SciTech Connect

    Dorf, Mikhail A.; Davidson, Ronald C.; Startsev, Edward A.

    2011-04-27

    An advanced spectral analysis of a mis-matched charged particle beam propagating through a periodic focusing transport lattice is utilized in particle-in-cell (PIC) simulations. It is found that the betatron frequency distribution function of a mismatched space-charge-dominated beam has a bump-on-tail structure attributed to the beam halo particles. Based on this observation, a new spectral method for halo particle definition is proposed that provides the opportunity to carry out a quantitative analysis of halo particle production by a beam mismatch. In addition, it is shown that the spectral analysis of the mismatch relaxation process provides important insights into the emittance growth attributed to the halo formation and the core relaxation processes. Finally, the spectral method is applied to the problem of space-charge transport limits.

  3. Human errors are symptoms of a mismatch between pilots, machines and the operating environment.

    PubMed

    Sarter, N B

    1996-10-01

    The author suggests that errors should be the starting point for analysis of aviation mishaps. The analysis should focus on human, automation, and environment interaction and determine any mismatch among these factors.

  4. A spectral method for halo particle definition in intense mismatched beams

    SciTech Connect

    Dorf, Mikhail A.; Davidson, Ronald C.; Startsev, Edward A.

    2011-04-15

    An advanced spectral analysis of a mismatched charged particle beam propagating through a periodic focusing transport lattice is utilized in particle-in-cell (PIC) simulations. It is found that the betatron frequency distribution function of a mismatched space-charge-dominated beam has a bump-on-tail structure attributed to the beam halo particles. Based on this observation, a new spectral method for halo particle definition is proposed that provides the opportunity to carry out a quantitative analysis of halo particle production by a beam mismatch. In addition, it is shown that the spectral analysis of the mismatch relaxation process provides important insights into the emittance growth attributed to the halo formation and the core relaxation processes. Finally, the spectral method is applied to the problem of space-charge transport limits.

  5. Patient - implant dimension mismatch in total knee arthroplasty: Is it worth worrying? An Indian scenario

    PubMed Central

    Thilak, Jai; George, Melvin J

    2016-01-01

    Background: The correct sizing of the components in both anteroposterior and mediolateral (ML) dimensions is crucial for the success of a total knee arthroplasty (TKA). The size of the implants selected is based on the intraoperative measurements. The currently used TKA implants available to us are based on morphometric measurements obtained from a Western/Caucasian population. Hence, the risk of component ML mismatch is more common in Asian sub-population, as they are of a smaller built and stature. This study aims to look into the following aspects agnitude of the ML mismatch between the femoral component and the patient's anatomical dimension, evaluation of gender variations in distal femur dimensions, and gender-wise and implant-wise correlation of ML mismatch. Materials and Methods: Intraoperatively, the distal femoral dimensions were measured using sterile calipers after removing the osteophytes and compared with the ML dimension of the implant used. ML mismatch length thus obtained is correlated with the various parameters. Results: Males showed larger distal femoral dimensions when compared to females. Males had larger ML mismatch. None of the implants used perfectly matched the patient's anatomical dimensions. Patients with larger mismatch had lower scorings at 2 years postoperative followup. Conclusion: Implant manufacturers need to design more options of femoral implants for a better fit in our subset of patients. The exact magnitude of mismatch which can cause functional implications need to be made out. The mismatch being one of the important factors for the success of the surgery, we should focus more on this aspect. PMID:27746494

  6. The incidence and etiology of the ventilation/perfusion reverse mismatch defect

    SciTech Connect

    Carvalho, P.; Lavender, J.P. )

    1989-08-01

    Kr-81m ventilation and Tc-99m perfusion images of 392 patients were examined retrospectively for the incidence and etiology of the reverse mismatch defect, which is characterized by a region of lung where the perfusion defect exceeds the ventilation defect. Forty-six patients (11.7%) showed such defects. The most frequent causes were pneumonia (15%), atelactasis (15%), pleural effusions (15%), chronic obstructive airway disease (24%), and bronchial obstruction (31%). The significance of the reverse mismatch defect is discussed.

  7. Detecting mismatches of bird migration stopover and tree phenology in response to changing climate.

    PubMed

    Kellermann, Jherime L; van Riper, Charles

    2015-08-01

    Migratory birds exploit seasonal variation in resources across latitudes, timing migration to coincide with the phenology of food at stopover sites. Differential responses to climate in phenology across trophic levels can result in phenological mismatch; however, detecting mismatch is sensitive to methodology. We examined patterns of migrant abundance and tree flowering, phenological mismatch, and the influence of climate during spring migration from 2009 to 2011 across five habitat types of the Madrean Sky Islands in southeastern Arizona, USA. We used two metrics to assess phenological mismatch: synchrony and overlap. We also examined whether phenological overlap declined with increasing difference in mean event date of phenophases. Migrant abundance and tree flowering generally increased with minimum spring temperature but depended on annual climate by habitat interactions. Migrant abundance was lowest and flowering was highest under cold, snowy conditions in high elevation montane conifer habitat while bird abundance was greatest and flowering was lowest in low elevation riparian habitat under the driest conditions. Phenological synchrony and overlap were unique and complementary metrics and should both be used when assessing mismatch. Overlap declined due to asynchronous phenologies but also due to reduced migrant abundance or flowering when synchrony was actually maintained. Overlap declined with increasing difference in event date and this trend was strongest in riparian areas. Montane habitat specialists may be at greatest risk of mismatch while riparian habitat could provide refugia during dry years for phenotypically plastic species. Interannual climate patterns that we observed match climate change projections for the arid southwest, altering stopover habitat condition.

  8. Detecting mismatches of bird migration stopover and tree phenology in response to changing climate

    USGS Publications Warehouse

    Kellermann, Jherime L.; Van Riper, Charles

    2015-01-01

    Migratory birds exploit seasonal variation in resources across latitudes, timing migration to coincide with the phenology of food at stopover sites. Differential responses to climate in phenology across trophic levels can result in phenological mismatch; however, detecting mismatch is sensitive to methodology. We examined patterns of migrant abundance and tree flowering, phenological mismatch, and the influence of climate during spring migration from 2009 to 2011 across five habitat types of the Madrean Sky Islands in southeastern Arizona, USA. We used two metrics to assess phenological mismatch: synchrony and overlap. We also examined whether phenological overlap declined with increasing difference in mean event date of phenophases. Migrant abundance and tree flowering generally increased with minimum spring temperature but depended on annual climate by habitat interactions. Migrant abundance was lowest and flowering was highest under cold, snowy conditions in high elevation montane conifer habitat while bird abundance was greatest and flowering was lowest in low elevation riparian habitat under the driest conditions. Phenological synchrony and overlap were unique and complementary metrics and should both be used when assessing mismatch. Overlap declined due to asynchronous phenologies but also due to reduced migrant abundance or flowering when synchrony was actually maintained. Overlap declined with increasing difference in event date and this trend was strongest in riparian areas. Montane habitat specialists may be at greatest risk of mismatch while riparian habitat could provide refugia during dry years for phenotypically plastic species. Interannual climate patterns that we observed match climate change projections for the arid southwest, altering stopover habitat condition.

  9. Mismatch repair regulates homologous recombination, but has little influence on antigenic variation, in Trypanosoma brucei.

    PubMed

    Bell, Joanna S; McCulloch, Richard

    2003-11-14

    Antigenic variation is critical in the life of the African trypanosome, as it allows the parasite to survive in the face of host immunity and enhance its transmission to other hosts. Much of trypanosome antigenic variation uses homologous recombination of variant surface glycoprotein (VSG)-encoding genes into specialized transcription sites, but little is known about the processes that regulate it. Here we describe the effects on VSG switching when two central mismatch repair genes, MSH2 and MLH1, are mutated. We show that disruption of the parasite mismatch repair system causes an increased frequency of homologous recombination, both between perfectly matched DNA molecules and between DNA molecules with divergent sequences. Mismatch repair therefore provides an important regulatory role in homologous recombination in this ancient eukaryote. Despite this, the mismatch repair system has no detectable role in regulating antigenic variation, meaning that VSG switching is either immune to mismatch selection or that mismatch repair acts in a subtle manner, undetectable by current assays.

  10. Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence

    PubMed Central

    Zheng, Ting; Hou, Yingzi; Zhang, Pingjing; Zhang, Zhenxi; Xu, Ying; Zhang, Letian; Niu, Leilei; Yang, Yi; Liang, Da; Yi, Fan; Peng, Wei; Feng, Wenjian; Yang, Ying; Chen, Jianxin; Zhu, York Yuanyuan; Zhang, Li-He; Du, Quan

    2017-01-01

    Targeting specificity is an essential issue in the development of CRISPR-Cas technology. Using a luciferase activation assay, off-target cleavage activity of sgRNA was systematically investigated on single nucleotide-mismatched targets. In addition to confirming that PAM-proximal mismatches are less tolerated than PAM-distal mismatches, our study further identified a “core” sequence that is highly sensitive to target-mismatch. This sequence is of 4-nucleotide long, located at +4 to +7 position upstream of PAM, and positioned in a steric restriction region when assembled into Cas9 endonuclease. Our study also found that, single or multiple target mismatches at this region abolished off-target cleavage mediated by active sgRNAs, thus proposing a principle for gene-specific sgRNA design. Characterization of a mismatch sensitive “core” sequence not only enhances our understanding of how this elegant system functions, but also facilitates our efforts to improve targeting specificity of a sgRNA. PMID:28098181

  11. Brain activity from stimuli that are not perceived: Visual mismatch negativity during binocular rivalry suppression.

    PubMed

    Jack, Bradley N; Widmann, Andreas; O'Shea, Robert P; Schröger, Erich; Roeber, Urte

    2017-02-20

    Predictive coding explains visual perception as the result of an interaction between bottom-up sensory input and top-down generative models at each level of the visual hierarchy. Evidence for this comes from the visual mismatch negativity (vMMN): a more negative ERP for rare, unpredictable visual stimuli-deviants, than for frequent, predictable visual stimuli-standards. Here, we show that the vMMN does not require conscious experience. We measured the vMMN from monocular luminance-decrement deviants that were either perceived or not during binocular rivalry dominance or suppression, respectively. We found that both sorts of deviants elicited the vMMN at about 250 ms after stimulus onset, with perceived deviants eliciting a bigger vMMN than not-perceived deviants. These results show that vMMN occurs in the absence of consciousness, and that consciousness enhances the processing underlying vMMN. We conclude that generative models of visual perception are tested, even when sensory input for those models is not perceived.

  12. Lattice-mismatched phosphide-based LEDs for color mixing white light applications

    NASA Astrophysics Data System (ADS)

    Alberi, Kirstin

    2011-03-01

    The most promising means of achieving high efficiency white light emitting diodes (LEDs) with high color rendering indices (CRI) is to combine individual red (615 nm), yellow (573 nm), green (535 nm) and blue (459 nm) solid-state LEDs in a four color RYGB architecture. Due to their high bandgaps and the availability of bulk substrates, phosphide-based alloys are currently leading candidates for achieving the longer wavelengths, of which AlGaInP lattice-matched to GaAs has been extensively explored. In a departure from this approach, we investigate phosphide alloys at compositions that are lattice-mismatched with respect to GaAs for color mixing white light applications. Lifting the lattice-matching requirement extends the options for active and cladding layer design and optimization, thereby providing additional avenues for reducing carrier loss pathways and improving device efficiency. This talk covers our work on issues central to the success of this technology: metamorphic growth of high quality epilayers, the competing trade-off between operating wavelength and intervalley carrier transfer loss, and the availability of optimal cladding layers for high power operation. Support from the DOE EERE-SSL and BES-DMS programs and the ~LDRD program at NREL is gratefully acknowledged.

  13. Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases.

    PubMed

    Vouillot, Léna; Thélie, Aurore; Pollet, Nicolas

    2015-01-07

    Genome editing using engineered nucleases is used for targeted mutagenesis. But because genome editing does not target all loci with similar efficiencies, the mutation hit-rate at a given locus needs to be evaluated. The analysis of mutants obtained using engineered nucleases requires specific methods for mutation detection, and the enzyme mismatch cleavage method is used commonly for this purpose. This method uses enzymes that cleave heteroduplex DNA at mismatches and extrahelical loops formed by single or multiple nucleotides. Bacteriophage resolvases and single-stranded nucleases are used commonly in the assay but have not been compared side-by-side on mutations obtained by engineered nucleases. We present the first comparison of the sensitivity of T7E1 and Surveyor EMC assays on deletions and point mutations obtained by zinc finger nuclease targeting in frog embryos. We report the mutation detection limits and efficiencies of T7E1 and Surveyor. In addition, we find that T7E1 outperforms the Surveyor nuclease in terms of sensitivity with deletion substrates, whereas Surveyor is better for detecting single nucleotide changes. We conclude that T7E1 is the preferred enzyme to scan mutations triggered by engineered nucleases.

  14. Comparison of T7E1 and Surveyor Mismatch Cleavage Assays to Detect Mutations Triggered by Engineered Nucleases

    PubMed Central

    Vouillot, Léna; Thélie, Aurore; Pollet, Nicolas

    2015-01-01

    Genome editing using engineered nucleases is used for targeted mutagenesis. But because genome editing does not target all loci with similar efficiencies, the mutation hit-rate at a given locus needs to be evaluated. The analysis of mutants obtained using engineered nucleases requires specific methods for mutation detection, and the enzyme mismatch cleavage method is used commonly for this purpose. This method uses enzymes that cleave heteroduplex DNA at mismatches and extrahelical loops formed by single or multiple nucleotides. Bacteriophage resolvases and single-stranded nucleases are used commonly in the assay but have not been compared side-by-side on mutations obtained by engineered nucleases. We present the first comparison of the sensitivity of T7E1 and Surveyor EMC assays on deletions and point mutations obtained by zinc finger nuclease targeting in frog embryos. We report the mutation detection limits and efficiencies of T7E1 and Surveyor. In addition, we find that T7E1 outperforms the Surveyor nuclease in terms of sensitivity with deletion substrates, whereas Surveyor is better for detecting single nucleotide changes. We conclude that T7E1 is the preferred enzyme to scan mutations triggered by engineered nucleases. PMID:25566793

  15. Lattice-mismatched In(0.40)Al(0.60)As window layers for indium phosphide solar cells

    NASA Technical Reports Server (NTRS)

    Jain, Raj K.; Landis, Geoffrey A.; Wilt, David M.; Flood, Dennis J.

    1993-01-01

    The efficiency of indium phosphide (InP) solar cells is limited by its high surface recombination velocity (approximately 10(exp 7) cm/s). This might be reduced by a wide-bandgap window layer. The performance of InP solar cells with wide-bandgap (1.8 eV) lattice-mismatched In(0.40)Al(0.60)As as a window layer was calculated. Because the required window layer thickness is less than the critical layer thickness, growth of strained (pseudomorphic) layers without interfacial misfit dislocations should be possible. Calculations using the PC-lD numerical code showed that the efficiencies of baseline and optimized p(+)n (p-on-n) cells are increased to more than 22 and 24 percent, (air mass zero (AMO), 25 C), respectively for a lattice-mismatched In(0.40)Al(0.60)As window layer of 10-nm thickness. Currently, most cell development work has been focused on n(+)p (n-on-p) structures although comparatively little improvement has been found for n(+)p cells.

  16. Pure Red Cell Aplasia in Major ABO-Mismatched Allogeneic Hematopoietic Stem Cell Transplantation Is Associated with Severe Pancytopenia.

    PubMed

    Aung, Fleur M; Lichtiger, Benjamin; Rondon, Gabriela; Yin, C Cameron; Alousi, Amin; Ahmed, Sairah; Andersson, Borje S; Bashir, Qaiser; Ciurea, Stefan O; Hosing, Chitra; Jones, Roy; Kebriaei, Partow; Khouri, Issa; Nieto, Yago; Oran, Betul; Parmar, Simrit; Qazilbash, Muzaffar; Shah, Nina; Shpall, Elizabeth J; Champlin, Richard E; Popat, Uday

    2016-05-01

    In major ABO-mismatched allogeneic hematopoietic stem cell transplantation (HSCT) persistence of antidonor isohemagglutinins leads to pure red cell aplasia (PRCA). To investigate severe pancytopenia noted in a previous study of PRCA, we analyzed all major ABO-mismatched HSCT between January 2003 and December 2012. Of 83 PRCA patients, 13 (16%) had severe pancytopenia. Severe pancytopenia was defined as an absolute neutrophil count (ANC) < 1.5 K/μL or requiring granulocyte colony-stimulating factor, platelets < 50 K/μL or transfusion dependent, and PRCA with RBC transfusion dependence at post-transplant day 90. In 6 patients (46%) severe pancytopenia resolved after PRCA resolution. Two patients (15%) received a second transplant because of persistent pancytopenia/secondary graft failure, 1 (8%) died from secondary graft failure despite a stem cell boost, 1 (8%) did not recover his platelet counts despite RBC/ANC recovery, and 3 patients (23%) died from disease relapse. We found that severe pancytopenia is frequently associated with PRCA in 16% of major ABO-incompatible HSCT with a higher incidence in males and pancytopenia resolved with resolution of PRCA in 46% of patients.

  17. Impact of Slow Blood Filling via Collaterals on Infarct Growth: Comparison of Mismatch and Collateral Status

    PubMed Central

    Son, Jeong Pyo; Lee, Mi Ji; Kim, Suk Jae; Chung, Jong-Won; Cha, Jihoon; Kim, Gyeong-Moon; Chung, Chin-Sang; Lee, Kwang Ho; Bang, Oh Young

    2017-01-01

    Background and Purpose Perfusion-diffusion mismatch has been evaluated to determine whether the presence of a target mismatch helps to identify patients who respond favorably to recanalization therapies. We compared the impact on infarct growth of collateral status and the presence of a penumbra, using magnetic resonance perfusion (MRP) techniques. Methods Consecutive patients who were candidates for recanalization therapy and underwent serial diffusion-weighted imaging (DWI) and MRP were enrolled. A collateral flow map derived from MRP source data was generated by automatic post-processing. The impact of a target mismatch (Tmax>6 s/apparent diffusion coefficient (ADC) volume≥1.8, ADC volume<70 mL; and Tmax>10 s for ADC volume<100 mL) on infarct growth was compared with MR-based collateral grading on day 7 DWI, using multivariate linear regression analysis. Results Among 73 patients, 55 (75%) showed a target mismatch, whereas collaterals were poor in 14 (19.2%), intermediate in 36 (49.3%), and good in 23 (31.5%) patients. After adjusting for initial severity of stroke, early recanalization (P<0.001) and the MR-based collateral grading (P=0.001), but not the presence of a target mismatch, were independently associated with infarct growth. Even in patients with a target mismatch and successful recanalization, the degree of infarct growth depended on the collateral status. Perfusion status at later Tmax time points (beyond the arterial phase) was more closely correlated with collateral status. Conclusions Patients with good collaterals show a favorable outcome in terms of infarct growth, regardless of the presence of a target mismatch pattern. The presence of slow blood filling predicts collateral status and infarct growth. PMID:28030891

  18. Formation of the BiAg2 surface alloy on lattice-mismatched interfaces

    NASA Astrophysics Data System (ADS)

    Abd El-Fattah, Z. M.; Lutz, P.; Piquero-Zulaica, I.; Lobo-Checa, J.; Schiller, F.; Bentmann, H.; Ortega, J. E.; Reinert, F.

    2016-10-01

    We report on the growth of a monolayer-thick BiAg2 surface alloy on thin Ag films grown on Pt(111) and Cu(111). Using low energy electron diffraction (LEED), angle resolved photoemission spectroscopy (ARPES), and scanning tunneling microscopy (STM) we show that the surface structure of the 1/3 ML Bi/x -ML Ag/Pt(111) system (x ≥2 ) is strongly affected by the annealing temperature required to form the alloy. As judged from the characteristic (√{3 }×√{3 } )R 30∘ LEED pattern, the BiAg2 alloy is partially formed at room temperature. A gentle, gradual increase in the annealing temperatures successively results in the formation of a pure BiAg2 phase, a combination of that phase with a (2 ×2 ) superstructure, and finally the pure (2 ×2 ) phase, which persists at higher annealing temperatures. These results complement recent work reporting the (2 ×2 ) as a predominant phase, and attributing the absence of BiAg2 alloy to the strained Ag/Pt interface. Likewise, we show that the growth of the BiAg2 alloy on similarly lattice-mismatched 1 and 2 ML Ag-Cu(111) interfaces also requires a low annealing temperature, whilst higher temperatures result in BiAg2 clustering and the formation of a BiCu2 alloy. The demonstration that the BiAg2 alloy can be formed on thin Ag films on different substrates presenting a strained interface has the prospect of serving as bases for technologically relevant systems, such as Rashba alloys interfaced with magnetic and semiconductor substrates.

  19. Overeducation and Educational-Occupational Mismatch: A Distinguishing Integration

    ERIC Educational Resources Information Center

    Moore, Sharon; Rosenbloom, Tova

    2016-01-01

    This article accounts for a renovation by enriching the existent literature regarding two major nowadays phenomena and their labor implications, which might require a rethinking regarding new career-development approaches: the overeducation phenomenon (academic graduates whose educational level exceeds the educational level required in their jobs)…

  20. Fibroblast growth factor-1 stimulation of quiescent NIH 3T3 cells increases G/T mismatch-binding protein expression.

    PubMed Central

    Donohue, P J; Feng, S L; Alberts, G F; Guo, Y; Peifley, K A; Hsu, D K; Winkles, J A

    1996-01-01

    Polypeptide growth factors promote cell-cycle progression in part by the transcriptional activation of a diverse group of specific genes. We have used an mRNA differential-display approach to identify several fibroblast growth factor (FGF)-1 (acidic FGF)-inducible genes in NIH 3T3 cells. Here we report that one of these genes, called FGF-regulated (FR)-3, is predicted to encode G/T mismatch-binding protein (GTBP), a component of the mammalian DNA mismatch correction system. The murine GTBP gene is transiently expressed after FGF-1 or calf serum treatment, with maximal mRNA levels detected at 12 and 18 h post-stimulation. FGF-1-stimulated NIH 3T3 cells also express an increased amount of GTBP as determined by immunoblot analysis. These results indicate that elevated levels of GTBP may be required during the DNA synthesis phase of the cell cycle for efficient G/T mismatch recognition and repair. PMID:8870641

  1. MSH-MLH complexes formed at a DNA mismatch are disrupted by the PCNA sliding clamp.

    PubMed

    Bowers, J; Tran, P T; Joshi, A; Liskay, R M; Alani, E

    2001-03-09

    In the yeast Saccharomyces cerevisiae, mismatch repair (MMR) is initiated by the binding of heterodimeric MutS homolog (MSH) complexes to mismatches that include single nucleotide and loop insertion/deletion mispairs. In in vitro experiments, the mismatch binding specificity of the MSH2-MSH6 heterodimer is eliminated if ATP is present. However, addition of the MutL homolog complex MLH1-PMS1 to binding reactions containing MSH2-MSH6, ATP, and mismatched substrate results in the formation of a stable ternary complex. The stability of this complex suggests that it represents an intermediate in MMR that is subsequently acted upon by other MMR factors. In support of this idea, we found that the replication processivity factor proliferating cell nuclear antigen (PCNA), which plays a critical role in MMR at step(s) prior to DNA resynthesis, disrupted preformed ternary complexes. These observations, in conjunction with experiments performed with streptavidin end-blocked mismatch substrates, suggested that PCNA interacts with an MSH-MLH complex formed on DNA mispairs.

  2. Role of energy-level mismatches in a multi-pathway complex of photosynthesis

    NASA Astrophysics Data System (ADS)

    Lim, James; Ryu, Junghee; Lee, Changhyoup; Yoo, Seokwon; Jeong, Hyunseok; Lee, Jinhyoung

    2011-10-01

    Considering a multi-pathway structure in a light-harvesting complex of photosynthesis, we investigated the role of energy-level mismatches between antenna molecules in transferring the absorbed energy to a reaction center (RC). We found a condition in which the antenna molecules faithfully play their roles: when their effective absorption ratios are larger than those of the receiver molecule directly coupled to the RC. In the absence of energy-level mismatches and dephasing noise, there arises quantum destructive interference between multiple paths that restricts the energy transfer. On the other hand, the destructive interference diminishes as asymmetrically biasing the energy-level mismatches and/or introducing quantum noise of dephasing for the antenna molecules, so that the transfer efficiency is greatly enhanced to nearly unity. Remarkably, the near-unity efficiency can be achieved at a wide range of asymmetric energy-level mismatches. Temporal characteristics are also optimized at the energy-level mismatches where the transfer efficiency is nearly unity. We discuss these effects, in particular, for the Fenna-Matthews-Olson complex.

  3. Assessing mismatches between ecosystem structure and function in Jiaozhou Bay by coordination degree algorithm

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoyan; Gao, Huiwang; Chen, Zhenhua; Yao, Xiaohong; Sun, Peng

    2017-04-01

    A healthy ecosystem depends on the coordination of ecosystem structure and function. The coordination among ecosystem components, however, is seldom taken into account in current ecosystem health assessments (EHA). Neglect of such coordination may lead to large degrees of uncertainty in EHA and fail to support ecosystem management. We propose an approach to quantify the level of dynamic mismatching between ecosystem structure and function and the impact on ecosystem health by incorporating the ecosystem coordination index into EHA. The coordination degree is calculated using variation coefficient of six proxies for ecosystem structure and functions. The ecosystem at Jiaozhou Bay, as a microcosm of China's coast, has been documented to fluctuate from healthy to unhealthy status over the past three decades. The results indicate that there is a 3%-17% lower health level than that calculated by common methods used in the literature, indicating that the health of Jiaozhou Bay has become worse than expected. Habitat change contributes 20%-52% to ecosystem mismatches and is the most uncoordinated factor. Mismatch-related declines account for approximately one-fourth of the total ecological declines. Restoration scenarios that aim to resolve ecosystem mismatches could increase efficiency by about 50% compared to restoration scenarios that do not consider mismatches. This study investigates ecological declines in a coastal bay due to 30 years of rapid economic development. In doing so, this study provides novel insights and enhances our understanding of the reasons for failure in ecological restoration.

  4. A P300 brain-computer interface based on a modification of the mismatch negativity paradigm.

    PubMed

    Jin, Jing; Sellers, Eric W; Zhou, Sijie; Zhang, Yu; Wang, Xingyu; Cichocki, Andrzej

    2015-05-01

    The P300-based brain-computer interface (BCI) is an extension of the oddball paradigm, and can facilitate communication for people with severe neuromuscular disorders. It has been shown that, in addition to the P300, other event-related potential (ERP) components have been shown to contribute to successful operation of the P300 BCI. Incorporating these components into the classification algorithm can improve the classification accuracy and information transfer rate (ITR). In this paper, a single character presentation paradigm was compared to a presentation paradigm that is based on the visual mismatch negativity. The mismatch negativity paradigm showed significantly higher classification accuracy and ITRs than a single character presentation paradigm. In addition, the mismatch paradigm elicited larger N200 and N400 components than the single character paradigm. The components elicited by the presentation method were consistent with what would be expected from a mismatch paradigm and a typical P300 was also observed. The results show that increasing the signal-to-noise ratio by increasing the amplitude of ERP components can significantly improve BCI speed and accuracy. The mismatch presentation paradigm may be considered a viable option to the traditional P300 BCI paradigm.

  5. Saturation of DNA mismatch repair and error catastrophe by a base analogue in Escherichia coli.

    PubMed Central

    Negishi, Kazuo; Loakes, David; Schaaper, Roel M

    2002-01-01

    Deoxyribosyl-dihydropyrimido[4,5-c][1,2]oxazin-7-one (dP) is a potent mutagenic deoxycytidine-derived base analogue capable of pairing with both A and G, thereby causing G. C --> A. T and A. T --> G. C transition mutations. We have found that the Escherichia coli DNA mismatch-repair system can protect cells against this mutagenic action. At a low dose, dP is much more mutagenic in mismatch-repair-defective mutH, mutL, and mutS strains than in a wild-type strain. At higher doses, the difference between the wild-type and the mutator strains becomes small, indicative of saturation of mismatch repair. Introduction of a plasmid containing the E. coli mutL(+) gene significantly reduces dP-induced mutagenesis. Together, the results indicate that the mismatch-repair system can remove dP-induced replication errors, but that its capacity to remove dP-containing mismatches can readily be saturated. When cells are cultured at high dP concentration, mutant frequencies reach exceptionally high levels and viable cell counts are reduced. The observations are consistent with a hypothesis in which dP-induced cell killing and growth impairment result from excess mutations (error catastrophe), as previously observed spontaneously in proofreading-deficient mutD (dnaQ) strains. PMID:12196386

  6. Is ABO mismatch another risk factor for allogeneic hematopoietic stem cell transplantation in pediatric thalassemic patients?

    PubMed

    Atay, Didem; Erbey, Fatih; Akcay, Arzu; Ozturk, Gulyuz

    2015-09-01

    The ABO incompatibility between donor and recipient is not considered a barrier to successful allogeneic HSCT. Nevertheless, conflicting data still exist about the influence of ABO incompatibility on transplant outcome in pediatric patients with thalassemia. Fifty-one children with beta-thalassemia major who underwent allogeneic HSCT were enrolled this study. Twenty-three of them (45%) received an ABO-incompatible transplant [minor ABO mismatch: six (26%), major ABO mismatch: fourteen (61%), and bidirectional mismatch: three (13%)]. In this study, ABO incompatibility did not significantly impair GVHD, VOD, neutrophil and platelet engraftment, TRM, OS and TFS. Particularly in major and bidirectional ABO-mismatched patients, a delayed erythroid recovery was recorded as compared to the group receiving an ABO-compatible graft (median time, 31 and 38 days vs. 19.5 days; p: 0.02 and p: 0.03). Median time to red cell transfusion independence was significantly longer in major ABO-incompatible patients (median time, 87 days vs. 32 days; p: 0.001). Therefore, whenever feasible, major ABO-mismatched donors should be avoided in HSCT recipients, to prevent delayed erythroid recovery with prolonged RBC transfusion needs and impaired quality of life.

  7. Significance of single ventilation/perfusion mismatches in krypton-81m/technetium-99m lung scintigraphy

    SciTech Connect

    Rosen, J.M.; Palestro, C.J.; Markowitz, D.; Alderson, P.O.

    1986-03-01

    The significance of a single area of ventilation/perfusion (V/P) mismatch in lung scans performed on patients suspected of pulmonary embolism (PE) was evaluated. Ten of 20 patients with this scan finding were found to have PE. An intermediate probability of PE was found with segmental (71%) or subsegmental (45%) single V/P mismatches. Seven of 16 patients with a single V/P mismatch and without a matching radiographic opacity had PE. Three of the four patients who had a V/P mismatch and a matching radiographic opacity were found to have PE. Multiview ventilation imaging with 81mKr was found to have advantages for the evaluation of single V/P mismatches. Based on the data available at this time, a single V/P mismatch suggests an intermediate probability of PE.

  8. MRD detection of leukemia relapse using HLA typing by FACS in combination with FISH after mismatched allogeneic stem cell transplantation.

    PubMed

    Miyachi, Mitsuru; Watanabe, Eri; Watanabe, Nobukazu; Tsuma, Yusuke; Kawashima-Goto, Sachiko; Tamura, Shinichi; Imamura, Toshihiko; Ishida, Hiroyuki; Hosoi, Hajime

    2014-08-01

    Loss of mismatched HLA is a cause of relapse following HLA-mismatched allo-SCT. We directly detected the loss of mismatched HLA alleles in relapsed leukemic cells at a MRD level using HLA typing by multicolor FACS (HLA-Flow) in combination with FISH in the BM of two patients with MLL-AF9-positive AML, at 6 and 10 months after mismatched allo-SCT. HLA-Flow with FISH analysis detected relapsed leukemic cells not expressing a mismatched HLA allele and harboring the MLL rearrangement. Simultaneously, real-time quantitative RT-PCR detected a low copy number of MLL-AF9 transcripts, consistent with MRD detection. HLA-Flow with FISH is a powerful method for detecting molecular relapse after mismatched allo-SCT and provides important information on the HLA expression status of the relapsed leukemic cells to help determine the next intervention.

  9. Feature versus gestalt representation of stimuli in the mismatch negativity system of 7- to 9-year-old children.

    PubMed

    Molholm, Sophie; Gomes, Hilary; Lobosco, Jacqueline; Deacon, Diana; Ritter, Walter

    2004-05-01

    We examined preattentive auditory change detection in 7- to 9-year-old children. The question of interest was whether the preattentive comparison of stimuli indexed by the scalp-recorded mismatch negativity (MMN) was performed on representations of individual stimulus features or on gestalt representations of their combined attributes. The design of the study, based on a work by D. Deacon, J. Nousak, M. Pilotti, W. Ritter, and C. Yang (Psychophysiology, 1998), was such that both feature and gestalt representations could have been available to the comparator mechanism generating the MMN. The data indicated that for the majority of the children-those that exhibited an inverse relationship between the amplitude of the MMN and the probability of the deviant-the MMN was based on feature-specific information. This study also provides a method to obtain MMNs to deviants in three different features in the time usually required to obtain an MMN to a single acoustic feature.

  10. Mismatch repair of heteroduplex DNA intermediates of extrachromosomal recombination in mammalian cells.

    PubMed Central

    Deng, W P; Nickoloff, J A

    1994-01-01

    Previous work indicated that extrachromosomal recombination in mammalian cells could be explained by the single-strand annealing (SSA) model. This model predicts that extrachromosomal recombination leads to nonconservative crossover products and that heteroduplex DNA (hDNA) is formed by annealing of complementary single strands. Mismatched bases in hDNA may subsequently be repaired to wild-type or mutant sequences, or they may remain unrepaired and segregate following DNA replication. We describe a system to examine the formation and mismatch repair of hDNA in recombination intermediates. Our results are consistent with extrachromosomal recombination occurring via SSA and producing crossover recombinant products. As predicted by the SSA model, hDNA was present in double-strand break-induced recombination intermediates. By placing either silent or frameshift mutations in the predicted hDNA region, we have shown that mismatches are efficiently repaired prior to DNA replication. Images PMID:8264607

  11. Daytime Locations in Spatial Mismatch: Job Accessibility and Employment at Reentry From Prison.

    PubMed

    Sugie, Naomi F; Lens, Michael C

    2017-04-01

    Individuals recently released from prison confront many barriers to employment. One potential obstacle is spatial mismatch-the concentration of low-skilled, nonwhite job-seekers within central cities and the prevalence of relevant job opportunities in outlying areas. Prior research has found mixed results about the importance of residential place for reentry outcomes. In this article, we propose that residential location matters for finding work, but this largely static measure does not capture the range of geographic contexts that individuals inhabit throughout the day. We combine novel, real-time GPS information on daytime locations and self-reported employment collected from smartphones with sophisticated measures of job accessibility to test the relative importance of spatial mismatch based on residence and daytime locations. Our findings suggest that the ability of low-skilled, poor, and urban individuals to compensate for their residential deficits by traveling to job-rich areas is an overlooked and salient consideration in spatial mismatch perspectives.

  12. Poorly repaired mismatches in heteroduplex DNA are hyper-recombinagenic in Saccharomyces cerevisiae

    SciTech Connect

    Manivasakam, P.; Hastings, P.J.; Rosenberg, S.M.

    1996-02-01

    In yeast meiotic recombination, alleles used as genetic markers fall into two classes as regards their fate when incorporated into heteroduplex DNA. Normal alleles are those that form heteroduplexes that are nearly always recognized and corrected by the mismatch repair system operating in meiosis. High PMS (postmeiotic segregation) alleles form heteroduplexes that are inefficiently mismatch repaired. We propose that this hyperrecombination is caused by the high PMS allele blocking a mismatch repair tract initiated from the normal allele, thus preventing corepair of the two alleles, which would prevent formation of recombinants. The results of three point crosses involving two PMS alleles and a normal allele suggest that high PMS alleles placed between two alleles that are normally corepaired block that corepair. 30 refs., 7 figs., 3 tabs.

  13. Manufacturer-provided effective orifice area index charts and the prevention of prosthesis-patient mismatch.

    PubMed

    House, Chad M; Nelson, William B; Kroshus, Timothy J; Dahiya, Ranjan; Pibarot, Philippe

    2012-01-01

    Prosthesis-patient mismatch (PPM) occurs when an implanted prosthesis is too small relative to the patient's body surface area (BSA). However, mismatch can often be prevented by indexing the expected effective orifice area (EOA) of a prosthesis to the patient's BSA and then selecting the largest implantable prosthesis to avoid mismatch. Previously, prosthesis manufacturers have attempted to simplify this process by providing charts that include the expected EOA for their prosthesis, already indexed into an array of BSA values. One caveat with these charts is that the expected EOA data must truly be reliable, or the charts will misguide the implanting surgeon. Manufacturer-provided charts could be improved by standardizing the EOA data, with one potential source being the hemodynamic data submitted to the United States Food and Drug Administration. This review discusses PPM, manufacturer-provided EOA charts, and the regulation of EOA data.

  14. Advancing the match-mismatch framework for large herbivores in the Arctic: Evaluating the evidence for a trophic mismatch in caribou

    USGS Publications Warehouse

    Gustine, David D.; Barboza, Perry; Adams, Layne G.; Griffith, Brad; Cameron, Raymond; Whitten, Kenneth R.

    2017-01-01

    Climate-induced shifts in plant phenology may adversely affect animals that cannot or do not shift the timing of their reproductive cycle. The realized effect of potential trophic “mismatches” between a consumer and its food varies with the degree to which species rely on dietary income and stored capital. Large Arctic herbivores rely heavily on maternal capital to reproduce and give birth near the onset of the growing season but are they vulnerable to trophic mismatch? We evaluated the long-term changes in the temperatures and characteristics of the growing seasons (1970–2013), and compared growing conditions and dynamics of forage quality for caribou at peak parturition, peak lactation, and peak forage biomass, and plant senescence between two distinct time periods over 36 years (1977 and 2011–13). Despite advanced thaw dates (7−12 days earlier), increased growing season lengths (15−21 days longer), and consistent parturition dates, we found no decline in forage quality and therefore no evidence within this dataset for a trophic mismatch at peak parturition or peak lactation from 1977 to 2011–13. In Arctic ungulates that use stored capital for reproduction, reproductive demands are largely met by body stores deposited in the previous summer and autumn, which reduces potential adverse effects of any mismatch between food availability and timing of parturition. Climate-induced effects on forages growing in the summer and autumn ranges, however, do correspond with the demands of female caribou and their offspring to gain mass for the next reproductive cycle and winter. Therefore, we suggest the window of time to examine the match-mismatch framework in Arctic ungulates is not at parturition but in late summer-autumn, where the multiplier effects of small changes in forage quality are amplified by forage abundance, peak forage intake, and resultant mass gains in mother-offspring pairs.

  15. Advancing the match-mismatch framework for large herbivores in the Arctic: Evaluating the evidence for a trophic mismatch in caribou

    PubMed Central

    Barboza, Perry; Adams, Layne; Griffith, Brad; Whitten, Kenneth

    2017-01-01

    Climate-induced shifts in plant phenology may adversely affect animals that cannot or do not shift the timing of their reproductive cycle. The realized effect of potential trophic “mismatches” between a consumer and its food varies with the degree to which species rely on dietary income and stored capital. Large Arctic herbivores rely heavily on maternal capital to reproduce and give birth near the onset of the growing season but are they vulnerable to trophic mismatch? We evaluated the long-term changes in the temperatures and characteristics of the growing seasons (1970–2013), and compared growing conditions and dynamics of forage quality for caribou at peak parturition, peak lactation, and peak forage biomass, and plant senescence between two distinct time periods over 36 years (1977 and 2011–13). Despite advanced thaw dates (7−12 days earlier), increased growing season lengths (15−21 days longer), and consistent parturition dates, we found no decline in forage quality and therefore no evidence within this dataset for a trophic mismatch at peak parturition or peak lactation from 1977 to 2011–13. In Arctic ungulates that use stored capital for reproduction, reproductive demands are largely met by body stores deposited in the previous summer and autumn, which reduces potential adverse effects of any mismatch between food availability and timing of parturition. Climate-induced effects on forages growing in the summer and autumn ranges, however, do correspond with the demands of female caribou and their offspring to gain mass for the next reproductive cycle and winter. Therefore, we suggest the window of time to examine the match-mismatch framework in Arctic ungulates is not at parturition but in late summer-autumn, where the multiplier effects of small changes in forage quality are amplified by forage abundance, peak forage intake, and resultant mass gains in mother-offspring pairs. PMID:28231256

  16. Educational mismatch and health status among foreign-born workers in Sweden.

    PubMed

    Dunlavy, A C; Garcy, A M; Rostila, M

    2016-04-01

    Foreign-born workers have been shown to experience poorer working conditions than native-born workers. Yet relationships between health and educational mismatch have been largely overlooked among foreign-born workers. This study uses objective and self-reported measures of educational mismatch to compare the prevalence of educational mismatch among native (n = 2359) and foreign-born (n = 1789) workers in Sweden and to examine associations between educational mismatch and poor self-rated health. Findings from weighted multivariate logistic regression which controlled for social position and individual-level demographic characteristics suggested that over-educated foreign-born workers had greater odds ratios for poor-self rated health compared to native-born matched workers. This association was particularly evident among men (OR = 2.14, 95% CI: 1.04-4.39) and women (OR = 2.13, 95% CI: 1.12-4.03) from countries outside of Western Europe, North America, and Australia/New Zealand. Associations between under-education and poor-self rated health were also found among women from countries outside of Western Europe, North America, and Australia/New Zealand (OR = 2.02, 95% CI: 1.27-3.18). These findings suggest that educational mismatch may be an important work-related social determinant of health among foreign-born workers. Future studies are needed to examine the effects of long-term versus short-term states of educational mismatch on health and to study relationships over time.

  17. Trophic mismatch and its effects on the growth of young in an Arctic herbivore.

    PubMed

    Doiron, Madeleine; Gauthier, Gilles; Lévesque, Esther

    2015-12-01

    In highly seasonal environments, timing of breeding of organisms is typically set to coincide with the period of highest resource availability. However, breeding phenology may not change at a rate sufficient to keep up with rapid changes in the environment in the wake of climate change. The lack of synchrony between the phenology of consumers and that of their resources can lead to a phenomenon called trophic mismatch, which may have important consequences on the reproductive success of herbivores. We analyzed long-term data (1991-2010) on climate, plant phenology and the reproduction of a long-distance Arctic migrant, the greater snow goose (Chen caerulescens atlantica), in order to examine the effects of mismatched reproduction on the growth of young. We found that geese are only partially able to adjust their breeding phenology to compensate for annual changes in the timing of high-quality food plants, leading to mismatches of up to 20 days between the two. The peak of nitrogen concentration in plants, an index of their nutritive quality for goslings, occurred earlier in warm springs with an early snow melt. Likewise, mismatch between hatch dates of young and date of peak nitrogen was more important in years with early snow melt. Gosling body mass and structural size at fledging was reduced when trophic mismatch was high, particularly when the difference between date of peak nitrogen concentration and hatching was >9 days. Our results support the hypothesis that trophic mismatch can negatively affect the fitness of Arctic herbivores and that this is likely to be exacerbated by rising global temperatures.

  18. Crosstalk between mismatch repair and base excision repair in human gastric cancer.

    PubMed

    Simonelli, Valeria; Leuzzi, Giuseppe; Basile, Giorgia; D'Errico, Mariarosaria; Fortini, Paola; Franchitto, Annapaola; Viti, Valentina; Brown, Ashley R; Parlanti, Eleonora; Pascucci, Barbara; Palli, Domenico; Giuliani, Alessandro; Palombo, Fabio; Sobol, Robert W; Dogliotti, Eugenia

    2016-06-20

    DNA repair gene expression in a set of gastric cancers suggested an inverse association between the expression of the mismatch repair (MMR) gene MLH1 and that of the base excision repair (BER) gene DNA polymerase β (Polβ). To gain insight into possible crosstalk of these two repair pathways in cancer, we analysed human gastric adenocarcinoma AGS cells over-expressing Polβ or Polβ active site mutants, alone or in combination with MLH1 silencing. Next, we investigated the cellular response to the alkylating agent methyl methanesulfonate (MMS) and the purine analogue 6-thioguanine (6-TG), agents that induce lesions that are substrates for BER and/or MMR. AGS cells over-expressing Polβ were resistant to 6-TG to a similar extent as when MLH1 was inactivated while inhibition of O6-methylguanine-DNA methyltransferase (MGMT) was required to detect resistance to MMS. Upon either treatment, the association with MLH1 down-regulation further amplified the resistant phenotype. Moreover, AGS cells mutated in Polβ were hypersensitive to both 6-TG and MMS killing and their sensitivity was partially rescued by MLH1 silencing. We provide evidence that the critical lethal lesions in this new pathway are double strand breaks that are exacerbated when Polβ is defective and relieved when MLH1 is silenced. In conclusion, we provide evidence of crosstalk between MLH1 and Polβ that modulates the response to alkylation damage. These studies suggest that the Polβ/MLH1 status should be taken into consideration when designing chemotherapeutic approaches for gastric cancer.

  19. Face configuration affects speech perception: Evidence from a McGurk mismatch negativity study.

    PubMed

    Eskelund, Kasper; MacDonald, Ewen N; Andersen, Tobias S

    2015-01-01

    We perceive identity, expression and speech from faces. While perception of identity and expression depends crucially on the configuration of facial features it is less clear whether this holds for visual speech perception. Facial configuration is poorly perceived for upside-down faces as demonstrated by the Thatcher illusion in which the orientation of the eyes and mouth with respect to the face is inverted (Thatcherization). This gives the face a grotesque appearance but this is only seen when the face is upright. Thatcherization can likewise disrupt visual speech perception but only when the face is upright indicating that facial configuration can be important for visual speech perception. This effect can propagate to auditory speech perception through audiovisual integration so that Thatcherization disrupts the McGurk illusion in which visual speech perception alters perception of an incongruent acoustic phoneme. This is known as the McThatcher effect. Here we show that the McThatcher effect is reflected in the McGurk mismatch negativity (MMN). The MMN is an event-related potential elicited by a change in auditory perception. The McGurk-MMN can be elicited by a change in auditory perception due to the McGurk illusion without any change in the acoustic stimulus. We found that Thatcherization disrupted a strong McGurk illusion and a correspondingly strong McGurk-MMN only for upright faces. This confirms that facial configuration can be important for audiovisual speech perception. For inverted faces we found a weaker McGurk illusion but, surprisingly, no MMN. We also found no correlation between the strength of the McGurk illusion and the amplitude of the McGurk-MMN. We suggest that this may be due to a threshold effect so that a strong McGurk illusion is required to elicit the McGurk-MMN.

  20. Visual mismatch negativity to masked stimuli presented at very brief presentation rates.

    PubMed

    Flynn, Maria; Liasis, Alki; Gardner, Mark; Towell, Tony

    2017-02-01

    Mismatch negativity (MMN) has been characterised as a 'pre-attentive' component of an event-related potential (ERP) that is related to discrimination and error prediction processes. The aim of the current experiment was to establish whether visual MMN could be recorded to briefly presented, backward and forward masked visual stimuli, given both below and above levels of subjective experience. Evidence of visual MMN elicitation in the absence of the ability to consciously report stimuli would provide strong evidence for the automaticity of the visual MMN mechanism. Using an oddball paradigm, two stimuli that differed in orientation from each other, a + and an ×, were presented on a computer screen. Electroencephalogram (EEG) was recorded from nine participants (six females), mean age 21.4 years. Results showed that for stimuli that were effectively masked at 7 ms presentation, there was little variation in the ERPs evoked to standard and deviant stimuli or in the subtraction waveform employed to delineate the visual MMN. At 14 ms stimulus presentation, when participants were able to report stimulus presence, an enhanced negativity at around 175 and 305 ms was observed to the deviant and was evident in the subtraction waveform. However, some of the difference observed in the ERPs can be attributed to stimulus characteristics, as the use of a 'lonely' deviant protocol revealed attenuated visual MMN components at 14 ms stimulus presentation. Overall, results suggest that some degree of conscious attention is required before visual MMN components emerge, suggesting visual MMN is not an entirely pre-attentive process.

  1. Perfusion-diffusion mismatch: does it identify who will benefit from reperfusion therapy?

    PubMed

    Powers, William J

    2012-06-01

    A method to determine which patients would benefit from reperfusion therapies after 4.5 h would greatly add to our ability to reduce the disability caused by stroke. The goal of magnetic resonance perfusion-diffusion imaging in hyperacute ischemic stroke is to identify regions of the brain that will die if untreated and will live and regain function if quickly reperfused. The clinical value of perfusion-diffusion imaging in hyperacute ischemic stroke can be proven only by demonstrating empirically in a randomized controlled trial (RCT) that there is an improvement in patient outcome that depends on the use of the neuroimaging modality to guide therapy. To date, there have been only a few RCTs that have evaluated whether perfusion-diffusion imaging can identify a subgroup of patients with ischemic stroke more than 4.5 h from onset in whom the overall benefit from reperfusion therapy outweighs the risk. None have met the rigorous design requirements of the three-group study necessary to adequately test this hypothesis, and none have even met their own criteria for demonstrating a clinical benefit. While studies are not sufficient to conclusively disprove the hypothesis there are no RCT data to support it, and thus, the clinical value of MRI perfusion-diffusion imaging in this setting remains unproven. It is worthy of further investigation in rigorously designed RCTs. However, the risks of symptomatic intracerebral hemorrhage with reperfusion therapies in acute ischemic stroke are proven. Unless RCT data are forthcoming to demonstrate that MRI perfusion-diffusion mismatch improves clinical outcome, it should not be used to guide delayed reperfusion therapy.

  2. Biotic interactions and macroevolution: extensions and mismatches across scales and levels.

    PubMed

    Jablonski, David

    2008-04-01

    Clade dynamics in the fossil record broadly fit expectations from the operation of competition, predation, and mutualism, but data from both modern and ancient systems suggest mismatches across scales and levels. Indirect effects, as when antagonistic or mutualistic interactions restrict geographic range and thereby elevate extinction risk, are probably widespread and may flow in both directions, as when species- or organismic-level factors increase extinction risk or speciation probabilities. Apparent contradictions across scales and levels have been neglected, including (1) the individualistic geographic shifts of species on centennial and millennial timescales versus evidence for fine-tuned coevolutionary relationships; (2) the extensive and dynamic networks of interactions faced by most species versus the evolution of costly enemy-specific defenses and finely attuned mutualisms; and (3) the macroevolutionary lags often seen between the origin and the diversification of a clade or an evolutionary novelty versus the rapid microevolution of advantageous phenotypes and the invasibility of most communities. Resolution of these and other cross-level tensions presumably hinges on how organismic interactions impinge on genetic population structures, geographic ranges, and the persistence of incipient species, but generalizations are not yet possible. Paleontological and neontological data are both incomplete and so the most powerful response to these problems will require novel integrative approaches. Promising research areas include more realistic approaches to modeling and empirical analysis of large-scale diversity dynamics of ostensibly competing clades; spatial and phylogenetic dissections of clades involved in escalatory dynamics (where prey respond evolutionarily to a broad and shifting array of enemies); analyses of the short- versus long-term consequences of mutualistic symbioses; and fuller use of abundant natural experiments on the evolutionary impacts of

  3. A rescaling method for correcting log-layer mismatch in detached eddy simulation

    NASA Astrophysics Data System (ADS)

    Hu, Ning

    2013-06-01

    In order to correct the unphysical log-layer mismatch commonly encountered in detached eddy simulation (DES) of flows with attached boundary layers, a function ℓM,ML, which has a multi-layer structure with scaling laws in each layer and a plateau related to the Kármán constant, is defined. The height of this plateau is found to be crucial for obtaining the correct log-layer. A target scaling function is designed which equals ℓM,ML in the near-wall region, but with the height of plateau determined analytically from the classical log-law. This scaling function is used as a target function according to which the resolved turbulent fluctuations are renormalized, in order to recover the height of plateau prescribed by the log-law. The renormalization procedure guarantees the height of ℓM,ML required by log-law, resulting in correct log layer slope. The method is also shown to maintain similar turbulent properties in the large eddy simulation (LES) region of DES method. Hence it predicts the turbulent intensity correctly. The results demonstrate the relationship between constant ℓM,ML and log-law profile of mean velocity, and relate the Kármán constant to turbulent fluctuations, implying a complete description of turbulent structural ensemble dynamics. The proposed method can be extended to more general flows with log layers since it uses only the log-law with Kármán constant as the input, while the intercept of log layer depends on the solution of Spalart-Allmaras (SA) model in the near-wall field, where Reynolds-averaged Navier-Stokes (RANS) solutions are accurate.

  4. Tuning thermal mismatch between turbine rotor parts with a thermal medium

    DOEpatents

    Schmidt, Mark Christopher

    2001-01-01

    In a turbine rotor, an aft shaft wheel and the final-stage wheel of the rotor are coupled together, including by a rabbeted joint. During shutdown and startup of the turbine, a thermal mismatch between the aft shaft wheel and final-stage wheel is avoided by respectively heating and cooling the aft shaft wheel to maintain the thermal mismatch within acceptable limits, thereby avoiding opening of the rabbeted joint and the potential for unbalancing the rotor and rotor vibration. The thermal medium may be supplied by piping in the aft bearing cavity into the cavity between the forward closure plate and the aft shaft wheel.

  5. Complete achromatic optical switching between two waveguides with a sign flip of the phase mismatch

    NASA Astrophysics Data System (ADS)

    Huang, Wei; Rangelov, Andon A.; Kyoseva, Elica

    2014-11-01

    We present a two-waveguide coupler which realizes complete achromatic all-optical switching. The coupling of the waveguides has a hyperbolic-secant shape, while the phase mismatch has a sign flip at the maximum of the coupling. We derive an analytic solution for the electric field propagation using coupled-mode theory and show that the light switching is robust against small to moderate variations in the coupling strength and phase mismatch. Thus, we realize an achromatic light switching between the two waveguides. We further consider the extended case of three coupled waveguides in an array and pay special attention to the case of equal bidirectional achromatic light beam splitting.

  6. Epitaxial growth of largely mismatched crystals on H-terminated Si(111) surfaces.

    PubMed

    Asaoka, Hidehito

    2010-12-01

    A strontium or strontium oxide epitaxial layer was grown using a monoatomic buffer layer of hydrogen on silicon, in spite of a huge lattice mismatch. The onset of the initial growth stage of strontium crystals occur with only one atomic layer deposition. To investigate the growth mechanism in the highly mismatched system, combination analysis using neutron reflection, reflection high-energy electron diffraction, x-ray photoelectron spectra, and stress measurements is employed. The interface structure has opened up a new way to fabricate novel heterostructures, consisting of various kinds of one-, two- or three-dimensional materials for future silicon-based technology.

  7. Tunable sound transmission at an impedance-mismatched fluidic interface assisted by a composite waveguide

    PubMed Central

    Zhang, Hui; Wei, Zhi; Fan, Li; Qu, Jianmin; Zhang, Shu-yi

    2016-01-01

    We report a composite waveguide fabricated by attaching a coupling aperture to a waveguide. The acoustic impedance of the composite waveguide can be regulated by merely controlling its coupling vibrations, depending on its structure size. By changing the size to adjust the acoustic impedance of the composite waveguide at an impedance-mismatched fluidic interface, tunable sound transmission at the desired frequencies is achieved. The reported composite waveguide provides a new method for sound regulation at a mismatched fluidic interface and has extensive frequency hopping and frequency agility applications in air-water sound communication. PMID:27698379

  8. Test report for twinax cable (Rockwell type MB0150-051). [effects of mismatched termination

    NASA Technical Reports Server (NTRS)

    Doland, G. D.

    1978-01-01

    A controlled impedance twisted pair shielded cable was tested to determine the frequency response and effects of mismatched termination. It was found that a long length of this cable, about 100 feet, exhibited a frequency sensitive attenuation roll-off greater than 1.5 db down at 5 MHz. It was also determined that improper termination resulted in losses of 1/2 to 1 db within the frequency range of 200 KHz to greater than 1-1/2 MHz. The test results indicate a possible problem where mismatched connectors are used in video signal cables.

  9. Detection of base-pair mismatches in DNA using graphene-based nanopore device

    NASA Astrophysics Data System (ADS)

    Kundu, Sourav; Karmakar, S. N.

    2016-04-01

    We present a unique way to detect base-pair mismatches in DNA, leading to a different epigenetic disorder by the method of nanopore sequencing. Based on a tight-binding formulation of a graphene-based nanopore device, using the Green’s function approach we study the changes in the electronic transport properties of the device as we translocate a double-stranded DNA through the nanopore embedded in a zigzag graphene nanoribbon. In the present work we are not only successful in detecting the usual AT and GC pairs but also a set of possible mismatches in the complementary base pairing.

  10. Collective pedagogical teacher culture, teacher-student ethno-racial mismatch, and teacher job satisfaction.

    PubMed

    Stearns, Elizabeth; Banerjee, Neena; Mickelson, Roslyn; Moller, Stephanie

    2014-05-01

    Teacher job satisfaction is critical to schools' successful functioning. Using a representative sample of kindergarten teachers from the Early Childhood Longitudinal Study, we investigate the association among professional learning community and teacher collaboration, teacher ethno-racial group, teacher-student ethno-racial mismatch, and teacher job satisfaction. We find that White teachers are significantly less satisfied than African-American and Latino teachers, especially when they teach in majority non-White classrooms. However, the existence of a professional community moderates the negative influence of teacher-student ethno-racial mismatch on White teachers' job satisfaction. In effect, strong professional communities serve as a cushion to bolster teacher job satisfaction.

  11. Solution of transport equations in layered media with refractive index mismatch using the PN-method.

    PubMed

    Phillips, Kevin G; Jacques, Steven L

    2009-10-01

    The PN-method is a spectral discretization technique used to obtain numerical solutions to the radiative transport equation. To the best of our knowledge, the PN-method has yet to be generalized to the case of refractive index mismatch in layered slabs used to numerically simulate skin. Our main contribution is the application of a collocation method that takes into account refractive index mismatch at layer interfaces. The stability, convergence, and accuracy of the method are established. Example calculations demonstrating the flexibility of the method are performed.

  12. Detection of base-pair mismatches in DNA using graphene-based nanopore device.

    PubMed

    Kundu, Sourav; Karmakar, S N

    2016-04-01

    We present a unique way to detect base-pair mismatches in DNA, leading to a different epigenetic disorder by the method of nanopore sequencing. Based on a tight-binding formulation of a graphene-based nanopore device, using the Green's function approach we study the changes in the electronic transport properties of the device as we translocate a double-stranded DNA through the nanopore embedded in a zigzag graphene nanoribbon. In the present work we are not only successful in detecting the usual AT and GC pairs but also a set of possible mismatches in the complementary base pairing.

  13. Tunable sound transmission at an impedance-mismatched fluidic interface assisted by a composite waveguide

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Wei, Zhi; Fan, Li; Qu, Jianmin; Zhang, Shu-Yi

    2016-10-01

    We report a composite waveguide fabricated by attaching a coupling aperture to a waveguide. The acoustic impedance of the composite waveguide can be regulated by merely controlling its coupling vibrations, depending on its structure size. By changing the size to adjust the acoustic impedance of the composite waveguide at an impedance-mismatched fluidic interface, tunable sound transmission at the desired frequencies is achieved. The reported composite waveguide provides a new method for sound regulation at a mismatched fluidic interface and has extensive frequency hopping and frequency agility applications in air-water sound communication.

  14. The effect of a visual/motion display mismatch in a single axis compensatory tracking task

    NASA Technical Reports Server (NTRS)

    Shirachi, D. K.; Shirley, R. S.

    1977-01-01

    An experiment was performed to determine the effect of a performance mismatch between the visual and motion display systems on a real time piloted aircraft simulation. Pilots performed a compensatory roll tracking task with dynamics typical of medium jet transports. Between 0 and 10 rad/sec, visual and motion system responses were equivalent to either unity or a first order lag at 4.8 rad/sec. Pilot describing functions and error scores were calculated. Results show that the mismatch between visual and motion display systems has no significant effect. It is the absence of high frequency visual and/or motion cues which significantly affects pilot performance.

  15. The Mismatch between Children's Health Needs and School Resources

    ERIC Educational Resources Information Center

    Knauer, Heather; Baker, Dian L.; Hebbeler, Kathleen; Davis-Alldritt, Linda

    2015-01-01

    There are increasing numbers of children with special health care needs (CSHCN) who require various levels of care each school day. The purpose of this study was to examine the role of public schools in supporting CSHCN through in-depth key informant interviews. For this qualitative study, the authors interviewed 17 key informants to identify key…

  16. Matched and Mismatched Metabolic Fuels in Lymphocyte Function

    PubMed Central

    Caro-Maldonado, Alfredo; Gerriets, Valerie A.; Rathmell, Jeffrey C.

    2012-01-01

    Immunological function requires metabolic support to suit the needs of lymphocytes at a variety of distinct differentiation and activation states. It is now evident that the signaling pathways that drive lymphocyte survival and activity can directly control cellular metabolism. This linkage provides a mechanism by which activation and specific signaling pathways provide a supply of appropriate and required nutrients to support cell functions in a pro-active supply rather than consumption-based metabolic model. In this way, the metabolism and fuel choices of lymphocytes are guided to specifically match the anticipated needs. If the fuel choice or metabolic pathways of lymphocytes are dysregulated, however, metabolic checkpoints can become activated to disrupt immunological function. These changes are now shown in several immunological diseases and may open new opportunities to selectively enhance or suppress specific immune functions through targeting of glucose, lipid, or amino acid metabolism. PMID:23290889

  17. Mental Ability, P300, and Mismatch Negativity: Analysis of Frequency and Duration Discrimination

    ERIC Educational Resources Information Center

    Troche, Stefan J.; Houlihan, Michael E.; Stelmack, Robert M.; Rammsayer, Thomas H.

    2009-01-01

    Individual differences in mental ability (MA) were examined with event-related potentials (ERP). In addition to using an auditory frequency discrimination task, a duration discrimination task was used to elicit P300 and mismatch negativity (MMN) components of the ERP. Frequency and duration P300 latencies explained 9% and 10% of variance of MAB…

  18. Nuclease stability of boron-modified nucleic acids: application to label-free mismatch detection.

    PubMed

    Reverte, Maëva; Vasseur, Jean-Jacques; Smietana, Michael

    2015-11-21

    5'-End boronic acid-modified oligonucleotides were evaluated against various nucleases at single and double stranded levels. The results show that these modifications induce a high resistance to degradation by calf-spleen and snake venom phosphodiesterases. More importantly, this eventually led to the development of a new label-free enzyme-assisted fluorescence-based method for single mismatch detection.

  19. High performance, high bandgap, lattice-mismatched, GaInP solar cells

    DOEpatents

    Wanlass, Mark W.; Carapella, Jeffrey J.; Steiner, Myles A.

    2014-07-08

    High performance, high bandgap, lattice-mismatched, photovoltaic cells (10), both transparent and non-transparent to sub-bandgap light, are provided as devices for use alone or in combination with other cells in split spectrum apparatus or other applications.

  20. Examining the Mismatch between Pupil and Teacher Knowledge in Acid-Base Chemistry.

    ERIC Educational Resources Information Center

    Erduran, Sibel

    2003-01-01

    Reports a mismatch between teacher and pupil knowledge of acid-base chemistry as a result of controversial episodes from three science lessons. Suggests that the teacher's knowledge is guided by textbook information while the pupil's knowledge is based on direct experimental experience. Proposes that classroom activities should support the…

  1. Educational Mismatches and Earnings: Extensions of Occupational Mobility Theory and Evidence of Human Capital Depreciation

    ERIC Educational Resources Information Center

    Rubb, Stephen

    2006-01-01

    Using a human capital theory framework, this study examines the impact of educational mismatches on earnings and occupational mobility. Occupational mobility theory suggests that overeducated workers observe greater upward occupational mobility and undereducated workers observe lower upward occupational mobility. By extension, this leads to…

  2. Strain compensation in a semiconducting device structure using an intentionally mismatched uniform buffer layer

    NASA Astrophysics Data System (ADS)

    Kujofsa, Tedi; Ayers, John E.

    2016-12-01

    The extent of strain relaxation in semiconducting device heterostructures has important implications in the design of high electron mobility transistors, light-emitting diodes, and laser diodes, in which the residual strain affects the device characteristics. In this work, we develop the theoretical framework for understanding strain compensation in a semiconductor device layer using a uniform buffer layer which can be intentionally mismatched to the material above. Specifically, we determined the critical condition for complete strain compensation in the device layer by intentionally introducing a compositional mismatch at the device-buffer interface. We present minimum energy calculations and show that for a given device layer with fixed mismatch and layer thickness, the buffer layer may be designed with the appropriate combination of thickness and mismatch such that the device layer will have zero residual strain in equilibrium. Such a structure can be referred to as a completely strain-compensated design. In the more general case, there may be partial strain compensation, and we give a simple physics-based Gaussian-type function describing the residual strain in the device layer. We have applied this general framework to In x Ga1-x As/GaAs (001) heterostructures for the purpose of illustration, but the work is applicable to any diamond or zinc blende (001) heteroepitaxial material system.

  3. High performance, high bandgap, lattice-mismatched, GaInP solar cells

    SciTech Connect

    Wanlass, Mark W; Carapella, Jeffrey J; Steiner, Myles A

    2016-11-01

    High performance, high bandgap, lattice-mismatched, photovoltaic cells (10), both transparent and non-transparent to sub-bandgap light, are provided as devices for use alone or in combination with other cells in split spectrum apparatus or other applications.

  4. Cultural Mismatch in Honduran Garifuna Communities: The Role of Culture, Race, and Language in Schools

    ERIC Educational Resources Information Center

    Kleyn, Tatyana

    2010-01-01

    The Garifuna are an Indigenous, Afro-Latino group in Honduras whose distinct cultural, ethnic, and linguistic background has been unacknowledged and frequently misunderstood on a societal level and, consequently, in the schools that serve them. This study argues for the utility of a cultural mismatch approach, one applied primarily to U.S.…

  5. The effect of matching and mismatching cognitive style and science instruction

    NASA Astrophysics Data System (ADS)

    Conwell, Catherine R.; Helgeson, Stanley L.; Wachowiak, Dale G.

    This study examined the effect of matching learners' cognitive styles with science learning activities on science knowledge and attitudes. Fifty-six elementary education majors who were identified as Sensing Feeling types on the Myers-Briggs Type Indicator participated in this study. The Sensing Feeling type is predominant among elementary school educators. The subjects participated in either nine science activities matched to the learning preferences of Sensing Feelers or nine science activities mismatched to their learning preferences. These mismatched activities were geared toward the learning preferences of Intuitive Thinkers, the dominant type among scientists. Results revealed no significant differences between matched and mismatched groups in knowledge of the material presented or overall attitude toward science and toward science teaching. Comparisons made subsequent to the hypothesized analyses did suggest that cognitive style may affect reactions to certain specific learning activities. The immediate reactions of forty non-Sensing Feeling types who also experienced the treatments were compared to those of the 56 Sensing Feeling subjects. Certain activities which were rated by judges prior to the onset of treatment as being particularly well-matched to the Sensing Feeling style did receive significantly more favorable ratings by the Sensing Feeling subjects than by other types. Conversely, the Sensing Feelers gave significantly lower ratings than other types to certain activities which, according to independent judges, were strongly mismatched to the Sensing Feeling style.

  6. Can Mismatch Negativity Be Linked to Synaptic Processes? A Glutamatergic Approach to Deviance Detection

    ERIC Educational Resources Information Center

    Strelnikov, Kuzma

    2007-01-01

    This article aims to provide a theoretical framework to elucidate the neurophysiological underpinnings of deviance detection as reflected by mismatch negativity. A six-step model of the information processing necessary for deviance detection is proposed. In this model, predictive coding of learned regularities is realized by means of long-term…

  7. Evaluating the Competency Mismatch between Master of Engineering Graduates and Industry Needs in China

    ERIC Educational Resources Information Center

    Peng, Lijun; Zhang, Shulin; Gu, Jibao

    2016-01-01

    This study investigates the mismatch between the educational attainment of a graduate with a Master of Engineering (MEng) degree and the industry needs in China. A competency list for MEng graduates from the perspective of industry needs was constructed. And a survey was conducted among MEng graduate students, alumni, and employers to assess the…

  8. Competition Effects in Phonological Priming: The Role of Mismatch Position between Primes and Targets

    ERIC Educational Resources Information Center

    Dufour, Sophie; Peereman, Ronald

    2009-01-01

    In three experiments, we examined lexical competition effects using the phonological priming paradigm in a shadowing task. Experiments 1A and 1B showed that an inhibitory priming effect occurred when the primes mismatched the targets on the last phoneme (/bagar/-/bagaj/). In contrast, a facilitatory priming effect was observed when the primes…

  9. A rare case mimicking positron emission tomography/computed tomography mismatch: Hepatic subcapsular hematoma

    PubMed Central

    Inanir, Sabahat; Oksuzoglu, Kevser; Aras, Mustafa; Tuney, Davut

    2015-01-01

    Subcapsular collections of bile, air or blood in the liver have been described following transhepatic procedures due to the leakage of bile and blood from the percutaneous puncture at the surface of the liver. Herein we presented the subcapsular collection led to a mismatch between functional and anatomical boundaries of the liver. PMID:26430331

  10. A rare case mimicking positron emission tomography/computed tomography mismatch: Hepatic subcapsular hematoma.

    PubMed

    Inanir, Sabahat; Oksuzoglu, Kevser; Aras, Mustafa; Tuney, Davut

    2015-01-01

    Subcapsular collections of bile, air or blood in the liver have been described following transhepatic procedures due to the leakage of bile and blood from the percutaneous puncture at the surface of the liver. Herein we presented the subcapsular collection led to a mismatch between functional and anatomical boundaries of the liver.

  11. Regional Differences in the Listener's Phonemic Inventory Affect Semantic Processing: A Mismatch Negativity (MMN) Study

    ERIC Educational Resources Information Center

    Brunelliere, Angele; Dufour, Sophie; Nguyen, Noel

    2011-01-01

    Using the mismatch negativity (MMN) response, we examined how Standard French and Southern French speakers access the meaning of words ending in /e/ or /[epsilon]/ vowels which are contrastive in Standard French but not in Southern French. In Standard French speakers, there was a significant difference in the amplitude of the brain response after…

  12. The Impact of Educational Mismatch on Firm Productivity: Evidence from Linked Panel Data

    ERIC Educational Resources Information Center

    Kampelmann, Stephan; Rycx, Francois

    2012-01-01

    We provide first evidence regarding the direct impact of educational mismatch on firm productivity. To do so, we rely on representative linked employer-employee panel data for Belgium covering the period 1999-2006. Controlling for simultaneity issues, time-invariant unobserved workplace characteristics, cohort effects and dynamics in the…

  13. A review of climate-driven mismatches between interdependent phenophases in terrestrial and aquatic ecosystems.

    PubMed

    Donnelly, Alison; Caffarra, Amelia; O'Neill, Bridget F

    2011-11-01

    Mismatches in phenology between mutually dependent species, resulting from climate change, can have far-reaching consequences throughout an ecosystem at both higher and lower trophic levels. Rising temperatures, due to climate warming, have resulted in advances in development and changes in behaviour of many organisms around the world. However, not all species or phenophases are responding to this increase in temperature at the same rate, thus creating a disruption to previously synchronised interdependent key life-cycle stages. Mismatches have been reported between plants and pollinators, predators and prey, and pests and hosts. Here, we review mismatches between interdependent phenophases at different trophic levels resulting from climate change. We categorized the studies into (1) terrestrial (natural and agricultural) ecosystems, and (2) aquatic (freshwater and marine) ecosystems. As expected, we found reports of 'winners' and 'losers' in each system, such as earlier emergence of prey enabling partial avoidance of predators, potential reductions in crop yield if herbivore pests emerge before their predators and possible declines in marine biodiversity due to disruption in plankton-fish phenologies. Furthermore, in the marine environment rising temperatures have resulted in synchrony in a previously mismatched prey and predator system, resulting in an abrupt population decline in the prey species. The examples reviewed suggest that more research into the complex interactions between species in terrestrial and aquatic ecosystems is necessary to make conclusive predictions of how climate warming may impact the fragile balances within ecosystems in future.

  14. Sector-Based Analysis of the Education-Occupation Mismatch in the Turkish Labor Market

    ERIC Educational Resources Information Center

    Mercan, Murat Anil; Karakas, Mesut; Citci, Sadettin Haluk; Babacan, Mehmet

    2015-01-01

    The aim of this study was to investigate the existence of sectorial undereducation and overeducation problems in the Turkish labor market. In order to cope with this issue, the 2009 Household Labor Force Survey (TurkStat), which covers 145,934 individuals within 27 sectors, was utilized. An objective measure of education-occupation mismatch based…

  15. STEM in the Ohio Labor Market: A Mismatch or a Missed Opportunity?

    ERIC Educational Resources Information Center

    Edwards, Stacia Lynn

    2013-01-01

    The relationship between the supply of educated workers and the talent demands of employers is complex. Declining educational attainment levels in the US have been identified as a possible cause for the reported mismatch between the availability of talent that businesses want to hire and the talent available in the labor market, especially in the…

  16. Labour Market Mismatch among UK Graduates: An Analysis Using REFLEX Data

    ERIC Educational Resources Information Center

    McGuinness, Seamus; Sloane, Peter J.

    2011-01-01

    There is much disagreement in the literature over the extent to which graduates are mismatched in the labour market and the reasons for this. In this paper we utilise the Flexible Professional in the Knowledge Society (REFLEX) data set to cast light on these issues, based on data for UK graduates. We find substantial pay penalties for…

  17. A quantitative model of bacterial mismatch repair as applied to studying induced mutagenesis

    NASA Astrophysics Data System (ADS)

    Belov, O. V.; Chuluunbaatar, O.; Kapralov, M. I.; Sweilam, N. H.

    2013-11-01

    The paper presents a mathematical model of the DNA mismatch repair system in Escherichia coli bacterial cells. The key pathways of this repair mechanism were simulated on the basis of modern experimental data. We have modelled in detail five main pathways of DNA misincorporation removal with different DNA exonucleases. Here we demonstrate an application of the model to problems of radiation-induced mutagenesis.

  18. Penalized or Protected? Gender and the Consequences of Nonstandard and Mismatched Employment Histories

    PubMed Central

    Pedulla, David S.

    2016-01-01

    Millions of workers are employed in positions that deviate from the full-time, standard employment relationship or work in jobs that are mismatched with their skills, education, or experience. Yet, little is known about how employers evaluate workers who have experienced these employment arrangements, limiting our knowledge about how part-time work, temporary agency employment, and skills underutilization affect workers’ labor market opportunities. Drawing on original field and survey experiment data, I examine three questions: (1) What are the consequences of having a nonstandard or mismatched employment history for workers’ labor market opportunities? (2) Are the effects of nonstandard or mismatched employment histories different for men and women? and (3) What are the mechanisms linking nonstandard or mismatched employment histories to labor market outcomes? The field experiment shows that skills underutilization is as scarring for workers as a year of unemployment, but that there are limited penalties for workers with histories of temporary agency employment. Additionally, although men are penalized for part-time employment histories, women face no penalty for part-time work. The survey experiment reveals that employers’ perceptions of workers’ competence and commitment mediate these effects. These findings shed light on the consequences of changing employment relations for the distribution of labor market opportunities in the “new economy.” PMID:27182069

  19. Optimizing the Face Paradigm of BCI System by Modified Mismatch Negative Paradigm

    PubMed Central

    Zhou, Sijie; Jin, Jing; Daly, Ian; Wang, Xingyu; Cichocki, Andrzej

    2016-01-01

    Many recent studies have focused on improving the performance of event-related potential (ERP) based brain computer interfaces (BCIs). The use of a face pattern has been shown to obtain high classification accuracies and information transfer rates (ITRs) by evoking discriminative ERPs (N200 and N400) in addition to P300 potentials. Recently, it has been proved that the performance of traditional P300-based BCIs could be improved through a modification of the mismatch pattern. In this paper, a mismatch inverted face pattern (MIF-pattern) was presented to improve the performance of the inverted face pattern (IF-pattern), one of the state of the art patterns used in visual-based BCI systems. Ten subjects attended in this experiment. The result showed that the mismatch inverted face pattern could evoke significantly larger vertex positive potentials (p < 0.05) and N400s (p < 0.05) compared to the inverted face pattern. The classification accuracy (mean accuracy is 99.58%) and ITRs (mean bit rate is 27.88 bit/min) of the mismatch inverted face pattern was significantly higher than that of the inverted face pattern (p < 0.05). PMID:27774046

  20. Graduates in Economics and Educational Mismatch: The Case Study of the University of Naples "Parthenope"

    ERIC Educational Resources Information Center

    Quintano, Claudio; Castellano, Rosalia; D'Agostino, Antonella

    2008-01-01

    The quality of jobs of economics graduates was studied in terms of educational mismatch. The returns of over-education on earnings and on the job-search were also investigated. The discussion regards the second wave of a longitudinal survey of a random sample of economics graduates from the University of Naples "Parthenope", a major…

  1. Affirmative Action in Higher Education in India: Targeting, Catch Up, and Mismatch

    ERIC Educational Resources Information Center

    Frisancho, Veronica; Krishna, Kala

    2016-01-01

    Using detailed data on the 2008 graduating class from an elite engineering institution in India, we evaluate the impact of affirmative action policies in higher education focusing on three issues: targeting, catch up, and mismatch. We find that admission preferences effectively target minority students who are poorer than average displaced…

  2. A simple ABO genotyping by PCR using sequence-specific primers with mismatched nucleotides.

    PubMed

    Taki, Takashi; Kibayashi, Kazuhiko

    2014-05-01

    In forensics, the specific ABO blood group is often determined by analyzing the ABO gene. Among various methods used, PCR employing sequence-specific primers (PCR-SSP) is simpler than other methods for ABO typing. When performing the PCR-SSP, the pseudo-positive signals often lead to errors in ABO typing. We introduced mismatched nucleotides at the second and the third positions from the 3'-end of the primers for the PCR-SSP method and examined whether reliable typing could be achieved by suppressing pseudo-positive signals. Genomic DNA was extracted from nail clippings of 27 volunteers, and the ABO gene was examined with PCR-SSP employing primers with and without mismatched nucleotides. The ABO blood group of the nail clippings was also analyzed serologically, and these results were compared with those obtained using PCR-SSP. When mismatched primers were employed for amplification, the results of the ABO typing matched with those obtained by the serological method. When primers without mismatched nucleotides were used for PCR-SSP, pseudo-positive signals were observed. Thus our method may be used for achieving more reliable ABO typing.

  3. Whose Reality? Mismatch of Perceptions of ESL Pupils and Teachers in Britain.

    ERIC Educational Resources Information Center

    Collet, R. J.

    The role of the specialist in English as a Second Language (ESL) in sensitizing colleagues, administrators and politicians to the mismatch of perceptions in the classroom and in helping establish and consolidate links with the minority communities is discussed. Seven factors said to contribute to the underachievement of children of Caribbean…

  4. The Extent of Skills Mismatch among Childhood Education Graduates of Princess Alia University College

    ERIC Educational Resources Information Center

    Nashash, Hyam M.

    2015-01-01

    This study is aimed at investigating the extent of skill mismatch between the skills the childhood education graduates at Al-Balqa Applied University--Princess Alia University College acquired during their studies and those demanded in the labor market. The descriptive survey design was adopted and the purposive sampling technique was employed to…

  5. A mismatch in the human realism of face and voice produces an uncanny valley.

    PubMed

    Mitchell, Wade J; Szerszen, Kevin A; Lu, Amy Shirong; Schermerhorn, Paul W; Scheutz, Matthias; Macdorman, Karl F

    2011-01-01

    The uncanny valley has become synonymous with the uneasy feeling of viewing an animated character or robot that looks imperfectly human. Although previous uncanny valley experiments have focused on relations among a character's visual elements, the current experiment examines whether a mismatch in the human realism of a character's face and voice causes it to be evaluated as eerie. The results support this hypothesis.

  6. DnaN clamp zones provide a platform for spatiotemporal coupling of mismatch detection to DNA replication.

    PubMed

    Lenhart, Justin S; Sharma, Anushi; Hingorani, Manju M; Simmons, Lyle A

    2013-02-01

    Mismatch repair (MMR) increases the fidelity of DNA replication by identifying and correcting replication errors. Processivity clamps are vital components of DNA replication and MMR, yet the mechanism and extent to which they participate in MMR remains unclear. We investigated the role of the Bacillus subtilis processivity clamp DnaN, and found that it serves as a platform for mismatch detection and coupling of repair to DNA replication. By visualizing functional MutS fluorescent fusions in vivo, we find that MutS forms foci independent of mismatch detection at sites of replication (i.e. the replisome). These MutS foci are directed to the replisome by DnaN clamp zones that aid mismatch detection by targeting the search to nascent DNA. Following mismatch detection, MutS disengages from the replisome, facilitating repair. We tested the functional importance of DnaN-mediated mismatch detection for MMR, and found that it accounts for 90% of repair. This high dependence on DnaN can be bypassed by increasing MutS concentration within the cell, indicating a secondary mode of detection in vivo whereby MutS directly finds mismatches without associating with the replisome. Overall, our results provide new insight into the mechanism by which DnaN couples mismatch recognition to DNA replication in living cells.

  7. HLAMatchmaker-based strategy to identify acceptable HLA class I mismatches for highly sensitized kidney transplant candidates.

    PubMed

    Duquesnoy, Rene J; Witvliet, Marian; Doxiadis, Ilias I N; de Fijter, Hans; Claas, Frans H J

    2004-01-01

    HLAMatchmaker determines HLA compatibility at the level of polymorphic amino acid triplets in antibody-accessible sequence positions. Recent studies have shown that among HLA-DR-matched kidney transplants, the HLA-A,B antigen mismatches which are compatible at the triplet level have almost identical graft survival rates as the zero-HLA-A,B antigen mismatches. This finding provides the basis of a new strategy to identify HLA-mismatched organs that have similar success rates as the zero-HLA-antigen mismatches. This report describes how in conjunction with the Acceptable Mismatch program in Eurotransplant, HLAMatchmaker can expand the pool of potential donors for highly sensitized patients, for whom it is very difficult to find a compatible transplant. Sera from 35 highly sensitized kidney transplant candidates with an average PRA of 96% were screened by lymphocytotoxicity with HLA-typed panels that included cells that were selectively mismatched for one or two HLA antigens for each patient. Acceptable and unacceptable HLA-A,B antigen mismatches were determined from the serum reactivity with the cell panel. HLAMatchmaker analysis was applied to identify additional HLA class I antigens that were matched at the triplet level. For each patient, we calculated the probability of finding a donor (PFD) in the different match categories from HLA gene frequencies in the kidney donor population. The median PFD for a zero-antigen mismatch was 0.025%. Matching at the triplet level increased the median PFD to 0.037% ( P = 0.008). The median PFD was 0.058% for a 0-1-triplet mismatch and 0.226% for a 0-2-triplet mismatch. Serum screening identified acceptable antigen mismatches for 28 of 35 highly sensitized patients, and the median PFD increased to 0.307% for a zero/acceptable antigen mismatch. The application of HLAMatchmaker permitted for 33 patients (or 92%) the identification of additional antigens that were acceptable at the triplet level, and the median PFD for a zero

  8. Camouflage mismatch in seasonal coat color due to decreased snow duration.

    PubMed

    Mills, L Scott; Zimova, Marketa; Oyler, Jared; Running, Steven; Abatzoglou, John T; Lukacs, Paul M

    2013-04-30

    Most examples of seasonal mismatches in phenology span multiple trophic levels, with timing of animal reproduction, hibernation, or migration becoming detached from peak food supply. The consequences of such mismatches are difficult to link to specific future climate change scenarios because the responses across trophic levels have complex underlying climate drivers often confounded by other stressors. In contrast, seasonal coat color polyphenism creating camouflage against snow is a direct and potentially severe type of seasonal mismatch if crypsis becomes compromised by the animal being white when snow is absent. It is unknown whether plasticity in the initiation or rate of coat color change will be able to reduce mismatch between the seasonal coat color and an increasingly snow-free background. We find that natural populations of snowshoe hares exposed to 3 y of widely varying snowpack have plasticity in the rate of the spring white-to-brown molt, but not in either the initiation dates of color change or the rate of the fall brown-to-white molt. Using an ensemble of locally downscaled climate projections, we also show that annual average duration of snowpack is forecast to decrease by 29-35 d by midcentury and 40-69 d by the end of the century. Without evolution in coat color phenology, the reduced snow duration will increase the number of days that white hares will be mismatched on a snowless background by four- to eightfold by the end of the century. This novel and visually compelling climate change-induced stressor likely applies to >9 widely distributed mammals with seasonal coat color.

  9. The Mismatch Between Children's Health Needs and School Resources.

    PubMed

    Knauer, Heather; Baker, Dian L; Hebbeler, Kathleen; Davis-Alldritt, Linda

    2015-10-01

    There are increasing numbers of children with special health care needs (CSHCN) who require various levels of care each school day. The purpose of this study was to examine the role of public schools in supporting CSHCN through in-depth key informant interviews. For this qualitative study, the authors interviewed 17 key informants to identify key themes, provide recommendations, and generate hypotheses for further statewide survey of school nurse services. Key informants identified successful strategies and challenges that public schools face in meeting the needs of all CSHCN. Although schools are well intentioned, there is wide variation in the ability of schools to meet the needs of CSHCN. Increased funding, monitoring of school health services, integration of services, and interagency collaboration are strategies that could improve the delivery of health services to CSHCN in schools.

  10. Effect of delay mismatch in Pyragas feedback control

    NASA Astrophysics Data System (ADS)

    Purewal, A. S.; Postlethwaite, C. M.; Krauskopf, B.

    2014-11-01

    Pyragas time-delayed feedback is a control scheme designed to stabilize unstable periodic orbits, which occur naturally in many nonlinear dynamical systems. It has been successfully implemented in a number of applications, including lasers and chemical systems. The control scheme targets a specific unstable periodic orbit by adding a feedback term with a delay chosen as the period of the unstable periodic orbit. However, in an experimental or industrial environment, obtaining the exact period or setting the delay equal to the exact period of the target periodic orbit may be difficult. This could be due to a number of factors, such as incomplete information on the system or the delay being set by inaccurate equipment. In this paper, we evaluate the effect of Pyragas control on the prototypical generic subcritical Hopf normal form when the delay is close to but not equal to the period of the target periodic orbit. Specifically, we consider two cases: first, a constant, and second, a linear approximation of the period. We compare these two cases to the case where the delay is set exactly to the target period, which serves as the benchmark case. For this comparison, we construct bifurcation diagrams and determine any regions where a stable periodic orbit close to the target is stabilized by the control scheme. In this way, we find that at least a linear approximation of the period is required for successful stabilization by Pyragas control.

  11. Electrical impedance tomography for assessing ventilation/perfusion mismatch for pulmonary embolism detection without interruptions in respiration.

    PubMed

    Nguyen, Doan Trang; Thiagalingam, Aravinda; Bhaskaran, Abhishek; Barry, Michael A; Pouliopoulos, Jim; Jin, Craig; McEwan, Alistair L

    2014-01-01

    Recent studies have shown high correlation between pulmonary perfusion mapping with impedance contrast enhanced Electrical Impedance Tomography (EIT) and standard perfusion imaging methods such as Computed Tomography (CT) and Single Photon Emission Computerized Tomography (SPECT). EIT has many advantages over standard imaging methods as it is highly portable and non-invasive. Contrast enhanced EIT uses hypertonic saline bolus instead of nephrotoxic contrast medium that are utilized by CT and nuclear Ventilation/Perfusion (V/Q) scans. However, current implementation of contrast enhanced EIT requires induction of an apnea period for perfusion measurement, rendering it disadvantageous compared with current gold standard imaging modalities. In the present paper, we propose the use of a wavelet denoising algorithm to separate perfusion signal from ventilation signal such that no interruption in patient's ventilation would be required. Furthermore, right lung to left lung perfusion ratio and ventilation ratio are proposed to assess the mismatch between ventilation and perfusion for detection of Pulmonary Embolism (PE). The proposed methodology was validated on an ovine model (n=3, 83.7±7.7 kg) with artificially induced PE in the right lung. The results showed a difference in right lung to left lung perfusion ratio between baseline and diseased states in all cases with all paired t-tests between baseline and PE yielding p <; 0.01, while the right lung to left lung ventilation ratio remained unchanged in two out of three experiments. Statistics were pooled from multiple repetitions of measurements per experiment.

  12. Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.

    PubMed

    Pan, Yongping; Priyakumar, U Deva; MacKerell, Alexander D

    2005-02-08

    Structure and energetic properties of base pair mismatches in duplex RNA have been the focus of numerous investigations due to their role in many important biological functions. Such efforts have contributed to the development of models for secondary structure prediction of RNA, including the nearest-neighbor model. In RNA duplexes containing GU mismatches, 5'-GU-3' tandem mismatches have a different thermodynamic stability than 5'-UG-3' mismatches. In addition, 5'-GU-3' mismatches in some sequence contexts do not follow the nearest-neighbor model for stability. To characterize the underlying atomic forces that determine the structural and thermodynamic properties of GU tandem mismatches, molecular dynamics (MD) simulations were performed on a series of 5'-GU-3' and 5'-UG-3' duplexes in different sequence contexts. Overall, the MD-derived structural models agree well with experimental data, including local deviations in base step helicoidal parameters in the region of the GU mismatches and the model where duplex stability is associated with the pattern of GU hydrogen bonding. Further analysis of the simulations, validated by data from quantum mechanical calculations, suggests that the experimentally observed differences in thermodynamic stability are dominated by GG interstrand followed by GU intrastrand base stacking interactions that dictate the one versus two hydrogen bonding scenarios for the GU pairs. In addition, the inability of 5'-GU-3' mismatches in different sequence contexts to all fit into the nearest-neighbor model is indicated to be associated with interactions of the central four base pairs with the surrounding base pairs. The results emphasize the role of GG and GU stacking interactions on the structure and thermodynamics of GU mismatches in RNA.

  13. Impact of Human Leukocyte Antigen Allele Mismatch in Unrelated Bone Marrow Transplantation with Reduced-Intensity Conditioning Regimen.

    PubMed

    Yokoyama, Hisayuki; Kanda, Junya; Fuji, Shigeo; Kim, Sung-Won; Fukuda, Takahiro; Najima, Yuho; Ohno, Hitoshi; Uchida, Naoyuki; Ueda, Yasunori; Eto, Tetsuya; Iwato, Koji; Kobayashi, Hikaru; Ozawa, Yukiyasu; Kondo, Tadakazu; Ichinohe, Tatsuo; Atsuta, Yoshiko; Kanda, Yoshinobu

    2017-02-01

    The impact of HLA mismatch in hematopoietic stem cell transplantation with reduced-intensity conditioning (RIC) has not been fully examined. We analyzed a total of 1130 cases to examine the effects of HLA allele mismatch in unrelated bone marrow transplantation (BMT) with RIC in the Japan Marrow Donor Program registry cohort. Compared with HLA 8/8-allele match (n = 720, 8/8 match), both 1 (n = 295, 7/8 match) and 2 allele mismatches (n = 115, 6/8 match) were associated with significant reduction of overall survival (OS) (hazard ratio [HR],  1.34; P = .0024 and HR, 1.33; P = .035 for 7/8 and 6/8 match, respectively). The incidence of grades 2 to 4 acute graft-versus-host disease (aGVHD) increased with increasing number of mismatched alleles (HR, 1.36 and HR, 2.08 for 7/8 and 6/8 match, respectively). Nonrelapse mortality showed a similar tendency to aGVHD (HR, 1.35 for 7/8 and HR, 1.63 for 6/8). One-allele mismatches at the HLA-A or -B and HLA-C loci were significantly associated with inferior OS compared with 8/8 match (HR, 1.64 for A or B mismatch and HR, 1.41 for C mismatch), whereas HLA-DRB1 allele mismatch was not (HR, 1.16; P = .30). However, the effect of HLA-A or -B and -C mismatch on OS was not observed in those who received RIC BMT since 2010, in contrast to recipients before 2010. These results suggested that in unrelated RIC BMT, 1-allele mismatch is associated with poorer outcome, and the impact of HLA mismatch may differ depending on the HLA locus, although these HLA mismatch effects may be different in recent cases.

  14. Length mismatch in random semiconductor alloys. III. Crystalline and amorphous SiGe

    NASA Astrophysics Data System (ADS)

    Mousseau, Normand; Thorpe, M. F.

    1992-12-01

    In the third paper of this series on the length mismatch problem, we study binary semiconductor alloys in both their crystalline and amorphous forms. We have concentratred on SiGe alloys. Applying the theory developed in paper I, we obtain the mean length for both nearest and next-nearest neighbors as well as the nearest-neighbor length distribution for the crystalline alloy. We show that the theoretical results fall within the limits set by experiment. We check our analytical results against computer simulations. We examine the effect of amorphization on the internal strain, using the Wooten, Winer, and Weaire model, and find that the disorders due to the length mismatch and due to amorphization decouple.

  15. Structural and thermodynamic studies on the adenine.guanine mismatch in B-DNA.

    PubMed Central

    Leonard, G A; Booth, E D; Brown, T

    1990-01-01

    The structure of the synthetic dodecamer d(CGCAAATTGGCG) has been shown by single crystal X-ray diffraction methods to be that of a B-DNA helix containing two A(anti).G(syn) base pairs. The refinement, based on data to a resolution of 2.25 A shows that the mismatch base pairs are held together by two hydrogen bonds. The syn-conformation of the guanine base of the mismatch is stabilised by hydrogen bonding to a network of solvent molecules in both the major and minor grooves. A pH-dependent ultraviolet melting study indicates that the duplex is stabilised by protonation, suggesting that the bases of the A.G mispair are present in their most common tautomeric forms and that the N(1)-atom of adenine is protonated. The structure refinement shows that there is some disorder in the sugar-phosphate backbone. PMID:2216754

  16. Position but not color deviants result in visual mismatch negativity in an active oddball task.

    PubMed

    Berti, Stefan

    2009-05-06

    Changes in the visual environment might be detected automatically. This function is provided by the sensory systems and showed, for instance, by the pop-out phenomenon. Automatic change detection is also observable within visual oddball paradigms, where rare changes are introduced in an irrelevant stimulus feature; the detection of deviant stimuli is accompanied by a negative component (so-called visual mismatch negativity) in the human event-related brain potential. In this study, the deviating stimulus feature was embedded in a task-relevant object presented in the focus of attention. With this, visual mismatch negativity was observable only with position deviants presented in the upper visual half field but not by lower half field presentation or color deviants.

  17. Energy losses of nanomechanical resonators induced by atomic force microscopy-controlled mechanical impedance mismatching

    NASA Astrophysics Data System (ADS)

    Rieger, Johannes; Isacsson, Andreas; Seitner, Maximilian J.; Kotthaus, Jörg P.; Weig, Eva M.

    2014-03-01

    Clamping losses are a widely discussed damping mechanism in nanoelectromechanical systems, limiting the performance of these devices. Here we present a method to investigate this dissipation channel. Using an atomic force microscope tip as a local perturbation in the clamping region of a nanoelectromechanical resonator, we increase the energy loss of its flexural modes by at least one order of magnitude. We explain this by a transfer of vibrational energy into the cantilever, which is theoretically described by a reduced mechanical impedance mismatch between the resonator and its environment. A theoretical model for this mismatch, in conjunction with finite element simulations of the evanescent strain field of the mechanical modes in the clamping region, allows us to quantitatively analyse data on position and force dependence of the tip-induced damping. Our experiments yield insights into the damping of nanoelectromechanical systems with the prospect of engineering the energy exchange in resonator networks.

  18. Energy losses of nanomechanical resonators induced by atomic force microscopy-controlled mechanical impedance mismatching

    PubMed Central

    Rieger, Johannes; Isacsson, Andreas; Seitner, Maximilian J.; Kotthaus, Jörg P.; Weig, Eva M.

    2014-01-01

    Clamping losses are a widely discussed damping mechanism in nanoelectromechanical systems, limiting the performance of these devices. Here we present a method to investigate this dissipation channel. Using an atomic force microscope tip as a local perturbation in the clamping region of a nanoelectromechanical resonator, we increase the energy loss of its flexural modes by at least one order of magnitude. We explain this by a transfer of vibrational energy into the cantilever, which is theoretically described by a reduced mechanical impedance mismatch between the resonator and its environment. A theoretical model for this mismatch, in conjunction with finite element simulations of the evanescent strain field of the mechanical modes in the clamping region, allows us to quantitatively analyse data on position and force dependence of the tip-induced damping. Our experiments yield insights into the damping of nanoelectromechanical systems with the prospect of engineering the energy exchange in resonator networks. PMID:24594876

  19. Maladaptation and phenotypic mismatch in hatchery-reared Atlantic salmon Salmo salar released in the wild.

    PubMed

    Stringwell, R; Lock, A; Stutchbury, C J; Baggett, E; Taylor, J; Gough, P J; Garcia de Leaniz, C

    2014-12-01

    Changes in body shape, fluctuating asymmetry (FA) and crypsis were compared among Atlantic salmon Salmo salar fry kept as controls in captivity and those released and subsequently recaptured in the wild according to a before-after-control-impact (BACI) design. Hatchery fish that survived in the wild became more cryptic and displayed a much lower incidence of fin erosion and of asymmetric individuals than control fish kept in captivity. Significant differences in body shape were also apparent, and survivors had longer heads, thicker caudal peduncles and a more streamlined body shape than hatchery controls as early as 20 days following stocking, most likely as a result of phenotypic plasticity and non-random, selective mortality of maladapted phenotypes. Hatchery-reared fish typically perform poorly in the wild and the results of this study indicate that this may be due to phenotypic mismatch, i.e. because hatcheries generate fish that are phenotypically mismatched to the natural environment.

  20. FAT-based adaptive control for pneumatic servo systems with mismatched uncertainties

    NASA Astrophysics Data System (ADS)

    Tsai, Yi-Chang; Huang, An-Chyau

    2008-08-01

    In this paper, a function approximation technique (FAT)-based adaptive controller is proposed for pneumatic servo systems with variable payload and uncertain disturbances. The system model is firstly described by a set of non-autonomous state equations with mismatched uncertainties. Since the uncertainties are time-varying and their variation bounds are not available, most traditional robust designs or adaptive strategies are not directly applicable. The FAT-based design is proposed here to estimate these uncertainties so that the closed-loop stability can be proved by using the Lyapunov-like theory. The problem in dealing with the mismatched uncertainties is circumvented by using the multiple-surface sliding control (MSSC) algorithm. Experimental results justify that the proposed scheme can give good performance regardless of various uncertainties.

  1. Phenological Dynamics and the Development of Trophic Mismatch in the Arctic

    NASA Astrophysics Data System (ADS)

    Post, E.; Boving, P.; Wilmers, C. C.; Pedersen, C.; Forchhammer, M. C.

    2008-12-01

    One of the ecological consequences of rising temperatures in the Arctic is an advancement of the timing of spring events such as the onset of the plant growing season. Here, we present data from Greenland illustrating that, while plant growth is occurring earlier there, the timing of arrival on breeding grounds by species such as caribou and muskoxen that are dependent upon those plants has not advanced. The result is a developing "trophic mismatch" between the timing of resource demand by reproducing females and the timing of resource availability by newly emergent forage plants. We will discuss the consequences this warming-induced trophic mismatch may pose for the persistence of mammalian herbivores in the Arctic.

  2. The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches.

    PubMed Central

    Carter, R J; Baeyens, K J; SantaLucia, J; Turner, D H; Holbrook, S R

    1997-01-01

    The X-ray crystallographic structure of the RNA duplex [r(CGCAIGCG)]2 has been refined to 2.5 A. It shows a symmetric internal loop of two non-Watson-Crick base pairs which form in the middle of the duplex. The tandem A-I/I-A pairs are related by a crystallographic two-fold axis. Both A(anti)-I(anti) mismatches are in a head-to-head conformation forming hydrogen bonds using the Watson-Crick positions. The octamer duplexes stack above one another in the cell forming a pseudo-infinite helix throughout the crystal. A hydrated calcium ion bridges between the 3'-terminal of one molecule and the backbone of another. The tandem A-I mismatches are incorporated with only minor distortion to the backbone. This is in contrast to the large helical perturbations often produced by sheared G-A pairs in RNA oligonucleotides. PMID:9321667

  3. Adaptive IF selection and IQ mismatch compensation in a low-IF GSM receiver

    NASA Astrophysics Data System (ADS)

    Cheng, Zhang; Lifang, Wang; Xi, Tan; Hao, Min

    2012-06-01

    This paper presents an algorithm that can adaptively select the intermediate frequency (IF) and compensate the IQ mismatch according to the power ratio of the adjacent channel interference to the desired signal in a low-IF GSM receiver. The IF can be adaptively selected between 100 and 130 kHz. Test result shows an improvement of phase error from 6.78° to 3.23°. Also a least mean squares (LMS) based IQ mismatch compensation algorithm is applied to improve image rejection ratio (IRR) for the desired signal along with strong adjacent channel interference. The IRR is improved from 29.1 to 44.3 dB in measurement. The design is verified in a low-IF GSM receiver fabricated in SMIC 0.13 μm RF CMOS process with a working voltage of 1.2 V.

  4. A review and summary of cell and module mismatch losses from theoretical and experimental studies

    NASA Technical Reports Server (NTRS)

    Lambarski, T. J.

    1983-01-01

    Studies on power loss due to photovoltaic (PV) cell and module parameter mismatch were reviewed. The losses result from the current voltage (I-V) characteristics of cells which vary over a manufactured lot. The peak power and the peak power I-V point vary from cell to cell. The largest parameter variation occurs in the cell photocurrent generation and the most significant loss occurs in series connections since all cells are essentially limited by the lowest photocurrent. Most theoretical studies address only photocurrent variation effects, which consider shunt and series resistance, ideality factor and saturation current to be comparatively insignificant. One study is identified which specifically configured the study of mismatch loss effects. Experimental results consist of estimates based on limited data not taken from specially configured tests.

  5. Surface reconstruction: An effective method for the growth of mismatched materials

    NASA Astrophysics Data System (ADS)

    Sun, Yu; Zheng, Beining; Wu, Xiaofeng; Yuan, Long; Wu, Jie; Guo, Hongping; Huang, Keke; Feng, Shouhua

    2016-01-01

    The crystalline quality of epitaxial films depends on the degree of lattice match between substrates and films. Here, we report a growth strategy for large mismatched epi-films to grow GaSb films on Si(1 1 1) substrates. The epitaxial strategy can be influenced by controlling the surface reconstructions of Sb-treated Si(1 1 1). The film with the best quality was grown on Si(1 1 1)-(5⿿3 ÿ 5⿿3)-Sb surface due to the stress release and the formation of a self-assembled 2D fishbone structure. Controlled surface engineering provides an effective pathway towards the growth of the large mismatched materials.

  6. Numerical study of supersonic combustors by multi-block grids with mismatched interfaces

    NASA Technical Reports Server (NTRS)

    Moon, Young J.

    1990-01-01

    A three dimensional, finite rate chemistry, Navier-Stokes code was extended to a multi-block code with mismatched interface for practical calculations of supersonic combustors. To ensure global conservation, a conservative algorithm was used for the treatment of mismatched interfaces. The extended code was checked against one test case, i.e., a generic supersonic combustor with transverse fuel injection, examining solution accuracy, convergence, and local mass flux error. After testing, the code was used to simulate the chemically reacting flow fields in a scramjet combustor with parallel fuel injectors (unswept and swept ramps). Computational results were compared with experimental shadowgraph and pressure measurements. Fuel-air mixing characteristics of the unswept and swept ramps were compared and investigated.

  7. Scalable solution-phase epitaxial growth of symmetry-mismatched heterostructures on two-dimensional crystal soft template

    PubMed Central

    Lin, Zhaoyang; Yin, Anxiang; Mao, Jun; Xia, Yi; Kempf, Nicholas; He, Qiyuan; Wang, Yiliu; Chen, Chih-Yen; Zhang, Yanliang; Ozolins, Vidvuds; Ren, Zhifeng; Huang, Yu; Duan, Xiangfeng

    2016-01-01

    Epitaxial heterostructures with precisely controlled composition and electronic modulation are of central importance for electronics, optoelectronics, thermoelectrics, and catalysis. In general, epitaxial material growth requires identical or nearly identical crystal structures with small misfit in lattice symmetry and parameters and is typically achieved by vapor-phase depositions in vacuum. We report a scalable solution-phase growth of symmetry-mismatched PbSe/Bi2Se3 epitaxial heterostructures by using two-dimensional (2D) Bi2Se3 nanoplates as soft templates. The dangling bond–free surface of 2D Bi2Se3 nanoplates guides the growth of PbSe crystal without requiring a one-to-one match in the atomic structure, which exerts minimal restriction on the epitaxial layer. With a layered structure and weak van der Waals interlayer interaction, the interface layer in the 2D Bi2Se3 nanoplates can deform to accommodate incoming layer, thus functioning as a soft template for symmetry-mismatched epitaxial growth of cubic PbSe crystal on rhombohedral Bi2Se3 nanoplates. We show that a solution chemistry approach can be readily used for the synthesis of gram-scale PbSe/Bi2Se3 epitaxial heterostructures, in which the square PbSe (001) layer forms on the trigonal/hexagonal (0001) plane of Bi2Se3 nanoplates. We further show that the resulted PbSe/Bi2Se3 heterostructures can be readily processed into bulk pellet with considerably suppressed thermal conductivity (0.30 W/m·K at room temperature) while retaining respectable electrical conductivity, together delivering a thermoelectric figure of merit ZT three times higher than that of the pristine Bi2Se3 nanoplates at 575 K. Our study demonstrates a unique epitaxy mode enabled by the 2D nanocrystal soft template via an affordable and scalable solution chemistry approach. It opens up new opportunities for the creation of diverse epitaxial heterostructures with highly disparate structures and functions. PMID:27730211

  8. A graphene solution to conductivity mismatch: spin injection from ferromagnetic metal/graphene tunnel contacts into silicon

    NASA Astrophysics Data System (ADS)

    van't Erve, Olaf

    2014-03-01

    New paradigms for spin-based devices, such as spin-FETs and reconfigurable logic, have been proposed and modeled. These devices rely on electron spin being injected, transported, manipulated and detected in a semiconductor channel. This work is the first demonstration on how a single layer of graphene can be used as a low resistance tunnel barrier solution for electrical spin injection into Silicon at room temperature. We will show that a FM metal / monolayer graphene contact serves as a spin-polarized tunnel barrier which successfully circumvents the classic metal / semiconductor conductivity mismatch issue for electrical spin injection. We demonstrate electrical injection and detection of spin accumulation in Si above room temperature, and show that the corresponding spin lifetimes correlate with the Si carrier concentration, confirming that the spin accumulation measured occurs in the Si and not in interface trap states. An ideal tunnel barrier should exhibit several key material characteristics: a uniform and planar habit with well-controlled thickness, minimal defect / trapped charge density, a low resistance-area product for minimal power consumption, and compatibility with both the FM metal and semiconductor, insuring minimal diffusion to/from the surrounding materials at temperatures required for device processing. Graphene, offers all of the above, while preserving spin injection properties, making it a compelling solution to the conductivity mismatch for spin injection into Si. Although Graphene is very conductive in plane, it exhibits poor conductivity perpendicular to the plane. Its sp2 bonding results in a highly uniform, defect free layer, which is chemically inert, thermally robust, and essentially impervious to diffusion. The use of a single monolayer of graphene at the Si interface provides a much lower RA product than any film of an oxide thick enough to prevent pinholes (1 nm). Our results identify a new route to low resistance-area product spin

  9. A Digital Differential Transmitter with Pseudo-LVDS Output Driver and Digital Mismatch Calibration

    NASA Astrophysics Data System (ADS)

    Bae, Jun-Hyun; Park, Sang-Hune; Sim, Jae-Yoon; Park, Hong-June

    A digital 3Gbps 0.2V differential transmitter is proposed using a voltage-mode pseudo-LVDS output driver. The delay mismatch between two pre-drivers is digitally calibrated by a modified digital DLL with the duty cycle correction. The height and width of eye opening are improved by 103% and 46%, respectively. The power consumption is 11.4mW at 1.2V with 0.18µm process.

  10. Robust Sierpiński triangle fractals on symmetry-mismatched Ag(100).

    PubMed

    Zhang, Xue; Li, Na; Liu, Liwei; Gu, Gaochen; Li, Chao; Tang, Hao; Peng, Lianmao; Hou, Shimin; Wang, Yongfeng

    2016-08-18

    Sierpiński triangle fractals were constructed on both Ag(111) and symmetry-mismatched fourfold Ag(100) surfaces through chemical reaction between H3PH molecules and Fe atoms under vacuum. Density functional theory calculations revealed that the fractals were stabilized by the strong coordination interaction between Fe and O atoms. In comparison, pure H3PH molecules formed fractals via moderately strong hydrogen bonds only on Ag(111), not on Ag(100).

  11. Questioning the role of phenology shifts and trophic mismatching in a planktonic food web

    NASA Astrophysics Data System (ADS)

    Atkinson, Angus; Harmer, Rachel A.; Widdicombe, Claire E.; McEvoy, Andrea J.; Smyth, Tim J.; Cummings, Denise G.; Somerfield, Paul J.; Maud, Jacqueline L.; McConville, Kristian

    2015-09-01

    In a warming climate, differential shifts in the seasonal timing of predators and prey have been suggested to lead to trophic "mismatches" that decouple primary, secondary and tertiary production. We tested this hypothesis using a 25-year time-series of weekly sampling at the Plymouth L4 site, comparing 57 plankton taxa spanning 4 trophic levels. During warm years, there was a weak tendency for earlier timings of spring taxa and later timings of autumn taxa. While this is in line with many previous findings, numerous exceptions existed and only a few taxa (e.g. Gyrodinium spp., Pseudocalanus elongatus, and Acartia clausi) showed consistent, strong evidence for temperature-related timing shifts, revealed by all 4 of the timing indices that we used. Also, the calculated offsets in timing (i.e. "mismatches") between predator and prey were no greater in extreme warm or cold years than during more average years. Further, the magnitude of these offsets had no effect on the "success" of the predator, in terms of their annual mean abundance or egg production rates. Instead numerous other factors override, including: inter-annual variability in food quantity, high food baseline levels, turnover rates and prolonged seasonal availability, allowing extended periods of production. Furthermore many taxa, notably meroplankton, increased well before the spring bloom. While theoretically a chronic mismatch, this likely reflects trade-offs for example in predation avoidance. Various gelatinous taxa (Phaeocystis, Noctiluca, ctenophores, appendicularians, medusae) may have reduced these predation constraints, with variable, explosive population outbursts likely responding to improved conditions. The match-mismatch hypothesis may apply for highly seasonal, pulsed systems or specialist feeders, but we suggest that the concept is being over-extended to other marine systems where multiple factors compensate.

  12. The effect of Hartmann-Hahn mismatching on polarization inversion spin exchange at the magic angle.

    PubMed

    Fu, Riqiang; Tian, Changlin; Kim, Hyeongnam; Smith, Scott A; Cross, Timothy A

    2002-12-01

    The effect of the Hartmann-Hahn mismatch delta = omega(eff)-omega(1S) during polarization inversion spin exchange at the magic angle (PISEMA) has been investigated, where omega(eff) and omega(1S) represent the amplitudes of the 1H effective spin-locking field at the magic angle and the 15N RF spin-locking field, respectively. During the PISEMA evolution period, the exact Hartmann-Hahn match condition (i.e., delta = 0) yields a maximum dipolar scaling factor of 0.816 for PISEMA experiments, while any mismatch results in two different effective fields for the first and second half of each frequency switched Lee-Goldburg (FSLG) cycle. The mismatch effect on the scaling factor depends strongly on the transition angle from one effective field to the other within each FSLG cycle as well as on the cycle time. At low RF spin-lock amplitudes in which the FSLG cycle time is relatively long, the scaling factor rapidly becomes smaller as omega(1S) becomes greater than omega(eff). On the other hand, when omega(1S) < omega(eff), there is relatively little effect on the scaling factor with variation in delta. As a result, the presence of RF inhomogeneities may significantly broaden the line-width in the dipolar dimension because of the mismatch effect. Higher RF spin-lock amplitudes result in a relatively small variation for the scaling factor. Furthermore, ramped amplitude of the 15N RF spin-lock field in synchronization with the flip-flop of the FSLG sequence minimizes the transition angle between the two effective fields within the FSLG cycle. It is shown experimentally that such a ramped amplitude not only gives rise to the same scaling factor but also results in a narrower dipolar line-width in comparison with the rectangular amplitude.

  13. Climate warming, ecological mismatch at arrival and population decline in migratory birds.

    PubMed

    Saino, Nicola; Ambrosini, Roberto; Rubolini, Diego; von Hardenberg, Jost; Provenzale, Antonello; Hüppop, Kathrin; Hüppop, Ommo; Lehikoinen, Aleksi; Lehikoinen, Esa; Rainio, Kalle; Romano, Maria; Sokolov, Leonid

    2011-03-22

    Climate is changing at a fast pace, causing widespread, profound consequences for living organisms. Failure to adjust the timing of life-cycle events to climate may jeopardize populations by causing ecological mismatches to the life cycle of other species and abiotic factors. Population declines of some migratory birds breeding in Europe have been suggested to depend on their inability to adjust migration phenology so as to keep track of advancement of spring events at their breeding grounds. In fact, several migrants have advanced their spring arrival date, but whether such advancement has been sufficient to compensate for temporal shift in spring phenophases or, conversely, birds have become ecologically mismatched, is still an unanswered question, with very few exceptions. We used a novel approach based on accumulated winter and spring temperatures (degree-days) as a proxy for timing of spring biological events to test if the progress of spring at arrival to the breeding areas by 117 European migratory bird species has changed over the past five decades. Migrants, and particularly those wintering in sub-Saharan Africa, now arrive at higher degree-days and may have therefore accumulated a 'thermal delay', thus possibly becoming increasingly mismatched to spring phenology. Species with greater 'thermal delay' have shown larger population decline, and this evidence was not confounded by concomitant ecological factors or by phylogenetic effects. These findings provide general support to the largely untested hypotheses that migratory birds are becoming ecologically mismatched and that failure to respond to climate change can have severe negative impacts on their populations. The novel approach we adopted can be extended to the analysis of ecological consequences of phenological response to climate change by other taxa.

  14. Projective synchronization of fractional-order memristive neural networks with switching jumps mismatch

    NASA Astrophysics Data System (ADS)

    Zhang, Lingzhong; Yang, Yongqing; Wang, Fei

    2017-04-01

    This paper investigates the projective synchronization of fractional-order memristor-based neural networks (FMNNs) with switching jumps mismatch and time-varying delays. According to the theory of discontinuous differential system (Filippov) and differential inclusions, a fractional order inequality was introduced. Based on notoriously Barbalat's lemma and Razumikhin-type stability theorem, some projective synchronization criteria of FMNNs are derived. These results extend the previous publications. To illustrate the effectiveness of the proposed results, two numerical examples are presented.

  15. Impact and Mitigation of Multiantenna Analog Front-End Mismatch in Transmit Maximum Ratio Combining

    NASA Astrophysics Data System (ADS)

    Liu, Jian; Khaled, Nadia; Petré, Frederik; Bourdoux, André; Barel, Alain

    2006-12-01

    Transmit maximum ratio combining (MRC) allows to extend the range of wireless local area networks (WLANs) by exploiting spatial diversity and array gains. These gains, however, depend on the availability of the channel state information (CSI). In this perspective, an open-loop approach in time-division-duplex (TDD) systems relies on channel reciprocity between up- and downlink to acquire the CSI. Although the propagation channel can be assumed to be reciprocal, the radio-frequency (RF) transceivers may exhibit amplitude and phase mismatches between the up- and downlink. In this contribution, we present a statistical analysis to assess the impact of these mismatches on the performance of transmit-MRC. Furthermore, we propose a novel mixed-signal calibration scheme to mitigate these mismatches, which allows to reduce the implementation loss to as little as a few tenths of a dB. Finally, we also demonstrate the feasibility of the proposed calibration scheme in a real-time wireless MIMO-OFDM prototyping platform.

  16. Fabrication and characterization of multiband solar cells based on highly mismatched alloys

    NASA Astrophysics Data System (ADS)

    López, N.; Braña, A. F.; García Núñez, C.; Hernández, M. J.; Cervera, M.; Martínez, M.; Yu, K. M.; Walukiewicz, W.; García, B. J.

    2015-10-01

    Multiband solar cells are one type of third generation photovoltaic devices in which an increase of the power conversion efficiency is achieved through the absorption of low energy photons while preserving a large band gap that determines the open circuit voltage. The ability to absorb photons from different parts of the solar spectrum originates from the presence of an intermediate energy band located within the band gap of the material. This intermediate band, acting as a stepping stone allows the absorption of low energy photons to transfer electrons from the valence band to the conduction band by a sequential two photons absorption process. It has been demonstrated that highly mismatched alloys offer a potential to be used as a model material system for practical realization of multiband solar cells. Dilute nitride GaAs1-xNx highly mismatched alloy with low mole fraction of N is a prototypical multiband semiconductor with a well-defined intermediate band. Currently, we are using chemical beam epitaxy to synthesize dilute nitride highly mismatched alloys. The materials are characterized by a variety of structural and optical methods to optimize their properties for multiband photovoltaic devices.

  17. Mismatch or allostatic load? Timing of life adversity differentially shapes gray matter volume and anxious temperament.

    PubMed

    Kuhn, Manuel; Scharfenort, Robert; Schümann, Dirk; Schiele, Miriam A; Münsterkötter, Anna L; Deckert, Jürgen; Domschke, Katharina; Haaker, Jan; Kalisch, Raffael; Pauli, Paul; Reif, Andreas; Romanos, Marcel; Zwanzger, Peter; Lonsdorf, Tina B

    2016-04-01

    Traditionally, adversity was defined as the accumulation of environmental events (allostatic load). Recently however, a mismatch between the early and the later (adult) environment (mismatch) has been hypothesized to be critical for disease development, a hypothesis that has not yet been tested explicitly in humans. We explored the impact of timing of life adversity (childhood and past year) on anxiety and depression levels (N = 833) and brain morphology (N = 129). Both remote (childhood) and proximal (recent) adversities were differentially mirrored in morphometric changes in areas critically involved in emotional processing (i.e. amygdala/hippocampus, dorsal anterior cingulate cortex, respectively). The effect of adversity on affect acted in an additive way with no evidence for interactions (mismatch). Structural equation modeling demonstrated a direct effect of adversity on morphometric estimates and anxiety/depression without evidence of brain morphology functioning as a mediator. Our results highlight that adversity manifests as pronounced changes in brain morphometric and affective temperament even though these seem to represent distinct mechanistic pathways. A major goal of future studies should be to define critical time periods for the impact of adversity and strategies for intervening to prevent or reverse the effects of adverse childhood life experiences.

  18. An interplay of the base excision repair and mismatch repair pathways in active DNA demethylation

    PubMed Central

    Grin, Inga; Ishchenko, Alexander A.

    2016-01-01

    Active DNA demethylation (ADDM) in mammals occurs via hydroxylation of 5-methylcytosine (5mC) by TET and/or deamination by AID/APOBEC family enzymes. The resulting 5mC derivatives are removed through the base excision repair (BER) pathway. At present, it is unclear how the cell manages to eliminate closely spaced 5mC residues whilst avoiding generation of toxic BER intermediates and whether alternative DNA repair pathways participate in ADDM. It has been shown that non-canonical DNA mismatch repair (ncMMR) can remove both alkylated and oxidized nucleotides from DNA. Here, a phagemid DNA containing oxidative base lesions and methylated sites are used to examine the involvement of various DNA repair pathways in ADDM in murine and human cell-free extracts. We demonstrate that, in addition to short-patch BER, 5-hydroxymethyluracil and uracil mispaired with guanine can be processed by ncMMR and long-patch BER with concomitant removal of distant 5mC residues. Furthermore, the presence of multiple mispairs in the same MMR nick/mismatch recognition region together with BER-mediated nick formation promotes proficient ncMMR resulting in the reactivation of an epigenetically silenced reporter gene in murine cells. These findings suggest cooperation between BER and ncMMR in the removal of multiple mismatches that might occur in mammalian cells during ADDM. PMID:26843430

  19. A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem.

    PubMed

    Thankachan, Sharma V; Apostolico, Alberto; Aluru, Srinivas

    2016-06-01

    Alignment-free sequence comparison methods are attracting persistent interest, driven by data-intensive applications in genome-wide molecular taxonomy and phylogenetic reconstruction. Among all the methods based on substring composition, the average common substring (ACS) measure admits a straightforward linear time sequence comparison algorithm, while yielding impressive results in multiple applications. An important direction of this research is to extend the approach to permit a bounded edit/hamming distance between substrings, so as to reflect more accurately the evolutionary process. To date, however, algorithms designed to incorporate k ≥ 1 mismatches have O(n(2)) worst-case time complexity, where n is the total length of the input sequences. On the other hand, accounting for mismatches has shown to lead to much improved classification, while heuristics can improve practical performance. In this article, we close the gap by presenting the first provably efficient algorithm for the k-mismatch average common string (ACSk) problem that takes O(n) space and O(n log(k) n) time in the worst case for any constant k. Our method extends the generalized suffix tree model to incorporate a carefully selected bounded set of perturbed suffixes, and can be applied to other complex approximate sequence matching problems.

  20. Applying different equations to evaluate the level of mismatch between students and school furniture.

    PubMed

    Castellucci, H I; Arezes, P M; Molenbroek, J F M

    2014-07-01

    The mismatch between students and school furniture is likely to result in a number of negative effects, such as uncomfortable body posture, pain, and ultimately, it may also affect the learning process. This study's main aim is to review the literature describing the criteria equations for defining the mismatch between students and school furniture, to apply these equations to a specific sample and, based on the results, to propose a methodology to evaluate school furniture suitability. The literature review comprises one publications database, which was used to identify the studies carried out in the field of the abovementioned mismatch. The sample used for testing the different equations was composed of 2261 volunteer subjects from 14 schools. Fifteen studies were found to meet the criteria of this review and 21 equations to test 6 furniture dimensions were identified. Regarding seat height, there are considerable differences between the two most frequently used equations. Although seat to desk clearance was evaluated by knee height, this condition seems to be based on the false assumption that students are sitting on a chair with a proper seat height. Finally, the proposed methodology for suitability evaluation of school furniture should allow for a more reliable analysis of school furniture.

  1. Mismatched partners that achieve postpairing behavioral similarity improve their reproductive success

    PubMed Central

    Laubu, Chloé; Dechaume-Moncharmont, François-Xavier; Motreuil, Sébastien; Schweitzer, Cécile

    2016-01-01

    Behavioral similarity between partners is likely to promote within-pair compatibility and to result in better reproductive success. Therefore, individuals are expected to choose a partner that is alike in behavioral type. However, mate searching is very costly and does not guarantee finding a matching partner. If mismatched individuals pair, they may benefit from increasing their similarity after pairing. We show in a monogamous fish species—the convict cichlid—that the behavioral similarity between mismatched partners can increase after pairing. This increase resulted from asymmetrical adjustment because only the reactive individual became more alike its proactive partner, whereas the latter did not change its behavior. The mismatched pairs that increased their similarity not only improved their reproductive success but also raised it up to the level of matched pairs. While most studies assume that assortative mating results from mate choice, our study suggests that postpairing adjustment could be an alternative explanation for the high behavioral similarity between partners observed in the field. It also explains why interindividual behavioral differences can be maintained within a given population. PMID:26973869

  2. Allocentric or Craniocentric Representation of Acoustic Space: An Electrotomography Study Using Mismatch Negativity

    PubMed Central

    Altmann, Christian F.; Getzmann, Stephan; Lewald, Jörg

    2012-01-01

    The world around us appears stable in spite of our constantly moving head, eyes, and body. How this is achieved by our brain is hardly understood and even less so in the auditory domain. Using electroencephalography and the so-called mismatch negativity, we investigated whether auditory space is encoded in an allocentric (referenced to the environment) or craniocentric representation (referenced to the head). Fourteen subjects were presented with noise bursts from loudspeakers in an anechoic environment. Occasionally, subjects were cued to rotate their heads and a deviant sound burst occurred, that deviated from the preceding standard stimulus either in terms of an allocentric or craniocentric frame of reference. We observed a significant mismatch negativity, i.e., a more negative response to deviants with reference to standard stimuli from about 136 to 188 ms after stimulus onset in the craniocentric deviant condition only. Distributed source modeling with sLORETA revealed an involvement of lateral superior temporal gyrus and inferior parietal lobule in the underlying neural processes. These findings suggested a craniocentric, rather than allocentric, representation of auditory space at the level of the mismatch negativity. PMID:22848643

  3. Compensation strategy to reduce geometry and mechanics mismatches in porous biomaterials built with Selective Laser Melting.

    PubMed

    Bagheri, Zahra S; Melancon, David; Liu, Lu; Johnston, R Burnett; Pasini, Damiano

    2016-05-06

    The accuracy of Additive Manufacturing processes in fabricating porous biomaterials is currently limited by their capacity to render pore morphology that precisely matches its design. In a porous biomaterial, a geometric mismatch can result in pore occlusion and strut thinning, drawbacks that can inherently compromise bone ingrowth and severely impact mechanical performance. This paper focuses on Selective Laser Melting of porous microarchitecture and proposes a compensation scheme that reduces the morphology mismatch between as-designed and as-manufactured geometry, in particular that of the pore. A spider web analog is introduced, built out of Ti-6Al-4V powder via SLM, and morphologically characterized. Results from error analysis of strut thickness are used to generate thickness compensation relations expressed as a function of the angle each strut formed with the build plane. The scheme is applied to fabricate a set of three-dimensional porous biomaterials, which are morphologically and mechanically characterized via micro Computed Tomography, mechanically tested and numerically analyzed. For strut thickness, the results show the largest mismatch (60% from the design) occurring for horizontal members, reduces to 3.1% upon application of the compensation. Similar improvement is observed also for the mechanical properties, a factor that further corroborates the merit of the design-oriented scheme here introduced.

  4. Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes

    PubMed Central

    Mishra, Sourav; Lahiri, Hiya; Banerjee, Siddhartha; Mukhopadhyay, Rupa

    2016-01-01

    So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for ‘lab-on-a-chip’ type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored. PMID:27025649

  5. Analysis of mismatch and shading effects in a photovoltaic array using different technologies

    NASA Astrophysics Data System (ADS)

    Guerrero, J.; Muñoz, Y.; Ibáñez, F.; Ospino, A.

    2014-06-01

    In this paper, we analyze the performance of a photovoltaic array implemented in the Universidad Politécnica de Valencia which consists of modules of different technologies and power, connected in series, in order to quantify the energy losses due to mismatch and the effect of the shadows. To do this, the performance of the modules was measured in operation under ambient conditions with field measurement equipment (AMPROBE Solar Analyzer, Solar - 4000), which allows the extrapolation of measures to standard conditions STC. For the data validation, measures under controlled conditions were taken to some modules in the flash test laboratory of the Institute of Energy Technology ITE of Valencia in Spain. Subsequently the array curves measured were validated with a photovoltaic array model developed in MATLAB-Simulink for the same conditions and technologies. The results of this particular array are lost up to 20% of the energy supplied due to the modules mismatch. The study shows the curves and the energy loss due to shadows modules. This result opens scenarios for conceivable modifications to the PV field configurations today, chosen during the design stage and unchangeable during the operating stage; and gives greater importance to the energy loss by mismatch in the PV array.

  6. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

    NASA Technical Reports Server (NTRS)

    Urakawa, Hidetoshi; El Fantroussi, Said; Smidt, Hauke; Smoot, James C.; Tribou, Erik H.; Kelly, John J.; Noble, Peter A.; Stahl, David A.

    2003-01-01

    The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

  7. Auditory cortical and hippocampal-system mismatch responses to duration deviants in urethane-anesthetized rats.

    PubMed

    Ruusuvirta, Timo; Lipponen, Arto; Pellinen, Eeva; Penttonen, Markku; Astikainen, Piia

    2013-01-01

    Any change in the invariant aspects of the auditory environment is of potential importance. The human brain preattentively or automatically detects such changes. The mismatch negativity (MMN) of event-related potentials (ERPs) reflects this initial stage of auditory change detection. The origin of MMN is held to be cortical. The hippocampus is associated with a later generated P3a of ERPs reflecting involuntarily attention switches towards auditory changes that are high in magnitude. The evidence for this cortico-hippocampal dichotomy is scarce, however. To shed further light on this issue, auditory cortical and hippocampal-system (CA1, dentate gyrus, subiculum) local-field potentials were recorded in urethane-anesthetized rats. A rare tone in duration (deviant) was interspersed with a repeated tone (standard). Two standard-to-standard (SSI) and standard-to-deviant (SDI) intervals (200 ms vs. 500 ms) were applied in different combinations to vary the observability of responses resembling MMN (mismatch responses). Mismatch responses were observed at 51.5-89 ms with the 500-ms SSI coupled with the 200-ms SDI but not with the three remaining combinations. Most importantly, the responses appeared in both the auditory-cortical and hippocampal locations. The findings suggest that the hippocampus may play a role in (cortical) manifestation of MMN.

  8. Segmental mismatch in crustacean appendages: the naupliar antennal exopod of Artemia (Crustacea, Branchiopoda, Anostraca).

    PubMed

    Maruzzo, Diego; Minelli, Alessandro; Fusco, Giuseppe

    2009-03-01

    Based on traditional techniques and confocal laser scanning microscopy for external morphology, and immunohistochemistry for the muscular system, we describe here the segmental features of the antennal exopod of Artemia nauplii. Two kinds of serial elements are present, i.e. setae (with cuticular folds at their base) and ringlets (serially arranged sclerites separated by joint-like cuticular folds not extending to form complete rings around the appendage). The two series are usually not in register. The cuticular folds of the setae and of the ringlets are also sites of intermediate insertions of the three exopod muscles: as the two tegumentary structures are discordant in periodicity, this is also mirrored in the pattern of muscle insertions on the two sides of the appendage. Similar cases of segmental mismatch are known for the trunk of several arthropods, but segmental mismatch along the appendages has received very little attention. The occurrence of segmental mismatch in the naupliar appendages of both extant and fossil crustaceans is reviewed and it is suggested here to be a primitive feature of the exopods of both second antennae and mandibles. Problems in the interpretation of morphological evidence are discussed, also in relation to development and evolution of segmentation of naupliar appendages.

  9. The effect of mismatched recording conditions on human and automatic speaker recognition in forensic applications.

    PubMed

    Alexander, A; Botti, F; Dessimoz, D; Drygajlo, A

    2004-12-02

    In this paper, we analyse mismatched technical conditions in training and testing phases of speaker recognition and their effect on forensic human and automatic speaker recognition. We use perceptual tests performed by non-experts and compare their performance with that of a baseline automatic speaker recognition system. The degradation of the accuracy of human recognition in mismatched recording conditions is contrasted with that of the automatic system under similar recording conditions. The conditions considered are of public switched telephone network (PSTN) and global system for mobile communications (GSM) transmission and background noise. The perceptual cues that the human subjects use to perceive differences in voices are studied along with their importance in different conditions. We discuss the possibility of increasing the accuracy of automatic systems using the perceptual cues that remain robust to mismatched conditions. We estimate the strength of evidence for both humans and automatic systems, calculating likelihood ratios using the perceptual scores for humans and the log-likelihood scores for automatic systems.

  10. Methylene blue treatment delays progression of perfusion-diffusion mismatch to infarct in permanent ischemic stroke.

    PubMed

    Rodriguez, Pavel; Jiang, Zhao; Huang, Shiliang; Shen, Qiang; Duong, Timothy Q

    2014-11-07

    Stroke is a leading cause of morbidity and mortality in the world. Low-dose methylene blue (MB), which has been used safely to treat methemoglobinemia and cyanide poisoning in humans, has energy enhancing and antioxidant properties. We tested the hypothesis that methylene blue treatment delays progression of at-risk tissue (ca. perfusion-diffusion mismatch) to infarct in permanent middle cerebral artery occlusion in rats at two MB treatment doses. Serial MRI was used to evaluate MB treatment efficacy. The major findings were: (i) MB significantly prolonged the perfusion-diffusion mismatch, (ii) MB mildly increased the CBF in the hypoperfused tissue, (iii) MB did not change the final infarct volume in permanent ischemic stroke, and (iv) there were no dose-dependent effects on mismatch progression for the 1 and 3mg/kg doses studied. This neuroprotective effect is likely the result of sustained ATP production and increased CBF to tissue at risk. This work has the potential to readily lead to clinical stroke trials given MB's excellent safety profile.

  11. Mismatch negativity at Fz in response to within-category changes of the vowel /i/.

    PubMed

    Marklund, Ellen; Schwarz, Iris-Corinna; Lacerda, Francisco

    2014-07-09

    The amplitude of the mismatch negativity response for acoustic within-category deviations in speech stimuli was investigated by presenting participants with different exemplars of the vowel /i/ in an odd-ball paradigm. The deviants differed from the standard either in terms of fundamental frequency, the first formant, or the second formant. Changes in fundamental frequency are generally more salient than changes in the first formant, which in turn are more salient than changes in the second formant. The mismatch negativity response was expected to reflect this with greater amplitude for more salient deviations. The fundamental frequency deviants did indeed result in greater amplitude than both first formant deviants and second formant deviants, but no difference was found between the first formant deviants and the second formant deviants. It is concluded that greater difference between standard and within-category deviants across different acoustic dimensions results in greater mismatch negativity amplitude, suggesting that the processing of linguistically irrelevant changes in speech sounds may be processed similar to nonspeech sound changes.

  12. The stress-coping (mis)match hypothesis for nature × nurture interactions.

    PubMed

    Homberg, Judith R

    2012-01-13

    There is high consensus that stress-related disorders like depression are shaped by nature×nurture interactions. However, the complexity appears larger than envisaged and nature×nurture research is progressing too slowly. An important reason is that mainstream research is focussing on the idea that a combination of genotypic stress-sensitivity and stress exposure inevitably leads to maladaptive stress-coping responses, and thereby stress-related disorders. However, stress-coping responses can also be adaptive and adhere to the expected norm. Here I elaborate the 'environment' mismatch hypothesis proposed by Mathias Schmidt (Psychoneuroendocrinology, 36, 330-338, 2011) to the stress-coping (mis)match (SCM) hypothesis postulating that stress-coping responses-as programmed by nature×age-dependent nurture interactions-are adaptive when they match current stress conditions, but maladaptive when they mismatch current stress conditions. For instance, acquisition of an active stress-coping response during nurture may lead to the programmed release of active coping responses in current life. This is adaptive when current stress is escapable, but maladaptive when current stress is inescapable, leading to agitation. A model par example for nature×nurture interactions is the serotonin transporter promoter polymorphism, which will be discussed in the framework of the SCM hypothesis. The potential role of the prefrontal-amygdala circuit and the therapeutic implications of the SCM hypothesis will also be discussed.

  13. Mismatch or allostatic load? Timing of life adversity differentially shapes gray matter volume and anxious temperament

    PubMed Central

    Kuhn, Manuel; Scharfenort, Robert; Schümann, Dirk; Schiele, Miriam A.; Münsterkötter, Anna L.; Deckert, Jürgen; Domschke, Katharina; Haaker, Jan; Kalisch, Raffael; Pauli, Paul; Reif, Andreas; Romanos, Marcel; Zwanzger, Peter

    2016-01-01

    Traditionally, adversity was defined as the accumulation of environmental events (allostatic load). Recently however, a mismatch between the early and the later (adult) environment (mismatch) has been hypothesized to be critical for disease development, a hypothesis that has not yet been tested explicitly in humans. We explored the impact of timing of life adversity (childhood and past year) on anxiety and depression levels (N = 833) and brain morphology (N = 129). Both remote (childhood) and proximal (recent) adversities were differentially mirrored in morphometric changes in areas critically involved in emotional processing (i.e. amygdala/hippocampus, dorsal anterior cingulate cortex, respectively). The effect of adversity on affect acted in an additive way with no evidence for interactions (mismatch). Structural equation modeling demonstrated a direct effect of adversity on morphometric estimates and anxiety/depression without evidence of brain morphology functioning as a mediator. Our results highlight that adversity manifests as pronounced changes in brain morphometric and affective temperament even though these seem to represent distinct mechanistic pathways. A major goal of future studies should be to define critical time periods for the impact of adversity and strategies for intervening to prevent or reverse the effects of adverse childhood life experiences. PMID:26568620

  14. Spring temperature, clutch initiation date and duck nest success: a test of the mismatch hypothesis.

    PubMed

    Drever, Mark C; Clark, Robert G

    2007-01-01

    1. Increases in average global temperature during the twentieth century have prompted calls for research on the effect of temperature variation on avian population dynamics. Particular attention has been paid to the hypothesis that increased temperatures may affect a species' ability to shift their breeding efforts to match the phenology of their prey, and thus result in reduced reproductive success (the 'mismatch hypothesis'). 2. We used data from a long-term study of breeding ducks to investigate how duck nest success varied with clutch initiation date, and to test whether spring temperature affected this relationship in a manner consistent with the mismatch hypothesis. We modelled five possible functional forms of how nest success might vary with clutch initiation date and spring temperature, and used an information-theoretic approach to determine which model best described the nesting outcomes of five dabbling duck species nesting in Saskatchewan, Canada. 3. Probability of nest success for the five species did not vary strongly with clutch initiation date, and we found evidence consistent with the mismatch hypothesis for one species, northern pintail Anas acuta, although weight of evidence was weak. 4. Overall nest success of all five species was positively associated with spring temperature. These results suggest that increasing spring temperature alone (within the range observed in this study) may not affect nest success in a manner that would result in lower populations of breeding ducks.

  15. Effects of impedance mismatch and coaxial cable length on absolute gravimeters

    NASA Astrophysics Data System (ADS)

    Křen, Petr; Pálinkáš, Vojtech; Mašika, Pavel; Vaľko, Miloš

    2017-04-01

    The systematic effects of absolute gravimeters have to be investigated to fully utilize their capabilities in metrology and geosciences. In Křen et al (2016 Metrologia 53 27–40) we found that for an FG5 gravimeter, even a few meter long coaxial cable used for transmission of fringe signal causes systematic features in residuals and errors at the level of 1–2 µGal. In this paper, we present experimental results and appropriate models to explain the effects that were found to be caused by impedance mismatches of electronic components and dispersion effects in coaxial cables of gravimeters. The experimental results have been obtained for analogue and transistor–transistor logic (TTL) compatible signals in the FG5-215 gravimeter and for a TTL signal in the FG5X-251 gravimeter. We found that dispersion and impedance mismatch effects are similar for both gravimeters. Furthermore, we describe a model of the dispersion that allows an evaluation of the effect/correction for a given range of the free-fall and thus it is also applicable to other gravimeters. The effect of impedance mismatch for the analogue fringe signal is modelled as an effect of the reflected electronic signal on the evaluation of zero-crossings. The applicability of this model for TTL signal is also discussed.

  16. Radio metric errors due to mismatch and offset between a DSN antenna beam and the beam of a troposphere calibration instrument

    NASA Technical Reports Server (NTRS)

    Linfield, R. P.; Wilcox, J. Z.

    1993-01-01

    Two components of the error of a troposphere calibration measurement were quantified by theoretical calculations. The first component is a beam mismatch error, which occurs when the calibration instrument senses a conical volume different from the cylindrical volume sampled by a Deep Space Network (DSN) antenna. The second component is a beam offset error, which occurs if the calibration instrument is not mounted on the axis of the DSN antenna. These two error sources were calculated for both delay (e.g., VLBI) and delay rate (e.g., Doppler) measurements. The beam mismatch error for both delay and delay rate drops rapidly as the beamwidth of the troposphere calibration instrument (e.g., a water vapor radiometer or an infrared Fourier transform spectrometer) is reduced. At a 10-deg elevation angle, the instantaneous beam mismatch error is 1.0 mm for a 6-deg beamwidth and 0.09 mm for a 0.5-deg beam (these are the full angular widths of a circular beam with uniform gain out to a sharp cutoff). Time averaging for 60-100 sec will reduce these errors by factors of 1.2-2.2. At a 20-deg elevation angle, the lower limit for current Doppler observations, the beam-mismatch delay rate error is an Allan standard deviation over 100 sec of 1.1 x 10(exp -14) with a 4-deg beam and 1.3 x 10(exp -l5) for a 0.5-deg beam. A 50-m beam offset would result in a fairly modest (compared to other expected error sources) delay error (less than or equal to 0.3 mm for 60-sec integrations at any elevation angle is greater than or equal to 6 deg). However, the same offset would cause a large error in delay rate measurements (e.g., an Allan standard deviation of 1.2 x 10(exp -14) over 100 sec at a 20-deg elevation angle), which would dominate over other known error sources if the beamwidth is 2 deg or smaller. An on-axis location is essential for accurate troposphere calibration of delay rate measurements. A half-power beamwidth (for a beam with a tapered gain profile) of 1.2 deg or smaller is

  17. A monofunctional platinum complex coordinated to a rhodium metalloinsertor selectively binds mismatched DNA in the minor groove.

    PubMed

    Weidmann, Alyson G; Barton, Jacqueline K

    2015-10-05

    We report the synthesis and characterization of a bimetallic complex derived from a new family of potent and selective metalloinsertors containing an unusual Rh-O axial coordination. This complex incorporates a monofunctional platinum center containing only one labile site for coordination to DNA, rather than two, and coordinates DNA nonclassically through adduct formation in the minor groove. This conjugate displays bifunctional, interdependent binding of mismatched DNA via metalloinsertion at a mismatch as well as covalent platinum binding. DNA sequencing experiments revealed that the preferred site of platinum coordination is not the traditional N7-guanine site in the major groove, but rather N3-adenine in the minor groove. The complex also displays enhanced cytotoxicity in mismatch repair-deficient and mismatch repair-proficient human colorectal carcinoma cell lines compared to the chemotherapeutic cisplatin, and it triggers cell death via an apoptotic pathway, rather than the necrotic pathway induced by rhodium metalloinsertors.

  18. Evidence for the role of German final devoicing in pre-attentive speech processing: a mismatch negativity study

    PubMed Central

    Truckenbrodt, Hubert; Steinberg, Johanna; Jacobsen, Thomas K.; Jacobsen, Thomas

    2014-01-01

    Results of a mismatch negativity experiment are reported in which the pre-attentive relevance of the German phonological alternation of final devoicing (FD) is shown in two ways. The experiment employs pseudowords. (1) A deviant [vus] paired with standard /vuzə/ did not show a mismatch effect for the voicing change in /z/ versus [s] because the two can be related by FD. When standard and deviant were reversed, the two could not be related by FD and a mismatch effect for the voicing difference occurred. (2) An ill-formed deviant that violates FD, *[vuz], triggered mismatch effects that were plausibly attributed to its ill-formedness. The results show that a syllable-related process like FD is already taken into account by the processing system in early pre-attentive processing. PMID:25505433

  19. Role of Cell Cycle Regulation and MLH1, A Key DNA Mismatch Repair Protein, In Adaptive Survival Responses. Final Report

    SciTech Connect

    David A. Boothman

    1999-08-11

    Due to several interesting findings on both adaptive survival responses (ASRs) and DNA mismatch repair (MMR), this grant was separated into two discrete Specific Aim sets (each with their own discrete hypotheses). The described experiments were simultaneously performed.

  20. Science-Technology-Society (STS) and ChemCom Courses versus College Chemistry Courses: Is There a Mismatch?

    ERIC Educational Resources Information Center

    Sanger, Michael J.; Greenbowe, Thomas J.

    1996-01-01

    This opinion paper discusses several issues surrounding questions of ChemCom and STS courses taken by science majors. Explores the basis for a potential mismatch students having an STS-based course may experience. Discusses objectivism and constructivism. (MKR)

  1. A Monofunctional Platinum Complex Coordinated to a Rhodium Metalloinsertor Selectively Binds Mismatched DNA in the Minor Groove

    PubMed Central

    Weidmann, Alyson G.; Barton, Jacqueline K.

    2015-01-01

    We report the synthesis and characterization of a bimetallic complex derived from a new family of potent and selective metalloinsertors containing an unusual Rh—O axial coordination. This complex incorporates a monofunctional platinum center containing only one labile site for coordination to DNA, rather than two, and coordinates DNA non-classically through adduct formation in the minor groove. This conjugate displays bifunctional, interdependent binding of mismatched DNA via metalloinsertion at a mismatch as well as covalent platinum binding. DNA sequencing experiments revealed that the preferred site of platinum coordination is not the traditional N7-guanine site in the major groove, but rather N3-adenine in the minor groove. The complex also displays enhanced cytotoxicity in mismatch repair-deficient and mismatch repair-proficient human colorectal carcinoma cell lines compared to the chemotherapeutic cisplatin, and triggers cell death via an apoptotic pathway, rather than the necrotic pathway induced by rhodium metalloinsertors. PMID:26397309

  2. Loss of DNA mismatch repair function and cancer predisposition in the mouse: animal models for human hereditary nonpolyposis colorectal cancer.

    PubMed

    Edelmann, Lisa; Edelmann, Winfried

    2004-08-15

    Germline mutations in DNA mismatch repair genes underlie one of the most common hereditary cancer predisposition syndromes known in humans, hereditary nonpolyposis colorectal cancer (HNPCC). Defects of the DNA mismatch repair system are also prevalent in sporadic colorectal cancers. The generation of mice with targeted inactivating mutations in the mismatch repair genes has facilitated the in vivo study of how these genes function and how their individual loss contributes to tumorigenesis. Although there are notable limitations when using murine models to study the molecular basis of human cancer, there is remarkable similarity between the two species with respect to the contribution of individual members of the mismatch repair system to cancer susceptibility, and mouse mutants have greatly enhanced our understanding of the normal role of these genes in mutation avoidance and suppression of tumorigenesis.

  3. Cascading MutS and MutL sliding clamps control DNA diffusion to activate mismatch repair.

    PubMed

    Liu, Jiaquan; Hanne, Jeungphill; Britton, Brooke M; Bennett, Jared; Kim, Daehyung; Lee, Jong-Bong; Fishel, Richard

    2016-11-24

    Mismatched nucleotides arise from polymerase misincorporation errors, recombination between heteroallelic parents and chemical or physical DNA damage. Highly conserved MutS (MSH) and MutL (MLH/PMS) homologues initiate mismatch repair and, in higher eukaryotes, act as DNA damage sensors that can trigger apoptosis. Defects in human mismatch repair genes cause Lynch syndrome or hereditary non-polyposis colorectal cancer and 10-40% of related sporadic tumours. However, the collaborative mechanics of MSH and MLH/PMS proteins have not been resolved in any organism. We visualized Escherichia coli (Ec) ensemble mismatch repair and confirmed that EcMutS mismatch recognition results in the formation of stable ATP-bound sliding clamps that randomly diffuse along the DNA with intermittent backbone contact. The EcMutS sliding clamps act as a platform to recruit EcMutL onto the mismatched DNA, forming an EcMutS-EcMutL search complex that then closely follows the DNA backbone. ATP binding by EcMutL establishes a second long-lived DNA clamp that oscillates between the principal EcMutS-EcMutL search complex and unrestricted EcMutS and EcMutL sliding clamps. The EcMutH endonuclease that targets mismatch repair excision only binds clamped EcMutL, increasing its DNA association kinetics by more than 1,000-fold. The assembly of an EcMutS-EcMutL-EcMutH search complex illustrates how sequential stable sliding clamps can modulate one-dimensional diffusion mechanics along the DNA to direct mismatch repair.

  4. The Combined Effect of Hydrophobic Mismatch and Bilayer Local Bending on the Regulation of Mechanosensitive Ion Channels.

    PubMed

    Bavi, Omid; Vossoughi, Manouchehr; Naghdabadi, Reza; Jamali, Yousef

    2016-01-01

    The hydrophobic mismatch between the lipid bilayer and integral membrane proteins has well-defined effect on mechanosensitive (MS) ion channels. Also, membrane local bending is suggested to modulate MS channel activity. Although a number of studies have already shown the significance of each individual factor, the combined effect of these physical factors on MS channel activity have not been investigated. Here using finite element simulation, we study the combined effect of hydrophobic mismatch and local bending on the archetypal mechanosensitive channel MscL. First we show how the local curvature direction impacts on MS channel modulation. In the case of MscL, we show inward (cytoplasmic) bending can more effectively gate the channel compared to outward bending. Then we indicate that in response to a specific local curvature, MscL inserted in a bilayer with the same hydrophobic length is more expanded in the constriction pore region compared to when there is a protein-lipid hydrophobic mismatch. Interestingly in the presence of a negative mismatch (thicker lipids), MscL constriction pore is more expanded than in the presence of positive mismatch (thinner lipids) in response to an identical membrane curvature. These results were confirmed by a parametric energetic calculation provided for MscL gating. These findings have several biophysical consequences for understanding the function of MS channels in response to two major physical stimuli in mechanobiology, namely hydrophobic mismatch and local membrane curvature.

  5. Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch.

    PubMed

    Kandasamy, Senthil K; Larson, Ronald G

    2006-04-01

    Hydrophobic mismatch, which is the difference between the hydrophobic length of trans-membrane segments of a protein and the hydrophobic width of the surrounding lipid bilayer, is known to play a role in membrane protein function. We have performed molecular dynamics simulations of trans-membrane KALP peptides (sequence: GKK(LA)nLKKA) in phospholipid bilayers to investigate hydrophobic mismatch alleviation mechanisms. By varying systematically the length of the peptide (KALP15, KALP19, KALP23, KALP27, and KALP31) and the lipid hydrophobic length (DLPC, DMPC, and DPPC), a wide range of mismatch conditions were studied. Simulations of durations of 50-200 ns show that under positive mismatch, the system alleviates the mismatch predominantly by tilting the peptide and to a smaller extent by increased lipid ordering in the immediate vicinity of the peptide. Under negative mismatch, alleviation takes place by a combination of local bilayer bending and the snorkeling of the lysine residues of the peptide. Simulations performed at a higher peptide/lipid molar ratio (1:25) reveal slower dynamics of both the peptide and lipid relative to those at a lower peptide/lipid ratio (1:128). The lysine residues have favorable interactions with specific oxygen atoms of the phospholipid headgroups, indicating the preferred localization of these residues at the lipid/water interface.

  6. The Combined Effect of Hydrophobic Mismatch and Bilayer Local Bending on the Regulation of Mechanosensitive Ion Channels

    PubMed Central

    Bavi, Omid; Vossoughi, Manouchehr; Naghdabadi, Reza; Jamali, Yousef

    2016-01-01

    The hydrophobic mismatch between the lipid bilayer and integral membrane proteins has well-defined effect on mechanosensitive (MS) ion channels. Also, membrane local bending is suggested to modulate MS channel activity. Although a number of studies have already shown the significance of each individual factor, the combined effect of these physical factors on MS channel activity have not been investigated. Here using finite element simulation, we study the combined effect of hydrophobic mismatch and local bending on the archetypal mechanosensitive channel MscL. First we show how the local curvature direction impacts on MS channel modulation. In the case of MscL, we show inward (cytoplasmic) bending can more effectively gate the channel compared to outward bending. Then we indicate that in response to a specific local curvature, MscL inserted in a bilayer with the same hydrophobic length is more expanded in the constriction pore region compared to when there is a protein-lipid hydrophobic mismatch. Interestingly in the presence of a negative mismatch (thicker lipids), MscL constriction pore is more expanded than in the presence of positive mismatch (thinner lipids) in response to an identical membrane curvature. These results were confirmed by a parametric energetic calculation provided for MscL gating. These findings have several biophysical consequences for understanding the function of MS channels in response to two major physical stimuli in mechanobiology, namely hydrophobic mismatch and local membrane curvature. PMID:26958847

  7. The effects of tautomerization and protonation on the adenine-cytosine mismatches: a density functional theory study.

    PubMed

    Masoodi, Hamid Reza; Bagheri, Sotoodeh; Abareghi, Mahsa

    2016-06-01

    In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.

  8. The MutSα-Proliferating Cell Nuclear Antigen Interaction in Human DNA Mismatch Repair*S⃞♦

    PubMed Central

    Iyer, Ravi R.; Pohlhaus, Timothy J.; Chen, Sihong; Hura, Gregory L.; Dzantiev, Leonid; Beese, Lorena S.; Modrich, Paul

    2008-01-01

    We have examined the interaction parameters, conformation, and functional significance of the human MutSα· proliferating cell nuclear antigen (PCNA) complex in mismatch repair. The two proteins associate with a 1:1 stoichiometry and a KD of 0.7 μm in the absence or presence of heteroduplex DNA. PCNA does not influence the affinity of MutSα for a mismatch, and mismatch-bound MutSα binds PCNA. Small angle x-ray scattering studies have established the molecular parameters of the complex, which are consistent with an elongated conformation in which the two proteins associate in an end-to-end fashion in a manner that does not involve an extended unstructured tether, as has been proposed for yeast MutSα and PCNA (Shell, S. S., Putnam, C. D., and Kolodner, R. D. (2007) Mol. Cell26 ,565 -57817531814). MutSα variants lacking the PCNA interaction motif are functional in 3′- or 5′-directed mismatch-provoked excision, but display a partial defect in 5′-directed mismatch repair. This finding is consistent with the modest mutability conferred by inactivation of the MutSα PCNA interaction motif and suggests that interaction of the replication clamp with other repair protein(s) accounts for the essential role of PCNA in MutSα-dependent mismatch repair. PMID:18326858

  9. Molecular Dynamics Simulations of Model Trans-Membrane Peptides in Lipid Bilayers: A Systematic Investigation of Hydrophobic Mismatch

    PubMed Central

    Kandasamy, Senthil K.; Larson, Ronald G.

    2006-01-01

    Hydrophobic mismatch, which is the difference between the hydrophobic length of trans-membrane segments of a protein and the hydrophobic width of the surrounding lipid bilayer, is known to play a role in membrane protein function. We have performed molecular dynamics simulations of trans-membrane KALP peptides (sequence: GKK(LA)nLKKA) in phospholipid bilayers to investigate hydrophobic mismatch alleviation mechanisms. By varying systematically the length of the peptide (KALP15, KALP19, KALP23, KALP27, and KALP31) and the lipid hydrophobic length (DLPC, DMPC, and DPPC), a wide range of mismatch conditions were studied. Simulations of durations of 50–200 ns show that under positive mismatch, the system alleviates the mismatch predominantly by tilting the peptide and to a smaller extent by increased lipid ordering in the immediate vicinity of the peptide. Under negative mismatch, alleviation takes place by a combination of local bilayer bending and the snorkeling of the lysine residues of the peptide. Simulations performed at a higher peptide/lipid molar ratio (1:25) reveal slower dynamics of both the peptide and lipid relative to those at a lower peptide/lipid ratio (1:128). The lysine residues have favorable interactions with specific oxygen atoms of the phospholipid headgroups, indicating the preferred localization of these residues at the lipid/water interface. PMID:16428278

  10. Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations.

    PubMed

    Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra

    2015-09-24

    Base excision of mismatched or damaged nucleotides catalyzed by glycosylase enzymes is the first step of the base excision repair system, a machinery preserving the integrity of DNA. Thymine DNA glycosylase recognizes and removes mismatched thymine by cleaving the C1'-N1 bond between the base and the sugar ring. Our quantum mechanical/molecular mechanical calculations of this reaction in human thymine DNA glycosylase reveal a requirement for a positive charge in the active site to facilitate C1'-N1 bond scission: protonation of His151 significantly lowers the free energy barrier for C1'-N1 bond dissociation compared to the situation with neutral His151. Shuttling a proton from His151 to the thymine base further reduces the activation free energy for glycosidic bond cleavage. Classical molecular dynamics simulations of the H151A mutant suggest that the mutation to the smaller, neutral, residue increases the water accessibility of the thymine base, rendering direct proton transfer from the bulk feasible. Quantum mechanical/molecular mechanical calculations of the glycosidic bond cleavage reaction in the H151A mutant show that the activation free energy is slightly lower than in the wild-type enzyme, explaining the experimentally observed higher reaction rates in this mutant.

  11. The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs.

    PubMed

    Bilbille, Yann; Vendeix, Franck A P; Guenther, Richard; Malkiewicz, Andrzej; Ariza, Xavier; Vilarrasa, Jaume; Agris, Paul F

    2009-06-01

    Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNA(Lys3), to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3'-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5'-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNA(Lys3). The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s(2)U(34), and pseudouridine, Psi(39), appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U(162)*Psi(39) and G(163)*A(38), that maintained a reasonable A-form helix diameter. The tRNA's s(2)U(34) stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Psi(39) stabilized the adjacent mismatched pairs.

  12. Variable flowering phenology and pollinator use in a community suggest future phenological mismatch

    NASA Astrophysics Data System (ADS)

    Petanidou, Theodora; Kallimanis, Athanasios S.; Sgardelis, Stefanos P.; Mazaris, Antonios D.; Pantis, John D.; Waser, Nickolas M.

    2014-08-01

    Recent anthropogenic climate change is strongly associated with average shifts toward earlier seasonal timing of activity (phenology) in temperate-zone species. Shifts in phenology have the potential to alter ecological interactions, to the detriment of one or more interacting species. Recent models predict that detrimental phenological mismatch may increasingly occur between plants and their pollinators. One way to test this prediction is to examine data from ecological communities that experience large annual weather fluctuations. Taking this approach, we analyzed interactions over a four-year period among 132 plant species and 665 pollinating insect species within a Mediterranean community. For each plant species we recorded onset and duration of flowering and number of pollinator species. Flowering onset varied among years, and a year of earlier flowering of a species tended to be a year of fewer species pollinating its flowers. This relationship was attributable principally to early-flowering species, suggesting that shifts toward earlier phenology driven by climate change may reduce pollination services due to phenological mismatch. Earlier flowering onset of a species also was associated with prolonged flowering duration, but it is not certain that this will counterbalance any negative effects of lower pollinator species richness on plant reproductive success. Among plants with different life histories, annuals were more severely affected by flowering-pollinator mismatches than perennials. Specialized plant species (those attracting a smaller number of pollinator species) did not experience disproportionate interannual fluctuations in phenology. Thus they do not appear to be faced with disproportionate fluctuations in pollinator species richness, contrary to the expectation that specialists are at greatest risk of losing mutualistic interactions because of climate change.

  13. Stability of DNA duplexes containing GG, CC, AA, and TT mismatches.

    PubMed

    Tikhomirova, Anna; Beletskaya, Irina V; Chalikian, Tigran V

    2006-09-05

    We employed salt-dependent differential scanning calorimetric measurements to characterize the stability of six oligomeric DNA duplexes (5'-GCCGGAXTGCCGG-3'/5'-CCGGCAYTCCGGC-3') that contain in the central XY position the GC, AT, GG, CC, AA, or TT base pair. The heat-induced helix-to-coil transitions of all the duplexes are associated with positive changes in heat capacity, DeltaC(p), ranging from 0.43 to 0.53 kcal/mol. Positive values of DeltaC(p) result in strong temperature dependences of changes in enthalpy, DeltaH degrees, and entropy, DeltaS degrees , accompanying duplex melting and cause melting free energies, DeltaG degrees, to exhibit characteristically curved shapes. These observations suggest that DeltaC(p) needs to be carefully taken into account when the parameters of duplex stability are extrapolated to temperatures distant from the transition temperature, T(M). Comparison of the calorimetric and van't Hoff enthalpies revealed that none of the duplexes studied in this work exhibits two-state melting. Within the context of the central AXT/TYA triplet, the thermal and thermodynamic stabilities of the duplexes in question change in the following order: GC > AT > GG > AA approximately TT > CC. Our estimates revealed that the thermodynamic impact of the GG, AA, and TT mismatches is confined within the central triplet. In contrast, the thermodynamic impact of the CC mismatch propagates into the adjacent helix domains and may involve 7-9 bp. We discuss implications of our results for understanding the origins of initial recognition of mismatched DNA sites by enzymes of the DNA repair machinery.

  14. Hydrophobic Mismatch Drives the Interaction of E5 with the Transmembrane Segment of PDGF Receptor

    PubMed Central

    Windisch, Dirk; Ziegler, Colin; Grage, Stephan L.; Bürck, Jochen; Zeitler, Marcel; Gor’kov, Peter L.; Ulrich, Anne S.

    2015-01-01

    The oncogenic E5 protein from bovine papillomavirus is a short (44 amino acids long) integral membrane protein that forms homodimers. It activates platelet-derived growth factor receptor (PDGFR) β in a ligand-independent manner by transmembrane helix-helix interactions. The nature of this recognition event remains elusive, as numerous mutations are tolerated in the E5 transmembrane segment, with the exception of one hydrogen-bonding residue. Here, we examined the conformation, stability, and alignment of the E5 protein in fluid lipid membranes of substantially varying bilayer thickness, in both the absence and presence of the PDGFR transmembrane segment. Quantitative synchrotron radiation circular dichroism analysis revealed a very long transmembrane helix for E5 of ∼26 amino acids. Oriented circular dichroism and solid-state 15N-NMR showed that the alignment and stability of this unusually long segment depend critically on the membrane thickness. When reconstituted alone in exceptionally thick DNPC lipid bilayers, the E5 helix was found to be inserted almost upright. In moderately thick bilayers (DErPC and DEiPC), it started to tilt and became slightly deformed, and finally it became aggregated in conventional DOPC, POPC, and DMPC membranes due to hydrophobic mismatch. On the other hand, when E5 was co-reconstituted with the transmembrane segment of PDGFR, it was able to tolerate even the most pronounced mismatch and was stabilized by binding to the receptor, which has the same hydrophobic length. As E5 is known to activate PDGFR within the thin membranes of the Golgi compartment, we suggest that the intrinsic hydrophobic mismatch of these two interaction partners drives them together. They seem to recognize each other by forming a closely packed bundle of mutually aligned transmembrane helices, which is further stabilized by a specific pair of hydrogen-bonding residues. PMID:26287626

  15. Characterisation of the oxysterol metabolising enzyme pathway in mismatch repair proficient and deficient colorectal cancer

    PubMed Central

    Swan, Rebecca; Alnabulsi, Abdo; Cash, Beatriz; Alnabulsi, Ayham; Murray, Graeme I.

    2016-01-01

    Oxysterols are oxidised derivatives of cholesterol, formed by the enzymatic activity of several cytochrome P450 enzymes and tumour-derived oxysterols have been implicated in tumour growth and survival. The aim of this study was to profile the expression of oxysterol metabolising enzymes in primary colorectal cancer and assess the association between expression and prognosis. Immunohistochemistry was performed on a colorectal cancer tissue microarray containing 650 primary colorectal cancers using monoclonal antibodies to CYP2R1, CYP7B1, CYP8B1, CYP27A1, CYP39A1, CYP46A1 and CYP51A1, which we have developed. Unsupervised hierarchical cluster analysis was used to examine the overall relationship of oxysterol metabolising enzyme expression with outcome and based on this identify an oxysterol metabolising enzyme signature associated with prognosis. Cluster analysis of the whole patient cohort identified a good prognosis group (mean survival=146 months 95% CI 127-165 months) that had a significantly better survival (δ2=12.984, p<0.001, HR=1.983, 95% CI 1.341-2.799) than the poor prognosis group (mean survival=107 months, 95% CI 98-123 months). For the mismatch repair proficient cohort, the good prognosis group had a significantly better survival (δ2=8.985, p=0.003, HR=1.845, 95% CI 1.227-2.774) than the poor prognosis group. Multi-variate analysis showed that cluster group was independently prognostically significant in both the whole patient cohort (p=0.02, HR=1.554, 95% CI 1.072-2.252) and the mismatch repair proficient group (p=0.04, HR=1.530, 95% CI 1.014-2.310). Individual oxysterol metabolising enzymes are overexpressed in colorectal cancer and an oxysterol metabolising enzyme expression profile associated with prognosis has been identified in the whole patient cohort and in mismatch repair proficient colorectal cancers. PMID:27341022

  16. Lattice mismatch induced ripples and wrinkles in planar graphene/boron nitride superlattices

    SciTech Connect

    Nandwana, Dinkar; Ertekin, Elif

    2015-06-21

    A continuum theory to describe periodic ripple formation in planar graphene/boron nitride superlattices is formulated. Due to the lattice mismatch between the two materials, it is shown that flat superlattices are unstable with respect to ripple formation of appropriate wavelengths. A competition between bending energy and transverse stretching energy gives rise to an optimal ripple wavelength that depends on the superlattice pitch. The optimal wavelengths predicted by the continuum theory are in good agreement with atomic scale total energy calculations previously reported by Nandwana and Ertekin [Nano Lett. 15, 1468 (2015)].

  17. Role of Deficient Mismatch Repair in the Personalized Management of Colorectal Cancer

    PubMed Central

    Zhang, Cong-Min; Lv, Jin-Feng; Gong, Liang; Yu, Lin-Yu; Chen, Xiao-Ping; Zhou, Hong-Hao; Fan, Lan

    2016-01-01

    Colorectal cancer (CRC) represents the third most common type of cancer in developed countries and one of the leading causes of cancer deaths worldwide. Personalized management of CRC has gained increasing attention since there are large inter-individual variations in the prognosis and response to drugs used to treat CRC owing to molecular heterogeneity. Approximately 15% of CRCs are caused by deficient mismatch repair (dMMR) characterized by microsatellite instability (MSI) phenotype. The present review is aimed at highlighting the role of MMR status in informing prognosis and personalized treatment of CRC including adjuvant chemotherapy, targeted therapy, and immune checkpoint inhibitor therapy to guide the individualized therapy of CRC. PMID:27618077

  18. Microsatellites in the Eukaryotic DNA Mismatch Repair Genes as Modulators of Evolutionary Mutation Rate

    NASA Technical Reports Server (NTRS)

    Chang, Dong Kyung; Metzgar, David; Wills, Christopher; Boland, C. Richard

    2003-01-01

    All "minor" components of the human DNA mismatch repair (MMR) system-MSH3, MSH6, PMS2, and the recently discovered MLH3-contain mononucleotide microsatellites in their coding sequences. This intriguing finding contrasts with the situation found in the major components of the DNA MMR system-MSH2 and MLH1-and, in fact, most human genes. Although eukaryotic genomes are rich in microsatellites, non-triplet microsatellites are rare in coding regions. The recurring presence of exonal mononucleotide repeat sequences within a single family of human genes would therefore be considered exceptional.

  19. Event-triggered reliable control for fuzzy Markovian jump systems with mismatched membership functions.

    PubMed

    Hou, Liyuan; Cheng, Jun; Qi, Wenhai

    2017-01-01

    The problem of event-triggered reliable control for fuzzy Markovian jump system (FMJS) with mismatched membership functions (MMFs) is addressed. Based on the mode-dependent reliable control and event-triggered communication scheme, the stability conditions and control design procedure are formulated. More precisely, a general actuator-failure is designed such that the FMJS is reliable in the sense of stochastically stable and reduce the utilization of network resources. Furthermore, the improved MMFs are introduced to reduce the conservativeness of obtained results. Finally, simulation results indicate the effectiveness of the proposed methodology.

  20. Mechanisms of ring and island formation in lattice mismatched droplet epitaxy

    NASA Astrophysics Data System (ADS)

    DeJarld, M.; Reyes, Kris; Smereka, P.; Millunchick, J. M.

    2013-04-01

    Lattice mismatched GaSb nanostructures were grown using droplet epitaxy. In this method, liquid Ga droplets are deposited on GaAs substrates and then exposed to a Sb flux at various temperatures. At increasing temperature and droplet volumes, the morphologies changed from two-dimensional islands to nanoholes, three-dimensional islands, rings, and clusters of islands. A theoretical model describes the relationship between the volume of the droplet and the final nanostructure, and is validated by kinetic Monte Carlo simulations. The combined experimental and simulation results demonstrate another process to obtain complex nanostructures, widening the design window for devices.

  1. Evaluation of hemangiomas with technetium 99m-labeled RBCs: the perfusion-blood pool mismatch

    SciTech Connect

    Front, D.; Israel, O.; Joachims, H.; Brown, Y.; Eliachar, I.

    1983-03-18

    A case report is presented of a woman with a tumor mass in the nasopharynx. Early and delayed scintigraphy with Technetium 99m-labeled RBCs showed a large area of increased uptake which was later shown to be a hemangioma by contrast angiography. The perfusion-blood pool mismatch observed in hemangiomas is characteristic of these lesions and has not been described in any other abnormalities. The Tc-RBC using both early and delayed scintigraphy is a simple, noninvasive method for assessing the vascular characteristics of these tumors. (JMT)

  2. Symmetry-mismatch reconstruction of genomes and associated proteins within icosahedral viruses using cryo-EM.

    PubMed

    Li, Xiaowu; Liu, Hongrong; Cheng, Lingpeng

    2016-01-01

    Although near-atomic resolutions have been routinely achieved for structural determination of many icosahedral viral capsids, structures of genomes and associated proteins within the capsids are still less characterized because the genome information is overlapped by the highly symmetric capsid information in the virus particle images. We recently developed a software package for symmetry-mismatch structural reconstruction and determined the structures of the genome and RNA polymerases within an icosahedral virus for the first time. Here, we describe the protocol used for this structural determination, which may facilitate structural biologists in investigating the structures of viral genome and associated proteins.

  3. Expectations of Competency: The Mismatch between Employers' and Graduates' Views of End-User Computing Skills Requirements in the Workplace

    ERIC Educational Resources Information Center

    Gibbs, Shirley; Steel, Gary; Kuiper, Alison

    2011-01-01

    The use of computers has become part of everyday life. The high prevalence of computer use appears to lead employers to assume that university graduates will have the good computing skills necessary in many graduate level jobs. This study investigates how well the expectations of employers match the perceptions of near-graduate students about the…

  4. Refinement of the definition of permissible HLA-DPB1 mismatches with predicted indirectly recognizable HLA-DPB1 epitopes.

    PubMed

    Thus, Kirsten A; Ruizendaal, Mieke T A; de Hoop, Talitha A; Borst, Eric; van Deutekom, Hanneke W M; Te Boome, Liane; Kuball, Jürgen; Spierings, Eric

    2014-11-01

    Hematopoietic stem cell transplantation with HLA-DPB1-mismatched donors leads to an increased risk of acute graft-versus-host disease (GVHD). Studies have indicated a prognostic value for classifying HLA-DPB1 mismatches based on T cell-epitope (TCE) groups. The aim of this study was to determine the contribution of indirect recognition of HLA-DP-derived epitopes, as determined with the Predicted Indirectly ReCognizable HLA Epitopes (PIRCHE) method. We therefore conducted a retrospective single-center analysis on 80 patients transplanted with a 10/10 matched unrelated donor that was HLA-DPB1 mismatched. HLA-DPB1 mismatches that were classified as GVH nonpermissive by the TCE algorithm correlated to higher numbers of HLA class I as well as HLA class II presented PIRCHE (PIRCHE-I and -II) compared with permissive or host-versus-graft nonpermissive mismatches. Patients with acute GVHD grades II to IV presented significantly higher numbers of PIRCHE-I compared with patients without acute GVHD (P < .05). Patients were divided into 2 groups based on the presence or absence of PIRCHE. Patients with PIRCHE-I or -II have an increased hazard of acute GVHD when compared with patients without PIRCHE-I or -II (hazard ratio [HR], 3.19; 95% confidence interval [CI], 1.10 to 9.19; P < .05; and HR, 4.07; 95% CI, .97 to 17.19; P = .06, respectively). Patients classified as having an HLA-DPB1 permissive mismatch by the TCE model had an increased risk of acute GVHD when comparing presence of PIRCHE-I with absence of PIRCHE-I (HR, 2.96; 95% CI, .84 to 10.39; P = .09). We therefore conclude that the data presented in this study describe an attractive and feasible possibility to better select permissible HLA-DPB1 mismatches by including both a direct and an indirect recognition model.

  5. Antagonism of ultraviolet-light mutagenesis by the methyl-directed mismatch-repair system of Escherichia coli.

    PubMed Central

    Liu, H; Hewitt, S R; Hays, J B

    2000-01-01

    Previous studies have demonstrated that the Escherichia coli MutHLS mismatch-repair system can process UV-irradiated DNA in vivo and that the human MSH2.MSH6 mismatch-repair protein binds more strongly in vitro to photoproduct/base mismatches than to "matched" photoproducts in DNA. We tested the hypothesis that mismatch repair directed against incorrect bases opposite photoproducts might reduce UV mutagenesis, using two alleles at E. coli lacZ codon 461, which revert, respectively, via CCC --> CTC and CTT --> CTC transitions. F' lacZ targets were mated from mut(+) donors into mutH, mutL, or mutS recipients, once cells were at substantial densities, to minimize spontaneous mutation prior to irradiation. In umu(+) mut(+) recipients, a range of UV fluences induced lac(+) revertant frequencies of 4-25 x 10(-8); these frequencies were consistently 2-fold higher in mutH, mutL, or mutS recipients. Since this effect on mutation frequency was unaltered by an Mfd(-) defect, it appears not to involve transcription-coupled excision repair. In mut(+) umuC122::Tn5 bacteria, UV mutagenesis (at 60 J/m(2)) was very low, but mutH or mutL or mutS mutations increased reversion of both lacZ alleles roughly 25-fold, to 5-10 x 10(-8). Thus, at UV doses too low to induce SOS functions, such as Umu(2)'D, most incorrect bases opposite occasional photoproducts may be removed by mismatch repair, whereas in heavily irradiated (SOS-induced) cells, mismatch repair may only correct some photoproduct/base mismatches, so UV mutagenesis remains substantial. PMID:10655206

  6. Changes in emotional tone and instrumental timbre are reflected by the mismatch negativity.

    PubMed

    Goydke, Katja N; Altenmüller, Eckart; Möller, Jürn; Münte, Thomas F

    2004-11-01

    The present study examined whether or not the brain is capable to preattentively discriminate tones differing in emotional expression or instrumental timbre. In two event-related potential (ERP) experiments single tones (600 ms) were presented which had been rated as happy or sad in a pretest. In experiment 1, 12 non-musicians passively listened to tone series comprising a frequent (standard) single musical tone played by a violin in a certain pitch and with a certain emotional connotation (happy or sad). Among these standard tones deviant tones differing in emotional valence, either in instrumental timbre or in pitch were presented. All deviants generated mismatch negativity (MMN) responses. The MMN scalp topography was similar for all of the three deviants but latency was shorter for pitch deviants than for the other two conditions. The topography of the mismatch responses was indistinguishable. In a second experiment, subjects actively detected the deviant tones by button press. All detected deviants generated P3b waves at parietal leads. These results indicate that the brain is not only able to use simple physical differences such as pitch for rapid preattentive categorization but can also perform similar operations on the basis of more complex differences between tones of the same pitch such as instrumental timbre and the subtle timbral differences associated with different emotional expression. This rapid categorization may serve as a basis for the further fine-grained analysis of musical (and other) sounds with regard to their emotional content.

  7. Measurement Matrix Optimization and Mismatch Problem Compensation for DLSLA 3-D SAR Cross-Track Reconstruction

    PubMed Central

    Bao, Qian; Jiang, Chenglong; Lin, Yun; Tan, Weixian; Wang, Zhirui; Hong, Wen

    2016-01-01

    With a short linear array configured in the cross-track direction, downward looking sparse linear array three-dimensional synthetic aperture radar (DLSLA 3-D SAR) can obtain the 3-D image of an imaging scene. To improve the cross-track resolution, sparse recovery methods have been investigated in recent years. In the compressive sensing (CS) framework, the reconstruction performance depends on the property of measurement matrix. This paper concerns the technique to optimize the measurement matrix and deal with the mismatch problem of measurement matrix caused by the off-grid scatterers. In the model of cross-track reconstruction, the measurement matrix is mainly affected by the configuration of antenna phase centers (APC), thus, two mutual coherence based criteria are proposed to optimize the configuration of APCs. On the other hand, to compensate the mismatch problem of the measurement matrix, the sparse Bayesian inference based method is introduced into the cross-track reconstruction by jointly estimate the scatterers and the off-grid error. Experiments demonstrate the performance of the proposed APCs’ configuration schemes and the proposed cross-track reconstruction method. PMID:27556471

  8. Columnar structured FePt films epitaxially grown on large lattice mismatched intermediate layer.

    PubMed

    Dong, K F; Deng, J Y; Peng, Y G; Ju, G; Chow, G M; Chen, J S

    2016-09-30

    The microstructure and magnetic properties of the FePt films grown on large mismatched ZrN (15.7%) intermediate layer were investigated. With using ZrN intermediate layer, FePt 10 nm films exhibited (001) texture except for some weaker FePt (110) texture. Good epitaxial relationships of FePt (001) <100>//ZrN (001) <100>//TiN (001) <100> among FePt and ZrN/TiN were revealed from the transmission electron microscopy (TEM) results. As compared with TiN intermediate layer, although FePt-SiO2-C films grown on ZrN/TiN intermediate layer showed isotropic magnetic properties, the large interfacial energy and lattice mismatch between FePt and ZrN would lead to form columnar structural FePt films with smaller grain size and improved isolation. By doping ZrN into the TiN layer, solid solution of ZrTiN was formed and the lattice constant is increased comparing with TiN and decreased comparing with ZrN. Moreover, FePt-SiO2-C films grown on TiN 2 nm-20 vol.% ZrN/TiN 3 nm intermediate layer showed an improved perpendicular magnetic anisotropy. Simultaneously, columnar structure with smaller grain size retained.

  9. Measurement Matrix Optimization and Mismatch Problem Compensation for DLSLA 3-D SAR Cross-Track Reconstruction.

    PubMed

    Bao, Qian; Jiang, Chenglong; Lin, Yun; Tan, Weixian; Wang, Zhirui; Hong, Wen

    2016-08-22

    With a short linear array configured in the cross-track direction, downward looking sparse linear array three-dimensional synthetic aperture radar (DLSLA 3-D SAR) can obtain the 3-D image of an imaging scene. To improve the cross-track resolution, sparse recovery methods have been investigated in recent years. In the compressive sensing (CS) framework, the reconstruction performance depends on the property of measurement matrix. This paper concerns the technique to optimize the measurement matrix and deal with the mismatch problem of measurement matrix caused by the off-grid scatterers. In the model of cross-track reconstruction, the measurement matrix is mainly affected by the configuration of antenna phase centers (APC), thus, two mutual coherence based criteria are proposed to optimize the configuration of APCs. On the other hand, to compensate the mismatch problem of the measurement matrix, the sparse Bayesian inference based method is introduced into the cross-track reconstruction by jointly estimate the scatterers and the off-grid error. Experiments demonstrate the performance of the proposed APCs' configuration schemes and the proposed cross-track reconstruction method.

  10. Screening for mutations in kidney-related genes using SURVEYOR nuclease for cleavage at heteroduplex mismatches.

    PubMed

    Voskarides, Konstantinos; Deltas, Constantinos

    2009-07-01

    SURVEYOR is a new mismatch-specific plant DNA endonuclease that is very efficient for mutation scanning in heteroduplex DNA. It is much faster, cheaper, more sensitive, and easier to perform than other "traditional" mutation detection methods such as single-strand conformation polymorphism analysis, denaturing high-performance liquid chromatography, heteroduplex analysis, and phage resolvases. This is the first comprehensive report on the use of SURVEYOR for screening genes implicated in a spectrum of inherited renal diseases. Of the 48.2 kb screened, 44 variations were identified, accounting for one variation per 1.1 kb. The re-sequencing of multiple samples did not reveal any variation that had not been identified by SURVEYOR, attesting to its high fidelity. Additionally, we tested this enzyme against 15 known variants, 14 of which it identified, thus showing a sensitivity of 93%. We showed that the genetic heterogeneity of renal diseases can be easily overcome using this enzyme with a high degree of confidence and no bias for any specific variations. We also showed for the first time that SURVEYOR does not demonstrate any preference regarding mismatch cleavage at specific positions. Disadvantages of using SURVEYOR include enhanced exonucleolytic activity for some polymerase chain reaction products and less than 100% sensitivity. We report that SURVEYOR can be used as a mutation detection method with a high degree of confidence, offering an excellent alternative for low-budget laboratories and for the rapid manipulation of multiple genes.

  11. The thermal mismatch hypothesis explains host susceptibility to an emerging infectious disease.

    PubMed

    Cohen, Jeremy M; Venesky, Matthew D; Sauer, Erin L; Civitello, David J; McMahon, Taegan A; Roznik, Elizabeth A; Rohr, Jason R

    2017-02-01

    Parasites typically have broader thermal limits than hosts, so large performance gaps between pathogens and their cold- and warm-adapted hosts should occur at relatively warm and cold temperatures, respectively. We tested this thermal mismatch hypothesis by quantifying the temperature-dependent susceptibility of cold- and warm-adapted amphibian species to the fungal pathogen Batrachochytrium dendrobatidis (Bd) using laboratory experiments and field prevalence estimates from 15 410 individuals in 598 populations. In both the laboratory and field, we found that the greatest susceptibility of cold- and warm-adapted hosts occurred at relatively warm and cool temperatures, respectively, providing support for the thermal mismatch hypothesis. Our results suggest that as climate change shifts hosts away from their optimal temperatures, the probability of increased host susceptibility to infectious disease might increase, but the effect will depend on the host species and the direction of the climate shift. Our findings help explain the tremendous variation in species responses to Bd across climates and spatial, temporal and species-level variation in disease outbreaks associated with extreme weather events that are becoming more common with climate change.

  12. Method for reducing or eliminating interface defects in mismatched semiconductor eiplayers

    DOEpatents

    Fitzgerald, Jr., Eugene A.; Ast, Dieter G.

    1991-01-01

    The present invention and process relates to crystal lattice mismatched semiconductor composite having a first semiconductor layer and a second semiconductor growth layer deposited thereon to form an interface wherein the growth layer can be deposited at thicknesses in excess of the critical thickness, even up to about 10x critical thickness. Such composite has an interface which is substantially free of interface defects. For example, the size of the growth areas in a mismatched In.sub.0.05 Ga.sub.0.95 As/(001)GaAs interface was controlled by fabricating 2-.mu.m high pillars of various lateral geometries and lateral dimensions before the epitaxial deposition of 3500.ANG. of In.sub.0.05 Ga.sub.0.95 As. The linear dislocation density at the interface was reduced from >5000 dislocations/cm to about zero for 25-.mu.m lateral dimensions and to less than 800 dislocations/cm for lateral dimensions as large as 100 .mu.m. The fabricated pillars control the lateral dimensions of the growth layer and block the glide of misfit dislocations with the resultant decrease in dislocation density.

  13. Method for reducing or eliminating interface defects in mismatched semiconductor epilayers

    DOEpatents

    Fitzgerald, Jr., Eugene A.; Ast, Dieter G.

    1992-01-01

    The present invention and process relates to crystal lattice mismatched semiconductor composite having a first semiconductor layer and a second semiconductor growth layer deposited thereon to form an interface wherein the growth layer can be deposited at thicknesses in excess of the critical thickness, even up to about 10.times. critical thickness. Such composite has an interface which is substantially free of interface defects. For example, the size of the growth areas in a mismatched In.sub.0.05 Ga.sub.0.95 As/(001)GaAs interface was controlled by fabricating 2-.mu.m high pillars of various lateral geometries and lateral dimensions before the epitaxial deposition of 3500.ANG. of In.sub.0.05 Ga.sub.0.95 As. The linear dislocation density at the interface was reduced from >5000 dislocations/cm to about zero for 25-.mu.m lateral dimensions and to less than 800 dislocations/cm for lateral dimensions as large as 100 .mu.m. The fabricated pillars control the lateral dimensions of the growth layer and block the glide of misfit dislocations with the resultant decrease in dislocation density.

  14. Method for reducing or eliminating interface defects in mismatched semiconductor epilayers

    DOEpatents

    Fitzgerald, E.A. Jr.; Ast, D.G.

    1992-10-20

    The present invention and process relates to crystal lattice mismatched semiconductor composite having a first semiconductor layer and a second semiconductor growth layer deposited thereon to form an interface wherein the growth layer can be deposited at thicknesses in excess of the critical thickness, even up to about 10[times] critical thickness. Such composite has an interface which is substantially free of interface defects. For example, the size of the growth areas in a mismatched In[sub 0.05]Ga[sub 0.95]As/(001)GaAs interface was controlled by fabricating 2-[mu]m high pillars of various lateral geometries and lateral dimensions before the epitaxial deposition of 3500 [angstrom] of In[sub 0.05]Ga[sub 0.95]As. The linear dislocation density at the interface was reduced from >5000 dislocations/cm to about zero for 25-[mu]m lateral dimensions and to less than 800 dislocations/cm for lateral dimensions as large as 100 [mu]m. The fabricated pillars control the lateral dimensions of the growth layer and block the glide of misfit dislocations with the resultant decrease in dislocation density. 7 figs.

  15. Assessing Dissimilarity of Genes by Comparing Their Rnase a Mismatch Cleavage Patterns

    PubMed Central

    Rzhetsky, A.; Dopazo, J.; Snyder, E.; Dangler, C. A.; Ayala, F. J.

    1996-01-01

    We propose a simple algorithm for estimating the number of nucleotide differences between a pair of RNA or DNA sequences through comparison of their RNAse A mismatch cleavage patterns. In the RNAse A mismatch cleavage technique two or more sample sequences are hybridized to the same RNA probe, the hybrids are partially digested with RNAse A, and the digestion products are compared on an electrophoretic gel. Here we provide an algorithm for converting the numbers of unique and matching electrophoretic bands into an estimate of the number of nucleotide differences between the sequences. Computer simulation indicates that the proposed method yields a robust estimate of the genetic distance despite stochastic errors and occasional violation of certain assumptions. Our study suggests that the method performs best when the distance between the sequences is <15 differences. When the sequences under analysis are likely to have larger distances, we advise to substitute one long riboprobe with a set of shorter nonoverlapping probes. The new algorithm is applied to infer the proximity of several strains of pseudorabies virus. PMID:8978080

  16. Columnar structured FePt films epitaxially grown on large lattice mismatched intermediate layer

    PubMed Central

    Dong, K. F.; Deng, J. Y.; Peng, Y. G.; Ju, G.; Chow, G. M.; Chen, J. S.

    2016-01-01

    The microstructure and magnetic properties of the FePt films grown on large mismatched ZrN (15.7%) intermediate layer were investigated. With using ZrN intermediate layer, FePt 10 nm films exhibited (001) texture except for some weaker FePt (110) texture. Good epitaxial relationships of FePt (001) <100>//ZrN (001) <100>//TiN (001) <100> among FePt and ZrN/TiN were revealed from the transmission electron microscopy (TEM) results. As compared with TiN intermediate layer, although FePt-SiO2-C films grown on ZrN/TiN intermediate layer showed isotropic magnetic properties, the large interfacial energy and lattice mismatch between FePt and ZrN would lead to form columnar structural FePt films with smaller grain size and improved isolation. By doping ZrN into the TiN layer, solid solution of ZrTiN was formed and the lattice constant is increased comparing with TiN and decreased comparing with ZrN. Moreover, FePt-SiO2-C films grown on TiN 2 nm-20 vol.% ZrN/TiN 3 nm intermediate layer showed an improved perpendicular magnetic anisotropy. Simultaneously, columnar structure with smaller grain size retained. PMID:27686046

  17. Photoacoustic generation for a spherical absorber with impedance mismatch with the surrounding media

    NASA Astrophysics Data System (ADS)

    Sun, J. M.; Gerstman, Bernard S.

    1999-05-01

    Pressure generation in a spherical absorber due to energy deposition from pulsed lasers is studied. For a variety of conditions, analytical solutions are derived that allow quick computation of exact results. For the special case of identical acoustic impedance, the pressure transient spreads to the surrounding medium by a single compressive pulse followed by a tensile pulse at the end of illumination. For the general case of impedance mismatch, the pressure transient is in the form of a series of dampened compressive and tensile pressure pulses. In this paper both the amplitude ratio and the sign of consecutive pressure pulses are determined analytically, and are shown to be dependent upon the impedance mismatch. For laser pulses of duration much less than the absorber's characteristic oscillation time, a stress confinement limit is reached for most of the absorber, but a sharp tensile stress in the core region of the sphere is predicted. This region of high stress is defined by r<=rc, and we show that rc is proportional to the laser pulse duration τ0. Upon further shortening of the laser pulse duration, the strength of this tensile stress continues to increase while its spatial distribution is sharpened. This observation has relevance to a number of experiments where laser-induced pressure transients cause the absorber to fracture.

  18. Matched, mismatched, and robust scatter matrix estimation and hypothesis testing in complex t-distributed data

    NASA Astrophysics Data System (ADS)

    Fortunati, Stefano; Gini, Fulvio; Greco, Maria S.

    2016-12-01

    Scatter matrix estimation and hypothesis testing are fundamental inference problems in a wide variety of signal processing applications. In this paper, we investigate and compare the matched, mismatched, and robust approaches to solve these problems in the context of the complex elliptically symmetric (CES) distributions. The matched approach is when the estimation and detection algorithms are tailored on the correct data distribution, whereas the mismatched approach refers to the case when the scatter matrix estimator and the decision rule are derived under a model assumption that is not correct. The robust approach aims at providing good estimation and detection performance, even if suboptimal, over a large set of possible data models, irrespective of the actual data distribution. Specifically, due to its central importance in both the statistical and engineering applications, we assume for the input data a complex t-distribution. We analyze scatter matrix estimators derived under the three different approaches and compare their mean square error (MSE) with the constrained Cramér-Rao bound (CCRB) and the constrained misspecified Cramér-Rao bound (CMCRB). In addition, the detection performance and false alarm rate (FAR) of the various detection algorithms are compared with that of the clairvoyant optimum detector.

  19. MEG Signatures of a Perceived Match or Mismatch between Individual and Group Opinions

    PubMed Central

    Zubarev, Ivan; Klucharev, Vasily; Ossadtchi, Alexei; Moiseeva, Victoria; Shestakova, Anna

    2017-01-01

    Humans often adjust their opinions to the perceived opinions of others. Neural responses to a perceived match or mismatch between individual and group opinions have been investigated previously, but some findings are inconsistent. In this study, we used magnetoencephalographic source imaging to investigate further neural responses to the perceived opinions of others. We found that group opinions mismatching with individual opinions evoked responses in the anterior and posterior medial prefrontal cortices, as well as in the temporoparietal junction and ventromedial prefrontal cortex in the 220–320 and 380–530 ms time windows. Evoked responses were accompanied by an increase in the power of theta oscillations (4–8 Hz) over a number of frontal cortical sites. Group opinions matching with individual opinions evoked an increase in amplitude of beta oscillations (13–30 Hz) in the anterior cingulate and ventral medial prefrontal cortices. Based on these results, we argue that distinct valuation and performance-monitoring neural circuits in the medial cortices of the brain may monitor compliance of individual behavior to the perceived group norms. PMID:28167897

  20. Loss of DNA mismatch repair facilitates reactivation of a reporter plasmid damaged by cisplatin

    PubMed Central

    Cenni, B; Kim, H-K; Bubley, G J; Aebi, S; Fink, D; Teicher, B A; Howell, S B; Christen, R D

    1999-01-01

    In addition to recognizing and repairing mismatched bases in DNA, the mismatch repair (MMR) system also detects cisplatin DNA adducts and loss of MMR results in resistance to cisplatin. A comparison was made of the ability of MMR-proficient and -deficient cells to remove cisplatin adducts from their genome and to reactivate a transiently transfected plasmid that had previously been inactivated by cisplatin to express the firefly luciferase enzyme. MMR deficiency due to loss of hMLH1 function did not change the extent of platinum (Pt) accumulation or kinetics of removal from total cellular DNA. However, MMR-deficient cells, lacking either hMLH1 or hMSH2, generated twofold more luciferase activity from a cisplatin-damaged reporter plasmid than their MMR-proficient counterparts. Thus, detection of the cisplatin adducts by the MMR system reduced the efficiency of reactivation of the damaged luciferase gene compared to cells lacking this detector. The twofold reduction in reactivation efficiency was of the same order of magnitude as the difference in cisplatin sensitivity between the MMR-proficient and -deficient cells. We conclude that although MMR-proficient and -deficient cells remove Pt from their genome at equal rates, the loss of a functional MMR system facilitates the reactivation of a cisplatin-damaged reporter gene. © 1999 Cancer Research Campaign PMID:10360646

  1. From coherent to incoherent mismatched interfaces. A generalized continuum formulation of surface stresses

    SciTech Connect

    Dingreville, Rémi; Hallil, Abdelmalek; Berbenni, Stéphane

    2014-08-19

    The equilibrium of coherent and incoherent mismatched interfaces is reformulated in the context of continuum mechanics based on the Gibbs dividing surface concept. Two surface stresses are introduced: a coherent surface stress and an incoherent surface stress, as well as a transverse excess strain. Additionally, the coherent surface stress and the transverse excess strain represent the thermodynamic driving forces of stretching the interface while the incoherent surface stress represents the driving force of stretching one crystal while holding the other fixed and thereby altering the structure of the interface. These three quantities fully characterize the elastic behavior of coherent and incoherent interfaces as a function of the in-plane strain, the transverse stress and the mismatch strain. The isotropic case is developed in detail and particular attention is paid to the case of interfacial thermo-elasticity. This exercise provides an insight on the physical significance of the interfacial elastic constants introduced in the formulation and illustrates the obvious coupling between the interface structure and its associated thermodynamics quantities. Finally, an example based on atomistic simulations of Cu/Cu2O interfaces is given to demonstrate the relevance of the generalized interfacial formulation and to emphasize the dependence of the interfacial thermodynamic quantities on the incoherency strain with an actual material system.

  2. From coherent to incoherent mismatched interfaces. A generalized continuum formulation of surface stresses

    DOE PAGES

    Dingreville, Rémi; Hallil, Abdelmalek; Berbenni, Stéphane

    2014-08-19

    The equilibrium of coherent and incoherent mismatched interfaces is reformulated in the context of continuum mechanics based on the Gibbs dividing surface concept. Two surface stresses are introduced: a coherent surface stress and an incoherent surface stress, as well as a transverse excess strain. Additionally, the coherent surface stress and the transverse excess strain represent the thermodynamic driving forces of stretching the interface while the incoherent surface stress represents the driving force of stretching one crystal while holding the other fixed and thereby altering the structure of the interface. These three quantities fully characterize the elastic behavior of coherent andmore » incoherent interfaces as a function of the in-plane strain, the transverse stress and the mismatch strain. The isotropic case is developed in detail and particular attention is paid to the case of interfacial thermo-elasticity. This exercise provides an insight on the physical significance of the interfacial elastic constants introduced in the formulation and illustrates the obvious coupling between the interface structure and its associated thermodynamics quantities. Finally, an example based on atomistic simulations of Cu/Cu2O interfaces is given to demonstrate the relevance of the generalized interfacial formulation and to emphasize the dependence of the interfacial thermodynamic quantities on the incoherency strain with an actual material system.« less

  3. Study of cover source mismatch in steganalysis and ways to mitigate its impact

    NASA Astrophysics Data System (ADS)

    Kodovský, Jan; Sedighi, Vahid; Fridrich, Jessica

    2014-02-01

    When a steganalysis detector trained on one cover source is applied to images from a different source, generally the detection error increases due to the mismatch between both sources. In steganography, this situation is recognized as the so-called cover source mismatch (CSM). The drop in detection accuracy depends on many factors, including the properties of both sources, the detector construction, the feature space used to represent the covers, and the steganographic algorithm. Although well recognized as the single most important factor negatively affecting the performance of steganalyzers in practice, the CSM received surprisingly little attention from researchers. One of the reasons for this is the diversity with which the CSM can manifest. On a series of experiments in the spatial and JPEG domains, we refute some of the common misconceptions that the severity of the CSM is tied to the feature dimensionality or their "fragility." The CSM impact on detection appears too difficult to predict due to the effect of complex dependencies among the features. We also investigate ways to mitigate the negative effect of the CSM using simple measures, such as by enlarging the diversity of the training set (training on a mixture of sources) and by employing a bank of detectors trained on multiple different sources and testing on a detector trained on the closest source.

  4. Expectation mismatch: differences between self-generated and cue-induced expectations.

    PubMed

    Gaschler, R; Schwager, S; Umbach, V J; Frensch, P A; Schubert, T

    2014-10-01

    Expectation of upcoming stimuli and tasks can lead to improved performance, if the anticipated situation occurs, while expectation mismatch can lead to less efficient processing. Researchers have used methodological approaches that rely on either self-generated expectations (predictions) or cue-induced expectations to investigate expectation mismatch effects. Differentiating these two types of expectations for different contents of expectation such as stimuli, responses, task sets and conflict level, we review evidence suggesting that self-generated expectations lead to larger facilitating effects and conflict effects on the behavioral and neural level - as compared to cue-based expectations. On a methodological level, we suggest that self-generated as compared to cue-induced expectations allow for a higher amount of experimental control in many experimental designs on expectation effects. On a theoretical level, we argue for qualitative differences in how cues vs. self-generated expectations influence performance. While self-generated expectations might generally involve representing the expected event in the focus of attention in working memory, cues might only lead to such representations under supportive circumstances (i.e., cue of high validity and attended).

  5. Femtomolar detection of single mismatches by discriminant analysis of DNA hybridization events using gold nanoparticles.

    PubMed

    Ma, Xingyi; Sim, Sang Jun

    2013-03-21

    Even though DNA-based nanosensors have been demonstrated for quantitative detection of analytes and diseases, hybridization events have never been numerically investigated for further understanding of DNA mediated interactions. Here, we developed a nanoscale platform with well-designed capture and detection gold nanoprobes to precisely evaluate the hybridization events. The capture gold nanoprobes were mono-laid on glass and the detection probes were fabricated via a novel competitive conjugation method. The two kinds of probes combined in a suitable orientation following the hybridization with the target. We found that hybridization efficiency was markedly dependent on electrostatic interactions between DNA strands, which can be tailored by adjusting the salt concentration of the incubation solution. Due to the much lower stability of the double helix formed by mismatches, the hybridization efficiencies of single mismatched (MMT) and perfectly matched DNA (PMT) were different. Therefore, we obtained an optimized salt concentration that allowed for discrimination of MMT from PMT without stringent control of temperature or pH. The results indicated this to be an ultrasensitive and precise nanosensor for the diagnosis of genetic diseases.

  6. Propagation dynamics and X-pulse formation in phase-mismatched second-harmonic generation

    SciTech Connect

    Valiulis, G.; Jukna, V.; Jedrkiewicz, O.; Clerici, M.; Rubino, E.; DiTrapani, P.

    2011-04-15

    This paper concerns the theoretical, numerical, and experimental study of the second-harmonic-generation (SHG) process under conditions of phase and group-velocity mismatch and aims to demonstrate the dimensionality transition of the SHG process caused by the change of the fundamental wave diameter. We show that SHG from a narrow fundamental beam leads to the spontaneous self-phase-matching process with, in addition, the appearance of angular dispersion for the off-axis frequency components generated. The angular dispersion sustains the formation of the short X pulse in the second harmonic (SH) and is recognized as three-dimensional (3D) dynamics. On the contrary, the large-diameter fundamental beam reduces the number of the degrees of freedom, does not allow the generation of the angular dispersion, and maintains the so-called one-dimensional (1D) SHG dynamics, where the self-phase-matching appears just for axial components and is accompanied by the shrinking of the SH temporal bandwidth, and sustains a long SH pulse formation. The transition from long SH pulse generation typical of the 1D dynamics to the short 3D X pulse is illustrated numerically and experimentally by changing the conditions from the self-defocusing to the self-focusing regime by simply tuning the phase mismatch. The numerical and experimental verification of the analytical results are also presented.

  7. Race, spatial mismatch, and job accessibility: evidence from a plant relocation.

    PubMed

    Fernandez, Roberto M

    2008-09-01

    One of the most prominent explanations for minority underachievement in the labor market is what has been termed the spatial mismatch hypothesis. The original formulation of the hypothesis by John Kain focused on the effects of racially segregated housing on workers' labor market outcomes assuming race-neutral employers. This paper reports the results of a case study designed to test Kain's original conception of this important hypothesis within the context of a longitudinal analysis of a relocating food processing plant. Because the workers in this study did not choose the firm's new location, the relocation can be treated as an exogenous, demand-side shock to the local labor market. This natural experiment design solves the major problem of extant approaches to the theory, i.e., the selective migration of minorities to areas with high concentrations of jobs. The study design also eliminates the confounding factor of non-race-neutral employers using space as a means to discriminate against minorities since the circumstances of this move make us confident that the firm is not moving for racial motives. We find support in favor of Kain's version of the spatial mismatch hypothesis. Despite the firm's best intentions and work to minimize the impact of the spatial disruption caused by the relocation, the racial segregation of the area's housing market hampered minorities' adjustments to the relocation. Consistent with Kain's formulation, spatially discriminating employers are not needed to produce race differences in job accessibility; racially segregated housing markets alone can generate such outcomes.

  8. Repair of mismatched basepairs in mammalian DNA. Progress report, March 1, 1990--February 28, 1991

    SciTech Connect

    Taylor, J.H.; Hare, J.T.

    1991-08-01

    We have concentrated on three specific areas of our research plan. Our greatest emphasis is on the role of single strand nicks in influencing template strand selection in mismatch repair. We have found, that the ability of a nick in one strand to influence which strand is repaired is not a simple function of distance from the mismatched site but rather that an hot spot where a nick is more likely to have an influence can exist. The second line was production of single-genotype heteroduplexes in order to examine independently the repair of T/G and A/C mispairs within the same sequence context as in our mixed mispair preparations. We have shown preparations of supercoiled heteroduplex can be prepared that were exclusively T/G or exclusively A/C at the mispair site. The third effort has been to understand the difference in repair bias of different cell lines or different transfection conditions as it may relate to different repair systems in the cell. We have identified some of the sources of variation, including cell cycle position. We hope to continue this work to more precisely identify the phase of the cell cycle.

  9. Mutations affecting a putative MutLα endonuclease motif impact multiple mismatch repair functions

    PubMed Central

    Erdeniz, Naz; Nguyen, Megan; Deschênes, Suzanne M.; Liskay, R. Michael

    2008-01-01

    Mutations in DNA mismatch repair (MMR) lead to increased mutation rates and higher recombination between similar, but not identical sequences, as well as resistance to certain DNA methylating agents. Recently, a component of human MMR machinery, MutLα, has been shown to display a latent endonuclease activity. The endonuclease active site appears to include a conserved motif, DQHA(X)2E(X)4E, within the COOH-terminus of human PMS2. Substitution of the glutamic acid residue (E705) abolished the endonuclease activity and mismatch-dependent excision in vitro. Previously, we showed that the PMS2-E705K mutation and the corresponding mutation in Saccharomyces cerevisiae were both recessive loss of function alleles for mutation avoidance in vivo. Here, we show that mutations impacting this endonuclease motif also significantly affect MMR-dependent suppression of homeologous recombination in yeast and responses to Sn1-type methylating agents in both yeast and mammalian cells. Thus, our in vivo results suggest that the endonuclease activity of MutLα is important not only in MMR-dependent mutation avoidance but also for recombination and damage response functions. PMID:17567544

  10. Thickness Mismatch of Coexisting Liquid Phases in Non-Canonical Lipid Bilayers

    PubMed Central

    Bleecker, Joan V.; Cox, Phillip A.; Foster, Rami N.; Litz, Jonathan P.; Blosser, Matthew C.; Castner, David G.; Keller, Sarah L.

    2016-01-01

    Lipid composition dictates membrane thickness, which in turn can influence membrane protein activity. Lipid composition also determines whether a membrane demixes into coexisting liquid-crystalline phases. Previous direct measurements of demixed lipid membranes have always found a liquid-ordered phase that is thicker than the liquid-disordered phase. Here we investigated non-canonical ternary lipid mixtures designed to produce bilayers with thicker disordered phases than ordered phases. The membranes were comprised of short, saturated (ordered) lipids; long, unsaturated (disordered) lipids; and cholesterol. We found that few of these systems yield coexisting liquid phases above 10 °C. For membranes that do demix into two liquid phases, we measured the thickness mismatch between the phases by atomic force microscopy and found that not one of the systems yields thicker disordered than ordered phases under standard experimental conditions. We found no monotonic relationship between demixing temperatures of these ternary systems and either estimated thickness mismatches between the liquid phases or the physical parameters of single-component membranes comprised of the individual lipids. These results highlight the robustness of a membrane’s liquid-ordered phase to be thicker than the liquid-disordered phase, regardless of the membrane’s lipid composition. PMID:26890258

  11. Plasticity in human pitch perception induced by tonotopically mismatched electro-acoustic stimulation.

    PubMed

    Reiss, L A J; Turner, C W; Karsten, S A; Gantz, B J

    2014-01-03

    Under normal conditions, the acoustic pitch percept of a pure tone is determined mainly by the tonotopic place of the stimulation along the cochlea. Unlike acoustic stimulation, electric stimulation of a cochlear implant (CI) allows for the direct manipulation of the place of stimulation in human subjects. CI sound processors analyze the range of frequencies needed for speech perception and allocate portions of this range to the small number of electrodes distributed in the cochlea. Because the allocation is assigned independently of the original resonant frequency of the basilar membrane associated with the location of each electrode, CI users who have access to residual hearing in either or both ears often have tonotopic mismatches between the acoustic and electric stimulation. Here we demonstrate plasticity of place pitch representations of up to three octaves in Hybrid CI users after experience with combined electro-acoustic stimulation. The pitch percept evoked by single CI electrodes, measured relative to acoustic tones presented to the non-implanted ear, changed over time in directions that reduced the electro-acoustic pitch mismatch introduced by the CI programming. This trend was particularly apparent when the allocations of stimulus frequencies to electrodes were changed over time, with pitch changes even reversing direction in some subjects. These findings show that pitch plasticity can occur more rapidly and on a greater scale in the mature auditory system than previously thought possible. Overall, the results suggest that the adult auditory system can impose perceptual order on disordered arrays of inputs.

  12. Plasticity in Human Pitch Perception Induced by Tonotopically Mismatched Electro-Acoustic Stimulation

    PubMed Central

    Reiss, Lina A.J.; Turner, Christopher W.; Karsten, Sue A.; Gantz, Bruce J.

    2013-01-01

    Under normal conditions, the acoustic pitch percept of a pure tone is determined mainly by the tonotopic place of the stimulation along the cochlea. Unlike acoustic stimulation, electric stimulation of a cochlear implant (CI) allows for the direct manipulation of the place of stimulation in human subjects. CI sound processors analyze the range of frequencies needed for speech perception and allocate portions of this range to the small number of electrodes distributed in the cochlea. Because the allocation is assigned independently of the original resonant frequency of the basilar membrane associated with the location of each electrode, CI users who have access to residual hearing in either or both ears often have tonotopic mismatches between the acoustic and electric stimulation. Here we demonstrate plasticity of place pitch representations of up to 3 octaves in Hybrid CI users after experience with combined electro-acoustic stimulation. The pitch percept evoked by single CI electrodes, measured relative to acoustic tones presented to the non-implanted ear, changed over time in directions that reduced the electro-acoustic pitch mismatch introduced by the CI programming. This trend was particularly apparent when the allocations of stimulus frequencies to electrodes were changed over time, with pitch changes even reversing direction in some subjects. These findings show that pitch plasticity can occur more rapidly and on a greater scale in the mature auditory system than previously thought possible. Overall, the results suggest that the adult auditory system can impose perceptual order on disordered arrays of inputs. PMID:24157931

  13. Columnar structured FePt films epitaxially grown on large lattice mismatched intermediate layer

    NASA Astrophysics Data System (ADS)

    Dong, K. F.; Deng, J. Y.; Peng, Y. G.; Ju, G.; Chow, G. M.; Chen, J. S.

    2016-09-01

    The microstructure and magnetic properties of the FePt films grown on large mismatched ZrN (15.7%) intermediate layer were investigated. With using ZrN intermediate layer, FePt 10 nm films exhibited (001) texture except for some weaker FePt (110) texture. Good epitaxial relationships of FePt (001) <100>//ZrN (001) <100>//TiN (001) <100> among FePt and ZrN/TiN were revealed from the transmission electron microscopy (TEM) results. As compared with TiN intermediate layer, although FePt-SiO2-C films grown on ZrN/TiN intermediate layer showed isotropic magnetic properties, the large interfacial energy and lattice mismatch between FePt and ZrN would lead to form columnar structural FePt films with smaller grain size and improved isolation. By doping ZrN into the TiN layer, solid solution of ZrTiN was formed and the lattice constant is increased comparing with TiN and decreased comparing with ZrN. Moreover, FePt-SiO2-C films grown on TiN 2 nm-20 vol.% ZrN/TiN 3 nm intermediate layer showed an improved perpendicular magnetic anisotropy. Simultaneously, columnar structure with smaller grain size retained.

  14. Iterative dual energy material decomposition from spatial mismatched raw data sets.

    PubMed

    Zhao, Xing; Hu, Jing-Jing; Zhao, Yun-Song; Zhang, Hui-Tao; Zhang, Peng

    2014-01-01

    Today's clinical dual energy computed tomography (DECT) scanners generally measure different rays for different energy spectra and acquire spatial mismatched raw data sets. The deficits in clinical DECT technologies suggest that mainly image based material decomposition methods are in use nowadays. However, the image based material decomposition is an approximate technique, and beam hardening artifacts remain in decomposition results. A recently developed image based iterative method for material decomposition from inconsistent rays (MDIR) can achieve much better image quality than the conventional image based methods. Inspired by the MDIR method, this paper proposes an iterative method to indirectly perform raw data based DECT even with completely mismatched raw data sets. The iterative process is initialized by density images that were obtained from an image based material decomposition. Then the density images are iteratively corrected by comparing the estimated polychromatic projections and the measured polychromatic projections. Only three iterations of the method are sufficient to greatly improve the qualitative and quantitative information in material density images. Compared with the MDIR method, the proposed method needs not to perform additional water precorrection. The advantages of the method are verified with numerical experiments from inconsistent noise free and noisy raw data.

  15. Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids.

    PubMed

    Fontenete, Silvia; Silvia, Fontenete; Barros, Joana; Joana, Barros; Madureira, Pedro; Pedro, Madureira; Figueiredo, Céu; Céu, Figueiredo; Wengel, Jesper; Jesper, Wengel; Azevedo, Nuno Filipe; Filipe, Azevedo Nuno

    2015-05-01

    In the past few years, several researchers have focused their attention on nucleic acid mimics due to the increasing necessity of developing a more robust recognition of DNA or RNA sequences. Fluorescence in situ hybridization (FISH) is an example of a method where the use of these novel nucleic acid monomers might be crucial to the success of the analysis. To achieve the expected accuracy in detection, FISH probes should have high binding affinity towards their complementary strands and discriminate effectively the noncomplementary strands. In this study, we investigate the effect of different chemical modifications in fluorescent probes on their ability to successfully detect the complementary target and discriminate the mismatched base pairs by FISH. To our knowledge, this paper presents the first study where this analysis is performed with different types of FISH probes directly in biological targets, Helicobacter pylori and Helicobacter acinonychis. This is also the first study where unlocked nucleic acids (UNA) were used as chemistry modification in oligonucleotides for FISH methodologies. The effectiveness in detecting the specific target and in mismatch discrimination appears to be improved using locked nucleic acids (LNA)/2'-O-methyl RNA (2'OMe) or peptide nucleic acid (PNA) in comparison to LNA/DNA, LNA/UNA, or DNA probes. Further, the use of LNA modifications together with 2'OMe monomers allowed the use of shorter fluorescent probes and increased the range of hybridization temperatures at which FISH would work.

  16. Effect of parameter mismatch on the dynamics of strongly coupled self sustained oscillators

    NASA Astrophysics Data System (ADS)

    Chakrabarty, Nilaj; Jain, Aditya; Lal, Nijil; Das Gupta, Kantimay; Parmananda, Punit

    2017-01-01

    In this paper, we present an experimental setup and an associated mathematical model to study the synchronization of two self-sustained, strongly coupled, mechanical oscillators (metronomes). The effects of a small detuning in the internal parameters, namely, damping and frequency, have been studied. Our experimental system is a pair of spring wound mechanical metronomes; coupled by placing them on a common base, free to move along a horizontal direction. We designed a photodiode array based non-contact, non-magnetic position detection system driven by a microcontroller to record the instantaneous angular displacement of each oscillator and the small linear displacement of the base, coupling the two. In our system, the mass of the oscillating pendula forms a significant fraction of the total mass of the system, leading to strong coupling of the oscillators. We modified the internal mechanism of the spring-wound "clockwork" slightly, such that the natural frequency and the internal damping could be independently tuned. Stable synchronized and anti-synchronized states were observed as the difference in the parameters was varied in the experiments. The simulation results showed a rapid increase in the phase difference between the two oscillators beyond a certain threshold of parameter mismatch. Our simple model of the escapement mechanism did not reproduce a complete 180° out of phase state. However, the numerical simulations show that increased mismatch in parameters leads to a synchronized state with a large phase difference.

  17. Dielectric Mismatch Mediates Carrier Mobility in Organic-Intercalated Layered TiS2.

    PubMed

    Wan, Chunlei; Kodama, Yumi; Kondo, Mami; Sasai, Ryo; Qian, Xin; Gu, Xiaokun; Koga, Kenji; Yabuki, Kazuhisa; Yang, Ronggui; Koumoto, Kunihito

    2015-10-14

    The dielectric constant is a key parameter that determines both optical and electronic properties of materials. It is desirable to tune electronic properties though dielectric engineering approach. Here, we present a systematic approach to tune carrier mobilities of hybrid inorganic/organic materials where layered two-dimensional transition-metal dichalcogenide TiS2 is electrochemically intercalated with polar organic molecules. By manipulating the dielectric mismatch using polar organic molecules with different dielectric constants, ranging from 10 to 41, the electron mobility of the TiS2 layers was changed three times due to the dielectric screening of the Coulomb-impurity scattering processes. Both the overall thermal conductivity and the lattice thermal conductivity were also found to decrease with an increasing dielectric mismatch. The enhanced electrical mobility along with the decreased thermal conductivity together gave rise to a significantly improved thermoelectric figure of merit of the hybrid inorganic/organic materials at room temperature, which might find applications in wearable electronics.

  18. Direct evidence of mismatching effect on H emission in laser-induced atmospheric helium gas plasma

    SciTech Connect

    Zener Sukra Lie; Koo Hendrik Kurniawan; May On Tjia; Rinda, Hedwig; Suliyanti, Maria Margaretha; Syahrun Nur Abdulmadjid; Nasrullah Idris; Alion Mangasi Marpaung; Marincan Pardede; Jobiliong, Eric; Muliadi Ramli; Heri Suyanto; Fukumoto, Kenichi; Kagawa, Kiichiro

    2013-02-07

    A time-resolved orthogonal double pulse laser-induced breakdown spectroscopy (LIBS) with helium surrounding gas is developed for the explicit demonstration of time mismatch between the passage of fast moving impurity hydrogen atoms and the formation of thermal shock wave plasma generated by the relatively slow moving major host atoms of much greater masses ablated from the same sample. Although this so-called 'mismatching effect' has been consistently shown to be responsible for the gas pressure induced intensity diminution of hydrogen emission in a number of LIBS measurements using different ambient gases, its explicit demonstration has yet to be reported. The previously reported helium assisted excitation process has made possible the use of surrounding helium gas in our experimental set-up for showing that the ablated hydrogen atoms indeed move faster than the simultaneously ablated much heavier major host atoms as signaled by the earlier H emission in the helium plasma generated by a separate laser prior to the laser ablation. This conclusion is further substantiated by the observed dominant distribution of H atoms in the forward cone-shaped target plasma.

  19. Impact of DNA mismatch repair system alterations on human fertility and related treatments*

    PubMed Central

    Hu, Min-hao; Liu, Shu-yuan; Wang, Ning; Wu, Yan; Jin, Fan

    2016-01-01

    DNA mismatch repair (MMR) is one of the biological pathways, which plays a critical role in DNA homeostasis, primarily by repairing base-pair mismatches and insertion/deletion loops that occur during DNA replication. MMR also takes part in other metabolic pathways and regulates cell cycle arrest. Defects in MMR are associated with genomic instability, predisposition to certain types of cancers and resistance to certain therapeutic drugs. Moreover, genetic and epigenetic alterations in the MMR system demonstrate a significant relationship with human fertility and related treatments, which helps us to understand the etiology and susceptibility of human infertility. Alterations in the MMR system may also influence the health of offspring conceived by assisted reproductive technology in humans. However, further studies are needed to explore the specific mechanisms by which the MMR system may affect human infertility. This review addresses the physiological mechanisms of the MMR system and associations between alterations of the MMR system and human fertility and related treatments, and potential effects on the next generation. PMID:26739522

  20. Cardiac complications after haploidentical HLA-mismatched hematopoietic stem cell transplantation using in vivo alemtuzumab.

    PubMed

    Oshima, K; Sakata-Yanagimoto, M; Asano-Mori, Y; Izutsu, K; Watanabe, T; Shoda, E; Ogawa, S; Motokura, T; Chiba, S; Kurokawa, M; Hirai, H; Kanda, Y

    2005-11-01

    Alemtuzumab is a humanized monoclonal antibody directed against human CD52 with a strong lympholytic effect. We have performed unmanipulated hematopoietic stem cell transplantation (HSCT) from 2- or 3-locus-mismatched family donors in 14 patients using in vivo alemtuzumab. All achieved complete donor cell engraftment and grade III-IV acute graft-versus-host disease was observed in only one patient. However, eight of the 14 patients developed grade II-IV cardiac complications according to Bearman's criteria. Next, we retrospectively analyzed the records of 142 adult patients who underwent allogeneic HSCT from 1995 to 2004 to evaluate whether the use of alemtuzumab was an independent risk factor for cardiac complications. Among several factors that increased the incidence of grade II-IV cardiac complications with at least borderline significance, a multivariate analysis identified the cumulative dose of anthracyclines (P=0.0016) and the use of alemtuzumab (P=0.0001) as independent significant risk factors. All of the cardiac complications in the alemtuzumab group were successfully treated with diuretics and/or catecholamines. Patient selection and close monitoring of cardiac function may be important in HLA-mismatched HSCT using in vivo alemtuzumab.

  1. Neisseria gonorrhoeae MutS Affects Pilin Antigenic Variation through Mismatch Correction and Not by pilE Guanine Quartet Binding

    PubMed Central

    Rotman, Ella

    2015-01-01

    ABSTRACT Many pathogens use homologous recombination to vary surface antigens to avoid immune surveillance. Neisseria gonorrhoeae achieves this in part by changing the properties of its surface pili in a process called pilin antigenic variation (AV). Pilin AV occurs by high-frequency gene conversion reactions that transfer silent pilS sequences into the expressed pilE locus and requires the formation of an upstream guanine quartet (G4) DNA structure to initiate this process. The MutS and MutL proteins of the mismatch correction (MMC) system act to correct mismatches after replication and prevent homeologous (i.e., partially homologous) recombination, but MutS orthologs can also bind to G4 structures. A previous study showed that mutation of MutS resulted in a 3-fold increase in pilin AV, which could be due to the loss of MutS antirecombination properties or loss of G4 binding. We tested two site-directed separation-of-function MutS mutants that are both predicted to bind to G4s but are not able to perform MMC. Pilus phase variation assays and DNA sequence analysis of pilE variants produced in these mutants showed that all three mutS mutants and a mutL mutant had similar increased frequencies of pilin AV. Moreover, the mutS mutants all showed similar increased levels of pilin AV-dependent synthetic lethality. These results show that antirecombination by MMC is the reason for the effect that MutS has on pilin AV and is not due to pilE G4 binding by MutS. IMPORTANCE Neisseria gonorrhoeae continually changes its outer surface proteins to avoid recognition by the immune system. N. gonorrhoeae alters the antigenicity of the pilus by directed recombination between partially homologous pilin copies in a process that requires a guanine quartet (G4) structure. The MutS protein of the mismatch correction (MMC) system prevents recombination between partially homologous sequences and can also bind to G4s. We confirmed that loss of MMC increases the frequency of pilin antigenic

  2. The DNA mismatch repair protein MutS forms a one-dimensional Tonks gas on DNA

    NASA Astrophysics Data System (ADS)

    Bundschuh, Ralf; Klajner, Piotr; Hanne, Jeungphill; Britton, Brooke M.; Liu, Jianquan; Park, Jonghyun; Lee, Jong-Bong; Fishel, Richard

    2014-03-01

    MutS is a protein involved in DNA mismatch repair. It recognizes the mismatch, forms a sliding clamp around the DNA, and displaces other proteins bound to the DNA prior to the actual repair process. Here, we present a quantitative model of an ensemble of MutS molecules on a short strand of DNA with one mismatch. We model the ensemble as a Tonks gas of passively diffusing one-dimensional particles of finite extension and include clamp formation at the mismatch and random detachment. The distributions of MutS number bound to the DNA for different mismatch positions and different MutS concentrations in solution fit very well with distributions determined by single molecule experiments, thereby establishing the Tonks gas as an excellent model of MutS action on DNA. This material is based upon work supported by the National Science Foundation under Grant No. 01105458 (RB), the National Institutes of Health under Grant No. CA67007 (RF), and the National Research Foundation of Korea under Grant No. 2011-0013901 (JBL).

  3. Circumpolar analysis of the Adélie Penguin reveals the importance of environmental variability in phenological mismatch.

    PubMed

    Youngflesh, Casey; Jenouvrier, Stephanie; Li, Yun; Ji, Rubao; Ainley, David G; Ballard, Grant; Barbraud, Christophe; Delord, Karine; Dugger, Katie M; Emmerson, Louise M; Fraser, William R; Hinke, Jefferson T; Lyver, Phil O'B; Olmastroni, Silvia; Southwell, Colin J; Trivelpiece, Susan G; Trivelpiece, Wayne Z; Lynch, Heather J

    2017-04-01

    Evidence of climate-change-driven shifts in plant and animal phenology have raised concerns that certain trophic interactions may be increasingly mismatched in time, resulting in declines in reproductive success. Given the constraints imposed by extreme seasonality at high latitudes and the rapid shifts in phenology seen in the Arctic, we would also expect Antarctic species to be highly vulnerable to climate-change-driven phenological mismatches with their environment. However, few studies have assessed the impacts of phenological change in Antarctica. Using the largest database of phytoplankton phenology, sea-ice phenology, and Adélie Penguin breeding phenology and breeding success assembled to date, we find that, while a temporal match between Penguin breeding phenology and optimal environmental conditions sets an upper limit on breeding success, only a weak relationship to the mean exists. Despite previous work suggesting that divergent trends in Adélie Penguin breeding phenology are apparent across the Antarctic continent, we find no such trends. Furthermore, we find no trend in the magnitude of phenological mismatch, suggesting that mismatch is driven by interannual variability in environmental conditions rather than climate-change-driven trends, as observed in other systems. We propose several criteria necessary for a species to experience a strong climate-change-driven phenological mismatch, of which several may be violated by this system.

  4. Synergism of Dam, MutH, and MutS in methylation-directed mismatch repair in Escherichia coli.

    PubMed

    Hu, Changkun; Zhao, Yunqi; Sun, Huiyun; Yang, Yixin

    2017-01-01

    DNA mismatch repair (MMR) is a critical mutation surveillance system for recognizing and repairing erroneous insertion, deletion, and disincorporation of base. Major components of mismatch repair system consist of MutH, MutL, and MutS. Dam methylates adenine to distinguish newly synthesized daughter strands from the parent strands. Employing a tyrosine-auxotrophic E. coli FX-11 strain, the mutation frequency can be determined by the number of tyrosine revertants and the cell viability of FX-11 with deficiencies in dam and mismatch repair proteins. This study showed that mutS defect produced a higher mutation frequency than mutH did. Interestingly, double defects in dam and mutS synergistically produced a dramatically higher spontaneous mutation frequency than the summation of mutation frequencies of FX-11 strains with individual deficiency of dam or mutS, suggesting that Dam may work with MutHL to partially accomplish the task of recognizing the mismatch sites to retain partial mismatch repair capacity.

  5. Assessment of primer/template mismatch effects on real-time PCR amplification of target taxa for GMO quantification.

    PubMed

    Ghedira, Rim; Papazova, Nina; Vuylsteke, Marnik; Ruttink, Tom; Taverniers, Isabel; De Loose, Marc

    2009-10-28

    GMO quantification, based on real-time PCR, relies on the amplification of an event-specific transgene assay and a species-specific reference assay. The uniformity of the nucleotide sequences targeted by both assays across various transgenic varieties is an important prerequisite for correct quantification. Single nucleotide polymorphisms (SNPs) frequently occur in the maize genome and might lead to nucleotide variation in regions used to design primers and probes for reference assays. Further, they may affect the annealing of the primer to the template and reduce the efficiency of DNA amplification. We assessed the effect of a minor DNA template modification, such as a single base pair mismatch in the primer attachment site, on real-time PCR quantification. A model system was used based on the introduction of artificial mismatches between the forward primer and the DNA template in the reference assay targeting the maize starch synthase (SSIIb) gene. The results show that the presence of a mismatch between the primer and the DNA template causes partial to complete failure of the amplification of the initial DNA template depending on the type and location of the nucleotide mismatch. With this study, we show that the presence of a primer/template mismatch affects the estimated total DNA quantity to a varying degree.

  6. Exonuclease processivity of archaeal replicative DNA polymerase in association with PCNA is expedited by mismatches in DNA

    PubMed Central

    Yoda, Takuya; Tanabe, Maiko; Tsuji, Toshiyuki; Yoda, Takao; Ishino, Sonoko; Shirai, Tsuyoshi; Ishino, Yoshizumi; Takeyama, Haruko; Nishida, Hirokazu

    2017-01-01

    Family B DNA polymerases comprise polymerase and 3′ −>5′ exonuclease domains, and detect a mismatch in a newly synthesized strand to remove it in cooperation with Proliferating cell nuclear antigen (PCNA), which encircles the DNA to provide a molecular platform for efficient protein–protein and protein–DNA interactions during DNA replication and repair. Once the repair is completed, the enzyme must stop the exonucleolytic process and switch to the polymerase mode. However, the cue to stop the degradation is unclear. We constructed several PCNA mutants and found that the exonuclease reaction was enhanced in the mutants lacking the conserved basic patch, located on the inside surface of PCNA. These mutants may mimic the Pol/PCNA complex processing the mismatched DNA, in which PCNA cannot interact rigidly with the irregularly distributed phosphate groups outside the dsDNA. Indeed, the exonuclease reaction with the wild type PCNA was facilitated by mismatched DNA substrates. PCNA may suppress the exonuclease reaction after the removal of the mismatched nucleotide. PCNA seems to act as a “brake” that stops the exonuclease mode of the DNA polymerase after the removal of a mismatched nucleotide from the substrate DNA, for the prompt switch to the DNA polymerase mode. PMID:28300173

  7. Multiple mismatches at the low expression HLA loci DP, DQ, and DRB3/4/5 associate with adverse outcomes in hematopoietic stem cell transplantation.

    PubMed

    Fernández-Viña, Marcelo A; Klein, John P; Haagenson, Michael; Spellman, Stephen R; Anasetti, Claudio; Noreen, Harriet; Baxter-Lowe, Lee Ann; Cano, Pedro; Flomenberg, Neal; Confer, Dennis L; Horowitz, Mary M; Oudshoorn, Machteld; Petersdorf, Effie W; Setterholm, Michelle; Champlin, Richard; Lee, Stephanie J; de Lima, Marcos

    2013-05-30

    A single mismatch in highly expressed HLA-A, -B, -C, and -DRB1 loci (HEL) is associated with worse outcomes in hematopoietic stem cell transplantation, while less is known about the cumulative impact of mismatches in the lesser expressed HLA loci DRB3/4/5, DQ, and DP (LEL). We studied whether accumulation of LEL mismatches is associated with deleterious effects in 3853 unrelated donor transplants stratified according to number of matches in the HEL. In the 8/8 matched HEL group, LEL mismatches were not associated with any adverse outcome. Mismatches at HLA-DRB1 were associated with occurrence of multiple LEL mismatches. In the 7/8 HEL group, patients with 3 or more LEL mismatches scored in the graft-versus-host vector had a significantly higher risk of mortality (1.45 and 1.43) and transplant-related mortality (1.68 and 1.54) than the subgroups with 0 or 1 LEL mismatches. No single LEL locus had a more pronounced effect on clinical outcome. Three or more LEL mismatches are associated with lower survival after 7/8 HEL matched transplantation. Prospective evaluation of matching for HLA-DRB3/4/5, -DQ, and -DP loci is warranted to reduce posttransplant risks in donor-recipient pairs matched for 7/8 HEL.

  8. Occupational stratification, job-mismatches, and child poverty: understanding the disadvantage of Black immigrants in the US.

    PubMed

    Thomas, Kevin J A

    2015-03-01

    This study examines the implications of occupational stratification and job mismatches for the welfare of children, using data from the 2005-2009 American Community Survey. The results show that Black children of immigrants have household heads that are more likely to have occupations with low SEI scores than children in US-born households. More importantly, they demonstrate that intersections between parental job-mismatches and employment in the bottom rather than upper levels of the occupational distribution have important implications for understanding poverty differences among children. Job mismatches within occupations with low SEI scores are associated with greater poverty risks among Black than White, Asian, or Hispanic children of immigrants. However, racial poverty disparities are considerably lower among children with household heads in the highest occupational strata.

  9. Contingency blindness: location-identity binding mismatches obscure awareness of spatial contingencies and produce profound interference in visual working memory.

    PubMed

    Fiacconi, Chris M; Milliken, Bruce

    2012-08-01

    The purpose of the present study was to highlight the role of location-identity binding mismatches in obscuring explicit awareness of a strong contingency. In a spatial-priming procedure, we introduced a high likelihood of location-repeat trials. Experiments 1, 2a, and 2b demonstrated that participants' explicit awareness of this contingency was heavily influenced by the local match in location-identity bindings. In Experiment 3, we sought to determine why location-identity binding mismatches produce such low levels of contingency awareness. Our results suggest that binding mismatches can interfere substantially with visual-memory performance. We attribute the low levels of contingency awareness to participants' inability to remember the critical location-identity binding in the prime on a trial-to-trial basis. These results imply a close interplay between object files and visual working memory.

  10. Longitudinal phonon modes in a ZnSe/ZnS(x)Se(1-x) lattice-mismatched superlattice

    NASA Astrophysics Data System (ADS)

    Xia, Hua; Jiang, S. S.; Zhang, Wei; Zhang, X. K.; Guan, Z. P.; Fan, X. W.

    1994-11-01

    Longitudinal acoustic and optical phonon modes of a ZnSe/ZnS(x)Se(1-x) (x approximately equals 0.20) lattice-mismatched superlattice, prepared with atmospheric metal organic chemical vapor deposition method, have been investigated by light scattering measurements. Despite a lattice mismatch as large as 1% between the alternating layers, the measured longitudinal elastic constants are in agreement with the calculated values of an unstrained effective medium model. Furthermore, a correlative study was made by fitting the spectra to a spatial correlation model, which reproduces line shapes of the observed confined longitudinal-optical modes without incorporating the strain effects. The results demonstrate that a combination of Brillouin and Raman spectroscopy provides a good method to determine accurately the elastic constants and strain information of the lattice-mismatched superlattices and heterostructures.

  11. Method based on chirp decomposition for dispersion mismatch compensation in precision absolute distance measurement using swept-wavelength interferometry.

    PubMed

    Lu, Cheng; Liu, Guodong; Liu, Bingguo; Chen, Fengdong; Hu, Tao; Zhuang, Zhitao; Xu, Xinke; Gan, Yu

    2015-12-14

    We establish a theoretical model of dispersion mismatch in absolute distance measurements using swept-wavelength interferometry (SWI) and propose a novel dispersion mismatch compensation method called chirp decomposition. This method separates the dispersion coefficient and distance under test, which ensures dispersion mismatch compensation without introducing additional random errors. In the measurement of a target located at 3.9 m, a measurement resolution of 45.9 μm is obtained, which is close to the theoretical resolution, and a standard deviation of 0.74 μm is obtained, which is better than the traditional method. The measurement results are compared to a single-frequency laser interferometer. The target moves from 1 m to 3.7 m, and the measurement precision using the new method is less than 0.81 μm.

  12. Influence of the Strength Mismatch of a Narrow Gap Welded Joint of SA508 on the Plastic η Factor

    NASA Astrophysics Data System (ADS)

    Koo, J. M.; Huh, Y.; Seok, C. S.

    2012-11-01

    In this article, the influence of the strength mismatch of a narrow gap welded joint of SA508 on the η factor was evaluated. The η factor is the principal parameter that determines the plastic portion of the J-integral. The specimens for tensile and hardness tests were collected from piping with narrow gap welding and the stress-strain curve and hardness were obtained from those. From these results, the Ramberg-Osgood (R-O) constant was obtained. Also, the finite element analysis was performed with variations in the strength mismatch and the weld width. The η factor equation considering the strength mismatch and the weld width of a narrow gap welded joint was suggested.

  13. Cross-scale feedbacks and scale mismatches as influences on cultural services and the resilience of protected areas.

    PubMed

    Maciejewski, Kristine; De Vos, Alta; Cumming, Graeme S; Moore, Christine; Biggs, Duan

    2015-01-01

    Protected areas are a central strategy for achieving global conservation goals, but their continued existence depends heavily on maintaining sufficient social and political support to outweigh economic interests or other motives for land conversion. Thus, the resilience of protected areas can be considered a function of their perceived benefits to society. Nature-based tourism (NBT), a cultural ecosystem service, provides a key source of income to protected areas, facilitating a sustainable solution to conservation. The ability of tourism to generate income depends, however, on both the scales at which this cultural service is provided and the scales at which tourists respond to services on offer. This observation raises a set of location-, context-, and scale-related questions that need to be confronted before we can understand and value cultural service provision appropriately. We combine elements of resilience analysis with a systems ecology framework and apply this to NBT in protected areas to investigate cross-scale interactions and scale mismatches. We postulate that cross-scale effects can either have a positive effect on protected area resilience or lead to scale mismatches, depending on their interactions with cross-scale feedbacks. To demonstrate this, we compare spatial scales and nested levels of institutions to develop a typology of scale mismatches for common scenarios in NBT. In our new typology, the severity of a scale mismatch is expressed as the ratio of spatial scale to institutional level, producing 25 possible outcomes with differing consequences for system resilience. We predict that greater differences between interacting scales and levels, and greater magnitudes of cross-scale interactions, will lead to greater magnitudes of scale mismatch. Achieving a better understanding of feedbacks and mismatches, and finding ways of aligning spatial and institutional scales, will be critical for strengthening the resilience of protected areas that

  14. Molecular recognition of T:G mismatched base pairs in DNA as studied by electrospray ionization mass spectrometry.

    PubMed

    Riccardi Sirtori, Federico; Aldini, Giancarlo; Colombo, Maristella; Colombo, Nicoletta; Malyszko, Jan; Vistoli, Giulio; D'Alessio, Roberto

    2012-06-01

    Postreplicative mismatch repair (MMR) is a cellular system involved in the recognition and correction of DNA polymerase errors that escape detection in proofreading. Of the various mismatched bases, T:G pairing in DNA is one of the more common mutations leading to the formation of tumors in humans. In addition, the absence of the MMR system can generate resistance to several chemotherapeutic agents, particularly DNA-damaging substances. The main purpose of this study was the setup and validation of an electrospray ionization (ESI) mass spectrometry method for the identification of small molecules that are able to recognize T:G mismatches in DNA targets. These findings could be useful for the discovery of new antitumor drugs. The analytical method is based on the ability of electrospray to preserve the noncovalent adducts present in solution and transfer them to the gas phase. Lexitropsin derivatives (polyimidazole compounds) have been previously described as selective for T:G mismatch binding by NMR and ITC studies. We synthesized and tested various polyimidazole derivatives, one of which in particular (NMS-057) showed a higher affinity for an oligonucleotide DNA sequence containing a T:G mismatched base pair. To rationalize these findings, molecular docking studies were performed using available NMR structures. Moreover, ESI-MS experiments, performed on an orbitrap mass spectrometer, highlighted the formation of heterodimeric complexes between DNA sequences, distamycin A, and polyimidazole compounds. Our results confirm that this ESI method could be a valuable tool for the identification of new molecules able to specifically recognize T:G mismatched base pairs.

  15. Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches.

    PubMed

    Green, Stefan J; Venkatramanan, Raghavee; Naqib, Ankur

    2015-01-01

    The polymerase chain reaction (PCR) is sensitive to mismatches between primer and template, and mismatches can lead to inefficient amplification of targeted regions of DNA template. In PCRs in which a degenerate primer pool is employed, each primer can behave differently. Therefore, inefficiencies due to different primer melting temperatures within a degenerate primer pool, in addition to mismatches between primer binding sites and primers, can lead to a distortion of the true relative abundance of targets in the original DNA pool. A theoretical analysis indicated that a combination of primer-template and primer-amplicon interactions during PCR cycles 3-12 is potentially responsible for this distortion. To test this hypothesis, we developed a novel amplification strategy, entitled "Polymerase-exonuclease (PEX) PCR", in which primer-template interactions and primer-amplicon interactions are separated. The PEX PCR method substantially and significantly improved the evenness of recovery of sequences from a mock community of known composition, and allowed for amplification of templates with introduced mismatches near the 3' end of the primer annealing sites. When the PEX PCR method was applied to genomic DNA extracted from complex environmental samples, a significant shift in the observed microbial community was detected. Furthermore, the PEX PCR method provides a mechanism to identify which primers in a primer pool are annealing to target gDNA. Primer utilization patterns revealed that at high annealing temperatures in the PEX PCR method, perfect match annealing predominates, while at lower annealing temperatures, primers with up to four mismatches with templates can contribute substantially to amplification. The PEX PCR method is simple to perform, is limited to PCR mixes and a single exonuclease step which can be performed without reaction cleanup, and is recommended for reactions in which degenerate primer pools are used or when mismatches between primers and

  16. Nitrogen fluxes at the root-soil interface show a mismatch of nitrogen fertilizer supply and sugarcane root uptake capacity

    NASA Astrophysics Data System (ADS)

    Inselsbacher, Erich; Schmidt, Susanne; Näsholm, Torgny; Robinson, Nicole; Guillou, Stéphane; Vinall, Kerry; Lakshmanan, Prakash; Brackin, Richard

    2016-04-01

    Nitrogen (N) uptake by agricultural crops is a key constituent of the global N cycle, as N captured by roots has a markedly different fate than N remaining in the soil. Global evidence indicates that only approximately 50% of applied N fertilizer is captured by crops, and the remainder can cause pollution via runoff and gaseous emissions. This inefficiency is of global concern, and requires innovation based on improved understanding of which N forms are available for and ultimately taken up by crops. However, current soil analysis methods based on destructive soil sampling provide little insight into delivery and acquisition of N forms by roots. Here, we present the results of a study in sugarcane fields receiving different fertilizer regimes comparing soil N supply rates with potential root N uptake rates. We applied microdialysis, a novel technique for in situ quantification of soil nutrient fluxes, to measure flux rates of inorganic N and amino acid N, and analyzed N uptake capacities of sugarcane roots using 15N labelled tracers. We found that in fertilized sugarcane soils, fluxes of inorganic N exceed the uptake capacities of sugarcane roots by several orders of magnitude. Contrary, fluxes of organic N closely matched roots' uptake capacity. These results indicate root uptake capacity constrains plant acquisition of inorganic N. This mismatch between soil N supply and root N uptake capacity is a likely key driver for low N efficiency in the studied crop system. Our results also suggest that the relative contribution of inorganic N for plant nutrition may be overestimated when relying on soil extracts as indicators for root-available N, and organic N may contribute more to crop N supply than is currently assumed. Overall, we show a new approach for examining in situ N relations in soil in context of crop N physiology, which provides a new avenue towards tailoring N fertilizer supply to match the specific uptake abilities and N demand of crops over the growth

  17. Phenological mismatch with abiotic conditions implications for flowering in Arctic plants.

    PubMed

    Wheeler, Helen C; Høye, Toke T; Schmidt, Niels Martin; Svenning, Jens-Christian; Forchhammer, Mads C

    2015-03-01

    Although many studies have examined the phenological mismatches between interacting organisms, few have addressed the potential for mismatches between phenology and seasonal weather conditions. In the Arctic, rapid phenological changes in many taxa are occurring in association with earlier snowmelt. The timing of snowmelt is jointly affected by the size of the late winter snowpack and the temperature during the spring thaw. Increased winter snowpack results in delayed snowmelt, whereas higher air temperatures and faster snowmelt advance the timing of snowmelt. Where interannual variation in snowpack is substantial, changes in the timing of snowmelt can be largely uncoupled from changes in air temperature. Using detailed, long-term data on the flowering phenology of four arctic plant species from Zackenberg, Greenland, we investigate whether there is a phenological component to the temperature conditions experienced prior to and during flowering. In particular, we assess the role of timing of flowering in determining pre-flowering exposure to freezing temperatures and to the temperatures-experienced prior to flowering. We then examine the implications of flowering phenology for flower abundance. Earlier snowmelt resulted in greater exposure to freezing conditions, suggesting an increased potential for a mismatch between the timing of flowering and seasonal weather conditions and an increased potential for negative consequences, such as freezing 'damage. We also found a parabolic relationship between the timing of flowering and the temperature experienced during flowering after taking interannual temperature effects into account. If timing of flowering advances to a cooler period of the growing season, this may moderate the effects of a general warming trend across years. Flower abundance was quadratically associated with the timing of flowering, such that both early and late flowering led to lower flower abundance than did intermediate flowering. Our results

  18. Influence of donor–recipient gender mismatch on graft function and survival following lung transplantation†

    PubMed Central

    Alvarez, Antonio; Moreno, Paula; Illana, Jennifer; Espinosa, Dionisio; Baamonde, Carlos; Arango, Elisabet; Algar, Francisco Javier; Salvatierra, Angel

    2013-01-01

    OBJECTIVES In current practice, donors and recipients are not matched for gender in lung transplantation. However, some data have suggested a possible effect of gender combinations on lung transplant outcomes. We examined whether donor–recipient (D/R) gender mismatch is related to adverse outcomes after lung transplantation in terms of early and long-term graft function and survival. METHODS We reviewed 256 donors and lung transplant recipients over a 14-year period. Patients were distributed into four groups: Group A (D/R: female/female), Group B (D/R: male/male), Group C (D/R: female/male), Group D (D/R: male/female). Donor and recipient variables were compared among groups, including early graft function, 30-day mortality, freedom from bronchiolitis obliterans syndrome (BOS), and long-term survival. RESULTS Group A: 57 (22%), Group B: 99 (39%), Group C: 62 (24%), Group D: 38 (15%) transplants (P = 0.001). Donor age was 29 ± 14, 27 ± 12, 33 ± 13 and 23 ± 12 years for Groups A, B, C and D, respectively (P = 0.004). Recipient age was 31 ± 15, 44 ± 17, 42 ± 16 and 30 ± 16 years for Groups A, B, C and D, respectively (P = 0.000). PaO2/FiO2 (mmHg) 24 h post-transplant was: Group A: 276 ± 144, Group B: 297 ± 131, Group C: 344 ± 133 and Group D: 238 ± 138 (P = 0.015). Primary graft dysfunction developed in 23, 14, 17 and 21% of recipients from Groups A, B, C and D, respectively (P = 0.45). Operative mortality was 4.4, 6.5, 5.2 and 2%, for recipients from Groups A, B, C and D, respectively (P = 0.66). Freedom from BOS was 73, 59 and 36% for gender-matched transplants vs 76, 67 and 40% for gender-mismatched transplants at 3, 5 and 10 years, respectively (P = 0.618), without differences among groups. A non-significant survival benefit was observed for female recipients, irrespective of the donor gender. CONCLUSIONS Donor–recipient gender mismatch does not have a negative impact on early graft function and mortality following lung transplantation. There is a

  19. Engineering Safety-Related Requirements for Software-Intensive Systems

    DTIC Science & Technology

    2006-03-01

    Climate Orbiter ($125 million) English vs. Metric units mismatch Mars Polar Lander Missing requirement concerning touchdown sensor behavior Therac – 25 ...Engineering Safety-Related Requirements for Software-Intensive Systems 25 Corresponding Safety Subfactors Safety SubfactorSafety Safety Problem Type Safety...station with the doors open for boarding, the horizontal gap between the station platform and the vehicle door threshold shall be no greater than 25 mm

  20. Effects of Emotional Intelligence on the Impression of Irony Created by the Mismatch between Verbal and Nonverbal Cues

    PubMed Central

    Jacob, Heike; Kreifelts, Benjamin; Nizielski, Sophia; Schütz, Astrid; Wildgruber, Dirk

    2016-01-01

    Emotional information is conveyed through verbal and nonverbal signals, with nonverbal cues often being considered the decisive factor in the judgment of others’ emotional states. The aim of the present study was to examine how verbal and nonverbal cues are integrated by perceivers. More specifically, we tested whether the mismatch between verbal and nonverbal information was perceived as an expression of irony. Moreover, we investigated the effects of emotional intelligence on the impression of irony. The findings revealed that the mismatch between verbal and nonverbal information created the impression of irony. Furthermore, participants higher in emotional intelligence were faster at rating such stimuli as ironic expressions. PMID:27716831

  1. Associations and clinical relevance of aortic-brachial artery stiffness mismatch, aortic reservoir function, and central pressure augmentation.

    PubMed

    Schultz, Martin G; Hughes, Alun D; Davies, Justin E; Sharman, James E

    2015-10-01

    Central augmentation pressure (AP) and index (AIx) predict cardiovascular events and mortality, but underlying physiological mechanisms remain disputed. While traditionally believed to relate to wave reflections arising from proximal arterial impedance (and stiffness) mismatching, recent evidence suggests aortic reservoir function may be a more dominant contributor to AP and AIx. Our aim was therefore to determine relationships among aortic-brachial stiffness mismatching, AP, AIx, aortic reservoir function, and end-organ disease. Aortic (aPWV) and brachial (bPWV) pulse wave velocity were measured in 359 individuals (aged 61 ± 9, 49% male). Central AP, AIx, and aortic reservoir indexes were derived from radial tonometry. Participants were stratified by positive (bPWV > aPWV), negligible (bPWV ≈ aPWV), or negative stiffness mismatch (bPWV < aPWV). Left-ventricular mass index (LVMI) was measured by two-dimensional-echocardiography. Central AP and AIx were higher with negative stiffness mismatch vs. negligible or positive stiffness mismatch (11 ± 6 vs. 10 ± 6 vs. 8 ± 6 mmHg, P < 0.001 and 24 ± 10 vs. 24 ± 11 vs. 21 ± 13%, P = 0.042). Stiffness mismatch (bPWV-aPWV) was negatively associated with AP (r = -0.18, P = 0.001) but not AIx (r = -0.06, P = 0.27). Aortic reservoir pressure strongly correlated to AP (r = 0.81, P < 0.001) and AIx (r = 0.62, P < 0.001) independent of age, sex, heart rate, mean arterial pressure, and height (standardized β = 0.61 and 0.12, P ≤ 0.001). Aortic reservoir pressure independently predicted abnormal LVMI (β = 0.13, P = 0.024). Positive aortic-brachial stiffness mismatch does not result in higher AP or AIx. Aortic reservoir function, rather than discrete wave reflection from proximal arterial stiffness mismatching, provides a better model description of AP and AIx and also has clinical relevance as evidenced by an independent association of aortic reservoir pressure with LVMI.

  2. Nanoscale self-templating for oxide epitaxy with large symmetry mismatch

    SciTech Connect

    Gao, Xiang; Lee, Shinbuhm; Nichols, John A.; Meyer, Tricia L.; Ward, Thomas Zac; Chisholm, Matthew F.; Lee, Ho Nyung

    2016-12-02

    Direct observations using scanning transmission electron microscopy unveil an intriguing interfacial bi-layer that enables epitaxial growth of a strain-free, monoclinic, bronze-phase VO2(B) thin film on a perovskite SrTiO3 (STO) substrate. For this study, we observe an ultrathin (2–3 unit cells) interlayer best described as highly strained VO2(B) nanodomains combined with an extra (Ti,V)O2 layer on the TiO2 terminated STO (001) surface. By forming a fully coherent interface with the STO substrate and a semi-coherent interface with the strain-free epitaxial VO2(B) film above, the interfacial bi-layer enables the epitaxial connection of the two materials despite their large symmetry and lattice mismatch.

  3. Warming, plant phenology and the spatial dimension of trophic mismatch for large herbivores

    PubMed Central

    Post, Eric; Pedersen, Christian; Wilmers, Christopher C; Forchhammer, Mads C

    2008-01-01

    Temporal advancement of resource availability by warming in seasonal environments can reduce reproductive success of vertebrates if their own reproductive phenology does not also advance with warming. Indirect evidence from large-scale analyses suggests, however, that migratory vertebrates might compensate for this by tracking phenological variation across landscapes. Results from our two-year warming experiment combined with seven years of observations of plant phenology and offspring production by caribou (Rangifer tarandus) in Greenland, however, contradict evidence from large-scale analyses. At spatial scales relevant to the foraging horizon of individual herbivores, spatial variability in plant phenology was reduced—not increased—by both experimental and observed warming. Concurrently, offspring production by female caribou declined with reductions in spatial variability in plant phenology. By highlighting the spatial dimension of trophic mismatch, these results reveal heretofore unexpected adverse consequences of climatic warming for herbivore population ecology. PMID:18495618

  4. Mitochondrial Cardiomyopathy with a Unique 99mTc-MIBI/123I-BMIPP Mismatch Pattern

    PubMed Central

    Tashiro, Ryosuke; Onoue, Noriko; Rikimaru, Hiroya; Tsukita, Kenichi; Fujita, Hiroshi; Yamaguchi, Nobuhiro; Ishizuka, Takeshi; Suzuki, Yasushi; Suzuki, Hiroyoshi; Shinozaki, Tsuyoshi

    2017-01-01

    A 42-year-old man was referred to our hospital due to chest pain, diabetes mellitus, and sensorineural hearing loss. Transthoracic echocardiography revealed diffuse left ventricular hypokinesis. He was diagnosed with mitochondrial disease and a c.A3243G mutation was identified in his mitochondrial DNA. This case of mitochondrial cardiomyopathy demonstrated a low uptake of 123I-BMIPP, while the uptake of 99mTc-MIBI was preserved. In contrast, previous reports have noted the increased uptake of123I-BMIPP and the decreased uptake of 99mTc-MIBI. This is the first study to show this unique 99mTc-MIBI/123I-BMIPP mismatch pattern. We also discuss the relationships among the cardiac scintigraphy, cardiac magnetic resonance imaging, and histopathology findings. PMID:28154277

  5. An Analytical Model for Top-Hat Long Transient Mode-Mismatched Thermal Lens Spectroscopy

    NASA Astrophysics Data System (ADS)

    Sabaeian, M.; Rezaei, H.

    2016-02-01

    It has been shown that a top-hat excitation beam gives rise to a more sensitive signal for the thermal lens spectroscopy (TLS). Recently, a numerical model has been presented for a top- hat excitation beam in a dual-beam mod-mismatched TLS [Opt. Lett. 33(13), 1464-1466 (2008)]. In this work, we present a full analytical version of this model. Our model was based on a new solution of time-dependent heat equation for a finite radius cylindrical sample exposed to a top-hat excitation laser beam. The Fresnel diffraction integration method was then used to calculate on-axis probe-beam intensity variations due to thermal lensing by taking the aberrant nature of the thermal lens into account. The model was confirmed with experimental data of LSCAS-2 with an excellent agreement.

  6. Neural mismatch indices of vowel discrimination in monolingually and bilingually exposed infants: does attention matter?

    PubMed

    Shafer, Valerie L; Yu, Yan H; Garrido-Nag, Karen

    2012-09-20

    Neurophysiological studies of infant speech suggest that mismatch responses (MMRs) have predictive value for later language. Their value, however, is diminished because unexplained differences in the MMR patterns are seen across studies. The current study aimed to identify the functional nature of infant MMRs by recording event-related-potentials (ERPs) to an infrequent English vowel change in internal or final positions of a sequence of ten vowels in six-month-old monolingually and bilingually exposed infants. Increased negativity of the MMR (infrequent minus frequent) was found in final compared to internal positions and correlated with an index of increased attention to the final position. This pattern helps explain the overall greater negativity to the speech sounds in the bilingually exposed female infants. These findings substantially advance our understanding of neural indices of speech perception development and show promise for furthering our understanding of bilingual language development.

  7. Lattice-Mismatched III-V Epilayers for High-Efficiency Photovoltaics

    SciTech Connect

    Ahrenkiel, Scott Phillip

    2013-06-30

    The project focused on development of new approaches and materials combinations to expand and improve the quality and versatility of lattice-mismatched (LMM) III-V semiconductor epilayers for use in high-efficiency multijunction photovoltaic (PV) devices. To address these goals, new capabilities for materials synthesis and characterization were established at SDSM&T that have applications in modern opto- and nano-electronics, including epitaxial crystal growth and transmission electron microscopy. Advances were made in analyzing and controlling the strain profiles and quality of compositional grades used for these technologies. In particular, quaternary compositional grades were demonstrated, and a quantitative method for characteristic X-ray analysis was developed. The project allowed enhanced collaboration between scientists at NREL and SDSM&T to address closely related research goals, including materials exchange and characterization.

  8. New Therapeutic Opportunities Based on DNA Mismatch Repair and BRAF Status in Metastatic Colorectal Cancer.

    PubMed

    Cohen, Romain; Svrcek, Magali; Dreyer, Chantal; Cervera, Pascale; Duval, Alex; Pocard, Marc; Fléjou, Jean-François; de Gramont, Aimery; André, Thierry

    2016-03-01

    Recently, colorectal cancer (CRC) subtyping consortium identified four consensus molecular subtypes (CMS1-4). CMS1 is enriched for deficient mismatch repair (dMMR) and BRAF (V600E) tumors. Intriguingly, this subtype has better relapse-free survival but worse overall survival after relapse compared with the other subtypes. Growing evidence is accumulating on the benefit of specific therapeutic strategies such as immune checkpoint inhibition therapy in dMMR tumors and mitogen-activated protein kinase (MAPK) pathway targeted therapy in tumors harboring BRAF (V600E) mutation. After reviewing dMMR prognostic value, immune checkpoints as major targets for dMMR carcinomas will be highlighted. Following, BRAF (V600E) prognostic impact will be reviewed and therapeutic strategies with the combination of cytotoxic agents and especially the combinations of BRAF and MAPK inhibitors will be discussed.

  9. Group velocity and pulse lengthening of mismatched laser pulses in plasma channels

    SciTech Connect

    Schroeder, Carl; Benedetti, Carlo; Esarey, Eric; van Tilborg, Jeroen; Leemans, Wim

    2011-07-07

    Analytic solutions are presented to the non-paraxial wave equation describing an ultra-short, low-power, laser pulse propagating in aplasma channel. Expressions for the laser pulse centroid motion and laser group velocity are derived, valid for matched and mismatchedpropagation in a parabolic plasma channel, as well as in vacuum, for an arbitrary Laguerre-Gaussian laser mode. The group velocity of amismatched laser pulse, for which the laser spot size is strongly oscillating, is found to be independent of propagation distance andsignificantly less than that of a matched pulse. Laser pulse lengthening of a mismatched pulse owing to laser mode slippage isexamined and found to dominate over that due to dispersive pulse spreading for sufficiently long pulses. Analytic results are shown tobe in excellent agreement with numerical solutions of the full Maxwell equations coupled to the plasma response. Implications for plasmachannel diagnostics are discussed.

  10. Variation in the Relationship Between Education and Marriage: Marriage Market Mismatch?

    PubMed Central

    Musick, Kelly; Brand, Jennie E.; Davis, Dwight

    2011-01-01

    Educational expansion has led to greater diversity in the social backgrounds of college students. We ask how schooling interacts with this diversity to influence marriage formation among men and women. Relying on data from the 1979 National Longitudinal Survey of Youth (N = 3208), we use a propensity score approach to group men and women into social strata and multilevel event history models to test differences in the effects of college attendance across strata. We find a statistically significant, positive trend in the effects of college attendance across strata, with the largest effects of college on first marriage among the more advantaged and the smallest—indeed, negative—effects among the least advantaged men and women. These findings appear consistent with a mismatch in the marriage market between individuals’ education and their social backgrounds. PMID:22563132

  11. Evidence that the DNA mismatch repair system removes 1-nucleotide Okazaki fragment flaps.

    PubMed

    Kadyrova, Lyudmila Y; Dahal, Basanta K; Kadyrov, Farid A

    2015-10-02

    The DNA mismatch repair (MMR) system plays a major role in promoting genome stability and suppressing carcinogenesis. In this work, we investigated whether the MMR system is involved in Okazaki fragment maturation. We found that in the yeast Saccharomyces cerevisiae, the MMR system and the flap endonuclease Rad27 act in overlapping pathways that protect the nuclear genome from 1-bp insertions. In addition, we determined that purified yeast and human MutSα proteins recognize 1-nucleotide DNA and RNA flaps. In reconstituted human systems, MutSα, proliferating cell nuclear antigen, and replication factor C activate MutLα endonuclease to remove the flaps. ATPase and endonuclease mutants of MutLα are defective in the flap removal. These results suggest that the MMR system contributes to the removal of 1-nucleotide Okazaki fragment flaps.

  12. Dynamics of Membrane Proteins within Synthetic Polymer Membranes with Large Hydrophobic Mismatch.

    PubMed

    Itel, Fabian; Najer, Adrian; Palivan, Cornelia G; Meier, Wolfgang

    2015-06-10

    The functioning of biological membrane proteins (MPs) within synthetic block copolymer membranes is an intriguing phenomenon that is believed to offer great potential for applications in life and medical sciences and engineering. The question why biological MPs are able to function in this completely artificial environment is still unresolved by any experimental data. Here, we have analyzed the lateral diffusion properties of different sized MPs within poly(dimethylsiloxane) (PDMS)-containing amphiphilic block copolymer membranes of membrane thicknesses between 9 and 13 nm, which results in a hydrophobic mismatch between the membrane thickness and the size of the proteins of 3.3-7.1 nm (3.5-5 times). We show that the high flexibility of PDMS, which provides membrane fluidities similar to phospholipid bilayers, is the key-factor for MP incorporation.

  13. Effect of photometric detector spectral response quality on white LED spectral mismatch correction factors.

    PubMed

    Rosas, E; Estrada-Hernández, A

    2016-07-01

    Light-emitting-diode (LED)-based solid-state lighting has become a real option for private and public lighting after achieving high total luminous flux (TLF) and luminous efficacy levels, thus promoting the development of energy efficient use regulation to be fulfilled by LED lamps and LED luminaires. Here, we propose a photometer-quality-based fast-checking criterion. This allows photometric technicians to perform a quick evaluation of the photometric head spectral response quality effect on the LED source spectral mismatch correction factor-when determining the TLF and luminous efficacy minimum approved levels-performance parameters subject to mandatory verification by the conformity assessment procedures technically supporting the corresponding regulation. The proposed criterion applies for a wide range of photometric detector heads' qualities (2.6%≤f1'≤36.4%).

  14. Matches, Mismatches, and Methods: Multiple-View Workflows for Energy Portfolio Analysis.

    PubMed

    Brehmer, Matthew; Ng, Jocelyn; Tate, Kevin; Munzner, Tamara

    2016-01-01

    The energy performance of large building portfolios is challenging to analyze and monitor, as current analysis tools are not scalable or they present derived and aggregated data at too coarse of a level. We conducted a visualization design study, beginning with a thorough work domain analysis and a characterization of data and task abstractions. We describe generalizable visual encoding design choices for time-oriented data framed in terms of matches and mismatches, as well as considerations for workflow design. Our designs address several research questions pertaining to scalability, view coordination, and the inappropriateness of line charts for derived and aggregated data due to a combination of data semantics and domain convention. We also present guidelines relating to familiarity and trust, as well as methodological considerations for visualization design studies. Our designs were adopted by our collaborators and incorporated into the design of an energy analysis software application that will be deployed to tens of thousands of energy workers in their client base.

  15. Role descriptions induce gender mismatch effects in eye movements during reading.

    PubMed

    Reali, Chiara; Esaulova, Yulia; Öttl, Anton; von Stockhausen, Lisa

    2015-01-01

    The present eye-tracking study investigates the effect of gender typicality on the resolution of anaphoric personal pronouns in English. Participants read descriptions of a person performing a typically male, typically female or gender-neutral occupational activity. The description was followed by an anaphoric reference (he or she) which revealed the referent's gender. The first experiment presented roles which were highly typical for men (e.g., blacksmith) or for women (e.g., beautician), the second experiment presented role descriptions with a moderate degree of gender typicality (e.g., psychologist, lawyer). Results revealed a gender mismatch effect in early and late measures in the first experiment and in early stages in the second experiment. Moreover, eye-movement data for highly typical roles correlated with explicit typicality ratings. The results are discussed from a cross-linguistic perspective, comparing natural gender languages and grammatical gender languages. An interpretation of the cognitive representation of typicality beliefs is proposed.

  16. Role descriptions induce gender mismatch effects in eye movements during reading

    PubMed Central

    Reali, Chiara; Esaulova, Yulia; Öttl, Anton; von Stockhausen, Lisa

    2015-01-01

    The present eye-tracking study investigates the effect of gender typicality on the resolution of anaphoric personal pronouns in English. Participants read descriptions of a person performing a typically male, typically female or gender-neutral occupational activity. The description was followed by an anaphoric reference (he or she) which revealed the referent's gender. The first experiment presented roles which were highly typical for men (e.g., blacksmith) or for women (e.g., beautician), the second experiment presented role descriptions with a moderate degree of gender typicality (e.g., psychologist, lawyer). Results revealed a gender mismatch effect in early and late measures in the first experiment and in early stages in the second experiment. Moreover, eye-movement data for highly typical roles correlated with explicit typicality ratings. The results are discussed from a cross-linguistic perspective, comparing natural gender languages and grammatical gender languages. An interpretation of the cognitive representation of typicality beliefs is proposed. PMID:26579003

  17. Residential Segregation,Spatial Mismatch and Economic Growth across US Metropolitan Area

    SciTech Connect

    Campbell, Dr Harrison; Li, Huiping

    2013-01-01

    Numerous studies have demonstrated the detrimental influence of residential segregation on poor inner-city residents. This study examines the impact of residential segregation on the welfare of populations in US metropolitan areas using economic growth as the indicator. Panel data of US metropolitan areas spanning 25 years, 1980 2005, are used to analyze the effect of segregation on economic growth. The results show that both racial and skill segregation have a negative impact on short and long-term economic growth, which have increased over time. Further, the negative impact of the variables associated with spatial mismatch is also revealed. The results clearly point to the need for mobility policies that favor non-White households and comprehensive strategies that promote economic opportunities in low-resource communities in the US.

  18. Phenotypic Heterogeneity by Germline Mismatch Repair Gene Defect in Lynch Syndrome Patients.

    PubMed

    Hernâni-Eusébio, Jorge; Barbosa, Elisabete

    2016-10-01

    Introdução: A síndrome de Lynch é a forma hereditária mais comum de cancro colo-rectal, sendo também responsável por cancro do endométrio e de outros tipos. Associa-se a mutações germinativas nos genes de mismatch repair do ADN e a instabilidade de microssatélites. As mutações MLH1 e MSH2 têm um fenótipo de síndrome de Lynch ‘clássico’, sendo o MSH2 mais associado a cancro extra-cólico. Mutações do MSH6 e PMS2 têm um fenótipo atípico. A expressão clínica é heterogénea, existindo uma correlação entre o gene mismatch repair mutado e o padrão fenotípico. Material e Métodos: Análise retrospetiva dos dados clínicos de doentes que cumpriam os critérios de Amesterdão ou que tinha mutações nos genes mismatch repair, entre setembro de 2012 e outubro de 2015. Resultados: Identificámos 28 doentes. Dezassete tinham cancro colo-rectal sendo a localização no cólon direito predominante. Cinco tiveram cancro do endométrio (mediana da idade de diagnóstico – 53), sem qualquer mutação no MSH6. Cinco desenvolveram outros cancros. Todos os casos com mutações mismatch repair estudados tinham instabilidade de microssatélites. Discussão: Na maioria dos casos foi encontrada mutação no MSH2 apesar de o MLH1 ser descrito na literatura como o gene mais frequentemente mutado. Interessa dizer que os doentes com cancro colo-rectal não evidenciam uma tendência para ter muito infiltrado inflamatório. Na maioria dos casos foi realizada colectomia parcial apesar da incidência elevada de lesões síncronas e metácronas associadas. Histerectomia e anexectomia profilática foi realizada em doentes em menopausa/perimenopausa. Conclusão: O registo standardizado dos dados dos doentes poderá levar a um melhor acompanhamento e conhecimento desta síndrome. O uso das Guidelines de Bethesda poderá identificar novos casos que escapam aos critérios de Amesterdão. A pesquisa de instabilidade de microssatélites deve ser feita em muito maior n

  19. Kinetic characterisation of primer mismatches in allele-specific PCR: a quantitative assessment.

    PubMed

    Waterfall, Christy M; Eisenthal, Robert; Cobb, Benjamin D

    2002-12-20

    A novel method of estimating the kinetic parameters of Taq DNA polymerase during rapid cycle PCR is presented. A model was constructed using a simplified sigmoid function to represent substrate accumulation during PCR in combination with the general equation describing high substrate inhibition for Michaelis-Menten enzymes. The PCR progress curve was viewed as a series of independent reactions where initial rates were accurately measured for each cycle. Kinetic parameters were obtained for allele-specific PCR (AS-PCR) amplification to examine the effect of mismatches on amplification. A high degree of correlation was obtained providing evidence of substrate inhibition as a major cause of the plateau phase that occurs in the later cycles of PCR.

  20. Piriform and trochanteric fossae. A drawing mismatch or a terminology error? A review.

    PubMed

    Papadakis, Stamatios A; Shepherd, Lane; Babourda, Eleni C; Papadakis, Stefanos

    2005-08-01

    The current literature indicates that the standard starting point for intramedullary nailing is the piriform fossa. The accuracy of the entry point for anterograde femoral intramedullary nailing between published texts and relevant illustrations was recorded. The piriform fossa is the site of insertion of the piriform tendon and represents a small, shallow depression located on the tip of the greater trochanter. The trochanteric fossa is a deep depression on the inner surface of the greater trochanter, and in the vast majority of the published data is indicated incorrectly as "piriform fossa". As a result of either a recurrent drawing mismatch or a terminology error, the correct entry point for anterograde femoral intramedullary nailing is confusing and should be indicated in the current literature. The trochanteric fossa appears to be the standard entry point that most surgeons recommend.

  1. Discrimination of stress in speech and music: a mismatch negativity (MMN) study.

    PubMed

    Peter, Varghese; McArthur, Genevieve; Thompson, William Forde

    2012-12-01

    The aim of this study was to determine if duration-related stress in speech and music is processed in a similar way in the brain. To this end, we tested 20 adults for their abstract mismatch negativity (MMN) event-related potentials to two duration-related stress patterns: stress on the first syllable or note (long-short), and stress on the second syllable or note (short-long). A significant MMN was elicited for both speech and music except for the short-long speech stimulus. The long-short stimuli elicited larger MMN amplitudes for speech and music compared to short-long stimuli. An extra negativity-the late discriminative negativity (LDN)-was observed only for music. The larger MMN amplitude for long-short stimuli might be due to the familiarity of the stress pattern in speech and music. The presence of LDN for music may reflect greater long-term memory transfer for music stimuli.

  2. When the face fits: recognition of celebrities from matching and mismatching faces and voices.

    PubMed

    Stevenage, Sarah V; Neil, Greg J; Hamlin, Iain

    2014-01-01

    The results of two experiments are presented in which participants engaged in a face-recognition or a voice-recognition task. The stimuli were face-voice pairs in which the face and voice were co-presented and were either "matched" (same person), "related" (two highly associated people), or "mismatched" (two unrelated people). Analysis in both experiments confirmed that accuracy and confidence in face recognition was consistently high regardless of the identity of the accompanying voice. However accuracy of voice recognition was increasingly affected as the relationship between voice and accompanying face declined. Moreover, when considering self-reported confidence in voice recognition, confidence remained high for correct responses despite the proportion of these responses declining across conditions. These results converged with existing evidence indicating the vulnerability of voice recognition as a relatively weak signaller of identity, and results are discussed in the context of a person-recognition framework.

  3. Robust control of nonlinear MAGLEV suspension system with mismatched uncertainties via DOBC approach.

    PubMed

    Yang, Jun; Zolotas, Argyrios; Chen, Wen-Hua; Michail, Konstantinos; Li, Shihua

    2011-07-01

    Robust control of a class of uncertain systems that have disturbances and uncertainties not satisfying "matching" condition is investigated in this paper via a disturbance observer based control (DOBC) approach. In the context of this paper, "matched" disturbances/uncertainties stand for the disturbances/uncertainties entering the system through the same channels as control inputs. By properly designing a disturbance compensation gain, a novel composite controller is proposed to counteract the "mismatched" lumped disturbances from the output channels. The proposed method significantly extends the applicability of the DOBC methods. Rigorous stability analysis of the closed-loop system with the proposed method is established under mild assumptions. The proposed method is applied to a nonlinear MAGnetic LEViation (MAGLEV) suspension system. Simulation shows that compared to the widely used integral control method, the proposed method provides significantly improved disturbance rejection and robustness against load variation.

  4. An Underreported Consequence of Obesity in Pregnancy: Patient-Prosthesis Mismatch

    PubMed Central

    Hartman, William R.; Arendt, Katherine W.; Rehfeldt, Kent H.

    2012-01-01

    As the rate of obesity increases in childbearing-aged women, so too will the complications of obesity in pregnancy. An uncommon and likely underreported complication occurs in obese women who have received prepregnancy cardiac valve replacement with a prosthesis that is inadequately sized for body habitus, a condition referred to as patient-prosthesis mismatch (PPM). The physiologic changes of pregnancy as well as the increased weight gain combine to exacerbate PPM. We report a case of PPM that necessitated prosthesis replacement at 16-week gestation. As the incidence of this clinical scenario increases, it is important to understand the implications of prosthesis sizing, as well as the repercussions of having cardiopulmonary surgery to correct the undersized valve prosthesis while pregnant. PMID:22830065

  5. Aortic annuloplasty with aortic root reconstruction to prevent patient-prosthesis mismatch.

    PubMed

    Hopkins, Richard A

    2006-07-01

    Part of the ongoing argument concerning patient-prosthesis mismatch (PPM) following aortic valve replacement (AVR) is due to the perception that aortic annulus enlargement procedures increase the risk and technical difficulty of aortic valve surgery. Here, an aortic root reconstruction that involves enlargement of the annulus and tailoring of the aortic root to accommodate larger stented prostheses is presented that has been personally performed in 196 patients with no technique-related surgical deaths or complications, and thus can be carried out without additional risk. This aortic root enlargement aortoplasty and annuloplasty method can be calibrated to all AVRs involving stented manufactured prostheses when these are deemed the prosthesis of choice for the patient with a relatively small annulus and/or aortic root, severe left ventricular hypertrophy, compromised LV function or a very active lifestyle, to achieve predicted EOA values > or = 1.00 cm2/m2.

  6. Nanoscale self-templating for oxide epitaxy with large symmetry mismatch

    NASA Astrophysics Data System (ADS)

    Gao, Xiang; Lee, Shinbuhm; Nichols, John; Meyer, Tricia L.; Ward, Thomas Z.; Chisholm, Matthew F.; Lee, Ho Nyung

    2016-12-01

    Direct observations using scanning transmission electron microscopy unveil an intriguing interfacial bi-layer that enables epitaxial growth of a strain-free, monoclinic, bronze-phase VO2(B) thin film on a perovskite SrTiO3 (STO) substrate. We observe an ultrathin (2–3 unit cells) interlayer best described as highly strained VO2(B) nanodomains combined with an extra (Ti,V)O2 layer on the TiO2 terminated STO (001) surface. By forming a fully coherent interface with the STO substrate and a semi-coherent interface with the strain-free epitaxial VO2(B) film above, the interfacial bi-layer enables the epitaxial connection of the two materials despite their large symmetry and lattice mismatch.

  7. Mode-mismatched confocal thermal-lens microscope with collimated probe beam

    SciTech Connect

    Cabrera, Humberto; Korte, Dorota; Franko, Mladen

    2015-05-15

    We report a thermal lens microscope (TLM) based on an optimized mode-mismatched configuration. It takes advantage of the coaxial counter propagating tightly focused excitation and collimated probe beams, instead of both focused at the sample, as it is in currently known TLM setups. A simple mathematical model that takes into account the main features of the instrument is presented. The confocal detection scheme and the introduction of highly collimated probe beam allow enhancing the versatility, limit of detection (LOD), and sensitivity of the instrument. The theory is experimentally verified measuring ethanol’s absorption coefficient at 532.8 nm. Additionally, the presented technique is applied for detection of ultra-trace amounts of Cr(III) in liquid solution. The achieved LOD is 1.3 ppb, which represents 20-fold enhancement compared to transmission mode spectrometric techniques and a 7.5-fold improvement compared to previously reported methods for Cr(III) based on thermal lens effect.

  8. Nanoscale self-templating for oxide epitaxy with large symmetry mismatch

    DOE PAGES

    Gao, Xiang; Lee, Shinbuhm; Nichols, John A.; ...

    2016-12-02

    Direct observations using scanning transmission electron microscopy unveil an intriguing interfacial bi-layer that enables epitaxial growth of a strain-free, monoclinic, bronze-phase VO2(B) thin film on a perovskite SrTiO3 (STO) substrate. For this study, we observe an ultrathin (2–3 unit cells) interlayer best described as highly strained VO2(B) nanodomains combined with an extra (Ti,V)O2 layer on the TiO2 terminated STO (001) surface. By forming a fully coherent interface with the STO substrate and a semi-coherent interface with the strain-free epitaxial VO2(B) film above, the interfacial bi-layer enables the epitaxial connection of the two materials despite their large symmetry and lattice mismatch.

  9. Functional mismatch in a bumble bee pollination mutualism under climate change.

    PubMed

    Miller-Struttmann, Nicole E; Geib, Jennifer C; Franklin, James D; Kevan, Peter G; Holdo, Ricardo M; Ebert-May, Diane; Lynn, Austin M; Kettenbach, Jessica A; Hedrick, Elizabeth; Galen, Candace

    2015-09-25

    Ecological partnerships, or mutualisms, are globally widespread, sustaining agriculture and biodiversity. Mutualisms evolve through the matching of functional traits between partners, such as tongue length of pollinators and flower tube depth of plants. Long-tongued pollinators specialize on flowers with deep corolla tubes, whereas shorter-tongued pollinators generalize across tube lengths. Losses of functional guilds because of shifts in global climate may disrupt mutualisms and threaten partner species. We found that in two alpine bumble bee species, decreases in tongue length have evolved over 40 years. Co-occurring flowers have not become shallower, nor are small-flowered plants more prolific. We argue that declining floral resources because of warmer summers have favored generalist foraging, leading to a mismatch between shorter-tongued bees and the longer-tubed plants they once pollinated.

  10. Biomarkers for immune therapy in colorectal cancer: mismatch-repair deficiency and others

    PubMed Central

    Bupathi, Manojkumar

    2016-01-01

    Colorectal cancer (CRC) is a heterogeneous disease for which the treatment backbone has primarily been cytotoxic chemotherapy. With better understanding of the involved molecular mechanisms, it is now known that there are a number of epigenetic and genetic events, which are involved in CRC pathogenesis. Specific biomarkers have been identified which can be used to determine the clinical outcome of patients beyond tumor staging and predict for treatment efficacy. Molecular testing is now routinely performed to select for patients that will benefit the most from targeted agents and immunotherapy. In addition to KRAS, NRAS, and BRAF mutation (MT), analysis of DNA mismatch repair (MMR) status, tumor infiltrating lymphocytes, and checkpoint protein expression may be helpful to determine whether patients are eligible for certain therapies. The focus of this article is to discuss present and upcoming biomarkers for immunotherapy in CRC. PMID:27747085

  11. Mismatch negativity to tonal contours suggests preattentive perception of prosodic content.

    PubMed

    Leitman, David I; Sehatpour, Pejman; Shpaner, Marina; Foxe, John J; Javitt, Daniel C

    2009-09-01

    Modulation of speech conveys information that is decoded within audio-sensory structures. For example, the termination of an utterance with a rise in pitch distinguishes statements and questions. This study evaluated the sensitivity of early auditory structures to such linguistic prosodic distinctions using mismatch negativity (MMN). MMN is a preattentive auditory event-related potential (ERP) sensitive to stimulus deviance. High-density ERP to pitch contour stimuli were collected in a passive listening oddball paradigm from 11 healthy subjects. Voltage analysis revealed significant MMN responses to declarative and interrogative oddball stimuli. Further, MMN was significantly larger to interrogative, than declarative, deviants, indicating non-symmetric brain processing. These MMNs demonstrate that pitch contour abstractions reflecting interrogative/ declarative distinctions can be represented in preattentive auditory sensory memory.

  12. Abstract phoneme representations in the left temporal cortex: magnetic mismatch negativity study.

    PubMed

    Shestakova, Anna; Brattico, Elvira; Huotilainen, Minna; Galunov, Valery; Soloviev, Alexei; Sams, Mikko; Ilmoniemi, Risto J; Näätänen, Risto

    2002-10-07

    We investigated the brain mechanisms enabling one automatically discriminate phoneme category irrespective of the large inter-speaker variability in the acoustic features of the voices. For this purpose, subjects were presented with 450 different speech stimuli, each uttered by a different speaker, belonging to three vowel categories, while a 306-channel magnetoencephalogram (MEG) was obtained to record the magnetic counterpart of the mismatch negativity (MMNm), elicited only when sensory memory traces for repetitive sounds are formed in the auditory cortex. Despite this wide acoustic variation, category changes elicited prominent MMNm responses, which were considerably stronger in the left than in the right hemisphere in the right-handed subjects. These results implicate the presence of long-term memory traces for vowels, which can recognize the vowel-specific invariant code enabling correct vowel percept even in the presence of realistic acoustic variation.

  13. Recombination dynamics and carrier lifetimes in highly mismatched ZnTeO alloys

    SciTech Connect

    Lin, Yan-Cheng E-mail: wuchingchou@mail.nctu.edu.tw; Tasi, Ming-Jui; Chou, Wu-Ching E-mail: wuchingchou@mail.nctu.edu.tw; Chang, Wen-Hao; Chen, Wei-Kuo; Tanaka, Tooru; Guo, Qixin; Nishio, Mitsuhiro

    2013-12-23

    This study investigates the recombination dynamics in highly mismatched ZnTeO alloys using time-resolved photoluminescence (PL) spectroscopy. The large PL energy redshift with increasing O content and the disappearance of the ZnTe emission verify the O-induced conduction band anticrossing effect. The incorporation of O generates electron localization below the E{sub −} conduction subband tail, which provide additional optical transitions and cause complex recombination mechanisms. Photoexcited free electrons in both the E{sub +} and the E{sub −} conduction subbands favor rapid relaxation to low energy states. Additionally, temperature-independent long carrier lifetimes (>130.0 ns) that are induced by localized electrons increase with O concentration.

  14. Somatic aphasia: Mismatch of body sensations with autonomic stress reactivity in psychopathy

    PubMed Central

    Gao, Yu; Raine, Adrian; Schug, Robert A.

    2012-01-01

    Background Although one of the main characteristics of psychopaths is a deficit in emotion, it is unknown whether they show a fundamental impairment in appropriately recognizing their own body sensations during an emotion-inducing task. Method Skin conductance and heart rate were recorded in 138 males during a social stressor together with subjective reports of body sensations. Psychopathic traits were assessed using the Psychopathy Checklist – Revised (PCL-R) 2nd edition (Hare, 2003). Results Nonpsychopathic controls who reported higher body sensations showed higher heart rate reactivity, but this verbal-autonomic consistency was not found in psychopathic individuals. This mind-body disconnection is particularly associated with the interpersonal-affective factor of psychopathy. Conclusions Findings are the first to document this body sensations– autonomic mismatch in psychopaths, and suggest that somatic aphasia the inaccurate identification and recognition of one‘s own somatic states may partly underlie the interpersonal-affective features of psychopaths. PMID:22490763

  15. Human DNA Polymerase Kappa Encircles DNA: Implicatins for Mismatch Extension and Lesion Bypass

    SciTech Connect

    Lone,S.; Townson, S.; Uljon, S.; Johnson, R.; Brahma, A.; Nair, D.; Prakash, S.; Prakash, L.; Aggarwal, A.

    2007-01-01

    Human DNA polymerase (Pol ) is a proficient extender of mispaired primer termini on undamaged DNAs and is implicated in the extension step of lesion bypass. We present here the structure of Pol catalytic core in ternary complex with DNA and an incoming nucleotide. The structure reveals encirclement of the DNA by a unique 'N-clasp' at the N terminus of Pol , which augments the conventional right-handed grip on the DNA by the palm, fingers, and thumb domains and the PAD and provides additional thermodynamic stability. The structure also reveals an active-site cleft that is constrained by the close apposition of the N-clasp and the fingers domain, and therefore can accommodate only a single Watson-Crick base pair. Together, DNA encirclement and other structural features help explain Pol 's ability to extend mismatches and to promote replication through various minor groove DNA lesions, by extending from the nucleotide incorporated opposite the lesion by another polymerase.

  16. Nanoscale self-templating for oxide epitaxy with large symmetry mismatch

    PubMed Central

    Gao, Xiang; Lee, Shinbuhm; Nichols, John; Meyer, Tricia L.; Ward, Thomas Z.; Chisholm, Matthew F.; Lee, Ho Nyung

    2016-01-01

    Direct observations using scanning transmission electron microscopy unveil an intriguing interfacial bi-layer that enables epitaxial growth of a strain-free, monoclinic, bronze-phase VO2(B) thin film on a perovskite SrTiO3 (STO) substrate. We observe an ultrathin (2–3 unit cells) interlayer best described as highly strained VO2(B) nanodomains combined with an extra (Ti,V)O2 layer on the TiO2 terminated STO (001) surface. By forming a fully coherent interface with the STO substrate and a semi-coherent interface with the strain-free epitaxial VO2(B) film above, the interfacial bi-layer enables the epitaxial connection of the two materials despite their large symmetry and lattice mismatch. PMID:27909313

  17. Predictive validity of the ASAM Patient Placement Criteria for naturalistically matched vs. mismatched alcoholism patients.

    PubMed

    Magura, Stephen; Staines, Graham; Kosanke, Nicole; Rosenblum, Andrew; Foote, Jeffrey; DeLuca, Alexander; Bali, Priti

    2003-01-01

    This study examined the predictive validity of the ASAM Patient Placement Criteria for matching alcoholism patients to recommended levels of care. A cohort of 248 patients newly admitted to inpatient rehabilitation, intensive outpatient, or regular outpatient care was evaluated using both a computerized algorithm and a clinical evaluation protocol to determine whether they were naturalistically matched or mismatched to care. Outcomes were assessed three months after intake. One common type of undertreatment (ie, receiving regular outpatient care when intensive outpatient care was recommended) predicted poorer drinking outcomes as compared with matched treatment, independent of actual level of care received. Overtreatment did not improve outcomes. There also was a trend for better outcomes with residential vs. intensive outpatient treatment, independent of matching. Results were robust for both methods of assessment. Corroboration by more research is needed, but the ASAM Criteria show promise for reducing both detrimental undertreatment and cost-inefficient overtreatment.

  18. Removal of N-6-methyladenine by the nucleotide excision repair pathway triggers the repair of mismatches in yeast gap-repair intermediates.

    PubMed

    Guo, Xiaoge; Jinks-Robertson, Sue

    2013-12-01

    Gap-repair assays have been an important tool for studying the genetic control of homologous recombination in yeast. Sequence analysis of recombination products derived when a gapped plasmid is diverged relative to the chromosomal repair template additionally has been used to infer structures of strand-exchange intermediates. In the absence of the canonical mismatch repair pathway, mismatches present in these intermediates are expected to persist and segregate at the next round of DNA replication. In a mismatch repair defective (mlh1Δ) background, however, we have observed that recombination-generated mismatches are often corrected to generate gene conversion or restoration events. In the analyses reported here, the source of the aberrant mismatch removal during gap repair was examined. We find that most mismatch removal is linked to the methylation status of the plasmid used in the gap-repair assay. Whereas more than half of Dam-methylated plasmids had patches of gene conversion and/or restoration interspersed with unrepaired mismatches, mismatch removal was observed in less than 10% of products obtained when un-methylated plasmids were used in transformation experiments. The methylation-linked removal of mismatches in recombination intermediates was due specifically to the nucleotide excision repair pathway, with such mismatch removal being partially counteracted by glycosylases of the base excision repair pathway. These data demonstrate that nucleotide excision repair activity is not limited to bulky, helix-distorting DNA lesions, but also targets removal of very modest perturbations in DNA structure. In addition to its effects on mismatch removal, methylation reduced the overall gap-repair efficiency, but this reduction was not affected by the status of excision repair pathways. Finally, gel purification of DNA prior to transformation reduced gap-repair efficiency four-fold in a nucleotide excision repair-defective background, indicating that the collateral

  19. Impedance Mismatch study between the Microwave Generator and the PUPR Plasma Machine

    SciTech Connect

    Gaudier, Jorge R.; Castellanos, Ligeia; Encarnacion, Kabir; Zavala, Natyaliz; Rivera, Ramon; Farahat, Nader; Leal, Edberto

    2006-12-04

    Impedance mismatch inside the connection from the microwave power generator to the plasma machine is studied. A magnetron power generator transmits microwaves of 2.45 GHz and variable power from 50W to 5000W, through a flexible rectangular waveguide to heat plasma inside a Mirror Cusp devise located at the Polytechnic University of Puerto Rico. Before the production of plasma, the residual gas of the devise must be extracted by a vacuum system (5Torr or better), then Argon gas is injected to the machine. The microwaves heat the Argon ions to initiate ionization and plasma is produced. A dielectric wall is used inside the rectangular waveguide to isolate the plasma machine and maintain vacuum. Even though the dielectric will not block the wave propagation, some absorption of microwaves will occur. This absorption will cause reflection, reducing the efficiency of the power transfer. Typically a thin layer of Teflon is used, but measurements using this dielectric show a significant reflection of power back to the generator. Due to the high-power nature of the generator (5KW), this mismatch is not desirable. An electromagnetic field solver based on the Finite Difference Time Domain Method(FDTD) is used to model the rectangular waveguide connection. The characteristic impedance of the simulation is compared with the analytical formula expression and a good agreement is obtain. Furthermore the Teflon-loaded guide is modeled using the above program and the input impedance is computed. The reflection coefficient is calculated based on the transmission line theory with the characteristic and input impedances. Based on the simulation results it is possible to optimize the thickness, shape and dielectric constant of the material, in order to seal the connection with a better match.

  20. Mismatch between perceived and objectively measured environmental obesogenic features in European neighbourhoods.

    PubMed

    Roda, C; Charreire, H; Feuillet, T; Mackenbach, J D; Compernolle, S; Glonti, K; Ben Rebah, M; Bárdos, H; Rutter, H; McKee, M; De Bourdeaudhuij, I; Brug, J; Lakerveld, J; Oppert, J-M

    2016-01-01

    Findings from research on the association between the built environment and obesity remain equivocal but may be partly explained by differences in approaches used to characterize the built environment. Findings obtained using subjective measures may differ substantially from those measured objectively. We investigated the agreement between perceived and objectively measured obesogenic environmental features to assess (1) the extent of agreement between individual perceptions and observable characteristics of the environment and (2) the agreement between aggregated perceptions and observable characteristics, and whether this varied by type of characteristic, region or neighbourhood. Cross-sectional data from the SPOTLIGHT project (n = 6037 participants from 60 neighbourhoods in five European urban regions) were used. Residents' perceptions were self-reported, and objectively measured environmental features were obtained by a virtual audit using Google Street View. Percent agreement and Kappa statistics were calculated. The mismatch was quantified at neighbourhood level by a distance metric derived from a factor map. The extent to which the mismatch metric varied by region and neighbourhood was examined using linear regression models. Overall, agreement was moderate (agreement < 82%, kappa < 0.3) and varied by obesogenic environmental feature, region and neighbourhood. Highest agreement was found for food outlets and outdoor recreational facilities, and lowest agreement was obtained for aesthetics. In general, a better match was observed in high-residential density neighbourhoods characterized by a high density of food outlets and recreational facilities. Future studies should combine perceived and objectively measured built environment qualities to better understand the potential impact of the built environment on health, particularly in low residential density neighbourhoods.

  1. The plant virus microscope image registration method based on mismatches removing.

    PubMed

    Wei, Lifang; Zhou, Shucheng; Dong, Heng; Mao, Qianzhuo; Lin, Jiaxiang; Chen, Riqing

    2016-01-01

    The electron microscopy is one of the major means to observe the virus. The view of virus microscope images is limited by making specimen and the size of the camera's view field. To solve this problem, the virus sample is produced into multi-slice for information fusion and image registration techniques are applied to obtain large field and whole sections. Image registration techniques have been developed in the past decades for increasing the camera's field of view. Nevertheless, these approaches typically work in batch mode and rely on motorized microscopes. Alternatively, the methods are conceived just to provide visually pleasant registration for high overlap ratio image sequence. This work presents a method for virus microscope image registration acquired with detailed visual information and subpixel accuracy, even when overlap ratio of image sequence is 10% or less. The method proposed focus on the correspondence set and interimage transformation. A mismatch removal strategy is proposed by the spatial consistency and the components of keypoint to enrich the correspondence set. And the translation model parameter as well as tonal inhomogeneities is corrected by the hierarchical estimation and model select. In the experiments performed, we tested different registration approaches and virus images, confirming that the translation model is not always stationary, despite the fact that the images of the sample come from the same sequence. The mismatch removal strategy makes building registration of virus microscope images at subpixel accuracy easier and optional parameters for building registration according to the hierarchical estimation and model select strategies make the proposed method high precision and reliable for low overlap ratio image sequence.

  2. Nucleation, growth, and strain relaxation of lattice-mismatched 3-5 semiconductor epitaxial layers

    NASA Technical Reports Server (NTRS)

    Welser, R. E.; Guido, L. J.

    1994-01-01

    We have investigated the early stages of evolution of highly strained 2-D InAs layers and 3-D InAs islands grown by metal-organic chemical vapor deposition (MOCVD) on (100) and (111)B GaAs substrates. The InAs epilayer/GaAs substrate combination has been chosen because the lattice-mismatch is severe (approximately 7.2 percent), yet these materials are otherwise very similar. By examining InAs-on-GaAs composites instead of the more common In(x)Ga(1-x)As alloy we remove an additional degree of freedom (x) and thereby simplify data interpretation. A matrix of experiments is described in which the MOCVD growth parameters - susceptor temperature, Thin flux, and AsH3 flux - have been varied over a wide range. Scanning electron microscopy, atomic force microscopy, transmission electron microscopy, and electron microprobe analysis have been employed to observe the thin film surface morphology. In the case of 3-D growth, we have extracted activation energies and power-dependent exponents that characterize the nucleation process. As a consequence, optimized growth conditions have been identified for depositing approximately 250 A thick (100) and (111)B oriented InAs layers with relatively smooth surfaces. Together with preliminary data on the strain relaxation of these layers, the above results on the evolution of thin InAs films indicate that the (111)B orientation is particularly promising for yielding lattice-mismatched films that are fully relaxed with only misfit dislocations at the epilayer/substrate interface.

  3. NMR studies of G:A mismatches in oligodeoxyribonucleotide duplexes modelled after ribozymes.

    PubMed Central

    Katahira, M; Sato, H; Mishima, K; Uesugi, S; Fujii, S

    1993-01-01

    The structures of two oligodeoxyribonucleotide duplexes, the base sequences of which were modelled after both a hammerhead ribozyme and a small metalloribozyme, were studied by NMR. Both duplexes contain adjacent G:A mismatches; one has a PyGAPu:PyGAPu sequence and the other a PyGAPy:PuGAPu sequence. It is concluded on the basis of many characteristic NOEs that in both duplexes G:A base pairs are formed in the unique 'sheared' form, where an amino proton instead of an imino proton of G is involved in the hydrogen bonding, and G and A bases are arranged 'side by side' instead of 'head to head'. A photo-CIDNP experiment, which gives unique and independent information on the solvent accessibility of nucleotide bases, also supports G:A base pairing rather than a bulged-out structure of G and A residues. This is the first demonstration that not only the PyGAPu:PyGAPu sequence but also the PyGAPy:PuGAPu sequence can form the unique sheared G:A base pairs. Taking the previous studies on G:A mismatches into account, the idea is suggested that a PyGA:GAPu sequence is a minimum and essential element for the formation of the sheared G:A base pairs. The sheared G:A base pairs in the PyGAPu:PyGAPu sequence are suggested to be more stable than those in the PyGAPy:PuGAPu sequence. This is explained rationally by the idea proposed above. PMID:8265358

  4. A typology of time-scale mismatches and behavioral interventions to diagnose and solve conservation problems

    USGS Publications Warehouse

    Wilson, Robyn S.; Hardisty, David J.; Epanchin-Niell, Rebecca S.; Runge, Michael C.; Cottingham, Kathryn L.; Urban, Dean L.; Maguire, Lynn A.; Hastings, Alan; Mumby, Peter J.; Peters, Debra P. C.

    2016-01-01

    Ecological systems often operate on time scales significantly longer or shorter than the time scales typical of human decision making, which causes substantial difficulty for conservation and management in socioecological systems. For example, invasive species may move faster than humans can diagnose problems and initiate solutions, and climate systems may exhibit long-term inertia and short-term fluctuations that obscure learning about the efficacy of management efforts in many ecological systems. We adopted a management-decision framework that distinguishes decision makers within public institutions from individual actors within the social system, calls attention to the ways socioecological systems respond to decision makers’ actions, and notes institutional learning that accrues from observing these responses. We used this framework, along with insights from bedeviling conservation problems, to create a typology that identifies problematic time-scale mismatches occurring between individual decision makers in public institutions and between individual actors in the social or ecological system. We also considered solutions that involve modifying human perception and behavior at the individual level as a means of resolving these problematic mismatches. The potential solutions are derived from the behavioral economics and psychology literature on temporal challenges in decision making, such as the human tendency to discount future outcomes at irrationally high rates. These solutions range from framing environmental decisions to enhance the salience of long-term consequences, to using structured decision processes that make time scales of actions and consequences more explicit, to structural solutions aimed at altering the consequences of short-sighted behavior to make it less appealing. Additional application of these tools and long-term evaluation measures that assess not just behavioral changes but also associated changes in ecological systems are needed.

  5. Evolution of structural and electronic properties of highly mismatched InSb films

    NASA Astrophysics Data System (ADS)

    Weng, X.; Goldman, R. S.; Partin, D. L.; Heremans, J. P.

    2000-12-01

    We have investigated the evolution of structural and electronic properties of highly mismatched InSb films, with thicknesses ranging from 0.1 to 1.5 μm. Atomic force microscopy, cross-sectional transmission electron microscopy, and high-resolution x-ray diffraction show that the 0.1 μm films are nearly fully relaxed and consist of partially coalesced islands, which apparently contain threading dislocations at their boundaries. As the film thickness increases beyond 0.2 μm, the island coalescence is complete and the residual strain is reduced. Although the epilayers have relaxed equally in the <110> in-plane directions, the epilayer rotation about an in-plane axis (epilayer tilt) is not equal in both <110> in-plane directions. Interestingly, the island-like surface features tend to be preferentially elongated along the axis of epilayer tilt. Furthermore, epilayer tilt which increases the substrate offcut (reverse tilt) is evident in the [110] direction. High-resolution transmission electron microscopy indicates that both pure-edge and 60° misfit dislocations contribute to the relaxation of strain. In addition, as the film thickness increases, the threading dislocation density decreases, while the corresponding room-temperature electron mobility increases. The other structural features, including the residual strain, and the surface and interface roughness, do not appear to impact the electron mobility in these InSb films. Together, these results suggest that free-carrier scattering from the threading dislocations is the primary room-temperature mobility-limiting mechanism in highly mismatched InSb films. Finally, we show quantitatively that free-carrier scattering from the lattice dilation associated with threading dislocations, rather than scattering from a depletion potential surrounding the dislocations, is the dominant factor limiting the electron mobility.

  6. Expression of Mismatch Repair Proteins in Early and Advanced Gastric Cancer in Poland

    PubMed Central

    Karpińska-Kaczmarczyk, Katarzyna; Lewandowska, Magdalena; Ławniczak, Małgorzata; Białek, Andrzej; Urasińska, Elżbieta

    2016-01-01

    Background Mutations in DNA of mismatch repair (MMR) genes result in failure to repair errors that occur during DNA replication in microsatellites, resulting in accumulation of frameshift mutations in these genes and leading to DNA mismatch replication errors and microsatellite instability. Gastric cancers (GCs) with high MSI (MSI-H) are a well-defined subset of carcinomas showing distinctive clinicopathological features. In this study we investigated the rate of MSI and the correlation between MSI status and clinicopathological features of GC. Material/Methods The study included 107 patients with GCs: 61 with advanced gastric cancers (AGC) and 46 with early gastric cancer (EGC). MSI deficiency in GCs was assessed by the immunohistochemical analysis of expression of MMR proteins – MLH1, MSH2, MSH6, and PMS2 – using formalin-fixed and paraffin-embedded tissue. Results A total of 6 (5.6%) MSI-H were observed. The loss of MMR proteins expression was associated with the intestinal type of GC in Lauren classification, and tubular and papillary architecture in WHO classification. There was no statistically significant association between negative MMR expression and other selected clinical parameters: age, sex, tumor location, depth of invasion (EGC and AGC), lymph nodes status, presence of the ulceration, and lymphocytic infiltrate. Conclusions In the present era of personalized medicine, the histological type of GC and MMR proteins status in cancer cells are very important for the proper surveillance of patients with familial GC and sporadic GCs, as well as for selecting the proper follow-up and treatment. Larger collaborative studies are needed to verify the features of MSI-H GCs in Poland. PMID:27527654

  7. Effects of suppressing the DNA mismatch repair system on homeologous recombination in tomato.

    PubMed

    Tam, Sheh May; Hays, John B; Chetelat, Roger T

    2011-12-01

    In plant breeding, the ability to manipulate genetic (meiotic) recombination would be beneficial for facilitating gene transfer from wild relatives of crop plants. The DNA mismatch repair (MMR) system helps maintain genetic integrity by correcting base mismatches that arise via DNA synthesis or damage, and antagonizes recombination between homeologous (divergent) DNA sequences. Previous studies have established that the genomes of cultivated tomato (Solanum lycopersicum) and the wild relative S. lycopersicoides are substantially diverged (homeologous) such that recombination between their chromosomes is strongly reduced. Here, we report the effects on homeologous recombination of suppressing endogenous MMR genes in S. lycopersicum via RNAi-induced silencing of SlMSH2 and SlMSH7 or overexpressing dominant negatives of Arabidopsis MSH2 (AtMSH2-DN) in an alien substitution line (SL-8) of S. lycopersicoides in tomato. We show that certain inhibitions of MMR (RNAi of SlMSH7, AtMSH2-DN) are associated with modest increases in homeologous recombination, ranging from 3.8 to 29.2% (average rate of 17.8%) compared to controls. Unexpectedly, only the AtMSH2-DN proteins but not RNAi-induced silencing of MSH2 was found to increase homeologous recombination. The ratio of single to double crossovers (SCO:DCO ratio) decreased by approximately 50% in progeny of the AtMSH2-DN parents. An increase in the frequency of heterozygous SL-8 plants was also observed in the progeny of the SlMSH7-RNAi parents. Our findings may contribute to acceleration of introgression in cultivated tomato.

  8. Visualization of uncorrelated, tandem symmetry mismatches in the internal genome packaging apparatus of bacteriophage T7.

    PubMed

    Guo, Fei; Liu, Zheng; Vago, Frank; Ren, Yue; Wu, Weimin; Wright, Elena T; Serwer, Philip; Jiang, Wen

    2013-04-23

    Motor-driven packaging of a dsDNA genome into a preformed protein capsid through a unique portal vertex is essential in the life cycle of a large number of dsDNA viruses. We have used single-particle electron cryomicroscopy to study the multilayer structure of the portal vertex of the bacteriophage T7 procapsid, the recipient of T7 DNA in packaging. A focused asymmetric reconstruction method was developed and applied to selectively resolve neighboring pairs of symmetry-mismatched layers of the portal vertex. However, structural features in all layers of the multilayer portal vertex could not be resolved simultaneously. Our results imply that layers with mismatched symmetries can join together in several different relative orientations, and that orientations at different interfaces assort independently to produce structural isomers, a process that we call combinatorial assembly isomerism. This isomerism explains rotational smearing in previously reported asymmetric reconstructions of the portal vertex of T7 and other bacteriophages. Combinatorial assembly isomerism may represent a new regime of structural biology in which globally varying structures assemble from a common set of components. Our reconstructions collectively validate previously proposed symmetries, compositions, and sequential order of T7 portal vertex layers, resolving in tandem the 5-fold gene product 10 (gp10) shell, 12-fold gp8 portal ring, and an internal core stack consisting of 12-fold gp14 adaptor ring, 8-fold bowl-shaped gp15, and 4-fold gp16 tip. We also found a small tilt of the core stack relative to the icosahedral fivefold axis and propose that this tilt assists DNA spooling without tangling during packaging.

  9. A typology of time-scale mismatches and behavioral interventions to diagnose and solve conservation problems.

    PubMed

    Wilson, Robyn S; Hardisty, David J; Epanchin-Niell, Rebecca S; Runge, Michael C; Cottingham, Kathryn L; Urban, Dean L; Maguire, Lynn A; Hastings, Alan; Mumby, Peter J; Peters, Debra P C

    2016-02-01

    Ecological systems often operate on time scales significantly longer or shorter than the time scales typical of human decision making, which causes substantial difficulty for conservation and management in socioecological systems. For example, invasive species may move faster than humans can diagnose problems and initiate solutions, and climate systems may exhibit long-term inertia and short-term fluctuations that obscure learning about the efficacy of management efforts in many ecological systems. We adopted a management-decision framework that distinguishes decision makers within public institutions from individual actors within the social system, calls attention to the ways socioecological systems respond to decision makers' actions, and notes institutional learning that accrues from observing these responses. We used this framework, along with insights from bedeviling conservation problems, to create a typology that identifies problematic time-scale mismatches occurring between individual decision makers in public institutions and between individual actors in the social or ecological system. We also considered solutions that involve modifying human perception and behavior at the individual level as a means of resolving these problematic mismatches. The potential solutions are derived from the behavioral economics and psychology literature on temporal challenges in decision making, such as the human tendency to discount future outcomes at irrationally high rates. These solutions range from framing environmental decisions to enhance the salience of long-term consequences, to using structured decision processes that make time scales of actions and consequences more explicit, to structural solutions aimed at altering the consequences of short-sighted behavior to make it less appealing. Additional application of these tools and long-term evaluation measures that assess not just behavioral changes but also associated changes in ecological systems are needed.

  10. Kinking in polymer composites and wood, and, Crack growth in mismatched welds

    NASA Astrophysics Data System (ADS)

    Moran, Peter Malcolm

    This thesis is written in two parts; the first deals with compressive kinking in uniaxial carbon fiber PEEK composites and wood, and the second concerns ductile/brittle fracture in mismatched welds. The parts are dealt with separately below. Kinking. This is the first time that kink band formation and propagation has been video taped. The pictures reveal that kinking in ductile matrix fiber composites occurs in three distinct stages; incipient kinking, transient kinking and steady-state band broadening. Based on these observations a new kinematic model for kinking is proposed. Unlike previous models the present model is able to explain how angled kink bands are formed without violating compatibility or volume preserving constraints. Theoretical predictions for kink band orientation and compression strength under steady-state band broadening are made. Further experiments were conducted that verified the predictions. The steady-state band broadening stress is a very useful design parameter. It is a material parameter and forms a lower bound to the peak stress. Therefore it may be used in the same way as plastic limit loads are used for metals. It is also useful in determining the damage tolerance of a specimen. Mismatched welds. In the ductile/brittle transition regime, the fracture resistance of steel weldments is controlled by the competition between ductile tearing and cleavage fracture. Under typical conditions, a crack in a weld initiates and grows by ductile tearing but, ultimately, failure occurs by catastrophic cleavage fracture. In this study ductile tearing is modeled using Gurson cell elements embedded in an elastic-plastic body. Cleavage fracture is based on a weakest link mechanism in conjunction with brittle microcrack statistics. This model is applied to compute the behavior of undermatched and overmatched welds. The fracture resistance and onset of cleavage fracture are calculated for different crack lengths, specimen geometries and weld widths.

  11. Who Is Overeducated and Why? Probit and Dynamic Mixed Multinomial Logit Analyses of Vertical Mismatch in East and West Germany

    ERIC Educational Resources Information Center

    Boll, Christina; Leppin, Julian Sebastian; Schömann, Klaus

    2016-01-01

    Overeducation potentially signals a productivity loss. With Socio-Economic Panel data from 1984 to 2011 we identify drivers of educational mismatch for East and West medium and highly educated Germans. Addressing measurement error, state dependence and unobserved heterogeneity, we run dynamic mixed multinomial logit models for three different…

  12. Increase in Speech Recognition Due to Linguistic Mismatch between Target and Masker Speech: Monolingual and Simultaneous Bilingual Performance

    ERIC Educational Resources Information Center

    Calandruccio, Lauren; Zhou, Haibo

    2014-01-01

    Purpose: To examine whether improved speech recognition during linguistically mismatched target-masker experiments is due to linguistic unfamiliarity of the masker speech or linguistic dissimilarity between the target and masker speech. Method: Monolingual English speakers (n = 20) and English-Greek simultaneous bilinguals (n = 20) listened to…

  13. Incidence and natural history of pure red cell aplasia in major ABO-mismatched haematopoietic cell transplantation

    PubMed Central

    Aung, Fleur M.; Lichtiger, Benjamin; Bassett, Roland; Liu, Ping; Alousi, Amin; Bashier, Qaiser; Ciurea, Stefan O.; de Lima, Marcos J.; Hosing, Chitra; Kebriaei, Partow; Nieto, Yago; Oran, Betul; Parmar, Simrit; Qazilbash, Muzaffar; Shah, Nina; Khouri, Issa; Champlin, Richard E.; Popat, Uday

    2014-01-01

    Summary Major ABO mismatching is not considered a contraindication to allogeneic haematopoietic stem cell transplantation (HSCT). Modern reduced-intensity conditioning and reduced-toxicity regimens cause much less myeloablation than conventional myeloablative regimens, such as cyclophosphamide with busulfan or total body irradiation, which may affect the incidence of pure red cell aplasia (PRCA). We estimated the incidence and described the natural history of PRCA in patients with major ABO-mismatched donor stem cells. Between 2007 and 2008, 161 (27% of all patients undergoing HSCT) underwent allogeneic HSCT with major ABO-mismatched stem cells and 12 (7·5%) of these patients developed PRCA. Thirty and ninety day T-cell and myeloid cell chimerism and neutrophil and platelet engraftment did not differ between patients who developed PRCA and those who did not. The only risk factor associated with PRCA was the use of a fludarabine/busulfan conditioning regimen. All patients with PRCA needed red cell transfusion for several months after HSCT resulting in significant iron overload. Pure red cell aplasia resolved spontaneously in the majority (seven patients) but only resolved after stopping tacrolimus in three patients. Hence, after major ABO-mismatched HSCT, the incidence of PRCA was 7·5% and it resolved spontaneously or after withdrawal of immunosuppression in the majority of patients. PMID:23330820

  14. Spontaneous frameshift mutations in Saccharomyces cerevisiae: accumulation during DNA replication and removal by proofreading and mismatch repair activities.

    PubMed Central

    Greene, C N; Jinks-Robertson, S

    2001-01-01

    The accumulation of frameshift mutations during DNA synthesis is determined by the rate at which frameshift intermediates are generated during DNA polymerization and the efficiency with which frameshift intermediates are removed by DNA polymerase-associated exonucleolytic proofreading activity and/or the postreplicative mismatch repair machinery. To examine the relative contributions of these factors to replication fidelity in Saccharomyces cerevisiae, we determined the reversion rates and spectra of the lys2 Delta Bgl +1 frameshift allele. Wild-type and homozygous mutant diploid strains with all possible combinations of defects in the exonuclease activities of DNA polymerases delta and epsilon (conferred by the pol3-01 and pol2-4 alleles, respectively) and in mismatch repair (deletion of MSH2) were analyzed. Although there was no direct correlation between homopolymer run length and frameshift accumulation in the wild-type strain, such a correlation was evident in the triple mutant strain lacking all repair capacity. Furthermore, examination of strains defective in one or two repair activities revealed distinct biases in the removal of the corresponding frameshift intermediates by exonucleolytic proofreading and/or mismatch repair. Finally, these analyses suggest that the mismatch repair machinery may be important for generating some classes of frameshift mutations in yeast. PMID:11560887

  15. Characterization of a Thermostable 8-Oxoguanine DNA Glycosylase Specific for GO/N Mismatches from the Thermoacidophilic Archaeon Thermoplasma volcanium

    PubMed Central

    Fujii, Miki; Hata, Chieri; Ukita, Munetada; Fukushima, Chie; Matsuura, Chihiro; Kawashima-Ohya, Yoshie; Tomobe, Koji

    2016-01-01

    The oxidation of guanine (G) to 7,8-dihydro-8-oxoguanine (GO) forms one of the major DNA lesions generated by reactive oxygen species (ROS). The GO can be corrected by GO DNA glycosylases (Ogg), enzymes involved in base excision repair (BER). Unrepaired GO induces mismatched base pairing with adenine (A); as a result, the mismatch causes a point mutation, from G paired with cytosine (C) to thymine (T) paired with adenine (A), during DNA replication. Here, we report the characterization of a putative Ogg from the thermoacidophilic archaeon Thermoplasma volcanium. The 204-amino acid sequence of the putative Ogg (TVG_RS00315) shares significant sequence homology with the DNA glycosylases of Methanocaldococcus jannaschii (MjaOgg) and Sulfolobus solfataricus (SsoOgg). The six histidine-tagged recombinant TVG_RS00315 protein gene was expressed in Escherichia coli and purified. The Ogg protein is thermostable, with optimal activity near a pH of 7.5 and a temperature of 60°C. The enzyme displays DNA glycosylase, and apurinic/apyrimidinic (AP) lyase activities on GO/N (where N is A, T, G, or C) mismatch; yet it cannot eliminate U from U/G or T from T/G, as mismatch glycosylase (MIG) can. These results indicate that TvoOgg-encoding TVG_RS00315 is a member of the Ogg2 family of T. volcanium. PMID:27799846

  16. Mismatched Perceptions and Expectations: An Exploration of Stakeholders' Views of Key and Technical Skills in Vocational Education and Training

    ERIC Educational Resources Information Center

    Saunders, Mark N. K.; Skinner, Denise; Beresford, Richard

    2005-01-01

    Purpose: To explore potential mismatches between stakeholders' perceptions and expectations of key and technical skills needed for an advanced modern apprentice within the UK. Design/methodology/approach: Using data collected from the automotive sector, the template process is used to establish lecturer, student and employee stakeholder group's…

  17. Associative Retrieval Processes in the Human Medial Temporal Lobe: Hippocampal Retrieval Success and CA1 Mismatch Detection

    ERIC Educational Resources Information Center

    Chen, Janice; Olsen, Rosanna K.; Preston, Alison R.; Glover, Gary H.; Wagner, Anthony D.

    2011-01-01

    Hippocampal subfields CA3 and CA1 are hypothesized to differentially support the generation of associative predictions and the detection of associative mismatches, respectively. Using high-resolution functional MRI, we examined hippocampal subfield activation during associative retrieval and during subsequent comparisons of memory to matching or…

  18. A 30-Year-Old Man with Three Primary Malignancies: A Case of Constitutional Mismatch Repair Deficiency.

    PubMed

    Rengifo-Cam, William; Jasperson, Kory; Garrido-Laguna, Ignacio; Colman, Howard; Scaife, Courtney; Samowitz, Wade; Samadder, N Jewel

    2017-01-01

    Constitutional mismatch repair deficiency (CMMRD) is a devastating cancer predisposition syndrome for which clinical manifestations, genetic screening, and cancer prevention strategies are limited. We report a case of CMMRD presenting with metachronous colorectal cancer and brain cancer. Oncologists and gastroenterologists should be aware of the CMMRD syndrome as a rare cause of very early-onset colorectal cancer.

  19. On Cambodian Higher Education and Skills Mismatch: Young People Choosing University Majors in a Context of Risk and Uncertainty

    ERIC Educational Resources Information Center

    Peou, Chivoin

    2017-01-01

    Cambodia has in the past 15 years been catching up with the global and regional trends of rapid expansion of higher education, but its specific socio-historical context has engendered particular life course and societal implications. Engaging with the current policy attention to the cause of skills mismatch in Cambodia, this article aims to…

  20. Simulating the effect of interaural mismatch in the insertion depth of bilateral cochlear implants on speech perception.

    PubMed

    van Besouw, Rachel M; Forrester, Lisa; Crowe, Nicholas D; Rowan, Daniel

    2013-08-01

    A bilateral advantage for diotically presented stimuli has been observed for cochlear implant (CI) users and is suggested to be dependent on symmetrical implant performance. Studies using CI simulations have not shown a true "bilateral" advantage, but a "better ear" effect and have demonstrated that performance decreases with increasing basalward shift in insertion depth. This study aimed to determine whether there is a bilateral advantage for CI simulations with interaurally matched insertions and the extent to which performance is affected by interaural insertion depth mismatch. Speech perception in noise and self-reported ease of listening were measured using matched bilateral, mismatched bilateral and unilateral CI simulations over four insertion depths for seventeen normal hearing listeners. Speech scores and ease of listening reduced with increasing basalward shift in (interaurally matched) insertion depth. A bilateral advantage for speech perception was only observed when the insertion depths were interaurally matched and deep. No advantage was observed for small to moderate interaural insertion-depth mismatches, consistent with a better ear effect. Finally, both measures were poorer than expected for a better ear effect for large mismatches, suggesting that misalignment of the electrode arrays may prevent a bilateral advantage and detrimentally affect perception of diotically presented speech.