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Sample records for adjacent mismatch base

  1. The effect of base pair mismatch on DNA strand displacement

    CERN Document Server

    Broadwater, Bo

    2016-01-01

    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 base pair 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 t...

  2. Single base mismatch detection by microsecond voltage pulses.

    Science.gov (United States)

    Fixe, F; Chu, V; Prazeres, D M F; Conde, J P

    2005-12-15

    A single square voltage pulse applied to metal electrodes underneath a silicon dioxide film upon which DNA probes are immobilized allows the discrimination of DNA targets with a single base mismatch during hybridization. Pulse duration, magnitude and slew rate of the voltage pulse are all key factors controlling the rates of electric field assisted hybridization. Although pulses with 1 V, lasting less than 1 ms and with a rise/fall times of 4.5 ns led to maximum hybridization of fully complementary strands, lack of stringency did not allow the discrimination of single base mismatches. However, by choosing pulse conditions that are slightly off the optimum, the selectivity for discriminating single base mismatches could be improved up to a factor approximately 5 when the mismatch was in the middle of the strand and up to approximately 1.5 when the mismatch was on the 5'-end and. These results demonstrate that hybridization with the appropriate electric field pulse provides a new, site-specific, approach to the discrimination of single nucleotide polymorphisms in the sub-millisecond time scale, for addressable DNA microarrays.

  3. Anthracene Modified Oligonucleotides as Fluorescent DNA Mismatch Sensors: Discrimination Between Various Base Pair Mismatches

    OpenAIRE

    Tucker, Jim; Hyde, Eva; Ludwig, Christian; Zhao, John

    2011-01-01

    Abstract A fluorescent anthracene-tagged DNA probe has been shown to respond to various DNA sequences by changes to its emission signal upon duplex formation. The fluorescence response for duplexes containing a single mismatch near the anthracene site has been found to be very sensitive to its composition, with the emission signal increasing for a CA mismatch and decreasing for CT and CC mismatches. (Tucker, Jim) (Hyde, Eva) c.ludw...

  4. Supercoiling DNA Locates Mismatches

    Science.gov (United States)

    Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu; Marko, John F.; Neuman, Keir C.

    2017-10-01

    We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.6 pN force and show that under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.

  5. Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch.

    Science.gov (United States)

    Hasegawa, Yusuke; Takada, Tadao; Nakamura, Mitsunobu; Yamana, Kazushige

    2017-08-01

    We describe the synthesis, binding, and electrochemical properties of ferrocene-conjugated oligonucleotides (Fc-oligos). The key step for the preparation of Fc-oligos contains the coupling of vinylferrocene to 5-iododeoxyuridine via Heck reaction. The Fc-conjugated deoxyuridine phosphoramidite was used in the Fc-oligonucleotide synthesis. We show that thiol-modified Fc-oligos deposited onto gold electrodes possess potential ability in electrochemical detection of DNA base mismatch. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Photoinduced excess electron injection into DNA duplexes containing mismatched base pairs.

    Science.gov (United States)

    Ito, Takeo; Kondo, Akiko; Hayashi, Aiko; Uchida, Tsukasa; Tanabe, Kazuhito; Nishimoto, Sei-ichi

    2008-01-01

    A series of DNA containing photoinduced electron donors and mismatched DNA base pairs have been prepared and applied for the chemical investigation of excess electron transfer (EET) in the duplex DNA. As the electron donors, phenothiazine (PTZ) with a flexible linker was tethered to the 5'-end or in the middle of the sequences, or diaminostilbene (DAS) was covalently linked to form a hairpin structure. The presence of mismatched base pair lowered EET efficiency in the DAS-capped DNA hairpins, on the other hand, efficient EET beyond the mismatch site was observed in the PTZ-conjugated DNA.

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

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    Piia Astikainen

    Full Text Available 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.

  8. Mismatch repair.

    Science.gov (United States)

    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. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Mismatch Repair*

    Science.gov (United States)

    Fishel, Richard

    2015-01-01

    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. PMID:26354434

  10. A Comparison of Relative Time to Peak and Tmax for Mismatch-Based Patient Selection

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    Anke Wouters

    2017-10-01

    Full Text Available Background and purposeThe perfusion-weighted imaging (PWI/diffusion-weighted imaging (DWI mismatch profile is used to select patients for endovascular treatment. A PWI map of Tmax is commonly used to identify tissue with critical hypoperfusion. A time to peak (TTP map reflects similar hemodynamic properties with the added benefit that it does not require arterial input function (AIF selection and deconvolution. We aimed to determine if TTP could substitute Tmax for mismatch categorization.MethodsImaging data of the DEFUSE 2 trial were reprocessed to generate relative TTP (rTTP maps. We identified the rTTP threshold that yielded lesion volumes comparable to Tmax > 6 s and assessed the effect of reperfusion according to mismatch status, determined based on Tmax and rTTP volumes.ResultsAmong 102 included cases, the Tmax > 6 s lesion volumes corresponded most closely with rTTP > 4.5 s lesion volumes: median absolute difference 6.9 mL (IQR: 2.3–13.0. There was 94% agreement in mismatch classification between Tmax and rTTP-based criteria. When mismatch was assessed by Tmax criteria, the odds ratio (OR for favorable clinical response associated with reperfusion was 7.4 (95% CI 2.3–24.1 in patients with mismatch vs. 0.4 (95% CI 0.1–2.6 in patients without mismatch. When mismatch was assessed with rTTP criteria, these ORs were 7.2 (95% CI 2.3–22.2 and 0.3 (95% CI 0.1–2.2, respectively.ConclusionrTTP yields lesion volumes that are comparable to Tmax and reliably identifies the PWI/DWI mismatch profile. Since rTTP is void of the problems associated with AIF selection, it is a suitable substitute for Tmax that could improve the robustness and reproducibility of mismatch classification in acute stroke.

  11. Mood As Cumulative Expectation Mismatch: A Test of Theory Based on Data from Non-verbal Cognitive Bias Tests

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    Camille M. C. Raoult

    2017-12-01

    Full Text Available Affective states are known to influence behavior and cognitive processes. To assess mood (moderately long-term affective states, the cognitive judgment bias test was developed and has been widely used in various animal species. However, little is known about how mood changes, how mood can be experimentally manipulated, and how mood then feeds back into cognitive judgment. A recent theory argues that mood reflects the cumulative impact of differences between obtained outcomes and expectations. Here expectations refer to an established context. Situations in which an established context fails to match an outcome are then perceived as mismatches of expectation and outcome. We take advantage of the large number of studies published on non-verbal cognitive bias tests in recent years (95 studies with a total of 162 independent tests to test whether cumulative mismatch could indeed have led to the observed mood changes. Based on a criteria list, we assessed whether mismatch had occurred with the experimental procedure used to induce mood (mood induction mismatch, or in the context of the non-verbal cognitive bias procedure (testing mismatch. For the mood induction mismatch, we scored the mismatch between the subjects’ potential expectations and the manipulations conducted for inducing mood whereas, for the testing mismatch, we scored mismatches that may have occurred during the actual testing. We then investigated whether these two types of mismatch can predict the actual outcome of the cognitive bias study. The present evaluation shows that mood induction mismatch cannot well predict the success of a cognitive bias test. On the other hand, testing mismatch can modulate or even inverse the expected outcome. We think, cognitive bias studies should more specifically aim at creating expectation mismatch while inducing mood states to test the cumulative mismatch theory more properly. Furthermore, testing mismatch should be avoided as much as possible

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

    Science.gov (United States)

    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.

  13. MEASURES OF OCCUPATIONAL MISMATCH

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    Monica Mihaela MAER MATEI

    2014-11-01

    Full Text Available The research developed in this paper is based on micro data available in Programme for the International Assessment of Adult Competencies (PIAAC. The research aimed to estimate the size of both forms of labour market mismatch: education mismatch and skill mismatch. The first measure of job mismatch is based on workers’ self-assessment. The second one uses the PIAAC assessment regarding the proficiency for each skill dimension (literacy, numeracy and problem solving in technology rich environments. The labor market mismatch was measured for Spain and Italy datasets for the higher education graduates whose occupations are included in Major Group two Professionals, according to the International Standard Classification of Occupations. The estimation results showed that the two measures of labour market mismatch are not correlated.

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

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    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.

  15. Non-target adjacent stimuli classification improves performance of classical ERP-based brain computer interface

    Science.gov (United States)

    Ceballos, G. A.; Hernández, L. F.

    2015-04-01

    Objective. The classical ERP-based speller, or P300 Speller, is one of the most commonly used paradigms in the field of Brain Computer Interfaces (BCI). Several alterations to the visual stimuli presentation system have been developed to avoid unfavorable effects elicited by adjacent stimuli. However, there has been little, if any, regard to useful information contained in responses to adjacent stimuli about spatial location of target symbols. This paper aims to demonstrate that combining the classification of non-target adjacent stimuli with standard classification (target versus non-target) significantly improves classical ERP-based speller efficiency. Approach. Four SWLDA classifiers were trained and combined with the standard classifier: the lower row, upper row, right column and left column classifiers. This new feature extraction procedure and the classification method were carried out on three open databases: the UAM P300 database (Universidad Autonoma Metropolitana, Mexico), BCI competition II (dataset IIb) and BCI competition III (dataset II). Main results. The inclusion of the classification of non-target adjacent stimuli improves target classification in the classical row/column paradigm. A gain in mean single trial classification of 9.6% and an overall improvement of 25% in simulated spelling speed was achieved. Significance. We have provided further evidence that the ERPs produced by adjacent stimuli present discriminable features, which could provide additional information about the spatial location of intended symbols. This work promotes the searching of information on the peripheral stimulation responses to improve the performance of emerging visual ERP-based spellers.

  16. Enhanced extended state observer-based control for systems with mismatched uncertainties and disturbances.

    Science.gov (United States)

    Castillo, A; García, P; Sanz, R; Albertos, P

    2017-12-19

    This paper presents an enhanced Extended State Observer (ESO)-based control strategy to deal with the disturbance attenuation problem for a class of non integral-chain systems subject to non-linear mismatched uncertainties and external disturbances. The proposed control strategy does not assume the integral-chain form and it is formed by a state-feedback plus a dynamic disturbance compensation term, which is designed to reject the disturbance effect in the system output. From a theoretical point of view, the proposed strategy is reduced to the conventional ESO when the integral chain form and the matched condition hold. In this sense, this paper is presented as an extension of the ESO principles to cover a wider class of systems. The theoretical results show that the internal zero-dynamics plays an important role in ESO-based control design. Also, the closed-loop stability is analyzed and some numerical simulations show the effectiveness of the proposal in comparison with previous ESO-based techniques. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  17. Low frequency of defective mismatch repair in a population-based series of upper urothelial carcinoma

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    Isfoss Björn L

    2005-03-01

    Full Text Available Abstract Background Upper urothelial cancer (UUC, i.e. transitional cell carcinomas of the renal pelvis and the ureter, occur at an increased frequency in patients with hereditary nonpolyposis colorectal cancer (HNPCC. Defective mismatch repair (MMR specifically characterizes HNPCC-associated tumors, but also occurs in subsets of some sporadic tumors, e.g. in gastrointestinal cancer and endometrial cancer. Methods We assessed the contribution of defective MMR to the development of UUC in a population-based series from the southern Swedish Cancer Registry, through microsatellite instability (MSI analysis and immunohistochemical evaluation of expression of the MMR proteins MLH1, PMS2, MSH2, and MSH6. Results A MSI-high phenotype was identified in 9/216 (4% successfully analyzed patients and a MSI-low phenotype in 5/216 (2%. Loss of MMR protein immunostaining was found in 11/216 (5% tumors, and affected most commonly MSH2 and MSH6. Conclusion This population-based series indicates that somatic MMR inactivation is a minor pathway in the development of UUC, but tumors that display defective MMR are, based on the immunohistochemical expression pattern, likely to be associated with HNPCC.

  18. Identifying PV module mismatch faults by a thermography-based temperature distribution analysis

    OpenAIRE

    Hu, Yihua; Cao, Wenping; Ma, Jien; Finney, Stephen J.; Li, David

    2014-01-01

    Photovoltaic (PV) solar power generation is proven to be effective and sustainable but is currently hampered by relatively high costs and low conversion efficiency. This paper addresses both issues by presenting a low-cost and efficient temperature distribution analysis for identifying PV module mismatch faults by thermography. Mismatch faults reduce the power output and cause potential damage to PV cells. This paper first defines three fault categories in terms of fault levels, which lead to...

  19. DREMECELS: A Curated Database for Base Excision and Mismatch Repair Mechanisms Associated Human Malignancies.

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    Ankita Shukla

    Full Text Available DNA repair mechanisms act as a warrior combating various damaging processes that ensue critical malignancies. DREMECELS was designed considering the malignancies with frequent alterations in DNA repair pathways, that is, colorectal and endometrial cancers, associated with Lynch syndrome (also known as HNPCC. Since lynch syndrome carries high risk (~40-60% for both cancers, therefore we decided to cover all three diseases in this portal. Although a large population is presently affected by these malignancies, many resources are available for various cancer types but no database archives information on the genes specifically for only these cancers and disorders. The database contains 156 genes and two repair mechanisms, base excision repair (BER and mismatch repair (MMR. Other parameters include some of the regulatory processes that have roles in these disease progressions due to incompetent repair mechanisms, specifically BER and MMR. However, our unique database mainly provides qualitative and quantitative information on these cancer types along with methylation, drug sensitivity, miRNAs, copy number variation (CNV and somatic mutations data. This database would serve the scientific community by providing integrated information on these disease types, thus sustaining diagnostic and therapeutic processes. This repository would serve as an excellent accompaniment for researchers and biomedical professionals and facilitate in understanding such critical diseases. DREMECELS is publicly available at http://www.bioinfoindia.org/dremecels.

  20. Validation of the spectral mismatch correction factor using an LED-based solar simulator

    DEFF Research Database (Denmark)

    Riedel, Nicholas; Santamaria Lancia, Adrian Alejo; Thorsteinsson, Sune

    LED-based solar simulators are gaining popularity in the PV characterization field. There are several reasons for this trend, but the primary interest is often the potential of tuning the light source spectrum to a closer match to the AM 1.5G reference spectrum than traditional Xenon or metal......-halide light sources provide. In this work we will use an EcoSun10L LED module tester from Ecoprogetti to perform short circuit current (ISC) measurements under various class A, B and C spectra. We will apply a spectral mismatch correction to the measured ISC under each test spectrum per IEC 60904-7. In all...... scenarios, a small area mono-Si cell is used the reference cell and a similar mono-Si cell is used as the PV device under test (DUT). Finally, we quantify the variation of the DUT’s measured and spectrally corrected Isc under the class A, B and C test spectra....

  1. Gold-based optical biosensor for single-mismatched DNA detection using salt-induced hybridization

    DEFF Research Database (Denmark)

    Zhan, Zongrui; Ma, Xingyi; Cao, Cuong

    2011-01-01

    DNA while Au-NPs modified with oligonucleotide detection sequences played a role in recognition and signal production. Due to the much lower stability of mismatched DNA strands caused by unstable duplex structures in solutions of relatively low salt concentration, hybridization efficiency...... in the presence of different buffers was well investigated, and thus, the optimized salt concentration allowed for discrimination of single-mismatched DNA (MMT) from perfectly matched DNA (PMT). Therefore, quantitative information concerning the target analyte was translated into a colorimetric signal, which...... could easily and quantitatively measured by low-cost UV–vis spectrophotometric analysis. The results indicated this to be a very simple and economic strategy for detection of single-mismatched DNA strands....

  2. Fast and quantitative differentiation of single-base mismatched DNA by initial reaction rate of catalytic hairpin assembly.

    Science.gov (United States)

    Li, Chenxi; Li, Yixin; Xu, Xiao; Wang, Xinyi; Chen, Yang; Yang, Xiaoda; Liu, Feng; Li, Na

    2014-10-15

    The widely used catalytic hairpin assembly (CHA) amplification strategy generally needs several hours to accomplish one measurement based on the prevailingly used maximum intensity detection mode, making it less practical for assays where high throughput or speed is desired. To make the best use of the kinetic specificity of toehold domain for circuit reaction initiation, we developed a mathematical model and proposed an initial reaction rate detection mode to quantitatively differentiate the single-base mismatch. Using the kinetic mode, assay time can be reduced substantially to 10 min for one measurement with the comparable sensitivity and single-base mismatch differentiating ability as were obtained by the maximum intensity detection mode. This initial reaction rate based approach not only provided a fast and quantitative differentiation of single-base mismatch, but also helped in-depth understanding of the CHA system, which will be beneficial to the design of highly sensitive and specific toehold-mediated hybridization reactions. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Localizing pre-attentive auditory memory-based comparison: magnetic mismatch negativity to pitch change.

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    Maess, Burkhard; Jacobsen, Thomas; Schröger, Erich; Friederici, Angela D

    2007-08-15

    Changes in the pitch of repetitive sounds elicit the mismatch negativity (MMN) of the event-related brain potential (ERP). There exist two alternative accounts for this index of automatic change detection: (1) A sensorial, non-comparator account according to which ERPs in oddball sequences are affected by differential refractory states of frequency-specific afferent cortical neurons. (2) A cognitive, comparator account stating that MMN reflects the outcome of a memory comparison between a neuronal model of the frequently presented standard sound with the sensory memory representation of the changed sound. Using a condition controlling for refractoriness effects, the two contributions to MMN can be disentangled. The present study used whole-head MEG to further elucidate the sensorial and cognitive contributions to frequency MMN. Results replicated ERP findings that MMN to pitch change is a compound of the activity of a sensorial, non-comparator mechanism and a cognitive, comparator mechanism which could be separated in time. The sensorial part of frequency MMN consisting of spatially dipolar patterns was maximal in the late N1 range (105-125 ms), while the cognitive part peaked in the late MMN-range (170-200 ms). Spatial principal component analyses revealed that the early part of the traditionally measured MMN (deviant minus standard) is mainly due to the sensorial mechanism while the later mainly due to the cognitive mechanism. Inverse modeling revealed sources for both MMN contributions in the gyrus temporales transversus, bilaterally. These MEG results suggest temporally distinct but spatially overlapping activities of non-comparator-based and comparator-based mechanisms of automatic frequency change detection in auditory cortex.

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

    Science.gov (United States)

    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…

  5. AA mismatched DNAs with a single base difference exhibit a large structural change and a propensity for the parallel-stranded conformation

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    Chulhyun Lee

    2010-03-01

    Full Text Available AA mismatches in DNA with different nearest-neighbor sequences were studied to understand the structural changes that accompany base-pair mismatches and the associated thermodynamics. Two synthesized duplexes, , 5' -d(CGACAATTGACG (called AA1 and 5' -d(CGAGAATTCACG (called AA2 as a palindrome sequences, had different nearest-neighbor sequences to the AA mismatches. This study focused on elucidating the structural and thermodynamic differences between these two molecules. A hydrogen bond between the mismatched adenines in AA1 was found, while no hydrogen bond in AA2. Both of the mismatched adenines in AA1 were stacked in the helix, while the mismatched adenine in AA2 surrounded by guanines was partially out of the helix and the other mismatched adenine surrounded by cytosines was stacked in the helix. Thermodynamically, AA1 was more stable than AA2. The melting temperature of the internal bases of AA1 was about 7 degree higher than that of AA2. The standard Gibbs free energy change for the duplex formation of AA1 was 1.30 Kcal/mol smaller than that of AA2. These thermal properties could be ascribed to the formation of the hydrogen bond. The conformational changes of these molecules at low pH were also investigated and compared. AA1 unambiguously assumed a parallel-stranded duplex at pH 4, while AA2 existed as a mixture of anti-parallel and parallel duplexes below pH 5.

  6. Adjacency Matrix-Based Transmit Power Allocation Strategies in Wireless Sensor Networks

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    Luca Consolini

    2009-07-01

    Full Text Available In this paper, we present an innovative transmit power control scheme, based on optimization theory, for wireless sensor networks (WSNs which use carrier sense multiple access (CSMA with collision avoidance (CA as medium access control (MAC protocol. In particular, we focus on schemes where several remote nodes send data directly to a common access point (AP. Under the assumption of finite overall network transmit power and low traffic load, we derive the optimal transmit power allocation strategy that minimizes the packet error rate (PER at the AP. This approach is based on modeling the CSMA/CA MAC protocol through a finite state machine and takes into account the network adjacency matrix, depending on the transmit power distribution and determining the network connectivity. It will be then shown that the transmit power allocation problem reduces to a convex constrained minimization problem. Our results show that, under the assumption of low traffic load, the power allocation strategy, which guarantees minimal delay, requires the maximization of network connectivity, which can be equivalently interpreted as the maximization of the number of non-zero entries of the adjacency matrix. The obtained theoretical results are confirmed by simulations for unslotted Zigbee WSNs.

  7. Adjacency Matrix-Based Transmit Power Allocation Strategies in Wireless Sensor Networks

    Science.gov (United States)

    Consolini, Luca; Medagliani, Paolo; Ferrari, Gianluigi

    2009-01-01

    In this paper, we present an innovative transmit power control scheme, based on optimization theory, for wireless sensor networks (WSNs) which use carrier sense multiple access (CSMA) with collision avoidance (CA) as medium access control (MAC) protocol. In particular, we focus on schemes where several remote nodes send data directly to a common access point (AP). Under the assumption of finite overall network transmit power and low traffic load, we derive the optimal transmit power allocation strategy that minimizes the packet error rate (PER) at the AP. This approach is based on modeling the CSMA/CA MAC protocol through a finite state machine and takes into account the network adjacency matrix, depending on the transmit power distribution and determining the network connectivity. It will be then shown that the transmit power allocation problem reduces to a convex constrained minimization problem. Our results show that, under the assumption of low traffic load, the power allocation strategy, which guarantees minimal delay, requires the maximization of network connectivity, which can be equivalently interpreted as the maximization of the number of non-zero entries of the adjacency matrix. The obtained theoretical results are confirmed by simulations for unslotted Zigbee WSNs. PMID:22346705

  8. Estimation of channel mismatches in time-interleaved analog-to-digital converters based on fractional delay and sine curve fitting.

    Science.gov (United States)

    Guo, Lianping; Tian, Shulin; Jiang, Jun

    2015-03-01

    This paper proposes an algorithm to estimate the channel mismatches in time-interleaved analog-to-digital converter (TIADC) based on fractional delay (FD) and sine curve fitting. Choose one channel as the reference channel and apply FD to the output samples of reference channel to obtain the ideal samples of non-reference channels with no mismatches. Based on least square method, the sine curves are adopted to fit the ideal and the actual samples of non-reference channels, and then the mismatch parameters can be estimated by comparing the ideal sine curves and the actual ones. The principle of this algorithm is simple and easily understood. Moreover, its implementation needs no extra circuits, lowering the hardware cost. Simulation results show that the estimation accuracy of this algorithm can be controlled within 2%. Finally, the practicability of this algorithm is verified by the measurement results of channel mismatch errors of a two-channel TIADC prototype.

  9. Extraction of Winter Wheat Area and Growth Analysis Based on Remote Sensing Imagery of Adjacent Tracks

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    LIN Fen

    2016-07-01

    Full Text Available Winter wheat is one of the most valuable crops in Northern China, so getting a good knowledge of real-time information of its area and growing situation can help the manager of agricultural production and financial departments to make better decisions, meanwhile it can also increase the output capacity and farmers' income. In this paper, Binzhou City and Dongying City of Shandong Province were taken as the research areas. We extracted the information of winter wheat from ETM+ remote sensing image based on a combined method of principal component analysis, supervised and unsupervised classification. The growing situation of winter wheat in Binzhou was estimated through clustering analysis in SPSS, and winter wheat growing situation in Dongying was predicted by building vegetation growing situation hierarchical model in adjacent tracks using the distance-weighted method. The results showed that the mean extracting precision was 93.79%. There was a clear tendency of its distribution with characteristics of concentrated in the west and in the south other than that in the east and in the north. Also the regions where the wheat was concentrately distributed had better growth in general. We found that the vegetation growing situation hierarchical model built with distance-weighted method in the overlapping areas could eliminate the time differences between two remote sensing images in adjacent tracks to some extent, and it was beneficial for winter wheat growth analysis in large-scale regions.

  10. Strong Optical Shock excitation in the mismatched regime of bubble plasma-wave based LWFA

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    Sahai, Aakash

    2017-10-01

    We present investigations into the excitation of a strong optical shock through slicing of a high intensity laser pulse driving a bubble plasma wave in a regime of mis-match between the incident laser waist-size and the bubble size ( = 2√{a0} c /ωpe). In the matched regime, it is well-known that over long timescales, the laser continuously undergoes differential frequency-shifts in different bubble phases, forming an optical shock. In the mis-matched regime, rapid laser waist and resulting bubble oscillations change the location of the peak laser ponderomotive force. This changes the location and the magnitude of the peak electron density interacting with the laser pulse. A sudden increase in the electron density during a laser radial squeeze event, slices the laser envelope longitudinally near its peak amplitude, exciting a strong optical shock state. This is shown to occur much earlier in laser evolution only over a narrow range of plasma densities where the imbalance between the longitudinal & radial ponderomotive forces excites elongated bubbles, injects ultra-low emittance electron beams and sustains ultra-high peak plasma fields. We acknowledge STFC Grants ST/J002062/1 and ST/P000835/1 for the John Adams Institute of Accelerator Science.

  11. The plant virus microscope image registration method based on mismatches removing.

    Science.gov (United States)

    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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Trifunctional fluorescent unnatural nucleoside: Label free detection of T-T/C-C base mismatches, abasic site and bulge DNA.

    Science.gov (United States)

    Bag, Subhendu Sekhar; Pradhan, Manoj Kumar; Talukdar, Sangita

    2017-08-01

    The detection and targeting of both the mismatched and abasic DNA is highly important which would ultimately help in designing new diagnostics and chemotherapeutics. Furthermore, sensing and targeting the bulge sequence with a fluorescent probe would be useful to study the role of bulges in nucleic acid function or could have significant therapeutic potential. Thus, detection of specific bulges by small fluorescent molecules is an attractive research area since the past several years. Many attempts have been made to prepare such compounds. We report herein a label free strategy for the detection of pyrimidine base mismatches (T/T and C/C), sensing of abasic site, and pyrimidine base bulge DNA using an unnatural tetrazolylpyrene nucleoside ( TPy B Do ) as a bare fluorescent probe. The H-bonding/hydrophobic force mediated interactions allow the sensing of all three deformed DNA via an enhancement of fluorescence signal using our simple "Just-Mix and Read" strategy. The binding of the probe to all the three deformed DNA duplexes is accompanied by an increase in the thermal melting stability of the deformed DNAs. That the probe binds efficiently to the minor groove near the deformed site was evident from spectroscopic studies. All the spectral evidences open up a multitude of possibilities for using our probe, tetrazolylpyrene nucleoside, as an efficient fluorescent light-up bio-probe for label free DNA detection. Copyright © 2017. Published by Elsevier B.V.

  13. Investigation of Nascent Base Pair and Polymerase Behavior in the Presence of Mismatches in DNA Polymerase I Using Molecular Dynamics.

    Science.gov (United States)

    Yeager, Andrew; Humphries, Kathryn; Farmer, Ellen; Cline, Gene; Miller, Bill R

    2018-02-26

    Optimizing DNA polymerases for a broad range of tasks requires an understanding of the factors influencing polymerase fidelity, but many details of polymerase behavior remain unknown, especially in the presence of mismatched nascent base pairs. Using molecular dynamics, the large fragment of Bacillus stearothermophilus DNA polymerase I is simulated in the presence of all 16 possible standard nucleoside triphosphate-template (dNTP-dN) pairs, including four Watson-Crick pairs and 12 mismatches. The precatalytic steps of nucleotide addition from nucleotide insertion to immediately preceding catalysis are explored using three starting structures representing different stages of nucleotide addition. From these simulations, interactions between dNTPs and the DNA-protein complex formed by the polymerase are elucidated. Patterns of large-scale conformational shifts, classification of nucleotide pairs based on composition, and investigation of the roles of residues interacting with dNTPs are completed on 50+ μs of simulation. The role of molecular dynamics in studies of polymerase behavior is discussed.

  14. Variable length adjacent partitioning for PTS based PAPR reduction of OFDM signal

    Energy Technology Data Exchange (ETDEWEB)

    Ibraheem, Zeyid T.; Rahman, Md. Mijanur; Yaakob, S. N.; Razalli, Mohammad Shahrazel; Kadhim, Rasim A. [School of Computer and Communication Engineering, Universiti Malaysia Perlis, 02600 Arau, Perlis (Malaysia)

    2015-05-15

    Peak-to-Average power ratio (PAPR) is a major drawback in OFDM communication. It leads the power amplifier into nonlinear region operation resulting into loss of data integrity. As such, there is a strong motivation to find techniques to reduce PAPR. Partial Transmit Sequence (PTS) is an attractive scheme for this purpose. Judicious partitioning the OFDM data frame into disjoint subsets is a pivotal component of any PTS scheme. Out of the existing partitioning techniques, adjacent partitioning is characterized by an attractive trade-off between cost and performance. With an aim of determining effects of length variability of adjacent partitions, we performed an investigation into the performances of a variable length adjacent partitioning (VL-AP) and fixed length adjacent partitioning in comparison with other partitioning schemes such as pseudorandom partitioning. Simulation results with different modulation and partitioning scenarios showed that fixed length adjacent partition had better performance compared to variable length adjacent partitioning. As expected, simulation results showed a slightly better performance of pseudorandom partitioning technique compared to fixed and variable adjacent partitioning schemes. However, as the pseudorandom technique incurs high computational complexities, adjacent partitioning schemes were still seen as favorable candidates for PAPR reduction.

  15. Stability and Mismatch Discrimination of Locked Nucleic Acid–DNA Duplexes

    Science.gov (United States)

    2011-01-01

    Locked nucleic acids (LNA; symbols of bases, +A, +C, +G, and +T) are introduced into chemically synthesized oligonucleotides to increase duplex stability and specificity. To understand these effects, we have determined thermodynamic parameters of consecutive LNA nucleotides. We present guidelines for the design of LNA oligonucleotides and introduce free online software that predicts the stability of any LNA duplex oligomer. Thermodynamic analysis shows that the single strand–duplex transition is characterized by a favorable enthalpic change and by an unfavorable loss of entropy. A single LNA modification confines the local conformation of nucleotides, causing a smaller, less unfavorable entropic loss when the single strand is restricted to the rigid duplex structure. Additional LNAs adjacent to the initial modification appear to enhance stacking and H-bonding interactions because they increase the enthalpic contributions to duplex stabilization. New nearest-neighbor parameters correctly forecast the positive and negative effects of LNAs on mismatch discrimination. Specificity is enhanced in a majority of sequences and is dependent on mismatch type and adjacent base pairs; the largest discriminatory boost occurs for the central +C·C mismatch within the +T+C+C sequence and the +A·G mismatch within the +T+A+G sequence. LNAs do not affect specificity in some sequences and even impair it for many +G·T and +C·A mismatches. The level of mismatch discrimination decreases the most for the central +G·T mismatch within the +G+G+C sequence and the +C·A mismatch within the +G+C+G sequence. We hypothesize that these discrimination changes are not unique features of LNAs but originate from the shift of the duplex conformation from B-form to A-form. PMID:21928795

  16. Analysis of the effects of mismatched errors on coherent beam combining based on a self-imaging waveguide

    Energy Technology Data Exchange (ETDEWEB)

    Tao, R; Wang, X; Pu Zhou; Lei Si [College of Optoelectric Science and Engineering, National University of Defense Technology, Changsha 410073 (China)

    2016-01-31

    A theoretical model of coherent beam combining (CBC) based on a self-imaging waveguide (SIW) is built and the effects of mismatched errors on SIW-based CBC are simulated and analysed numerically. With the combination of the theoretical model and the finite difference beam propagation method, two main categories of errors, assembly and nonassembly errors, are numerically studied to investigate their effect on the beam quality by using the M{sup 2} factor. The optimisation of the SIW and error control principle of the system is briefly discussed. The generalised methodology offers a good reference for investigating waveguide-based high-power coherent combining of fibre lasers in a comprehensive way. (lasers and laser beams)

  17. Comparison of Adjacency and Distance-Based Approaches for Spatial Analysis of Multimodal Traffic Crash Data

    Science.gov (United States)

    Gill, G.; Sakrani, T.; Cheng, W.; Zhou, J.

    2017-09-01

    Many studies have utilized the spatial correlations among traffic crash data to develop crash prediction models with the aim to investigate the influential factors or predict crash counts at different sites. The spatial correlation have been observed to account for heterogeneity in different forms of weight matrices which improves the estimation performance of models. But very rarely have the weight matrices been compared for the prediction accuracy for estimation of crash counts. This study was targeted at the comparison of two different approaches for modelling the spatial correlations among crash data at macro-level (County). Multivariate Full Bayesian crash prediction models were developed using Decay-50 (distance-based) and Queen-1 (adjacency-based) weight matrices for simultaneous estimation crash counts of four different modes: vehicle, motorcycle, bike, and pedestrian. The goodness-of-fit and different criteria for accuracy at prediction of crash count reveled the superiority of Decay-50 over Queen-1. Decay-50 was essentially different from Queen-1 with the selection of neighbors and more robust spatial weight structure which rendered the flexibility to accommodate the spatially correlated crash data. The consistently better performance of Decay-50 at prediction accuracy further bolstered its superiority. Although the data collection efforts to gather centroid distance among counties for Decay-50 may appear to be a downside, but the model has a significant edge to fit the crash data without losing the simplicity of computation of estimated crash count.

  18. Optimal technique of linear accelerator-based stereotactic radiosurgery for tumors adjacent to brainstem.

    Science.gov (United States)

    Chang, Chiou-Shiung; Hwang, Jing-Min; Tai, Po-An; Chang, You-Kang; Wang, Yu-Nong; Shih, Rompin; Chuang, Keh-Shih

    2016-01-01

    Stereotactic radiosurgery (SRS) is a well-established technique that is replacing whole-brain irradiation in the treatment of intracranial lesions, which leads to better preservation of brain functions, and therefore a better quality of life for the patient. There are several available forms of linear accelerator (LINAC)-based SRS, and the goal of the present study is to identify which of these techniques is best (as evaluated by dosimetric outcomes statistically) when the target is located adjacent to brainstem. We collected the records of 17 patients with lesions close to the brainstem who had previously been treated with single-fraction radiosurgery. In all, 5 different lesion catalogs were collected, and the patients were divided into 2 distance groups-1 consisting of 7 patients with a target-to-brainstem distance of less than 0.5cm, and the other of 10 patients with a target-to-brainstem distance of ≥ 0.5 and radiosurgery: dynamic conformal arcs (DCA), intensity-modulated radiosurgery (IMRS), and volumetric modulated arc radiotherapy (VMAT). All techniques included multiple noncoplanar beams or arcs with or without intensity-modulated delivery. The volume of gross tumor volume (GTV) ranged from 0.2cm(3) to 21.9cm(3). Regarding the dose homogeneity index (HIICRU) and conformity index (CIICRU) were without significant difference between techniques statistically. However, the average CIICRU = 1.09 ± 0.56 achieved by VMAT was the best of the 3 techniques. Moreover, notable improvement in gradient index (GI) was observed when VMAT was used (0.74 ± 0.13), and this result was significantly better than those achieved by the 2 other techniques (p < 0.05). For V4Gy of brainstem, both VMAT (2.5%) and IMRS (2.7%) were significantly lower than DCA (4.9%), both at the p < 0.05 level. Regarding V2Gy of normal brain, VMAT plans had attained 6.4 ± 5%; this was significantly better (p < 0.05) than either DCA or IMRS plans, at 9.2 ± 7% and 8.2 ± 6%, respectively. Owing to

  19. A mismatch-based model for memory reconsolidation and extinction in attractor networks.

    Directory of Open Access Journals (Sweden)

    Remus Osan

    Full Text Available The processes of memory reconsolidation and extinction have received increasing attention in recent experimental research, as their potential clinical applications begin to be uncovered. A number of studies suggest that amnestic drugs injected after reexposure to a learning context can disrupt either of the two processes, depending on the behavioral protocol employed. Hypothesizing that reconsolidation represents updating of a memory trace in the hippocampus, while extinction represents formation of a new trace, we have built a neural network model in which either simple retrieval, reconsolidation or extinction of a stored attractor can occur upon contextual reexposure, depending on the similarity between the representations of the original learning and reexposure sessions. This is achieved by assuming that independent mechanisms mediate Hebbian-like synaptic strengthening and mismatch-driven labilization of synaptic changes, with protein synthesis inhibition preferentially affecting the former. Our framework provides a unified mechanistic explanation for experimental data showing (a the effect of reexposure duration on the occurrence of reconsolidation or extinction and (b the requirement of memory updating during reexposure to drive reconsolidation.

  20. Image contrast enhancement using adjacent-blocks-based modification for local histogram equalization

    Science.gov (United States)

    Wang, Yang; Pan, Zhibin

    2017-11-01

    Infrared images usually have some non-ideal characteristics such as weak target-to-background contrast and strong noise. Because of these characteristics, it is necessary to apply the contrast enhancement algorithm to improve the visual quality of infrared images. Histogram equalization (HE) algorithm is a widely used contrast enhancement algorithm due to its effectiveness and simple implementation. But a drawback of HE algorithm is that the local contrast of an image cannot be equally enhanced. Local histogram equalization algorithms are proved to be the effective techniques for local image contrast enhancement. However, over-enhancement of noise and artifacts can be easily found in the local histogram equalization enhanced images. In this paper, a new contrast enhancement technique based on local histogram equalization algorithm is proposed to overcome the drawbacks mentioned above. The input images are segmented into three kinds of overlapped sub-blocks using the gradients of them. To overcome the over-enhancement effect, the histograms of these sub-blocks are then modified by adjacent sub-blocks. We pay more attention to improve the contrast of detail information while the brightness of the flat region in these sub-blocks is well preserved. It will be shown that the proposed algorithm outperforms other related algorithms by enhancing the local contrast without introducing over-enhancement effects and additional noise.

  1. Extraction of mismatch negativity using a resampling-based spatial filtering method

    Science.gov (United States)

    Lin, Yanfei; Wu, Wei; Wu, Chaohua; Liu, Baolin; Gao, Xiaorong

    2013-04-01

    Objective. It is currently a challenge to extract the mismatch negativity (MMN) waveform on the basis of a small number of EEG trials, which are typically unbalanced between conditions. Approach. In order to address this issue, a method combining the techniques of resampling and spatial filtering is proposed in this paper. Specifically, the first step of the method, termed ‘resampling difference’, randomly samples the standard and deviant sweeps, and then subtracts standard sweeps from deviant sweeps. The second step of the method employs the spatial filters designed by a signal-to-noise ratio maximizer (SIM) to extract the MMN component. The SIM algorithm can maximize the signal-to-noise ratio for event-related potentials (ERPs) to improve extraction. Simulation data were used to evaluate the influence of three parameters (i.e. trial number, repeated-SIM times and sampling times) on the performance of the proposed method. Main results. Results demonstrated that it was feasible and reliable to extract the MMN waveform using the method. Finally, an oddball paradigm with auditory stimuli of different frequencies was employed to record a few trials (50 trials of deviant sweeps and 250 trials of standard sweeps) of EEG data from 11 adult subjects. Results showed that the method could effectively extract the MMN using the EEG data of each individual subject. Significance. The extracted MMN waveform has a significantly larger peak amplitude and shorter latencies in response to the more deviant stimuli than in response to the less deviant stimuli, which agreed with the MMN properties reported in previous literature using grand-averaged EEG data of multi-subjects.

  2. Adenomatous Polyposis Coli, mismatch repair, and microsatellite instability in colorectal cancer based on different locations.

    Science.gov (United States)

    Effendi-Y S, Rustam; Zain, Lukman H; Siregar, Gontar A; Lubis, Harun R; Damanik, Harun A; Laksmi, Lidya I; Chrestella, Jessy

    2013-10-01

    to examine the protein expression negative (PEN) of Adenomatous Polyposis Coli (APC), Mismatch Repair (MMR), and Microsatellite Instability (MSI) status of colorectal cancer (CRC), and establish a comparison of those molecular characteristics in CRC location among Indonesian patients in Adam Malik Hospital, Pirngadi Hospital, and other hospitals within the network of Faculty of Medicine University of Sumatera Utara Medan Indonesia. this prospective study was conducted from April to December 2012. Fresh tissues were obtained from colorectal tumor patients. The APC-PEN, MMR (MLH1, MSH2, PMS2, MSH6)-PEN, were assessed by immunohistochemistry, and MSI by PCR using 5 microsatellite markers (BAT25, BAT26, D2S123, D5S346, D17S250), as independent variables. The tumour locations as dependent variables were divided into proximal colon (caecum, ascending colon, transverse colon); distal colon (splenic flexure, descending colon, sigmoid) and rectum. The comparative study were done by bivariate and multivariate analysis. there were 77 cases of colorectal adenocarsinoma. MMR-PEN was found in 54 of 77 (70.1%). MLH1-PEN was different between distal colon and rectal cancer (p=0.008); MSH6-PEN was different between proximal colon and rectal cancer (p= 0.020). Multivariate analysis showed: MLH1-PEN was related to cancer location (p=0.006) with OR 0.12 (95% CI 0.026-0.547). It had 0.12 times probability to be found in distal than rectum. MLH1-PEN had 10 times higher probability to be found in proximal than in distal (p=0.037). MSH6-PEN was related to the location (p=0.026) with OR 0.165 (95% CI 0.034-0.803), and had 0.165 times probability to be found in proximal than rectum; and 11 times higher probability in distal than proximal colon (p=0.043). APC-PEN was related to the location (p=0.020), with OR 6.897 (95% CI 1.359-34.995), and 6.89 times higher probability in distal than in rectum, with other variables controlled. MSI-H was found in 29 of 77 (37.7%) and MSI-L/MSS in 48 (62

  3. Artificial lateral line based local sensing between two adjacent robotic fish.

    Science.gov (United States)

    Zheng, Xingwen; Wang, Chen; Fan, Ruifeng; Xie, Guangming

    2017-09-26

    Lateral line system (LLS) is a mechanoreceptive organ system with which fish and aquatic amphibians can effectively sense the surrounding flow field. The reverse Kármán vortex street (KVS), known as a typical thrust-producing wake, is commonly observed in fish-like locomotion and is known to be generated by fish tail. The vortex street generally reflects the motion information of fish. Fish can use LLS to detect such vortex streets generated by its neighboring fish, thus sensing its own states and the states of its neighbors in fish school. Inspired by such a typical biological phenomenon, we design a robotic fish with an onboard artificial lateral line system (ALLS) composed of pressure sensor arrays and use it to detect the reverse KVS-like vortex wake generated by its adjacent robotic fish. Specifically, the vortex wake results in the hydrodynamic pressure variation (HPV) existed in flow field. Through measuring the HPV using ALLS and extracting meaningful information from the pressure sensor readings, the oscillating frequency/amplitude/offset of the adjacent robotic fish, the relative vertical distance and the relative yaw/pitch/roll angle between the robotic fish and its neighbour are sensed efficiently. This work investigates the hydrodynamic characteristics of the reverse KVS-like vortex wake using ALLS. Besides, this work demonstrates the effectiveness and practicability of artificial lateral line in local sensing for adjacent underwater robots, indicating that it is promising to improve the close-range interaction and the cooperation for a group of underwater vehicles with the application of ALLS in the near future. © 2017 IOP Publishing Ltd.

  4. MRI-based mismatch detection in acute ischemic stroke: Optimal PWI maps and thresholds validated with PET.

    Science.gov (United States)

    Zaro-Weber, Olivier; Moeller-Hartmann, Walter; Siegmund, Dora; Kandziora, Alexandra; Schuster, Alexander; Heiss, Wolf-Dieter; Sobesky, Jan

    2017-09-01

    Perfusion-weighted (PW) magnetic resonance imaging (MRI) is used to detect penumbral tissue in acute stroke, but the selection of optimal PW-maps and thresholds for tissue at risk detection remains a matter of debate. We validated the performance of PW-maps with 15O-water-positron emission tomography (PET) in a large comparative PET-MR cohort of acute stroke patients. In acute and subacute stroke patients with back-to-back MRI and PET imaging, PW-maps were validated with 15O-water-PET. We pooled two different cerebral blood flow (CBF) PET-maps to define the critical flow (CF) threshold, (i) quantitative (q)CBF-PET with the CF threshold 6.1 s (AUC = 0.94) and non-deconvolved PW-time-to-peak (TTP) >4.8 s (AUC = 0.93) showed the best performance to detect the CF threshold as defined by PET. PW-Tmax with a threshold >6.1 s and TTP with a threshold >4.8 s are the most predictive in detecting the CF threshold for MR-based mismatch definition.

  5. Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences.

    Science.gov (United States)

    Cilli, Piera; Minoprio, Anna; Bossa, Cecilia; Bignami, Margherita; Mazzei, Filomena

    2015-10-23

    The cellular pool of ribonucleotide triphosphates (rNTPs) is higher than that of deoxyribonucleotide triphosphates. To ensure genome stability, DNA polymerases must discriminate against rNTPs and incorporated ribonucleotides must be removed by ribonucleotide excision repair (RER). We investigated DNA polymerase β (POL β) capacity to incorporate ribonucleotides into trinucleotide repeated DNA sequences and the efficiency of base excision repair (BER) and RER enzymes (OGG1, MUTYH, and RNase H2) when presented with an incorrect sugar and an oxidized base. POL β incorporated rAMP and rCMP opposite 7,8-dihydro-8-oxoguanine (8-oxodG) and extended both mispairs. In addition, POL β was able to insert and elongate an oxidized rGMP when paired with dA. We show that RNase H2 always preserves the capacity to remove a single ribonucleotide when paired to an oxidized base or to incise an oxidized ribonucleotide in a DNA duplex. In contrast, BER activity is affected by the presence of a ribonucleotide opposite an 8-oxodG. In particular, MUTYH activity on 8-oxodG:rA mispairs is fully inhibited, although its binding capacity is retained. This results in the reduction of RNase H2 incision capability of this substrate. Thus complex mispairs formed by an oxidized base and a ribonucleotide can compromise BER and RER in repeated sequences. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences*

    Science.gov (United States)

    Cilli, Piera; Minoprio, Anna; Bossa, Cecilia; Bignami, Margherita; Mazzei, Filomena

    2015-01-01

    The cellular pool of ribonucleotide triphosphates (rNTPs) is higher than that of deoxyribonucleotide triphosphates. To ensure genome stability, DNA polymerases must discriminate against rNTPs and incorporated ribonucleotides must be removed by ribonucleotide excision repair (RER). We investigated DNA polymerase β (POL β) capacity to incorporate ribonucleotides into trinucleotide repeated DNA sequences and the efficiency of base excision repair (BER) and RER enzymes (OGG1, MUTYH, and RNase H2) when presented with an incorrect sugar and an oxidized base. POL β incorporated rAMP and rCMP opposite 7,8-dihydro-8-oxoguanine (8-oxodG) and extended both mispairs. In addition, POL β was able to insert and elongate an oxidized rGMP when paired with dA. We show that RNase H2 always preserves the capacity to remove a single ribonucleotide when paired to an oxidized base or to incise an oxidized ribonucleotide in a DNA duplex. In contrast, BER activity is affected by the presence of a ribonucleotide opposite an 8-oxodG. In particular, MUTYH activity on 8-oxodG:rA mispairs is fully inhibited, although its binding capacity is retained. This results in the reduction of RNase H2 incision capability of this substrate. Thus complex mispairs formed by an oxidized base and a ribonucleotide can compromise BER and RER in repeated sequences. PMID:26338705

  7. Using Agent-Based Modeling to Assess Liquidity Mismatch in Open-End Bond Funds

    Directory of Open Access Journals (Sweden)

    Donald J. Berndt

    2017-12-01

    Full Text Available In this paper, we introduce a small-scale heterogeneous agent-based model of the US corporate bond market. The model includes a realistic micro-grounded ecology of investors that trade a set of bonds through dealers. Using the model, we simulate market dynamics that emerge from agent behaviors in response to basic exogenous factors (such as interest rate shocks and the introduction of regulatory policies and constraints. A first experiment focuses on the liquidity transformation provided by mutual funds and investigates the conditions under which redemption-driven bond sales may trigger market instability. We simulate the effects of increasing mutual fund market shares in the presence of market-wide repricing of risk (in the form of a 100 basis point increase in the expected returns. The simulations highlight robust-yet-fragile aspects of the growing liquidity transformation provided by mutual funds, with an inflection point beyond which redemption-driven negative feedback loops trigger market instability.

  8. Diagnosis of Constitutional Mismatch Repair-Deficiency Syndrome Based on Microsatellite Instability and Lymphocyte Tolerance to Methylating Agents.

    Science.gov (United States)

    Bodo, Sahra; Colas, Chrystelle; Buhard, Olivier; Collura, Ada; Tinat, Julie; Lavoine, Noémie; Guilloux, Agathe; Chalastanis, Alexandra; Lafitte, Philippe; Coulet, Florence; Buisine, Marie-Pierre; Ilencikova, Denisa; Ruiz-Ponte, Clara; Kinzel, Miriam; Grandjouan, Sophie; Brems, Hilde; Lejeune, Sophie; Blanché, Hélène; Wang, Qing; Caron, Olivier; Cabaret, Odile; Svrcek, Magali; Vidaud, Dominique; Parfait, Béatrice; Verloes, Alain; Knappe, Ulrich J; Soubrier, Florent; Mortemousque, Isabelle; Leis, Alexander; Auclair-Perrossier, Jessie; Frébourg, Thierry; Fléjou, Jean-François; Entz-Werle, Natacha; Leclerc, Julie; Malka, David; Cohen-Haguenauer, Odile; Goldberg, Yael; Gerdes, Anne-Marie; Fedhila, Faten; Mathieu-Dramard, Michèle; Hamelin, Richard; Wafaa, Badre; Gauthier-Villars, Marion; Bourdeaut, Franck; Sheridan, Eamonn; Vasen, Hans; Brugières, Laurence; Wimmer, Katharina; Muleris, Martine; Duval, Alex

    2015-10-01

    Patients with bi-allelic germline mutations in mismatch repair (MMR) genes (MLH1, MSH2, MSH6, or PMS2) develop a rare but severe variant of Lynch syndrome called constitutional MMR deficiency (CMMRD). This syndrome is characterized by early-onset colorectal cancers, lymphomas or leukemias, and brain tumors. There is no satisfactory method for diagnosis of CMMRD because screens for mutations in MMR genes are noninformative for 30% of patients. MMR-deficient cancer cells are resistant to genotoxic agents and have microsatellite instability (MSI), due to accumulation of errors in repetitive DNA sequences. We investigated whether these features could be used to identify patients with CMMRD. We examined MSI by PCR analysis and tolerance to methylating or thiopurine agents (functional characteristics of MMR-deficient tumor cells) in lymphoblastoid cells (LCs) from 3 patients with CMMRD and 5 individuals with MMR-proficient LCs (controls). Using these assays, we defined experimental parameters that allowed discrimination of a series of 14 patients with CMMRD from 52 controls (training set). We then used the same parameters to assess 23 patients with clinical but not genetic features of CMMRD. In the training set, we identified parameters, based on MSI and LC tolerance to methylation, that detected patients with CMMRD vs controls with 100% sensitivity and 100% specificity. Among 23 patients suspected of having CMMRD, 6 had MSI and LC tolerance to methylation (CMMRD highly probable), 15 had neither MSI nor LC tolerance to methylation (unlikely to have CMMRD), and 2 were considered doubtful for CMMRD based on having only 1 of the 2 features. The presence of MSI and tolerance to methylation in LCs identified patients with CMMRD with 100% sensitivity and specificity. These features could be used in diagnosis of patients. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

  9. Pms2 and uracil-DNA glycosylases act jointly in the mismatch repair pathway to generate Ig gene mutations at A-T base pairs.

    Science.gov (United States)

    Girelli Zubani, Giulia; Zivojnovic, Marija; De Smet, Annie; Albagli-Curiel, Olivier; Huetz, François; Weill, Jean-Claude; Reynaud, Claude-Agnès; Storck, Sébastien

    2017-04-03

    During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis. In this study, we show that uracils generated in the G1 phase in B cells can generate equal proportions of A-T and G-C mutations, which suggests that UNG and MMR can operate within the same time frame during SHM. Furthermore, we show that Ung-/-Pms2-/- mice display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T bases depend on two additional uracil glycosylases, thymine-DNA glycosylase and SMUG1. These results demonstrate that Pms2/Mlh1 and multiple uracil glycosylases act jointly, each one with a distinct strand bias, to enlarge the immunoglobulin gene mutation spectrum from G-C to A-T bases. © 2017 Girelli Zubani et al.

  10. An Analysis of Skill Mismatch Using Direct Measures of Skills

    OpenAIRE

    Desjardins, R

    2011-01-01

    The focus of this study is on the potential causes of skill mismatch, the extent of skill mismatch, the sociodemographic make-up of skill mismatch, and the consequences of skill mismatch in terms of earnings as well as employer sponsored adult education/training. A distinction is made between skill mismatch and education mismatch. The analysis is based on the 2003-2007 Adult Literacy and Lifeskills Survey (ALLS) – a dataset similar to the one that is forthcoming from the Programme for Interna...

  11. Accurate and visual discrimination of single-base mismatch by utilization of binary DNA probes in gold nanoparticles-based biosensing strategy.

    Science.gov (United States)

    Zhou, Weijun; Ren, Jiangtao; Zhu, Jinbo; Zhou, Zhixue; Dong, Shaojun

    2016-12-01

    Herein we report a colorimetric biosensing strategy to discriminate single-nucleotide mutation in DNA with high selectivity using unmodified gold nanoparticles (AuNPs) as indicators. In the AuNPs-based colorimetric strategy, binary DNA probes were produced by splitting a long DNA probe in the middle for sensitive differentiation of single-base mismatch. The detection limit of this method toward target DNA was 5nM. The developed system has superior advantages of utilization of inexpensive materials, simplicity and visualization. Moreover, binary DNA probes not only can distinguish single-base mutation in the target DNA very well, as compared to long DNA probe, but also can construct "AND" logic gate using two distinct target DNAs as inputs, which holds great potential for increasing the accuracy of disease diagnosis in clinical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Cancer spectrum in DNA mismatch repair gene mutation carriers: results from a hospital based Lynch syndrome registry.

    Science.gov (United States)

    Pande, Mala; Wei, Chongjuan; Chen, Jinyun; Amos, Christopher I; Lynch, Patrick M; Lu, Karen H; Lucio, Laura A; Boyd-Rogers, Stephanie G; Bannon, Sarah A; Mork, Maureen E; Frazier, Marsha L

    2012-09-01

    The spectrum of cancers seen in a hospital based Lynch syndrome registry of mismatch repair gene mutation carriers was examined to determine the distribution of cancers and examine excess cancer risk. Overall there were 504 cancers recorded in 368 mutation carriers from 176 families. These included 236 (46.8 %) colorectal and 268 (53.2 %) extracolonic cancers. MLH1 mutation carriers had a higher frequency of colorectal cancers whereas MSH2, MSH6 and PMS2 mutation carriers had more extracolonic cancers although these differences were not statistically significant. Men had fewer extracolonic cancers than colorectal (45.3 vs. 54.7 %), whereas women had more extracolonic than colorectal cancers (59.0 vs. 41.0 %). The mean age at diagnosis overall for extracolonic cancers was older than for colorectal, 49.1 versus 44.8 years (P ≤ 0.001). As expected, the index cancer was colorectal in 58.1 % of patients and among the extracolonic index cancers, endometrial was the most common (13.8 %). A significant number of non-Lynch syndrome index cancers were recorded including breast (n = 5) prostate (n = 3), thyroid (n = 3), cervix (n = 3), melanoma (n = 3), and 1 case each of thymoma, sinus cavity, and adenocarcinoma of the lung. However, standardized incidence ratios calculated to assess excess cancer risk showed that only those cancers known to be associated with Lynch syndrome were significant in our sample. We found that Lynch syndrome patients can often present with cancers that are not considered part of Lynch syndrome. This has clinical relevance both for diagnosis of Lynch syndrome and surveillance for cancers of different sites during follow-up of these patients.

  13. Educational Mismatch and Retirement

    Science.gov (United States)

    Bender, Keith A.; Heywood, John S.

    2017-01-01

    Using a panel data set of scientists in the US, we examine the hypothesis that workers in jobs poorly matched to their education are more likely to retire. In pooled estimates, we confirm that the mismatched are more likely to retire and that among retirees, the mismatched retire at younger ages. Hazard function estimates also support the…

  14. Fixed-Base Comb with Window-Non-Adjacent Form (NAF) Method for Scalar Multiplication

    Science.gov (United States)

    Seo, Hwajeong; Kim, Hyunjin; Park, Taehwan; Lee, Yeoncheol; Liu, Zhe; Kim, Howon

    2013-01-01

    Elliptic curve cryptography (ECC) is one of the most promising public-key techniques in terms of short key size and various crypto protocols. For this reason, many studies on the implementation of ECC on resource-constrained devices within a practical execution time have been conducted. To this end, we must focus on scalar multiplication, which is the most expensive operation in ECC. A number of studies have proposed pre-computation and advanced scalar multiplication using a non-adjacent form (NAF) representation, and more sophisticated approaches have employed a width-w NAF representation and a modified pre-computation table. In this paper, we propose a new pre-computation method in which zero occurrences are much more frequent than in previous methods. This method can be applied to ordinary group scalar multiplication, but it requires large pre-computation table, so we combined the previous method with ours for practical purposes. This novel structure establishes a new feature that adjusts speed performance and table size finely, so we can customize the pre-computation table for our own purposes. Finally, we can establish a customized look-up table for embedded microprocessors. PMID:23881143

  15. Fixed-Base Comb with Window-Non-Adjacent Form (NAF Method for Scalar Multiplication

    Directory of Open Access Journals (Sweden)

    Yeoncheol Lee

    2013-07-01

    Full Text Available Elliptic curve cryptography (ECC is one of the most promising public-key techniques in terms of short key size and various crypto protocols. For this reason, many studies on the implementation of ECC on resource-constrained devices within a practical execution time have been conducted. To this end, we must focus on scalar multiplication, which is the most expensive operation in ECC. A number of studies have proposed pre-computation and advanced scalar multiplication using a non-adjacent form (NAF representation, and more sophisticated approaches have employed a width-w NAF representation and a modified pre-computation table. In this paper, we propose a new pre-computation method in which zero occurrences are much more frequent than in previous methods. This method can be applied to ordinary group scalar multiplication, but it requires large pre-computation table, so we combined the previous method with ours for practical purposes. This novel structure establishes a new feature that adjusts speed performance and table size finely, so we can customize the pre-computation table for our own purposes. Finally, we can establish a customized look-up table for embedded microprocessors.

  16. Native and non-native speech sound processing and the neural mismatch responses: A longitudinal study on classroom-based foreign language learning.

    Science.gov (United States)

    Jost, Lea B; Eberhard-Moscicka, Aleksandra K; Pleisch, Georgette; Heusser, Veronica; Brandeis, Daniel; Zevin, Jason D; Maurer, Urs

    2015-06-01

    Learning a foreign language in a natural immersion context with high exposure to the new language has been shown to change the way speech sounds of that language are processed at the neural level. It remains unclear, however, to what extent this is also the case for classroom-based foreign language learning, particularly in children. To this end, we presented a mismatch negativity (MMN) experiment during EEG recordings as part of a longitudinal developmental study: 38 monolingual (Swiss-) German speaking children (7.5 years) were tested shortly before they started to learn English at school and followed up one year later. Moreover, 22 (Swiss-) German adults were recorded. Instead of the originally found positive mismatch response in children, an MMN emerged when applying a high-pass filter of 3 Hz. The overlap of a slow-wave positivity with the MMN indicates that two concurrent mismatch processes were elicited in children. The children's MMN in response to the non-native speech contrast was smaller compared to the native speech contrast irrespective of foreign language learning, suggesting that no additional neural resources were committed to processing the foreign language speech sound after one year of classroom-based learning. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Zero energy buildings and mismatch compensation factors

    DEFF Research Database (Denmark)

    Lund, Henrik; Marszal, Anna Joanna; Heiselberg, Per

    2011-01-01

    of the energy production unit. Based on historical data for the electricity supply area in western Denmark, this paper makes a first attempt to quantify mismatch compensation factors. The results indicate that such compensation factors are a little below one for buildings with photovoltaics (PV) and a little......This paper takes an overall energy system approach to analysing the mismatch problem of zero energy and zero emission buildings (ZEBs). The mismatch arises from hourly differences in energy production and consumption at the building level and results in the need for exchange of electricity via...... the public grid even though the building has an annual net-exchange of zero. This paper argues that, when looked upon from the viewpoint of the overall electricity supply system, a mismatch can be both negative and positive. Moreover, there are often both an element of levelling out mismatches between...

  18. The Eukaryotic Mismatch Recognition Complexes Track with the Replisome during DNA Synthesis.

    Directory of Open Access Journals (Sweden)

    Joanna E Haye

    2015-12-01

    Full Text Available During replication, mismatch repair proteins recognize and repair mispaired bases that escape the proofreading activity of DNA polymerase. In this work, we tested the model that the eukaryotic mismatch recognition complex tracks with the advancing replisome. Using yeast, we examined the dynamics during replication of the leading strand polymerase Polε using Pol2 and the eukaryotic mismatch recognition complex using Msh2, the invariant protein involved in mismatch recognition. Specifically, we synchronized cells and processed samples using chromatin immunoprecipitation combined with custom DNA tiling arrays (ChIP-chip. The Polε signal was not detectable in G1, but was observed at active origins and replicating DNA throughout S-phase. The Polε signal provided the resolution to track origin firing timing and efficiencies as well as replisome progression rates. By detecting Polε and Msh2 dynamics within the same strain, we established that the mismatch recognition complex binds origins and spreads to adjacent regions with the replisome. In mismatch repair defective PCNA mutants, we observed that Msh2 binds to regions of replicating DNA, but the distribution and dynamics are altered, suggesting that PCNA is not the sole determinant for the mismatch recognition complex association with replicating regions, but may influence the dynamics of movement. Using biochemical and genomic methods, we provide evidence that both MutS complexes are in the vicinity of the replisome to efficiently repair the entire spectrum of mutations during replication. Our data supports the model that the proximity of MutSα/β to the replisome for the efficient repair of the newly synthesized strand before chromatin reassembles.

  19. A Fast Motion Parameters Estimation Method Based on Cross-Correlation of Adjacent Echoes for Wideband LFM Radars

    Directory of Open Access Journals (Sweden)

    Yi-Xiong Zhang

    2017-05-01

    Full Text Available In wideband radar systems, the performance of motion parameters estimation can significantly affect the performance of object detection and the quality of inverse synthetic aperture radar (ISAR imaging. Although the traditional motion parameters estimation methods can reduce the range migration (RM and Doppler frequency migration (DFM effects in ISAR imaging, the computational complexity is high. In this paper, we propose a new fast non-parameter-searching method for motion parameters estimation based on the cross-correlation of adjacent echoes (CCAE for wideband LFM signals. A cross-correlation operation is carried out for two adjacent echo signals, then the motion parameters can be calculated by estimating the frequency of the correlation result. The proposed CCAE method can be applied directly to the stretching system, which is commonly adopted in wideband radar systems. Simulation results demonstrate that the new method can achieve better estimation performances, with much lower computational cost, compared with existing methods. The experimental results on real radar datasets are also evaluated to verify the effectiveness and superiority of the proposed method compared to the state-of-the-art existing methods.

  20. Use case scenarios - space based receiver assessment : GPS Adjacent Band Compatibility Assessment Workshop VI.

    Science.gov (United States)

    2017-03-30

    This workshop presentation discusses space based receiver applications, NASA developed receivers, the TriG receiver, on-orbit assessment parameters, the TriG GNSS-RO antenna gain pattern, the GNSS-RO antenna beam Earth grazing coverage area, assessme...

  1. Benthic habitat quality assessment based on biological indices in Xiaoqing River estuary and its adjacent sea of Laizhou Bay, China

    Science.gov (United States)

    Luo, Xianxiang; Lin, Song; Yang, Jianqiang; Shen, Jiayu; Fan, Yuqing; Zhang, Longjun

    2017-06-01

    Based on the macrofauna data (2008-2011) in Xiaoqing River estuary and its adjacent sea, Laizhou Bay of Bohai Sea, China, the AZTI Marine Biotic Index (AMBI) and Multivariate AMBI (M-AMBI) were used for benthic habitat quality (BHQ) assessment. Results showed that BHQ presented an obvious trend of improvement along the direction of stream channel and river mouth, and in the coastal areas. AMBI and M-AMBI were significantly related to environmental pressure gradient data. Therefore, the two indices can well indicate BHQ in the studied area. However, there were significant differences between results of the two indices. In the cases of low taxa number and high abundance of single species, AMBI might overestimate BHQ. We thus adjusted its thresholds to solve this problem. And M-AMBI might overestimate BHQ when benthic assemblage was dominated by the opportunistic species. Then we could raise the weight of AMBI in the calculation of M-AMBI to handle the problem.

  2. Adjacency-Based Data Reordering Algorithm for Acceleration of Finite Element Computations

    Directory of Open Access Journals (Sweden)

    Min Zhou

    2010-01-01

    Full Text Available Effective use of the processor memory hierarchy is an important issue in high performance computing. In this work, a part level mesh topological traversal algorithm is used to define a reordering of both mesh vertices and regions that increases the spatial locality of data and improves overall cache utilization during on processor finite element calculations. Examples based on adaptively created unstructured meshes are considered to demonstrate the effectiveness of the procedure in cases where the load per processing core is varied but balanced (e.g., elements are equally distributed across cores for a given partition. In one example, the effect of the current ajacency-based data reordering is studied for different phases of an implicit analysis including element-data blocking, element-level computations, sparse-matrix filling and equation solution. These results are compared to a case where reordering is applied to mesh vertices only. The computations are performed on various supercomputers including IBM Blue Gene (BG/L and BG/P, Cray XT (XT3 and XT5 and Sun Constellation Cluster. It is observed that reordering improves the per-core performance by up to 24% on Blue Gene/L and up to 40% on Cray XT5. The CrayPat hardware performance tool is used to measure the number of cache misses across each level of the memory hierarchy. It is determined that the measured decrease in L1, L2 and L3 cache misses when data reordering is used, closely accounts for the observed decrease in the overall execution time.

  3. Matching/Mismatching in Web-Based Learning: A Perspective Based on Cognitive Styles and Physiological Factors

    Science.gov (United States)

    Huang, Yueh-Min; Hwang, Jan-Pan; Chen, Sherry Y.

    2016-01-01

    Cognitive styles have been regarded as a crucial factor that affects the effectiveness of web-based learning (WBL). Previous research indicated that educational settings that match with students' cognitive styles can enhance students' learning performance, which is, however, linked to their emotion. Various physiological signals can be applied to…

  4. Multi-domain feature selection in auditory MisMatch Negativity via PARAFAC-based template matching approach.

    Science.gov (United States)

    Pouryazdian, Saeed; Chang, Andrew; Bosnyak, Dan J; Trainor, Laurel J; Beheshti, Soosan; Krishnan, Sridhar

    2016-08-01

    MisMatch Negativity (MMN) is a small event-related potential (ERP) that provide an index of sensory learning and perceptual accuracy for the cognitive research. Group-level analysis plays an important role for detecting differences at group or condition level, especially when the signal-to-noise ratio is low. Tensor factorization has provided a framework for group-level analysis of ERPs by exploiting more information of brain responses in more domains simultaneously. A 4-way ERP tensor of time × frequency × channel × subjects/condition is generated and decomposed via PARAFAC. A crucial step after PARAFAC decomposition is to select the component that corresponds to the event of interest and moreover differentiates the two groups\\conditions. This is usually done manually, which is tedious when the number of components is high. Here we propose a technique to select the multi-domain feature of an ERP among all extracted features by a template matching approach, that uses the MMN temporal and spectral signatures. Following a statistical test, the selected feature significantly discriminated subjects for the two experimental conditions.

  5. Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods.

    Science.gov (United States)

    Arora, Sanjeevani; Huwe, Peter J; Sikder, Rahmat; Shah, Manali; Browne, Amanda J; Lesh, Randy; Nicolas, Emmanuelle; Deshpande, Sanat; Hall, Michael J; Dunbrack, Roland L; Golemis, Erica A

    2017-07-03

    The cancer-predisposing Lynch Syndrome (LS) arises from germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1, MSH2, MSH6, and PMS2. A major challenge for clinical diagnosis of LS is the frequent identification of variants of uncertain significance (VUS) in these genes, as it is often difficult to determine variant pathogenicity, particularly for missense variants. Generic programs such as SIFT and PolyPhen-2, and MMR gene-specific programs such as PON-MMR and MAPP-MMR, are often used to predict deleterious or neutral effects of VUS in MMR genes. We evaluated the performance of multiple predictive programs in the context of functional biologic data for 15 VUS in MLH1, MSH2, and PMS2. Using cell line models, we characterized VUS predicted to range from neutral to pathogenic on mRNA and protein expression, basal cellular viability, viability following treatment with a panel of DNA-damaging agents, and functionality in DNA damage response (DDR) signaling, benchmarking to wild-type MMR proteins. Our results suggest that the MMR gene-specific classifiers do not always align with the experimental phenotypes related to DDR. Our study highlights the importance of complementary experimental and computational assessment to develop future predictors for the assessment of VUS.

  6. Ovarian cancer at young age: the contribution of mismatch-repair defects in a population-based series of epithelial ovarian

    DEFF Research Database (Denmark)

    Domanska, K; Malander, S; Måsbäck, A

    2007-01-01

    At least one of ten patients with ovarian cancer is estimated to develop their tumor because of heredity with the breast and ovarian cancer syndrome due to mutations in the BRCA1 and BRCA2 genes and hereditary nonpolyposis colorectal cancer (HNPCC) being the major genetic causes. Cancer at young...... age is a hallmark of heredity, and ovarian cancers associated with HNPCC have been demonstrated to develop at a particularly early age. We used the Swedish Cancer Registry to identify a population-based series of 98 invasive epithelial ovarian cancers that developed before 40 years. Mucinous...... and endometrioid cancers were overrepresented and were diagnosed in 27% and 16% of the tumors, respectively. Immunostaining using antibodies against MLH1, PMS2, MSH2, and MSH6 was used to assess the mismatch-repair status and revealed loss of expression of MLH1/PMS2 in two cases, loss of MSH2/MSH6 in one case...

  7. Mismatch and G-stack modulated probe signals on SNP microarrays.

    Directory of Open Access Journals (Sweden)

    Hans Binder

    Full Text Available BACKGROUND: Single nucleotide polymorphism (SNP arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates. METHODOLOGY/PRINCIPAL FINDINGS: The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G and the particular type of mismatched pairings formed in cross-allelic probe/target duplexes constitute sources of systematic biases of the probe signals with consequences for genotyping and copy number estimates. The poly-G effect seems to be related to the crowded arrangement of probes which facilitates complex formation of neighboring probes with at minimum three adjacent G's in their sequence. CONCLUSIONS: The applied method of "triple-averaging" represents a model-free approach to estimate the mean intensity contributions of different sequence motifs which can be applied in calibration algorithms to correct signal values for sequence effects. Rules for appropriate sequence corrections are suggested.

  8. High resolution CT evaluation on the morphologic characteristics and variations of foramen ovale and adjacent foramina in the skull base

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyun Sook; Kim, Dong Ik [Yonsei University College of Medicine, Seoul (Korea, Republic of)

    1995-07-15

    To evaluate the morphologic characteristics and anatomical variation of the foramen ovale(FO) and its relationship with adjacent foramina. We evaluated 305 HRCT studies of the temporal bone in patients without having any disease that might alter the foraminal anatomy. This study focused on the variations in presence, shape, size, location and relationship with each other. The shapes of FO were 6 types (ovoid: 75.2%, pyriform, elongated, round, polygonal and figure of 8). The average size was 7.4 mm 1.3 in ling diameter and 4.3 mm 0.9 in short diameter. The position of the posterior margin of FO in respective to the line connecting the both mandibular fossa of temporal bone was various(on the line: 62.3%, anterior: 30.2%, posterior: 7.5%). FO had communication with the foramen spinosum (FS) in 4.1% and with the foramen vesalius(FV) in 1.9%. FV was present in 47.5%(bilateral: 26.2%, right: 10.2%, left: 11.1%). The shapes were round or ovoid. The distance from the midline was 18.9 mm 1.7. No data showed statistically significant differences between right and left. There was no inverse relationship between the presence of FV and the size of FO. Three continuous sections in one patient showed variations in the formation of foramen ovale and foramen spinosum; one pyriform shaped foramen ovale and one foramen spinosum on the lower section, one round shaped foramen ovale and two foramen spinosum on the midsection, assimilation of two foramen spinosum into one elongated foramen spinosum on the upper section. The canaliculus innominatus was observed in 9%. Skull base foramina of the middle cranial fossa have various shape, size, location, presence and relationship with each other. It is important to recognize foraminal varients not to misinterprete as disease.

  9. Heterogenous mismatch-repair status in colorectal cancer

    DEFF Research Database (Denmark)

    Joost, Patrick; Veurink, Nynke; Holck, Susanne

    2014-01-01

    BACKGROUND: Immunohistochemical staining for mismatch repair proteins is efficient and widely used to identify mismatch repair defective tumors. The tumors typically show uniform and widespread loss of MMR protein staining. We identified and characterized colorectal cancers with alternative......, heterogenous mismatch repair protein staining in order to delineate expression patterns and underlying mechanisms. METHODS: Heterogenous staining patterns that affected at least one of the mismatch repair proteins MLH1, PMS2, MSH2 and MSH6 were identified in 14 colorectal cancers. Based on alternative....... CONCLUSIONS: Heterogenous mismatch repair status can be demonstrated in colorectal cancer. Though rare, attention to this phenomenon is recommended since it corresponds to differences in mismatch repair status that are relevant for correct classification. VIRTUAL SLIDES: The virtual slide(s) for this article...

  10. Investigating the optimal passive and active vibration controls of adjacent buildings based on performance indices using genetic algorithms

    Science.gov (United States)

    Hadi, Muhammad N. S.; Uz, Mehmet E.

    2015-02-01

    This study proposes the optimal passive and active damper parameters for achieving the best results in seismic response mitigation of coupled buildings connected to each other by dampers. The optimization to minimize the H2 and H∞ norms in the performance indices is carried out by genetic algorithms (GAs). The final passive and active damper parameters are checked for adjacent buildings connected to each other under El Centro NS 1940 and Kobe NS 1995 excitations. Using real coded GA in H∞ norm, the optimal controller gain is obtained by different combinations of the measurement as the feedback for designing the control force between the buildings. The proposed method is more effective than other metaheuristic methods and more feasible, although the control force increased. The results in the active control system show that the response of adjacent buildings is reduced in an efficient manner.

  11. GPS-corrected and GIS-based remapping of the Kalahari Gemsbok National Park and the adjacent area in Botswana

    Directory of Open Access Journals (Sweden)

    J. du P. Bothma

    1993-09-01

    Full Text Available GPS-equipment was used to map the interior roads, major pans and the location of all windmills and solar-equipped boreholes in the Kalahari Gemsbok National Park and the adjacent areas of Botswana. The final map was generated with GIS-equipment, and supplies managers and planners with the first error-free map of the area. The major errors of previous maps are indicated.

  12. Streptococcus mutans counts in plaque adjacent to orthodontic brackets bonded with resin-modified glass ionomer cement or resin-based composite

    Directory of Open Access Journals (Sweden)

    Solange Machado Mota

    2008-03-01

    Full Text Available This study investigated the number of Streptococcus mutans CFU (colony forming units in the saliva and plaque adjacent to orthodontic brackets bonded with a glass ionomer cement - GIC (Fuji Ortho or a resin-based composite - RC (Concise. Twenty male and female patients, aged 12 to 20 years, participated in the study. Saliva was collected before and after placement of appliances. Plaque was collected from areas adjacent to brackets and saliva was again collected on the 15th, 30th, and 45th day after placement. On the 30th day, 0.4% stannous fluoride gel was applied for 4 minutes. No significant modification in the number of Streptococcus mutans CFU in saliva was observed after placement of the fixed orthodontic appliances. On the 15th day, the percentage of Streptococcus mutans CFU in plaque was statistically lower in sites adjacent to GIC-bonded brackets (mean = 0.365 than in those adjacent to RC-bonded brackets (mean = 0.935. No evidence was found of a contribution of GIC to the reduction of CFU in plaque after the 15th day. Topical application of stannous fluoride gel on the 30th day reduced the number of CFU in saliva, but not in plaque. This study suggests that the antimicrobial activity of GIC occurs only in the initial phase and is not responsible for a long-term anticariogenic property.

  13. Mechanisms in E. coli and Human Mismatch Repair (Nobel Lecture).

    Science.gov (United States)

    Modrich, Paul

    2016-07-18

    DNA molecules are not completely stable, they are subject to chemical or photochemical damage and errors that occur during DNA replication resulting in mismatched base pairs. Through mechanistic studies Paul Modrich showed how replication errors are corrected by strand-directed mismatch repair in Escherichia coli and human cells. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. The Mismatch between Students' Mental Models of Acids/Bases and Their Sources and Their Teacher's Anticipations Thereof

    Science.gov (United States)

    Lin, Jing-Wen; Chiu, Mei-Hung

    2010-01-01

    The aim of this study is to compare the characteristics and sources of students' mental models of acids and bases with a teacher's anticipations and, based on this comparison, to explore some possible explanations why motivated students might fail to learn from a subject-knowledgeable chemistry teacher. The study involves a chemistry teacher and…

  15. Deciphering the Mismatch Recognition Cycle in MutS and MSH2-MSH6 Using Normal-Mode Analysis

    OpenAIRE

    Mukherjee, Shayantani; Law, Sean M.; Feig, Michael

    2009-01-01

    Postreplication DNA mismatch repair is essential for maintaining the integrity of genomic information in prokaryotes and eukaryotes. The first step in mismatch repair is the recognition of base-base mismatches and insertions/deletions by bacterial MutS or eukaryotic MSH2-MSH6. Crystal structures of both proteins bound to mismatch DNA reveal a similar molecular architecture but provide limited insight into the detailed molecular mechanism of long-range allostery involved in mismatch recognitio...

  16. Potential for DNA-based identification of Great Lakes fauna: Match and mismatch between taxa inventories and DNA barcode libraries

    Science.gov (United States)

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However, the abi...

  17. Minimally invasive procedure reduces adjacent segment degeneration and disease: New benefit-based global meta-analysis.

    Science.gov (United States)

    Li, Xiao-Chuan; Huang, Chun-Ming; Zhong, Cheng-Fan; Liang, Rong-Wei; Luo, Shao-Jian

    2017-01-01

    Adjacent segment pathology (ASP) is a common complication presenting in patients with axial pain and dysfunction, requiring treatment or follow-up surgery. However, whether minimally invasive surgery (MIS), including MIS transforaminal / posterior lumbar interbody fusion (MIS-TLIF/PLIF) decreases the incidence rate of ASP remains unknown. The aim of this meta-analysis was to compare the incidence rate of ASP in patients undergoing MIS versus open procedures. This systematic review was undertaken by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement. We searched electronic databases, including PubMed, EMBASE, SinoMed, and the Cochrane Library, without language restrictions, to identify clinical trials comparing MIS to open procedures. The results retrieved were last updated on June 15, 2016. Overall, 9 trials comprising 770 patients were included in the study; the quality of the studies included 4 moderate and 5 low-quality studies. The pooled data analysis demonstrated low heterogeneity between the trials and a significantly lower ASP incidence rate in patients who underwent MIS procedure, compared with those who underwent open procedure (p = 0.0001). Single-level lumbar interbody fusion was performed in 6 trials of 408 patients and we found a lower ASP incidence rate in MIS group, compared with those who underwent open surgery (p = 0.002). Moreover, the pooled data analysis showed a significant reduction in the incidence rate of adjacent segment disease (ASDis) (p = 0.0003) and adjacent segment degeneration (ASDeg) (p = 0.0002) for both procedures, favoring MIS procedure. Subgroup analyses showed no difference in follow-up durations between the procedures (p = 0.93). Therefore, we conclude that MIS-TLIF/PLIF can reduce the incidence rate of ASDis and ASDeg, compared with open surgery. Although the subgroup analysis did not indicate a difference in follow-up duration between the two procedures, larger-scale, well

  18. Diagnosis of Constitutional Mismatch Repair-Deficiency Syndrome Based on Microsatellite Instability and Lymphocyte Tolerance to Methylating Agents

    DEFF Research Database (Denmark)

    Bodo, Sahra; Colas, Chrystelle; Buhard, Olivier

    2015-01-01

    in repetitive DNA sequences. We investigated whether these features could be used to identify patients with CMMRD. METHODS: We examined MSI by PCR analysis and tolerance to methylating or thiopurine agents (functional characteristics of MMR-deficient tumor cells) in lymphoblastoid cells (LCs) from 3 patients...... features of CMMRD. RESULTS: In the training set, we identified parameters, based on MSI and LC tolerance to methylation, that detected patients with CMMRD vs controls with 100% sensitivity and 100% specificity. Among 23 patients suspected of having CMMRD, 6 had MSI and LC tolerance to methylation (CMMRD...

  19. Metrology of ground-based satellite validation: co-location mismatch and smoothing issues of total ozone comparisons

    Directory of Open Access Journals (Sweden)

    T. Verhoelst

    2015-12-01

    Full Text Available Comparisons with ground-based correlative measurements constitute a key component in the validation of satellite data on atmospheric composition. The error budget of these comparisons contains not only the measurement errors but also several terms related to differences in sampling and smoothing of the inhomogeneous and variable atmospheric field. A versatile system for Observing System Simulation Experiments (OSSEs, named OSSSMOSE, is used here to quantify these terms. Based on the application of pragmatic observation operators onto high-resolution atmospheric fields, it allows a simulation of each individual measurement, and consequently, also of the differences to be expected from spatial and temporal field variations between both measurements making up a comparison pair. As a topical case study, the system is used to evaluate the error budget of total ozone column (TOC comparisons between GOME-type direct fitting (GODFITv3 satellite retrievals from GOME/ERS2, SCIAMACHY/Envisat, and GOME-2/MetOp-A, and ground-based direct-sun and zenith–sky reference measurements such as those from Dobsons, Brewers, and zenith-scattered light (ZSL-DOAS instruments, respectively. In particular, the focus is placed on the GODFITv3 reprocessed GOME-2A data record vs. the ground-based instruments contributing to the Network for the Detection of Atmospheric Composition Change (NDACC. The simulations are found to reproduce the actual measurements almost to within the measurement uncertainties, confirming that the OSSE approach and its technical implementation are appropriate. This work reveals that many features of the comparison spread and median difference can be understood as due to metrological differences, even when using strict co-location criteria. In particular, sampling difference errors exceed measurement uncertainties regularly at most mid- and high-latitude stations, with values up to 10 % and more in extreme cases. Smoothing difference errors only

  20. Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries

    Science.gov (United States)

    Trebitz, Anett S.; Hoffman, Joel C.; Grant, George W.; Billehus, Tyler M.; Pilgrim, Erik M.

    2015-07-01

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Visual Detection of Single-Base Mismatches in DNA Using Hairpin Oligonucleotide with Double-Target DNA Binding Sequences and Gold Nanoparticles

    Science.gov (United States)

    He, Yuqing; Zhang, Xibao; Zhang, Sanquan; Kris, Mak Ka Long; Man, Fong Chi; Liu, Guodong

    2014-01-01

    We describe a hairpin oligonucleotide (HO) with double-target DNA binding sequences in the loop and 11-base in the stem for visual detection of single-base mismatches (SBM) in DNA with highly specificity. The thiol-modified HO was immobilized on gold nanoparticle (Au-NP) surface through a self-assembling process. The strategy of detecting SBM depends on the unique molecular recognition properties of HO to the perfect-matched DNA and SBM to generate different quantities of duplex DNA on the Au-NP surface, which are captured on the test zone of lateral flow test strip via the DNA hybridization reaction between the duplex DNA and preimmobilized DNA probe. Accumulation of Au-NPs produces the characteristic red bands, enabling visual detection of SBM. It was found that the ability of HO to differentiate perfect-matched DNA and SBM was increased dramatically by incorporating double-target DNA binding sequences in the loop of HO. The signal ratio between perfect-matched DNA and SBM was up to 28, which is much higher than that of conventional HO or molecular beacon. The approach was applied to detect the mutation sites, Arg142Cys and Gly529Ile, of transglutaminase 1 gene in autosomal recessive congenital ichthyosis. The results presented here show that the new HO is a potential molecular recognition probe for the future development of nucleic acid-based biosensors and bioassays. The approach can be used for point-of-care diagnosis of genetic diseases and detecting infectious agents or warning against bio-warfare agents. PMID:22386491

  3. A Calibration Method for Nonlinear Mismatches in M-Channel Time-Interleaved Analog-to-Digital Converters Based on Hadamard Sequences

    Directory of Open Access Journals (Sweden)

    Husheng Liu

    2016-11-01

    Full Text Available The time-interleaved analog-to-digital converter (TIADC is an architecture used to achieve a high sampling rate and high dynamic performance. However, estimation and compensation methods are required to maintain the dynamic performance of the constituent analog-to-digital converters (ADCs due to channel mismatches. This paper proposes a blind adaptive method to calibrate the nonlinear mismatches in M-channel TIADCs (M-TIADCs. The nonlinearity-induced error signal is reconstructed by the proposed multiplier Hadamard transform (MHT structure, and the nonlinear parameters are estimated by the filtered-X least-mean square (FxLMS algorithm. The performance of cascade calibration is also analyzed. The numerical simulation results show that the proposed method consumes much less hardware resources while maintaining the calibration performance.

  4. DNA Mismatch Repair in Eukaryotes and Bacteria

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    Kenji Fukui

    2010-01-01

    Full Text Available DNA mismatch repair (MMR corrects mismatched base pairs mainly caused by DNA replication errors. The fundamental mechanisms and proteins involved in the early reactions of MMR are highly conserved in almost all organisms ranging from bacteria to human. The significance of this repair system is also indicated by the fact that defects in MMR cause human hereditary nonpolyposis colon cancers as well as sporadic tumors. To date, 2 types of MMRs are known: the human type and Escherichia coli type. The basic features of the former system are expected to be universal among the vast majority of organisms including most bacteria. Here, I review the molecular mechanisms of eukaryotic and bacterial MMR, emphasizing on the similarities between them.

  5. Utility of a Computed Tomography-Based Navigation System (O-Arm) for En Bloc Partial Vertebrectomy for Lung Cancer Adjacent to the Thoracic Spine: Technical Case Report.

    Science.gov (United States)

    Kobayashi, Kazuyoshi; Imagama, Shiro; Ito, Zenya; Ando, Kei; Yokoi, Kohei; Ishiguro, Naoki

    2016-04-01

    We describe successful vertebrectomy from a posterior approach using a computed tomography (CT)-based navigation system (O-arm) in a 53-year-old man with adenocarcinoma of the posterior apex of the right lung with invasion of the adjacent rib, thoracic wall, and T2 and T3 vertebral bodies. En bloc partial vertebrectomy for lung cancer adjacent to the thoracic spine was planned using O-arm. First, laminectomy was performed from right T2 to T3, and pedicles and transverse processes of T2 to T3 were resected. O-arm was used to confirm the location of the cutting edge in the T2 to 3 right vertebral internal body, and osteotomy to the anterior cortex was performed with a chisel. Next, the patient was placed in a left decubitus position. The surgical specimen was extracted en bloc. This case shows that O-arm can be used reliably and easily in vertebrectomy from a posterior approach and can facilitate en bloc resection.

  6. Elastic-plastic fracture mechanics of strength-mismatching

    Energy Technology Data Exchange (ETDEWEB)

    Parks, D.M.; Ganti, S.; McClintock, F.A. [Massachusetts Institute of Technology, Cambridge, MA (United States)

    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.

  7. Seismic structure beneath the Gulf of Aqaba and adjacent areas based on the tomographic inversion of regional earthquake data

    Science.gov (United States)

    El Khrepy, Sami; Koulakov, Ivan; Al-Arifi, Nassir; Petrunin, Alexey G.

    2016-06-01

    We present the first 3-D model of seismic P and S velocities in the crust and uppermost mantle beneath the Gulf of Aqaba and surrounding areas based on the results of passive travel time tomography. The tomographic inversion was performed based on travel time data from ˜ 9000 regional earthquakes provided by the Egyptian National Seismological Network (ENSN), and this was complemented with data from the International Seismological Centre (ISC). The resulting P and S velocity patterns were generally consistent with each other at all depths. Beneath the northern part of the Red Sea, we observed a strong high-velocity anomaly with abrupt limits that coincide with the coastal lines. This finding may indicate the oceanic nature of the crust in the Red Sea, and it does not support the concept of gradual stretching of the continental crust. According to our results, in the middle and lower crust, the seismic anomalies beneath the Gulf of Aqaba seem to delineate a sinistral shift (˜ 100 km) in the opposite flanks of the fault zone, which is consistent with other estimates of the left-lateral displacement in the southern part of the Dead Sea Transform fault. However, no displacement structures were visible in the uppermost lithospheric mantle.

  8. Dynamics of DNA Mismatch Repair

    Science.gov (United States)

    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.

  9. Bioimaging of geographically adjacent proteins in a single cell by quantum dot-based fluorescent resonance energy transfer.

    Science.gov (United States)

    Kang, Won Jun; Ko, Mee Hyang; Lee, Dong Soo; Kim, Soonhag

    2009-12-01

    Thousands of proteins are simultaneously involved in the maintenance of a single cancer cell. Fluorescent resonance energy transfer (FRET) is one of the most general techniques for imaging biologically interacting molecules in a cell. Here, we applied FRET to image the co-localization of two proteins that do not interact biologically (nucleolin and integrin α(v) β(3),) both of which are highly expressed in the plasma membrane of cancer cells. AS1411 aptamer, which targets nucleolin, was labeled by Cy3 (Cy3-AS1411) and arginine-glycine-aspartic acid (RGD) peptide, which targets integrin α(v) β(3) , was conjugated with quantum dot (525 nm, Qd) Qd arginine-glycine-aspartic acid (Qd-RGD). FRET activities between Cy3-AS1411 and Qd-RGD were measured in HeLa cells, a human cervical cancer cell line. FRET phenomena between Qd and Cy3 showed good compatibility according to proximity. The fluorescence signature using Qd-RGD and Cy3-AS1411 showed that nucleolin and integrin α(v) β(3) proteins were highly expressed in HeLa cells. Co-incubation of Qd-RGD and Cy3-AS1411 in a single HeLa cell demonstrated that the fluorescence overlay by FRET was quantitatively and geographically quite different from that of individual confocal images. These results suggest that Qd-based FRET analysis can provide information on geographical co-localization of proteins in naïve cells, which is very important for determining the molecular and cellular functions of genes involved in cancers and other clinical diseases. Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. PARP-1 enhances the mismatch-dependence of 5′-directed excision in human mismatch repair in vitro

    Science.gov (United States)

    Liu, Yiyong; Kadyrov, Farid A.; Modrich, Paul

    2011-01-01

    End-directed mismatch-provoked excision has been reconstituted in several purified systems. While 3′-directed excision displays a mismatch dependence similar to that observed in nuclear extracts (≈ 20-fold), the mismatch dependence of 5′-directed excision is only 3 to 4-fold, significantly less than that in extracts (8 to 10-fold). Utilizing a fractionation-based approach, we have isolated a single polypeptide that enhances mismatch dependence of reconstituted 5′-directed excision and have shown it to be identical to poly[ADP-ribose] polymerase 1 (PARP-1). Titration of reconstituted excision reactions or PARP-1-depleted HeLa nuclear extract with purified PARP-1 showed that the protein specifically enhances mismatch dependence of 5′-directed excision. Analysis of a set of PARP-1 mutants revealed that the DNA binding domain and BRCT fold contribute to the regulation of excision specificity. Involvement of the catalytic domain is restricted to its ability to poly(ADP-ribosyl)ate PARP-1 in the presence of NAD+, likely through interference with DNA binding. Analysis of protein-protein interactions demonstrated that PARP-1 interacts with mismatch repair proteins MutSα, exonuclease 1, replication protein A (RPA), and as previously shown by others, replication factor C (RFC) and proliferating cell nuclear antigen (PCNA) as well. The BRCT fold plays an important role in the interaction of PARP-1 with the former three proteins. PMID:21945626

  11. Bond-based linear indices of the non-stochastic and stochastic edge-adjacency matrix. 1. Theory and modeling of ChemPhys properties of organic molecules.

    Science.gov (United States)

    Marrero-Ponce, Yovani; Martínez-Albelo, Eugenio R; Casañola-Martín, Gerardo M; Castillo-Garit, Juan A; Echevería-Díaz, Yunaimy; Zaldivar, Vicente Romero; Tygat, Jan; Borges, José E Rodriguez; García-Domenech, Ramón; Torrens, Francisco; Pérez-Giménez, Facundo

    2010-11-01

    Novel bond-level molecular descriptors are proposed, based on linear maps similar to the ones defined in algebra theory. The kth edge-adjacency matrix (E(k)) denotes the matrix of bond linear indices (non-stochastic) with regard to canonical basis set. The kth stochastic edge-adjacency matrix, ES(k), is here proposed as a new molecular representation easily calculated from E(k). Then, the kth stochastic bond linear indices are calculated using ES(k) as operators of linear transformations. In both cases, the bond-type formalism is developed. The kth non-stochastic and stochastic total linear indices are calculated by adding the kth non-stochastic and stochastic bond linear indices, respectively, of all bonds in molecule. First, the new bond-based molecular descriptors (MDs) are tested for suitability, for the QSPRs, by analyzing regressions of novel indices for selected physicochemical properties of octane isomers (first round). General performance of the new descriptors in this QSPR studies is evaluated with regard to the well-known sets of 2D/3D MDs. From the analysis, we can conclude that the non-stochastic and stochastic bond-based linear indices have an overall good modeling capability proving their usefulness in QSPR studies. Later, the novel bond-level MDs are also used for the description and prediction of the boiling point of 28 alkyl-alcohols (second round), and to the modeling of the specific rate constant (log k), partition coefficient (log P), as well as the antibacterial activity of 34 derivatives of 2-furylethylenes (third round). The comparison with other approaches (edge- and vertices-based connectivity indices, total and local spectral moments, and quantum chemical descriptors as well as E-state/biomolecular encounter parameters) exposes a good behavior of our method in this QSPR studies. Finally, the approach described in this study appears to be a very promising structural invariant, useful not only for QSPR studies but also for similarity

  12. On String Matching with Mismatches

    Directory of Open Access Journals (Sweden)

    Marius Nicolae

    2015-05-01

    Full Text Available In this paper, we consider several variants of the pattern matching with mismatches problem. In particular, given a text \\(T=t_1 t_2\\cdots t_n\\ and a pattern \\(P=p_1p_2\\cdots p_m\\, we investigate the following problems: (1 pattern matching with mismatches: for every \\(i, 1\\leq i \\leq n-m+1\\ output, the distance between \\(P\\ and \\(t_i t_{i+1}\\cdots t_{i+m-1}\\; and (2 pattern matching with \\(k\\ mismatches: output those positions \\(i\\ where the distance between \\(P\\ and \\(t_i t_{i+1}\\cdots t_{i+m-1}\\ is less than a given threshold \\(k\\. The distance metric used is the Hamming distance. We present some novel algorithms and techniques for solving these problems. We offer deterministic, randomized and approximation algorithms. We consider variants of these problems where there could be wild cards in either the text or the pattern or both. We also present an experimental evaluation of these algorithms. The source code is available at http://www.engr.uconn.edu/\\(\\sim\\man09004/kmis.zip.

  13. Regularity extraction from non-adjacent sounds.

    Science.gov (United States)

    Bendixen, Alexandra; Schröger, Erich; Ritter, Walter; Winkler, István

    2012-01-01

    The regular behavior of sound sources helps us to make sense of the auditory environment. Regular patterns may, for instance, convey information on the identity of a sound source (such as the acoustic signature of a train moving on the rails). Yet typically, this signature overlaps in time with signals emitted from other sound sources. It is generally assumed that auditory regularity extraction cannot operate upon this mixture of signals because it only finds regularities between adjacent sounds. In this view, the auditory environment would be grouped into separate entities by means of readily available acoustic cues such as separation in frequency and location. Regularity extraction processes would then operate upon the resulting groups. Our new experimental evidence challenges this view. We presented two interleaved sound sequences which overlapped in frequency range and shared all acoustic parameters. The sequences only differed in their underlying regular patterns. We inserted deviants into one of the sequences to probe whether the regularity was extracted. In the first experiment, we found that these deviants elicited the mismatch negativity (MMN) component. Thus the auditory system was able to find the regularity between the non-adjacent sounds. Regularity extraction was not influenced by sequence cohesiveness as manipulated by the relative duration of tones and silent inter-tone-intervals. In the second experiment, we showed that a regularity connecting non-adjacent sounds was discovered only when the intervening sequence also contained a regular pattern, but not when the intervening sounds were randomly varying. This suggests that separate regular patterns are available to the auditory system as a cue for identifying signals coming from distinct sound sources. Thus auditory regularity extraction is not necessarily confined to a processing stage after initial sound grouping, but may precede grouping when other acoustic cues are unavailable.

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

    Directory of Open Access Journals (Sweden)

    Scott A Lujan

    Full Text Available 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.

  15. Evaluating the Effectiveness of Conservation on Mangroves: A Remote Sensing-Based Comparison for Two Adjacent Protected Areas in Shenzhen and Hong Kong, China

    Directory of Open Access Journals (Sweden)

    Mingming Jia

    2016-07-01

    Full Text Available Mangroves are ecologically important ecosystems and globally protected. The purpose of this study was to evaluate the effectiveness of mangrove conservation efforts in two adjacent protected areas in China that were under the management policies of the Ramsar Convention (Mai Po Marshes Nature Reserve (MPMNR, Hong Kong and China’s National Nature Reserve System (Futian Mangrove National Nature Reserve (FMNNR, Shenzhen. To achieve this goal, eleven Landsat images were chosen and classified, areal extent and landscape metrics were then calculated. The results showed that: from 1973–2015, the areal extent of mangroves in both reserves increased, but the net change for the MPMNR (281.43 hm2 was much higher than those of the FMNNR (101.97 hm2. In general, the area-weighted centroid of the mangroves in FMNNR moved seaward by approximately 120 m, whereas in the MPMNR, the centroid moved seaward even farther (410 m. Although both reserves saw increased integrality and connectivity of the mangrove patches, the patches in the MPMNR always had higher integrality than those in the FMNNR. We concluded that the mangroves in the MPMNR were more effectively protected than those in the FMNNR. This study may provide assistance to the formulation of generally accepted criteria for remote sensing-based evaluation of conservation effectiveness, and may facilitate the development of appropriate mangrove forest conservation and management strategies in other counties.

  16. Relationship between DNA Mismatch Repair Deficiency and Endometrial Cancer

    Directory of Open Access Journals (Sweden)

    Kenta Masuda

    2011-01-01

    Full Text Available Some cases of endometrial cancer are associated with a familial tumor and are referred to as hereditary nonpolyposis colorectal cancer (HNPCC or Lynch syndrome. Lynch syndrome is thought to be induced by germline mutation of the DNA mismatch repair (MMR gene. An aberration in the MMR gene prevents accurate repair of base mismatches produced during DNA replication. This phenomenon can lead to an increased frequency of errors in target genes involved in carcinogenesis, resulting in cancerization of the cell. On the other hand, aberrant DNA methylation is thought to play a key role in sporadic endometrial carcinogenesis. Hypermethylation of unmethylated CpG islands in the promoter regions of cancer-related genes associated with DNA repair leads to the cell becoming cancerous. Thus, both genetic and epigenetic changes are intricately involved in the process through which cells become cancerous. In this review, we introduce the latest findings on the DNA mismatch repair pathway in endometrial cancer.

  17. Visual assessment of perfusion-diffusion mismatch is inadequate to select patients for thrombolysis.

    Science.gov (United States)

    Campbell, Bruce C V; Christensen, Søren; Foster, Sarah J; Desmond, Patricia M; Parsons, Mark W; Butcher, Kenneth S; Barber, P Alan; Levi, Christopher R; Bladin, Christopher F; Donnan, Geoffrey A; Davis, Stephen M

    2010-01-01

    For MR perfusion-diffusion mismatch to be clinically useful as a means of selecting patients for thrombolysis, it needs to occur in real time at the MRI console. Visual mismatch assessment has been used clinically and in trials but has not been systematically validated. We compared the accuracy of visually rating console-generated images with offline volumetric measurements using data from the Echoplanar Imaging Thrombolytic Evaluation Trial (EPITHET). Perfusion time-to-peak (TTP) and diffusion-weighted images (DWI) (as generated by commercial MRI console software) and T(max) perfusion maps (which required offline calculation) were visually rated. Perfusion-diffusion mismatch, defined as a ratio of perfusion:diffusion lesion volume of >1.2, was independently scored by 1 expert and 2 inexperienced raters blinded to calculated volumes and clinical information. Visual mismatch was compared with region-of-interest-based volumetric calculation, which was used as the gold standard. Volumetric calculation demonstrated perfusion-diffusion mismatch in 85/99 patients. Visual TTP-DWI mismatch was correctly classified by the experienced rater in 82% of the cases (sensitivity: 0.86; specificity: 0.54) compared to 73% for the inexperienced raters (sensitivity: 0.75; specificity: 0.57). The interrater reliability for TTP-DWI mismatch was moderate (kappa = 0.50). Visual T(max)-DWI mismatch performed better (agreement - 93 and 87%, sensitivity - 95 and 88%, specificity - 77 and 82% for the experienced and inexperienced raters, respectively). The assessment of visual TTP-DWI mismatch at the MRI console is insufficiently reliable for use in clinical trials. Differences in perfusion analysis technique and visual inaccuracies combine to make visual TTP-DWI mismatch substantially different to volumetric T(max)-DWI mismatch. Automated software that applies perfusion thresholds may improve the reproducibility of real-time mismatch assessment. Copyright 2010 S. Karger AG, Basel.

  18. BEPS Action 2: Neutralizing the Effects on Hybrid Mismatch Arrangements

    NARCIS (Netherlands)

    de Boer, R.; Marres, O.

    2015-01-01

    Curbing tax arbitrage is one of the main priorities of the Organization for Economic Cooperation and Development (OECD) (endorsed by the G20 and the G8) ever since the public debate on base erosion fully erupted. Neutralizing the effect of hybrid mismatch arrangements has become Action No. 2 of the

  19. A neurocomputational model of the mismatch negativity.

    Directory of Open Access Journals (Sweden)

    Falk Lieder

    Full Text Available The mismatch negativity (MMN is an event related potential evoked by violations of regularity. Here, we present a model of the underlying neuronal dynamics based upon the idea that auditory cortex continuously updates a generative model to predict its sensory inputs. The MMN is then modelled as the superposition of the electric fields evoked by neuronal activity reporting prediction errors. The process by which auditory cortex generates predictions and resolves prediction errors was simulated using generalised (Bayesian filtering--a biologically plausible scheme for probabilistic inference on the hidden states of hierarchical dynamical models. The resulting scheme generates realistic MMN waveforms, explains the qualitative effects of deviant probability and magnitude on the MMN - in terms of latency and amplitude--and makes quantitative predictions about the interactions between deviant probability and magnitude. This work advances a formal understanding of the MMN and--more generally--illustrates the potential for developing computationally informed dynamic causal models of empirical electromagnetic responses.

  20. Selective nanoscale growth of lattice mismatched materials

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung-Chang; Brueck, Steven R. J.

    2017-06-20

    Exemplary embodiments provide materials and methods of forming high-quality semiconductor devices using lattice-mismatched materials. In one embodiment, a composite film including one or more substantially-single-particle-thick nanoparticle layers can be deposited over a substrate as a nanoscale selective growth mask for epitaxially growing lattice-mismatched materials over the substrate.

  1. The nature of the transition mismatches with Watson-Crick architecture: the G*·T or G·T* DNA base mispair or both? A QM/QTAIM perspective for the biological problem.

    Science.gov (United States)

    Brovarets', Ol'ha O; Hovorun, Dmytro M

    2015-01-01

    This study provides the first accurate investigation of the tautomerization of the biologically important guanine*·thymine (G*·T) DNA base mispair with Watson-Crick geometry, involving the enol mutagenic tautomer of the G and the keto tautomer of the T, into the G·T* mispair (∆G = .99 kcal mol(-1), population = 15.8% obtained at the MP2 level of quantum-mechanical theory in the continuum with ε = 4), formed by the keto tautomer of the G and the enol mutagenic tautomer of the T base, using DFT and MP2 methods in vacuum and in the weakly polar medium (ε = 4), characteristic for the hydrophobic interfaces of specific protein-nucleic acid interactions. We were first able to show that the G*·T↔G·T* tautomerization occurs through the asynchronous concerted double proton transfer along two antiparallel O6H···O4 and N1···HN3 H-bonds and is assisted by the third N2H···O2 H-bond, that exists along the entire reaction pathway. The obtained results indicate that the G·T* base mispair is stable from the thermodynamic point of view complex, while it is dynamically unstable structure in vacuum and dynamically stable structure in the continuum with ε = 4 with lifetime of 6.4·10(-12) s, that, on the one side, makes it possible to develop all six low-frequency intermolecular vibrations, but, on the other side, it is by three orders less than the time (several ns) required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication. One of the more significant findings to emerge from this study is that the short-lived G·T* base mispair, which electronic interaction energy between the bases (-23.76 kcal mol(-1)) exceeds the analogical value for the G·C Watson-Crick nucleobase pair (-20.38 kcal mol(-1)), "escapes from the hands" of the DNA replication machinery by fast transforming into the G*·T mismatch playing an indirect role of its supplier during the DNA replication. So

  2. Metamer mismatching in practice versus theory.

    Science.gov (United States)

    Zhang, Xiandou; Funt, Brian; Mirzaei, Hamidreza

    2016-03-01

    Metamer mismatching (the phenomenon that two objects matching in color under one illuminant may not match under a different illuminant) potentially has important consequences for color perception. Logvinenko et al. [PLoS ONE10, e0135029 (2015)] show that in theory the extent of metamer mismatching can be very significant. This paper examines metamer mismatching in practice by computing the volumes of the empirical metamer mismatch bodies and comparing them to the volumes of the theoretical mismatch bodies. A set of more than 25 million unique reflectance spectra is assembled using datasets from several sources. For a given color signal (e.g., CIE XYZ) recorded under a given first illuminant, its empirical metamer mismatch body for a change to a second illuminant is computed as follows: the reflectances having the same color signal when lit by the first illuminant (i.e., reflect metameric light) are computationally relit by the second illuminant, and the convex hull of the resulting color signals then defines the empirical metamer mismatch body. The volume of these bodies is shown to vary systematically with Munsell value and chroma. The empirical mismatch bodies are compared to the theoretical mismatch bodies computed using the algorithm of Logvinenko et al. [IEEE Trans. Image Process.23, 34 (2014)]. There are three key findings: (1) the empirical bodies are found to be substantially smaller than the theoretical ones; (2) the sizes of both the empirical and theoretical bodies show a systematic variation with Munsell value and chroma; and (3) applied to the problem of color-signal prediction, the centroid of the empirical metamer mismatch body is shown to be a better predictor of what a given color signal might become under a specified illuminant than state-of-the-art methods.

  3. Discriminating DNA mismatches by electrochemical and gravimetric techniques.

    Science.gov (United States)

    Mazouz, Zouhour; Fourati, Najla; Zerrouki, Chouki; Ommezine, Asma; Rebhi, Lamia; Yaakoubi, Nourdin; Kalfat, Rafik; Othmane, Ali

    2013-10-15

    A silicon nitride functionalized electrode and a 104 MHz lithium tantalate (LiTaO₃) surface acoustic wave (SAW) sensor have been used to investigate target-probe recognition processes. Electrochemical and gravimetric measurements have been considered to monitor hybridization of single base mismatch (SBM) in synthetic oligonucleotides and single-nucleotide polymorphisms ApoE in real clinical genotypes. Obvious discrimination of SBM in nucleotides has been shown by both gravimetric and electrochemical techniques, without labeling nor amplification. Investigations on mismatches nature and position have also been considered. For guanine-adenine (GA), guanine-thymine (GT) and guanine-guanine (GG) mismatches, the sensors responses present a dependence upon positions. Considering the capacitance variations and hybridization rates, results showed that gravimetric transduction is more sensitive than electrochemical one. Moreover, the highest value of GT hybridization rate (in the middle position) was found in accordance with the nearest-neighbor model, where the considered configuration appears as the most thermodynamically stable. For the real samples, where the electrochemical transduction, by combining capacitance and flat-band potential measurements, were found more sensitive, the results show that the realized sensor permits an unambiguous discrimination of recognition between fully complementary, non-complementary and single base mismatched targets, and even between the combination of differently matched strands. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Enhancement of RecA-mediated self-assembly in DNA nanostructures through basepair mismatches and single-strand nicks

    Science.gov (United States)

    Corbett, Sybilla Louise; Sharma, Rajan; Davies, Alexander Giles; Wälti, Christoph

    2017-01-01

    The use of DNA as a structural material for nanometre-scale construction has grown extensively over the last decades. The development of more advanced DNA-based materials would benefit from a modular approach enabling the direct assembly of additional elements onto nanostructures after fabrication. RecA-based nucleoprotein filaments encapsulating short ssDNA have been demonstrated as a tool for highly efficient and fully programmable post-hoc patterning of duplex DNA scaffold. However, the underlying assembly process is not fully understood, in particular when patterning complex DNA topologies. Here, we report the effect of basepair-mismatched regions and single-strand nicks in the double-stranded DNA scaffold on the yield of RecA-based assembly. Significant increases in assembly yield are observed upon the introduction of unpaired basepairs directly adjacent to the assembly region. However, when the unpaired regions were introduced further from the assembly site the assembly yield initially decreased as the length of the unpaired region was increased. These results suggest that an unpaired region acts as a kinetic trap for RecA-based nucleoprotein filaments, impeding the assembly mechanism. Conversely, when the unpaired region is located directly adjacent to the assembly site, it leads to an increase in efficiency of RecA patterning owing to increased breathing of the assembly site.

  5. Lower incidence of acute GVHD is associated with the rapid recovery of CD4+CD25+CD45RA+regulatory T cells in patients who received haploidentical allografts from NIMA-mismatched donors: A retrospective (development) and prospective (validation) cohort-based study.

    Science.gov (United States)

    Wang, Yu; Zhao, Xiang-Yu; Xu, Lan-Ping; Zhang, Xiao-Hui; Han, Wei; Chen, Huan; Wang, Feng-Rong; Mo, Xiao-Dong; Zhang, Yuan-Yuan; Zhao, Xiao-Su; Y, Kong; Liua, Kai-Yan; Huang, Xiao-Jun; Yu, Xue-Zhong; Chang, Ying-Jun

    2016-01-01

    To investigate the effects of non-inherited maternal antigen (NIMA) on clinical outcomes and immune recovery, especially of regulatory T cells (Tregs), in patients who underwent unmanipulated haploidentical transplantation. A retrospective cohort (n = 57) and a prospective cohort (n = 88) were included. All patients received haploidentical allografts from sibling donors. Reconstitution of immune subsets, including Tregs, was determined using multicolor flow cytometry. In the retrospective cohort, the cumulative incidence of grades II-IV acute GVHD in patients with NIMA-mismatched donors was significantly lower than that of cases with NIPA-mismatched donors (14.8% vs. 43.30%, p = 0.018). Patients with higher percentages of CD4 + CD25 + CD45RA + T cells (naive Tregs) within CD4 + T cells recovered on day 30 (≥1.55%) experienced a significantly lower incidence of grades II-IV acute GVHD than that of cases with lower percentages of naive Tregs (NIMA mismatch and the percentages of naive Tregs were associated with the incidence of grades II-IV acute GVHD [ p = 0.050, and 0.031, respectively]. In the prospective cohort, the association of NIMA mismatch [HR = 0.365, 95% CI, 0.169-0.786, p = 0.010] or higher percentages of naive Tregs recovered on day 30 (≥1.55%) [HR = 0.114, 95% CI, 0.027-0.479, p = 0.003] with a lower cumulative incidence of grades II-IV acute GVHD was further demonstrated. No effects of NIMA mismatch on chronic GVHD, transplant-related mortality, relapse, disease-free survival, or overall survival were found. Our results confirmed the role of NIMA mismatch in acute GVHD and provided the first demonstration, based on clinical data, that recovered Tregs may be involved in the effects of NIMA on acute GVHD in a haploidentical transplant setting.

  6. Electrochemical Investigation of Interaction between a Bifunctional Probe and GG Mismatch Duplex.

    Science.gov (United States)

    Li, Jiao; He, Hanping; Peng, Xiaoqian; Huang, Min; Zhang, Xiuhua; Wang, Shengfu

    2015-01-01

    A bifunctional probe (FecNC), containing a recognition part and an electrochemical active center, was applied to electrochemical detection of GG mismatch duplexes. The preparation of gold electrodes modified by mismatch and complementatry duplexes was characterized by electrochemical impedance spectroscopy (EIS) and optimized for better detection in terms of self-assembly time, hybridization time, and incubation time. The interaction between FecNC and DNA duplexes modified on the surface of a gold electrode was explored by square wave voltammetry (SWV) and EIS. The results showed that the DNA duplexes with GG mismatch on the surface of a gold electrode was easily detected by the largest electrochemical signal of the bifunctional probe because of its selective binding to GG mismatches. The bifunctional probe could offer a simple, effective electrochemical detection of GG mismatches, and theoretical bases for development of electrochemical biosensors. Further, the method would be favorable for diagnosis of genetic diseases.

  7. DNA Mismatch Repair and Oxidative DNA Damage: Implications for Cancer Biology and Treatment

    Energy Technology Data Exchange (ETDEWEB)

    Bridge, Gemma; Rashid, Sukaina; Martin, Sarah A., E-mail: sarah.martin@qmul.ac.uk [Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ (United Kingdom)

    2014-08-05

    Many components of the cell, including lipids, proteins and both nuclear and mitochondrial DNA, are vulnerable to deleterious modifications caused by reactive oxygen species. If not repaired, oxidative DNA damage can lead to disease-causing mutations, such as in cancer. Base excision repair and nucleotide excision repair are the two DNA repair pathways believed to orchestrate the removal of oxidative lesions. However, recent findings suggest that the mismatch repair pathway may also be important for the response to oxidative DNA damage. This is particularly relevant in cancer where mismatch repair genes are frequently mutated or epigenetically silenced. In this review we explore how the regulation of oxidative DNA damage by mismatch repair proteins may impact on carcinogenesis. We discuss recent studies that identify potential new treatments for mismatch repair deficient tumours, which exploit this non-canonical role of mismatch repair using synthetic lethal targeting.

  8. Modeling of channel mismatch in time-interleaved SAR ADC

    Science.gov (United States)

    Dengquan, Li; Liang, Zhang; Zhangming, Zhu; Yintang, Yang

    2015-09-01

    In a time-interleaved analog-to-digital converter (TI ADC), several individual ADCs operate in parallel to achieve a higher sampling rate. Low power consumption as well as good linearity can be obtained by applying successive approximation register (SAR) converters as sub-channel ADCs. In spite of the advantages, this structure suffers from three mismatches, which are offset mismatch, gain mismatch, and time skew. This paper focuses on a TI SAR ADC with a number of channels. The mismatch effects in the frequency domain are analyzed and the derived close form formulas are verified based on Matlab. In addition, we clarify that the standard deviation of DNL and INL of an M-channel TI ADC is reduced by a factor of \\sqrt M compared to a single channel ADC. The formulas can be used to derive the corresponding requirements when designing a TI ADC. Our analysis process is able to inform the study of calibration algorithms. Project supported by the National Natural Science Foundation of China (Nos. 61234002, 61322405, 61306044, 61376033) and the National High-Tech Program of China (No. 2013AA014103).

  9. Phase mismatched optical parametric generation in semiconductor magnetoplasma

    Science.gov (United States)

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

    2017-05-01

    Optical parametric generation involves the interaction of pump, signal, and idler waves satisfying law of conservation of energy. Phase mismatch parameter plays important role for the spatial distribution of the field along the medium. In this paper instead of exactly matching wave vector, a small mismatch is admitted with a degree of phase velocity mismatch between these waves. Hence the medium must possess certain finite coherence length. This wave mixing process is well explained by coupled mode theory and one dimensional hydrodynamic model. Based on this scheme, expressions for threshold pump field and transmitted intensity have been derived. It is observed that the threshold pump intensity and transmitted intensity can be manipulated by varying doping concentration and magnetic field under phase mismatched condition. A compound semiconductor crystal of n-InSb is assumed to be shined at 77 K by a 10.6μm CO2 laser with photon energy well below band gap energy of the crystal, so that only free charge carrier influence the optical properties of the medium for the I.R. parametric generation in a semiconductor plasma medium. Favorable parameters were explored to incite the said process keeping in mind the cost effectiveness and conversion efficiency of the process.

  10. Hydrolytic function of Exo1 in mammalian mismatch repair

    Science.gov (United States)

    Shao, Hongbing; Baitinger, Celia; Soderblom, Erik J.; Burdett, Vickers; Modrich, Paul

    2014-01-01

    Genetic and biochemical studies have previously implicated exonuclease 1 (Exo1) in yeast and mammalian mismatch repair, with results suggesting that function of the protein in the reaction depends on both its hydrolytic activity and its ability to interact with other components of the repair system. However, recent analysis of an Exo1-E109K knockin mouse has concluded that Exo1 function in mammalian mismatch repair is restricted to a structural role, a conclusion based on a prior report that N-terminal His-tagged Exo1-E109K is hydrolytically defective. Because Glu-109 is distant from the nuclease hydrolytic center, we have compared the activity of untagged full-length Exo1-E109K with that of wild type Exo1 and the hydrolytically defective active site mutant Exo1-D173A. We show that the activity of Exo1-E109K is comparable to that of wild type enzyme in a conventional exonuclease assay and that in contrast to a D173A active site mutant, Exo1-E109K is fully functional in mismatch-provoked excision and repair. We conclude that the catalytic function of Exo1 is required for its participation in mismatch repair. We also consider the other phenotypes of the Exo1-E109K mouse in the context of Exo1 hydrolytic function. PMID:24829455

  11. Refining the perfusion-diffusion mismatch hypothesis.

    Science.gov (United States)

    Butcher, K S; Parsons, M; MacGregor, L; Barber, P A; Chalk, J; Bladin, C; Levi, C; Kimber, T; Schultz, D; Fink, J; Tress, B; Donnan, G; Davis, S

    2005-06-01

    The Echoplanar Imaging Thrombolysis Evaluation Trial (EPITHET) tests the hypothesis that perfusion-weighted imaging (PWI)-diffusion-weighted imaging (DWI) mismatch predicts the response to thrombolysis. There is no accepted standardized definition of PWI-DWI mismatch. We compared common mismatch definitions in the initial 40 EPITHET patients. Raw perfusion images were used to generate maps of time to peak (TTP), mean transit time (MTT), time to peak of the impulse response (Tmax) and first moment transit time (FMT). DWI, apparent diffusion coefficient (ADC), and PWI volumes were measured with planimetric and thresholding techniques. Correlations between mismatch volume (PWIvol-DWIvol) and DWI expansion (T2(Day 90-vol)-DWI(Acute-vol)) were also assessed. Mean age was 68+/-11, time to MRI 4.5+/-0.7 hours, and median National Institutes of Health Stroke Scale (NIHSS) score 11 (range 4 to 23). Tmax and MTT hypoperfusion volumes were significantly lower than those calculated with TTP and FMT maps (P or =20% was observed in 89% (Tmax) to 92% (TTP/FMT/MTT) of patients. Application of a +4s (relative to the contralateral hemisphere) PWI threshold reduced the frequency of positive mismatch volumes (TTP 73%/FMT 68%/Tmax 54%/MTT 43%). Mismatch was not significantly different when assessed with ADC maps. Mismatch volume, calculated with all parameters and thresholds, was not significantly correlated with DWI expansion. In contrast, reperfusion was correlated inversely with infarct growth (R=-0.51; P=0.009). Deconvolution and application of PWI thresholds provide more conservative estimates of tissue at risk and decrease the frequency of mismatch accordingly. The precise definition may not be critical; however, because reperfusion alters tissue fate irrespective of mismatch.

  12. Digital three-dimensional model of lumbar region 4-5 and its adjacent structures based on a virtual Chinese human.

    Science.gov (United States)

    Yang, Bo; Fang, Shi-bing; Li, Chang-shu; Yin, Biao; Wang, Le; Wan, Sheng-yu; Xie, Jing-kai; Ding, Qiang; Tang, Lei; Zhong, Shi-zhen

    2013-05-01

    To study the methods for constructing a digitized three-dimensional (3D) model of a virtual lumbar region and its adjacent structures in order to assist anatomical study and virtual surgery. Images of DSCF5375-p1 to DSCF5745-p1 were taken from the database of the digitized Virtual Chinese human of Southern Medical University in Guangzhou. This region encompasses the superior facet joint of L4 to the inferior edge of the intervertebral body of L5. The regions of interest were interactively segmented from the images utilizing Adobe Photoshop software. The images were further processed using format conversion and segmentation. Finally, a 3D model of the L4-5 region and its neighboring structures was reconstructed with the assistance of Mimics 10.01 software. A digitized 3D model of this part of the virtual lumbar spine and its adjacent structures was reconstructed. This model allows all constructed structures to be displayed individually or jointly, moved or rotated arbitrarily, setting of different transparencies and convenient measurement of the diameters and angles of the reconstructed structures. The 3D model precisely displays the anatomical relationships between all structures and provides a reliable 3D model for a spinal endoscopic surgery simulation system. Visualization of the digitized 3D reconstruction of the virtual lower lumbar region displays this region and its adjacent structures stereoscopically and in actuality, thus providing morphological data concerning anatomy, image diagnosis and virtual operations in this region. © 2013 Chinese Orthopaedic Association and Wiley Publishing Asia Pty Ltd.

  13. SKILLS MISMATCH OF THE YOUNG PEOPLE AT THE EUROPEAN LEVEL

    Directory of Open Access Journals (Sweden)

    Hatos Roxana

    2015-07-01

    Full Text Available Transition from school to work is a main issue with many fields of study. Studies on transition from school to work, have highlight the importance of two categories of factors at the level of the individual formal proceedings which may affect how easy it is to graduate to integrate into the labor market: 1 so far as the educational systems are transmitting specific competences as compared with those general and 2 so far as there are direct links between employers and the education system. In this way, are reduced the costs of selection and allocation for employers. A poor articulation between educational institutions and the labor market produce a high level of unmatched competences of assimilated by formal education and competencies required of the labor market (skill mismatch (Parodi et al., 2012. The surveys with European employers reflect particular difficulties that they are experiencing in employment vacancies. Investigation on the European companies in the spring of 2013 found that 40% of the firms in the EU have difficulty in finding employees with suitable qualification (CEDEFOP-European Center for the Development of the Vocational Training, 2014. Skills mismatch is a generic term that refers to various types of imbalances between skills and competences offered and those required in the labor market. Concept has become one intensely discussed and submitted to measurement in international research on the background concerns the under-utilization human resource. Numerous opinion polls with employers come to the same unexpected conclusion - that despite high unemployment many posts can't find occupants satisfactorily prepared and identify the causes: most of them criticized the lack of skills of the candidates or the absence of skills specific to the workplace. Based on the latest studies on international databases have built a set of questions that, through secondary analysis, we tried to find answers. Questions that we try to give answer

  14. A mismatch index based on the difference between measured left ventricular ejection fraction and that estimated by infarct size at three months following reperfused acute myocardial infarction

    DEFF Research Database (Denmark)

    Carlsen, Esben A; Bang, Lia E; Lønborg, Jacob

    2014-01-01

    BACKGROUND AND AIM: The reduction of left ventricular ejection fraction (LVEF) following ST-segment elevation myocardial infarction (STEMI) is a result of infarcted myocardium and may involve dysfunctional but viable myocardium. An index that may quantitatively determine whether LVEF is reduced...... beyond the expected value when considering only infarct size (IS) has previously been presented based on cardiac magnetic resonance (CMR). The purpose of this study was to introduce the index based on the electrocardiogram (ECG) and compare indices based on ECG and CMR. METHOD AND RESULTS: In 55 patients...

  15. Improved DNA clamps by stacking to adjacent nucleobases

    DEFF Research Database (Denmark)

    Fatthalla, M.I.; Pedersen, Erik Bjerregaard

    2012-01-01

    to the underlying non-planar base triplet in the formed triplex. This type of triplexes has a substantially higher thermal melting temperature which can be further improved by inserting locked nucleic acids (LNAs) in the Hoogsteen part of the clamp. An extremely high sensitivity to mismatches is observed...

  16. A teleofunctional account of evolutionary mismatch.

    Science.gov (United States)

    Cofnas, Nathan

    When the environment in which an organism lives deviates in some essential way from that to which it is adapted, this is described as "evolutionary mismatch," or "evolutionary novelty." The notion of mismatch plays an important role, explicitly or implicitly, in evolution-informed cognitive psychology, clinical psychology, and medicine. The evolutionary novelty of our contemporary environment is thought to have significant implications for our health and well-being. However, scientists have generally been working without a clear definition of mismatch. This paper defines mismatch as deviations in the environment that render biological traits unable, or impaired in their ability, to produce their selected effects (i.e., to perform their proper functions in Neander's sense). The machinery developed by Millikan in connection with her account of proper function, and with her related teleosemantic account of representation, is used to identify four major types, and several subtypes, of evolutionary mismatch. While the taxonomy offered here does not in itself resolve any scientific debates, the hope is that it can be used to better formulate empirical hypotheses concerning the effects of mismatch. To illustrate, it is used to show that the controversial hypothesis that general intelligence evolved as an adaptation to handle evolutionary novelty can, contra some critics, be formulated in a conceptually coherent way.

  17. A label-free G-quadruplex-based mercury detection assay employing the exonuclease III-mediated cleavage of T?Hg2+?T mismatched DNA

    OpenAIRE

    Wang, Wanhe; Kang, Tian-Shu; Chan, Philip Wai Hong; Lu, Jin-Jian; Chen, Xiu-Ping; Leung, Chung-Hang; Ma, Dik-Lung

    2015-01-01

    We report herein the use of an exonuclease III and G-quadruplex probe to construct a G-quadruplex-based luminescence detection platform for Hg2+. Unlike common DNA-based Hg2+ detection methods, when using the dsDNA probe to monitor the hairpin formation, the intercalation of the dsDNA probe may be influenced by the distortion of dsDNA. This ?mix-and-detect? methodology utilized the G-quadruplex probe as the signal transducer and is simple, rapid, convenient to use and can detect down to 20 nM...

  18. Learning Non-Adjacent Regularities at Age 0 ; 7

    Science.gov (United States)

    Gervain, Judit; Werker, Janet F.

    2013-01-01

    One important mechanism suggested to underlie the acquisition of grammar is rule learning. Indeed, infants aged 0 ; 7 are able to learn rules based on simple identity relations (adjacent repetitions, ABB: "wo fe fe" and non-adjacent repetitions, ABA: "wo fe wo", respectively; Marcus et al., 1999). One unexplored issue is…

  19. Donor selection in pediatric kidney transplantation using DR and DQ eplet mismatching: A new histocompatibility paradigm.

    Science.gov (United States)

    Bryan, Christopher F; Chadha, Vimal; Warady, Bradley A

    2016-11-01

    It is now appreciated that more HLA-DR mismatching at the time of the first renal transplant is associated with higher degrees of sensitization, lower rates and longer times to retransplantation, and worse graft outcomes in children who are subsequently retransplanted. As such, our pediatric renal transplant program preferentially uses 0 or 1 HLA-DR-mismatched kidneys and reserves 2 DR-mismatched kidneys for recipients with an eminent need for a kidney. Based on a new HLA class II epitope matching strategy that is designed to minimize dnDSA production to DR and DQ antigens, we evaluated the prevalence of DR and DQ eplet mismatching for dd offers made to our pediatric wait-listed candidates. Each candidate/dd pair were HLA-DR (β1 and β3 and/or β5) and DQ (α1 and β1) allele typed by rSSO and were then evaluated for eplet mismatches by the HLAMatchmaker program. We evaluated 78 offers made to 16 children on our UNOS waiting list from 27 consecutive dd from 4/14/14 to 3/23/15. The data show that 40% (8/20) of the 1 DR-mismatched dd offers and 64% (37/58) of the 2 DR-mismatched offers were in the high-risk category for both DR and DQ dnDSA development. Whereas only 15% (3/20) of the 1 DR-mismatched offers and 5% (3/58) of the 2 DR-mismatched offers were in the low-risk category for both DR and DQ dnDSA development, 55% and 33% of the 1 DR- and 2 DR-mismatched offers, respectively, had a favorable DQ eplet mismatch threshold. In summary, HLA class II eplet mismatching is common in potential pediatric transplant recipient/donor pairs. Additional study will be necessary to validate the DR and DQ eplet threshold levels in children and to determine whether eplet mismatching strategies in donor selection result in improved transplant outcome and decreased dnDSA production. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Skill mismatch of graduates in a local labour market

    OpenAIRE

    Enrico Marelli; Dario Sciulli; Marcello Signorelli

    2014-01-01

    In this paper we first review the (potential and actual) role of the Universities for the local economies in which they operate, especially considering the implications deriving from the degree of skill mismatch (over-education) in a local labour market. Then, in the second part of the paper, we realise an empirical investigation based on administrative information of an Italian University matched with the data of the job centres of the local (provincial) labour market in order to...

  1. Ovarian cancer at young age: the contribution of mismatch-repair defects in a population-based series of epithelial ovarian

    DEFF Research Database (Denmark)

    Domanska, K; Malander, S; Måsbäck, A

    2007-01-01

    At least one of ten patients with ovarian cancer is estimated to develop their tumor because of heredity with the breast and ovarian cancer syndrome due to mutations in the BRCA1 and BRCA2 genes and hereditary nonpolyposis colorectal cancer (HNPCC) being the major genetic causes. Cancer at young......, and loss of MSH6 only in three tumors. A microsatellite instability-high phenotype was verified in five of six tumors. Based on the identified mutations and family history of cancer, several of these individuals are likely to be affected by HNPCC. We conclude that although the causes of the vast majority...... of epithelial ovarian cancer at young age are unknown, HNPCC should be considered because of the high risk of metachronous colorectal cancer in the individual and the possibility of preventing additional cancers in the family through control programs....

  2. Low radiation dose C-arm cone-beam CT based on prior image constrained compressed sensing (PICCS): including compensation for image volume mismatch between multiple data acquisitions

    Science.gov (United States)

    Nett, Brian; Tang, Jie; Aagaard-Kienitz, Beverly; Rowley, Howard; Chen, Guang-Hong

    2009-02-01

    C-arm based cone-beam CT (CBCT) has evolved into a routine clinical imaging modality to provide threedimensional tomographic image guidance before, during, and after an interventional procedure. It is often used to update the clinician to the state of the patient anatomy and interventional tool placement. Due to the repeatedly use of CBCT, the accumulated radiation dose in an interventional procedure has become a concern. There is a strong desire from both patients and health care providers to reduce the radiation exposure required for these exams. The overall objective of this work is to propose and validate a method to significantly reduce the total radiation dose used during a CBCT image guided intervention. The basic concept is that the first cone-beam CT scan acquired at the full dose will be used to constrain the reconstruction of the later CBCT scans acquired at a much lower radiation dose. A recently developed new image reconstruction algorithm, Prior Image Constrained Compressed Sensing (PICCS), was used to reconstruct subsequent CBCT images with lower dose. This application differs from other applications of the PICCS algorithm, such as time-resolved CT or fourdimensional CBCT (4DCBCT), because the patient position may be frequently changed from one CBCT scan to another during the procedure. Thus, an image registration step to account for the change in patient position is indispensable for use of the PICCS image reconstruction algorithm. In this paper, the image registration step is combined with the PICCS algorithm to enable radiation dose reduction in CBCT image guided interventions. Experimental results acquired from a clinical C-arm system using a human cadaver were used to validate the PICCS algorithm based radiation dose reduction scheme. Using the proposed method in this paper, it has been demonstrated that, instead of 300 view angles, this technique requires about 20 cone-beam view angles to reconstruct CBCT angiograms. This signals a radiation

  3. Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base.

    Science.gov (United States)

    Mukherjee, Sanjukta; Dohno, Chikara; Asano, Kaori; Nakatani, Kazuhiko

    2016-09-06

    A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the sequence 5'-T-3'/5'-GG-3' (T/GG) with the formation of a 1:1 complex, which is one of possible structural elements involved in the higher order structures of (TGG)n repeat DNA triggering the genome microdeletion. Surface plasmon resonance assay also showed the binding of CMBL4: with TGG repeat DNA. Potassium permanganate oxidation studies of CMBL4: -bound duplex containing the T/GG site showed that the CMBL4: -binding accelerated the oxidation of thymine at that site, which suggests the flipping out of the thymine base from a π-stack. Preferential binding was observed for CMBL4: compared with its acyclic variants, which suggests the marked significance of the macrocyclic structure for the recognition of the T/GG site. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Sedimentary and crustal thicknesses and Poisson's ratios for the NE Tibetan Plateau and its adjacent regions based on dense seismic arrays

    Science.gov (United States)

    Wang, Weilai; Wu, Jianping; Fang, Lihua; Lai, Guijuan; Cai, Yan

    2017-03-01

    The sedimentary and crustal thicknesses and Poisson's ratios of the NE Tibetan Plateau and its adjacent regions are estimated by the h- κ stacking and CCP image of receiver functions from the data of 1,317 stations. The horizontal resolution of the obtained results is as high as 0.5° × 0.5°, which can be used for further high resolution model construction in the region. The crustal thicknesses from Airy's equilibrium are smaller than our results in the Sichuan Basin, Qilian tectonic belt, northern Alxa block and Qaidam Basin, which is consistent with the high densities in the mantle lithosphere and may indicate that the high-density lithosphere drags crust down overall. High Poisson's ratios and low velocity zones are found in the mid- and lower crust beneath eastern Qilian tectonic belt and the boundary areas of the Ordos block, indicating that partial melting may exist in these regions. Low Poisson's ratios and low-velocity anomalies are observed in the crust in the NE Tibetan Plateau, implying that the mafic lower crust is thinning or missing and that the mid- and lower crust does not exhibit melting or partial melting in the NE Tibetan Plateau, and weak flow layers are not likely to exist in this region.

  5. Fuzzy Backstepping Sliding Mode Control for Mismatched Uncertain System

    Directory of Open Access Journals (Sweden)

    H. Q. Hou

    2014-06-01

    Full Text Available Sliding mode controllers have succeeded in many control problems that the conventional control theories have difficulties to deal with; however it is practically impossible to achieve high-speed switching control. Therefore, in this paper an adaptive fuzzy backstepping sliding mode control scheme is derived for mismatched uncertain systems. Firstly fuzzy sliding mode controller is designed using backstepping method based on the Lyapunov function approach, which is capable of handling mismatched problem. Then fuzzy sliding mode controller is designed using T-S fuzzy model method, it can improve the performance of the control systems and their robustness. Finally this method of control is applied to nonlinear system as a case study; simulation results are also provided the performance of the proposed controller.

  6. JOB MISMATCH – EFFECTS ON WORK PRODUCTIVITY

    Directory of Open Access Journals (Sweden)

    Magdalena Velciu

    2017-12-01

    Full Text Available Job matching and finding the best person to the right job inside the right company has become one of the most important and actual challenges of productivity. Not only full employment but the match between the employee and the job, in terms of educational level or field of activity, qualifications and skills of workforce; all have been the new gain of work productivity. Present article synthesizes the theoretical and empirical findings on effects of job mismatch by selecting the main findings about influence of job mismatches on work productivity including both employees and companies sides. on short term overeducation and overqualification could have a positive effect on productivity for one company, but on long term, mismatched worker would be affected by decreasing job satisfaction and lower wages. Also, at macroeconomic level, from a perspective of economy as a whole, job mismatches mean a loss of resources and human capital and could have negative effects on overall productivity. The opposite effects stay at the crossing between the employees, companies, policies and future development. In fact the effects of skill mismatch and productivity is a lost of work potential through inefficient resource (reallocation.

  7. Status of the engineering treatment model for mis-matched welds (ETM-MM) handbook

    Energy Technology Data Exchange (ETDEWEB)

    Schwalbe, K.H.; Hao, S.; Cornec, A.; Kocak, M. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Materialforschung

    1997-12-31

    The Engineering Treatment Model (ETM) has been extended to heterogeneous structures such as yield strength mismatched welded joints. The document ETM-MM describes four levels with increasing complexity. On the first level mismatch can be ignored if specific conditions are satisfied. The second level refers to the ETM for homogeneous structures, and mismatch is accounted for by using the lowest yield strength and hardening exponent of the weld metal and base plate, respectively. Within a specified window the third level can be used which is based on all weld metal configurations. If the mismatch yield load solution is available the fourth level can be applied which represents a solution of general validity. Some examples for validation are presented. (orig.)

  8. Educational mismatch in the Czech Labour Market

    Directory of Open Access Journals (Sweden)

    Mysíková Martina

    2016-06-01

    Full Text Available Educational mismatch in labour markets is a phenomenon that has been widely analysed, mainly with respect to rising concerns about a possible oversupply of graduates. Like most European countries, the Czech Republic has experienced a boom in tertiary education in the last decade. The incidence and determinants of over- and undereducation vary substantially depending both on the mismatch measurement approach and the data source applied. Educational mismatch is also reflected in wage levels: overeducated workers have lower wages and undereducated workers have higher wages than workers with the same education whose jobs match their education level. Second, overeducated workers earn more and undereducated workers earn less than their co-workers with exactly the required level of education. The effects are qualitatively the same regardless of the data source and measurement approach applied, but their sizes differ slightly.

  9. Mismatch and noise in modern IC processes

    CERN Document Server

    Marshall, Andrew

    2009-01-01

    Component variability, mismatch, and various noise effects are major contributors to design limitations in most modern IC processes. Mismatch and Noise in Modern IC Processes examines these related effects and how they affect the building block circuits of modern integrated circuits, from the perspective of a circuit designer.Variability usually refers to a large scale variation that can occur on a wafer to wafer and lot to lot basis, and over long distances on a wafer. This phenomenon is well understood and the effects of variability are included in most integrated circuit design with the use

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

    Science.gov (United States)

    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.

  11. Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis.

    Science.gov (United States)

    Mukherjee, Shayantani; Law, Sean M; Feig, Michael

    2009-03-04

    Postreplication DNA mismatch repair is essential for maintaining the integrity of genomic information in prokaryotes and eukaryotes. The first step in mismatch repair is the recognition of base-base mismatches and insertions/deletions by bacterial MutS or eukaryotic MSH2-MSH6. Crystal structures of both proteins bound to mismatch DNA reveal a similar molecular architecture but provide limited insight into the detailed molecular mechanism of long-range allostery involved in mismatch recognition and repair initiation. This study describes normal-mode calculations of MutS and MSH2-MSH6 with and without DNA. The results reveal similar protein flexibilities and suggest common dynamic and functional characteristics. A strongly correlated motion is present between the lever domain and ATPase domains, which suggests a pathway for long-range allostery from the N-terminal DNA binding domain to the C-terminal ATPase domains, as indicated by experimental studies. A detailed analysis of individual low-frequency modes of both MutS and MSH2-MSH6 shows changes in the DNA-binding domains coupled to the ATPase sites, which are interpreted in the context of experimental data to arrive at a complete molecular-level mismatch recognition cycle. Distinct conformational states are proposed for DNA scanning, mismatch recognition, repair initiation, and sliding along DNA after mismatch recognition. Hypotheses based on the results presented here form the basis for further experimental and computational studies.

  12. Translating genomic discoveries to cure ultrahypermutant mismatch ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Translating genomic discoveries to cure ultrahypermutant mismatch repair deficient brain tumours. Les tumeurs malignes au cerveau sont la cause la plus courante de décès chez les enfants atteints du cancer, mais il n'y a pas de traitement connu. Ce projet permettra de faire avancer la recherche dans ce domaine ...

  13. Preventing mismatch answers in standardized survey interviews

    NARCIS (Netherlands)

    Ongena, Yfke P.; Dijkstra, Wil

    Interaction analysis of question–answer sequences from a telephone survey shows that so-called mismatch answers, i.e. answers that do not correspond to the required answering format, are the most frequently occurring problematic verbal behavior. They also are likely to trigger suggestive interviewer

  14. Educational Mismatch and Wages: A Panel Analysis.

    Science.gov (United States)

    Bauer, Thomas K.

    2002-01-01

    Using a large German Socioeconomic Panel data set for the period 1984-98, investigates the wage effects of two different measures of educational mismatch, overeducation and undereducation, when controlling for unobserved heterogeneity. Finds that wages differences between overeducated and undereducated workers totally disappear in most cases.…

  15. Distributivity and Agreement mismatches in Serbian

    NARCIS (Netherlands)

    Bosnic, Ana

    2016-01-01

    This paper presents a truth value judgment study done on two types of numerals in the Serbian numerical system and corresponding verbal agreement mismatch that is characteristic for the numerals in question. Recent work on agreement and distributivity suggests that singular verbal marking promotes

  16. Wavelength mismatch effect in electromagnetically induced absorption

    Energy Technology Data Exchange (ETDEWEB)

    Bharti, Vineet [Department of Physics, Indian Institute of Science, Bangalore 560012 (India); Wasan, Ajay [Department of Physics, Indian Institute of Technology, Roorkee 247667 (India); Natarajan, Vasant [Department of Physics, Indian Institute of Science, Bangalore 560012 (India)

    2016-07-15

    We present a theoretical investigation of the phenomenon of electromagnetically induced absorption (EIA) in a 4-level system consisting of vee and ladder subsystems. The four levels are coupled using one weak probe field, and two strong control fields. We consider an experimental realization using energy levels of Rb. This necessitates dealing with different conditions of wavelength mismatch—near-perfect match where all three wavelengths are approximately equal; partial mismatch where the wavelength of one control field is less than the other fields; and complete mismatch where all three wavelengths are unequal. We present probe absorption profiles with Doppler averaging at room temperature to account for experiments in a room temperature Rb vapor cell. Our analysis shows that EIA resonances can be studied using Rydberg states excited with diode lasers. - Highlights: • Wavelength mismatch effect is investigated in electromagnetically induced absorption (EIA). • An experimental realization of 4-level vee + ladder system using energy levels of rubidium atom is presented. • EIA resonances are studied under different conditions of wavelength mismatch. • Possibility of observation of EIA using Rydberg states excited with diode lasers.

  17. Aortic mismatch in heart transplantation: readaptation.

    Science.gov (United States)

    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.

  18. Mismatch brain response to speech-sound changes in rats

    Directory of Open Access Journals (Sweden)

    Mustak eAhmed

    2011-10-01

    Full Text Available Understanding speech is based on neural representations of individual speech sounds. In humans, such representations are capable of supporting an automatic and memory-based mechanism for auditory change detection, as reflected by the mismatch negativity of event-related potentials. There are also findings of neural representations of speech sounds in animals, but it is not known whether these representations can support the change detection mechanism analogous to that underlying the mismatch negativity in humans. To this end, we presented synthesized spoken syllables to urethane-anesthetized rats while local field potentials were epidurally recorded above their primary auditory cortex. In an oddball condition, a deviant stimulus /ga/ or /ba/ (probability 1:12 for each was rarely and randomly interspersed between frequently presented standard stimulus /da/ (probability 10:12. In an equiprobable condition, 12 syllables, including /da/, /ga/, and /ba/, were presented in a random order (probability 1:12 for each. We found evoked responses of higher amplitude to the deviant /ba/, albeit not to /ga/, relative to the standard /da/ in the oddball condition. Furthermore, the responses to /ba/ were higher in amplitude in the oddball condition than in the equiprobable condition. The findings suggest that anaesthetized rat’s brain can form representations of human speech sounds, and that these representations can support the memory-based change detection mechanism analogous to that underlying the mismatch negativity in humans. Our findings show a striking parallel in speech processing between humans and rodents and may thus pave the way for feasible animal models of memory-based change detection.

  19. Circuit mismatch influence on performance of paralleling silicon carbide MOSFETs

    DEFF Research Database (Denmark)

    Li, Helong; Munk-Nielsen, Stig; Pham, Cam

    2014-01-01

    This paper focuses on circuit mismatch influence on performance of paralleling SiC MOSFETs. Power circuit mismatch and gate driver mismatch influences are analyzed in detail. Simulation and experiment results show the influence of circuit mismatch and verify the analysis. This paper aims to give...... suggestions on paralleling discrete SiC MOSFETs and designing layout of power modules with paralleled SiC MOSFETs dies....

  20. Ecologic and geographic distributions of the vascular plants of southern Nye County, and adjacent parts of Clark, Lincoln, and Esmeralda Counties, Nevada. [Based on collections made in 1970

    Energy Technology Data Exchange (ETDEWEB)

    Beatley, J. C.

    1971-01-01

    A catalog is compiled of the vascular plants indiginous to Nye, Clark, Lincoln, and Esmeralda Counties of Nevada based on collections made in 1970. This compilation is an update of previous collections in these areas and is a supplement to report, UCLA--12-705. (ERB)

  1. Mismatch repair proteins collaborate with methyltransferases in the repair of O6-methylguanine

    Science.gov (United States)

    Rye, Peter T.; Delaney, James C.; Netirojjanakul, Chawita; Sun, Dana X.; Liu, Jenny Z.; Essigmann, John M.

    2010-01-01

    DNA repair is essential for combatting the adverse effects of damage to the genome. One example of base damage is O6-methylguanine (O6mG), which stably pairs with thymine during replication and thereby creates a promutagenic O6mG:T mismatch. This mismatch has also been linked with cellular toxicity. Therefore, in the absence of repair, O6mG:T mismatches can lead to cell death or result in G:C→A:T transition mutations upon the next round of replication. Cysteine thiolate residues on the Ada and Ogt methyltransferase (MTase) proteins directly reverse the O6mG base damage to yield guanine. When a cytosine is opposite the lesion, MTase repair restores a normal G:C pairing. However, if replication past the lesion has produced an O6mG:T mismatch, MTase conversion to a G:T mispair must still undergo correction to avoid mutation. Two mismatch repair pathways in E. coli that convert G:T mispairs to native G:C pairings are methyl-directed mismatch repair (MMR) and very short patch repair (VSPR). This work examined the possible roles that proteins in these pathways play in coordination with the canonical MTase repair of O6mG:T mismatches. The possibility of this repair network was analyzed by probing the efficiency of MTase repair of a single O6mG residue in cells deficient in individual mismatch repair proteins (Dam, MutH, MutS, MutL, or Vsr). We found that MTase repair in cells deficient in Dam or MutH showed wild-type levels of MTase repair. In contrast, cells lacking any of the VSPR proteins MutS, MutL, or Vsr showed a decrease in repair of O6mG by the Ada and Ogt MTases. Evidence is presented that the VSPR pathway positively influences MTase repair of O6mG:T mismatches, and assists the efficiency of restoring these mismatches to native G:C base pairs. PMID:17951114

  2. Immigrants' Educational Mismatch and the Penalty of Over-Education

    Science.gov (United States)

    Kalfa, Eleni; Piracha, Matloob

    2017-01-01

    This paper analyses immigrants' educational mismatch and its impact on wages in Spain. The incidence of immigrants' education-occupation mismatch in the Spanish labour market can largely be explained by the mismatch in the last job held in the home country. The probability of having been over-educated in the home country has a higher effect on the…

  3. MutS recognition: Multiple mismatches and sequence context effects

    Indian Academy of Sciences (India)

    ... which we established more directly by studying two identical single mismatches in an altered sequence background. A mismatch, upon simply being flipped at the same location, elicits changes in MutS specific contacts, thereby underscoring the importance of sequence context in modulating MutS binding to mismatches.

  4. Mismatch repair defects in human carcinogenesis.

    Science.gov (United States)

    Eshleman, J R; Markowitz, S D

    1996-01-01

    Mismatch repair defects are carcinogenic. This conclusion comes some 80 years after the original description of a type of familial colorectal cancer in which mismatch repair defects are involved, and from decades of dedicated basic science research into fundamental mechanisms cells use to repair their DNA. Mismatch repair (MMR) was described first in bacteria, later in yeast and finally in higher eukaryotes. In bacteria, one of its roles is the rapid repair of replicative errors thereby providing the genome with a 100-1000-fold level of protection against mutation. It also guards the genome by preventing recombination between non-homologous regions of DNA. The information gained from bacteria suddenly became relevant to human neoplasia in 1993 when the RER phenotype of microsatellite instability was discovered in human cancers and was rapidly shown to be due to defects in mismatch repair. Evidence supporting the role of MMR defects in carcinogenesis comes from a variety of independent sources including: (i) theoretical considerations of the requirement for a mutator phenotype as a step in multistage carcinogenesis; (ii) discovering that MMR defects cause a 'mutator phenotype' destabilizing endogenous expressed genes including those integral to carcinogenesis; (iii) finding MMR defects in the germline of HNPCC kindred members; (iv) finding that such defects behave as classic tumor suppressor genes in both familial and sporadic colorectal cancers; (v) discovering that MMR 'knockout' mice have an increased incidence of tumors; and (vi) discovering that genetic complementation of MMR defective cells stabilizes the MMR deficiency-associated microsatellite instability. Models of carcinogenesis now must integrate the concepts of a MMR defect induced mutator phenotype (Loeb) with the concepts of multistep colon carcinogenesis (Fearon and Vogelstein) and clonal heterogeneity/selection (Nowell).

  5. Lattice mismatch modeling of aluminum alloys

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Dongwon; Roy, Shibayan; Watkins, Thomas R.; Shyam, Amit

    2017-10-01

    We present a theoretical framework to accurately predict the lattice mismatch between the fcc matrix and precipitates in the multi-component aluminum alloys as a function of temperature and composition. We use a computational thermodynamic approach to model the lattice parameters of the multi-component fcc solid solution and θ'-Al2Cu precipitate phase. Better agreement between the predicted lattice parameters of fcc aluminum in five commercial alloys (206, 319, 356, A356, and A356 + 0.5Cu) and experimental data from the synchrotron X-ray diffraction (SXD) has been obtained when simulating supersaturated rather than equilibrium solid solutions. We use the thermal expansion coefficient of thermodynamically stable θ-Al2Cu to describe temperature-dependent lattice parameters of meta-stable θ' and to show good agreement with the SXD data. Both coherent and semi-coherent interface mismatches between the fcc aluminum matrix and θ' in Al-Cu alloys are presented as a function of temperature. Our calculation results show that the concentration of solute atoms, particularly Cu, in the matrix greatly affects the lattice mismatch

  6. The effect of S-substitution at the O6-guanine site on the structure and dynamics of a DNA oligomer containing a G:T mismatch.

    Directory of Open Access Journals (Sweden)

    Elaine Ann Moore

    Full Text Available The effect of S-substitution on the O6 guanine site of a 13-mer DNA duplex containing a G:T mismatch is studied using molecular dynamics. The structure, dynamic evolution and hydration of the S-substituted duplex are compared with those of a normal duplex, a duplex with S-substitution on guanine, but no mismatch and a duplex with just a G:T mismatch. The S-substituted mismatch leads to cell death rather than repair. One suggestion is that the G:T mismatch recognition protein recognises the S-substituted mismatch (GS:T as G:T. This leads to a cycle of futile repair ending in DNA breakage and cell death. We find that some structural features of the helix are similar for the duplex with the G:T mismatch and that with the S-substituted mismatch, but differ from the normal duplex, notably the helical twist. These differences arise from the change in the hydrogen-bonding pattern of the base pair. However a marked feature of the S-substituted G:T mismatch duplex is a very large opening. This showed considerable variability. It is suggested that this enlarged opening would lend support to an alternative model of cell death in which the mismatch protein attaches to thioguanine and activates downstream damage-response pathways. Attack on the sulphur by reactive oxygen species, also leading to cell death, would also be aided by the large, variable opening.

  7. The molecular marker-based comparison of Azotobacter spp. populations isolated from industrial soils of Cracow-Nowa Huta steelworks (southern Poland) and the adjacent agricultural soils.

    Science.gov (United States)

    Lenart-Boroń, Anna M; Wolny-Koładka, Katarzyna A; Boroń, Piotr M; Mitka, Józef R

    2014-01-01

    The occurrence of Azotobacter spp., which has beneficial effects on plant development, is related to various soil properties, such as pH and fertility. This study evaluated the prevalence of Azotobacter spp. in industrial (H) and agricultural soils (P) in Nowa Huta, Cracow and determined the phenotypic and genetic diversity of these bacteria. The examined bacteria were present in 40% of H and in 50% of P soils. Taxonomic identification of the bacterial isolates indicated the presence of three species--A. salinestris, A. chroococcum and A. vinelandii. The genetic diversity, determined using two fingerprinting methods--Random Analysis of Polymorphic DNA (RAPD) and Rep-PCR (BOX) revealed high level of population diversity. In AMOVA analysis most of diversity was attributed to within-population variation (76-85%), and only 3.78-6.18% was associated with among-group H and P variation. Global test of differences revealed distinct population structure within bacterial strains isolated from H and P areas only for BOX markers (Fst = 0.05732, P = 0.00275). Phenetic analyses: UPGMA and DCA better discriminated H and P groups based on RAPD data. Both BOX and RAPD methods provided an insight into the genetic complexity of Azotobacter spp. variation in soils of different land-use types.

  8. Thermodynamic characterization of tandem mismatches found in naturally occurring RNA

    Science.gov (United States)

    Christiansen, Martha E.; Znosko, Brent M.

    2009-01-01

    Although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [Christiansen,M.E. and Znosko,B.M. (2008) Biochemistry, 47, 4329–4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. Since experimental data is preferred over a predictive model, the thermodynamic parameters for 25 frequently occurring tandem mismatches were determined. These new experimental values, on average, are 1.0 kcal/mol different from the values predicted for these mismatches using the previous model. The data for the sequence asymmetric tandem mismatches reported here were then combined with the data for 72 sequence asymmetric tandem mismatches that were published previously, and the parameters used to predict the thermodynamics of previously unmeasured sequence asymmetric tandem mismatches were updated. The average absolute difference between the measured values and the values predicted using these updated parameters is 0.5 kcal/mol. This updated model improves the prediction for tandem mismatches that were predicted rather poorly by the previous model. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA duplexes containing tandem mismatches, and, furthermore, should allow for improved prediction of secondary structure from sequence. PMID:19509311

  9. Variability of adjacency effects in sky reflectance measurements.

    Science.gov (United States)

    Groetsch, Philipp M M; Gege, Peter; Simis, Stefan G H; Eleveld, Marieke A; Peters, Steef W M

    2017-09-01

    Sky reflectance Rsky(λ) is used to correct in situ reflectance measurements in the remote detection of water color. We analyzed the directional and spectral variability in Rsky(λ) due to adjacency effects against an atmospheric radiance model. The analysis is based on one year of semi-continuous Rsky(λ) observations that were recorded in two azimuth directions. Adjacency effects contributed to Rsky(λ) dependence on season and viewing angle and predominantly in the near-infrared (NIR). For our test area, adjacency effects spectrally resembled a generic vegetation spectrum. The adjacency effect was weakly dependent on the magnitude of Rayleigh- and aerosol-scattered radiance. The reflectance differed between viewing directions 5.4±6.3% for adjacency effects and 21.0±19.8% for Rayleigh- and aerosol-scattered Rsky(λ) in the NIR. Under which conditions in situ water reflectance observations require dedicated correction for adjacency effects is discussed. We provide an open source implementation of our method to aid identification of such conditions.

  10. Solution conformation of an oligonucleotide containing a G.G mismatch determined by nuclear magnetic resonance and molecular mechanics.

    OpenAIRE

    Cognet, J A; Gabarro-Arpa, J; Le Bret, M; van der Marel, G A; van Boom, J H; Fazakerley, G V

    1991-01-01

    We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three dimensional solution structure of the non-selfcomplementary oligonucleotide, d(GAGGAGGCACG). d(CGTGCGTCCTC) in which the central base pair is G.G. This is the first structural determination of a G.G mismatch in a oligonucleotide. Two dimensional nuclear magnetic resonance spectra show that the bases of the mismatched pair are stacked into the helix and that the helix adopts ...

  11. A new incision technique to reduce tibiofemoral mismatch in rotationplasty.

    Science.gov (United States)

    Ossendorf, Christian; Exner, Gerhard U; Fuchs, Bruno

    2010-05-01

    Rotationplasty provides stable and durable biologic reconstruction after tumor resection around the knee and renders reliable results, in young patients. However, after resection of the tumor, there is often a mismatch between the circumference of the proximal (femoral) and the distal (tibial) parts. Because rotationplasty includes an intercalary amputation where the ends are readapted, there is always a mismatch of the proximal and distal circumferences of the soft tissue envelope. To facilitate skin closure without tension and to avoid impaired wound healing and subsequent infections, the type of incision is critical and must be carefully planned. We present a new incision technique for rotationplasty about the knee. Half of the difference of the incision length of the proximal and distal circumferences represents the base of the triangle proximally, medially and laterally of the thigh. After adapting both ends, the peak of this flat triangle is distally adapted via a vertical incision which allows it to match unequal circumferences. This technique was used in eight patients, in all of whom the wounds healed uneventfully.

  12. Sequence-dependent cleavage of mismatched DNA by Ban I restriction endonuclease.

    Science.gov (United States)

    Gao, Weimin; Zhu, Dan; Keohavong, Phouthone

    2017-10-01

    Restriction enzymes have previously shown the ability to cleave DNA substrates with mismatched base(s) in recognition sequences; in this study, Ban I endonuclease demonstrated this same ability. Single base substitutions were introduced, and fragments containing various types of unpaired base(s) (heteroduplex fragments) within the Ban I endonuclease recognition sequence, 5'-G|GPyPuCC-3', were generated. Each of the heteroduplex fragments was treated with Ban I endonuclease and analyzed by denaturing gradient gel electrophoresis. Our results showed that heteroduplex fragments containing mismatched bases at either the first or third position of the Ban I recognition sequence or, because of the symmetrical structure of the sequence, the sixth or fourth position on the opposite strand were cleaved by the enzyme. Furthermore, these cleaved fragments contained at least one strand corresponding to the original Ban I recognition sequence. Fragments with mismatches formed by an A (noncanonical, nc) opposite a purine (canonical, ca) or a T (nc) opposite a pyrimidine (ca) were cleaved more efficiently than other types of mismatched bases. These results may help elucidate the mechanisms by which DNA and protein interact during the process of DNA cleavage by Ban I endonuclease. Copyright © 2017 John Wiley & Sons, Ltd.

  13. Receiver IQ mismatch estimation in PDM CO-OFDM system using training symbol

    Science.gov (United States)

    Peng, Dandan; Ma, Xiurong; Yao, Xin; Zhang, Haoyuan

    2017-07-01

    Receiver in-phase/quadrature (IQ) mismatch is hard to mitigate at the receiver via using conventional method in polarization division multiplexed (PDM) coherent optical orthogonal frequency division multiplexing (CO-OFDM) system. In this paper, a novel training symbol structure is proposed to estimate IQ mismatch and channel distortion. Combined this structure with Gram Schmidt orthogonalization procedure (GSOP) algorithm, we can get lower bit error rate (BER). Meanwhile, based on this structure one estimation method is deduced in frequency domain which can achieve the estimation of IQ mismatch and channel distortion independently and improve the system performance obviously. Numerical simulation shows that the proposed two methods have better performance than compared method at 100 Gb/s after 480 km fiber transmission. Besides, the calculation complexity is also analyzed.

  14. Scale Mismatches in Management of Urban Landscapes

    Directory of Open Access Journals (Sweden)

    Sara T. Borgström

    2006-12-01

    Full Text Available Urban landscapes constitute the future environment for most of the world's human population. An increased understanding of the urbanization process and of the effects of urbanization at multiple scales is, therefore, key to ensuring human well-being. In many conventional natural resource management regimes, incomplete knowledge of ecosystem dynamics and institutional constraints often leads to institutional management frameworks that do not match the scale of ecological patterns and processes. In this paper, we argue that scale mismatches are particularly pronounced in urban landscapes. Urban green spaces provide numerous important ecosystem services to urban citizens, and the management of these urban green spaces, including recognition of scales, is crucial to the well-being of the citizens. From a qualitative study of the current management practices in five urban green spaces within the Greater Stockholm Metropolitan Area, Sweden, we found that 1 several spatial, temporal, and functional scales are recognized, but the cross-scale interactions are often neglected, and 2 spatial and temporal meso-scales are seldom given priority. One potential effect of the neglect of ecological cross-scale interactions in these highly fragmented landscapes is a gradual reduction in the capacity of the ecosystems to provide ecosystem services. Two important strategies for overcoming urban scale mismatches are suggested: 1 development of an integrative view of the whole urban social-ecological landscape, and 2 creation of adaptive governance systems to support practical management.

  15. Ollier's disease in association with adjacent fibromatosis.

    Science.gov (United States)

    Al-Ismail, Khalid; Torreggiani, William C; Munk, Peter L; O'Connell, John X; Nicolaou, Savvakis; Masri, Bassam A

    2002-08-01

    Ollier's disease (enchondromatosis) is a nonhereditary disorder of mesodermal dysplasia. It is characterized by the presence of multiple enchondromas that typically affect the metaphyseal ends of bones. The association of Ollier's disease with adjacent fibromatosis has, to our knowledge, not been previously described. We report a case of Ollier's disease in association with soft tissue fibromatosis adjacent to the involved upper arm.

  16. Skill mismatch and skill use in developed countries: Evidence from the PIAAC study

    OpenAIRE

    Allen, J.P.; Levels, M.; van der Velden, R.K.W.

    2013-01-01

    In this paper we develop and test a new set of measures of skill mismatches, based on data on skill levels and skill use in the domains of literacy and numeracy from the PIAAC project. The measures we develop represent the extent of skill use relative to one’s own skill level. We test the measures by examining their relation to a number of labour market outcomes. We subsequently examine how mismatches are distributed across and within a large number of countries, and use our results to reflec...

  17. Resolution of Mismatched Overlap Holliday Junction Intermediates by the Tyrosine Recombinase IntDOT.

    Science.gov (United States)

    Ringwald, Kenneth; Yoneji, Sumiko; Gardner, Jeffrey

    2017-05-15

    CTnDOT is an integrated conjugative element found in Bacteroides species. CTnDOT contains and transfers antibiotic resistance genes. The element integrates into and excises from the host chromosome via a Holliday junction (HJ) intermediate as part of a site-specific recombination mechanism. The CTnDOT integrase, IntDOT, is a tyrosine recombinase with core-binding, catalytic, and amino-terminal (N) domains. Unlike well-studied tyrosine recombinases, such as lambda integrase (Int), IntDOT is able to resolve Holliday junctions containing heterology (mismatched bases) between the sites of strand exchange. All known natural isolates of CTnDOT contain mismatches in the overlap region between the sites of strand exchange. Previous work showed that IntDOT was unable to resolve synthetic Holliday junctions containing mismatched bases to products in the absence of the arm-type sites and a DNA-bending protein. We constructed synthetic HJs with the arm-type sites and tested them with the Bacteroides host factor (BHFa). We found that the addition of BHFa stimulated resolution of HJ intermediates with mismatched overlap regions to products. In addition, the L1 site is required for directionality of the reaction, particularly when the HJ contains mismatches. BHFa is required for product formation when the overlap region contains mismatches, and it stimulates resolution to products when the overlap region is identical. Without this DNA bending, the N domain of IntDOT is likely unable to bind the L1 arm-type site. These findings suggest that BHFa bends DNA into the necessary conformation for the higher-order complexes, including the L1 site, that are required for product formation.IMPORTANCE CTnDOT is a mobile element that carries antibiotic resistance genes and moves by site-selective recombination and subsequent conjugation. The recombination reaction is catalyzed by an integrase IntDOT that is a member of the tyrosine recombinase family. The reaction proceeds through ordered

  18. Designing of highly effective complementary and mismatch siRNAs for silencing a gene.

    Science.gov (United States)

    Ahmed, Firoz; Raghava, Gajendra P S

    2011-01-01

    In past, numerous methods have been developed for predicting efficacy of short interfering RNA (siRNA). However these methods have been developed for predicting efficacy of fully complementary siRNA against a gene. Best of author's knowledge no method has been developed for predicting efficacy of mismatch siRNA against a gene. In this study, a systematic attempt has been made to identify highly effective complementary as well as mismatch siRNAs for silencing a gene.Support vector machine (SVM) based models have been developed for predicting efficacy of siRNAs using composition, binary and hybrid pattern siRNAs. We achieved maximum correlation 0.67 between predicted and actual efficacy of siRNAs using hybrid model. All models were trained and tested on a dataset of 2182 siRNAs and performance was evaluated using five-fold cross validation techniques. The performance of our method desiRm is comparable to other well-known methods. In this study, first time attempt has been made to design mutant siRNAs (mismatch siRNAs). In this approach we mutated a given siRNA on all possible sites/positions with all possible nucleotides. Efficacy of each mutated siRNA is predicted using our method desiRm. It is well known from literature that mismatches between siRNA and target affects the silencing efficacy. Thus we have incorporated the rules derived from base mismatches experimental data to find out over all efficacy of mutated or mismatch siRNAs. Finally we developed a webserver, desiRm (http://www.imtech.res.in/raghava/desirm/) for designing highly effective siRNA for silencing a gene. This tool will be helpful to design siRNA to degrade disease isoform of heterozygous single nucleotide polymorphism gene without depleting the wild type protein.

  19. The mouse mismatch repair protein, MSH3, is a nucleoplasmic protein that aggregates into denser nuclear bodies under conditions of stress.

    NARCIS (Netherlands)

    Holt, I.; Thanh Lam, L.; Tome, S.; Wansink, D.G.; Riele, H. te; Gourdon, G.; Morris, G.E.

    2011-01-01

    The mismatch repair protein, MSH3, together with MSH2, forms the MutSbeta heterodimer which recognizes and repairs base pair mismatches and larger insertion/deletion loops in DNA. Lack of specific antibodies against mouse MSH3 has hampered studies of its expression and localization. Mouse MSH3 is

  20. Skill mismatch and skill use in developed countries: Evidence from the PIAAC study

    NARCIS (Netherlands)

    Allen, J.P.; Levels, M.; van der Velden, R.K.W.

    2013-01-01

    In this paper we develop and test a new set of measures of skill mismatches, based on data on skill levels and skill use in the domains of literacy and numeracy from the PIAAC project. The measures we develop represent the extent of skill use relative to one’s own skill level. We test the measures

  1. Skill mismatch and use in developed countries: Evidence from the PIAAC study

    NARCIS (Netherlands)

    Allen, J.P.; Levels, M.; van der Velden, R.K.W.

    2013-01-01

    In this paper we develop and test a new set of measures of skill mismatches, based on data on skill levels and skill use in the domains of literacy and numeracy from the PIAAC project. The measures we develop represent the extent of skill use relative to one’s own skill level. We test the measures

  2. L-band AlGaN/GaN Power Amplifier with Protection Against Load Mismatch

    NARCIS (Netherlands)

    Heijningen, M. van; Bent, G. van der; Houwen, E.H. van der; Chowdhary, A.; Vliet, F.E. van

    2013-01-01

    Solid-state power amplifiers need protection at the output to handle high reflections due to mismatch. Normally this is implemented by using a ferrite-based isolator. These are however large and bulky components. This paper presents a Gallium-Nitride power amplifier module with automatic protection

  3. Mismatch negativity (MMN: Translating the potential.

    Directory of Open Access Journals (Sweden)

    Juanita eTodd

    2013-12-01

    Full Text Available The mismatch negativity (MMN component of the auditory event-related potential has become a valuable tool in cognitive neuroscience. Its reduced size in persons with schizophrenia is of unknown origin but theories proposed include links to problems in experience-dependent plasticity reliant on N-methyl-d-aspartate glutamate receptors. In this review we address the utility of this tool in revealing the nature and time course of problems in perceptual inference in this illness together with its potential for use in translational research testing animal models of schizophrenia-related phenotypes. Specifically, we review the reasons for interest in MMN in schizophrenia, issues pertaining to the measurement of MMN, its use as a vulnerability index for the development of schizophrenia, the pharmacological sensitivity of MMN and the progress in developing animal models of MMN. Within this process we highlight the challenges posed by knowledge gaps pertaining to the tool and the pharmacology of the underlying system.

  4. Optimizing the face Paradigm of BCI system by modified Mismatch Negative paradigm

    Directory of Open Access Journals (Sweden)

    Siejie Zhou

    2016-10-01

    Full Text Available 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.

  5. Skill Mismatch of Graduates in a Local Labour Market

    Directory of Open Access Journals (Sweden)

    Enrico Marelli

    2014-06-01

    Full Text Available In this paper we first review the (potential and actual role of the Universities for the local economies in which they operate, especially considering the implications deriving from the degree of skill mismatch (over-education in a local labour market. Then, in the second part of the paper, we realise an empirical investigation based on administrative information of an Italian University matched with the data of the job centres of the local (provincial labour market in order to reconstruct the characteristics of the university-to-work transitions of graduates. Our results have important policy implications, since for local development it is crucial, among other things, to make the best use of all human resources and especially those with the highest educational level.

  6. Mismatch-Shaped Pseudo-Passive Two-Capacitor DAC

    DEFF Research Database (Denmark)

    Steensgaard-Madsen, Jesper; Moon, Un-Ku; Temes, Gabor C.

    1999-01-01

    A simple mismatch-shaping scheme is proposed for a two-capacitor DAC. Unlike in other mismatch-shaping systems, the shaped error is generated by direct filtering of a well-defined bounded signal, which can be generated as white noise. The operation is closely related to a specific digital...

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

  9. Lexical influence in phonetic decision making: Evidence from subcategorical mismatches

    NARCIS (Netherlands)

    McQueen, J.M.; Norris, D.; Cutler, A.

    1999-01-01

    In a series of experiments, listeners heard words and nonwords, some cross-spliced so that they contained acoustic-phonetic mismatches. Performance was worse on mismatching than on matching items. Words cross-spliced with words and words cross-spliced with nonwords produced parallel results. But in

  10. Influence of halo doping profiles on MOS transistor mismatch

    NARCIS (Netherlands)

    Andricciola, P.; Tuinhout, H.

    2009-01-01

    Halo implants are used in modern CMOS technology to reduce the short channel effect. However, the lateral non-uniformity of the channel doping has been proven to degenerate the mismatch performance. With this paper we want to discuss the influence of the halo profile on MOS transistor mismatch. The

  11. The 'adjacent Possible' is Relational

    Science.gov (United States)

    Kauffman, Stuart

    There really is no science of complexity. Rather we have a fairly well developed set of tools to examine diverse complex and complex adaptive systems. These tools include now familiar ideas of nonlinear dynamical systems, bifurcation theory, and stochastic models, as well as agent-based models such as BOIDS. These tools have been well developed in the past 30 years and we are now underway with the applications of such tools. As B. Arthur noted in analogy, the railways in Britain caused a surge in their stock values, which then fell as the bubble burst, but most of the track was laid afterwards. So, too, complexity burst upon the scene in the late 1980s, largely at the Santa Fe Institute. If that messianic era is now, naturally, past, we are enabled to lay enormous tracks as we proceed...

  12. Repair of naturally occurring mismatches can induce mutations in flanking DNA

    Science.gov (United States)

    Chen, Jia; Miller, Brendan F; Furano, Anthony V

    2014-01-01

    ‘Normal’ genomic DNA contains hundreds of mismatches that are generated daily by the spontaneous deamination of C (U/G) and methyl-C (T/G). Thus, a mutagenic effect of their repair could constitute a serious genetic burden. We show here that while mismatches introduced into human cells on an SV40-based episome were invariably repaired, this process induced mutations in flanking DNA at a significantly higher rate than no mismatch controls. Most mutations involved the C of TpC, the substrate of some single strand-specific APOBEC cytidine deaminases, similar to the mutations that can typify the ‘mutator phenotype’ of numerous tumors. siRNA knockdowns and chromatin immunoprecipitation showed that TpC preferring APOBECs mediate the mutagenesis, and siRNA knockdowns showed that both the base excision and mismatch repair pathways are involved. That naturally occurring mispairs can be converted to mutators, represents an heretofore unsuspected source of genetic changes that could underlie disease, aging, and evolutionary change. DOI: http://dx.doi.org/10.7554/eLife.02001.001 PMID:24843013

  13. Investigation on the influence of BBO thermal-induced phase mismatching in 266nm UV laser conversion efficiency

    Science.gov (United States)

    Yu, Kai; Jin, Guangyong; Yu, Miao; Huang, Zhulong; Zhai, Ruizhi; Wang, Lei

    2014-12-01

    266nm UV laser has a wide range of applications in many fields, such as laser medical treatment, laser processing, precision measure and other applications for the reason of its advantages in wavelength, small diffraction effects, high single-photon energy, and high resolution and so on. BBO crystals absorb parts of the fundamental laser energy and second harmonic laser energy are unavoidable, and thus the temperature raise, so that the existing crystal phase matching conditions change, resulting in phase mismatching in the high-power frequency doubling, greatly influence the 266nm UV laser conversion efficiency. To further study the effect of phase mismatching to conversion efficiency, and improve the conversion efficiency, output power and other output characteristics of 266nm laser, the article mainly describe from the following three aspects. Firstly, took the use of three-dimensional nonlinear crystal temperature distribution which is obtained, the process of BBO crystal thermal-induced phase mismatching is analyzed. Secondly, based on frequency doubling theory, the effects of the thermal-induced phase mismatching affected of conversion in crystals are analyzed. Combining with the phase mismatching of the three-dimensional distributions, the fourth harmonic conversion efficiency with thermal phase mismatching changes of BBO 266nm UV laser are simulated for the first time. Thirdly, by using MATLAB software, the effects of phase mismatching to conversion efficiency in crystal for different waist radius, 532nm laser power and the fundamental beam quality are simulated. The results indicate a good physical interpretation of reasons of high power laser frequency doubling system. It shows that the model established explains the reason of the reduction of conversion efficiency, output power and the beam quality excellently. All results make a leading sense to the research on the compensating of the phase mismatching and on the improvement of conversion efficiency.

  14. Comparison of arterial spin labeling and bolus perfusion-weighted imaging for detecting mismatch in acute stroke.

    Science.gov (United States)

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

    2012-07-01

    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 patients with stroke. This was a retrospective study drawn from all 1.5-T MRI studies performed in 2010 at a single institution. Inclusion criteria were: symptom onset10 mL, and acquisition of both PWI and ASL. DWI and PWI time to maximum>6 seconds 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. Fifty-one 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 border zone sign), resulting in 44 studies for comparison. Interrater 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 of 44 cases (57%). In the 16 of 19 discrepant cases (84%), ASL overestimated the PWI lesion size. In 34 of 44 cases (77%), they agreed regarding the presence of mismatch versus no mismatch. Mismatch classification based on ASL and PWI agrees frequently but not perfectly. ASL tends to overestimate the PWI time to maximum lesion volume. Improved ASL methodologies and/or higher field strength are necessary before ASL can be recommended for routine use in acute stroke.

  15. Visual mismatch negativity reveals automatic detection of sequential regularity violation.

    Science.gov (United States)

    Stefanics, Gábor; Kimura, Motohiro; Czigler, István

    2011-01-01

    Sequential regularities are abstract rules based on repeating sequences of environmental events, which are useful to make predictions about future events. Here, we tested whether the visual system is capable to detect sequential regularity in unattended stimulus sequences. The visual mismatch negativity (vMMN) component of the event-related potentials is sensitive to the violation of complex regularities (e.g., object-related characteristics, temporal patterns). We used the vMMN component as an index of violation of conditional (if, then) regularities. In the first experiment, to investigate emergence of vMMN and other change-related activity to the violation of conditional rules, red and green disk patterns were delivered in pairs. The majority of pairs comprised of disk patterns with identical colors, whereas in deviant pairs the colors were different. The probabilities of the two colors were equal. The second member of the deviant pairs elicited a vMMN with longer latency and more extended spatial distribution to deviants with lower probability (10 vs. 30%). In the second (control) experiment the emergence of vMMN to violation of a simple, feature-related rule was studied using oddball sequences of stimulus pairs where deviant colors were presented with 20% probabilities. Deviant colored patterns elicited a vMMN, and this component was larger for the second member of the pair, i.e., after a shorter inter-stimulus interval. This result corresponds to the SOA/(v)MMN relationship, expected on the basis of a memory-mismatch process. Our results show that the system underlying vMMN is sensitive to abstract, conditional rules. Representation of such rules implicates expectation of a subsequent event, therefore vMMN can be considered as a correlate of violated predictions about the characteristics of environmental events.

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

    Science.gov (United States)

    Wadgymar, Susana M; Weis, Arthur E

    2017-06-01

    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

  17. Mechanism of DNA strand exchange at liposome surfaces investigated using mismatched DNA.

    Science.gov (United States)

    Frykholm, Karolin; Nordén, Bengt; Westerlund, Fredrik

    2009-02-03

    DNA strand exchange is of great importance in vivo for genetic recombination and DNA repair. The detailed mechanism of strand exchange is not understood in full detail despite extensive studies. Simplistic model systems in which molecular parameters can be varied independently are therefore of interest to study. We chose the surface of a positively charged liposome as a scaffold, which we recently demonstrated to be able to catalyze the exchange of fully complementary DNA oligonucleotides. We here study how single base pair mismatches affect the rate of strand exchange on the liposome surface. Interestingly, the rate of the exchange does not simply follow the stability of the duplex in solution, as determined by melting temperatures, but also depends sensitively on the position of the mismatch. For duplexes with similar melting temperatures, the exchange is much faster for a mismatch close to the end than for a mismatch in the middle of the sequence. Our results suggest that the single strands are stabilized by the liposome surface; therefore, the duplex is fraying more and the DNA opens up in a zipperlike fashion on the surface, increasing the probability of strand exchange. We also show that the competition between greater stability (higher Tm in solution) and higher concentration is important for the final composition of the duplex when a large excess of single strands is added to a complementary double-stranded DNA. Finally, the similar exchange rate constants for fully base-paired duplexes on the liposome surface when adding fully matched single strands or single strands with a mismatched base indicate that the rate is governed largely by separation of the initial duplex and not by the formation of the product duplex.

  18. A conditioning platform based on fludarabine, busulfan, and 2 days of rabbit antithymocyte globulin results in promising results in patients undergoing allogeneic transplantation from both matched and mismatched unrelated donor.

    Science.gov (United States)

    Devillier, Raynier; Fürst, Sabine; Crocchiolo, Roberto; El-Cheikh, Jean; Castagna, Luca; Harbi, Samia; Granata, Angela; D'Incan, Evelyne; Coso, Diane; Chabannon, Christian; Picard, Christophe; Etienne, Anne; Calmels, Boris; Schiano, Jean-Marc; Lemarie, Claude; Stoppa, Anne-Marie; Bouabdallah, Reda; Vey, Norbert; Blaise, Didier

    2014-01-01

    Conditioning regimen including fludarabine, intravenous busulfan (Bx), and 5 mg/kg total dose of rabbit antithymocyte globulin (r-ATG) (FBx-ATG) results in low incidence of graft-versus-host disease (GVHD) and non-relapse mortality (NRM) after allogeneic hematopoietic stem cell transplantation (Allo-HSCT) from HLA-matched related or unrelated donors (MUD). However, whether this platform produces similar results in the setting of one mismatch unrelated donor (MMUD) Allo-HSCT is not known. We retrospectively analyzed patients aged less than 65 years who were diagnosed with hematological malignancies and received FBx-ATG regimen prior to Allo-HSCT from MUD (N = 74) or MMUD (N = 40). We compared outcome of MUD versus MMUD patients. There was no difference in the cumulative incidence of grades II-IV acute GVHD (MUD: 34% vs. MMUD: 35%, P = 0.918), but MMUD patients developed more grade III-IV acute GVHD (MUD: 5% vs. MMUD: 15%, P = 0.016). The cumulative incidences of overall chronic GVHD (MUD: 33% vs. MMUD: 22%, P = 0.088) and extensive chronic GVHD (MUD: 20% vs. MMUD: 19%, P = 0.594) were comparable. One-year NRM was similar in both groups (MUD: 16% vs. MMUD: 14%, P = 0.292); similarly, progression-free survival (MUD: 59% vs. MMUD: 55%, P = 0.476) and overall survival (MUD: 63% vs. MMUD: 61%, P = 0.762) were not different between both groups. With a median follow up of 24 months, 35 of 74 MUD patients (47%) and 19 of 40 MMUD patients (48%) were free of both disease progression and immunosuppressive treatment. We conclude that the FBx-ATG regimen results in low incidences of NRM and GVHD in both MUD and the MMUD recipients. Copyright © 2013 Wiley Periodicals, Inc.

  19. Moving beyond a single perfusion threshold to define penumbra: a novel probabilistic mismatch definition.

    Science.gov (United States)

    Nagakane, Yoshinari; Christensen, Soren; Ogata, Toshiyasu; Churilov, Leonid; Ma, Henry; Parsons, Mark W; Desmond, Patricia M; Levi, Christopher R; Butcher, Kenneth S; Davis, Stephen M; Donnan, Geoffrey A

    2012-06-01

    The mismatch lesion volumes defined by perfusion-weighted imaging exceeding diffusion-weighted imaging have been used as a marker of ischemic penumbral tissue. Defining the perfusion lesion by thresholding has shown promise as a practical tool; several positron emission tomography studies have indicated a more probabilistic relationship between perfusion and infarction. Here, we used a randomized controlled trial dataset of tissue-type plasminogen activator 3 to 6 hours after stroke to: (1) quantify the relationship between severity of hypoperfusion (measured by Tmax) and risk of infarction; (2) exploit this relationship to present a novel definition of mismatch based on infarct probabilities rather than dichotomies; and (3) examine the treatment response in the subgroup of patients with mismatch by the new definition. Patients from the Echoplanar Imaging Thrombolytic Evaluation Trial (EPITHET) were included. Baseline perfusion-weighted imaging and 90-day T2-weighted imaging were coregistered. Perfusion-weighted imaging lesion volumes were divided into 10 Tmax delay strata, and infarct risk was defined as the fraction of the tissue at a given Tmax strata that progressed to infarction by day 90. Sixty-two patients were studied. Infarct risk was an increasing function of Tmax for all subgroups, including the whole cohort. The probabilistic approach outperformed all Tmax thresholds, with exception of the Tmax ≥ 10 threshold, for which it was only favored by a trend. Infarct risk and treatment effect increased with severity of perfusion abnormalities. This suggests that a severity-weighted mismatch definition may define penumbral tissue more accurately.

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

    Science.gov (United States)

    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.

  1. A technique to measure wavenumber mismatch between quadratically interacting modes

    Energy Technology Data Exchange (ETDEWEB)

    Hajj, M.R. [Coll. of Engineering, Univ. of Texas, Austin, TX (United States); Davila, J.B. [Coll. of Engineering, Univ. of Texas, Austin, TX (United States); Miksad, R.W. [Coll. of Engineering, Univ. of Texas, Austin, TX (United States); Powers, E.J. [Coll. of Engineering, Univ. of Texas, Austin, TX (United States)

    1995-02-01

    Nonlinear energy cascade by means of three-wave resonant interactions is a characteristic feature of transitioning and turbulent flows. Resonant wavenumber mismatch between these interacting modes can arise from the dispersive characteristics of the interacting waves and from spectral broadening due to random effects. In this paper, a general technique is presented to estimate the average level of instantaneous wavenumber mismatch, left angle {Delta}k right angle = left angle k{sub m}-k{sub i}-k{sub j} right angle , between components whose frequencies obey the resonant selection condition, f{sub m}-f{sub i}-f{sub j}=0. Cross-correlation of the auto-bispectrum is used to quantify the level of mismatch. The concept of bispectrum coupling coherency is introduced to determine the confidence level in the wavenumber mismatch estimates. These techniques are then applied to measure wavenumber mismatch in the transitioning field of a plane wake. The results show that the average of the instantaneous mismatch between the actual interacting modes left angle k{sub m}-k{sub i}-k{sub j} right angle is in general not equal to the mismatch between the average wavenumbers of each interacting mode left angle k{sub m} right angle - left angle k{sub i} right angle - left angle k{sub j} right angle . (orig.)

  2. The Immunogenicity of HLA Class II Mismatches: The Predicted Presentation of Nonself Allo-HLA-Derived Peptide by the HLA-DR Phenotype of the Recipient Is Associated with the Formation of DSA.

    Science.gov (United States)

    Jucaud, Vadim

    2017-01-01

    The identification of permissible HLA class II mismatches can prevent DSA in mismatched transplantation. The HLA-DR phenotype of recipients contributes to DSA formation by presenting allo-HLA-derived peptides to T-helper cells, which induces the differentiation of B cells into plasma cells. Comparing the binding affinity of self and nonself allo-HLA-derived peptides for recipients' HLA class II antigens may distinguish immunogenic HLA mismatches from nonimmunogenic ones. The binding affinities of allo-HLA-derived peptides to recipients' HLA-DR and HLA-DQ antigens were predicted using the NetMHCIIpan 3.1 server. HLA class II mismatches were classified based on whether they induced DSA and whether self or nonself peptide was predicted to bind with highest affinity to recipients' HLA-DR and HLA-DQ. Other mismatch characteristics (eplet, hydrophobic, electrostatic, and amino acid mismatch scores and PIRCHE-II) were evaluated. A significant association occurred between DSA formation and the predicted HLA-DR presentation of nonself peptides (P = 0.0169; accuracy = 80%; sensitivity = 88%; specificity = 63%). In contrast, mismatch characteristics did not differ significantly between mismatches that induced DSA and the ones that did not, except for PIRCHE-II (P = 0.0094). This methodology predicts DSA formation based on HLA mismatches and recipients' HLA-DR phenotype and may identify permissible HLA mismatches to help optimize HLA matching and guide donor selection.

  3. The Immunogenicity of HLA Class II Mismatches: The Predicted Presentation of Nonself Allo-HLA-Derived Peptide by the HLA-DR Phenotype of the Recipient Is Associated with the Formation of DSA

    Science.gov (United States)

    2017-01-01

    The identification of permissible HLA class II mismatches can prevent DSA in mismatched transplantation. The HLA-DR phenotype of recipients contributes to DSA formation by presenting allo-HLA-derived peptides to T-helper cells, which induces the differentiation of B cells into plasma cells. Comparing the binding affinity of self and nonself allo-HLA-derived peptides for recipients' HLA class II antigens may distinguish immunogenic HLA mismatches from nonimmunogenic ones. The binding affinities of allo-HLA-derived peptides to recipients' HLA-DR and HLA-DQ antigens were predicted using the NetMHCIIpan 3.1 server. HLA class II mismatches were classified based on whether they induced DSA and whether self or nonself peptide was predicted to bind with highest affinity to recipients' HLA-DR and HLA-DQ. Other mismatch characteristics (eplet, hydrophobic, electrostatic, and amino acid mismatch scores and PIRCHE-II) were evaluated. A significant association occurred between DSA formation and the predicted HLA-DR presentation of nonself peptides (P = 0.0169; accuracy = 80%; sensitivity = 88%; specificity = 63%). In contrast, mismatch characteristics did not differ significantly between mismatches that induced DSA and the ones that did not, except for PIRCHE-II (P = 0.0094). This methodology predicts DSA formation based on HLA mismatches and recipients' HLA-DR phenotype and may identify permissible HLA mismatches to help optimize HLA matching and guide donor selection. PMID:28331856

  4. A systematic review of definitions and classification systems of adjacent segment pathology.

    Science.gov (United States)

    Kraemer, Paul; Fehlings, Michael G; Hashimoto, Robin; Lee, Michael J; Anderson, Paul A; Chapman, Jens R; Raich, Annie; Norvell, Daniel C

    2012-10-15

    Systematic review. To undertake a systematic review to determine how "adjacent segment degeneration," "adjacent segment disease," or clinical pathological processes that serve as surrogates for adjacent segment pathology are classified and defined in the peer-reviewed literature. Adjacent segment degeneration and adjacent segment disease are terms referring to degenerative changes known to occur after reconstructive spine surgery, most commonly at an immediately adjacent functional spinal unit. These can include disc degeneration, instability, spinal stenosis, facet degeneration, and deformity. The true incidence and clinical impact of degenerative changes at the adjacent segment is unclear because there is lack of a universally accepted classification system that rigorously addresses clinical and radiological issues. A systematic review of the English language literature was undertaken and articles were classified using the Grades of Recommendation Assessment, Development, and Evaluation criteria. RESULTS.: Seven classification systems of spinal degeneration, including degeneration at the adjacent segment, were identified. None have been evaluated for reliability or validity specific to patients with degeneration at the adjacent segment. The ways in which terms related to adjacent segment "degeneration" or "disease" are defined in the peer-reviewed literature are highly variable. On the basis of the systematic review presented in this article, no formal classification system for either cervical or thoracolumbar adjacent segment disorders currently exists. No recommendations regarding the use of current classification of degeneration at any segments can be made based on the available literature. A new comprehensive definition for adjacent segment pathology (ASP, the now preferred terminology) has been proposed in this Focus Issue, which reflects the diverse pathology observed at functional spinal units adjacent to previous spinal reconstruction and balances

  5. Mismatch-Shaping Serial Digital-to-Analog Converter

    DEFF Research Database (Denmark)

    Steensgaard-Madsen, Jesper; Moon, Un-Ku; Temes, Gabor C.

    1999-01-01

    A simple but accurate pseudo-passive mismatch-shaping D/A converter is described. A digital state machine is used to control the switching sequence of a symmetric two-capacitor network that performs the D/A conversion. The error caused by capacitor mismatch is uncorrelated with the input signal a...... and has only little power in the signal band. The system has been simulated assuming a 0.1% capacitor mismatch, and the achieved SNDR performance was 100 dB for an oversampling ratio of 7....

  6. Adjacent tooth trauma in complicated mandibular third molar surgery: Risk degree classification and digital surgical simulation.

    Science.gov (United States)

    Ye, Zhou-Xi; Yang, Chi; Ge, Jing

    2016-12-15

    Analysis of adjacent tooth resistance is essential in wisdom teeth extraction to prevent adjacent tooth trauma, however it lacks adequate attention nowadays. This study aims at suggesting special extraction methods based on adjacent tooth resistance analysis for prevention of adjacent tooth damage. In this study, 136 complicated mandibular third molars extracted using piezosurgery were reviewed and classified based on the adjacent teeth resistances shown in orthopantomogram (OPG) during their mesio-distal rotations: degree I refers to teeth with no adjacent teeth resistance; degree II refers to teeth with resistance released after mesial-half crown sectioning; degree III refers to teeth which still had resistance after mesial-half crown sectioning. With the use of surgical simulations using cone beam computerized tomography (CBCT) reconstruction, all teeth in degree I were designed to rotate mesio-distally; 86.36%(38/44) teeth in degree II were designed to rotate mesio-distally after mesio-half crown sectioning; 69.09%(36/55) teeth in degree III were designed to rotate bucco-lingually. All teeth were extracted successfully, and only one adjacent tooth was subluxated due to the incomplete bone removal. Our study suggested that in order to prevent adjacent teeth trauma, complete bone removal is of importance, and impacted teeth with higher adjacent teeth trauma risks should consider bucco-lingual rotations.

  7. Development of improved connection details for adjacent prestressed member bridges.

    Science.gov (United States)

    2017-06-01

    Adjacent prestressed member girder bridges are economical systems for short spans and generally come in two types: adjacent box beam bridges and adjacent voided slab bridges. Each type provides the advantages of having low clearances because of their...

  8. Understanding the Consequences of Property Rights Mismatches: a Case Study of New Zealand's Marine Resources

    Directory of Open Access Journals (Sweden)

    Tracy Yandle

    2007-12-01

    Full Text Available Within fisheries and natural resource management literature, there is considerable discussion about the key roles that property rights can play in building biologically and socially sustainable resource management regimes. A key point of agreement is that secure long-term property rights provide an incentive for resource users to manage the resource sustainably. However, property rights mismatches create ambiguity and conflict in resource use. Though the term mismatches is usually associated with problems in matching temporal and spatial resource characteristics with institutional characteristics, I expand it here to include problems that can arise when property rights are incompletely defined or incompletely distributed. Property rights mismatches are particularly likely to occur over marine resources, for which multiple types of resource and resource user can be engaged and managed under a variety of regulatory regimes. I used New Zealand's marine resources to examine the causes and consequences of these property rights mismatches. New Zealand is particularly interesting because its property-rights-based commercial fishing regime, in the form of individual transferable quotas, has attracted considerable positive attention. However, my review of the marine natural resource management regime from a broader property rights perspective highlights a series of problems caused by property rights mismatches, including competition for resources among commercial, customary, and recreational fishers; spatial conflict among many marine resource users; and conflicting incentives and objectives for the management of resources over time. The use of a property rights perspective also highlights some potential solutions such as the layering of institutional arrangements and the improvement of how property rights are defined to encourage long-term sustainability.

  9. Association between CTL precursor frequency to HLA-C mismatches and HLA-C antigen cell surface expression

    Directory of Open Access Journals (Sweden)

    Moshe eIsraeli

    2014-10-01

    Full Text Available Previous studies showed the relevance of the cytotoxic T cell precursor frequency assay (CTLp for prediction of the outcome of HLA mismatched hematopoietic cell transplantation (HCT. Recently it has been shown that HLA-C cell surface expression is correlated with virus specific cytotoxic T cell responses and viremia control in HIV patients.The aim of the current study was to investigate the association between HLA-C antigen expression and the CTLp frequency to the mismatched HLA-C antigen.In total 115 recipient–donor pairs, for whom a successful CTLp assay was performed, were evaluated for this pilot study. All donor-recipient pairs were matched at 9/10 alleles with a single mismatch at the HLA-C locus. Antigen expression level of the mismatched HLA-C allele for each recipient and donor was based on the MFI values as described by Apps et al (Science, 2013.The cell surface expression of recipient’s mismatched HLA-C antigen was significantly lower among CTLp negative (n=59 compared to CTLp positive (n=56 pairs (154 and 193 MFI units, respectively; p=0.0031. This difference was more pronounced in donor-recipient pairs that were mismatched for amino-acid residue-116 located in the groove of the HLA-C antigen, suggesting the importance of peptide binding in the allo-recognition. Furthermore, in the particular case of low expression of the recipient mismatched HLA-C antigen (MFI<115, CTLp reactivity depended on HLA-C expression level in the donor; the median MFI of donor’s mismatched HLA-C antigen was 114 in CTLp negative cases (n=26, while in CTLp positive cases (n=15 the median MFI of donor’s HLA-C antigen was 193. (P=0.0093.We conclude that the expression level of the donor and recipient mismatched HLA-C antigens affect CTLp outcome. HLA-C antigen expression levels in combination with the CTLp assay may prove useful for the prediction of the clinical outcome of HLA-C mismatched HCT.

  10. lower oluwa river and adjacent floodplains

    African Journals Online (AJOL)

    2005-02-23

    Feb 23, 2005 ... Abstract. The ecology of sympatric African bony tongue fish, Heterotis niloticus and the catfish, Clarias gariepinus were compared during the dry and rainy conditions in the lower Oluwa River and its adjacent floodplains. Both ..... trade amounting to over N15 million in the coastal detritus materials for growth.

  11. User image mismatch in anaesthesia alarms: a cognitive systems analysis.

    Science.gov (United States)

    Raymer, Karen E; Bergström, Johan

    2013-01-01

    In this study, principles of Cognitive Systems Engineering are used to better understand the human-machine interaction manifesting in the use of anaesthesia alarms. The hypothesis is that the design of the machine incorporates built-in assumptions of the user that are discrepant with the anaesthesiologist's self-assessment, creating 'user image mismatch'. Mismatch was interpreted by focusing on the 'user image' as described from the perspectives of both machine and user. The machine-embedded image was interpreted through document analysis. The user-described image was interpreted through user (anaesthesiologist) interviews. Finally, an analysis was conducted in which the machine-embedded and user-described images were contrasted to identify user image mismatch. It is concluded that analysing user image mismatch expands the focus of attention towards macro-elements in the interaction between man and machine. User image mismatch is interpreted to arise from complexity of algorithm design and incongruity between alarm design and tenets of anaesthesia practice. Cognitive system engineering principles are applied to enhance the understanding of the interaction between anaesthesiologist and alarm. The 'user image' is interpreted and contrasted from the perspectives of machine as well as the user. Apparent machine-user mismatch is explored pertaining to specific design features.

  12. Mismatch Repair Deficiency and Response to Immune Checkpoint Blockade

    Science.gov (United States)

    Lee, Valerie; Murphy, Adrian; Le, Dung T.

    2016-01-01

    More than 1.6 million new cases of cancer will be diagnosed in the U.S. in 2016, resulting in more than 500,000 deaths. Although chemotherapy has been the mainstay of treatment in advanced cancers, immunotherapy development, particularly with PD-1 inhibitors, has changed the face of treatment for a number of tumor types. One example is the subset of tumors characterized by mismatch repair deficiency and microsatellite instability that are highly sensitive to PD-1 blockade. Hereditary forms of cancer have been noted for more than a century, but the molecular changes underlying mismatch repair-deficient tumors and subsequent microsatellite unstable tumors was not known until the early 1990s. In this review article, we discuss the history and pathophysiology of mismatch repair, the process of testing for mismatch repair deficiency and microsatellite instability, and the role of immunotherapy in this subset of cancers. Implications for Practice: Mismatch repair deficiency has contributed to our understanding of carcinogenesis for the past 2 decades and now identifies a subgroup of traditionally chemotherapy-insensitive solid tumors as sensitive to PD-1 blockade. This article seeks to educate oncologists regarding the nature of mismatch repair deficiency, its impact in multiple tumor types, and its implications for predicting the responsiveness of solid tumors to immune checkpoint blockade. PMID:27412392

  13. Dynamics of MutS-mismatched DNA complexes are predictive of their repair phenotypes.

    Science.gov (United States)

    DeRocco, Vanessa C; Sass, Lauryn E; Qiu, Ruoyi; Weninger, Keith R; Erie, Dorothy A

    2014-04-01

    MutS recognizes base-base mismatches and base insertions/deletions (IDLs) in newly replicated DNA. Specific interactions between MutS and these errors trigger a cascade of protein-protein interactions that ultimately lead to their repair. The inability to explain why different DNA errors are repaired with widely varying efficiencies in vivo remains an outstanding example of our limited knowledge of this process. Here, we present single-molecule Förster resonance energy transfer measurements of the DNA bending dynamics induced by Thermus aquaticus MutS and the E41A mutant of MutS, which is known to have error specific deficiencies in signaling repair. We compared three DNA mismatches/IDLs (T-bulge, GT, and CC) with repair efficiencies ranging from high to low. We identify three dominant DNA bending states [slightly bent/unbent (U), intermediately bent (I), and significantly bent (B)] and find that the kinetics of interconverting among states varies widely for different complexes. The increased stability of MutS-mismatch/IDL complexes is associated with stabilization of U and lowering of the B to U transition barrier. Destabilization of U is always accompanied by a destabilization of B, supporting the suggestion that B is a "required" precursor to U. Comparison of MutS and MutS-E41A dynamics on GT and the T-bulge suggests that hydrogen bonding to MutS facilitates the changes in base-base hydrogen bonding that are required to achieve the U state, which has been implicated in repair signaling. Taken together with repair propensities, our data suggest that the bending kinetics of MutS-mismatched DNA complexes may control the entry into functional pathways for downstream signaling of repair.

  14. Association Between IHC and MSI Testing to Identify Mismatch Repair–Deficient Patients with Ovarian Cancer

    OpenAIRE

    Lee, Ji-Hyun; Cragun, Deborah; Thompson, Zachary; Coppola, Domenico; Nicosia, Santo V.; Akbari, Mohammad; Zhang, Shiyu; McLaughlin, John; Narod, Steven; Schildkraut, Joellen; Sellers, Thomas A.; Pal, Tuya

    2014-01-01

    Objective: In epithelial ovarian cancer, concordance between results of microsatellite instability (MSI) and immunohistochemical (IHC) testing has not been demonstrated. This study evaluated the association of MSI-high (MSI-H) status with loss of expression (LoE) of mismatch repair (MMR) proteins on IHC and assessed for potential factors affecting the strength of the association. Methods: Tumor specimens from three population-based studies of epithelial ovarian cancer were stained for MMR pro...

  15. [Characteristics and Outcomes of Treatment in Patients with Stage IV Colorectal Cancer with Mismatch Repair Deficiency].

    Science.gov (United States)

    Ishibashi, Keiichiro; Chika, Noriyasu; Suzuki, Okihide; Ito, Tetsuya; Amano, Kunihiko; Kumamoto, Kensuke; Fukuchi, Minoru; Kumagai, Youichi; Mochiki, Erito; Ishida, Hideyuki

    2016-11-01

    Mismatch repair(MMR)protein deficiency in colorectal cancer is well correlated with high-level microsatellite instability (MSI-H). There are little data on mismatch repair deficiency(dMMR)colorectal cancers in Japan. In addition, we have no available data on the therapeutic efficacy of oxaliplatin(oxa)-based chemotherapy, one of the standard treatment regimens for metastatic colorectal cancer, for patients with dMMR colorectal cancer. The subjects were 254 patients with Stage IV colorectal cancer whose tumors were immunohistochemically stained for MMR proteins, MLH1, MSH2, MSH6, and PMS2. Patients who underwent R0 resection were excluded. Clinicopathologic factors and the efficacy of oxa-based chemotherapy were compared between patients with dMMR colorectal cancer and those with mismatch repair proficient(pMMR)colorectal cancer. There were 7(2.8%)patients with dMMR. Four patients demonstrated both MLH1 and PMS2 loss, while 3 patients demonstrated both MSH2 and MSH6 loss. Though the dMMR had a higher frequency in female patients(p=0.02) and a lower frequency in those with liver metastasis(pcolorectal cancers was lower than those(4-11%)reported in Western countries. Therefore, the clinical significance of universal screeningfor dMMR in all colorectal cancer samples may not be valid. Concerningsurvival benefit, oxa-based chemotherapy seems to be an effective alternative in clinical practice for metastatic colorectal cancer patients with dMMR.

  16. Synergism of Dam, MutH, and MutS in methylation-directed mismatch repair in Escherichia coli.

    Science.gov (United States)

    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. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Vibration reduces thermal pain in adjacent dermatomes.

    Science.gov (United States)

    Yarnitsky, D; Kunin, M; Brik, R; Sprecher, E

    1997-01-01

    Spatial summation of thermal pain crosses dermatomal boundaries. In this study we examined whether a vibrational stimulus applied to adjacent or remote dermatomes affects thermal pain perception to the volar forearm. Contact heat at 2 degrees C above thermal pain threshold was applied, and a Visual Analog Scale (VAS) was used for pain assessment. We found a significant decrease in mean VAS rating when simultaneous vibratory stimuli were given to the dermatome adjacent to that receiving thermal stimulation, or to the same dermatome on the contralateral side. There was no change in VAS rating when vibration was given two or more dermatomes away. Vibration within the same dermatome also did not yield a significant change in VAS rating, possibly due to difficulty in magnitude assessment of stimuli given simultaneously within a single dermatome. The finding that vibration can reduce pain across dermatomes may allow for more flexible design of stimulation therapy for pain.

  18. Parametric Adaptive Radar Detector with Enhanced Mismatched Signals Rejection Capabilities

    Directory of Open Access Journals (Sweden)

    Liu Bin

    2010-01-01

    Full Text Available We consider the problem of adaptive signal detection in the presence of Gaussian noise with unknown covariance matrix. We propose a parametric radar detector by introducing a design parameter to trade off the target sensitivity with sidelobes energy rejection. The resulting detector merges the statistics of Kelly's GLRT and of the Rao test and so covers Kelly's GLRT and the Rao test as special cases. Both invariance properties and constant false alarm rate (CFAR behavior for this detector are studied. At the analysis stage, the performance of the new receiver is assessed and compared with several traditional adaptive detectors. The results highlight better rejection capabilities of this proposed detector for mismatched signals. Further, we develop two two-stage detectors, one of which consists of an adaptive matched filter (AMF followed by the aforementioned detector, and the other is obtained by cascading a GLRT-based Subspace Detector (SD and the proposed adaptive detector. We show that the former two-stage detector outperforms traditional two-stage detectors in terms of selectivity, and the latter yields more robustness.

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

    Science.gov (United States)

    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

  20. Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR

    Directory of Open Access Journals (Sweden)

    Seiki Kuramitsu

    2013-03-01

    Full Text Available Polymerase chain reaction (PCR-related technologies are hampered mainly by two types of error: nonspecific amplification and DNA polymerase-generated mutations. Here, we report that both errors can be suppressed by the addition of a DNA mismatch-recognizing protein, MutS, from a thermophilic bacterium. Although it had been expected that MutS has a potential to suppress polymerase-generated mutations, we unexpectedly found that it also reduced nonspecific amplification. On the basis of this finding, we propose that MutS binds a mismatched primer-template complex, thereby preventing the approach of DNA polymerase to the 3' end of the primer. Our simple methodology improves the efficiency and accuracy of DNA amplification and should therefore benefit various PCR-based applications, ranging from basic biological research to applied medical science.

  1. Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids

    DEFF Research Database (Denmark)

    Fontenete, Sílvia; Joana, Barros; Pedro, Madureira

    2015-01-01

    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...

  2. Direct Mismatch Characterization of femto-Farad Capacitors

    KAUST Repository

    Omran, Hesham

    2015-08-17

    Reducing the capacitance of programmable capacitor arrays, commonly used in analog integrated circuits, is necessary for low-energy applications. However, limited mismatch data is available for small capacitors. We report mismatch measurement for a 2fF poly-insulator-poly (PIP) capacitor, which is the smallest reported PIP capacitor to the best of the authors’ knowledge. Instead of using complicated custom onchip circuitry, direct mismatch measurement is demonstrated and verified using Monte Carlo Simulations and experimental measurements. Capacitive test structures composed of 9 bit programmable capacitor arrays (PCAs) are implemented in a low-cost 0:35m CMOS process. Measured data is compared to mismatch of large PIP capacitors, theoretical models, and recently published data. Measurement results indicate an estimated average relative standard deviation of 0.43% for the 2fF unit capacitor, which is better than the reported mismatch of metal-oxide-metal (MOM) fringing capacitors implemented in an advanced 32nm CMOS process.

  3. HLA Mismatching Strategies for Solid Organ Transplantation - a Balancing Act

    Directory of Open Access Journals (Sweden)

    Andrea A. Zachary

    2016-12-01

    Full Text Available 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. Further, 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.

  4. Baseband I/Q regeneration Method for Direct Conversion Receiver to nullify effect of I/Q mismatch

    Directory of Open Access Journals (Sweden)

    M. Shah

    2016-11-01

    Full Text Available Direct Conversion Receiver is the choice of the today’s designer for low power compact wireless receiver. DCR is attractive due to low power, small size and highly monolithic integratable structure, but distortions affect its performance.  I/Q mismatch is the one of the major distortion which is responsible for performance degradation.  In this paper, a novel method for Direct Conversion Receiver is suggested, which makes it insensitive to the I/Q mismatch. Here the classical homodyne architecture is modified to nullify effect of I/Q mismatch. The proposed method can be implemented in the Digital Signal Processing (DSP back-end section also.  This feature makes it acceptable in the already designed/functioning classical homodyne architecture based receiver.

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

    Science.gov (United States)

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Applying different equations to evaluate the level of mismatch between students and school furniture.

    Science.gov (United States)

    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. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  7. Mismatch repair and treatment resistance in ovarian cancer

    Directory of Open Access Journals (Sweden)

    van der Burg Maria EL

    2006-07-01

    Full Text Available Abstract Background The treatment of ovarian cancer is hindered by intrinsic or acquired resistance to platinum-based chemotherapy. The aim of this study is to determine the frequency of mismatch repair (MMR inactivation in ovarian cancer and its association with resistance to platinum-based chemotherapy. Methods We determined, microsatellite instability (MSI as a marker for MMR inactivation (analysis of BAT25 and BAT26, MLH1 promoter methylation status (methylation specific PCR on bisulfite treated DNA and mRNA expression of MLH1, MSH2, MSH3, MSH6 and PMS2 (quantitative RT-PCR in 75 ovarian carcinomas and eight ovarian cancer cell lines Results MSI was detected in three of the eight cell lines i.e. A2780 (no MLH1 mRNA expression due to promoter methylation, SKOV3 (no MLH1 mRNA expression and 2774 (no altered expression of MMR genes. Overall, there was no association between cisplatin response and MMR status in these eight cell lines. Seven of the 75 ovarian carcinomas showed MLH1 promoter methylation, however, none of these showed MSI. Forty-six of these patients received platinum-based chemotherapy (11 non-responders, 34 responders, one unknown response. The resistance seen in the eleven non-responders was not related to MSI and therefore also not to MMR inactivation. Conclusion No MMR inactivation was detected in 75 ovarian carcinoma specimens and no association was seen between MMR inactivation and resistance in the ovarian cancer cell lines as well as the ovarian carcinomas. In the discussion, the results were compared to that of twenty similar studies in the literature including in total 1315 ovarian cancer patients. Although no association between response and MMR status was seen in the primary tumor the possible role of MMR inactivation in acquired resistance deserves further investigation.

  8. Hydrophobic mismatch triggering texture defects in membrane gel domains

    DEFF Research Database (Denmark)

    Dreier, J.; Brewer, J.R.; Simonsen, Adam Cohen

    2013-01-01

    The orientational texture of gel-phase lipid bilayers is a phenomenon that can structure membrane domains. Using two-photon polarized fluorescence microscopy and image analysis, we map the lateral variation of the lipid orientation (the texture) in single domains. With this method, we uncover...... a lipid-induced transition between vortex and uniform textures in binary phospholipid bilayers. By tuning the lipid composition, the hydrophobic mismatch at the domain boundary can be varied systematically as monitored by AFM. Low hydrophobic mismatch correlates with domains having uniform texture, while...... higher mismatch values correlate with a vortex-type texture. The defect pattern created during early growth persists in larger domains, and a minimal model incorporating the anisotropic line tension and the vortex energy can rationalize this finding. The results suggest that the lipid composition...

  9. Bilayer thickness mismatch controls domain size in biomimetic membranes

    Science.gov (United States)

    Heberle, Frederick A.; Petruzielo, Robin S.; Pan, Jianjun; Drazba, Paul; Kučerka, Norbert; Standaert, Robert F.; Feigenson, Gerald W.; Katsara, John

    2013-03-01

    In order to promote functionality, cells may alter the spatial organization of membrane lipids and proteins, including separation of liquid phases into distinct domains. In model membranes, domain size and morphology depend strongly on composition and temperature, but the physicochemical mechanisms controlling them are poorly understood. Theoretical work suggests a role for interfacial energy at domain boundaries, which may be driven in part by thickness mismatch between a domain and its surrounding bilayer. However, no direct evidence linking thickness mismatch to domain size in free-standing bilayers has been reported. We describe the use of Small Angle Neutron Scattering (SANS) to detect domains in simplified lipid-only models that mimic the composition of plasma membrane. We find that domain size is controlled by the degree of acyl chain unsaturation of low-melting temperature lipids, and that this size transition is correlated to changes in the thickness mismatch between coexisting liquid phases.

  10. A Statistic-Based Calibration Method for TIADC System

    Directory of Open Access Journals (Sweden)

    Kuojun Yang

    2015-01-01

    Full Text Available Time-interleaved technique is widely used to increase the sampling rate of analog-to-digital converter (ADC. However, the channel mismatches degrade the performance of time-interleaved ADC (TIADC. Therefore, a statistic-based calibration method for TIADC is proposed in this paper. The average value of sampling points is utilized to calculate offset error, and the summation of sampling points is used to calculate gain error. After offset and gain error are obtained, they are calibrated by offset and gain adjustment elements in ADC. Timing skew is calibrated by an iterative method. The product of sampling points of two adjacent subchannels is used as a metric for calibration. The proposed method is employed to calibrate mismatches in a four-channel 5 GS/s TIADC system. Simulation results show that the proposed method can estimate mismatches accurately in a wide frequency range. It is also proved that an accurate estimation can be obtained even if the signal noise ratio (SNR of input signal is 20 dB. Furthermore, the results obtained from a real four-channel 5 GS/s TIADC system demonstrate the effectiveness of the proposed method. We can see that the spectra spurs due to mismatches have been effectively eliminated after calibration.

  11. Mismatch repair genes in Lynch syndrome: a review

    OpenAIRE

    Silva,Felipe Cavalcanti Carneiro da; Valentin, Mev Dominguez; Ferreira, Fábio de Oliveira; Carraro, Dirce Maria; Rossi, Benedito Mauro

    2009-01-01

    Lynch syndrome represents 1-7% of all cases of colorectal cancer and is an autosomal-dominant inherited cancer predisposition syndrome caused by germline mutations in deoxyribonucleic acid (DNA) mismatch repair genes. Since the discovery of the major human genes with DNA mismatch repair function, mutations in five of them have been correlated with susceptibility to Lynch syndrome: mutS homolog 2 (MSH2); mutL homolog 1 (MLH1); mutS homolog 6 (MSH6); postmeiotic segregation increased 2 (PMS2); ...

  12. Advanced radar detection schemes under mismatched signal models

    CERN Document Server

    Bandiera, Francesco

    2009-01-01

    Adaptive detection of signals embedded in correlated Gaussian noise has been an active field of research in the last decades. This topic is important in many areas of signal processing such as, just to give some examples, radar, sonar, communications, and hyperspectral imaging. Most of the existing adaptive algorithms have been designed following the lead of the derivation of Kelly's detector which assumes perfect knowledge of the target steering vector. However, in realistic scenarios, mismatches are likely to occur due to both environmental and instrumental factors. When a mismatched signal

  13. Interobserver variability in the evaluation of mismatch repair protein immunostaining

    DEFF Research Database (Denmark)

    Klarskov, Louise Laurberg; Ladelund, Steen; Holck, Susanne

    2010-01-01

    Immunohistochemical staining for mismatch repair proteins has during recent years been established as a routine analysis in many pathology laboratories with the aim to identify tumors linked to the hereditary nonpolyposis colorectal cancer syndrome. Despite widespread application, data...... in hereditary nonpolyposis colorectal cancer, the interobserver variability identified highlights the need for quality assessment programs, including guidelines for classification of different expression patterns....... on reliability are lacking. We therefore evaluated interobserver variability among 6 pathologists, 3 experienced gastrointestinal pathologists and 3 residents. In total, 225 immunohistochemically stained colorectal cancers were evaluated as having normal, weak, loss of, or nonevaluable mismatch repair protein...

  14. Visual mismatch negativity in the dorsal stream is independent of concurrent visual task difficulty

    Directory of Open Access Journals (Sweden)

    Jan eKremlacek

    2013-07-01

    Full Text Available The manipulation of attention can produce mismatch negativity-like components that are not necessarily connected to the unintentional sensory registration of the violation of probability-based regularity. For clinical purposes, attentional bias should be quantified because it can vary substantially among subjects and can decrease the specificity of the examination. This experiment targets the role of attention in the generation of visual mismatch negativity (vMMN.The visual regularity generated by a sequence of two radial motions while subjects focused on visual tasks in the central part of the display. Attentional load was systematically varied and had three levels, no-load, easy, and difficult. Rare deviant and frequent standard motions were presented with a 10/60 ratio in oddball sequences.Data from 12 subjects was recorded from 64 channels and processed. vMMN was identified within the interval of 142-198 ms. The mean amplitude was evaluated during the aforementioned interval in the parietal and fronto-central regions. A general linear model for repeated measures was applied to the mean amplitude with a three-factor design and showed a significant difference (F(1,11 = 17.40, p = 0.002 between standard and deviant stimuli and between regions (F(1,11 = 8.40, p = 0.01; however, no significant effect of the task (F(2,22 = 1.26, p = 0.30 was observed. The unintentional detection of irregularity during the processing of the visual motion was independent of the attentional load associated with handling the central visual task.The experiment did not demonstrate an effect of attentional load manipulation on mismatch negativity induced by the motion-sequence, which supports the clinical utility of this examination. However, used stimulation paradigm should be further optimized to generate mismatch negativity that is stable enough to be usable not only for group comparisons but also for a single subject assessment.

  15. Variants of sequence family B Thermococcus kodakaraensis DNA polymerase with increased mismatch extension selectivity.

    Directory of Open Access Journals (Sweden)

    Claudia Huber

    Full Text Available Fidelity and selectivity of DNA polymerases are critical determinants for the biology of life, as well as important tools for biotechnological applications. DNA polymerases catalyze the formation of DNA strands by adding deoxynucleotides to a primer, which is complementarily bound to a template. To ensure the integrity of the genome, DNA polymerases select the correct nucleotide and further extend the nascent DNA strand. Thus, DNA polymerase fidelity is pivotal for ensuring that cells can replicate their genome with minimal error. DNA polymerases are, however, further optimized for more specific biotechnological or diagnostic applications. Here we report on the semi-rational design of mutant libraries derived by saturation mutagenesis at single sites of a 3'-5'-exonuclease deficient variant of Thermococcus kodakaraensis DNA polymerase (KOD pol and the discovery for variants with enhanced mismatch extension selectivity by screening. Sites of potential interest for saturation mutagenesis were selected by their proximity to primer or template strands. The resulting libraries were screened via quantitative real-time PCR. We identified three variants with single amino acid exchanges-R501C, R606Q, and R606W-which exhibited increased mismatch extension selectivity. These variants were further characterized towards their potential in mismatch discrimination. Additionally, the identified enzymes were also able to differentiate between cytosine and 5-methylcytosine. Our results demonstrate the potential in characterizing and developing DNA polymerases for specific PCR based applications in DNA biotechnology and diagnostics.

  16. Clinical characteristics of unknown symptom onset stroke patients with and without diffusion-weighted imaging and fluid-attenuated inversion recovery mismatch

    DEFF Research Database (Denmark)

    Thomalla, Götz; Boutitie, Florent; Fiebach, Jochen B.

    2018-01-01

    Background Diffusion-weighted imaging (DWI) and fluid-attenuated inversion recovery (FLAIR) mismatch was suggested to identify stroke patients with unknown time of symptom onset likely to be within the time window for thrombolysis. Aims We aimed to study clinical characteristics associated with DWI......-FLAIR mismatch in patients with unknown onset stroke. Methods We analyzed baseline MRI and clinical data from patients with acute ischemic stroke proven by DWI from WAKE-UP, an investigator-initiated, randomized, placebo-controlled trial of MRI-based thrombolysis in stroke patients with unknown time of symptom...... symptom onset stroke patients with and without DWI-FLAIR mismatch. DWI-FLAIR mismatch as an indicator of stroke onset within 4.5 h shows no relevant association with commonly collected clinical characteristics of stroke patients. Clinical Trial Registration URL: http://www.clinicaltrials.gov . Unique...

  17. Cross-scale feedbacks and scale mismatches as influences on cultural services and the resilience of protected areas.

    Science.gov (United States)

    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

  18. Log-layer mismatch and modeling of the fluctuating wall stress in wall-modeled large-eddy simulations

    Science.gov (United States)

    Yang, Xiang I. A.; Park, George Ilhwan; Moin, Parviz

    2017-10-01

    Log-layer mismatch refers to a chronic problem found in wall-modeled large-eddy simulation (WMLES) or detached-eddy simulation, where the modeled wall-shear stress deviates from the true one by approximately 15 % . Many efforts have been made to resolve this mismatch. The often-used fixes, which are generally ad hoc, include modifying subgrid-scale stress models, adding a stochastic forcing, and moving the LES-wall-model matching location away from the wall. An analysis motivated by the integral wall-model formalism suggests that log-layer mismatch is resolved by the built-in physics-based temporal filtering. In this work we investigate in detail the effects of local filtering on log-layer mismatch. We show that both local temporal filtering and local wall-parallel filtering resolve log-layer mismatch without moving the LES-wall-model matching location away from the wall. Additionally, we look into the momentum balance in the near-wall region to provide an alternative explanation of how LLM occurs, which does not necessarily rely on the numerical-error argument. While filtering resolves log-layer mismatch, the quality of the wall-shear stress fluctuations predicted by WMLES does not improve with our remedy. The wall-shear stress fluctuations are highly underpredicted due to the implied use of LES filtering. However, good agreement can be found when the WMLES data are compared to the direct numerical simulation data filtered at the corresponding WMLES resolutions.

  19. Auditory processing in autism spectrum disorder : Mismatch negativity deficits

    NARCIS (Netherlands)

    Vlaskamp, Chantal|info:eu-repo/dai/nl/413985679; Oranje, Bob|info:eu-repo/dai/nl/217177409; Madsen, Gitte Falcher; Møllegaard Jepsen, Jens Richardt; Durston, Sarah|info:eu-repo/dai/nl/243083912; Cantio, Cathriona; Glenthøj, Birte; Bilenberg, Niels

    2017-01-01

    Children with autism spectrum disorders (ASD) often show changes in (automatic) auditory processing. Electrophysiology provides a method to study auditory processing, by investigating event-related potentials such as mismatch negativity (MMN) and P3a-amplitude. However, findings on MMN in autism are

  20. Mismatch-shaping switching for two-capacitor DAC

    DEFF Research Database (Denmark)

    Steensgaard-Madsen, Jesper; Moon, U.; Temes, G.C.

    1998-01-01

    A mismatch-shaping scheme is proposed for a two-capacitor digital-to-analogue converter (DAC). It uses a delta-sigma loop for finding the optimal switching sequence for each input word. Simulations indicate that the scheme can be used for the realisation of DACs with 16 bit linearity and SNR...

  1. Mismatch repair proficiency is not required for radioenhancement by gemcitabine

    NARCIS (Netherlands)

    van Bree, Chris; Rodermond, Hans M.; de Vos, Judith; Haveman, Jaap; Franken, Nicolaas A. P.

    2005-01-01

    Purpose: Mismatch repair (MMR) proficiency has been reported to either increase or decrease radioenhancement by 24-h incubations with gemcitabine. This study aimed to establish the importance of MMR for radioenhancement by gemcitabine after short-exposure, high-dose treatment and long-exposure,

  2. Pathological assessment of mismatch repair gene variants in Lynch syndrome

    DEFF Research Database (Denmark)

    Rasmussen, Lene Juel; Heinen, Christopher D; Royer-Pokora, Brigitte

    2012-01-01

    Lynch syndrome (LS) is caused by germline mutations in DNA mismatch repair (MMR) genes and is the most prevalent hereditary colorectal cancer syndrome. A significant proportion of variants identified in MMR and other common cancer susceptibility genes are missense or noncoding changes whose conse...

  3. DNA mismatch repair: Dr. Jekyll and Mr. Hyde?

    Science.gov (United States)

    Hsieh, Peggy

    2012-09-14

    In this issue, Peña-Diaz et al. (2012) describe a pathway for somatic mutation in nonlymphoid cells termed noncanonical DNA mismatch repair, whereby the error-prone translesion polymerase Pol-η substitutes for high-fidelity replicative polymerases to resynthesize excised regions opposite DNA damage. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Closed-form mismatched filter synthesis for complementary range response

    Science.gov (United States)

    Bell, Thomas

    2017-04-01

    The combined response of a pair of complementary waveforms has zero range sidelobes and could significantly improve synthetic aperture radar (SAR) image quality by reducing multiplicative noise. However, complementary waveforms may not be practical for SAR imaging for reasons such as Doppler tolerance and unimodular waveform constraints. By using mismatched filters to achieve either a complementary or near-complementary response, two or more practical waveforms could be employed and SAR image quality improved. A closed-form approach was developed that calculates mismatched filters so that the coherent sum of the range responses from each waveform and its corresponding mismatched filter is complementary. A second approach reduced sidelobes while retaining a frequency response close to the waveforms' frequency responses. Images processed using X-band radar data collected under the Air Force Gotcha program exhibited improvements in image quality over those processed using matched filters. The closed-form approach is presented for both complementary and reduced-sidelobe mismatched filters and image quality is quantified. The approach developed in this work offers improved image quality, is suitable for near real-time operation, and is independent of the waveforms.

  5. Conformations of MutS in DNA mismatch repair

    NARCIS (Netherlands)

    F.S. Groothuizen (Flora)

    2015-01-01

    markdownabstract__Abstract__ Prior to cell division, the DNA containing the genetic information of a cell has to be copied. During this process, errors are sometimes incorporated (so-called mismatches), which may cause genetic abnormalities in future cells. To prevent this, cells contain a DNA

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

    Science.gov (United States)

    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…

  7. A possible mechanism for exonuclease 1-independent eukaryotic mismatch repair

    Science.gov (United States)

    Kadyrov, Farid A.; Genschel, Jochen; Fang, Yanan; Penland, Elisabeth; Edelmann, Winfried; Modrich, Paul

    2009-01-01

    Mismatch repair contributes to genetic stability, and inactivation of the mammalian pathway leads to tumor development. Mismatch correction occurs by an excision-repair mechanism and has been shown to depend on the 5′ to 3′ hydrolytic activity exonuclease 1 (Exo1) in eukaryotic cells. However, genetic and biochemical studies have indicated that one or more Exo1-independent modes of mismatch repair also exist. We have analyzed repair of nicked circular heteroduplex DNA in extracts of Exo1-deficient mouse embryo fibroblast cells. Exo1-independent repair under these conditions is MutLα-dependent and requires functional integrity of the MutLα endonuclease metal-binding motif. In contrast to the Exo1-dependent reaction, we have been unable to detect a gapped excision intermediate in Exo1-deficient extracts when repair DNA synthesis is blocked. A possible explanation for this finding has been provided by analysis of a purified system comprised of MutSα, MutLα, replication factor C, proliferating cell nuclear antigen, replication protein A, and DNA polymerase δ that supports Exo1-independent repair in vitro. Repair in this system depends on MutLα incision of the nicked heteroduplex strand and dNTP-dependent synthesis-driven displacement of a DNA segment spanning the mismatch. Such a mechanism may account, at least in part, for the Exo1-independent repair that occurs in eukaryotic cells, and hence the modest cancer predisposition of Exo1-deficient mammalian cells. PMID:19420220

  8. Channel normalization technique for speech recognition in mismatched conditions

    CSIR Research Space (South Africa)

    Kleynhans, N

    2008-11-01

    Full Text Available , where one wishes to use any available training data for a variety of purposes. Research into a new channel normalization (CN) technique for channel mismatched speech recognition is presented. A process of inverse linear filtering is used in order...

  9. Review: Clinical aspects of hereditary DNA Mismatch repair gene mutations

    NARCIS (Netherlands)

    Sijmons, Rolf H.; Hofstra, Robert M. W.

    Inherited mutations of the DNA Mismatch repair genes MLH1, MSH2, MSH6 and PMS2 can result in two hereditary tumor syndromes: the adult-onset autosomal dominant Lynch syndrome, previously referred to as Hereditary Non-Polyposis Colorectal Cancer (HNPCC) and the childhood-onset autosomal recessive

  10. Clinicopathologic factors identify sporadic mismatch repair-defective colon cancers

    DEFF Research Database (Denmark)

    Halvarsson, Britta; Anderson, Harald; Domanska, Katarina

    2008-01-01

    Identification of sporadic mismatch repair (MMR)-defective colon cancers is increasingly demanded for decisions on adjuvant therapies. We evaluated clinicopathologic factors for the identification of these prognostically favorable tumors. Histopathologic features in 238 consecutive colon cancers...... and excluded 61.5% of the tumors from MMR testing. This clinicopathologic index thus successfully selects MMR-defective colon cancers. Udgivelsesdato: 2008-Feb...

  11. Understanding the Mismatch Between Coaches' and Players' Perceptions of Exertion

    NARCIS (Netherlands)

    Brink, Michel S.; Kersten, Anna W.; Frencken, Wouter G. P.

    A mismatch between the training exertion intended by a coach and the exertion perceived by players is well established in sports. However, it is unknown whether coaches can accurately observe exertion of individual players during training. Furthermore, the discrepancy in coaches' and players'

  12. Mismatch negativity to pitch pattern deviants in schizophrenia.

    Science.gov (United States)

    Haigh, Sarah M; Matteis, Mario De; Coffman, Brian A; Murphy, Timothy K; Butera, Christiana D; Ward, Kayla L; Leiter-McBeth, Justin R; Salisbury, Dean F

    2017-09-01

    Simple mismatch negativity (MMN) to infrequent pitch deviants is impaired in individuals with long-term schizophrenia (Sz). The complex MMN elicited by pattern deviance often manifes is cut from here]->ts later after deviant onset than simple MMN and can ascertain deficits in abstracting relationships between stimuli. Sz exhibit reduced complex MMN, but so far this has only been measured when deviance detection relies on a grouping rule. We measured MMN to deviants in pitch-based rules to see whether MMN is also abnormal in Sz under these conditions. Three experiments were conducted. Twenty-seven Sz and 28 healthy matched controls (HC) participated in Experiments 1 and 2, and 24 Sz and 26 HC participated in Experiment 3. Experiment 1 was a standard pitch MMN task, and Sz showed the expected MMN reduction (~ 115 ms) in the simple pitch deviant compared to HC. Experiment 2 comprised standard groups of six tones that ascended in pitch, and deviant groups where the last tone descended in pitch. Complex MMN was late (~ 510 ms) and significantly blunted in Sz. Experiment 3 comprised standard groups of 12 tones (six tones ascending in pitch followed by six tones descending in pitch, like a scale), and deviant groups containing two repetitions of six ascending tones (the scale restarted midstream). Complex MMN was also late (~ 460 ms) and significantly blunted in Sz. These results identify a late pitch pattern deviance-related MMN that is deficient in schizophrenia. This suggests specific deficits in later more complex deviance detection in schizophrenia for abstract patterns. © 2017 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  13. Does mismatch of the femoral component aspect ratio

    Directory of Open Access Journals (Sweden)

    JIA Yu-tao

    2012-06-01

    Full Text Available 【Abstract】Objective: To study whether the range of knee flexion (ROF is affected by geometrical mismatch of the femoral component and the resultant change in the pos-terior condylar offset (PCO after high-flexion posterior-sta-bilized total knee arthroplasty (TKA. Methods: One hundred osteoarthritic patients (50 males and 50 females underwent femoral osteotomy by the ante-rior referencing technique. The PCO for each patient was measured from lateral radiographs before, during and 2 years after TKA. The thickness of the joint cartilage was mea-sured by magnetic resonance imaging before TKA and added onto the radiographic measurement. The relationship be-tween changes in the PCO and improvements in the ROF before, during and 2 years after TKA were statistically analyzed. Results: Compared with the preoperative value, the PCO was reduced by (3.45±3.28 mm after TKA, with a sig-nificantly larger reduction observed in female patients than male patients (P<0.05. When examining the subject popu-lation as a whole, there was a significant positive correla-tion between PCO and ROF improvement during TKA (P< 0.05, but this improvement was not maintained 2 years after TKA (P>0.05. However, when male and female patients were analyzed separately, there was a significant positive corre-lation between PCO change and ROF improvement for both sexes at both time points (all P<0.05. Conclusions: Restoration of PCO plays an important role in the optimization of knee flexion even after posterior-stabilized TKA. Femoral components based on Caucasian anatomic characteristics could not match the native anatomy of distal femurs in Chinese population especially female Chinese. Rotated resection of distal femur with anterior re-ferencing technique usually leads to a decreased PCO and therefore reduces maximal obtainable flexion. Key words: Arthroplasty, replacement, knee; Pros-thesis design; Range of motion, articular; Femur

  14. Evaluating Mismatch Repair Deficiency in Pancreatic Adenocarcinoma: Challenges and Recommendations.

    Science.gov (United States)

    Hu, Zishuo I; Shia, Jinru; Stadler, Zsofia K; Varghese, Anna M; Capanu, Marinela; Salo-Mullen, Erin; Lowery, Maeve A; Diaz, Luis A; Mandelker, Diana; Yu, Kenneth H; Zervoudakis, Alice; Kelsen, David P; Iacobuzio-Donahue, Christine A; Klimstra, David S; Saltz, Leonard B; Sahin, Ibrahim H; O'Reilly, Eileen M

    2018-01-24

    Purpose: Immune checkpoint inhibition has been shown to generate profound and durable responses in mismatch repair deficient (MMR-D) solid tumors and has elicited interest in detection tools and strategies to guide therapeutic decision-making. Herein we address questions on the appropriate screening, detection methods, patient selection, and initiation of therapy for MMR-D pancreatic ductal adenocarcinoma (PDAC) and assess the utility of next-generation sequencing (NGS) in providing additional prognostic and predictive information for MMR-D PDAC. Experimental Design: Archival and prospectively acquired samples and matched normal DNA from N = 833 PDAC cases were analyzed using a hybridization capture-based, NGS assay designed to perform targeted deep sequencing of all exons and selected introns of 341 to 468 cancer-associated genes. A computational program using NGS data derived the MSI status from the tumor-normal paired genome sequencing data. Available germline testing, IHC, and microsatellite instability (MSI) PCR results were reviewed to assess and confirm MMR-D and MSI status. Results: MMR-D in PDAC is a rare event among PDAC patients (7/833), occurring at a frequency of 0.8%. Loss of MMR protein expression by IHC, high mutational load, and elevated MSIsensor scores were correlated with MMR-D PDAC. All 7 MMR-D PDAC patients in the study were found to have Lynch syndrome. Four (57%) of the MMR-D patients treated with immune checkpoint blockade had treatment benefit (1 complete response, 2 partial responses, 1 stable disease). Conclusions: An integrated approach of germline testing and somatic analyses of tumor tissues in advanced PDAC using NGS may help guide future development of immune and molecularly directed therapies in PDAC patients. Clin Cancer Res; 24(6); 1-11. ©2018 AACR. ©2018 American Association for Cancer Research.

  15. Band anticrossing effects in highly mismatched semiconductor alloys

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Junqiao [Univ. of California, Berkeley, CA (United States)

    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

  16. In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus.

    Science.gov (United States)

    Banasik, Michał; Stanisławska-Sachadyn, Anna; Hildebrandt, Ewa; Sachadyn, Paweł

    2017-06-20

    The mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront this with the properties of those from E. coli and T. thermophilus. The analyses which included mobility gel-shift assay, colorimetric and qPCR estimation of MutS-bound DNA clearly showed that D. radiodurans MutS exhibited much higher affinity towards mismatched DNA in vitro than its counterparts from E. coli and T. thermophilus. In addition, D. radiodurans MutS displayed a significantly higher specificity of DNA mismatch binding than the two other orthologues. The specificity expressed as the ratio of mismatched to fully complementary DNA bound reached over 4 and 20-fold higher values for D. radiodurans than for T. thermophilus and E. coli MutS, respectively. The results demonstrate mainly the biotechnological potential of D. radiodurans MutS but the in vitro characteristics of the MutS orthologues could reflect substantial differences in DNA mismatch binding activities existing in vivo. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Worst case estimate of mismatch induced distortion in complementary CMOS current mirrors

    DEFF Research Database (Denmark)

    Bruun, Erik

    1998-01-01

    Mismatching between the MOS transistors in a current mirror causes harmonic distortion. In a complementary class AB current mirror, mismatching of threshold voltages, geometries and transconductance parameters causes a distortion which cannot be eliminated by circuit techniques but which can...

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

    Science.gov (United States)

    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 HLA mismatches. PMID:24408320

  19. Understanding mismatches in body size, speed and power among adolescent rugby union players.

    Science.gov (United States)

    Krause, Lyndon M; Naughton, Geraldine A; Denny, Greg; Patton, Declan; Hartwig, Tim; Gabbett, Tim J

    2015-05-01

    With adolescent sport increasingly challenged by mismatches in size, new strategies are important to maximize participation. The objectives were to (1) improve the understanding of mismatches in physical size, speed and power in adolescent rugby union players, (2) explore associations between size and performance with demographic, playing-history, and injury profiles, and (3) explore the applicability of existing criteria for age/body mass-based dispensation (playing-down) strategies. Cross-sectional study. Four hundred and eighty-five male community rugby union players were recruited from three Australian states selected to represent community-based U12, U13, U14 and U15 players. Body mass, stature, speed (10, 30, and 40 m sprints) and lower-leg power (relative peak power and relative peak force) were measured. Independent student t-tests, linear regressions and Chi square analyses were undertaken. Mean values in age groups for size, speed and power masked considerable overlap in the ranges within specific age groups of adolescent rugby players. Only a small proportion of players (approximately 5%) shared the highest and lowest tertiles for speed, relative peak power and body mass. Physical size was not related to injury. The mean body mass of current community rugby union players was above the 75th percentile on normative growth-charts. The notion that bigger, faster, and more powerful characteristics occur simultaneously in adolescent rugby players was not supported in the present study. Current practices in body mass-based criteria for playing down an age group lack a sufficient evidence for decision-making. Dispensation solely based on body mass may not address mismatch in junior rugby union. Copyright © 2014 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  20. Iterative dual energy material decomposition from spatial mismatched raw data sets.

    Science.gov (United States)

    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.

  1. The adjacency-Jacobsthal-circulant sequence in groups

    Science.gov (United States)

    Deveci, Ömür; Adıgüzel, Zafer

    2017-04-01

    In this work, we study the adjacency-Jacobsthal-circulant sequence modulo α and we obtain the cyclic groups from the generating matrix of the adjacency-Jacobsthal-circulant numbers when read modulo α. Then, we derive the relationship among the periods of the adjacency-Jacobsthal-circulant sequence modulo α and the orders of the cyclic groups obtained. Furthermore, we extend the adjacency-Jacobsthal-circulant sequence to groups. Finally, we obtain the length of the period of the adjacency-Jacobsthal-circulant sequence in the quaternion group Q8 as applications of the results obtained.

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

    Science.gov (United States)

    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…

  3. Skill effort: A new theoretical perspective on the relation between skills, skill use, mismatches, and wages

    NARCIS (Netherlands)

    van der Velden, Rolf; Bijlsma, Ineke

    2017-01-01

    Mismatches between workers’ skills and job demands have large negative effects on productivity, job satisfaction, and other outcomes. Current approaches to measure the impact of skills and skill mismatches on wages fail to specify the mechanism through which skills and mismatches may affect

  4. Skill effort: a new theoretical perspective on the relation between skills, skill use, mismatches, and wages

    NARCIS (Netherlands)

    van der Velden, Rolf; Bijlsma, Ineke

    2017-01-01

    Mismatches between workers’ skills and job demands have large negative effects on productivity, job satisfaction, and other outcomes. Current approaches to measure the impact of skills and skill mismatches on wages fail to specify the mechanism through which skills and mismatches may affect

  5. Compensation of multi-channel mismatches in high-speed high-resolution photonic analog-to-digital converter.

    Science.gov (United States)

    Yang, Guang; Zou, Weiwen; Yu, Lei; Wu, Kan; Chen, Jianping

    2016-10-17

    We demonstrate a method to compensate multi-channel mismatches that intrinsically exist in a photonic analog-to-digital converter (ADC) system. This system, nominated time-wavelength interleaved photonic ADC (TWI-PADC), is time-interleaved via wavelength demultiplexing/multiplexing before photonic sampling, wavelength demultiplexing channelization, and electronic quantization. Mismatches among multiple channels are estimated in frequency domain and hardware adjustment are used to approach the device-limited accuracy. A multi-channel mismatch compensation algorithm, inspired from the time-interleaved electronic ADC, is developed to effectively improve the performance of TWI-PADC. In the experiment, we configure out a 4-channel TWI-PADC system with 40 GS/s sampling rate based on a 10-GHz actively mode-locked fiber laser. After multi-channel mismatch compensation, the effective number of bit (ENOB) of the 40-GS/s TWI-PADC system is enhanced from ~6 bits to >8.5 bits when the RF frequency is within 0.1-3.1 GHz and from ~6 bits to >7.5 bits within 3.1-12.1 GHz. The enhanced performance of the TWI-PADC system approaches the limitation determined by the timing jitter and noise.

  6. Mismatch Negativity Based Neurofeedback for Cochlear Implant Users

    NARCIS (Netherlands)

    Luckmann, Annika; Başkent, Deniz; Jolij, Jacob

    2015-01-01

    Cochlear implant (CI) users experience great difficulty when it comes to pitch discrimination. This leads to problems during daily interactions, due to poor speech perception, but also a very low pleasure ratings for music. Improving pitch perception and discrimination in CI users would improve

  7. Stress Wave Interaction Between Two Adjacent Blast Holes

    Science.gov (United States)

    Yi, Changping; Johansson, Daniel; Nyberg, Ulf; Beyglou, Ali

    2016-05-01

    Rock fragmentation by blasting is determined by the level and state of stress in the rock mass subjected to blasting. With the application of electronic detonators, some researchers stated that it is possible to achieve improved fragmentation through stress wave superposition with very short delay times. This hypothesis was studied through theoretical analysis in the paper. First, the stress in rock mass induced by a single-hole shot was analyzed with the assumptions of infinite velocity of detonation and infinite charge length. Based on the stress analysis of a single-hole shot, the stress history and tensile stress distribution between two adjacent holes were presented for cases of simultaneous initiation and 1 ms delayed initiation via stress superposition. The results indicated that the stress wave interaction is local around the collision point. Then, the tensile stress distribution at the extended line of two adjacent blast holes was analyzed for a case of 2 ms delay. The analytical results showed that the tensile stress on the extended line increases due to the stress wave superposition under the assumption that the influence of neighboring blast hole on the stress wave propagation can be neglected. However, the numerical results indicated that this assumption is unreasonable and yields contrary results. The feasibility of improving fragmentation via stress wave interaction with precise initiation was also discussed. The analysis in this paper does not support that the interaction of stress waves improves the fragmentation.

  8. Policy Debate | Education and Employment Mismatch

    Directory of Open Access Journals (Sweden)

    Mona Mourshed

    2014-12-01

    Full Text Available Editor’s note: These papers are contributions to the ‘Policy Debate’ section of International Development Policy. In this section, academics, policy-makers and practioners engage in a dialogue on global development challenges. Papers are copy-edited but not peer-reviewed. Instead, the initial thematic contribution is followed by critical comments and reactions from scholars and/or policy-makers.Authored by McKinsey’s research team, the initial paper addresses the Education to Employment challenge. It is based on McKinsey’s study, which looked at skill development in 25 different countries and investigated education-to-employment initiatives. The authors claim that the most successful efforts are those where different stakeholders interact intensively and frequently. Employers need to get involved in education, and educators should play a bigger role in employment.The paper is followed by critical comments by two authors, Beatriz Cardoso, Executive Director of Laboratório de Educação, Brazil, and Shailaja Fennell lecturer at the Centre of Development Studies, University of Cambridge, UK.This debate can be pursued on the Journal’s blog http://devpol.hypotheses.org/423.

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

    DEFF Research Database (Denmark)

    Guérit, François; Santurette, Sébastien; Chalupper, Josef

    2014-01-01

    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...

  10. Interobserver variability in the evaluation of mismatch repair protein immunostaining

    DEFF Research Database (Denmark)

    Klarskov, Louise; Ladelund, Steen; Holck, Susanne

    2010-01-01

    Immunohistochemical staining for mismatch repair proteins has during recent years been established as a routine analysis in many pathology laboratories with the aim to identify tumors linked to the hereditary nonpolyposis colorectal cancer syndrome. Despite widespread application, data on reliabi......Immunohistochemical staining for mismatch repair proteins has during recent years been established as a routine analysis in many pathology laboratories with the aim to identify tumors linked to the hereditary nonpolyposis colorectal cancer syndrome. Despite widespread application, data...... staining. Full consensus was achieved in 51% of the stainings for MLH1, 61% for PMS2, 83% for MSH2, and 45% for MSH6. Weak stainings were the main cause of reduced consensus, whereas contradictory evaluations with normal as well as loss of staining were reported in 2% to 6% of the tumors. Interobserver...

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

    Science.gov (United States)

    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. Copyright 2009 Elsevier Ltd. All rights reserved.

  12. Phenotypic mismatches reveal escape from arms-race coevolution.

    Directory of Open Access Journals (Sweden)

    Charles T Hanifin

    2008-03-01

    Full Text Available 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.

  13. Feature-specific transition from positive mismatch response to mismatch negativity in early infancy: mismatch responses to vowels and initial consonants.

    Science.gov (United States)

    Cheng, Ying-Ying; Wu, Hsin-Chi; Tzeng, Yu-Lin; Yang, Ming-Tao; Zhao, Lu-Lu; Lee, Chia-Ying

    2015-05-01

    This study investigated how phonological saliency, deviance size, and maturation affect mismatch responses (MMRs) in early infancy. MMRs to Mandarin vowels and initial consonants were measured using a multi-deviant oddball paradigm in adults, newborns, and 6-month-olds. The vowel condition consisted of Mandarin syllable da as the standard, du as the large deviant and di as small deviant. As for initial consonant condition, we took syllable ba as standard, ga as large deviant, and ba as small deviant. While adults showed typical mismatch negativities (MMNs), newborns demonstrated broad positive MMRs (P-MMRs) to both initial consonants and vowels. For 6-month-olds, deviance size affected the polarity of MMRs to vowels. The large deviant du/da contrast elicited an adult-like MMN, while the small deviant di/da contrast elicited a P-MMR. Initial consonant changes elicited only P-MMRs, regardless of deviance size. In summary, MMRs to vowels switched from P-MMR at birth to MMN at 6 months. However, the polarity transition was not found for MMRs to initial consonants. The developmental trajectories of MMRs to vowels and initial consonants further support the phonological saliency hypothesis. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Halo formation from mismatched beam-beam interactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Infra-red parametric generation: Phase mismatch condition

    Science.gov (United States)

    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.

  16. ZOOGEOGRAPHICAL ZONING OF THE MEDITERRANEAN AND ADJACENT TERRITORIES

    Directory of Open Access Journals (Sweden)

    H. A. Ketenchiev

    2013-01-01

    Full Text Available Abstract. Aim. The article considers the zoogeographical zoning of the Mediterranean and adjacent territories with the purpose of specification of the scheme of zoogeographic zoning of land on the basis of the distribution of dragonflies.Methods. Use common methods of entomological research, mapping and analysis of the fauna.Results. On the based on our analysis of the composition and distribution of odonatofauna Mediterranean zoogeographical subregion is offered to divide into 5 provinces: Caucasian, South-European, Pyrenees, Asian and African. Analysis of the existing schemes zoning of land based on the distribution of taxa dragonflies, installed the advantages and disadvantages presented by different authors, the result of which is proposed to change the borders between the Holarctic and Subholarctic areas of the Boreal fauna Kingdom (BFK. It is connected with the fact that the dividing them into subdomains and evaluation role in the establishment of regional odonatofauna not always convincing. In this regard, the article proposed to abolish the Holarctic region sub-region: European and Mongolian-Kazakh, and in Subholarctic - add 1 sub-region of Central Asia. In a new form Subholarctic region becomes clear and logical configuration, but her name becomes inadequate, therefore, we re-name it in Paleosubtropical.The scope of the results. In fundamental research on systematics of animals, ecology and biogeography.Main conclusions. Based on the study of the composition and distribution of taxa of dragonflies in the Mediterranean and adjacent territories proposed the division of the Mediterranean subregion 5 provinces and refined scheme of zoogeographic zoning of land.

  17. Numerical simulations of material mismatch and ductile crack growth

    Energy Technology Data Exchange (ETDEWEB)

    Oestby, Erling

    2002-07-01

    Both the global geometry and inhomogeneities in material properties will influence the fracture behaviour of structures in presence of cracks. In this thesis numerical simulations have been used to investigate how some aspects of both these issues affect the conditions at the crack-tip. The thesis is organised in an introduction chapter, summarising the major findings and conclusions, a review chapter, presenting the main aspects of the developments in the field of fracture mechanics, and three research papers. Paper I considers the effect of mismatch in hardening exponent on the local near-tip stress field for stationary interface cracks in bi-materials under small scale yielding conditions. It is demonstrated that the stress level in the weaker material increases compared to what is found in the homogeneous material for the same globally applied load level, with the effect being of increasing importance as the crack-tip is approached. Although a coupling between the radial and angular dependence of the stress fields exists, the evolving stress field can still be normalised with the applied J. The effect on the increase in stress level can closely be characterised by the difference in hardening exponent, {delta}n, termed the hardening mismatch, and is more or less independent of the absolute level of hardening in the two materials. Paper II and Ill deal with the effects of geometry, specimen size, hardening level and yield stress mismatch in relation to ductile crack growth. The ductile crack growth is simulated through use of the Gurson model. In Paper H the effect of specimen size on the crack growth resistance is investigated for deep cracked bend and shallow cracked tensile specimens. At small amounts of crack growth the effect of specimen size on the crack growth resistance is small, but a more significant effect is found for larger amounts of crack growth. The crack growth resistance decreases in smaller specimens loaded in tension, whereas the opposite is

  18. Recruitment variability in North Atlantic cod and match-mismatch dynamics.

    Science.gov (United States)

    Kristiansen, Trond; Drinkwater, Kenneth F; Lough, R Gregory; Sundby, Svein

    2011-03-07

    Fisheries exploitation, habitat destruction, and climate are important drivers of variability in recruitment success. Understanding variability in recruitment can reveal mechanisms behind widespread decline in the abundance of key species in marine and terrestrial ecosystems. For fish populations, the match-mismatch theory hypothesizes that successful recruitment is a function of the timing and duration of larval fish abundance and prey availability. However, the underlying mechanisms of match-mismatch dynamics and the factors driving spatial differences between high and low recruitment remain poorly understood. We used empirical observations of larval fish abundance, a mechanistic individual-based model, and a reanalysis of ocean temperature data from 1960 to 2002 to estimate the survival of larval cod (Gadus morhua). From the model, we quantified how survival rates changed during the warmest and coldest years at four important cod spawning sites in the North Atlantic. The modeled difference in survival probability was not large for any given month between cold or warm years. However, the cumulative effect of higher growth rates and survival through the entire spawning season in warm years was substantial with 308%, 385%, 154%, and 175% increases in survival for Georges Bank, Iceland, North Sea, and Lofoten cod stocks, respectively. We also found that the importance of match-mismatch dynamics generally increased with latitude. Our analyses indicate that a key factor for enhancing survival is the duration of the overlap between larval and prey abundance and not the actual timing of the peak abundance. During warm years, the duration of the overlap between larval fish and their prey is prolonged due to an early onset of the spring bloom. This prolonged season enhances cumulative growth and survival, leading to a greater number of large individuals with enhanced potential for survival to recruitment.

  19. Recruitment variability in North Atlantic cod and match-mismatch dynamics.

    Directory of Open Access Journals (Sweden)

    Trond Kristiansen

    Full Text Available BACKGROUND: Fisheries exploitation, habitat destruction, and climate are important drivers of variability in recruitment success. Understanding variability in recruitment can reveal mechanisms behind widespread decline in the abundance of key species in marine and terrestrial ecosystems. For fish populations, the match-mismatch theory hypothesizes that successful recruitment is a function of the timing and duration of larval fish abundance and prey availability. However, the underlying mechanisms of match-mismatch dynamics and the factors driving spatial differences between high and low recruitment remain poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We used empirical observations of larval fish abundance, a mechanistic individual-based model, and a reanalysis of ocean temperature data from 1960 to 2002 to estimate the survival of larval cod (Gadus morhua. From the model, we quantified how survival rates changed during the warmest and coldest years at four important cod spawning sites in the North Atlantic. The modeled difference in survival probability was not large for any given month between cold or warm years. However, the cumulative effect of higher growth rates and survival through the entire spawning season in warm years was substantial with 308%, 385%, 154%, and 175% increases in survival for Georges Bank, Iceland, North Sea, and Lofoten cod stocks, respectively. We also found that the importance of match-mismatch dynamics generally increased with latitude. CONCLUSIONS/SIGNIFICANCE: Our analyses indicate that a key factor for enhancing survival is the duration of the overlap between larval and prey abundance and not the actual timing of the peak abundance. During warm years, the duration of the overlap between larval fish and their prey is prolonged due to an early onset of the spring bloom. This prolonged season enhances cumulative growth and survival, leading to a greater number of large individuals with enhanced potential for

  20. Scolopendromorpha of New Guinea and adjacent islands (Myriapoda, Chilopoda).

    Science.gov (United States)

    Schileyko, Arkady A; Stoev, Pavel E

    2016-08-04

    The centipede fauna of the second largest island in the world, New Guinea, and its adjacent islands, is poorly known, with most information deriving from the first half of the 20th century. Here we present new data on the order Scolopendromorpha based on material collected in the area in the last 40 years, mainly by Bulgarian and Latvian zoologists. The collections comprise eleven species of six genera and three families. The diagnosis of Cryptops (Trigonocryptops) is emended in the light of the recent findings. The old and doubtful record of Scolopendra multidens Newport, 1844 from New Guinea is referred to S. subspinipes Leach, 1815 and the species is here excluded from the present day list of New Guinean scolopendromorphs. Cryptops nepalensis Lewis, 1999 is here recorded from New Guinea for the first time. An annotated list and an identification key to the scolopendromorphs of the studied region are presented.

  1. Migration of PCBs from Sealants to Adjacent Material

    DEFF Research Database (Denmark)

    Andersen, Helle Vibeke; Gunnarsen, Lars Bo; Kampmann, Kristoffer

    2015-01-01

    PCB in sealants can migrate into porous surfaces like concrete and brick and contaminate these materials. The study focuses on an analysis of concentration profiles in relation to alleviation of PCB contamination. The PCB content was determined in 20 samples of concrete and 6 samples of brick...... to the concentration of the adjacent material. The profiles of PCB concentration into the materials showed some variation, though in general there is a tendency of relative higher concentration near the primary source in concrete and longer migration at low concentrations in brick. The concentration profiles seemed...... to fit an exponential function for concrete and a power function for brick. Based on the sample series, a worst case scenario for migration was defined. For concrete, it showed that a concentration of less than 50 ppm in the material (hazardous waste) was reached at a distance of 5 cm, whereas for bricks...

  2. Clinical characteristics of unknown symptom onset stroke patients with and without diffusion-weighted imaging and fluid-attenuated inversion recovery mismatch.

    Science.gov (United States)

    Thomalla, Götz; Boutitie, Florent; Fiebach, Jochen B; Simonsen, Claus Z; Pedraza, Salvador; Lemmens, Robin; Nighoghossian, Norbert; Roy, Pascal; Muir, Keith W; Ebinger, Martin; Ford, Ian; Cheng, Bastian; Galinovic, Ivana; Cho, Tae-Hee; Puig, Josep; Thijs, Vincent; Endres, Matthias; Fiehler, Jens; Gerloff, Christian

    2018-01-01

    Background Diffusion-weighted imaging (DWI) and fluid-attenuated inversion recovery (FLAIR) mismatch was suggested to identify stroke patients with unknown time of symptom onset likely to be within the time window for thrombolysis. Aims We aimed to study clinical characteristics associated with DWI-FLAIR mismatch in patients with unknown onset stroke. Methods We analyzed baseline MRI and clinical data from patients with acute ischemic stroke proven by DWI from WAKE-UP, an investigator-initiated, randomized, placebo-controlled trial of MRI-based thrombolysis in stroke patients with unknown time of symptom onset. Clinical characteristics were compared between patients with and without DWI-FLAIR mismatch. Results Of 699 patients included, 418 (59.8%) presented with DWI-FLAIR mismatch. A shorter delay between last seen well and symptom recognition (p = 0.0063), a shorter delay between symptom recognition and arrival at hospital (p = 0.0025), and history of atrial fibrillation (p = 0.19) were predictors of DWI-FLAIR mismatch in multivariate analysis. All other characteristics were comparable between groups. Conclusions There are only minor differences in measured clinical characteristics between unknown symptom onset stroke patients with and without DWI-FLAIR mismatch. DWI-FLAIR mismatch as an indicator of stroke onset within 4.5 h shows no relevant association with commonly collected clinical characteristics of stroke patients. Clinical Trial Registration URL: http://www.clinicaltrials.gov . Unique identifier: NCT01525290; URL: https://www.clinicaltrialsregister.eu . Unique identifier: 2011-005906-32.

  3. Feasibility of HLA-haploidentical hematopoietic stem cell transplantation between noninherited maternal antigen (NIMA)-mismatched family members linked with long-term fetomaternal microchimerism.

    Science.gov (United States)

    Ichinohe, Tatsuo; Uchiyama, Takashi; Shimazaki, Chihiro; Matsuo, Keitaro; Tamaki, Shigehisa; Hino, Masayuki; Watanabe, Arata; Hamaguchi, Motohiro; Adachi, Souichi; Gondo, Hisashi; Uoshima, Nobuhiko; Yoshihara, Takao; Hatanaka, Kazuo; Fujii, Hiroshi; Kawa, Keisei; Kawanishi, Kazunobu; Oka, Koji; Kimura, Hideo; Itoh, Mitsuru; Inukai, Takeshi; Maruya, Etsuko; Saji, Hiroh; Kodera, Yoshihisa

    2004-12-01

    Based on the hypothesis that long-term fetomaternal microchimerism is associated with acquired immunologic hyporesponsiveness to noninherited maternal antigens (NIMAs) or inherited paternal antigens (IPAs), several groups have recently reported successful cases of non-T-cell-depleted hematopoietic stem cell transplantation (SCT) from HLA-haploidentical family members mismatched for NIMAs. In this study, we examined the outcomes of 35 patients with advanced hematologic malignancies who underwent HLA-2-antigen- or HLA-3-antigen-incompatible SCT from a microchimeric NIMA-mismatched donor. After standard-intensity or reduced-intensity preparative regimens, all patients had sustained hematopoietic recovery with tacrolimus-based graft-versus-host disease (GVHD) prophylaxis. Grade II/IV acute GVHD occurred in 19 (56%) of 34 evaluable patients, while extensive chronic GVHD developed in 13 (57%) of 23 patients who could be evaluated. Multivariate analysis demonstrated that NIMA mismatch in the GVH direction was associated with a lower risk of severe grade III-IV acute GVHD when compared with IPA mismatch (P = .03). Fifteen patients were alive and 14 of them were disease-free with a median follow-up of 20 (range, 8 to 37) months. These results indicate that T cell-replete SCT from an HLA-haploidentical NIMA-mismatched donor can offer durable remission with an acceptable risk of GVHD in selected patients with advanced hematologic malignancies who lack immediate access to a conventional stem cell source.

  4. Measurement Matrix Optimization and Mismatch Problem Compensation for DLSLA 3-D SAR Cross-Track Reconstruction.

    Science.gov (United States)

    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.

  5. Efficient engineering of chromosomal ribosome binding site libraries in mismatch repair proficient Escherichia coli.

    Science.gov (United States)

    Oesterle, Sabine; Gerngross, Daniel; Schmitt, Steven; Roberts, Tania Michelle; Panke, Sven

    2017-09-26

    Multiplexed gene expression optimization via modulation of gene translation efficiency through ribosome binding site (RBS) engineering is a valuable approach for optimizing artificial properties in bacteria, ranging from genetic circuits to production pathways. Established algorithms design smart RBS-libraries based on a single partially-degenerate sequence that efficiently samples the entire space of translation initiation rates. However, the sequence space that is accessible when integrating the library by CRISPR/Cas9-based genome editing is severely restricted by DNA mismatch repair (MMR) systems. MMR efficiency depends on the type and length of the mismatch and thus effectively removes potential library members from the pool. Rather than working in MMR-deficient strains, which accumulate off-target mutations, or depending on temporary MMR inactivation, which requires additional steps, we eliminate this limitation by developing a pre-selection rule of genome-library-optimized-sequences (GLOS) that enables introducing large functional diversity into MMR-proficient strains with sequences that are no longer subject to MMR-processing. We implement several GLOS-libraries in Escherichia coli and show that GLOS-libraries indeed retain diversity during genome editing and that such libraries can be used in complex genome editing operations such as concomitant deletions. We argue that this approach allows for stable and efficient fine tuning of chromosomal functions with minimal effort.

  6. Foot-to-shoe mismatch and rates of referral in Special Olympics athletes.

    Science.gov (United States)

    Jenkins, David W; Cooper, Kimbal; O'Connor, Rachel; Watanabe, Liane

    2012-01-01

    Improperly fitted shoes are frequently seen in athletes participating in Special Olympics competitions. This foot-to-shoe mismatch may result in deformities as well as discomfort and reduced performance or injuries in competitions. A primary purpose for providing medical screenings is to identify conditions unknown and to promptly refer to an appropriate provider for evaluation and care. This study attempts to determine the prevalence of improperly fitted shoes and the rate of referral for Special Olympics athletes screened at Fit Feet venues. To evaluate the foot-to-shoe mismatch and rate of referral, 4,094 Fit Feet screenings of Special Olympics athletes participating in US competitions in 2005 to 2009 were analyzed. The participants were 58.5% male and 41.5% female, with a median age of 25.6 years. A power analysis and the χ(2) test were used. The athletes voluntarily underwent a foot screening that followed the standardized Special Olympics Fit Feet protocol. The Brannock Device for measuring feet was used to assess proper fit. A proper fit was found in 58.56% of the athletes, with 28.60% wearing shoes too big and 12.84% wearing shoes too small. Unrelated to shoe fit, 20% of the athletes required referrals for professional follow-up based on abnormal clinical findings. There is a significant (41.44%) mismatch of foot to shoe in Special Olympics athletes. The most common mismatch is a shoe too big, with a much smaller number of athletes having shoes too small. Awareness of this foot-to-shoe incompatibility may be useful for the development of shoes better designed for athletes with a foot structure not consistent with conventional shoes. Because 20% of the athletes required a referral for professional follow-up, Fit Feet examinations are important for identifying athletes with conditions that can be more readily evaluated and treated, thus improving the athletes' comfort and performance. Beyond knowing the rate of referral, future studies can determine the

  7. JOINTING PROCESS OF THE SAE 1020 WITH MAG WELD'S REGION HAVE BEEN INVESTIGATED AND FACTOR OF MISMATCH DETERMINED

    Directory of Open Access Journals (Sweden)

    Cevdet MERİÇ

    1997-03-01

    Full Text Available In this study, the jointing process of the SAE 1020 low carbon steel, generally used in the industry, has been done by the MAG weld method. The aim of this study is to examine the mismatch between base and weld metal. After the jointing process, mechanical and metalographical properties of the weld region, HAZ, and the weld metal of the samples considered here were searched, and CTOD (Crack Tip Opening Displacement was identified.

  8. JOINTING PROCESS OF THE SAE 1020 WITH MAG WELD'S REGION HAVE BEEN INVESTIGATED AND FACTOR OF MISMATCH DETERMINED

    OpenAIRE

    Cevdet MERİÇ; Mesut TOKDEMİR

    1997-01-01

    In this study, the jointing process of the SAE 1020 low carbon steel, generally used in the industry, has been done by the MAG weld method. The aim of this study is to examine the mismatch between base and weld metal. After the jointing process, mechanical and metalographical properties of the weld region, HAZ, and the weld metal of the samples considered here were searched, and CTOD (Crack Tip Opening Displacement) was identified.

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

    Directory of Open Access Journals (Sweden)

    Hui-yan Sun

    2015-01-01

    Full Text Available 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.

  10. The dual nature of mismatch repair as antimutator and mutator

    DEFF Research Database (Denmark)

    Bak, Sara Thornby; Sakellariou, Despoina; Pena Diaz, Javier

    2014-01-01

    DNA is constantly under attack by a number of both exogenous and endogenous agents that challenge its integrity. Among the mechanisms that have evolved to counteract this deleterious action, mismatch repair (MMR) has specialized in removing DNA biosynthetic errors that occur when replicating...... of oxidative damage. Surprisingly, MMR is also required for certain mutagenic processes. The mutagenic MMR has beneficial consequences contributing to the generation of a vast repertoire of antibodies through class switch recombination and somatic hypermutation processes. However, this non-canonical mutagenic...

  11. Identity Management Mismatch Challenges in the Danish Municipality Administration System

    DEFF Research Database (Denmark)

    Andersen, Mads Schaarup; Christensen, Henrik Bærbak

    2010-01-01

    municipality administration system, called Opus BRS, a system that integrates SAP, legacy mainframe systems, and other systems present in the individual municipalities. Each of these systems defines their own access control model and architecture, which leads to architectural mismatch that impacts security......, usability, as well as maintainability. We outline a three-year research project and discuss our research method that will include elements of action research as well as experiments using architectural prototyping. The project is carried out in cooperation with KMD, one of the largest Danish IT companies...

  12. Quasisynchronization in Quorum Sensing Systems with Parameter Mismatches

    Directory of Open Access Journals (Sweden)

    Jianbao Zhang

    2014-01-01

    Full Text Available The paper investigates quasisynchronization in a communication system, which consists of cells communicating through quorum sensing. With the help of Lyapunov function method and Lur’e system approach, some sufficient conditions for quasisynchronization are presented, and a bound on the synchronization errors is derived. The obtained theoretical results show that the synchronization quality is influenced by two parameters detrimentally: the error bound depends almost linearly on the mismatches between cells and depends sensitively on the diffusion rates of the signals inward the cell membrane. Numerical experiments are carried out to verify the theoretical results.

  13. Copper(II)-Controlled Molecular Glue for Mismatched DNA.

    Science.gov (United States)

    Kotera, Naoko; Guillot, Régis; Teulade-Fichou, Marie-Paule; Granzhan, Anton

    2017-04-04

    Isothermal hybridization of two DNA strands bearing three thymine-thymine (T:T) mismatches can be brought about in the presence of a stoichiometric amount of a bis-naphthalene macrocycle, 2,7-BisNP-NH. This process can be reverted by addition of a Cu II salt due to formation of a dinuclear metal complex which does not bind to DNA. Subsequent sequestration of Cu II releases the macrocycle and restores the hybridization state of DNA strands, thus allowing implementation of a fast fluorescent two-state DNA switch. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Model mismatch analysis and compensation for modal phase measuring deflectometry.

    Science.gov (United States)

    Huang, Lei; Xue, Junpeng; Gao, Bo; McPherson, Chris; Beverage, Jacob; Idir, Mourad

    2017-01-23

    The correspondence residuals due to the discrepancy between the reality and the shape model in use are analyzed for the modal phase measuring deflectometry. Slope residuals are calculated from these discrepancies between the modal estimation and practical acquisition. Since the shape mismatch mainly occurs locally, zonal integration methods which are good at dealing with local variations are used to reconstruct the height residual for compensation. Results of both simulation and experiment indicate the proposed height compensation method is effective, which can be used as a post-complement for the modal phase measuring deflectometry.

  15. Improved connection details for adjacent prestressed bridge beams.

    Science.gov (United States)

    2015-03-01

    Bridges with adjacent box beams and voided slabs are simply and rapidly constructed, and are well suited to : short to medium spans. The traditional connection between the adjacent members is a shear key lled with a : conventional non-shrink grout...

  16. Learning Non-Adjacent Dependencies: A Mechanism for Language Acquisition

    NARCIS (Netherlands)

    Grama, I.C.|info:eu-repo/dai/nl/339459646

    2017-01-01

    This dissertation explores the human ability for non-adjacent dependency-learning, which allows adults and infants to detect the relationship between a and b in an aXb string. I use artificial grammar learning with adults and infants to investigate whether non-adjacent dependency-learning could

  17. Unconscious improvement in foreign language learning using mismatch negativity neurofeedback: A preliminary study.

    Science.gov (United States)

    Chang, Ming; Iizuka, Hiroyuki; Kashioka, Hideki; Naruse, Yasushi; Furukawa, Masahiro; Ando, Hideyuki; Maeda, Taro

    2017-01-01

    When people learn foreign languages, they find it difficult to perceive speech sounds that are nonexistent in their native language, and extensive training is consequently necessary. Our previous studies have shown that by using neurofeedback based on the mismatch negativity event-related brain potential, participants could unconsciously achieve learning in the auditory discrimination of pure tones that could not be consciously discriminated without the neurofeedback. Here, we examined whether mismatch negativity neurofeedback is effective for helping someone to perceive new speech sounds in foreign language learning. We developed a task for training native Japanese speakers to discriminate between 'l' and 'r' sounds in English, as they usually cannot discriminate between these two sounds. Without participants attending to auditory stimuli or being aware of the nature of the experiment, neurofeedback training helped them to achieve significant improvement in unconscious auditory discrimination and recognition of the target words 'light' and 'right'. There was also improvement in the recognition of other words containing 'l' and 'r' (e.g., 'blight' and 'bright'), even though these words had not been presented during training. This method could be used to facilitate foreign language learning and can be extended to other fields of auditory and clinical research and even other senses.

  18. Unconscious improvement in foreign language learning using mismatch negativity neurofeedback: A preliminary study.

    Directory of Open Access Journals (Sweden)

    Ming Chang

    Full Text Available When people learn foreign languages, they find it difficult to perceive speech sounds that are nonexistent in their native language, and extensive training is consequently necessary. Our previous studies have shown that by using neurofeedback based on the mismatch negativity event-related brain potential, participants could unconsciously achieve learning in the auditory discrimination of pure tones that could not be consciously discriminated without the neurofeedback. Here, we examined whether mismatch negativity neurofeedback is effective for helping someone to perceive new speech sounds in foreign language learning. We developed a task for training native Japanese speakers to discriminate between 'l' and 'r' sounds in English, as they usually cannot discriminate between these two sounds. Without participants attending to auditory stimuli or being aware of the nature of the experiment, neurofeedback training helped them to achieve significant improvement in unconscious auditory discrimination and recognition of the target words 'light' and 'right'. There was also improvement in the recognition of other words containing 'l' and 'r' (e.g., 'blight' and 'bright', even though these words had not been presented during training. This method could be used to facilitate foreign language learning and can be extended to other fields of auditory and clinical research and even other senses.

  19. Multiple scale model for cell migration in monolayers: Elastic mismatch between cells enhances motility.

    Science.gov (United States)

    Palmieri, Benoit; Bresler, Yony; Wirtz, Denis; Grant, Martin

    2015-07-02

    We propose a multiscale model for monolayer of motile cells that comprise normal and cancer cells. In the model, the two types of cells have identical properties except for their elasticity; cancer cells are softer and normal cells are stiffer. The goal is to isolate the role of elasticity mismatch on the migration potential of cancer cells in the absence of other contributions that are present in real cells. The methodology is based on a phase-field description where each cell is modeled as a highly-deformable self-propelled droplet. We simulated two types of nearly confluent monolayers. One contains a single cancer cell in a layer of normal cells and the other contains normal cells only. The simulation results demonstrate that elasticity mismatch alone is sufficient to increase the motility of the cancer cell significantly. Further, the trajectory of the cancer cell is decorated by several speed "bursts" where the cancer cell quickly relaxes from a largely deformed shape and consequently increases its translational motion. The increased motility and the amplitude and frequency of the bursts are in qualitative agreement with recent experiments.

  20. PCNA function in the activation and strand direction of MutLα endonuclease in mismatch repair

    Science.gov (United States)

    Pluciennik, Anna; Dzantiev, Leonid; Iyer, Ravi R.; Constantin, Nicoleta; Kadyrov, Farid A.; Modrich, Paul

    2010-01-01

    MutLα (MLH1–PMS2) is a latent endonuclease that is activated in a mismatch-, MutSα-, proliferating cell nuclear antigen (PCNA)-, replication factor C (RFC)-, and ATP-dependent manner, with nuclease action directed to the heteroduplex strand that contains a preexisting break. RFC depletion experiments and use of linear DNAs indicate that RFC function in endonuclease activation is limited to PCNA loading. Whereas nicked circular heteroduplex DNA is a good substrate for PCNA loading and for endonuclease activation on the incised strand, covalently closed, relaxed circular DNA is a poor substrate for both reactions. However, covalently closed supercoiled or bubble-containing relaxed heteroduplexes, which do support PCNA loading, also support MutLα activation, but in this case cleavage strand bias is largely abolished. Based on these findings we suggest that PCNA has two roles in MutLα function: The clamp is required for endonuclease activation, an effect that apparently involves interaction of the two proteins, and by virtue of its loading orientation, PCNA determines the strand direction of MutLα incision. These results also provide a potential mechanism for activation of mismatch repair on nonreplicating DNA, an effect that may have implications for the somatic phase of triplet repeat expansion. PMID:20713735

  1. Shape forming by thermal expansion mismatch and shape memory locking in polymer/elastomer laminates

    Science.gov (United States)

    Yuan, Chao; Ding, Zhen; Wang, T. J.; Dunn, Martin L.; Qi, H. Jerry

    2017-10-01

    This paper studies a novel method to fabricate three-dimensional (3D) structure from 2D thermo-responsive shape memory polymer (SMP)/elastomer bilayer laminate. In this method, the shape change is actuated by the thermal mismatch strain between the SMP and the elastomer layers upon heating. However, the glass transition behavior of the SMP locks the material into a new 3D shape that is stable even upon cooling. Therefore, the second shape becomes a new permanent shape of the laminate. A theoretical model that accounts for the temperature-dependent thermomechanical behavior of the SMP material and thermal mismatch strain between the two layers is developed to better understand the underlying physics. Model predictions and experiments show good agreement and indicate that the theoretical model can well predict the bending behavior of the bilayer laminate. The model is then used in the optimal design of geometrical configuration and material selection. The latter also illustrates the requirement of thermomechanical behaviors of the SMP to lock the shape. Based on the fundamental understandings, several self-folding structures are demonstrated by the bilayer laminate design.

  2. Mismatched single stranded antisense oligonucleotides can induce efficient dystrophin splice switching

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    Kole Ryszard

    2011-10-01

    Full Text Available Abstract Background Antisense oligomer induced exon skipping aims to reduce the severity of Duchenne muscular dystrophy by redirecting splicing during pre-RNA processing such that the causative mutation is by-passed and a shorter but partially functional Becker muscular dystrophy-like dystrophin isoform is produced. Normal exons are generally targeted to restore the dystrophin reading frame however, an appreciable subset of dystrophin mutations are intra-exonic and therefore have the potential to compromise oligomer efficiency, necessitating personalised oligomer design for some patients. Although antisense oligomers are easily personalised, it remains unclear whether all patient polymorphisms within antisense oligomer target sequences will require the costly process of producing and validating patient specific compounds. Methods Here we report preclinical testing of a panel of splice switching antisense oligomers, designed to excise exon 25 from the dystrophin transcript, in normal and dystrophic patient cells. These patient cells harbour a single base insertion in exon 25 that lies within the target sequence of an oligomer shown to be effective at removing exon 25. Results It was anticipated that such a mutation would compromise oligomer binding and efficiency. However, we show that, despite the mismatch an oligomer, designed and optimised to excise exon 25 from the normal dystrophin mRNA, removes the mutated exon 25 more efficiently than the mutation-specific oligomer. Conclusion This raises the possibility that mismatched AOs could still be therapeutically applicable in some cases, negating the necessity to produce patient-specific compounds.

  3. Simple detection of germline microsatellite instability for diagnosis of constitutional mismatch repair cancer syndrome.

    Science.gov (United States)

    Ingham, Danielle; Diggle, Christine P; Berry, Ian; Bristow, Claire A; Hayward, Bruce E; Rahman, Nazneen; Markham, Alexander F; Sheridan, Eamonn G; Bonthron, David T; Carr, Ian M

    2013-06-01

    Heterozygous mutations in DNA mismatch repair (MMR) genes result in predisposition to colorectal cancer (hereditary nonpolyposis colorectal cancer or Lynch syndrome). Patients with biallelic mutations in these genes, however, present earlier, with constitutional mismatch repair deficiency cancer syndrome (CMMRD), which is characterized by a spectrum of rare childhood malignancies and café-au-lait skin patches. The hallmark of MMR deficiency, microsatellite instability (MSI), is readily detectable in tumor DNA in Lynch syndrome, but is also present in constitutional DNA of CMMRD patients. However, detection of constitutional or germline MSI (gMSI) has hitherto relied on technically difficult assays that are not routinely applicable for clinical diagnosis. Consequently, we have developed a simple high-throughput screening methodology to detect gMSI in CMMRD patients based on the presence of stutter peaks flanking a dinucleotide repeat allele when amplified from patient blood DNA samples. Using the three different microsatellite markers, the gMSI ratio was determined in a cohort of normal individuals and 10 CMMRD patients, with biallelic germline mutations in PMS2 (seven patients), MSH2 (one patient), or MSH6 (two patients). Subjects with either PMS2 or MSH2 mutations were easily identified; however, this measure was not altered in patients with CMMRD due to MSH6 mutation. © 2013 Wiley Periodicals, Inc.

  4. Adjacent Joint Kinematics After Ankle Arthrodesis During Cadaveric Gait Simulation.

    Science.gov (United States)

    Sturnick, Daniel R; Demetracopoulos, Constantine A; Ellis, Scott J; Queen, Robin M; Kolstov, Jayme C B; Deland, Jonathan T; Baxter, Josh R

    2017-11-01

    Arthrodesis is an effective and reliable treatment for end-stage ankle arthritis; however, many patients develop ipsilateral adjacent joint arthritis following surgery. The mechanism that drives adjacent joint arthritis remains uncertain. Cadaveric simulation permits direct investigation of the effects of both arthrodesis and movement strategy on adjacent joints during simulated walking. The objective of this study was to identify the isolated effect of ankle arthrodesis on adjacent joint kinematics during simulated walking. Effects of ankle arthrodesis on adjacent joint kinematics were assessed in 8 cadaveric foot and ankle specimens using a robotic gait simulator. Gait parameters acquired from healthy adults and patients with ankle arthrodesis were used as inputs for simulations. Three-dimensional subtalar and talonavicular joint kinematics were directly measured before and after ankle arthrodesis, and healthy- and arthrodesis-gait parameters were applied to identify the isolated effect of the ankle arthrodesis on adjacent joint kinematics. Ankle arthrodesis increased subtalar and talonavicular joint motion during early and midstance independent of which gait parameters were used as inputs to the gait simulator. However, adjacent joint motions did not differ between the control and arthrodesis condition during late stance, when the healthy gait parameters were used as inputs. Conversely, adjacent joint motion decreased during late stance following arthrodesis when simulating gait using parameters typical in arthrodesis patients. Regardless of the gait parameter inputs, subtalar and talonavicular joint motions increased from normal kinematics, which likely increase the biomechanical burden placed on these adjacent joints and may lead to joint degeneration. Increased motion of the adjacent joints caused by ankle arthrodesis may explain the articular degeneration observed clinically.

  5. Optimal definition for PWI/DWI mismatch in acute ischemic stroke patients.

    Science.gov (United States)

    Kakuda, Wataru; Lansberg, Maarten G; Thijs, Vincent N; Kemp, Stephanie M; Bammer, Roland; Wechsler, Lawrence R; Moseley, Michael E; Marks, Michael P; Parks, Michael P; Albers, Gregory W

    2008-05-01

    Although the perfusion-weighted imaging/diffusion-weighted imaging (PWI/DWI) mismatch model has been proposed to identify acute stroke patients who benefit from reperfusion therapy, the optimal definition of a mismatch is uncertain. We evaluated the odds ratio for a favorable clinical response in mismatch patients with reperfusion compared with no reperfusion for various mismatch ratio thresholds in patients enrolled in the diffusion and perfusion imaging evaluation for understanding stroke evolution (DEFUSE) study. A mismatch ratio of 2.6 provided the highest sensitivity (90%) and specificity (83%) for identifying patients in whom reperfusion was associated with a favorable response. Defining mismatch with a larger PWI/DWI ratio may provide greater power for detecting beneficial effects of reperfusion.

  6. Spatial mismatch, wages and unemployment in metropolitan areas in Brazil

    Directory of Open Access Journals (Sweden)

    Ana Maria Bonomi Barufi

    2017-12-01

    Full Text Available The spatial mismatch hypothesis states that a lack of connection to job opportunities may affect an individual’s prospects in the labour market, especially for low-skilled workers. This phenomenon is especially observed in large urban areas, in which low-skilled minorities tend to live far away from jobs and face geographical barriers to finding and keeping jobs. This paper aims to investigate whether this negative relationship between spatial mismatch and labour market outcomes is valid in Brazil after controlling for individual characteristics. Our conclusions indicate that there is no clear relation between different measures of accessibility to jobs and the probability of being unemployed. However, for wages there is a clear correlation, which is stronger in larger metropolitan areas in the country. Given the exploratory nature of this work, our results still rely on strong identification hypotheses to avoid potential bias related to simultaneous location decisions of workers and firms within the city. Even if these conditions do not hold, the results are still meaningful as they provide a better understanding of the conditional distribution of wages and the unemployment rate in the biggest metropolitan areas of Brazil.

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

    Science.gov (United States)

    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).

  8. The grain size of auditory mismatch response in speech perception

    Science.gov (United States)

    Zhang, Yang; Kuhl, Patricia; Imada, Toshiaki; Imada, Toshiaki; Kotani, Makoto

    2005-09-01

    This phonetic study examined neural encoding of within-and cross- category information as a function of language experience. Behavioral and magnetoencephalography (MEG) measures for synthetic /ba-wa/ and /ra-la/ stimuli were obtained from ten American and ten Japanese subjects. The MEG experiments employed the oddball paradigm in two conditions. One condition used single exemplars to represent the phonetic categories, and the other introduced within-category variations for both the standard and deviant stimuli. Behavioral results showed three major findings: (a) a robust phonetic boundary effect was observed only in the native listeners; (b) all listeners were able to detect within-category differences on an acoustic basis; and (c) both within- and cross- category discriminations were strongly influenced by language experience. Consistent with behavioral findings, American listeners had larger mismatch field (MMF) responses for /ra-la/ in both conditions but not for /ba-wa/ in either. Moreover, American listeners showed a significant MMF reduction in encoding within-category variations for /ba-wa/ but not for /ra-la/, and Japanese listeners had MMF reductions for both. These results strongly suggest that the grain size of auditory mismatch response is determined not only by experience-dependent phonetic knowledge, but also by the specific characteristics of speech stimuli. [Work supported by NIH.

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

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    Ellis Allan G

    2010-07-01

    Full Text Available Abstract Background There are few predictions about the directionality or extent of morphological trait (mismatches 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.

  10. Polarity, Intensity and Mismatch: a Superlative Construction of Absolute States

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    Neusa Salim Miranda

    2014-06-01

    Full Text Available Assuming the sociocognitive and constructionist perspective taken by Cognitive Linguistic and by the Models of Use from the Construction Grammar, this work aims at investigating the mismatched feature of a construction, here called as Superlative Synthetic Construction of Absolute States (SSCAS. It is a morphological construction built from the integration of a chore which refers to a non-gradable absolute state (desempregada, casada, grávida / unemployed, married, pregnant with a superlative scale operator (-íssimo/a – very. The result of this integration is types such as: desempregadíssima, casadíssima, gravidíssima, formadíssima. The configuration of SSCAS points to the mismatch phenomenon (FRANCIS & MICHAELIS, 2000; TRAUGOTT, 2007; TRAUGOTT, 2006; GOLDBERG, 1995, 2006, due to the fact that it makes clear the incompatibilities between the formal-semantic properties of the units which integrate this pattern – the superlative affix -íssimo – and the lexical item graduated by it. The incompatibility of this construction is approached from the polar relations of contrariety and contradiction, as they were described by Israel (2004.

  11. Saccharomyces cerevisiae MutLα IS A MISMATCH REPAIR ENDONUCLEASE*

    Science.gov (United States)

    Kadyrov, Farid A.; Holmes, Shannon F.; Arana, Mercedes E.; Lukianova, Olga A.; O’Donnell, Mike; Kunkel, Thomas A.; Modrich, Paul

    2008-01-01

    MutL homologs are crucial for mismatch repair and genetic stability, but their function is not well understood. Human MutLα (MLH1-PMS2 heterodimer) harbors a latent endonuclease that is dependent on integrity of a PMS2 DQHA(X)2E(X)4E motif (Kadyrov et al. (2006) Cell 126, 297-308). This sequence element is conserved in many MutL homologs, including the PMS1 subunit of Saccharomyces cerevisiae MutLα, but is absent in MutL proteins from bacteria like Escherichia coli that rely on d(GATC) methylation for strand directionality. We show that yeast MutLα is a strand-directed endonuclease that incises DNA in a reaction that depends on a mismatch, yMutSα, yRFC, yPCNA, ATP, and a pre-existing strand break, whereas E. coli MutL is not. Amino acid substitution within the PMS1 DQHA(X)2E(X)4E motif abolishes yMutLα endonuclease activity in vitro and confers strong genetic instability in vivo, but does not affect yMutLα ATPase activity or the ability of the protein to support assembly of the yMutLα•yMutSα•heteroduplex ternary complex. The loaded form of yPCNA may play an important effector role in directing yMutLα incision to the discontinuous strand of a nicked heteroduplex. PMID:17951253

  12. Mismatch repair proficiency and in vitro response to 5-fluorouracil.

    Science.gov (United States)

    Carethers, J M; Chauhan, D P; Fink, D; Nebel, S; Bresalier, R S; Howell, S B; Boland, C R

    1999-07-01

    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. We determined growth selection by cell enrichment assay and cloning efficiency after treatment with 5 micromol/L 5-FU, assayed nucleic 3H-5-FU incorporation, and analyzed the cell cycle by flow cytometry. 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. 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.

  13. Mismatch negativity, social cognition, and functioning in schizophrenia patients.

    Science.gov (United States)

    Wynn, Jonathan K; Sugar, Catherine; Horan, William P; Kern, Robert; Green, Michael F

    2010-05-15

    Cognition and social cognition have been found to influence functional outcome in schizophrenia patients. However, little is known about the underlying neural substrates that are associated with social cognition or daily functioning. Prior studies found associations between mismatch negativity (MMN), an event-related potential response indexing early auditory processing, and functioning in schizophrenia patients. In this study, we examined MMN, social cognition (social perception and theory of mind), and four domains of functioning (work, independent living, social networks, and family networks) in 33 schizophrenia patients and 42 demographically comparable healthy control subjects. Schizophrenia patients exhibited reduced MMN activity at frontocentral electrode sites compared with healthy control subjects. Within the schizophrenia sample, greater MMN activity at frontocentral sites correlated with better work and independent living (but not social or family networks) and with better social perception. These results suggest that MMN activity is more closely tied to some outcome domains (work and independent living) than others. Mismatch negativity has been previously shown to be associated with basic cognition and functional outcome in schizophrenia, but these findings are the first, to our knowledge, to show MMN associations with social cognition. These results are consistent with cascade models of information processing in which deficits in early perceptual processing have a downstream impact on higher order social cognition and community functioning. Published by Elsevier Inc.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  16. Somatosensory mismatch response in young and elderly adults

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    Juho M. Strömmer

    2014-10-01

    Full Text Available Aging is associated with cognitive decline and alterations in early perceptual processes. Studies in the auditory and visual modalities have shown that the mismatch negativity (or the mismatch response, MMR, an event-related potential (ERP elicited by a deviant stimulus in a background of homogenous events, diminishes with aging and cognitive decline. However, the effects of aging on the somatosensory MMR are not known. In the current study, we recorded ERPs to electrical pulses to different fingers of the left hand in a passive oddball experiment in young (22–36 years and elderly (66–95 years adults engaged in a visual task. The MMR was found to deviants as compared to standards at two latency ranges: 180–220 ms and 250–290 ms post-stimulus onset. At 180–220 ms, within the young, the MMR was found at medial electrode sites, whereas aged did not show any amplitude difference between the stimulus types at the same latency range. At 250–290 ms, the MMR was evident with attenuated amplitude and narrowed scalp distribution among aged (Fz compared to young (fronto-centrally and lateral parietal sites. Hence, the results reveal that the somatosensory change detection mechanism is altered in aging. The somatosensory MMR can be used as a reliable measure of age-related changes in sensory-cognitive functions.

  17. Loading effects of anterior cervical spine fusion on adjacent segments

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    Chien-Shiung Wang

    2012-11-01

    Full Text Available Adjacent segment degeneration typically follows anterior cervical spine fusion. However, the primary cause of adjacent segment degeneration remains unknown. Therefore, in order to identify the loading effects that cause adjacent segment degeneration, this study examined the loading effects to superior segments adjacent to fused bone following anterior cervical spine fusion. The C3–C6 cervical spine segments of 12 sheep were examined. Specimens were divided into the following groups: intact spine (group 1; and C5–C6 segments that were fused via cage-instrumented plate fixation (group 2. Specimens were cycled between 20° flexion and 15° extension with a displacement control of 1°/second. The tested parameters included the range of motion (ROM of each segment, torque and strain on both the body and inferior articular process at the superior segments (C3–C4 adjacent to the fused bone, and the position of the neutral axis of stress at under 20° flexion and 15° extension. Under flexion and Group 2, torque, ROM, and strain on both the bodies and facets of superior segments adjacent to the fused bone were higher than those of Group 1. Under extension and Group 2, ROM for the fused segment was less than that of Group 1; torque, ROM, and stress on both the bodies and facets of superior segments adjacent to the fused bone were higher than those of Group 1. These analytical results indicate that the muscles and ligaments require greater force to achieve cervical motion than the intact spine following anterior cervical spine fusion. In addition, ROM and stress on the bodies and facets of the joint segments adjacent to the fused bone were significantly increased. Under flexion, the neutral axis of the stress on the adjacent segment moved backward, and the stress on the bodies of the segments adjacent to the fused bone increased. These comparative results indicate that increased stress on the adjacent segments is caused by stress-shielding effects

  18. Uplink scheduling and adjacent-channel coupling loss analysis for TD-LTE deployment.

    Science.gov (United States)

    Yeo, Woon-Young; Moon, Sung Ho; Kim, Jae-Hoon

    2014-01-01

    TD-LTE, one of the two duplexing modes in LTE, operates in unpaired spectrum and has the advantages of TDD-based technologies. It is expected that TD-LTE will be more rapidly deployed in near future and most of WiMax operators will upgrade their networks to TD-LTE gradually. Before completely upgrading to TD-LTE, WiMax may coexist with TD-LTE in an adjacent frequency band. In addition, multiple TD-LTE operators may deploy their networks in adjacent bands. When more than one TDD network operates in adjacent frequency bands, severe interference may happen due to adjacent channel interference (ACI) and unsynchronized operations. In this paper, coexistence issues between TD-LTE and other systems are analyzed and coexistence requirements are provided. This paper has three research objectives. First, frame synchronization between TD-LTE and WiMax is discussed by investigating possible combinations of TD-LTE and WiMax configurations. Second, an uplink scheduling algorithm is proposed to utilize a leakage pattern of ACI in synchronized operations. Third, minimum requirements for coexistence in unsynchronized operations are analyzed by introducing a concept of adjacent-channel coupling loss. From the analysis and simulation results, we can see that coexistence of TD-LTE with other TDD systems is feasible if the two networks are synchronized. For the unsynchronized case, some special cell-site engineering techniques may be required to reduce the ACI.

  19. Gas explosion in a room with a window and passage to an adjacent room

    Directory of Open Access Journals (Sweden)

    Polandov Yuri

    2016-01-01

    Full Text Available Some publications describe an effect, produced during a physical model experiment, when an adjacent gas-free room influences the gas explosion pressure in a room with a window. The explosion pressure in this case significantly exceeds (2.5 times the explosion pressure in a room without an adjacent room. This result has been confirmed by our studies. Based on other available information about the influence of the ignition point location on the explosion pressure in one room, it was suggested that this could be true for an explosion in two rooms. In our studies we used a test unit with two connected chambers, each having a volume of 1.125 m3. It turned out that this influence of the adjacent volume was not so unambiguous as it was described in those publications. It was found out that the maximum effect of explosion pressure amplification by the adjacent room is achieved, when the igniter is located in the chamber filled with a gas-air mixture in the area between the center of the chamber and the window (maximum amplification by more than 3 times. This effect is lower directly by the window (1.8 times and is practically absent in case of ignition within the area near the passage connecting the chamber with the adjacent room. This suggests that the effect discovered earlier is a special case of the general dependence of the gas explosion pressure in two chambers on the igniter location.

  20. Fluorides leaching from restorative materials and the effect on adjacent teeth.

    Science.gov (United States)

    Qvist, Vibeke; Poulsen, Agneta; Teglers, Poul Thorpen; Mjör, Ivar A

    2010-06-01

    Placing a Class II restoration in a tooth changes the local environment, including that for the adjacent tooth. Apart from the change to a less- or non-cariogenic environment for the restored tooth, the effect of leachable components from a restoration in the adjacent tooth should be taken into consideration. Practice-based clinical studies comprising of 1341 unrestored proximal surfaces in contact with Class II restorations using different restorative materials were reviewed to assess the effect on the caries development on the adjacent teeth. The caries status of the adjacent un-restored proximal surface was assessed as being clinically sound, having active caries with or without cavitation, or having arrested caries. Restorations from nine clinicians were reviewed. They had attended annual meetings where all aspects of the investigation had been discussed. The surfaces were followed for up to eight years. A reduced rate of caries development and progression were found on surfaces in contact with fluoride releasing materials like glass ionomers, resin modified glass ionomers and compomers compared to surfaces in contact with amalgam. Fluoride releasing materials reduce the development and progression of primary caries on adjacent proximal surfaces.

  1. Mutagenesis of the HMGB (high-mobility group B) protein Cmb1 (cytosine-mismatch binding 1) of Schizosaccharomyces pombe: effects on recognition of DNA mismatches and damage.

    OpenAIRE

    Kunz, Christophe; Zurbriggen, Karin; Fleck, Oliver

    2003-01-01

    Cmb1 (cytosine-mismatch binding 1) is a high-mobility group (HMG) protein of Schizosaccharomyces pombe, which consists of 223 amino acids and has a single HMG domain at the C-terminal end. We have created several mutant and deletion forms of the Cmb1 protein and studied the effects on general DNA binding and specific binding to DNA mismatches and damaged DNA. Cmb1Delta41 (i.e. Cmb1 from which the 41 N-terminal amino acids have been deleted) bound specifically to cytosine-containing mismatches...

  2. Frequent mismatch-repair defects link prostate cancer to Lynch syndrome

    DEFF Research Database (Denmark)

    Dominguez-Valentin, Mev; Joost, Patrick; Therkildsen, Christina

    2016-01-01

    BACKGROUND: A possible role for prostate cancer in Lynch syndrome has been debated based on observations of mismatch-repair defective tumors and reports of an increased risk of prostate cancer in mutation carriers. Potential inclusion of prostate cancer in the Lynch syndrome tumor spectrum...... is relevant for family classification, risk estimates and surveillance recommendations in mutation carriers. METHODS: We used the population-based Danish HNPCC-register to identify all prostate cancers that developed in mutation carriers and in their first-degree relatives from 288 Lynch syndrome families...... at age 70 was 3.7 % (95 % CI: 2.3-4.9). CONCLUSION: We provide evidence to link prostate cancer to Lynch syndrome through demonstration of MMR defective tumors and an increased risk of the disease, which suggests that prostate cancer should be considered in the diagnostic work-up of Lynch syndrome....

  3. Mode-mismatched confocal thermal-lens microscope with collimated probe beam

    Energy Technology Data Exchange (ETDEWEB)

    Cabrera, Humberto, E-mail: hcabrera@ictp.it [SPIE-ICTP Anchor Research Laboratory, International Centre for Theoretical Physics (ICTP), Strada Costiera 11, Trieste (Italy); Centro Multidisciplinartio de Ciencias, Instituto Venezolano de Investigaciones Científicas (IVIC), Mérida 5101 (Venezuela, Bolivarian Republic of); Korte, Dorota; Franko, Mladen [Laboratory for Environmental Research, University of Nova Gorica, Vipavska 13, 5000 Nova Gorica (Slovenia)

    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.

  4. Twisting right to left: A…A mismatch in a CAG trinucleotide repeat overexpansion provokes left-handed Z-DNA conformation.

    Directory of Open Access Journals (Sweden)

    Noorain Khan

    2015-04-01

    Full Text Available Conformational polymorphism of DNA is a major causative factor behind several incurable trinucleotide repeat expansion disorders that arise from overexpansion of trinucleotide repeats located in coding/non-coding regions of specific genes. Hairpin DNA structures that are formed due to overexpansion of CAG repeat lead to Huntington's disorder and spinocerebellar ataxias. Nonetheless, DNA hairpin stem structure that generally embraces B-form with canonical base pairs is poorly understood in the context of periodic noncanonical A…A mismatch as found in CAG repeat overexpansion. Molecular dynamics simulations on DNA hairpin stems containing A…A mismatches in a CAG repeat overexpansion show that A…A dictates local Z-form irrespective of starting glycosyl conformation, in sharp contrast to canonical DNA duplex. Transition from B-to-Z is due to the mechanistic effect that originates from its pronounced nonisostericity with flanking canonical base pairs facilitated by base extrusion, backbone and/or base flipping. Based on these structural insights we envisage that such an unusual DNA structure of the CAG hairpin stem may have a role in disease pathogenesis. As this is the first study that delineates the influence of a single A…A mismatch in reversing DNA helicity, it would further have an impact on understanding DNA mismatch repair.

  5. Performing arts attendance and geographic adjacency

    NARCIS (Netherlands)

    C.B.G. Langeveld (Cees); M. Van Stiphout

    2013-01-01

    markdownabstract__Abstract__ Much research has been conducted on the willingness of audiences to travel to access the performing arts. Most studies are based on surveys filled in by arts consumers. The general findings indicate an average distance that audiences are willing to travel for

  6. Prophylactic adjacent-segment vertebroplasty following kyphoplasty for a single osteoporotic vertebral fracture and the risk of adjacent fractures: a retrospective study and clinical experience.

    Science.gov (United States)

    Eichler, Martin C; Spross, Christian; Ewers, Alexander; Mayer, Ryan; Külling, Fabrice A

    2016-10-01

    OBJECTIVE This study investigated the benefit of prophylactic vertebroplasty of the adjacent vertebrae in single-segment osteoporotic vertebral body fractures treated with kyphoplasty. METHODS All patients treated with kyphoplasty for osteoporotic single-segment fractures between January 2007 and August 2012 were included in this retrospective study. The patients received either kyphoplasty alone (kyphoplasty group) or kyphoplasty with additional vertebroplasty of the adjacent segment (vertebroplasty group). The segmental kyphosis with the rate of adjacent-segment fractures (ASFs) and remote fractures were studied on plain lateral radiographs preoperatively, postoperatively, at 3 months, and at final follow-up. RESULTS Thirty-seven (82%) of a possible 45 patients were included for the analysis, with a mean follow-up of 16 months (range 3-54 months). The study population included 31 women, and the mean age of the total patient population was 72 years old (range 53-86 years). In 21 patients (57%), the fracture was in the thoracolumbar junction. Eighteen patients were treated with additional vertebroplasty and 19 with kyphoplasty only. The segmental kyphosis increased in both groups at final follow-up. A fracture through the primary treated vertebra (kyphoplasty) was found in 4 (22%) of the vertebroplasty group and in 3 (16%) of the kyphoplasty group (p = 0.6). An ASF was found in 50% (n = 9) of the vertebroplasty group and in 16% (n = 3) of the kyphoplasty group (p = 0.03). Remote fractures occurred in 1 patient in each group (p = 1.0). CONCLUSIONS Prophylactic vertebroplasty of the adjacent vertebra in patients with single-segment osteoporotic fractures as performed in this study did not decrease the rate of adjacent fractures. Based on these retrospective data, the possible benefits of prophylactic vertebroplasty do not compensate for the possible risks of an additional cement augmentation.

  7. Asymmetric ATP Binding and Hydrolysis Activity of the Thermus aquaticus MutS Dimer Is Key to Modulation of Its Interactions with Mismatched DNA†

    Science.gov (United States)

    Antony, Edwin; Hingorani, Manju M.

    2010-01-01

    Prokaryotic MutS and eukaryotic Msh proteins recognize base pair mismatches and insertions or deletions in DNA and initiate mismatch repair. These proteins function as dimers (and perhaps higher order oligomers) and possess an ATPase activity that is essential for DNA repair. Previous studies of Escherichia coli MutS and eukaryotic Msh2–Msh6 proteins have revealed asymmetry within the dimer with respect to both DNA binding and ATPase activities. We have found the Thermus aquaticus MutS protein amenable to detailed investigation of the nature and role of this asymmetry. Here, we show that (a) in a MutS dimer one subunit (S1) binds nucleotide with high affinity and the other (S2) with 10-fold weaker affinity, (b) S1 hydrolyzes ATP rapidly while S2 hydrolyzes ATP at a 30–50-fold slower rate, (c) mismatched DNA binding to MutS inhibits ATP hydrolysis at S1 but slow hydrolysis continues at S2, and (d) interaction between mismatched DNA and MutS is weakened when both subunits are occupied by ATP but remains stable when S1 is occupied by ATP and S2 by ADP. These results reveal key MutS species in the ATPase pathway; S1ADP–S2ATP is formed preferentially in the absence of DNA or in the presence of fully matched DNA, while S1ATP–S2ATP and S1ATP–S2ADP are formed preferentially in the presence of mismatched DNA. These MutS species exhibit differences in interaction with mismatched DNA that are likely important for the mechanism of MutS action in DNA repair. PMID:15476405

  8. Gas samples of Afghanistan and adjacent areas (gasafg.shp)

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This shapefile contains points that describe the location of gas samples collected in Afghanistan and adjacent areas and the results of organic geochemical analysis.

  9. Systems of pillarless working of adjacent, sloped and inclined seams

    Energy Technology Data Exchange (ETDEWEB)

    Batmanov, Yu.K.; Bakhtin, A.F.; Bulavka, E.I.

    1979-01-01

    An analysis is made (advantages and disadvantages) of existing and recommended (pillarless) systems of working adjacent, sloped, and inclined seams. The economic benefits, area and extent of those systems are indicated. 8 references, 4 figures.

  10. Community conservation adjacent to Ruaha National Park, Tanzania

    Science.gov (United States)

    Sue Stolberger

    2007-01-01

    In the areas adjacent to Ruaha National Park where rural communities exist, much more work and education is required to enable them to benefit directly and indirectly from tourism and managing their own natural resources.

  11. Influence of cantilevered sheet pile deflection on adjacent roadways.

    Science.gov (United States)

    2009-06-01

    Cantilevered sheet pile walls are often used adjacent roadways as temporary support during construction. Excess movement of these walls has led to excessive roadway distress causing additional repairs to be necessary. This study assessed the effects ...

  12. Ollier's disease in association with adjacent fibromatosis

    Energy Technology Data Exchange (ETDEWEB)

    Al-Ismail, Khalid; Torreggiani, William C.; Munk, Peter L. [Department of Radiology, Vancouver General Hospital, University of British Columbia, 899 West l2th Avenue, Vancouver, BC (Canada); O' Connell, John X.; Nicolaou, Savvakis [Department of Pathology, Vancouver General Hospital, University of British Columbia, 899 West l2th Avenue, Vancouver, BC (Canada); Masri, Bassam A. [Department of Orthopaedics, Vancouver General Hospital, University of British Columbia, 899 West l2th Avenue, Vancouver, BC (Canada)

    2002-08-01

    Ollier's disease (enchondromatosis) is a nonhereditary disorder of mesodermal dysplasia. It is characterized by the presence of multiple enchondromas that typically affect the metaphyseal ends of bones. The association of Ollier's disease with adjacent fibromatosis has, to our knowledge, not been previously described. We report a case of Ollier's disease in association with soft tissue fibromatosis adjacent to the involved upper arm. (orig.)

  13. Disownership and disembodiment of the real limb without visuoproprioceptive mismatch.

    Science.gov (United States)

    Newport, Roger; Preston, Catherine

    2011-01-01

    The brain is able to sustain multiple bodily representations, and it is still unclear whether real body parts can be disembodied during the embodiment of fake or illusory body parts. The current experiment attempted to disembody the real hand without the visuoproprioceptive mismatch thought to compromise disembodiment in the rubber hand illusion by providing asynchronous feedback of the hand viewed in its actual location. Participants disowned their real hand and claimed ownership of a synchronous fake hand as measured by ownership questionnaires and skin conductance responses to perceived threat. In contrast, the body schema, as indexed by manual pointing, was only mildly affected, further supporting the distinction between bodily representations. Conflicts in time were more disruptive than conflicts in space for body ownership, while the effect was less so for body schema, schema being more affected by the proximity of vision and proprioception.

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

    Science.gov (United States)

    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. © London School of Economics and Political Science 2014.

  15. Mismatch repair status and synchronous metastases in colorectal cancer

    DEFF Research Database (Denmark)

    Nordholm-Carstensen, Andreas; Krarup, Peter-Martin; Morton, Dion

    2015-01-01

    logistic- and Cox-regression and proportional excess hazards analyses were used for confounder adjustment and to adjust for the general population mortality. In total, 983 of 6,692 patients (14.7%) had dMMR and 935 (14.0%) had SCCM. dMMR was associated with a decreased risk of SCCM, adjusted Odds Ratio (a......The causality between the metastatic potential, mismatch repair status (MMR) and survival in colorectal cancer (CRC) is complex. This study aimed to investigate the impact of MMR in CRC on the occurrence of synchronous metastases (SCCM) and survival in patients with SCCM on a national basis....... A nationwide cohort study of 6,692 patients diagnosed with CRC between 2010 and 2012 was conducted. Data were prospectively entered into the Danish Colorectal Cancer Group's database and merged with data from the Danish Pathology Registry and the National Patient Registry. Multivariable and multinomial...

  16. DNA mismatch repair and its many roles in eukaryotic cells

    DEFF Research Database (Denmark)

    Liu, Dekang; Keijzers, Guido; Rasmussen, Lene Juel

    2017-01-01

    in the clinic, and as a biomarker of cancer susceptibility in animal model systems. Prokaryotic MMR is well-characterized at the molecular and mechanistic level; however, MMR is considerably more complex in eukaryotic cells than in prokaryotic cells, and in recent years, it has become evident that MMR plays......DNA mismatch repair (MMR) is an important DNA repair pathway that plays critical roles in DNA replication fidelity, mutation avoidance and genome stability, all of which contribute significantly to the viability of cells and organisms. MMR is widely-used as a diagnostic biomarker for human cancers...... novel roles in eukaryotic cells, several of which are not yet well-defined or understood. Many MMR-deficient human cancer cells lack mutations in known human MMR genes, which strongly suggests that essential eukaryotic MMR components/cofactors remain unidentified and uncharacterized. Furthermore...

  17. Efficient and reproducible identification of mismatch repair deficient colon cancer

    DEFF Research Database (Denmark)

    Joost, Patrick; Bendahl, Pär-Ola; Halvarsson, Britta

    2013-01-01

    BACKGROUND: The identification of mismatch-repair (MMR) defective colon cancer is clinically relevant for diagnostic, prognostic and potentially also for treatment predictive purposes. Preselection of tumors for MMR analysis can be obtained with predictive models, which need to demonstrate ease...... of application and favorable reproducibility. METHODS: We validated the MMR index for the identification of prognostically favorable MMR deficient colon cancers and compared performance to 5 other prediction models. In total, 474 colon cancers diagnosed ≥ age 50 were evaluated with correlation between...... and efficiently identifies MMR defective colon cancers with high sensitivity and specificity. The model shows stable performance with low inter-observer variability and favorable performance when compared to other MMR predictive models....

  18. Fast damping in mismatched high intensity beam transportation

    Directory of Open Access Journals (Sweden)

    V. Variale

    2001-08-01

    Full Text Available 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.

  19. Memory reactivation or reinstatement and the mismatch negativity.

    Science.gov (United States)

    Ritter, Walter; Sussman, Elyse; Molholm, Sophie; Foxe, John J

    2002-03-01

    Previous studies have suggested that the memory underlying the mismatch negativity (MMN) can be deactivated by a period of silence and later reactivated. An alternative is that the memory becomes inapplicable due to a period of silence and subsequently reinstated. Both interpretations rest on the absence of a MMN for a deviant in Position 1 of a train (showing deactivation or inapplicability of the memory) and the presence of a MMN in Position 2 of the train (evidencing reactivation or reinstatement of the memory). In these studies, the standards were fixed across all trains of a given condition. Hence, it is not clear if the MMN elicited in Position 2 requires presentation of multiple trains with identical standards or only a single train. Experiment 1 showed that a single train is sufficient. With data from recent studies, Experiment 2 showed that MMNs in Position 2 of trains are due to reinstatement rather than reactivation of the memory.

  20. Diagnostic criteria for constitutional mismatch repair deficiency syndrome

    DEFF Research Database (Denmark)

    Wimmer, Katharina; Kratz, Christian P; Vasen, Hans F A

    2014-01-01

    Constitutional mismatch repair deficiency (CMMRD) syndrome is a distinct childhood cancer predisposition syndrome that results from biallelic germline mutations in one of the four MMR genes, MLH1, MSH2, MSH6 or PMS2. The tumour spectrum is very broad, including mainly haematological, brain...... and intestinal tract tumours. Patients show a variety of non-malignant features that are indicative of CMMRD. However, currently no criteria that should entail diagnostic evaluation of CMMRD exist. We present a three-point scoring system for the suspected diagnosis CMMRD in a paediatric/young adult cancer....... They include multiple hyperpigmented and hypopigmented skin areas, brain malformations, pilomatricomas, a second childhood malignancy, a Lynch syndrome (LS)-associated tumour in a relative and parental consanguinity. According to the scoring system, CMMRD should be suspected in any cancer patient who reaches...

  1. Microsatellite Instability Use in Mismatch Repair Gene Sequence Variant Classification

    Directory of Open Access Journals (Sweden)

    Bryony A. Thompson

    2015-03-01

    Full Text Available Inherited mutations in the DNA mismatch repair genes (MMR can cause MMR deficiency and increased susceptibility to colorectal and endometrial cancer. Microsatellite instability (MSI is the defining molecular signature of MMR deficiency. The clinical classification of identified MMR gene sequence variants has a direct impact on the management of patients and their families. For a significant proportion of cases sequence variants of uncertain clinical significance (also known as unclassified variants are identified, constituting a challenge for genetic counselling and clinical management of families. The effect on protein function of these variants is difficult to interpret. The presence or absence of MSI in tumours can aid in determining the pathogenicity of associated unclassified MMR gene variants. However, there are some considerations that need to be taken into account when using MSI for variant interpretation. The use of MSI and other tumour characteristics in MMR gene sequence variant classification will be explored in this review.

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

    Science.gov (United States)

    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

  3. Primary angioplasty for heart attack: mismatch between expectations and reality?

    Science.gov (United States)

    Astin, Felicity; Closs, S José; McLenachan, Jim; Hunter, Stacey; Priestley, Claire

    2009-01-01

    This paper is a report of a study to explore patients' experiences of primary angioplasty and assess their illness perceptions during early recovery. Primary angioplasty is recognized as the gold standard treatment for patients with ST elevation myocardial infarction, yet little is known about patients' experiences of this treatment. Recent policy change has emphasized the need for clinical practice to be more patient-centred. One way to achieve this is to understand patients' experiences of treatment better. A mixed methods exploratory study was carried out in 2006-2007 with a purposive sample of 29 patients. Data were collected 3-12 days after hospital discharge using (a) semi-structured interviews to explore participants' experiences and (b) The Illness Perception Questionnaire to evaluate illness perceptions. Interview data were analysed using the Framework approach. Questionnaire data were used to inform the qualitative findings. Participants were very positive about their treatment but experienced considerable emotional shock, which was exacerbated by the speed with which events occurred. Patients' experiences were characterized by a mismatch between their expectations and reality. Questionnaire data supported the notion that they experienced difficulty in 'making sense' of their condition in a coherent way. They tended to see their condition as 'acute' rather than 'chronic' and their treatment as curative. Patient education should include focused discussions addressing the 'mismatches' that may occur between their expectations and reality. In this way, a more coherent understanding can be promoted, with greater awareness of heart disease as a long-term condition requiring ongoing self-management.

  4. Involvement of the DNA mismatch repair system in cisplatin sensitivity of testicular germ cell tumours

    DEFF Research Database (Denmark)

    Rudolph, Christiane; Melau, Cecilie; Nielsen, John E.

    2017-01-01

    BackgroundTesticular germ cell tumours (TGCT) are highly sensitive to cisplatin-based chemotherapy, but patients with tumours containing differentiated teratoma components are less responsive to this treatment. The cisplatin sensitivity in TGCT has previously been linked to the embryonic phenotype...... in the majority of tumours, although the underlying mechanism largely remains to be elucidated. The aim of this study was to investigate the role of the DNA mismatch repair (MMR) system in the cisplatin sensitivity of TGCT. MethodsThe expression pattern of key MMR proteins, including MSH2, MSH6, MLH1 and PMS2......, were investigated during testis development and in the pathogenesis of TGCT, including germ cell neoplasia in situ (GCNIS). The TGCT-derived cell line NTera2 was differentiated using retinoic acid (10 μM, 6 days) after which MMR protein expression and activity, as well as cisplatin sensitivity, were...

  5. Heat Mismatch of future Net Zero Energy Buildings within district heating areas in Denmark

    DEFF Research Database (Denmark)

    Nielsen, Steffen; Möller, Bernd

    . NZEBs are characterized by having a greatly reduced energy demand that on an annual basis can be balanced out by an equivalent generation of energy from RES. Most buildings in Denmark are connected electricity grids and around half to district heating (DH) systems. Connecting buildings to larger energy...... instead of wasting the energy. The objective in this paper is find how large an area of NZEBs is to be built within DH areas and how the heat mismatch of NZEBs influence different types of Danish DH systems. In the analyses nine different scenarios are analyzed. The examination is from a technical......The long-term goal for Denmark is to develop an energy system solely based on renewable energy sources (RES) in 2050. To reach this goal energy savings in buildings are essential. Therefore, a focus on energy efficient measures in buildings and net zero energy buildings (NZEBs) have increased...

  6. Mismatch repair gene mutation spectrum in the Swedish Lynch syndrome population

    DEFF Research Database (Denmark)

    Lagerstedt-Robinson, Kristina; Rohlin, Anna; Aravidis, Christos

    2016-01-01

    Lynch syndrome caused by constitutional mismatch‑repair defects is one of the most common hereditary cancer syndromes with a high risk for colorectal, endometrial, ovarian and urothelial cancer. Lynch syndrome is caused by mutations in the mismatch repair (MMR) genes i.e., MLH1, MSH2, MSH6 and PMS2....... After 20 years of genetic counseling and genetic testing for Lynch syndrome, we have compiled the mutation spectrum in Sweden with the aim to provide a population-based perspective on the contribution from the different MMR genes, the various types of mutations and the influence from founder mutations....... Mutation data were collected on a national basis from all laboratories involved in genetic testing. Mutation analyses were performed using mainly Sanger sequencing and multiplex ligation-dependent probe amplification. A total of 201 unique disease-predisposing MMR gene mutations were identified in 369...

  7. Arterial spin-labeled perfusion imaging to predict mismatch in acute ischemic stroke.

    Science.gov (United States)

    Niibo, Takeya; Ohta, Hajime; Yonenaga, Kazuma; Ikushima, Ichiro; Miyata, Shirou; Takeshima, Hideo

    2013-09-01

    We assigned a threshold to arterial spin-labeling (ASL) perfusion-weighted images (PWI) from patients with acute ischemic stroke and compared them with dynamic susceptibility contrast perfusion images to examine whether mismatch can be determined. Pseudocontinuous ASL was combined with dynamic susceptibility contrast PWI in 23 patients with acute ischemic stroke. Scans were obtained within 24 hours of symptom onset. PWI volumes were defined by ASL cerebral blood flow (10 s) that show a strong association with cerebral blood flow PWI and the baseline diffusion-weighted imaging lesion, respectively, and the final infarct volume were assessed. The lesion volumes defined by MTT>10 s and ASL10 s and ASLPWI lesions defined by ASL10 s. In acute ischemic stroke, PWI lesions based on ASL threshold of 10 s.

  8. Dynamic four-dimensional computed tomography for preoperative assessment of lung cancer invasion into adjacent structures†.

    Science.gov (United States)

    Choong, Cliff K C; Pasricha, Sundeep S; Li, Xun; Briggs, Peter; Ramdave, Shakher; Crossett, Marcus; Troupis, John M

    2015-02-01

    The 320-slice computed tomography (CT) provides three-dimensional and dynamic imaging resulting in the ability to assess motion analysis between two adjacent structures (the fourth dimension). Differential movements between two adjacent structures would indicate that there is no fixation between the two structures. Eight patients with non-small-cell lung cancers located adjacent to vital structures (e.g. the great vessels) (n = 4), mediastinum (n = 1) or chest wall (n = 3) where conventional CT was unable to exclude local invasion underwent dynamic four-dimensional (4D) CT assessment. In 3 patients, the lung tumour was abutting the chest wall and 1 patient had tumour abutting the mediastinum. The remaining patients included a patient with a large 14-cm left lower lobe cancer abutting the descending thoracic aorta who had previous pleurodesis; a patient with an apical right upper lobe 6-cm cancer with static imaging appearances suggestive of tumour invasion into the apex, the mediastinal surface and superior vena cava (SVC); a patient with a 3.5-cm cancer which had a broad 2.5-cm base abutting the distal aortic arch and a patient with a 14-cm left upper lobe cancer abutting the aortic arch, descending thoracic aorta and chest wall. Differential movements between the tumour and adjacent structure on 4D CT were considered indicative of the absence of frank invasion. Dynamic 4D imaging revealed differential movements between the tumour and the adjacent structures in 7 cases, suggesting the absence of overt malignant invasion. Intraoperative assessments confirmed the findings. In 1 case, a small area of fixation seen on dynamic CT corresponded intraoperatively to superficial invasion of the adventitia of the SVC. Dynamic 4D 320-slice CT is useful in the preoperative assessment of the direct invasion of lung cancer into adjacent structures and hence its resectability. © The Author 2014. Published by Oxford University Press on behalf of the European Association for

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

    Science.gov (United States)

    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…

  10. University Graduates' Skills Mismatches in Central Asia: Employers' Perspectives from Post-Soviet Tajikistan

    Science.gov (United States)

    Jonbekova, Dilrabo

    2015-01-01

    This paper examines employers' perspectives about university graduates' skills and preparation for employment in post-Soviet Tajikistan. It explores the mismatch between the skills university graduates acquire and the skills required in the job market, and addresses some of the underlying reasons for the perceived skills mismatch. Thematic…

  11. Job mismatches and their labour-market effects among school-leavers in Europe

    NARCIS (Netherlands)

    Wolbers, M.H.J.

    2003-01-01

    In this article, we investigate the determinants of job mismatches with regard to the field of education among school-leavers in Europe. We also examine the effects of job mismatches on the labour-market position of school-leavers. Special attention is paid to cross-national differences in this

  12. Skill mismatch among migrant workers: evidence from a large multi-country dataset

    NARCIS (Netherlands)

    Visintin, S.; Tijdens, K.; van Klaveren, M.

    2015-01-01

    This article unravels the migrants’ incidence of skill mismatch taking into consideration different migration flows. Mismatch is the situation in which workers have jobs for which lower skill levels are required compared to their education. We use a dataset (from a large multi-country web survey)

  13. Educational mismatches for second generation migrants. An analysis of applied science graduates in the Netherlands

    NARCIS (Netherlands)

    Falcke, Swantje; Meng, Christoph; Nollen, Romy

    2016-01-01

    Educational mismatches, i.e. diferences between the education attained and required for a job have been found to negatively affect earnings and job satisfaction and thus lead to a lower return to education. In this paper we aim to see whether immigrants are more prone to educational mismatches and

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

    Science.gov (United States)

    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…

  15. Immunotherapy holds the key to cancer treatment and prevention in constitutional mismatch repair deficiency (CMMRD) syndrome

    NARCIS (Netherlands)

    Westdorp, Harm; Kolders, Sigrid; Hoogerbrugge, Nicoline; de Vries, I Jolanda M; Jongmans, Marjolijn C.J.; Schreibelt, Gerty

    2017-01-01

    Monoallelic germline mutations in one of the DNA mismatch repair (MMR) genes cause Lynch syndrome, with a high lifetime risks of colorectal and endometrial cancer at adult age. Less well known, is the constitutional mismatch repair deficiency (CMMRD) syndrome caused by biallelic germline mutations

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

    Science.gov (United States)

    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…

  17. Analytical Expressions for Harmonic Distortion at Low Frequencies due to Device Mismatch in CMOS Current Mirrors

    DEFF Research Database (Denmark)

    Bruun, Erik

    1999-01-01

    One of the origins of harmonic distortion in current mirrors is the inevitable mismatch between the mirror transistors. In this brief we examine both single current mirrors and complementary class AB current mirrors and develop analytical expressions for the mismatch induced harmonic distortion...

  18. Earthquake response of adjacent structures with viscoelastic and friction dampers

    Directory of Open Access Journals (Sweden)

    Žigić Miodrag

    2015-01-01

    Full Text Available We study the seismic response of two adjacent structures connected with a dry friction damper. Each of them consists of a viscoelastic rod and a rigid block, which can slide without friction along the moving base. A simplified earthquake model is used for modeling the horizontal ground motion. Energy dissipation is taken by the presence of the friction damper, which is modeled by the set-valued Coulomb friction law. Deformation of viscoelastic rods during the relative motion of the blocks represents another way of energy dissipation. The constitutive equation of a viscoelastic body is described by the fractional Zener model, which includes fractional derivatives of stress and strain. The problem merges fractional derivatives as non-local operators and theory of set-valued functions as the non-smooth ones. Dynamical behaviour of the problem is governed by a pair of coupled multi-valued differential equations. The posed Cauchy problem is solved by use of the Grünwald-Letnikov numerical scheme. The behaviour of the system is analyzed for different values of system parameters.

  19. Association between the perfusion/diffusion and diffusion/FLAIR mismatch: data from the AXIS2 trial.

    Science.gov (United States)

    Wouters, Anke; Dupont, Patrick; Ringelstein, Erich B; Norrving, Bo; Chamorro, Angel; Grond, Martin; Laage, Rico; Schneider, Armin; Wilms, Guido; Thomalla, Götz; Lemmens, Robin; Thijs, Vincent N

    2015-10-01

    The perfusion-/diffusion-weighted imaging (PWI/DWI) mismatch and the diffusion/fluid attenuated inversion recovery (DWI/FLAIR) mismatch are magnetic resonance imaging (MRI) markers of evolving brain ischemia. We examined whether the DWI/FLAIR mismatch was independently associated with the PWI/DWI mismatch. Furthermore, we determined whether the presence of the DWI/FLAIR mismatch in patients with the PWI/DWI mismatch would provide additional information regarding last seen normal time (LTM). We used data from the 'AX200 for ischemic stroke' trial (AXIS 2 study NCT00927836). We studied the association between the presence of the DWI/FLAIR and PWI/DWI mismatch, baseline National Institute of Health Stroke Scale (NIHSS), age, ischemic-core volume, gender, intravenous (IV) tissue plasminogen activator (tPA), and perfusion-mismatch volume in univariate analysis. Significant variables (PPWI/DWI and the DWI/FLAIR mismatch. Patients with the double mismatch pattern had a shorter LTM than patients with the PWI/DWI mismatch alone (Median difference 90 minutes, PPWI/DWI mismatch are strongly associated, independent from LTM. Furthermore, in the presence of the PWI/DWI mismatch, the DWI/FLAIR pattern indicates a shorter LTM. This could have implications in selecting patients for reperfusion therapy.

  20. Scale Mismatches in Social-Ecological Systems: Causes, Consequences, and Solutions

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    Graeme S. Cumming

    2006-06-01

    Full Text Available Scale is a concept that transcends disciplinary boundaries. In ecology and geography, scale is usually defined in terms of spatial and temporal dimensions. Sociological scale also incorporates space and time, but adds ideas about representation and organization. Although spatial and temporal location determine the context for social and ecological dynamics, social-ecological interactions can create dynamic feedback loops in which humans both influence and are influenced by ecosystem processes. We hypothesize that many of the problems encountered by societies in managing natural resources arise because of a mismatch between the scale of management and the scale(s of the ecological processes being managed. We use examples from southern Africa and the southern United States to address four main questions: (1 What is a "scale mismatch?" (2 How are scale mismatches generated? (3 What are the consequences of scale mismatches? (4 How can scale mismatches be resolved? Scale mismatches occur when the scale of environmental variation and the scale of social organization in which the responsibility for management resides are aligned in such a way that one or more functions of the social-ecological system are disrupted, inefficiencies occur, and/or important components of the system are lost. They are generated by a wide range of social, ecological, and linked social-ecological processes. Mismatches between the scales of ecological processes and the institutions that are responsible for managing them can contribute to a decrease in social-ecological resilience, including the mismanagement of natural resources and a decrease in human well-being. Solutions to scale mismatches usually require institutional changes at more than one hierarchical level. Long-term solutions to scale mismatch problems will depend on social learning and the development of flexible institutions that can adjust and reorganize in response to changes in ecosystems. Further research is

  1. Ischemic diffusion lesion reversal is uncommon and rarely alters perfusion-diffusion mismatch.

    Science.gov (United States)

    Chemmanam, T; Campbell, B C V; Christensen, S; Nagakane, Y; Desmond, P M; Bladin, C F; Parsons, M W; Levi, C R; Barber, P A; Donnan, G A; Davis, S M

    2010-09-21

    The use of diffusion-weighted imaging (DWI) to define irreversibly damaged infarct core is challenged by data suggesting potential partial reversal of DWI abnormalities. However, previous studies have not considered infarct involution. We investigated the prevalence of DWI lesion reversal in the EPITHET Trial. EPITHET randomized patients 3-6 hours from onset of acute ischemic stroke to tissue plasminogen activator (tPA) or placebo. Pretreatment DWI and day 90 T2-weighted images were coregistered. Apparent reversal of the acute ischemic lesion was defined as DWI lesion not incorporated into the final infarct. Voxels of CSF at follow-up were subtracted from regions of apparent DWI lesion reversal to adjust for infarct atrophy. All cases were visually cross-checked to exclude volume loss and coregistration inaccuracies. In 60 patients, apparent reversal involved a median 46% of the baseline DWI lesion (median volume 4.9 mL, interquartile range 2.6-9.5 mL) and was associated with less severe baseline hypoperfusion (p < 0.001). Apparent reversal was increased by reperfusion, regardless of the severity of baseline hypoperfusion (p = 0.02). However, the median volume of apparent reversal was reduced by 45% when CSF voxels were subtracted (2.7 mL, interquartile range 1.6-6.2 mL, p < 0.001). Perfusion-diffusion mismatch classification only rarely altered after adjusting the baseline DWI volume for apparent reversal. Visual comparison of acute DWI to subacute DWI or day 90 T2 identified minor regions of true DWI lesion reversal in only 6 of 93 patients. True DWI lesion reversal is uncommon in ischemic stroke patients. The volume of apparent lesion reversal is small and would rarely affect treatment decisions based on perfusion-diffusion mismatch.

  2. MISMATCH REPAIR-DEPENDENT ITERATIVE EXCISION AT IRREPARABLE O6-METHYLGUANINE LESIONS IN HUMAN NUCLEAR EXTRACTS*

    Science.gov (United States)

    York, Sally J.; Modrich, Paul

    2008-01-01

    The response of mammalian cells to SN1 DNA methylators depends on functional MutSα and MutLα. Cells deficient in either of these activities are resistant to the cytotoxic effects of this class of chemotherapeutic drug. Because killing by SN1 methylators has been attributed to O6-methylguanine (MeG), we have constructed nicked circular heteroduplexes that contain a single MeG-T mispair and have examined processing of these molecules by mismatch repair in nuclear extracts of human cells. Excision provoked by MeG-T is restricted to the incised heteroduplex strand, leading to removal of the MeG when it resides on this strand. However, when the MeG is located on the continuous strand, the heteroduplex is irreparable. MeG-T-dependent repair DNA synthesis is observed on both reparable and irreparable, 3’ and 5’ heteroduplexes as judged by [32P]dAMP incorporation. Labeling with [α-32P]dATP followed by a cold dATP chase has demonstrated that newly synthesized DNA on irreparable molecules is subject to re-excision in a reaction that is MutLα-dependent, an effect attributable to presence of MeG on the template strand. Processing of the irreparable 3’ heteroduplex is also associated with incision of the discontinuous strand of a few percent of molecules near the thymidylate of the MeG-T base pair. These results provide the first direct evidence for mismatch repair-mediated iterative processing of DNA methylator damage, an effect that may be relevant to damage signaling events triggered by this class of chemotherapeutic agent. PMID:16772289

  3. Maturation of teeth adjacent to dental agenesis site.

    Science.gov (United States)

    Ben-Bassat, Yocheved; Babadzhanov, Daniel; Brin, Ilana; Hazan-Molina, Hagai; Aizenbud, Dror

    2014-10-01

    The purpose of this study was to evaluate the developmental stage of teeth adjacent to the agenesis site in comparison to their antimeres. Panoramic views of 39 patients with unilateral dental agenesis and 42 normal controls were evaluated. The dental developmental stage (normal or delayed) of the teeth adjacent to the agenesis site was determined for each patient using the Haavikko's method, while the overall dental age was determined by Becker's method. No statistically significant difference was found in the developmental stage of teeth adjacent to the agenesis, compared to their antimere and to the same teeth in the normal control group. However, the prevalence of cases with no difference in development was almost double for the tooth distal to the agenesis site compared to the tooth mesial to the agenesis site in the hypodontia group (84.6% distal and 43.6% mesial; p teeth adjacent to the agenesis site and their antimeres. (2) Teeth mesial to the agenesis site showed some delay in development compared to teeth distal to the agenesis site, in this study. (3) The 1st molars, which were in most of the cases the distal adjacent tooth to the site of agenesis, showed developmental stability. (4) Additional longitudinal studies are needed to examine the dental developmental pattern in patients with agenesis.

  4. Novel cancerization marker, TP53, and its role in distinguishing normal tissue adjacent to cancerous tissue from normal tissue adjacent to benign tissue

    Directory of Open Access Journals (Sweden)

    Liu Guo-Yan

    2012-11-01

    Full Text Available Abstract Background The histopathological and molecular heterogeneity of normal tissue adjacent to cancerous tissue (NTAC and normal tissue adjacent to benign tissue (NTAB, and the availability of limited specimens make deciphering the mechanisms of carcinogenesis challenging. Our goal was to identify histogenetic biomarkers that could be reliably used to define a transforming fingerprint using RNA in situ hybridization. Methods We evaluated 15 tumor-related RNA in situ hybridization biomarkers using tumor microarray and samples of seven tumor-adjacent normal tissues from 314 patients. Biomarkers were determined using comprehensive statistical methods (significance of support vector machine-based artificial intelligence and area under curve scoring of classification distribution. Results TP53 was found to be a most reliable index (P -7; area under curve >87% for distinguishing NTAC from NTAB, according to the results of a significance panel (BCL10, BECN1, BRCA2, FITH, PTCH11 and TP53. Conclusions The genetic alterations in TP53 between NTAC and NTAB may provide new insight into the field of cancerization and tumor transformation.

  5. Novel cancerization marker, TP53, and its role in distinguishing normal tissue adjacent to cancerous tissue from normal tissue adjacent to benign tissue

    Science.gov (United States)

    2012-01-01

    Background The histopathological and molecular heterogeneity of normal tissue adjacent to cancerous tissue (NTAC) and normal tissue adjacent to benign tissue (NTAB), and the availability of limited specimens make deciphering the mechanisms of carcinogenesis challenging. Our goal was to identify histogenetic biomarkers that could be reliably used to define a transforming fingerprint using RNA in situ hybridization. Methods We evaluated 15 tumor-related RNA in situ hybridization biomarkers using tumor microarray and samples of seven tumor-adjacent normal tissues from 314 patients. Biomarkers were determined using comprehensive statistical methods (significance of support vector machine-based artificial intelligence and area under curve scoring of classification distribution). Results TP53 was found to be a most reliable index (P 87%) for distinguishing NTAC from NTAB, according to the results of a significance panel (BCL10, BECN1, BRCA2, FITH, PTCH11 and TP53). Conclusions The genetic alterations in TP53 between NTAC and NTAB may provide new insight into the field of cancerization and tumor transformation. PMID:23170979

  6. A review on eigen values of adjacency matrix of graph with cliques

    Science.gov (United States)

    Carnia, Ema; Suyudi, Moch.; Aisah, Isah; Supriatna, Asep K.

    2017-08-01

    The paper reviews the applications of eigen value in different areas. One of the area is in the analysis of graphs coming from networks. The development of theory regarding the eigenvalues and its maximum eigenvalue of the adjacency matrix arising from a general graph is already well-established. Here we review some notions from different context, i.e. led by observation of some simple experiments regarding the relation between graph, cliques, and the eigen values of the adjacency matrix. We focus on regular graphs having one or more cliques in their graph structures. We do some numerical experiment on the computation of the eigen values of the adjacency matrix and show some patterns on the relation between the structure of the graph (e.g. the maximum cliques, chromatic number) and the eigen values of the adjacency matrix. By observing these patterns we find some conclusion, such as: i. the maximum clique of a complete graph is given by the largest eigen value plus one; ii. the maximum clique of a cycle graph (simple incomplete regular graph) equals the largest eigen value, in which the value is two; iii. the maximum multiplicity of the eigen values of a cycle graph is two. Future direction of the development is also presented based on the careful analysis of the existing development.

  7. Emission of pesticides during drilling and deposition in adjacent areas

    Directory of Open Access Journals (Sweden)

    Heimbach, Udo

    2014-02-01

    Full Text Available In seven experiments seeds of maize, oil seed rape and barley, treated with neonicotinoids, were sown using pneumatic drilling equipment with deflectors attached in case of pneumatic suction systems. Directly adjacent to the drilled area of usually about 50 m width were replicated areas with bare soil as well as with crops. During maize (Zea mays drilling flowering oil seed rape (Brassica napus and during drilling of barley (Hordeum vulgare and oil seed rape flowering white mustard (Sinapis alba was adjacent. The amount of residues in the adjacent non crop areas in Petri dishes being distributed on the bare soil declined only slowly from 1 to 20 m distance from the area drilled. Seed batches with more abrasion and higher content of active substances in the dust resulted in higher residues off crop. After drilling of maize in four experiments in Petri dishes in adjacent non crop areas in 1-5 m distance between 0.02 and 0.40 g a.s./ha of neonicotinoids and in the adjacent oil seed rape a total of 0.05–0.80 g a.s./ha were detected. After drilling oil seed rape or barley these values were only 0.02–0.06 g a.s./ha in Petri dishes in non crop areas and 0.03-0.08 g a.s./ha in total in adjacent white mustard. In gauze net samplers installed vertically in 3 m distance in non crop areas up to seven times higher values were detected compared to Petri dishes.

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

    Science.gov (United States)

    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.

  9. When some is not every: dissociating scalar implicature generation and mismatch.

    Science.gov (United States)

    Shetreet, Einat; Chierchia, Gennaro; Gaab, Nadine

    2014-04-01

    Making inferences beyond the literal meaning of sentences occurs with certain scalar expressions via scalar implicatures. For example, adults usually interpret some as some but not all. On the basis of behavioral research, it has been suggested that processing implicatures is cognitively costly. However, many studies have used cases where sentences with some did not match the context in which they were presented. Our study aimed to examine whether the processing cost is linked to implicature generation, to the mismatch between the implicature and the context, or to both processes. To do so, we explored the neural patterns of implicature generation and implicature mismatch using fMRI. Thirteen participants performed a sentence-picture matching task (where pictures determined the context) with mismatched implicatures, successful implicatures or no implicature conditions. Several brain regions were identified when comparing cases of implicature mismatch and cases without implicatures. One of these regions, left-IFG, was jointly activated for mismatched and successful implicatures, as observed in a conjunction analysis. By contrast, left-MFG and medial-frontal-gyrus, were identified when comparing cases of implicature mismatch with cases of successful implicatures. Thus, the left IFG can be interpreted as being linked to implicature generation, whereas the other two areas seem to participate in the processing of the mismatch between the implicature and its context. Our results indicate that scalar implicatures induce processing cost in different ways. This should be considered in future research. Copyright © 2013 Wiley Periodicals, Inc.

  10. Quality of Experience for Large Ultra-High-Resolution Tiled Displays with Synchronization Mismatch

    Directory of Open Access Journals (Sweden)

    Deshpande Sachin

    2011-01-01

    Full Text Available This paper relates to quality of experience when viewing images, video, or other content on large ultra-high-resolution displays made from individual display tiles. We define experiments to measure vernier acuity caused by synchronization mismatch for moving images. The experiments are used to obtain synchronization mismatch acuity threshold as a function of object velocity and as a function of occlusion or gap width. Our main motivation for measuring the synchronization mismatch vernier acuity is its relevance in the application of tiled display systems, which create a single contiguous image using individual discrete panels arranged in a matrix with each panel utilizing a distributed synchronization algorithm to display parts of the overall image. We also propose a subjective assessment method for perception evaluation of synchronization mismatch for large ultra-high-resolution tiled displays. For this, we design a synchronization mismatch measurement test video set for various tile configurations for various interpanel synchronization mismatch values. The proposed method for synchronization mismatch perception can evaluate tiled displays with or without tile bezels. The results from this work can help during design of low-cost tiled display systems, which utilize distributed synchronization mechanisms for a contiguous or bezeled image display.

  11. Skin Flaps for the Repair of Multiple Adjacent Tumors.

    Science.gov (United States)

    Suárez-Valladares, M J; Pérez-Bustillo, A; González-Sixto, B; Otero-Rivas, M; Rodríguez-Prieto, M A

    2016-03-01

    In daily clinical practice, the dermatologic surgeon frequently has to excise closely adjacent tumors in the facial region. In such cases, planning of an appropriate reconstruction technique is essential. The aim is to treat all of the lesions in a single surgical intervention, if possible, and to achieve a good functional and cosmetic outcome. We present 5 patients in whom a single flap was used to repair multiple adjacent defects. Copyright © 2015 AEDV. Published by Elsevier España, S.L.U. All rights reserved.

  12. Nonlinear spin wave coupling in adjacent magnonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Sadovnikov, A. V., E-mail: sadovnikovav@gmail.com; Nikitov, S. A. [Laboratory “Metamaterials,” Saratov State University, Saratov 410012 (Russian Federation); Kotel' nikov Institute of Radioengineering and Electronics, Russian Academy of Sciences, Moscow 125009 (Russian Federation); Beginin, E. N.; Morozova, M. A.; Sharaevskii, Yu. P.; Grishin, S. V.; Sheshukova, S. E. [Laboratory “Metamaterials,” Saratov State University, Saratov 410012 (Russian Federation)

    2016-07-25

    We have experimentally studied the coupling of spin waves in the adjacent magnonic crystals. Space- and time-resolved Brillouin light-scattering spectroscopy is used to demonstrate the frequency and intensity dependent spin-wave energy exchange between the side-coupled magnonic crystals. The experiments and the numerical simulation of spin wave propagation in the coupled periodic structures show that the nonlinear phase shift of spin wave in the adjacent magnonic crystals leads to the nonlinear switching regime at the frequencies near the forbidden magnonic gap. The proposed side-coupled magnonic crystals represent a significant advance towards the all-magnonic signal processing in the integrated magnonic circuits.

  13. Recommended practice for fracture toughness testing of weldments with strength mismatch; Recommandations pratiques pour la determination experimentale de la tenacite de joints soudes en situation de mismatching

    Energy Technology Data Exchange (ETDEWEB)

    Hornet, P.; Eripret, C. [Electricite de France (EDF), 92 - Clamart (France); Wang, Y.Y.; Kirk, M.T.; Gordon, J.R. [Edison Welding Institute, Columbus, Ohio (United States)

    1997-10-01

    Fracture toughness testing requires relationships between experimentally measured quantities, such as load and displacement, and J and crack tip opening displacement (CTOD).The relationships provided in the presently codified procedures (ASTM E813, E1152, E1290 et BSI 7848:Part 1) were derived under the assumption that the specimens have homogeneous mechanical properties. However, these codified procedures are frequently used for testing of weldments despite their strong mechanical properties variations. As a result, the accuracy of the toughness values (J or CCTOD) is sometimes in question. Systematic finite element studies of mismatched single-edge-notched-bend specimens (SENB) having a crack on the centerline have been conducted to resolve this question. The effect of various parameters on these relationships, such as weld size, degree of mismatch, and crack depth, is investigated. The accuracy of the codified J and CTOD testing procedures when applied to the mismatched SE(B) specimens is examined. This systematic examination is extended to several newly proposed procedures, such as those from Joch et al. and Hornet and Eripret. New J and CTOD estimations procedures are proposed. The expected error in applying the codified and the new procedures are shown are proposed. The expected error in applying the codified and the new procedures are shown in terms of mismatch level and level width. Recommendations are made on the use of those procedures for a variety of weld mismatch and crack depth conditions. (authors).

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Integrated analysis of mismatch repair system in malignant astrocytomas.

    Directory of Open Access Journals (Sweden)

    Irene Rodríguez-Hernández

    Full Text Available Malignant astrocytomas are the most aggressive primary brain tumors with a poor prognosis despite optimal treatment. Dysfunction of mismatch repair (MMR system accelerates the accumulation of mutations throughout the genome causing uncontrolled cell growth. The aim of this study was to characterize the MMR system defects that could be involved in malignant astrocytoma pathogenesis. We analyzed protein expression and promoter methylation of MLH1, MSH2 and MSH6 as well as microsatellite instability (MSI and MMR gene mutations in a set of 96 low- and high-grade astrocytomas. Forty-one astrocytomas failed to express at least one MMR protein. Loss of MSH2 expression was more frequent in low-grade astrocytomas. Loss of MLH1 expression was associated with MLH1 promoter hypermethylation and MLH1-93G>A promoter polymorphism. However, MSI was not related with MMR protein expression and only 5% of tumors were MSI-High. Furthermore, the incidence of tumors carrying germline mutations in MMR genes was low and only one glioblastoma was associated with Lynch syndrome. Interestingly, survival analysis identified that tumors lacking MSH6 expression presented longer overall survival in high-grade astrocytoma patients treated only with radiotherapy while MSH6 expression did not modify the prognosis of those patients treated with both radiotherapy and chemotherapy. Our findings suggest that MMR system alterations are a frequent event in malignant astrocytomas and might help to define a subgroup of patients with different outcome.

  16. Impairment in Mismatch Negativity but not Repetition Suppression in Schizophrenia.

    Science.gov (United States)

    Coffman, Brian A; Haigh, Sarah M; Murphy, Tim K; Salisbury, Dean F

    2017-07-01

    Schizophrenia is characterized by impaired auditory-evoked potentials (AEPs), mismatch negativity (MMN), and sensory gating of AEPs to repeated stimuli (repetition suppression, RS). In the predictive modeling framework, MMN and RS reflect encoding of prediction error and model sharpening, respectively. We compared P50, N100, P200 RS, and pitch and duration MMN in 26 participants diagnosed with schizophrenia (SZ) and 26 matched healthy controls (HC), and assessed relationships between MMN, RS, and SZ diagnosis. RS was measured by comparing responses to individual tones presented as 5-tone groups (1 kHz, 75 dB, 50 ms, 5 ms rise/fall times, 330 ms SOA), separated by a 750 ms inter-trial interval. For MMN, the same tones were presented, with occasional pitch (1.2 kHz, 10%) or duration deviants (100 ms, 10%) interspersed. Pitch and duration MMN were reduced in SZ (p  0.1). Importantly, although pitch and duration MMN both correlated with RS of AEPs within the MMN time range (p's  0.93). We suggest that reduced MMN in SZ is related to deficits in encoding prediction error but not repetition suppression.

  17. Expectation of Strings with Mismatches under Markov Chain Distribution

    Science.gov (United States)

    Pizzi, Cinzia; Bianco, Mauro

    We study a problem related to the extraction of over-represented words from a given source text x, of length n. The words are allowed to occur with k mismatches, and x is produced by a source over an alphabet Σ according to a Markov chain of order p. We propose an online algorithm to compute the expected number of occurrences of a word y of length m in O(mk |Σ| p + 1). We also propose an offline algorithm to compute the probability of any word that occurs in the text in O(k|Σ|2) after O(nk |Σ| p + 1) pre-processing. This algorithm allows us to compute the expectation for all the words in a text of length n in O(kn 2|Σ|2 + nk |Σ| p + 1), rather than in O(n 3 |Σ| p + 1) that can be obtained with other methods. Although this study was motivated by the motif discovery problem in bioinformatics, the results find their applications in any other domain involving combinatorics on words.

  18. Treatment 'mismatch' in early prostate cancer: do treatment choices take patient quality of life into account?

    Science.gov (United States)

    Chen, Ronald C; Clark, Jack A; Manola, Judith; Talcott, James A

    2008-01-01

    Pretreatment urinary, bowel, and sexual dysfunction may increase the toxicity of prostate cancer treatments or preclude potential benefits. Using patient-reported baseline dysfunction from a prospective cohort study, we determined the proportion of patients receiving relatively contraindicated ('mismatched') treatments. Baseline obstructive uropathy and bowel dysfunction relatively contraindicate brachytherapy (BT) and external beam radiation therapy (EBRT), respectively, because they increase patients' vulnerability to treatment-related toxicity. Baseline sexual dysfunction renders moot the intended benefit of nerve-sparing radical prostatectomy (NSRP), which is to preserve sexual function. We categorized patients' clinical circumstances by increasing complexity and counted the mismatches in each, expecting weaker or multiple contraindications to increase mismatched treatments. Of 438 eligible patients, 389 (89%) reported preexisting dysfunction, and more than one-third received mismatched treatments. Mismatches did not significantly increase with clinical complexity, and watchful waiting was very infrequent, even when all treatment options were contraindicated. Patient age and comorbidity, but not preexisting dysfunction, were associated with treatment choice. As expected, mismatched BT and EBRT led to worsened urinary and bowel symptoms, respectively, and NSRP did not improve outcomes after baseline sexual dysfunction. Pretreatment dysfunction does not appear to reliably influence treatment choices, and patients receiving mismatched treatments had worse outcomes. Further study is needed to determine why mismatched treatments were chosen, including the role of incomplete patient-physician communication of baseline dysfunction, and whether using a validated questionnaire before treatment decision-making would bypass this difficulty. Treatment mismatch may be a useful outcome indicator of the quality of patient-centered decisions. 2007 American Cancer Society

  19. The Prevalence of Patient-Prosthesis Mismatch Can Be Reduced Using the Trifecta Aortic Prosthesis.

    Science.gov (United States)

    Hernandez-Vaquero, Daniel; Diaz, Rocio; Pascual, Isaac; Rozado, Jose; De la Hera, Jesus M; Leon, Victor; Avanzas, Pablo; Martín, Maria; García-Iglesias, Daniel; Calvo, David; Silva, Jacobo; Moris, César

    2018-01-01

    Some important studies have shown that patient-prosthesis mismatch is a frequent occurrence after surgical aortic valve replacement that impairs survival. The Trifecta valve (St. Jude Medical Inc, St. Paul, MN) has special architecture designed to achieve the best hemodynamic profile. The aim of this study was to determine the prevalence of mismatch when using this prosthesis. This study included 1,302 patients at 3 months postoperatively, 339 patients with a Trifecta prosthesis and 963 patients (the control group) with a Mitroflow aortic valve (Sorin Group Inc, Mitroflow Division, Vancouver, Canada). Multinomial multivariate logistic regression was calculated to estimate the association between the Trifecta prosthesis and moderate or severe patient-prosthesis mismatch. Any degree of mismatch was present in 5.9% of the Trifecta group and in 42.4% in the Mitroflow group. Moderate patient-prosthesis mismatch was present in 3.8% of the patients with a Trifecta valve and in 32.6% in the Mitroflow group. Severe mismatch was present in 2.1% of the patients with a Trifecta prosthesis and in 9.8% of the patients with a Mitroflow valve. All differences were statistically significant (p < 0.001). The odds ratio of the Trifecta prosthesis as protector against mismatch was 16.9 (95% confidence interval, 9.5 to 30.4) and 11.9 (95% confidence interval, 5.3 to 26.7) for moderate or severe mismatch, respectively. The prevalence of patient-prosthesis mismatch using the Trifecta aortic prosthesis is extraordinary low. This finding may have great clinical repercussions in patients undergoing surgical aortic valve replacement. Copyright © 2018 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  20. Capacitor Mismatch Error Cancellation Technique for a Successive Approximation A/D Converter

    DEFF Research Database (Denmark)

    Zheng, Zhiliang; Moon, Un-Ku; Steensgaard-Madsen, Jesper

    1999-01-01

    An error cancellation technique is described for suppressing capacitor mismatch in a successive approximation A/D converter. At the cost of a 50% increase in conversion time, the first-order capacitor mismatch error is cancelled. Methods for achieving top-plate parasitic insensitive operation...... are described, and the use of a gain- and offset-compensated opamp is explained. SWITCAP simulation results show that the proposed 16-bit SAR ADC can achieve an SNDR of over 91 dB under non-ideal conditions, including 1% 3 sigma nominal capacitor mismatch, 10-20% randomized parasitic capacitors, 66 dB opamp...

  1. Group- and phase-velocity-mismatch fringes in triple sum-frequency spectroscopy

    Science.gov (United States)

    Morrow, Darien J.; Kohler, Daniel D.; Wright, John C.

    2017-12-01

    The effects of group- and phase-velocity mismatch are well known in optical harmonic generation, but the nondegenerate cases remain unexplored. In this work we develop an analytic model which predicts velocity mismatch effects in nondegenerate triple sum-frequency mixing, TSF. We verify this model experimentally using two tunable, ultrafast, short-wave IR lasers to demonstrate spectral fringes in the TSF output from a 500-μ m -thick sapphire plate. We find the spectral dependence of the TSF depends strongly on both the phase-velocity and the group-velocity differences between the input and output fields. We define practical strategies for mitigating the impact of velocity mismatches.

  2. Hydrologic Connection Between Geysers and Adjacent Thermal Pools, Two Examples: El Tatio, Chile and Yellowstone, USA

    Science.gov (United States)

    Munoz Saez, C.; Fauria, K.; Manga, M.; Hurwitz, S.; Namiki, A.

    2014-12-01

    Geyser eruption cycles can be influenced by adjacent and distant thermals sources, suggesting a hydraulic connection through permeable pathways. Diffusion of fluid pressure can be responsible for the communication between geysers. In this study we examine the processes linking two different geysers with adjacent thermal pools. The first was Vega Rinconada, located at El Tatio geyser field, Chile, where we measured temperature inside the conduit between the ground surface and a depth of seven meters, at one-meter intervals. The second was Lone Star Geyser in Yellowstone National Park, where we measured temperature of the overflow water at the base of the cone. Concurrently, we measured temperature and the water level in pools adjacent to both geysers. We found common elements in both geyser - pool systems: First, water temperature in both adjacent pools was below the boiling point and cooler than water in the geysers. Second, changes in pool water levels were correlated with eruptions of the geysers. During the quiescent period of the geysers, the water level increased in adjacent pools, while water level in the pools deceased during eruptions. Additionally, measurements inside of the conduit in Vega Rinconada Geyser showed that water temperature increased in the deepest part of the conduit during eruptions, while water temperature decreased in the shallow part of the geyser conduit (~1 to 2 m). These drops in temperature in the shallow conduit were coincident with the drop in water level in the adjacent pool. This suggests that after the initiation of an eruption, water may drain from the pool to the geyser. Furthermore, we observed a temperature drop of 3oC in the shallow conduit immediately preceding the end of an eruption. This suggests that flow from the pool to geyser contributes to eruption shut off. Our observations of geyser-pool systems indicate a hydrologic connection between the geysers and their adjacent pools. In the case of Vega Rinconada, cold water

  3. 33 CFR 334.730 - Waters of Santa Rosa Sound and Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving...

    Science.gov (United States)

    2010-07-01

    ... Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving Ground Command, Eglin Air Force Base... Sound and Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving Ground Command, Eglin Air... regulations. (1) Experimental test operations will be conducted by the U.S. Air Force within the prohibited...

  4. An investigation of the weld region of the SAE 1020 joined with metal active gas and determination of the mismatch factor

    Science.gov (United States)

    Meric, C.; Tokdemir, M.

    1999-10-01

    In this study, the joining process of SAE 1020 low carbon steel, generally used in the industry, has been completed using the metal active gas (MAG) weld method. The goal of this study was to examine the mismatch between base and weld metal. After the joining process, mechanical properties of the samples of the base metal (BM), the heat affected zone (HAZ), and the weld metal (WM) were investigated, and the crack tip opening displacement (CTOD) test was performed.

  5. Measurement Methods to Determine Air Leakage Between Adjacent Zones

    Energy Technology Data Exchange (ETDEWEB)

    Hult, Erin L. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Dickerhoff, Darryl J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Price, Phillip N. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2012-09-01

    Air leakage between adjacent zones of a building can lead to indoor air quality and energy efficiency concerns, however there is no existing standard for measuring inter-zonal leakage. In this study, synthesized data and field measurements are analyzed in order to explore the uncertainty associated with different methods for collecting and analyzing fan pressurization measurements to calculate interzone leakage.

  6. Concurrent statistical learning of adjacent and nonadjacent dependencies

    NARCIS (Netherlands)

    Vuong, L.C.; Meyer, A.S.; Christiansen, M.H.

    2016-01-01

    When children learn their native language, they have to deal with a confusing array of dependencies between various elements in an utterance. The dependent elements may be adjacent to one another or separated by intervening material. Prior studies suggest that nonadjacent dependencies are hard to

  7. Herpetology of the American Madrean Archipelago and adjacent valleys

    Science.gov (United States)

    Lawrence L. C. Jones

    2005-01-01

    Approximately 110 species of amphibians (18 frogs and toads, and 1 salamander) and reptiles (47 snakes, 39 lizards, and 5 turtles) are known from the American Madrean Archipelago and adjacent valleys. The high diversity of the herpetofauna comes from a variety of factors, including a convergence of biotic communities representing deserts, grasslands, and mountains....

  8. PROBABILISTIC ZONING OF ADJACENT CATCHMENTS BY PHYSICAL MODELING

    Directory of Open Access Journals (Sweden)

    Yu. B. Andreev

    2012-01-01

    Full Text Available Now the probabilistic zoning of avalanche sites is being made either on the basis of the available field data, or using the mathematical and physical modeling of avalanche dynamics processes. The work purpose consisted in research of interaction and compiling probabilistic zoning maps of two adjacent avalanche sites by a physical modeling method. For the two adjacent sites № 9 and 10 on the slope of northern exposition ofTchegetMountain(Elbrus region,Caucasus the model of this slope with the scale of 1: 2 500 was created. The model dimension is 0,82 × 1,1 ×0,57 m. This model was produced using the 4-mm plywood sheets imposed against each other. The model horizontals correspond to the10 mnatural ones. The model slope was also surfaced by thin gypsum lay and then varnished. The fine-grained sawdust (0.1 mm with a natural friction angle of 43º has been chosen as the loose material modeling snow. A series of experiments on modeling avalanche releases from the two sites were carried out resulted in the measurements of avalanche deposit parameters such as run-out distance and length, width and thickness of deposits. The similarity criteria were used during the experiments. The morphometric features of adjacent sites interaction are revealed. The basic result of the carried out work will consist in the probabilistic zoning map of two adjacent sites № 9 and 10.

  9. Experimental Tape Casting of Adjacently Graded Materials for Magnetic Refrigeration

    DEFF Research Database (Denmark)

    Bulatova, Regina

    graded thin films. The motivation to create such adjacently segmented structures stemmed from a search of material and a materials design alternative to the expensive rare earth element gadolinium which is widely used as a magnetic regenerator in the emerging magnetic refrigeration technology...

  10. Bird use of banana plantations adjacent to Kibale National Park ...

    African Journals Online (AJOL)

    Bird use of banana plantations adjacent to Kibale National Park, Uganda: evaluating the conservation value of a matrix habitat. ... may provide suitable habitat for some nectarivores, but are of limited value for small birds that eat invertebrates and fruit. Keywords: agriculture, biodiversity, bird community, forest fragmentation ...

  11. Optimal induced universal graphs and adjacency labeling for trees

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Dahlgaard, Søren; Knudsen, Mathias Bæk Tejs

    2015-01-01

    bound. The lower bound and previously best upper bounds were presented in Alstrup and Rauhe (FOCS'02). Our upper bounds are obtained through a log2 n + O(1) labeling scheme for adjacency queries in forests. We hereby solve an open problem being raised repeatedly over decades, e.g. in Kannan, Naor...

  12. in cross River Estuary and Adjacent Coastal waters

    African Journals Online (AJOL)

    Studies on the length distribution of bonga, Ethmalosa fimbriata, in the Cross River estuary and adjacent coastal waters were conducted from October 1999 to December 2000. A total of 15,182 specimens of bonga from gill nets, purse seine and boat seine fisheries were measured. Post-larvae measuring between 2 cm and ...

  13. Realisation of two adjacent high tones: Acoustic evidence from ...

    African Journals Online (AJOL)

    We present findings of a multi-speaker production study that was undertaken to investigate the realisation of two adjacent high tones within the verb word in Northern Sotho, a Southern Bantu language. Experimental tokens are selected to ensure that the high tones originate from different combinations of morphosyntactic ...

  14. DNA mismatch repair preferentially protects genes from mutation.

    Science.gov (United States)

    Belfield, Eric J; Ding, Zhong Jie; Jamieson, Fiona J C; Visscher, Anne M; Zheng, Shao Jian; Mithani, Aziz; Harberd, Nicholas P

    2017-12-12

    Mutation is the source of genetic variation and fuels biological evolution. Many mutations first arise as DNA replication errors. These errors subsequently evade correction by cellular DNA repair, for example, by the well-known DNA mismatch repair (MMR) mechanism. Here, we determine the genome-wide effects of MMR on mutation. We first identify almost 9000 mutations accumulated over five generations in eight MMR-deficient mutation accumulation (MA) lines of the model plant species, Arabidopsis thaliana We then show that MMR deficiency greatly increases the frequency of both smaller-scale insertions and deletions (indels) and of single-nucleotide variant (SNV) mutations. Most indels involve A or T nucleotides and occur preferentially in homopolymeric (poly A or poly T) genomic stretches. In addition, we find that the likelihood of occurrence of indels in homopolymeric stretches is strongly related to stretch length, and that this relationship causes ultrahigh localized mutation rates in specific homopolymeric stretch regions. For SNVs, we show that MMR deficiency both increases their frequency and changes their molecular mutational spectrum, causing further enhancement of the GC to AT bias characteristic of organisms with normal MMR function. Our final genome-wide analyses show that MMR deficiency disproportionately increases the numbers of SNVs in genes, rather than in nongenic regions of the genome. This latter observation indicates that MMR preferentially protects genes from mutation and has important consequences for understanding the evolution of genomes during both natural selection and human tumor growth. © 2018 Belfield et al.; Published by Cold Spring Harbor Laboratory Press.

  15. Chronic effects of cannabis use on the auditory mismatch negativity.

    Science.gov (United States)

    Greenwood, Lisa-Marie; Broyd, Samantha J; Croft, Rodney; Todd, Juanita; Michie, Patricia T; Johnstone, Stuart; Murray, Robin; Solowij, Nadia

    2014-03-15

    Cannabis use is associated with the development of psychotic symptoms and increased risk for schizophrenia. The mismatch negativity (MMN) is a brain event-related potential marker of change detection thought to index glutamatergic N-methyl-D-aspartate receptor-mediated neurotransmission, which is known to be deficient in schizophrenia. This study examined auditory MMN in otherwise healthy chronic cannabis users compared with nonuser control subjects. Forty-two chronic cannabis users and 44 nonuser healthy control subjects completed a multi-feature MMN paradigm, which included duration, frequency, and intensity deviants (deviants 6%; standards 82%). The MMN was compared between users and control subjects as well as between long- and short-term users and age- and gender-matched control subjects. Associations between MMN, cannabis use measures, and symptoms were examined. The MMN amplitude was significantly reduced to frequency but not duration or intensity deviants in overall cannabis users relative to control subjects. Frequency MMN was similarly attenuated in short- and long-term users relative to control subjects. Long-term users also exhibited reduced duration MMN relative to control subjects and short-term users and this was correlated with increased duration of exposure to cannabis and increased psychotic-like experiences during intoxication. In short-term users, a younger age of onset of regular cannabis use and greater frequency of use were associated with greater psychotic-like experiences and symptomatic distress. These results suggest impaired sensory memory that might reflect N-methyl-D-aspartate receptor dysfunction in chronic cannabis users. The pattern of MMN alterations in cannabis users differed from that typically observed in patients with schizophrenia, indicating overlapping but distinct underlying pathology. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  16. Auditory processing in autism spectrum disorder: Mismatch negativity deficits.

    Science.gov (United States)

    Vlaskamp, Chantal; Oranje, Bob; Madsen, Gitte Falcher; Møllegaard Jepsen, Jens Richardt; Durston, Sarah; Cantio, Cathriona; Glenthøj, Birte; Bilenberg, Niels

    2017-06-22

    Children with autism spectrum disorders (ASD) often show changes in (automatic) auditory processing. Electrophysiology provides a method to study auditory processing, by investigating event-related potentials such as mismatch negativity (MMN) and P3a-amplitude. However, findings on MMN in autism are highly inconsistent, partly due to small sample sizes in the studies and differences in MMN paradigms. Therefore, in the current study, MMN and P3a amplitude were assessed in a relatively large sample of children with ASD, using a more extensive MMN paradigm and compared with that of typically developing children (TDC). Thirty-five children (aged 8-12 years) with ASD and 38 age and gender matched TDC were assessed with a MMN paradigm with three types of deviants, i.e., frequency, duration and a combination of these two. MMN elicited by duration and frequency-duration deviants was significantly reduced in the ASD group. P3a-amplitude elicited by duration deviants was significantly increased in the ASD group. Reduced MMN in children with ASD suggests that children with ASD may be less responsive to environmentally deviant stimuli at an early (sensory) level. P3a-amplitude was increased in ASD, implying a hyper-responsivity at the attentional level. In addition, as similar MMN deficits are found in schizophrenia, these MMN results may explain some of the frequently reported increased risk of children with ASD to develop schizophrenia later in life. Autism Res 2017. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.

  17. Approaches to diagnose DNA mismatch repair gene defects in cancer.

    Science.gov (United States)

    Peña-Diaz, Javier; Rasmussen, Lene Juel

    2016-02-01

    The DNA repair pathway mismatch repair (MMR) is responsible for the recognition and correction of DNA biosynthetic errors caused by inaccurate nucleotide incorporation during replication. Faulty MMR leads to failure to address the mispairs or insertion deletion loops (IDLs) left behind by the replicative polymerases and results in increased mutation load at the genome. The realization that defective MMR leads to a hypermutation phenotype and increased risk of tumorigenesis highlights the relevance of this pathway for human disease. The association of MMR defects with increased risk of cancer development was first observed in colorectal cancer patients that carried inactivating germline mutations in MMR genes and the disease was named as hereditary non-polyposis colorectal cancer (HNPCC). Currently, a growing list of cancers is found to be MMR defective and HNPCC has been renamed Lynch syndrome (LS) partly to include the associated risk of developing extra-colonic cancers. In addition, a number of non-hereditary, mostly epigenetic, alterations of MMR genes have been described in sporadic tumors. Besides conferring a strong cancer predisposition, genetic or epigenetic inactivation of MMR genes also renders cells resistant to some chemotherapeutic agents. Therefore, diagnosis of MMR deficiency has important implications for the management of the patients, the surveillance of their relatives in the case of LS and for the choice of treatment. Some of the alterations found in MMR genes have already been well defined and their pathogenicity assessed. Despite this substantial wealth of knowledge, the effects of a large number of alterations remain uncharacterized (variants of uncertain significance, VUSs). The advent of personalized genomics is likely to increase the list of VUSs found in MMR genes and anticipates the need of diagnostic tools for rapid assessment of their pathogenicity. This review describes current tools and future strategies for addressing the relevance

  18. Bilayer thickness mismatch controls domain size in model membranes.

    Science.gov (United States)

    Heberle, Frederick A; Petruzielo, Robin S; Pan, Jianjun; Drazba, Paul; Kučerka, Norbert; Standaert, Robert F; Feigenson, Gerald W; Katsaras, John

    2013-05-08

    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-dioleoyl-sn-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.

  19. Bilayer Thickness Mismatch Controls Domain Size in Model Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Heberle, Frederick A [ORNL; Petruzielo, Robin S [ORNL; Pan, Jianjun [ORNL; Drazba, Paul [ORNL; Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Feigenson, Gerald [Cornell University; Katsaras, John [ORNL

    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.

  20. Processing of unattended facial emotions: a visual mismatch negativity study.

    Science.gov (United States)

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

    2012-02-01

    Facial emotions express our internal states and are fundamental in social interactions. Here we explore whether the repetition of unattended facial emotions builds up a predictive representation of frequently encountered emotions in the visual system. Participants (n=24) were presented peripherally with facial stimuli expressing emotions while they performed a visual detection task presented in the center of the visual field. Facial stimuli consisted of four faces of different identity, but expressed the same emotion (happy or fearful). Facial stimuli were presented in blocks of oddball sequence (standard emotion: p=0.9, deviant emotion: p=0.1). Event-related potentials (ERPs) to the same emotions were compared when the emotions were deviant and standard, respectively. We found visual mismatch negativity (vMMN) responses to unattended deviant emotions in the 170-360 ms post-stimulus range over bilateral occipito-temporal sites. Our results demonstrate that information about the emotional content of unattended faces presented at the periphery of the visual field is rapidly processed and stored in a predictive memory representation by the visual system. We also found evidence that differential processing of deviant fearful faces starts already at 70-120 ms after stimulus onset. This finding shows a 'negativity bias' under unattended conditions. Differential processing of fearful deviants were more pronounced in the right hemisphere in the 195-275 ms and 360-390 ms intervals, whereas processing of happy deviants evoked larger differential response in the left hemisphere in the 360-390 ms range, indicating differential hemispheric specialization for automatic processing of positive and negative affect. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Impact of momentum mismatch on 2D van der Waals tunnel field-effect transistors

    Science.gov (United States)

    Cao, Jiang; Logoteta, Demetrio; Pala, Marco G.; Cresti, Alessandro

    2018-02-01

    We numerically investigate electron quantum transport in 2D van der Waals tunnel field-effect-transistors in the presence of lateral momentum mismatch induced by lattice mismatch or rotational misalignment between the two-dimensional layers. We show that a small momentum mismatch induces a threshold voltage shift without altering the subthreshold swing. On the contrary, a large momentum mismatch produces significant potential variations and ON-current reduction. Short-range scattering, such as that due to phonons or system edges, enables momentum variations, thus enhancing interlayer tunneling. The coupling of electrons with acoustic phonons is shown to increase the ON current without affecting the subthreshold swing. In the case of optical phonons, the ON-current increase is accompanied by a subthreshold swing degradation due to the inelastic nature of the scattering.

  2. DNA-mismatch repair. The intricacies of eukaryotic spell-checking.

    Science.gov (United States)

    Kunkel, T A

    1995-10-01

    Recent work suggests that the eukaryotic system responsible for repairing DNA mismatches, and so correcting replication errors, is more complex than was thought; its multiple components have many cellular functions.

  3. Infection risk decreases with increasing mismatch in host and pathogen environmental tolerances.

    Science.gov (United States)

    Nowakowski, A Justin; Whitfield, Steven M; Eskew, Evan A; Thompson, Michelle E; Rose, Jonathan P; Caraballo, Benjamin L; Kerby, Jacob L; Donnelly, Maureen A; Todd, Brian D

    2016-09-01

    The fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused the greatest known wildlife pandemic, infecting over 500 amphibian species. It remains unclear why some host species decline from disease-related mortality whereas others persist. We introduce a conceptual model that predicts that infection risk in ectotherms will decrease as the difference between host and pathogen environmental tolerances (i.e. tolerance mismatch) increases. We test this prediction using both local-scale data from Costa Rica and global analyses of over 11 000 Bd infection assays. We find that infection prevalence decreases with increasing thermal tolerance mismatch and with increasing host tolerance of habitat modification. The relationship between environmental tolerance mismatches and Bd infection prevalence is generalisable across multiple amphibian families and spatial scales, and the magnitude of the tolerance mismatch effect depends on environmental context. These findings may help explain patterns of amphibian declines driven by a global wildlife pandemic. © 2016 John Wiley & Sons Ltd/CNRS.

  4. Role of Energy-Level Mismatches in a Multi-Pathway Complex of Photosynthesis

    CERN Document Server

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

    2013-01-01

    Considering a multi-pathway structure in a light-harvesting complex of photosynthesis, we investigate the role of energy-level mismatches between antenna molecules in transferring the absorbed energy to a reaction center. We find a condition in which the antenna molecules faithfully play their roles: Their effective absorption ratios are larger than those of the receiver molecule directly coupled to the reaction center. 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 near 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 mismat...

  5. Association of common variants in mismatch repair genes and breast cancer susceptibility: a multigene study

    Directory of Open Access Journals (Sweden)

    Pina Julieta

    2009-09-01

    Full Text Available Abstract Background MMR is responsible for the repair of base-base mismatches and insertion/deletion loops. Besides this, MMR is also associated with an anti-recombination function, suppressing homologous recombination. Losses of heterozygosity and/or microsatellite instability have been detected in a large number of skin samples from breast cancer patients, suggesting a potential role of MMR in breast cancer susceptibility. Methods We carried out a hospital-based case-control study in a Caucasian Portuguese population (287 cases and 547 controls to estimate the susceptibility to non-familial breast cancer associated with some polymorphisms in mismatch repair genes (MSH3, MSH4, MSH6, MLH1, MLH3, PMS1 and MUTYH. Results Using unconditional logistic regression we found that MLH3 (L844P, G>A polymorphism GA (Leu/Pro and AA (Pro/Pro genotypes were associated with a decreased risk: OR = 0.65 (0.45-0.95 (p = 0.03 and OR = 0.62 (0.41-0.94 (p = 0.03, respectively. Analysis of two-way SNP interaction effects on breast cancer revealed two potential associations to breast cancer susceptibility: MSH3 Ala1045Thr/MSH6 Gly39Glu - AA/TC [OR = 0.43 (0.21-0.83, p = 0.01] associated with a decreased risk; and MSH4 Ala97Thr/MLH3 Leu844Pro - AG/AA [OR = 2.35 (1.23-4.49, p = 0.01], GG/AA [OR = 2.11 (1.12-3,98, p = 0.02], and GG/AG [adjusted OR = 1.88 (1.12-3.15, p = 0.02] all associated with an increased risk for breast cancer. Conclusion It is possible that some of these common variants in MMR genes contribute significantly to breast cancer susceptibility. However, further studies with a large sample size will be needed to support our results.

  6. Substrate Deformation Curvatures Due to Film Mismatch Strain for Spatially Varying Substrate and Film Thicknesses (Preprint)

    Science.gov (United States)

    2017-04-13

    AFRL-RX-WP-JA-2017-0338 SUBSTRATE DEFORMATION CURVATURES DUE TO FILM MISMATCH STRAIN FOR SPATIALLY VARYING SUBSTRATE AND FILM ...22 July 2013 – 13 March 2017 4. TITLE AND SUBTITLE SUBSTRATE DEFORMATION CURVATURES DUE TO FILM MISMATCH STRAIN FOR SPATIALLY VARYING SUBSTRATE...AND FILM THICKNESSES (PREPRINT) 5a. CONTRACT NUMBER IN-HOUSE 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 1) Craig P

  7. The curious case of the coding and self-ratings mismatches

    DEFF Research Database (Denmark)

    Panattoni, Katherine; McLean, Kate C.

    2018-01-01

    In this paper, we investigate methodological and theoretical constraints implicated by findings of low correlations between researcher codings and participant ratings of conceptually similar narrative features. We discuss potential explanations for these puzzling mismatches from a measurement...... perspective and from theoretical perspectives drawn from personality, developmental, and cognitive literatures. The mismatches raise questions for traditional theoretical assumptions of narrative identity as being internalized and subjective and may reflect different narrative constructs created through two...

  8. Educational mismatches for second generation migrants. An analysis of applied science graduates in the Netherlands

    OpenAIRE

    Falcke, Swantje; Meng, Christoph; Nollen, Romy

    2016-01-01

    Educational mismatches, i.e. diferences between the education attained and required for a job have been found to negatively affect earnings and job satisfaction and thus lead to a lower return to education. In this paper we aim to see whether immigrants are more prone to educational mismatches and unemployment than their native counterparts. Using a cross-sectional data set among recent applied science graduates in the Netherlands between 2006 and 2014 we are able to look at a very homogeneou...

  9. Sets of Waveform and Mismatched Filter Pairs for Clutter Suppression in Marine Radar Application

    OpenAIRE

    I.V. Koshevyy; Victoria Popova

    2017-01-01

    Sets of waveform and mismatched filter pairs are used. On the contrary with Golays matched waveform filter pair the mismatched waveform filter pair does exist for all N (number pulses in waveform). Using corresponding shapes of filter good Doppler tolerance may be provided. This property together with a good range side-lobs level suppression makes it’s attractable for use in marine radar.

  10. MutL traps MutS at a DNA mismatch

    Science.gov (United States)

    Qiu, Ruoyi; Sakato, Miho; Sacho, Elizabeth J.; Wilkins, Hunter; Zhang, Xingdong; Modrich, Paul; Hingorani, Manju M.; Erie, Dorothy A.; Weninger, Keith R.

    2015-01-01

    DNA mismatch repair (MMR) identifies and corrects errors made during replication. In all organisms except those expressing MutH, interactions between a DNA mismatch, MutS, MutL, and the replication processivity factor (β-clamp or PCNA) activate the latent MutL endonuclease to nick the error-containing daughter strand. This nick provides an entry point for downstream repair proteins. Despite the well-established significance of strand-specific nicking in MMR, the mechanism(s) by which MutS and MutL assemble on mismatch DNA to allow the subsequent activation of MutL’s endonuclease activity by β-clamp/PCNA remains elusive. In both prokaryotes and eukaryotes, MutS homologs undergo conformational changes to a mobile clamp state that can move away from the mismatch. However, the function of this MutS mobile clamp is unknown. Furthermore, whether the interaction with MutL leads to a mobile MutS–MutL complex or a mismatch-localized complex is hotly debated. We used single molecule FRET to determine that Thermus aquaticus MutL traps MutS at a DNA mismatch after recognition but before its conversion to a sliding clamp. Rather than a clamp, a conformationally dynamic protein assembly typically containing more MutL than MutS is formed at the mismatch. This complex provides a local marker where interaction with β-clamp/PCNA could distinguish parent/daughter strand identity. Our finding that MutL fundamentally changes MutS actions following mismatch detection reframes current thinking on MMR signaling processes critical for genomic stability. PMID:26283381

  11. Prosthesis-Patient Mismatch After Aortic Valve Replacement: Effect on Long-Term Survival.

    Science.gov (United States)

    Swinkels, Ben M; de Mol, Bas A; Kelder, Johannes C; Vermeulen, Freddy E; ten Berg, Jurriën M

    2016-04-01

    Mean follow-up in previous studies on the effect of prosthesis-patient mismatch on long-term survival after aortic valve replacement (AVR) is confined to a maximum of one decade. This retrospective longitudinal cohort study was performed to determine the effect on long-term survival of prosthesis-patient mismatch after AVR with a mean follow-up of almost two decades. Kaplan-Meier survival analysis was used to determine long-term survival after AVR in a cohort of 673 consecutive patients, divided into 163 patients (24.2%) with prosthesis-patient mismatch (indexed effective orifice area ≤ 0.85 cm(2)/m(2)) and 510 patients (75.8%) without prosthesis-patient mismatch (indexed effective orifice area >0.85 cm(2)/m(2)). Effective orifice area values of the prosthetic valves were retrieved from the literature or obtained from the charts of the prosthetic valve manufacturers. Cox multiple regression analysis was used to identify possible independent predictors, including prosthesis-patient mismatch, of decreased long-term survival. Median sizes of the implanted mechanical (n = 430) and biologic (n = 243) prostheses were 25 and 23 mm, respectively. Mean follow-up after AVR was 17.8 ± 1.8 years. Prosthesis-patient mismatch was not an independent predictor of decreased long-term survival (hazard ratio, 0.828; 95% confidence interval, 0.669 to 1.025; p = 0.083). Severe prosthesis-patient mismatch (indexed effective orifice area ≤ 0.65 cm(2)/m(2)), occurring in only 17 patients (2.5%), showed an insignificant trend toward decreased long-term survival (hazard ratio, 1.68; 95% confidence interval, 0.97 to 2.91; p = 0.066). Prosthesis-patient mismatch was not an independent predictor of decreased long-term survival after AVR. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  12. [Adjacent segment degeneration after lumbosacral fusion in spondylolisthesis: a retrospective radiological and clinical analysis].

    Science.gov (United States)

    Zencica, P; Chaloupka, R; Hladíková, J; Krbec, M

    2010-04-01

    Whereas the posterior lumbar interbody fusion (PLIF) technique with pedicle screw fixation has shown satisfactory clinical results, solid fusion has been reported to accelerate degenerative changes at adjacent unfused levels, especially at the cranial level. The aim of this retrospective study was to evaluate a group of patients with adjacent segment disease (ASD) developed after 360-degrees lumbar fusion for spondylolisthesis performed by PLIF with transpedicular fixation and posterolateral fusion (PLF).Radiographic examinations were focused on the origin or progression of degenerative changes at the adjacent segments after the operation, with statistical evaluation of some parameters. Clinical evaluations included back pain or neurologic symptomatology which emerged later in the post-operative period in patients with adjacent segment degeneration. The authors performed a retrospective analysis on a group of 91 patients (49 females, 42 males) with isthmic, degenerative or dysplastic spondylolisthesis at the L4-L5 level who had undergone the PLIF technique on L4/L5 or L5/S1 with transpedicular fixation surgery and PLF in the period from 1990 to 2001. Isthmic spondylolisthesis was observed in 70 patients, degenerative or dysplastic forms were found in 14 and 7 patients, respectively.The patients were operated on at 40.8 years on average, and were followed-up for an average of 6.1 years. Seven patients had isthmic, two had degenerative and one had dysplastic spondylolisthesis. The data for the patients with ASD were obtained retrospectively, based on radiographic examinations and clinical sequential follow-up examinations. The radiographs were analysed with regard to degeneration at the adjacent levels pre- operatively, immediately after surgery and at the time of the last follow-up visit. The origin or progression of L3-L4, L4-5 or L5-S1 segment degeneration was defined, as a condition giving rise to segmental instability (defined by White and Panjabi), significant

  13. Experimental estimation of mismatch uncertainty in radio – frequency power and attenuation measurements

    Directory of Open Access Journals (Sweden)

    Patel Kamlesh

    2015-01-01

    Full Text Available In this paper, the effects of the input quantity representations in linear and complex forms are analyzed to estimate mismatch uncertainty separately for one-port and two-port components. The mismatch uncertainties in power and attenuation measurements are evaluated for direct, ratio and substitution techniques with the use of a vector network analyzer system in the range of 1 to 18 GHz. The estimated mismatch uncertainties were compared for the same device under test and these values have verified that their evaluation is dependent on the representations of input quantities. In power measurements, the mismatch uncertainty is reduced when evaluating from the voltage standing wave ratio or reflection coefficient magnitudes in comparison to the complex reflection coefficients. The mismatch uncertainty in the attenuation measurements, are found higher and linearly increasing while estimating from the linear magnitude values than those from the S-parameters of the attenuator. Thus in practice, the mismatch uncertainty is estimated more accurately using the quantities measured in the same representations as of measuring quantity.

  14. Binaural Benefit with and without a Bilateral Spectral Mismatch in Acoustic Simulations of Cochlear Implant Processing

    Science.gov (United States)

    Yoon, Yang-soo; Shin, You-Ree; Fu, Qian-Jie

    2012-01-01

    Objectives This study investigated whether a spectral mismatch across ears influences the benefit of redundancy, squelch, and head shadow differently in speech perception using acoustic simulation of bilateral cochlear implant (CI) processing. Design Ten normal hearing subjects participated in the study, and acoustic simulations of CIs were used to test these subjects. Sentence recognition, presented unilaterally and bilaterally, was measured at +5 dB and +10 dB signal-to-noise ratios (SNRs) with bilaterally matched and mismatched conditions. Unilateral and bilateral CIs were simulated using 8-channel sine-wave vocoders. Binaural spectral mismatch was introduced by changing the relative simulated insertion depths across ears. Subjects were tested while listening with headphones; head-related transfer functions were applied before the vocoder processing to preserve natural interaural level and time differences. Results For both SNRs, greater and more consistent binaural benefit of squelch and redundancy occurred for the matched condition while binaural interference of squelch and redundancy occurred for the mismatched condition. However, significant binaural benefit of head shadow existed irrespective of spectral mismatches and SNRs. Conclusions The results suggest that bilateral spectral mismatch may have a negative impact on the binaural benefit of squelch and redundancy for bilateral CI users. The results also suggest that clinical mapping should be carefully administrated for bilateral CI users to minimize the difference in spectral patterns between the two CIs. PMID:22968427

  15. Protein roadblocks and helix discontinuities are barriers to the initiation of mismatch repair

    Science.gov (United States)

    Pluciennik, Anna; Modrich, Paul

    2007-01-01

    The hemimethylated d(GATC) sequence that directs Escherichia coli mismatch repair can reside on either side of a mismatch at a separation distance of 1,000 bp or more. Initiation of repair involves the mismatch-, MutS-, and MutL-dependent activation of MutH endonuclease, which incises the unmethylated strand at the d(GATC) sequence, with the ensuing strand break serving as the loading site for the appropriate 3′-to-5′ or 5′-to-3′ excision system. However, the mechanism responsible for the coordinated recognition of the mismatch and a hemimodified d(GATC) site is uncertain. We show that a protein roadblock (EcoRIE111Q, a hydrolytically defective form of EcoRI endonuclease) placed on the helix between the two DNA sites inhibits MutH activation by 70–80% and that events that escape inhibition are attributable, at least in part, to diffusion of EcoRIE111Q away from its recognition site. We also demonstrate that a double-strand break located within the shorter path linking the mismatch and a d(GATC) site in a circular heteroduplex abolishes MutH activation, whereas a double-strand break within the longer path is without effect. These findings support the idea that initiation of mismatch repair involves signaling along the helix contour. PMID:17620611

  16. Discoloration of Moso-chiku (Phyllostachys pubescens) leaves in an area adjacent to an aluminium refinery

    Energy Technology Data Exchange (ETDEWEB)

    Ishikawa, H.; Ishida, N.; Iwatsubo, G.; Kitao, K.; Kitayama, S.

    1976-09-01

    Injury to plants due to air pollution is found in the ares adjacent to such chemical factories as aluminium refineries due to the gaseous fluoride compounds generated. The authors observed the gradual discoloration of Moso-chiku (Phyllostachys pubescens) leaves from tip to base in accordance with the degree of injury in the area adjacent to an aluminium refinery in Ehime Pref. The fluoride contents of the leaves were also determined. It was found that the closer to the factory, the more remarkable the discoloration of the leaves. The discoloration of Moso-chiku leaves was correlated to the fluoride contents of the leaves. The areal distribution of discolored Moso-chiku leaves showed the range of fluoride air pollution affecting the growth of the plant. For this reason, Moso-chiku is useful as an indicator plant of air pollution by fluoride.

  17. Mechanical analysis about the influence of tunnel excavation on vertical effect of adjacent bridge pile

    Science.gov (United States)

    Tian, Xiaoyan

    2017-08-01

    Tunnel excavation will bring additional deformation and internal force of adjacent bridge piles, if the deformation is large, it will threat the upper structure safety of the bridge. According to the complexity of the existing three - dimensional numerical simulation modeling and the time - consuming calculation, a two - stage analysis method of tunnel excavation based on Winkler foundation model was proposed. Firstly, Loganathan and Polous solutions were used to obtain the vertical displacement of the soil free field at the pile position when tunnel excavated, and the corresponding polynomial fitting displacement curve was taken. Secondly, the differential equation was established by means of the equilibrium condition of micro - element physical force and considering the pile group effect. Then, through the logical derivation, the calculation expressions of the tunnel excavation on the effect of the adjacent bridge pile (settlement, axial force and friction resistance) were obtained. Finally, based on the background of the tunnel project of Yanxing Door Station ∼ Xianning Road Station in Xi’an Metro Line 3, the feasibility and applicability of the proposed method were proved by comparing the calculated values with the numerical simulation values. It provides theoretical guidance for the effective analysis about the influence of tunnel excavation on the adjacent pile foundation effect.

  18. Is thymidine glycol containing DNA a substrate of E. coli DNA mismatch repair system?

    Science.gov (United States)

    Perevozchikova, Svetlana A; Trikin, Roman M; Heinze, Roger J; Romanova, Elena A; Oretskaya, Tatiana S; Friedhoff, Peter; Kubareva, Elena A

    2014-01-01

    The DNA mismatch repair (MMR) system plays a crucial role in the prevention of replication errors and in the correction of some oxidative damages of DNA bases. In the present work the most abundant oxidized pyrimidine lesion, 5,6-dihydro-5,6-dihydroxythymidine (thymidine glycol, Tg) was tested for being recognized and processed by the E. coli MMR system, namely complex of MutS, MutL and MutH proteins. In a partially reconstituted MMR system with MutS-MutL-MutH proteins, G/Tg and A/Tg containing plasmids failed to provoke the incision of DNA. Tg residue in the 30-mer DNA duplex destabilized double helix due to stacking disruption with neighboring bases. However, such local structural changes are not important for E. coli MMR system to recognize this lesion. A lack of repair of Tg containing DNA could be due to a failure of MutS (a first acting protein of MMR system) to interact with modified DNA in a proper way. It was shown that Tg in DNA does not affect on ATPase activity of MutS. On the other hand, MutS binding affinities to DNA containing Tg in G/Tg and A/Tg pairs are lower than to DNA with a G/T mismatch and similar to canonical DNA. Peculiarities of MutS interaction with DNA was monitored by Förster resonance energy transfer (FRET) and fluorescence anisotropy. Binding of MutS to Tg containing DNAs did not result in the formation of characteristic DNA kink. Nevertheless, MutS homodimer orientation on Tg-DNA is similar to that in the case of G/T-DNA. In contrast to G/T-DNA, neither G/Tg- nor A/Tg-DNA was able to stimulate ADP release from MutS better than canonical DNA. Thus, Tg residue in DNA is unlikely to be recognized or processed by the E. coli MMR system. Probably, the MutS transformation to active "sliding clamp" conformation on Tg-DNA is problematic.

  19. A reversible histone H3 acetylation cooperates with mismatch repair and replicative polymerases in maintaining genome stability.

    Directory of Open Access Journals (Sweden)

    Lyudmila Y Kadyrova

    2013-10-01

    Full Text Available Mutations are a major driving force of evolution and genetic disease. In eukaryotes, mutations are produced in the chromatin environment, but the impact of chromatin on mutagenesis is poorly understood. Previous studies have determined that in yeast Saccharomyces cerevisiae, Rtt109-dependent acetylation of histone H3 on K56 is an abundant modification that is introduced in chromatin in S phase and removed by Hst3 and Hst4 in G2/M. We show here that the chromatin deacetylation on histone H3 K56 by Hst3 and Hst4 is required for the suppression of spontaneous gross chromosomal rearrangements, base substitutions, 1-bp insertions/deletions, and complex mutations. The rate of base substitutions in hst3Δ hst4Δ is similar to that in isogenic mismatch repair-deficient msh2Δ mutant. We also provide evidence that H3 K56 acetylation by Rtt109 is important for safeguarding DNA from small insertions/deletions and complex mutations. Furthermore, we reveal that both the deacetylation and acetylation on histone H3 K56 are involved in mutation avoidance mechanisms that cooperate with mismatch repair and the proofreading activities of replicative DNA polymerases in suppressing spontaneous mutagenesis. Our results suggest that cyclic acetylation and deacetylation of chromatin contribute to replication fidelity and play important roles in the protection of nuclear DNA from diverse spontaneous mutations.

  20. Mutagenesis of the HMGB (high-mobility group B) protein Cmb1 (cytosine-mismatch binding 1) of Schizosaccharomyces pombe: effects on recognition of DNA mismatches and damage.

    Science.gov (United States)

    Kunz, Christophe; Zurbriggen, Karin; Fleck, Oliver

    2003-06-01

    Cmb1 (cytosine-mismatch binding 1) is a high-mobility group (HMG) protein of Schizosaccharomyces pombe, which consists of 223 amino acids and has a single HMG domain at the C-terminal end. We have created several mutant and deletion forms of the Cmb1 protein and studied the effects on general DNA binding and specific binding to DNA mismatches and damaged DNA. Cmb1Delta41 (i.e. Cmb1 from which the 41 N-terminal amino acids have been deleted) bound specifically to cytosine-containing mismatches, to the cisplatin-induced intrastrand cross-links cis -GG and cis -AG and to an O (6)-methylguanine lesion. DNA binding was not affected when the 45 N-terminal amino acids were deleted, but was abolished in the absence of the 50 N-terminal amino acids, and was reduced when Cmb1 was truncated by between five and eleven C-terminal amino acids. Cmb1, both with and without the C-terminal truncations, retained its DNA binding affinity after heating at 95 degrees C. The cmb1 gene was induced when S. pombe cells were treated with cisplatin. Mitotic mutation rates were increased in a S. pombe cmb1 null mutant and in a cmb1-(1-212) mutant, which encodes a Cmb1 protein lacking the 11 C-terminal amino acids. We conclude that mutation avoidance by Cmb1 is distinct from Msh2-dependent mismatch repair, but related to nucleotide excision repair.

  1. Intratumoral budding as a potential parameter of tumor progression in mismatch repair-proficient and mismatch repair-deficient colorectal cancer patients.

    Science.gov (United States)

    Lugli, Alessandro; Vlajnic, Tatjana; Giger, Olivier; Karamitopoulou, Eva; Patsouris, Efstratios S; Peros, George; Terracciano, Luigi M; Zlobec, Inti

    2011-12-01

    In colorectal cancer, tumor budding at the invasive front (peritumoral budding) is an established prognostic parameter and decreased in mismatch repair-deficient tumors. In contrast, the clinical relevance of tumor budding within the tumor center (intratumoral budding) is not yet known. The aim of the study was to determine the correlation of intratumoral budding with peritumoral budding and mismatch repair status and the prognostic impact of intratumoral budding using 2 independent patient cohorts. Following pancytokeratin staining of whole-tissue sections and multiple-punch tissue microarrays, 2 independent cohorts (group 1: n = 289; group 2: n = 222) with known mismatch repair status were investigated for intratumoral budding and peritumoral budding. In group 1, intratumoral budding was strongly correlated to peritumoral budding (r = 0.64; P budding was associated with right-sided location (P = .024), advanced T stage (P = .001) and N stage pN (P tumor margin (P = .003), and shorter survival time (P = .014). In mismatch repair-deficient cancers, high intratumoral budding was linked to higher tumor grade (P = .004), vascular invasion (P = .009), infiltrating tumor margin (P = .005), and more unfavorable survival time (P = .09). These associations were confirmed in group 2. High-grade intratumoral budding was a poor prognostic factor in univariate (P budding is an independent prognostic factor, supporting the future investigation of intratumoral budding in larger series of both preoperative and postoperative rectal and colon cancer specimens. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. An improved method for measuring mismatch negativity using ensemble empirical mode decomposition.

    Science.gov (United States)

    Hsu, Chun-Hsien; Lee, Chia-Ying; Liang, Wei-Kuang

    2016-05-01

    Mismatch negativity (MMN) is a component of event-related potentials (ERPs). Conventional approaches to measuring MMN include recording a large number of trials (e.g., 1000 trials per participant) and extracting signals within a low frequency band, e.g., between 2Hz and 8Hz. Ensemble empirical mode decomposition (EEMD) is a method to decompose time series data into intrinsic mode functions (IMFs). Each IMF has a dominant frequency. Similar to ERP measurement, averaging IMFs across trials allows measurement of event-related modes (ERMs). This paper demonstrates a protocol that adopts EEMD and Hilbert spectral analyses and uses ERMs to extract MMN-related activity based on electroencephalography data recorded from 18 participants in an MMN paradigm. The effect of deviants was demonstrated by manipulating changes in lexical tones. The mean amplitudes of ERMs revealed a significant effect of lexical tone on MMN. Based on effect size statistics, a significant effect of lexical tone on MMN could be observed using ERM measurements over fewer trials (about 300 trials per participant) in a small sample size (five to six participants). The EEMD method provided ERMs with remarkably high signal-to-noise ratios and yielded a strong effect size. Furthermore, the experimental requirements for recording MMN (i.e., the number of trials and the sample size) could be reduced while using the suggested analytic method. ERMs may be useful for applying the MMN paradigm in clinical populations and children. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Association between IHC and MSI testing to identify mismatch repair-deficient patients with ovarian cancer.

    Science.gov (United States)

    Lee, Ji-Hyun; Cragun, Deborah; Thompson, Zachary; Coppola, Domenico; Nicosia, Santo V; Akbari, Mohammad; Zhang, Shiyu; McLaughlin, John; Narod, Steven; Schildkraut, Joellen; Sellers, Thomas A; Pal, Tuya

    2014-04-01

    In epithelial ovarian cancer, concordance between results of microsatellite instability (MSI) and immunohistochemical (IHC) testing has not been demonstrated. This study evaluated the association of MSI-high (MSI-H) status with loss of expression (LoE) of mismatch repair (MMR) proteins on IHC and assessed for potential factors affecting the strength of the association. Tumor specimens from three population-based studies of epithelial ovarian cancer were stained for MMR proteins through manual or automated methods, and results were interpreted by one of two pathologists. Tumor and germline DNA was extracted and MSI testing performed. Multivariable logistic regression models were fitted to predict loss of IHC expression based on MSI status after adjusting for staining method and reading pathologist. Of 834 cases, 564 (67.6%) were concordant; 41 were classified as MSI-H with LoE and 523 as microsatellite stable (MSS) with no LoE. Of the 270 discordant cases, 83 were MSI-H with no LoE and 187 were MSS with LoE. Both IHC staining method and reading pathologist were strongly associated with discordant results. Lack of concordance in the current study may be related to inconsistencies in IHC testing methods and interpretation. Results support the need for validation studies before routine screening of ovarian tumors is implemented in clinical practice for the purpose of identifying Lynch syndrome.

  4. New adjacent Bis-tetrahydrofuran Annonaceous acetogenins from Annona muricata.

    Science.gov (United States)

    Chang, Fang-Rong; Liaw, Chih-Chuang; Lin, Chih-Yuan; Chou, Chi-Jung; Chiu, Hui-Fen; Wu, Yang-Chang

    2003-03-01

    Bioactivity-guided fractionation led to the isolation of two new Annonaceous acetogenins, annocatacin A ( 1). and annocatacin B ( 2). from the seeds and the leaves, respectively, of Annona muricata. Compounds 1 and 2 are the first examples where the adjacent bis-tetrahydrofuran ring system is located at C-15. The new structures were elucidated and characterized by spectral and chemical methods. Both Annonaceous acetogenins 1 and 2 showed significant in vitro cytotoxicity toward the human hepatoma cell lines, Hep G2 and 2,2,15, and were compared with the known adjacent bis-tetrahydrofuran acetogenins, neoannonin ( 3). desacetyluvaricin ( 4). bullatacin ( 5). asimicin ( 6). annoglaucin ( 7). squamocin ( 8). and rollimusin ( 9).

  5. Adjacency labeling schemes and induced-universal graphs

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Kaplan, Haim; Thorup, Mikkel

    2015-01-01

    , matching a $\\Omega(n^k)$ lower bound. The lower bound and previously best upper bounds were presented in Alstrup and Rauhe (FOCS'02). Our upper bounds are obtained through a $\\log_2 n +\\Oh(1)$ labeling scheme for adjacency queries in forests. We hereby solve an open problem being raised repeatedly over...... decades, e.g. in Kannan, Naor, Rudich (STOC 1988), Chung (J. of Graph Theory 1990), Fraigniaud and Korman (SODA 2010)....

  6. Processing multiple non-adjacent dependencies: evidence from sequence learning

    Science.gov (United States)

    de Vries, Meinou H.; Petersson, Karl Magnus; Geukes, Sebastian; Zwitserlood, Pienie; Christiansen, Morten H.

    2012-01-01

    Processing non-adjacent dependencies is considered to be one of the hallmarks of human language. Assuming that sequence-learning tasks provide a useful way to tap natural-language-processing mechanisms, we cross-modally combined serial reaction time and artificial-grammar learning paradigms to investigate the processing of multiple nested (A1A2A3B3B2B1) and crossed dependencies (A1A2A3B1B2B3), containing either three or two dependencies. Both reaction times and prediction errors highlighted problems with processing the middle dependency in nested structures (A1A2A3B3_B1), reminiscent of the ‘missing-verb effect’ observed in English and French, but not with crossed structures (A1A2A3B1_B3). Prior linguistic experience did not play a major role: native speakers of German and Dutch—which permit nested and crossed dependencies, respectively—showed a similar pattern of results for sequences with three dependencies. As for sequences with two dependencies, reaction times and prediction errors were similar for both nested and crossed dependencies. The results suggest that constraints on the processing of multiple non-adjacent dependencies are determined by the specific ordering of the non-adjacent dependencies (i.e. nested or crossed), as well as the number of non-adjacent dependencies to be resolved (i.e. two or three). Furthermore, these constraints may not be specific to language but instead derive from limitations on structured sequence learning. PMID:22688641

  7. Adjacent segment disease in degenerative pathologies with posterior instrumentation

    OpenAIRE

    Olvera, Ana Guadalupe Ramírez; Arroyo, Manuel Villarreal; Martínez, Luis Mario Hinojosa; Pérez, Enrique Méndez; Hinojosa, Luis Romeo Ramos

    2015-01-01

    OBJECTIVE: To establish the real incidence of adjacent segment disease after fusion, and to identify the levels and predisposing factors for the pathology, as well as the functional results. METHODS: a retrospective case series study with level of evidence IIB, in a sample of 179 patients diagnosed with stenosis of the lumbar spine, spondylolisthesis and degenerative scoliosis, submitted to surgery in the period 2005 to December 2013, with posterior instrumentation and posterolateral fusion, ...

  8. Gap application results for adjacent electron beams treatment

    Energy Technology Data Exchange (ETDEWEB)

    Sampaio, Francisco G.A., E-mail: francisampaio@pg.ffclrp.usp.br [Departamento de Fisica - FFCLRP, Universidade de Sao Paulo - USP, Av. dos Bandeirantes 3900, CEP 14040-901, Ribeirao Preto, SP (Brazil); Del Lama, Lucas S., E-mail: lucasdellama@yahoo.com.br [Departamento de Fisica - FFCLRP, Universidade de Sao Paulo - USP, Av. dos Bandeirantes 3900, CEP 14040-901, Ribeirao Preto, SP (Brazil); Petchevist, Paulo C.D., E-mail: petchevist12@yahoo.com.br [Departamento de Fisica - FFCLRP, Universidade de Sao Paulo - USP, Av. dos Bandeirantes 3900, CEP 14040-901, Ribeirao Preto, SP (Brazil); Instituto de Radioterapia e Megavoltagem de Ribeirao Preto - IRMEV, Rua Sete de Setembro 1150, CEP 14010-180, Ribeirao Preto, SP (Brazil); Moreira, Marcos V., E-mail: marcos_vasques@yahoo.com.br [Departamento de Fisica - FFCLRP, Universidade de Sao Paulo - USP, Av. dos Bandeirantes 3900, CEP 14040-901, Ribeirao Preto, SP (Brazil); Instituto de Radioterapia e Megavoltagem de Ribeirao Preto - IRMEV, Rua Sete de Setembro 1150, CEP 14010-180, Ribeirao Preto, SP (Brazil); Almeida, Adelaide de, E-mail: dalmeida@ffclrp.usp.br [Departamento de Fisica - FFCLRP, Universidade de Sao Paulo - USP, Av. dos Bandeirantes 3900, CEP 14040-901, Ribeirao Preto, SP (Brazil)

    2011-12-15

    Nowadays, electron beams from high-energy linear accelerators (LINAC) are widely used in a variety of radiotherapy treatments being suitable especially for superficial tumors. Since this sort of ionizing radiation has stopping power higher than photons, deeper and healthier tissues can be preserved. On the other hand, when applying adjacent electron beams, 'hot' spots can be observed, due to penumbra and/or scattering, contributing to the increase of the absorbed dose in the target volume. In this sense, the objective of this work was to investigate the effects of parallel adjacent electron beams using the chemical dosimeter Fricke Xylenol Gel (FXG) and compare the experimental results with ones acquired using Monte Carlo simulation. Thus, 10 Multiplication-Sign 10, 15 Multiplication-Sign 15 and 20 Multiplication-Sign 20 cm{sup 2} fields were irradiated with 5, 8 and 10 MeV electron beams applying different gap widths. The experimental results and the simulations indicated overdose values up to 40% from the prescribed one for the specific tumor. This demonstrates that specific gaps are necessary in the case of treatments with parallel adjacent electron beams in order to prevent overdoses in the depth of interest.

  9. Remineralizing effects of glass ionomer restorations on adjacent interproximal caries.

    Science.gov (United States)

    Jang, K T; Garcia-Godoy, F; Donly, K J; Segura, A

    2001-01-01

    The purpose of this study was to examine the in vitro remineralization of incipient caries lesions on teeth adjacent interproximally to teeth with Class II glass ionomer cement restorations. Sixty-four extracted molars were selected and 1 x 5 mm artificial caries lesions were created at the interproximal contact point. One hundred micrometer sections were obtained at the caries sites, and polarized-light photomicrographs were obtained. The sections were covered with varnish, leaving only the external section site exposed, and were placed back into the original tooth. In another sixty-four molars, Class II cavities were prepared. Equal numbers of preparations were filled with Fuji IX GP, Vitremer, Ketac-Molar, or Z 250. These sixty-four teeth were mounted to have interproximal contact with the adjacent teeth containing the artificial caries lesions. Specimens were placed in closed environments of artificial saliva for one month. After thirty days, the same sections were photographed again under polarized light, and areas of the lesions were quantitated. Decrease in the size of caries lesions indicated the glass ionomers had significantly greater remineralization effects on adjacent caries than the nonfluoridated composite resin (ANOVA p < 0.05). There were no significant differences among the three glass ionomers tested.

  10. Sliding mode control for generalized robust synchronization of mismatched fractional order dynamical systems and its application to secure transmission of voice messages.

    Science.gov (United States)

    Muthukumar, P; Balasubramaniam, P; Ratnavelu, K

    2017-07-26

    This paper proposes a generalized robust synchronization method for different dimensional fractional order dynamical systems with mismatched fractional derivatives in the presence of function uncertainty and external disturbance by a designing sliding mode controller. Based on the proposed theory of generalized robust synchronization criterion, a novel audio cryptosystem is proposed for sending or sharing voice messages secretly via insecure channel. Numerical examples are given to verify the potency of the proposed theories. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    David Gustine

    Full Text Available 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.

  12. Late Permian to Triassic intraplate orogeny of the southern Tianshan and adjacent regions, NW China

    Directory of Open Access Journals (Sweden)

    Wei Ju

    2014-01-01

    Based on previous studies and recent geochronogical data, we suggest that the final collision between the Tarim Craton and the North Asian continent occurred during the late Carboniferous. Therefore, the Permian was a period of intracontinental environment in the southern Tianshan and adjacent regions. We propose that an earlier, small-scale intraplate orogenic stage occurred in late Permian to Triassic time, which was the first intraplate process in the South Tianshan Orogen and adjacent regions. The later large-scale and well-known Neogene to Quaternary intraplate orogeny was induced by the collision between the India subcontinent and the Eurasian plate. The paper presents a new evolutionary model for the South Tianshan Orogen and adjacent regions, which includes seven stages: (I late Ordovician–early Silurian opening of the South Tianshan Ocean; (II middle Silurian–middle Devonian subduction of the South Tianshan Ocean beneath an active margin of the North Asian continent; (III late Devonian–late Carboniferous closure of the South Tianshan Ocean and collision between the Kazakhstan-Yili and Tarim continental blocks; (IV early Permian post-collisional magmatism and rifting; (V late Permian–Triassic the first intraplate orogeny; (VI Jurassic–Palaeogene tectonic stagnation and (VII Neocene–Quaternary intraplate orogeny.

  13. Clusters of adjacent and similarly expressed genes across normal human tissues complicate comparative transcriptomic discovery.

    Science.gov (United States)

    Liu, Chang; Ghosh, Sujoy; Searls, David B; Saunders, Ann M; Cossman, Jeffrey; Roses, Allen D

    2005-01-01

    Transcriptomic techniques are valuable tools with which to validate genetic and biological hypotheses and are now widely available for research. However, with the exception of tumor biology, comparative genomics analyses have been difficult to use as discovery engines to describe biologically relevant expression changes. We propose that physical proximity of human genes correlates with similar mRNA expression, so that increased expression might include a disease-relevant gene and many other genes in the adjacent region. To increase the efficiency of combining susceptibility gene mapping and interpretation of transcriptomics, we developed a method to identify clusters of adjacent and similarly expressed genes. Gene expression profiles for 28,945 genes across 101 normal human tissues were obtained from the Gene Logic BioExpress system. The expression similarity for genes in sliding-windows was measured using average pair-wise Pearson correlation coefficients. We identified 187 clusters (p < 10e-4) of co-regulated genes, including 2648 genes, or 9.1% of all genes considered and termed these "clusters of adjacent and similarly expressed genes" (CASEGs). Genes in 15 (8.2%) of these clusters demonstrate a significant co-expression enrichment (p < 10e-10). This study demonstrates the coordinate expression of neighboring genes and provides a comprehensive view of expression-based compartmentalization of the human genome, which can be overlaid on genetic susceptibility gene maps.

  14. Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue.

    Science.gov (United States)

    Geybels, Milan S; Zhao, Shanshan; Wong, Chao-Jen; Bibikova, Marina; Klotzle, Brandy; Wu, Michael; Ostrander, Elaine A; Fan, Jian-Bing; Feng, Ziding; Stanford, Janet L

    2015-12-01

    Aberrant DNA methylation may promote prostate carcinogenesis. We investigated epigenome-wide DNA methylation profiles in prostate cancer (PCa) compared to adjacent benign tissue to identify differentially methylated CpG sites. The study included paired PCa and adjacent benign tissue samples from 20 radical prostatectomy patients. Epigenetic profiling was done using the Infinium HumanMethylation450 BeadChip. Linear models that accounted for the paired study design and False Discovery Rate Q-values were used to evaluate differential CpG methylation. mRNA expression levels of the genes with the most differentially methylated CpG sites were analyzed. In total, 2,040 differentially methylated CpG sites were identified in PCa versus adjacent benign tissue (Q-value < 0.001), the majority of which were hypermethylated (n = 1,946; 95%). DNA methylation profiles accurately distinguished between PCa and benign tissue samples. Twenty-seven top-ranked hypermethylated CpGs had a mean methylation difference of at least 40% between tissue types, which included 25 CpGs in 17 genes. Furthermore, for 10 genes over 50% of promoter region CpGs were hypermethylated in PCa versus benign tissue. The top-ranked differentially methylated genes included three genes that were associated with both promoter hypermethylation and reduced gene expression: SCGB3A1, HIF3A, and AOX1. Analysis of The Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. This study of PCa versus adjacent benign tissue showed many differentially methylated CpGs and regions in and outside gene promoter regions, which may potentially be used for the development of future epigenetic-based diagnostic tests or as therapeutic targets. © 2015 Wiley Periodicals, Inc.

  15. Direct observation of breathing dynamics at the mismatch induced DNA bubble with nanometre accuracy: a smFRET study.

    Science.gov (United States)

    Paul, Tapas; Bera, Subhas C; Mishra, Padmaja P

    2017-05-11

    The detailed conformational dynamics of the melted region in double-stranded DNA has been studied using a combination of ensemble and single-molecule FRET techniques. We monitored the millisecond time scale fluctuation kinetics of the two strands at the bubble region that varies with the size of the bubble. As the individual strands at the melting bubble behave as single-stranded DNA, and hence fluctuate dynamically to attain energetically favored configurations, the rates of these fluctuations increase with increase in the bubble size. In different short DNAs under investigation, the two strands never cross each other to form a knot, irrespective of the number of base pair mismatches present. Rather, they prefer to stay apart from each other, as the size of the bubble increases and follow exactly an opposite trend for bubbles of smaller size. The range within which the bubble strands fluctuate are monitored with great accuracy in the nanometre resolution from the single-molecule FRET measurements. The shape of the bubble that plays a crucial role in determining the activity of the DNA was speculated. These results shall be useful in quantifying the chemical processes within DNA as well as to develop a deeper understanding of the activity of the DNA due to induced mismatches.

  16. Bronchopulmonary dysplasia: clinical grading in relation to ventilation/perfusion mismatch measured by single photon emission computed tomography.

    Science.gov (United States)

    Kjellberg, Malin; Björkman, Karin; Rohdin, Malin; Sanchez-Crespo, Alejandro; Jonsson, Baldvin

    2013-12-01

    Bronchopulmonary dysplasia (BPD) is a significant cause of morbidity in the preterm population. Clinical severity grading based on the need for supplemental oxygen and/or need for positive airway pressure at 36 weeks postmenstrual age does not yield reproducible predictive values for later pulmonary morbidity. Single photon emission computed tomography (SPECT) was used to measure the distribution of lung ventilation (V) and perfusion (Q) in 30 BPD preterm infants at a median age of 37 weeks postmenstrual age. The V and Q were traced with 5 MBq Technegas and Technetium-labeled albumin macro aggregates, respectively, and the V/Q match-mismatch was used to quantify the extent of lung function impairment. The latter was then compared with the clinical severity grading at 36 weeks, and time spent on mechanical ventilation, continuous positive airway pressure (CPAP) and supplemental oxygen. Of those with mild and moderate BPD 3/9 and 3/11 patients, respectively, showed significant V/Q mismatches. By contrast, 4/10 patients with severe BPD showed a satisfactory V/Q matching distribution. An unsatisfactory V/Q match was not correlated with time spent on supplemental oxygen or CPAP, but was significantly negatively correlated with time spent on mechanical ventilation. SPECT provides unique additional information about regional lung function. The results suggest that the current clinical severity grading can be improved and/or complemented with SPECT. © 2013 Wiley Periodicals, Inc.

  17. In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair

    Science.gov (United States)

    Burdett, Vickers; Baitinger, Celia; Viswanathan, Mohan; Lovett, Susan T.; Modrich, Paul

    2001-01-01

    Biochemical studies with model DNA heteroduplexes have implicated RecJ exonuclease, exonuclease VII, exonuclease I, and exonuclease X in Escherichia coli methyl-directed mismatch correction. However, strains deficient in the four exonucleases display only a modest increase in mutation rate, raising questions concerning involvement of these activities in mismatch repair in vivo. The quadruple mutant deficient in the four exonucleases, as well as the triple mutant deficient in RecJ exonuclease, exonuclease VII, and exonuclease I, grow poorly in the presence of the base analogue 2-aminopurine, and exposure to the base analogue results in filament formation, indicative of induction of SOS DNA damage response. The growth defect and filamentation phenotypes associated with 2-aminopurine exposure are effectively suppressed by null mutations in mutH, mutL, mutS, or uvrD/mutU, which encode activities that act upstream of the four exonucleases in the mechanism for the methyl-directed reaction that has been proposed based on in vitro studies. The quadruple exonuclease mutant is also cold-sensitive, having a severe growth defect at 30°C. This phenotype is suppressed by a uvrD/mutU defect, and partially suppressed by mutH, mutL, or mutS mutations. These observations confirm involvement of the four exonucleases in methyl-directed mismatch repair in vivo and suggest that the low mutability of exonuclease-deficient strains is a consequence of under recovery of mutants due to a reduction in viability and/or chromosome loss associated with activation of the mismatch repair system in the absence of RecJ exonuclease, exonuclease VII, exonuclease I, and exonuclease X. PMID:11381137

  18. InSb heterostructure nanowires: MOVPE growth under extreme lattice mismatch.

    Science.gov (United States)

    Caroff, Philippe; Messing, Maria E; Mattias Borg, B; Dick, Kimberly A; Deppert, Knut; Wernersson, Lars-Erik

    2009-12-09

    We demonstrate the growth of InSb-based nanowire heterostructures by metalorganic vapour phase epitaxy and use it to integrate InSb on extremely lattice-mismatched III-V nanowire templates made of InAs, InP, and GaAs. Influence of temperature, V/III ratio, and diameter are investigated in order to investigate the growth rate and morphology. The range of growth temperatures used for InSb nanowire growth is very similar to that used for planar growth due to the nature of the precursor decomposition. This makes optimization of growth parameters very important, and more difficult than for most other nanowire III-V materials. Analysis of the InSb nanowire epitaxial quality when grown on InAs, InP, and GaAs, along with InSb segment and particle compositions are reported. This successful direct integration of InSb nanowires, on nanowire templates with unprecedented strain levels show great promise for fabrication of vertical InSb devices.

  19. Potential contamination effects of neuronal refractoriness on the speech-evoked mismatch negativity response.

    Science.gov (United States)

    Cranford, Jerry L; Walker, Letitia J; Stuart, Andrew; Elangovan, Saravanan; Pravica, David

    2003-07-01

    The mismatch negativity response (MMN) is an event-related potential that is believed to reflect the automatic (possibly preconscious) neural processing of changes in ongoing environmental sounds. The MMN involves a negative voltage shift of baseline electroencephalographic (EEG) activity in the approximate latency window of the N1 and P2 cortical potentials in response to new or novel sounds. The most commonly used laboratory tests for extracting the MMN from EEG activity all involve oddball stimulus presentation procedures in which the interstimulus intervals (ISIs) of the frequently occurring standard sounds are shorter in length then that of the infrequently occurring deviant sounds. This presents the possibility that the MMN response could be affected by neuronal refractory or recovery events. The present study tested 12 young females, using the syllabic events /da/ and /ga/ as standard and deviant stimuli, and found evidence that, with certain experimental protocols, ISI-dependent neural refractory effects can affect the morphology of the MMN, possibly resulting in misinterpretation of the underlying neural bases of the response.

  20. Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.

    Science.gov (United States)

    Halvey, Patrick J; Wang, Xiaojing; Wang, Jing; Bhat, Ajaz A; Dhawan, Punita; Li, Ming; Zhang, Bing; Liebler, Daniel C; Slebos, Robbert J C

    2014-01-01

    A growing body of genomic data on human cancers poses the critical question of how genomic variations translate to cancer phenotypes. We used standardized shotgun proteomics and targeted protein quantitation platforms to analyze a panel of 10 colon cancer cell lines differing by mutations in DNA mismatch repair (MMR) genes. In addition, we performed transcriptome sequencing (RNA-seq) to enable detection of protein sequence variants from the proteomic data. Biologic replicate cultures yielded highly consistent proteomic inventories with a cumulative total of 6,513 protein groups with a protein false discovery rate of 3.17% across all cell lines. Networks of coexpressed proteins with differential expression based on MMR status revealed impact on protein folding, turnover and transport, on cellular metabolism and on DNA and RNA synthesis and repair. Analysis of variant amino acid sequences suggested higher stability of proteins affected by naturally occurring germline polymorphisms than of proteins affected by somatic protein sequence changes. The data provide evidence for multisystem adaptation to MMR deficiency with a stress response that targets misfolded proteins for degradation through the ubiquitin-dependent proteasome pathway. Enrichment analysis suggested epithelial-to-mesenchymal transition in RKO cells, as evidenced by increased mobility and invasion properties compared with SW480. The observed proteomic profiles demonstrate previously unknown consequences of altered DNA repair and provide an expanded basis for mechanistic interpretation of MMR phenotypes.

  1. Automated auditory mismatch negativity paradigm improves coma prognostic accuracy after cardiac arrest and therapeutic hypothermia.

    Science.gov (United States)

    Rossetti, Andrea O; Tzovara, Athina; Murray, Micah M; De Lucia, Marzia; Oddo, Mauro

    2014-08-01

    EEG and somatosensory evoked potential are highly predictive of poor outcome after cardiac arrest; their accuracy for good recovery is however low. We evaluated whether addition of an automated mismatch negativity-based auditory discrimination paradigm (ADP) to EEG and somatosensory evoked potential improves prediction of awakening. EEG and ADP were prospectively recorded in 30 adults during therapeutic hypothermia and in normothermia. We studied the progression of auditory discrimination on single-trial multivariate analyses from therapeutic hypothermia to normothermia, and its correlation to outcome at 3 months, assessed with cerebral performance categories. At 3 months, 18 of 30 patients (60%) survived; 5 had severe neurologic impairment (cerebral performance categories = 3) and 13 had good recovery (cerebral performance categories = 1-2). All 10 subjects showing improvements of auditory discrimination from therapeutic hypothermia to normothermia regained consciousness: ADP was 100% predictive for awakening. The addition of ADP significantly improved mortality prediction (area under the curve, 0.77 for standard model including clinical examination, EEG, somatosensory evoked potential, versus 0.86 after adding ADP, P = 0.02). This automated ADP significantly improves early coma prognostic accuracy after cardiac arrest and therapeutic hypothermia. The progression of auditory discrimination is strongly predictive of favorable recovery and appears complementary to existing prognosticators of poor outcome. Before routine implementation, validation on larger cohorts is warranted.

  2. Upper tract urothelial carcinomas: frequency of association with mismatch repair protein loss and lynch syndrome.

    Science.gov (United States)

    Harper, Holly L; McKenney, Jesse K; Heald, Brandie; Stephenson, Andrew; Campbell, Steven C; Plesec, Thomas; Magi-Galluzzi, Cristina

    2017-01-01

    Increased risk for upper tract urothelial carcinoma is described in patients with Lynch syndrome, caused by germline mutations in mismatch repair genes. We aimed to identify the frequency of mismatch repair protein loss in upper tract urothelial carcinoma and its potential for identifying an association with Lynch syndrome. We queried our database to identify upper tract urothelial carcinomas. Patients were cross-referenced for history of colorectal carcinoma or other common Lynch syndrome-associated neoplasms to enrich for potential Lynch syndrome cases. Tumor histopathologic characteristics were reviewed and each case was analyzed for loss of mismatch repair proteins, MLH1, MSH2, MSH6, and PMS2, by immunohistochemistry. Of 444 patients with upper tract urothelial carcinoma, a subset of 215 (encompassing 30 with upper tract urothelial carcinoma and another common Lynch syndrome-associated neoplasm) was analyzed for loss of mismatch repair protein expression. Of 30 patients with Lynch syndrome-associated neoplasms, six had documented Lynch syndrome, including two with Muir-Torre syndrome. Mismatch repair protein loss was identified in 7% of total upper tract urothelial carcinomas and 30% of patients with Lynch syndrome-associated neoplasms (including all patients with Lynch syndrome/Muir-Torre syndrome). Of patients without history of Lynch syndrome-associated neoplasms, 5 of 184 (2.7%) had loss of mismatch repair protein expression. Twelve cases with mismatch repair protein loss demonstrated loss of MSH2 and MSH6, and 2 had isolated loss of MSH6. MLH1 and PMS2 expression were consistently retained. Although increased intratumoral lymphocytes, inverted growth, pushing tumor-stromal interface, and lack of nuclear pleomorphism were more commonly seen in cases with mismatch repair protein loss, only intratumoral lymphocytes and presence of pushing borders were statistically significant. MLH1 and PMS2 testing appear to have little utility in upper tract urothelial

  3. Susceptibility-diffusion mismatch in middle cerebral artery territory acute ischemic stroke: clinical and imaging implications.

    Science.gov (United States)

    Payabvash, Seyedmehid; Taleb, Shayandokht; Benson, John C; Hoffman, Benjamin; Oswood, Mark C; McKinney, Alexander M; Rykken, Jeffrey B

    2017-07-01

    Background Recent studies have suggested a correlation between susceptibility-diffusion mismatch and perfusion-diffusion mismatch in acute ischemic stroke patients. Purpose To determine the clinical and imaging associations of susceptibility-diffusion mismatch in patients with acute ischemic stroke in the middle cerebral artery (MCA) territory. Material and Methods Consecutive patients with MCA territory acute ischemic stroke, who had magnetic resonance imaging (MRI) performed with susceptibility-weighted imaging (SWI) and diffusion-weighted imaging (DWI) within 24 h of symptom onset or time last-seen-well, were included. Two neuroradiologists reviewed SWI scans for SWI-DWI mismatch defined by regionally increased vessel number or diameter on SWI extending beyond the DWI hyperintensity territory in the affected hemisphere. The stroke severity at admission was evaluated using the National Institutes of Health Stroke Scale (NIHSS) score. Poor clinical outcome was defined by a 3-month modified Rankin Scale (mRS) score >2. Results The SWI-DWI mismatch was identified in 44 (29.3%) of 150 patients included in this study. Patients with SWI-DWI mismatch had smaller admission infarct volumes (31.2 ± 44.7 versus 55.9 ± 117.7 mL, P = 0.045) and were younger (60.4 ± 18.9 versus 67.1 ± 15.5, P = 0.026). After correction for age, admission NIHSS score, and infarct volume, the SWI-DWI mismatch was associated with a 22.6% lower rate of poor clinical outcome using propensity score matching ( P = 0.032). In our cohort, thrombolytic therapy showed no significant effect on outcome. Conclusion The presence of SWI-DWI mismatch in acute MCA territory ischemic infarct is associated with smaller infarct volume. Moreover, SWI-DWI mismatch was associated with better outcome after correction for infarct size, severity of admission symptoms, and age.

  4. Comparison of phylogeographic structure and population history of two Phrynocephalus species in the Tarim Basin and adjacent areas.

    Science.gov (United States)

    Zhang, Qian; Xia, Lin; He, Jingbo; Wu, Yonghua; Fu, Jinzhong; Yang, Qisen

    2010-12-01

    An aridification of the Tarim Basin and adjacent areas since middle Pleistocene has produced significant genetic structuring of the local fauna. We examined the phylogeographic patterns, population structure and history of Phrynocephalus axillaris and Phrynocephalus forsythii using a mitochondrial fragment ND4-tRNA(LEU). Phylogenetic hypotheses were constructed using maximum parsimony and Bayesian inference, and the divergence times of major lineages were estimated by BEAST. Population structure and history were inferred by nested clade analysis, neutrality tests, mismatch distribution, and isolation by distance analysis. The two species might have experienced different evolutionary history throughout their current distribution. For P. forsythii, a vicariant event, as a consequence of geological isolation and desert expansion, might have produced the significant divergence between the Tarim and the Yanqi populations. For P. axillaris, populations of the Yanqi, Turpan and Hami Basins might have been established through dispersal during demographic expansion. Climatic fluctuations caused alternate expansion and shrinkage of rivers and oases several times, which likely led to habitat fragmentation for both species. Interaction between vicariance, dispersal and habitat fragmentation produced the current distribution and genetic diversity. The observed difference between the two species may be due partially to their different reproductive modes (ovoviviparous vs. oviparous). Copyright © 2010 Elsevier Inc. All rights reserved.

  5. Mismatch negativity in children with specific language impairment and auditory processing disorder

    Directory of Open Access Journals (Sweden)

    Caroline Nunes Rocha-Muniz

    2015-08-01

    Full Text Available INTRODUCTION: Mismatch negativity, an electrophysiological measure, evaluates the brain's capacity to discriminate sounds, regardless of attentional and behavioral capacity. Thus, this auditory event-related potential is promising in the study of the neurophysiological basis underlying auditory processing.OBJECTIVE: To investigate complex acoustic signals (speech encoded in the auditory nervous system of children with specific language impairment and compare with children with auditory processing disorders and typical development through the mismatch negativity paradigm.METHODS: It was a prospective study. 75 children (6-12 years participated in this study: 25 children with specific language impairment, 25 with auditory processing disorders, and 25 with typical development. Mismatch negativity was obtained by subtracting from the waves obtained by the stimuli /ga/ (frequent and /da/ (rare. Measures of mismatch negativity latency and two amplitude measures were analyzed.RESULTS: It was possible to verify an absence of mismatch negativity in 16% children with specific language impairment and 24% children with auditory processing disorders. In the comparative analysis, auditory processing disorders and specific language impairment showed higher latency values and lower amplitude values compared to typical development.CONCLUSION: These data demonstrate changes in the automatic discrimination of crucial acoustic components of speech sounds in children with specific language impairment and auditory processing disorders. It could indicate problems in physiological processes responsible for ensuring the discrimination of acoustic contrasts in pre-attentional and pre-conscious levels, contributing to poor perception.

  6. On pattern matching with k mismatches and few don't cares.

    Science.gov (United States)

    Nicolae, Marius; Rajasekaran, Sanguthevar

    2017-02-01

    We consider the problem of pattern matching with k mismatches, where there can be don't care or wild card characters in the pattern. Specifically, given a pattern P of length m and a text T of length n, we want to find all occurrences of P in T that have no more than k mismatches. The pattern can have don't care characters, which match any character. Without don't cares, the best known algorithm for pattern matching with k mismatches has a runtime of [Formula: see text]. With don't cares in the pattern, the best deterministic algorithm has a runtime of O(nk polylog m). Therefore, there is an important gap between the versions with and without don't cares. In this paper we give an algorithm whose runtime increases with the number of don't cares. We define an island to be a maximal length substring of P that does not contain don't cares. Let q be the number of islands in P. We present an algorithm that runs in [Formula: see text] time. If the number of islands q is O(k) this runtime becomes [Formula: see text], which essentially matches the best known runtime for pattern matching with k mismatches without don't cares. If the number of islands q is O(k2), this algorithm is asymptotically faster than the previous best algorithm for pattern matching with k mismatches with don't cares in the pattern.

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

    Science.gov (United States)

    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.

  8. Mismatch negativity in children with specific language impairment and auditory processing disorder.

    Science.gov (United States)

    Rocha-Muniz, Caroline Nunes; Befi-Lopes, Débora Maria; Schochat, Eliane

    2015-01-01

    Mismatch negativity, an electrophysiological measure, evaluates the brain's capacity to discriminate sounds, regardless of attentional and behavioral capacity. Thus, this auditory event-related potential is promising in the study of the neurophysiological basis underlying auditory processing. To investigate complex acoustic signals (speech) encoded in the auditory nervous system of children with specific language impairment and compare with children with auditory processing disorders and typical development through the mismatch negativity paradigm. It was a prospective study. 75 children (6-12 years) participated in this study: 25 children with specific language impairment, 25 with auditory processing disorders, and 25 with typical development. Mismatch negativity was obtained by subtracting from the waves obtained by the stimuli /ga/ (frequent) and /da/ (rare). Measures of mismatch negativity latency and two amplitude measures were analyzed. It was possible to verify an absence of mismatch negativity in 16% children with specific language impairment and 24% children with auditory processing disorders. In the comparative analysis, auditory processing disorders and specific language impairment showed higher latency values and lower amplitude values compared to typical development. These data demonstrate changes in the automatic discrimination of crucial acoustic components of speech sounds in children with specific language impairment and auditory processing disorders. It could indicate problems in physiological processes responsible for ensuring the discrimination of acoustic contrasts in pre-attentional and pre-conscious levels, contributing to poor perception. Copyright © 2015 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

  9. Mismatches in Self-Reported and Meta-Perceived Ethnic Identification across the High School Years.

    Science.gov (United States)

    Nishina, Adrienne; Bellmore, Amy; Witkow, Melissa R; Nylund-Gibson, Karen; Graham, Sandra

    2018-01-01

    Ethnic identification (i.e., one's self-reported ethnicity) is a social construction and therefore subject to misperceptions by others. When adolescents' self-views and others' perceptions are not aligned, adolescents may experience adjustment challenges. The present study examined mismatches between adolescents' ethnic identification (i.e., self-reported ethnicity) and meta-perceptions (i.e., what ethnicity they believed their schoolmates presumed them to be), as well as longitudinal associations between mismatches and adjustment across the high school years. Participants (M age =  14.5; 57% girls) were an ethnically diverse sample of 1151 low-income high school students who had participated in an earlier longitudinal study during middle school. Although ethnic identification was largely consistent across the high school years, many students (46%) experienced at least occasional mismatches between their self-reported ethnic identification and meta-perceptions, with students who ever identified as multiethnic experiencing more mismatches than their monoethnic counterparts. Experiencing a mismatch was associated with more depressive symptoms, physical symptoms, and lower self-worth.

  10. Incidence and Impact of Patient-Prosthesis Mismatch in Isolated Aortic Valve Surgery.

    Science.gov (United States)

    Dumani, Selman; Likaj, Ermal; Kacani, Andi; Dibra, Laureta; Petrela, Elizana; Beca, Vera; Refatllari, Ali

    2015-12-15

    The mains topics of this work are the incidence of patient-prosthesis mismatch and the influence in the early results of isolated aortic valve surgery. In 193 patients isolated aortic valve surgery was performed. The study population was divided in three subgroups: 20 patients with severe, 131 patients with moderate and 42 patients without patient-prosthesis mismatch. The indexed effective orifice area was used to define the subgroups. Operative mortality and perioperative complications were considered the indicators of the early results of aortic valve surgery. The incidence of severe and moderate patient-prosthesis mismatch was respectively 10.3% and 67.8%. Hospital mortality and perioperative complications were: mortality 5% vs. 3.1% vs. 2.4% (p = 0.855), low cardiac output 5% vs. 6.9% vs. 4.8% (p = 0.861); pulmonary complications 5% vs. 3.1 vs. 0.0% (p = 0.430); exploration for bleeding 5% vs. 0.8% vs. 2.4% (p = 0.319); atrial fibrillation 30% vs. 19.8% vs. 11.9% (p = 0.225); wound infection 5% vs. 0.8% vs. 0.00% (p = 0.165), respectively for the group with severe, moderate and without patient-prosthesis mismatch. Patient-prosthesis mismatch is a common occurrence in aortic valve surgery. This phenomenon does not affect the early results of aortic valve surgery.

  11. Influences of Device and Circuit Mismatches on Paralleling Silicon Carbide MOSFETs

    DEFF Research Database (Denmark)

    Li, Helong; Munk-Nielsen, Stig; Wang, Xiongfei

    2016-01-01

    This paper addresses the influences of device and circuit mismatches on paralleling the Silicon Carbide (SiC) MOSFETs. Comprehensive theoretical analysis and experimental validation from paralleled discrete devices to paralleled dies in multichip power modules are first presented. Then, the influ......This paper addresses the influences of device and circuit mismatches on paralleling the Silicon Carbide (SiC) MOSFETs. Comprehensive theoretical analysis and experimental validation from paralleled discrete devices to paralleled dies in multichip power modules are first presented. Then......, the influence of circuit mismatch on paralleling SiC MOSFETs is investigated and experimentally evaluated for the first time. It is found that the mismatch of the switching loop stray inductance can also lead to on-state current unbalance with inductive output current, in addition to the on-state resistance...... of the device. It further reveals that circuit mismatches and a current coupling among the paralleled dies exist in a SiC MOSFET multichip power module, which is critical for the transient current distribution in the power module. Thus, a power module layout with an auxiliary source connection is developed...

  12. The relative effects of age and learning style mismatch on adult students' academic achievement and perception of instructors

    OpenAIRE

    Garrett, Clayton W.

    1996-01-01

    This study investigated the relationship between students' age, achievement, evaluation of the instructors and the match-mismatch of students' and instructors' learning styles. Seventeen (17) business instructors and 302 business students comprised the population. The students were selected as an intact group enrolled in the participating faculty members' class. The relationship between age and learning style mismatch and evaluation and age and learning style mismatch an...

  13. Biomechanical Evaluation of Lumbar Decompression Adjacent to Instrumented Segments.

    Science.gov (United States)

    Grunert, Peter; Reyes, Phillip M; Newcomb, Anna G U S; Towne, Sara B; Kelly, Brian P; Theodore, Nicholas; Härtl, Roger

    2016-12-01

    Multilevel lumbar stenosis, in which 1 level requires stabilization due to spondylolisthesis, is routinely treated with multilevel open laminectomy and fusion. We hypothesized that a minimally invasive (MI) decompression is biomechanically superior to open laminectomy and may allow decompression of the level adjacent the spondylolisthesis without additional fusion. To study the mechanical effect of various decompression procedures adjacent to instrumented segments in cadaver lumbar spines. Conditions tested were (1) L4-L5 instrumentation, (2) L3-L4 MI decompression, (3) addition of partial facetectomy at L3-L4, and (4) addition of laminectomy at L3-L4. Flexibility tests were performed for range of motion (ROM) analysis by applying nonconstraining, pure moment loading during flexion-extension, lateral bending, and axial rotation. Compression flexion tests were performed for motion distribution analysis. After instrumentation, MI decompression increased flexion-extension ROM at L3-L4 by 13% (P = .03) and axial rotation by 23% (P = .003). Partial facetectomy further increased axial rotation by 15% (P = .03). After laminectomy, flexion-extension ROM further increased by 12% (P = .05), a 38% increase from baseline, and axial rotation by 17% (P = .02), a 58% increase from baseline. MI decompression yielded no significant increase in segmental contribution of motion at L3-L4, in contrast to partial facetectomy and laminectomy (<.05). MI tubular decompression is biomechanically superior to open laminectomy adjacent to instrumented segments. These results lend support to the concept that in patients in whom a multilevel MI decompression is performed, the fusion might be limited to the segments with actual instability. MI, minimally invasive.

  14. Microwave treatment of renal cell carcinoma adjacent to renal sinus

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yongyan, E-mail: gaoyongyan7@163.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Department of Ultrasound, The General Hospital of Chinese People’s Armed Police Forces, 69 Yongding Road, Beijing, 100039 (China); Liang, Ping, E-mail: liangping301@hotmail.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Yu, Xiaoling, E-mail: 784107477@qq.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Yu, Jie, E-mail: 1411495161@qq.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Cheng, Zhigang, E-mail: 13691367317@163.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Han, Zhiyu, E-mail: hanzhiyu122@163.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Duan, Shaobo, E-mail: Dustin2662@163.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Huang, Hui, E-mail: 309hh@sina.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China)

    2016-11-15

    Highlights: • This study shows US-guided microwave ablation appears to be a promising method to treat renal cell carcinoma adjacent to renal sinus. • The estimated 1-, 3- and 5-year RCC-related survival were 100%, 93.3% and 93.3%, respectively. • The estimated 1-, 3- and 5-year overall survival were 97.1%, 87.8%, 83.6%, respectively. • For patients with RCC ≤4 cm, initial ablation success was 100% (29/29) and the estimated 5-year disease-free survival were 81.5%. - Abstract: Purpose: To evaluate the efficacy and safety of ultrasound (US)-guided percutaneous microwave ablation (MWA) for renal cell carcinoma (RCC) adjacent to renal sinus. Materials and methods: This retrospective study included 41 patients who underwent US-guided percutaneous MWA of 41 RCCs adjacent to the renal sinus from April 2006 to December 2015. Contrast-enhanced images of US and computed tomography (CT) or magnetic resonance (MR) imaging were performed at pre-ablation and 1 day, 1 month, 3 months, and every 6 months after ablation. Initial ablation success (IAS), disease-free survival (DFS), RCC-related survival (RRS), and overall survival (OS) were recorded at the follow-up visits. Results: IAS was achieved in 92.7% (38/41) of the study subjects. The IAS significantly differed between patients with RCCs ≤4 cm (100%, 29/29) and RCCs >4 cm (75%, 9/12, p = 0.021). During the median follow-up of 37.6 (range, 3.0–97.3) months, the estimated 1-, 3-, and 5-year DFS of patients with an initial tumor of ≤4 cm were 100%, 89.7%, and 81.5%, respectively. The 1-, 3-, and 5-year RRS were 100%, 93.3%, and 93.3%, respectively. The 1-, 3-, and 5-year OS were 97.1%, 87.8%, and 83.6%, respectively. The multivariate analysis using the Cox proportional hazard model revealed no independent predictor of recurrence among all the variables. There were no MWA-related deaths among the study subjects. One patient developed a retroperitoneal abscess after ablation. Conclusion: US-guided percutaneous MWA

  15. Osteoid Osteoma of Cervical Spine in two adjacent Vertebrae

    Directory of Open Access Journals (Sweden)

    MR Etemadifar

    2005-09-01

    Full Text Available Osteoid osteoma is a benign bone tumor, mainly seen in 10-30 years male. Spine is a relatively common site and almost always, posterior elements are involved. Plain X-Ray-, CT scan and Isotope scan help to identify and localize spine lesions. We described one 18 years old boy with 3 years low neck pain. Isotope scan, MRI and CT scan showed two lesions in C7 and T1. Gross inspection and histopathology examination confirmed osteoid osteoma in two adjacent vertebrae which has not been reported elsewhere in the literature. Key words: Osteoid Osteoma, Spine, Multifocal

  16. Application of the simplified J-estimation scheme Aramis to mismatching welds in CCP; Application du concept d`integrale J dans l`outil Aramis aux effets de mismatch sur des eprouvettes CCP

    Energy Technology Data Exchange (ETDEWEB)

    Eripret, C.; Franco, C.; Gilles, P.

    1995-12-31

    The J-based criteria give reasonable predictions of the failure behaviour of ductile cracked metallic structures, even if the material characterization may be sensitive to the size of the specimens. However in cracked welds, this phenomenon due to stress triaxiality effects could be enhanced. Furthermore, the application of conventional methods of toughness measurement (ESIS or ASTM standard) have evidenced a strong influence of the portion of the weld metal in the specimen. Several authors have shown the inadequacy of the simplified J-estimation methods developed for homogeneous materials. These heterogeneity effects mainly related to the mismatch ratio (ratio of weld metal yield strength upon base metal yield strength) as well as to the geometrical parameter h/W-a (weld width upon ligament size). In order to make decisive progress in this field, the Atomic Energy Commission (CEA), the PWR manufacturer FRAMATOME, and the French utility (EDF) have launched a large research program on cracked piping welds behaviour. As part of this program, a new J-estimation scheme, so called ARAMIS, has been developed to account for the influence of both materials, i.e. base metal and weld metal, on the structural resistance of cracked welds. It has been shown that, when the mismatch is high, and when the ligament size is small compared to the weld width, a classical J-based method using the softer material properties is very conservative. On the opposite the ARAMIS method provides a good estimate of J, because it predicts pretty well the shift of the cracked weld limit load, due to the presence of the weld. the influence of geometrical parameters such as crack size, weld width, or specimen length is property accounted for. (authors). 23 refs., 8 figs., 1 tab., 1 appendix.

  17. The influence of intrinsic disc degeneration of the adjacent segments on its stress distribution after one-level lumbar fusion.

    Science.gov (United States)

    Kim, Ho-Joong; Kang, Kyoung-Tak; Chun, Heoung-Jae; Lee, Choon-Ki; Chang, Bong-Soon; Yeom, Jin S

    2015-04-01

    The presence of degeneration alters the stress within that particular degenerated disc. Therefore, the state of degeneration of the disc at the level adjacent to a single level fusion would influence the rate of subsequent further degeneration of that same adjacent disc. Therefore, the purpose of this study was to investigate the biomechanical effect of the disc degeneration at the adjacent segment on the stress of the corresponding segment after one segment lumbar fusion using validated finite element (FE) models. Three validated L2-L5 FE models with different grades of disc degeneration (normal, mild, moderate) at the L2-L5 were simulated. Based on the intact models that represented each grade of disc degeneration, the matched L3-L4 instrumented fusion models were developed. Therefore, three intact models and three matched fusion models were simulated. Under the 400-N pre-compressive follower loading, 7.5 Nm moments simulating flexion, extension, lateral bending, and torsion in five steps were imposed on the L2 superior endplate of three intact models. The hybrid loading protocol was utilized for the fusion models. The intradiscal pressure and the maximal von Mises stress of the annulus fibrosus in the L2-L3 and L4-L5 segments were analyzed and compared between fusion and intact models with each grade of disc degeneration. Disc degeneration led to an increase of maximal von Mises stress of annulus fibrosus at this degenerated disc, related to disc degeneration under flexion, extension, lateral bending and torsion moments. Furthermore, the fusion also increased a maximal von Mises stress of annulus fibrous at both proximal and distal adjacent segments under hybrid protocol. The increases of annular stress were greater at the proximal adjacent segment than those at distal adjacent segment. However, the contribution of the fusion surgery to the increment rate of annulus fibrosus stress at the adjacent segment did not increase in relation with disc degeneration

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

    Science.gov (United States)

    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.

  19. Reducing thermal mismatch stress in anodically bonded silicon-glass wafers: theoretical estimation

    Science.gov (United States)

    Sinev, Leonid S.; Ryabov, Vladimir T.

    2017-01-01

    This paper reports the theoretical study and estimations of thermal mismatch stress reduction in anodically bonded silicon-glass stacks by justifiable selection of bonding temperature and glass thickness. This can be done only after prior thorough study of temperature dependence of the linear thermal expansion coefficient of the glass and silicon to be used. We show by analyzing such a dependence of several glass brands that the usual idea of decreasing the bonding process temperature as a solution to the thermal mismatch stress problem can be a failure. Interchanging glass brands during device design is shown to produce very contrasting changes in residual stresses. These results are in good agreement with finite-element modeling. This paper reports there is proportion between glass and silicon wafer thicknesses minimizing thermal mismatch stress at unbonded side of the silicon independently of the bonding or working temperatures chosen.

  20. Principal Mismatch Patterns Across a Simplified Highly Renewable European Electricity Network

    Directory of Open Access Journals (Sweden)

    Mads Raunbak

    2017-11-01

    Full Text Available Due to its spatio-temporal variability, the mismatch between the weather and demand patterns challenges the design of highly renewable energy systems. A principal component analysis is applied to a simplified networked European electricity system with a high share of wind and solar power generation. It reveals a small number of important mismatch patterns, which explain most of the system’s required backup and transmission infrastructure. Whereas the first principal component is already able to reproduce most of the temporal mismatch variability for a solar dominated system, a few more principal components are needed for a wind dominated system. Due to its monopole structure the first principal component causes most of the system’s backup infrastructure. The next few principal components have a dipole structure and dominate the transmission infrastructure of the renewable electricity network.

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

    Science.gov (United States)

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

  2. Adjacent segment disease in degenerative pathologies with posterior instrumentation

    Directory of Open Access Journals (Sweden)

    Ana Guadalupe Ramírez Olvera

    2015-03-01

    Full Text Available OBJECTIVE: To establish the real incidence of adjacent segment disease after fusion, and to identify the levels and predisposing factors for the pathology, as well as the functional results. METHODS: a retrospective case series study with level of evidence IIB, in a sample of 179 patients diagnosed with stenosis of the lumbar spine, spondylolisthesis and degenerative scoliosis, submitted to surgery in the period 2005 to December 2013, with posterior instrumentation and posterolateral fusion, with follow-up from 2007 until May 2014, in which the symptomology and radiographic findings were evaluated, to establish the diagnosis and treatment. RESULTS: the study included 179 patients diagnosed with stenosis of the lumbar spine (n=116, isthmic and degenerative spondylolisthesis (n=50 and degenerative scoliosis (n=13; during the study, 20 cases of adjacent level segment were identified, 80% of which were treated surgically with extension of the instrumentation, while 20% were treated conservatively with NSAIDs and therapeutic blocks. CONCLUSION: An incidence of 11% was found, with an average of 3.25 years in diagnosis and treatment, a prevalence of females and diagnosis of stenosis of the lumbar canal on posterior instrumentation, a predominance of levels L4-L5; 80% were treated with extension of the instrumentation. The complications were persistent radiculopathy, infection of the surgical wound, and one death due to causes not related to the lumbar pathology.

  3. Class II Eplet Mismatch Modulates Tacrolimus Trough Levels Required to Prevent Donor-Specific Antibody Development.

    Science.gov (United States)

    Wiebe, Chris; Rush, David N; Nevins, Thomas E; Birk, Patricia E; Blydt-Hansen, Tom; Gibson, Ian W; Goldberg, Aviva; Ho, Julie; Karpinski, Martin; Pochinco, Denise; Sharma, Atul; Storsley, Leroy; Matas, Arthur J; Nickerson, Peter W

    2017-11-01

    Despite more than two decades of use, the optimal maintenance dose of tacrolimus for kidney transplant recipients is unknown. We hypothesized that HLA class II de novo donor-specific antibody (dnDSA) development correlates with tacrolimus trough levels and the recipient's individualized alloimmune risk determined by HLA-DR/DQ epitope mismatch. A cohort of 596 renal transplant recipients with 50,011 serial tacrolimus trough levels had HLA-DR/DQ eplet mismatch determined using HLAMatchmaker software. We analyzed the frequency of tacrolimus trough levels below a series of thresholds tacrolimus levels before dnDSA development in the context of HLA-DR/DQ eplet mismatch. HLA-DR/DQ eplet mismatch was a significant multivariate predictor of dnDSA development. Recipients treated with a cyclosporin regimen had a 2.7-fold higher incidence of dnDSA development than recipients on a tacrolimus regimen. Recipients treated with tacrolimus who developed HLA-DR/DQ dnDSA had a higher proportion of tacrolimus trough levels tacrolimus trough levels in the 6 months before dnDSA development were significantly lower than the levels >6 months before dnDSA development in the same patients. Recipients with a high-risk HLA eplet mismatch score were less likely to tolerate low tacrolimus levels without developing dnDSA. We conclude that HLA-DR/DQ eplet mismatch and tacrolimus trough levels are independent predictors of dnDSA development. Recipients with high HLA alloimmune risk should not target tacrolimus levels <5 ng/ml unless essential, and monitoring for dnDSA may be advisable in this setting. Copyright © 2017 by the American Society of Nephrology.

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

    Science.gov (United States)

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Cervical Cord-Canal Mismatch: A New Method for Identifying Predisposition to Spinal Cord Injury.

    Science.gov (United States)

    Nouri, Aria; Montejo, Julio; Sun, Xin; Virojanapa, Justin; Kolb, Luis E; Abbed, Khalid M; Cheng, Joseph S

    2017-12-01

    The risk for spinal cord injuries (SCIs) ranging from devastating traumatic injuries, compression because of degenerative pathology, and neurapraxia is increased in patients with congenital spinal stenosis. Classical diagnostic criteria include an absolute anteroposterior diameter of cord, which varies across patients, independent of canal size. Recent large magnetic resonance imaging studies of population cohorts have allowed newer methods to emerge that account for both cord and canal size by measuring a spinal cord occupation ratio (SCOR). A SCOR defined as ≥70% on midsagittal imaging or ≥80% on axial imaging appears to be an effective method of identifying cord-canal mismatch, but requires further validation. Cord-canal size mismatch predisposes patients to SCI because of 1) less space within the canal lowering the amount of degenerative changes needed for cord compression, and 2) less cerebrospinal fluid surrounding the spinal cord decreasing the ability to absorb kinetic forces directed at the spine. Patients with cord-canal mismatch have been reported to be at a substantially higher risk of traumatic SCI, and present with degenerative cervical myelopathy at a younger age than patients without cord-canal mismatch. However, neurologic outcome after SCI has occurred does not appear to be different in patients with or without a cord-canal mismatch. Recognition that canal and cord size are both factors which predispose to SCI supports that cord-canal size mismatch rather than a narrow cervical canal in isolation should be viewed as the underlying mechanism predisposing to SCI. Copyright © 2017. Published by Elsevier Inc.

  6. Characterizing sensitivity of longwave infrared hyperspectral target detection with respect to signature mismatch and dimensionality reduction

    Science.gov (United States)

    Meola, Joseph

    2017-05-01

    Hyperspectral target detection typically relies upon libraries of material reflectance and emissivity signatures. Application to real-world, airborne data requires estimation of atmospheric properties in order to convert reflectance/emissivity signatures to the sensor data domain. In the longwave infrared, an additional nuisance parameter of surface temperature exists that further complicates the signature conversion process. A significant amount of work has been done in atmospheric compensation and temperature-emissivity-separation techniques. This work examines the sensitivity of target detection performance for various materials with respect to target signature mismatch introduced from atmospheric compensation error or target temperature mismatch. Additionally, the impact of dimensionality reduction via principal components analysis is assessed.

  7. Job Mismatches and their Labour Market Effects among School-leavers in Europe

    OpenAIRE

    Maarten Wolbers

    2002-01-01

    In this paper, we investigate the determinants of job mismatches with respect to field of education among school-leavers in Europe. In addition, the effects of having a job mismatch on the labour market position of school-leavers are examined. Special attention is paid to cross-country variation in this respect. The data that are used come from the EU LFS 2000 ad hoc module on school-to-work transitions. The results of the empirical analysis show that several individual, job, and structural c...

  8. Spin splitting of electron states in lattice-mismatched (110)-oriented quantum wells

    Science.gov (United States)

    Nestoklon, M. O.; Tarasenko, S. A.; Benchamekh, R.; Voisin, P.

    2016-09-01

    We show that for lattice-mismatched zinc-blende-type (110)-grown quantum wells a significant contribution to the zero-magnetic-field spin splitting of electron subbands comes from strain-induced spin-orbit coupling. Combining the envelope function theory and atomistic tight-binding approach, we calculate spin-orbit splitting constants for realistic quantum wells. It is found that the strain due to lattice mismatch in conventional GaAs/AlGaAs structures may noticeably modify the spin splitting while in InGaAs/GaAs structures it plays a major role and may even change the sign of the spin splitting constant.

  9. Prevalence and prognostic role of mismatch repair gene defect in endometrial cancer patients.

    Science.gov (United States)

    Tangjitgamol, Siriwan; Kittisiam, Thannaporn; Tanvanich, Sujitra

    2017-09-01

    The study was to evaluate the prevalence of mismatch repair gene defect among Thai patients with endometrial cancer and its association with clinico-pathological features and survivals. The formalin fixed paraffin-embedded blocks of EMC tissue from hysterectomy specimens of patients having surgery in our institution between 1 Jan 1995 and 31 December 2016 were assessed for the immunohistochemical expression of 4 mismatch repair proteins (MLH1, PMS, MSH2, MSH 6). Mismatch repair gene defect was determined by a negative expression of at least 1 protein. Among 385 EMC patients included in the study, mean age was 57.3 ± 10.8 years with 62.3% aged ⩽ 60 years. The most frequent mismatch repair gene defect was MSH6 (38.7%), followed by PMS2 (34.3%), MLH1 (33.2%), and MSH2 (16.4%). Overall, 55.1% showed negative expression of at least one protein. We found significantly higher mismatch repair gene defect in patients aged ⩽ 60 years, with early stage disease, and negative lymph node status than the other comparative groups: 59.2% vs 48.3% for age (p = 0.037), 58.2% vs 45.2% (p = 0.027) for stage, and 58.1% vs 44.6% (p = 0.048) for nodal status. The 5-year progression-free survival, overall survival, and endometrial cancer-specific survival of patients with mismatch repair gene defect was higher than those without gene defect. The differences were statistically significant for only progression-free survival and endometrial cancer-specific survival: 87.7% (95% confidence interval = 83.0%-92.4%) vs 81.5% (95% confidence interval = 75.4%-87.6%) (p = 0.049) for progression-free survival and 91.0% (95% confidence interval = 86.9%-95.1%) vs 85.5% (95% confidence interval = 80.0%-91.0%) (p = 0.044) for endometrial cancer-specific survival, respectively. In conclusion, more than half of Thai endometrial cancer patients had mismatch repair gene defect. The patients with mismatch repair gene defect had significantly younger age (⩽ 60 years) and better prognosis in terms of

  10. 3D-2D image registration for target localization in spine surgery: investigation of similarity metrics providing robustness to content mismatch.

    Science.gov (United States)

    De Silva, T; Uneri, A; Ketcha, M D; Reaungamornrat, S; Kleinszig, G; Vogt, S; Aygun, N; Lo, S-F; Wolinsky, J-P; Siewerdsen, J H

    2016-04-21

    In image-guided spine surgery, robust three-dimensional to two-dimensional (3D-2D) registration of preoperative computed tomography (CT) and intraoperative radiographs can be challenged by the image content mismatch associated with the presence of surgical instrumentation and implants as well as soft-tissue resection or deformation. This work investigates image similarity metrics in 3D-2D registration offering improved robustness against mismatch, thereby improving performance and reducing or eliminating the need for manual masking. The performance of four gradient-based image similarity metrics (gradient information (GI), gradient correlation (GC), gradient information with linear scaling (GS), and gradient orientation (GO)) with a multi-start optimization strategy was evaluated in an institutional review board-approved retrospective clinical study using 51 preoperative CT images and 115 intraoperative mobile radiographs. Registrations were tested with and without polygonal masks as a function of the number of multistarts employed during optimization. Registration accuracy was evaluated in terms of the projection distance error (PDE) and assessment of failure modes (PDE  >  30 mm) that could impede reliable vertebral level localization. With manual polygonal masking and 200 multistarts, the GC and GO metrics exhibited robust performance with 0% gross failures and median PDE registration to fail at a rate of >14%; however, GO maintained robustness with a 0% gross failure rate. Overall, the GI, GC, and GS metrics were susceptible to registration errors associated with content mismatch, but GO provided robust registration (median PDE  =  5.5 mm, 2.6 mm IQR) without manual masking and with an improved runtime (29.3 s). The GO metric improved the registration accuracy and robustness in the presence of strong image content mismatch. This capability could offer valuable assistance and decision support in spine level localization in a manner consistent with

  11. T2-FLAIR Mismatch, an Imaging Biomarker for IDH and 1p/19q Status in Lower-grade Gliomas: A TCGA/TCIA Project.

    Science.gov (United States)

    Patel, Sohil H; Poisson, Laila M; Brat, Daniel J; Zhou, Yueren; Cooper, Lee; Snuderl, Matija; Thomas, Cheddhi; Franceschi, Ana M; Griffith, Brent; Flanders, Adam E; Golfinos, John G; Chi, Andrew S; Jain, Rajan

    2017-10-15

    Purpose: Lower-grade gliomas (WHO grade II/III) have been classified into clinically relevant molecular subtypes based on IDH and 1p/19q mutation status. The purpose was to investigate whether T2/FLAIR MRI features could distinguish between lower-grade glioma molecular subtypes. Experimental Design: MRI scans from the TCGA/TCIA lower grade glioma database ( n = 125) were evaluated by two independent neuroradiologists to assess (i) presence/absence of homogenous signal on T2WI; (ii) presence/absence of "T2-FLAIR mismatch" sign; (iii) sharp or indistinct lesion margins; and (iv) presence/absence of peritumoral edema. Metrics with moderate-substantial agreement underwent consensus review and were correlated with glioma molecular subtypes. Somatic mutation, DNA copy number, DNA methylation, gene expression, and protein array data from the TCGA lower-grade glioma database were analyzed for molecular-radiographic associations. A separate institutional cohort ( n = 82) was analyzed to validate the T2-FLAIR mismatch sign. Results: Among TCGA/TCIA cases, interreader agreement was calculated for lesion homogeneity [ κ = 0.234 (0.111-0.358)], T2-FLAIR mismatch sign [ κ = 0.728 (0.538-0.918)], lesion margins [ κ = 0.292 (0.135-0.449)], and peritumoral edema [ κ = 0.173 (0.096-0.250)]. All 15 cases that were positive for the T2-FLAIR mismatch sign were IDH -mutant, 1p/19q non-codeleted tumors ( P IDH -mutant, 1p/19q non-codeleted tumors ( P IDH -mutant, 1p/19q non-codeleted molecular subtype. Clin Cancer Res; 23(20); 6078-85. ©2017 AACR . ©2017 American Association for Cancer Research.

  12. 3D-2D image registration for target localization in spine surgery: investigation of similarity metrics providing robustness to content mismatch

    Science.gov (United States)

    De Silva, T.; Uneri, A.; Ketcha, M. D.; Reaungamornrat, S.; Kleinszig, G.; Vogt, S.; Aygun, N.; Lo, S.-F.; Wolinsky, J.-P.; Siewerdsen, J. H.

    2016-04-01

    In image-guided spine surgery, robust three-dimensional to two-dimensional (3D-2D) registration of preoperative computed tomography (CT) and intraoperative radiographs can be challenged by the image content mismatch associated with the presence of surgical instrumentation and implants as well as soft-tissue resection or deformation. This work investigates image similarity metrics in 3D-2D registration offering improved robustness against mismatch, thereby improving performance and reducing or eliminating the need for manual masking. The performance of four gradient-based image similarity metrics (gradient information (GI), gradient correlation (GC), gradient information with linear scaling (GS), and gradient orientation (GO)) with a multi-start optimization strategy was evaluated in an institutional review board-approved retrospective clinical study using 51 preoperative CT images and 115 intraoperative mobile radiographs. Registrations were tested with and without polygonal masks as a function of the number of multistarts employed during optimization. Registration accuracy was evaluated in terms of the projection distance error (PDE) and assessment of failure modes (PDE  >  30 mm) that could impede reliable vertebral level localization. With manual polygonal masking and 200 multistarts, the GC and GO metrics exhibited robust performance with 0% gross failures and median PDE  14% however, GO maintained robustness with a 0% gross failure rate. Overall, the GI, GC, and GS metrics were susceptible to registration errors associated with content mismatch, but GO provided robust registration (median PDE  =  5.5 mm, 2.6 mm IQR) without manual masking and with an improved runtime (29.3 s). The GO metric improved the registration accuracy and robustness in the presence of strong image content mismatch. This capability could offer valuable assistance and decision support in spine level localization in a manner consistent with clinical workflow.

  13. Broca's region: A causal role in implicit processing of grammars with crossed non-adjacent dependencies

    NARCIS (Netherlands)

    Uddén, J.U.; Ingvar, M.; Hagoort, P.; Petersson, K.M.

    2017-01-01

    Non-adjacent dependencies are challenging for the language learning machinery and are acquired later than adjacent dependencies. In this transcranial magnetic stimulation (TMS) study, we show that participants successfully discriminated between grammatical and non-grammatical sequences after having

  14. Adjacent Lumbar Disc Herniation after Lumbar Short Spinal Fusion

    Directory of Open Access Journals (Sweden)

    Koshi Ninomiya

    2014-01-01

    Full Text Available A 70-year-old outpatient presented with a chief complaint of sudden left leg motor weakness and sensory disturbance. He had undergone L4/5 posterior interbody fusion with L3–5 posterior fusions for spondylolisthesis 3 years prior, and the screws were removed 1 year later. He has been followed up for 3 years, and there had been no adjacent segment problems before this presentation. Lumbar magnetic resonance imaging (MRI showed a large L2/3 disc hernia descending to the L3/4 level. Compared to the initial MRI, this hernia occurred in an “intact” disc among multilevel severely degenerated discs. Right leg paresis and bladder dysfunction appeared a few days after admission. Microscopic lumbar disc herniotomy was performed. The right leg motor weakness improved just after the operation, but the moderate left leg motor weakness and difficulty in urination persisted.

  15. Adjacent Lumbar Disc Herniation after Lumbar Short Spinal Fusion

    Science.gov (United States)

    Iwatsuki, Koichi; Ohnishi, Yu-ichiro; Yoshimine, Toshiki

    2014-01-01

    A 70-year-old outpatient presented with a chief complaint of sudden left leg motor weakness and sensory disturbance. He had undergone L4/5 posterior interbody fusion with L3–5 posterior fusions for spondylolisthesis 3 years prior, and the screws were removed 1 year later. He has been followed up for 3 years, and there had been no adjacent segment problems before this presentation. Lumbar magnetic resonance imaging (MRI) showed a large L2/3 disc hernia descending to the L3/4 level. Compared to the initial MRI, this hernia occurred in an “intact” disc among multilevel severely degenerated discs. Right leg paresis and bladder dysfunction appeared a few days after admission. Microscopic lumbar disc herniotomy was performed. The right leg motor weakness improved just after the operation, but the moderate left leg motor weakness and difficulty in urination persisted. PMID:25276453

  16. Edge scour in current adjacent to stone covers

    DEFF Research Database (Denmark)

    Petersen, Thor Ugelvig; Sumer, B. Mutlu; Meyer, Knud Erik

    The present paper reports some early results of an experimental investigation of edge scour in currents. Two kinds of measurements are made (1) Particle Image Velocimetry (PIV) measurements of secondary currents that take place near a junction between the stone cover and the sand bed in a clear...... the sediment and puts into suspension, and the secondary flow carries it away from the junction between the stone layer and the sand bed, resulting in a scour hole forming adjacent to the toe of the stone layer.......-water experiment; and (2) scour measurements in actual scour experiment in the live-bed regime. The early results indicate that edge scour in a steady current propagating in-line with a stone layer is caused by the combined action of two effects; (1) Primary flow and (2) Secondary flow. The primary flow stirs up...

  17. Analysis of blasting damage in adjacent mining excavations

    Directory of Open Access Journals (Sweden)

    Nick Yugo

    2015-06-01

    Full Text Available Following a small-scale wedge failure at Yukon Zinc's Wolverine Mine in Yukon, Canada, a vibration monitoring program was added to the existing rockbolt pull testing regime. The failure in the 1150 drift occurred after numerous successive blasts in an adjacent tunnel had loosened friction bolts passing through an unmapped fault. Analysis of blasting vibration revealed that support integrity is not compromised unless there is a geological structure to act as a failure plane. The peak particle velocity (PPV rarely exceeded 250 mm/s with a frequency larger than 50 Hz. As expected, blasting more competent rock resulted in higher PPVs. In such cases, reducing the round length from 3.5 m to 2.0 m was an effective means of limiting potential rock mass and support damage.

  18. The Role of Education Pathways in the Relationship between Job Mismatch, Wages and Job Satisfaction: A Panel Estimation Approach

    Science.gov (United States)

    Mavromaras, Kostas; Sloane, Peter; Wei, Zhang

    2012-01-01

    This paper examines the outcome of over-skilling and over-education on wages and job satisfaction of full-time employees in Australia between 2001 and 2008. We employ a random effects probit model with Mundlak corrections. We find differences by type of mismatch, education pathway, and gender. We categorise reported mismatches as genuine…

  19. FLAIR-hyperintense vessel sign, diffusion-perfusion mismatch and infarct growth in acute ischemic stroke without vascular recanalisation therapy.

    Science.gov (United States)

    Gawlitza, Matthias; Gragert, Jasmin; Quäschling, Ulf; Hoffmann, Karl Titus

    2014-10-01

    To investigate the relation between DWI-PWI mismatch and FLAIR-hyperintense vessel (FHV) sign and their influence on the prediction of the infarct growth in stroke patients without vessel recanalising therapy. Thirty-three patients with non-lacunar acute stroke and not eligible for recanalisation therapy received cerebral MRI at the day of admission and after 7±1 days. DWI and PWI lesion volumes, DWI-PWI mismatch volumes, infarct growth, relative mismatch and relative infarct growth were assessed. FHV sign was subdivided into (i) proximal or (ii) distal, the latter graded as either (i) prominent or (ii) subtle. FHV sign did not predict absolute or relative infarct growth. Significantly larger DWI lesions, PWI lesions and mismatch volumes were observed in FHV-positive infarcts. There were significant correlations between the degree of FHV sign and PWI lesion volume (r=0.52; PPWI mismatch and relative infarct growth (r=0.91; PPWI lesion volumes and DWI-to-PWI mismatch volumes in acute stroke and thus seems to be an indicator of collateral flow. However, it is unsuitable to predict infarct growth. The latter occurred when DWI-to-PWI mismatches were present with bigger relative mismatch volumes making subsequent infarct growth more likely. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  20. Localization by interaural time difference (ITD): Effects of interaural frequency mismatch

    Energy Technology Data Exchange (ETDEWEB)

    Bonham, B.H. [Department of Otolaryngology and W. M. Keck Center for Integrative Neuroscience, Box 0732, University of California, San Francisco, California 94143-0732 (United States); Lewis, E.R. [Department of Electrical Engineering and Computer Science, University of California, Berkeley, California 94720 (United States)

    1999-07-01

    A commonly accepted physiological model for lateralization of low-frequency sounds by interaural time delay (ITD) stipulates that binaural comparison neurons receive input from frequency-matched channels from each ear. Here, the effects of hypothetical interaural frequency mismatches on this model are reported. For this study, the cat{close_quote}s auditory system peripheral to the binaural comparison neurons was represented by a neurophysiologically derived model, and binaural comparison neurons were represented by cross-correlators. The results of the study indicate that, for binaural comparison neurons receiving input from one cochlear channel from each ear, interaural CF mismatches may serve to either augment or diminish the effective difference in ipsilateral and contralateral axonal time delays from the periphery to the binaural comparison neuron. The magnitude of this increase or decrease in the effective time delay difference can be up to 400 {mu}s for CF mismatches of 0.2 octaves or less for binaural neurons with CFs between 250 Hz and 2.5 kHz. For binaural comparison neurons with nominal CFs near 500 Hz, the 25-{mu}s effective time delay difference caused by a 0.012-octave CF mismatch is equal to the ITD previously shown to be behaviorally sufficient for the cat to lateralize a low-frequency sound source. {copyright} {ital 1999 Acoustical Society of America.}

  1. Aortic valve prosthesis-patient mismatch and exercise capacity in adult patients with congenital heart disease

    NARCIS (Netherlands)

    van Slooten, Ymkje J.; Melle, van Joost P.; Freling, Hendrik G.; Bouma, Berto J.; van Dijk, Arie P. J.; Jongbloed, Monique R. M.; Post, Martijn C.; Sieswerda, Gertjan T.; in 't Veld, Anna Huis; Ebels, Tjark; Voors, Adriaan A.; Pieper, Petronella G.

    Objectives To report the prevalence of aortic valve prosthesis patient mismatch (PPM) in an adult population with congenital heart disease (CHD) and its impact on exercise capacity. Adults with congenital heart disease (ACHD) with a history of aortic valve replacement may outgrow their prosthesis

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

    Science.gov (United States)

    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.

  3. Developmental changes in mismatch responses to mandarin consonants and lexical tones from early to middle childhood.

    Directory of Open Access Journals (Sweden)

    Huei-Mei Liu

    Full Text Available The purpose of this study was to use mismatch responses (MMRs to explore the dynamic changes of Mandarin speech perception abilities from early to middle childhood. Twenty preschoolers, 18 school-aged children, and 26 adults participated in this study. Two sets of synthesized speech stimuli varying in Mandarin consonant (alveolo-palatal affricate vs. fricative and lexical tone features (rising vs. contour tone were used to examine the developmental course of speech perception abilities. The results indicated that only the adult group demonstrated typical early mismatch negativity (MMN responses, suggesting that the ability to discriminate specific speech cues in Mandarin consonant and lexical tone is a continuing process in preschool- and school-aged children. Additionally, distinct MMR patterns provided evidence indicating diverse developmental courses to different speech characteristics. By incorporating data from the two speech conditions, we propose using MMR profiles consisting of mismatch negativity (MMN, positive mismatch response (p-MMR, and late discriminative negativity (LDN as possible brain indices to investigate speech perception development.

  4. Second-harmonic generation with zero group-velocity mismatch in nonlinear photonic crystal fibers

    DEFF Research Database (Denmark)

    Bache, Morten; Lægsgaard, Jesper; Bang, Ole

    2006-01-01

    wavelength above 780 nm. The phase-velocity mismatch has a lower limit with coherence lengths in the micron range. The nonlinear strength is optimized when the fundamental has maximum confinement in the core. The conversion bandwidth allows for fs-pulse conversion and 4-180%/(Wmiddotcm2) relative...

  5. A skill mismatch for migrant workers? Evidence from WageIndicator survey data

    NARCIS (Netherlands)

    Tijdens, K.; van Klaveren, M.; Galgóczi, B.; Leschke, J.; Watt, A.

    2012-01-01

    Are overeducation and undereducation more common among migrants compared to domestic workers? If so, are overeducation and undereducation similar across migrants from various home countries and across various host countries? This chapter is aimed at unravelling the incidence of skill mismatch,

  6. Selecting patients with young-onset colorectal cancer for mismatch repair gene analysis

    DEFF Research Database (Denmark)

    Walker, M; O'Sullivan, B; Perakath, B

    2007-01-01

    BACKGROUND: Young patients with colorectal cancer are at increased risk of carrying a germline mutation in mismatch repair (MMR) genes. This study investigated the role of clinical criteria and immunohistochemistry for MMR proteins in selecting young patients for mutation testing. METHODS: A cohort...

  7. The match-mismatch model of emotion processing styles and emotion regulation strategies in fibromyalgia.

    NARCIS (Netherlands)

    Geenen, R.; Ooijen-van der Linden, L. van; Lumley, M.A.; Bijlsma, J.W.J.; Middendorp, H. van

    2012-01-01

    OBJECTIVE: Individuals differ in their style of processing emotions (e.g., experiencing affects intensely or being alexithymic) and their strategy of regulating emotions (e.g., expressing or reappraising). A match-mismatch model of emotion processing styles and emotion regulation strategies is

  8. Nuclear localization of human DNA mismatch repair protein exonuclease 1 (hEXO1)

    DEFF Research Database (Denmark)

    Knudsen, Nina Østergaard; Nielsen, Finn Cilius; Vinther, Lena

    2007-01-01

    Human exonuclease 1 (hEXO1) is implicated in DNA mismatch repair (MMR) and mutations in hEXO1 may be associated with hereditary nonpolyposis colorectal cancer (HNPCC). Since the subcellular localization of MMR proteins is essential for proper MMR function, we characterized possible nuclear locali...

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

    Science.gov (United States)

    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.

  10. A match-mismatch test of a stage model of behaviour change in tobacco smoking

    NARCIS (Netherlands)

    Dijkstra, A; Conijn, B; De Vries, H

    Aims An innovation offered by stage models of behaviour change is that of stage-matched interventions. Match-mismatch studies are the primary test of this idea but also the primary test of the validity of stage models. This study aimed at conducting such a test among tobacco smokers using the Social

  11. Wage effects of job-worker mismatches: Heterogeneous skills or institutional effects?

    NARCIS (Netherlands)

    Allen, J.P.; Badillo-Amador, L.; van der Velden, R.K.W.

    2013-01-01

    The strong wage effects related to mismatches between a worker’s education and that required in the job are usually attributed to assignment theory. This theory asserts that productivity and wages depend on the education-job match, which determines the utilization of skills. However, recent research

  12. What do Educational Mismatches tell us about Skill Mismachtes? A Cross-country Analysis

    NARCIS (Netherlands)

    Allen, Jim; de Weert, Egbert

    2007-01-01

    The relationship between higher education and employment is commonly interpreted in terms of the extent to which the higher education sector is providing graduates with the knowledge and skills to match employment needs. It is assumed that a mismatch between working in a job and level or field of

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

    Science.gov (United States)

    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…

  14. Zebrafish with mutations in mismatch repair genes develop neurofibromas and other tumors.

    NARCIS (Netherlands)

    Feitsma, H.; Kuiper, R.V.; Korving, J.; Nijman, I.J.; Cuppen, E.

    2008-01-01

    Defective mismatch repair (MMR) in humans causes hereditary nonpolyposis colorectal cancer. This genetic predisposition to colon cancer is linked to heterozygous familial mutations, and loss-of-heterozygosity is necessary for tumor development. In contrast, the rare cases with biallelic MMR

  15. Impact of prosthesis-patient mismatch on early and late mortality after aortic valve replacement

    NARCIS (Netherlands)

    Koene, Bart M.; Hamad, Mohamed A. Soliman; Bouma, Wobbe; Mariani, Massimo A.; Peels, Kathinka C.; van Dantzig, Jan-Melle; van Straten, Albert H.

    2013-01-01

    Background: The influence of prosthesis-patient mismatch (PPM) on survival after aortic valve replacement (AVR) remains controversial. In this study, we sought to determine the effect of PPM on early (30 days) after AVR or AVR combined with coronary artery bypass grafting (AVR with CABG). Methods:

  16. Mismatching between circulating strains and vaccine strains of influenza: Effect on Hajj pilgrims from both hemispheres.

    Science.gov (United States)

    Alfelali, Mohammad; Khandaker, Gulam; Booy, Robert; Rashid, Harunor

    2016-03-03

    The trivalent seasonal influenza vaccine is expected to provide optimum protection if the vaccine strains match the circulating strains. The effect of worldwide mismatch between the vaccine strains and extant strains on travelers attending Hajj pilgrimage is not known. Annually 2-3 million Muslims coming from north and south hemispheres congregate at Hajj in Mecca, Saudi Arabia, where intense congestion amplifies the risk of respiratory infection up to eight fold. In order to estimate, to what extent mismatching increases the risk of vaccine failure in Hajj pilgrims, we have examined the global data on influenza epidemiology since 2003, in light of the available data from Hajj. These data demonstrate that globally mismatching between circulating and vaccine strains has occurred frequently over the last 12 years, and the mismatch seems to have affected the Hajj pilgrims, however, influenza virus characteristics were studied only in a limited number of Hajj seasons. When the vaccines are different, dual vaccination of travelers by vaccines for southern and northern hemispheres should be considered for Hajj pilgrims whenever logistically feasible. Consideration should also be given to the use of vaccines with broader coverage, i.e., quadrivalent, or higher immunogenicity. Continuous surveillance of influenza at Hajj is important.

  17. Scales of Disconnection: Mismatches Shaping the Geographies of Emerging Energy Landscapes

    Directory of Open Access Journals (Sweden)

    Warren Charles R.

    2014-07-01

    Full Text Available The networked nature of energy systems produces geographies of connection, but the focus of this paper is on geographies of disconnection, exploring the multi-scalar processes which shape the context in which energy landscapes emerge. It does so, first, by presenting a case study of farmers' attitudes to perennial energy crops in south-west Scotland. Their strong antipathy to converting farmland to short-rotation coppice, and the reasons for their negative attitudes, exemplify some of the wider mismatches and disconnects which the paper goes on to discuss. These include socio-political and socio-cultural mismatches, and a range of essentially geographical disconnects which are scalar in nature, such as the familiar local-global tension and the mismatch between the scales (both temporal and spatial at which environmental and human systems organise and function. The discussion shows how these disjunctions not only affect energy geographies but also raise far-reaching questions about the ability of current governance structures and liberal democratic systems to respond swiftly and effectively to global challenges. The way that these mismatches are negotiated will mould both the character of future energy landscapes and the speed at which they take shape.

  18. Mental Ability and the Effect of Pattern Violation Discrimination on P300 and Mismatch Negativity

    Science.gov (United States)

    Sculthorpe, Lauren D.; Stelmack, Robert M.; Campbell, Kenneth B.

    2009-01-01

    The relation between mental ability and the ability to detect auditory pattern violations was examined using event-related potential measures, specifically P300 and mismatch negativity (MMN). Thirty female volunteers were presented with a two tone alternating pattern containing infrequent repetition violations in passive (ignore) then active…

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

    Science.gov (United States)

    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…

  20. The role of mismatch repair in small-cell lung cancer cells

    DEFF Research Database (Denmark)

    Hansen, L T; Thykjaer, T; Ørntoft, T F

    2003-01-01

    The role of mismatch repair (MMR) in small-cell lung cancer (SCLC) is controversial, as the phenotype of a MMR-deficiency, microsatellite instability (MSI), has been reported to range from 0 to 76%. We studied the MMR pathway in a panel of 21 SCLC cell lines and observed a highly heterogeneous...

  1. Variation in physical development in schoolboy rugby players: can maturity testing reduce mismatch?

    Science.gov (United States)

    Hamilton, David F; Hutchison, James D; Mitchell, Martin J; Simpson, A Hamish RW; MacLean, James G B

    2012-01-01

    Objectives This study set out to pursue means of reducing mismatch in schoolboy rugby players. The primary objective was to determine whether application of previously reported thresholds of height and grip strength could be used to distinguish those 15-year-old boys appropriate to play under-18 school rugby from their peers. A secondary objective was to obtain normative data for height, weight and grip strength and to assess the variation within that data of current schoolboy rugby players. Design Cross-sectional cohort study. Setting 3 Scottish schools and ‘Regional Assessment Centres’ organised by the Scottish Rugby Union. Participants 472 rugby playing youths aged 15 years (Regional Assessment Centres) and 382 schoolboys aged between 12 and 18 years (three schools). Outcome measures Height, weight and grip strength. Results 97% of 15-year-olds achieved the height and grip strength thresholds based on previous reported values. Larger mean values and wide variation of height, weight and grip strength were recorded in the schoolboy cohort. However, using the mean values of the cohort of 17-year-olds as a new threshold, only 7.7% of 15-year-olds would pass these thresholds. Conclusions Large morphological variation was observed in schoolboy rugby players of the same age. Physical maturity tests described in earlier literature as pre-participation screening for contact sports were not applicable to current day 15-year-old rugby players. New criteria were measured and found to be better at identifying those 15-year-old players who had sufficient physical development to play senior school rugby. PMID:22786947

  2. Abnormal auditory mismatch response in tinnitus sufferers with high-frequency hearing loss is associated with subjective distress level

    Directory of Open Access Journals (Sweden)

    Berg Patrick

    2004-03-01

    Full Text Available Abstract Background Tinnitus is an auditory sensation frequently following hearing loss. After cochlear injury, deafferented neurons become sensitive to neighbouring intact edge-frequencies, guiding an enhanced central representation of these frequencies. As psychoacoustical data 123 indicate enhanced frequency discrimination ability for edge-frequencies that may be related to a reorganization within the auditory cortex, the aim of the present study was twofold: 1 to search for abnormal auditory mismatch responses in tinnitus sufferers and 2 relate these to subjective indicators of tinnitus. Results Using EEG-mismatch negativity, we demonstrate abnormalities (N = 15 in tinnitus sufferers that are specific to frequencies located at the audiometrically normal lesion-edge as compared to normal hearing controls (N = 15. Groups also differed with respect to the cortical locations of mismatch responsiveness. Sources in the 90–135 ms latency window were generated in more anterior brain regions in the tinnitus group. Both measures of abnormality correlated with emotional-cognitive distress related to tinnitus (r ~ .76. While these two physiological variables were uncorrelated in the control group, they were correlated in the tinnitus group (r = .72. Concerning relationships with parameters of hearing loss (depth and slope, slope turned out to be an important variable. Generally, the steeper the hearing loss is the less distress related to tinnitus was reported. The associations between slope and the relevant neurophysiological variables are in agreement with this finding. Conclusions The present study is the first to show near-to-complete separation of tinnitus sufferers from a normal hearing control group based on neurophysiological variables. The finding of lesion-edge specific effects and associations with slope of hearing loss corroborates the assumption that hearing loss is the basis for tinnitus development. It is likely that some central

  3. Match or mismatch: the influence of phenology on size-dependent life history and divergence in population structure

    Science.gov (United States)

    Borcherding, Jost; Beeck, Peter; DeAngelis, Donald L.; Scharf, Werner R.

    2010-01-01

    Summary 1. In gape-limited predators, body size asymmetries determine the outcome of predator-prey interactions. Due to ontogenetic changes in body size, the intensity of intra- and interspecific interactions may change rapidly between the match situation of a predator-prey system and the mismatch situation in which competition, including competition with the prey, dominates. 2. Based on a physiologically structured population model using the European perch (Perca fluviatilis), analysis was performed on how prey density (bream, Abramis brama), initial size differences in the young-of-the-year (YOY) age cohort of the predator, and phenology (time-gap in hatching of predator and prey) influence the size structure of the predator cohort. 3. In relation to the seasonality of reproduction, the match situation of the predator-prey system occurred when perch hatched earlier than bream and when no gape-size limitations existed, leading to decreased size divergence in the predator age cohort. Decreased size divergence was also found when bream hatched much earlier than perch, preventing perch predation on bream occurring, which, in turn, increased the competitive interaction of the perch with bream for the common prey, zooplankton; i.e. the mismatch situation in which also the mean size of the age cohort of the predator decreased. 4. In between the total match and the mismatch, however, only the largest individuals of the perch age cohort were able to prey on the bream, while smaller conspecifics got trapped in competition with each other and with bream for zooplankton, leading to enlarged differences in growth that increased size divergence. 5. The modelling results were combined with 7 years of field data in a lake, where large differences in the length-frequency distribution of YOY perch were observed after their first summer. These field data corroborate that phenology and prey density per predator are important mechanisms in determining size differences within the YOY

  4. Genotyping of vitamin D receptor gene polymorphisms using mismatched amplification mutation assay in neonatal sepsis patients of Odisha, eastern India.

    Science.gov (United States)

    Das, Biswadeep; Patra, Saumya; Behera, Chinmay; Suar, Mryutunjay

    2016-11-01

    Vitamin D has potent antimicrobial and anti-inflammatory properties. Vitamin D deficiency has been shown to be associated with the risk of vulnerability to different infectious diseases, such as neonatal sepsis. Polymorphisms in vitamin D receptor (VDR) gene can influence the expression of vitamin D in individuals. Hence, it is essential to study the vitamin D status and VDR gene polymorphisms for assessing neonatal sepsis risk. In this study, we assessed the serum 25(OH)D, the main circulating form of vitamin D and VDR polymorphism on 120 subjects in a case-control approach, recruiting 60 subjects in each category. We genotyped Fok1, Bsm1, Apa1 and Taq1 gene polymorphisms in VDR by developing a unique mismatch amplification mutation assay (MAMA) and studied their association in both populations. VDR-MAMA primers were designed by addition of dual mismatches (DM) near the 3' end and were selected based on high ΔCt values in comparison to single mismatch (SM) primers using SYBR-Green RT-PCR, which were eventually used for VDR genotyping. Genotyping was also performed using PCR-RFLP for further confirmation. Serum 25(OH)D ELISA revealed that cases were vitamin D insufficient (Median=12.16ng/ml, 95% CI: 3.84-22.22) and controls were vitamin D sufficient (Median=30.22ng/ml, 95% CI: 20.08-46.78; pneonatal sepsis or 25(OH)D serum levels. The distributions of the Fok1, Bsm1, and Taq1 genotypes were not consistent with Hardy-Weinberg equilibrium in the control group. Future studies in larger populations are required to establish whether the VDR polymorphisms can be potentially used as genetic markers for early screening towards predisposition to neonatal sepsis risk. In this study, we describe a simple, inexpensive and rapid screening of VDR gene polymorphisms using VDR MAMA-PCR, which can be used in both clinical and research laboratories. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Stoichiometric Mismatch between Consumers and Resources Mediates the Growth of Rocky Intertidal Suspension Feeders.

    Science.gov (United States)

    Bracken, Matthew E S

    2017-01-01

    The concept of ecological stoichiometry-the balancing of elemental ratios in ecological interactions-has transformed our thinking about processes in natural systems. Here, this perspective is applied to rocky shore ecosystems to explore the consequences of variation in internal nutrient ratios across two trophic levels. Specifically, I measured the internal concentrations of carbon (C) and nitrogen (N) in mussels (Mytilus spp.) and particulate organic matter (POM) to evaluate the effects of stoichiometric mismatch-the difference in the carbon-to-nitrogen ratio (C:N) between a consumer and its resources-on mussel growth at sites on the coasts of Oregon, USA, and the South Island of New Zealand. As POM quality (i.e., Chl a, a proxy for phytoplankton availability in the POM) increased, C:N of the POM declined, but C:N of mussels increased. This resulted in a greater mismatch in C:N between mussels and their food source at low Chl a. Mussel growth across sites was positively associated with Chl a, particulate organic carbon (POC), and particulate organic nitrogen (PON) but negatively associated with stoichiometric mismatch. Overall, as the elemental ratios of consumers became more different from those of their resources, growth declined, likely due to the energetic cost associated with processing lower quality food. Furthermore, the effect of food quantity on growth depended on stoichiometric mismatch. In New Zealand, where mismatch was high-i.e., consumer C:N differed substantially from resource C:N-consumer growth was strongly affected by resource quantity (Chl a or POC). However, in Oregon, where mismatch was low, the relationship between resource quantity and growth was considerably weaker. This interaction between resource quantity and mismatch was not apparent for PON, which is consistent with variation in PON underlying variation in POM C:N and highlights the role of N in limiting growth. Previous research has neglected the importance of ecological stoichiometry

  6. Disc height and anteroposterior translation in fused and adjacent segments after lumbar spine fusion

    Directory of Open Access Journals (Sweden)

    Frobin, Wolfgang

    2003-09-01

    Full Text Available In a series of 46 patients the effects of spinal fusion upon intervertebral height and sagittal alignment in operated and non-operated segments were retrospectively evaluated on digitized radiographs. Data was compared with age- and gender-normalized standard values. The objective was to evaluate the influence of different types of spine fusions primarily upon adjacent segments, particularly in terms of degeneration and sagittal profile of the lumbar spine. Incidence of adjacent segment degeneration (ASD is still highly controversial. However, not every degeneration adjacent to spinal fusion must be caused by the fusion and responsibility of the fusion for ASD may vary with its range and type. Distortion Corrected Roentgen Analysis (DCRA was utilized. DCRA is a proven valid, reliable, observer-independent, and accurate tool for assessment of these parameters over time and in comparison with "normal" cohorts. With this method the exact posture of the patients needs not to be known.There was little evidence for serious fusion-related ASD within an average of 40 months follow-up. No difference could be detected for rigid vs. non-rigid fusion and instrumented vs. non-instrumented techniques. Temporary postoperative distraction effects could be detected in operated and non-operated segments. Absolute preoperative values for intervertebral height and vertebral slip were age-related. Retrospectively, the choice of segments for fusion was clearly based upon radiological criteria. Thus we conclude that radiological parameters have an obvious clinical relevance for decision-making and need to be quantified. Within the limitations of this pilot study, true fusion related ASD seems to be infrequent.

  7. Agricultural Intensification Exacerbates Spillover Effects on Soil Biogeochemistry in Adjacent Forest Remnants

    Science.gov (United States)

    Didham, Raphael K.; Barker, Gary M.; Bartlam, Scott; Deakin, Elizabeth L.; Denmead, Lisa H.; Fisk, Louise M.; Peters, Jennifer M. R.; Tylianakis, Jason M.; Wright, Hannah R.; Schipper, Louis A.

    2015-01-01

    Land-use intensification is a central element in proposed strategies to address global food security. One rationale for accepting the negative consequences of land-use intensification for farmland biodiversity is that it could ‘spare’ further expansion of agriculture into remaining natural habitats. However, in many regions of the world the only natural habitats that can be spared are fragments within landscapes dominated by agriculture. Therefore, land-sparing arguments hinge on land-use intensification having low spillover effects into adjacent protected areas, otherwise net conservation gains will diminish with increasing intensification. We test, for the first time, whether the degree of spillover from farmland into adjacent natural habitats scales in magnitude with increasing land-use intensity. We identified a continuous land-use intensity gradient across pastoral farming systems in New Zealand (based on 13 components of farmer input and soil biogeochemistry variables), and measured cumulative off-site spillover effects of fertilisers and livestock on soil biogeochemistry in 21 adjacent forest remnants. Ten of 11 measured soil properties differed significantly between remnants and intact-forest reference sites, for both fenced and unfenced remnants, at both edge and interior. For seven variables, the magnitude of effects scaled significantly with magnitude of surrounding land-use intensity, through complex interactions with fencing and edge effects. In particular, total C, total N, δ15N, total P and heavy-metal contaminants of phosphate fertilizers (Cd and U) increased significantly within remnants in response to increasing land-use intensity, and these effects were exacerbated in unfenced relative to fenced remnants. This suggests movement of livestock into surrounding natural habitats is a significant component of agricultural spillover, but pervasive changes in soil biogeochemistry still occur through nutrient spillover channels alone, even in fenced

  8. Agricultural intensification exacerbates spillover effects on soil biogeochemistry in adjacent forest remnants.

    Directory of Open Access Journals (Sweden)

    Raphael K Didham

    Full Text Available Land-use intensification is a central element in proposed strategies to address global food security. One rationale for accepting the negative consequences of land-use intensification for farmland biodiversity is that it could 'spare' further expansion of agriculture into remaining natural habitats. However, in many regions of the world the only natural habitats that can be spared are fragments within landscapes dominated by agriculture. Therefore, land-sparing arguments hinge on land-use intensification having low spillover effects into adjacent protected areas, otherwise net conservation gains will diminish with increasing intensification. We test, for the first time, whether the degree of spillover from farmland into adjacent natural habitats scales in magnitude with increasing land-use intensity. We identified a continuous land-use intensity gradient across pastoral farming systems in New Zealand (based on 13 components of farmer input and soil biogeochemistry variables, and measured cumulative off-site spillover effects of fertilisers and livestock on soil biogeochemistry in 21 adjacent forest remnants. Ten of 11 measured soil properties differed significantly between remnants and intact-forest reference sites, for both fenced and unfenced remnants, at both edge and interior. For seven variables, the magnitude of effects scaled significantly with magnitude of surrounding land-use intensity, through complex interactions with fencing and edge effects. In particular, total C, total N, δ15N, total P and heavy-metal contaminants of phosphate fertilizers (Cd and U increased significantly within remnants in response to increasing land-use intensity, and these effects were exacerbated in unfenced relative to fenced remnants. This suggests movement of livestock into surrounding natural habitats is a significant component of agricultural spillover, but pervasive changes in soil biogeochemistry still occur through nutrient spillover channels alone

  9. Involvement of the β Clamp in Methyl-directed Mismatch Repair in Vitro*

    Science.gov (United States)

    Pluciennik, Anna; Burdett, Vickers; Lukianova, Olga; O'Donnell, Mike; Modrich, Paul

    2009-01-01

    We have examined function of the bacterial β replication clamp in the different steps of methyl-directed DNA mismatch repair. The mismatch-, MutS-, and MutL-dependent activation of MutH is unaffected by the presence or orientation of loaded β clamp on either 3′ or 5′ heteroduplexes. Similarly, β is not required for 3′ or 5′ mismatch-provoked excision when scored in the presence of γ complex or in the presence of γ complex and DNA polymerase III core components. However, mismatch repair does not occur in the absence of β, an effect we attribute to a requirement for the clamp in the repair DNA synthesis step of the reaction. We have confirmed previous findings that β clamp interacts specifically with MutS and MutL (López de Saro, F. J., Marinus, M. G., Modrich, P., and O'Donnell, M. (2006) J. Biol. Chem. 281, 14340–14349) and show that the mutator phenotype conferred by amino acid substitution within the MutS N-terminal β-interaction motif is the probable result of instability coupled with reduced activity in multiple steps of the repair reaction. In addition, we have found that the DNA polymerase III α catalytic subunit interacts strongly and specifically with both MutS and MutL. Because interactions of polymerase III holoenzyme components with MutS and MutL appear to be of limited import during the initiation and excision steps of mismatch correction, we suggest that their significance might lie in the control of replication fork events in response to the sensing of DNA lesions by the repair system. PMID:19783657

  10. How semantic biases in simple adjacencies affect learning a complex structure with non-adjacencies in AGL: a statistical account

    Science.gov (United States)

    Poletiek, Fenna H.; Lai, Jun

    2012-01-01

    A major theoretical debate in language acquisition research regards the learnability of hierarchical structures. The artificial grammar learning methodology is increasingly influential in approaching this question. Studies using an artificial centre-embedded AnBn grammar without semantics draw conflicting conclusions. This study investigates the facilitating effect of distributional biases in simple AB adjacencies in the input sample—caused in natural languages, among others, by semantic biases—on learning a centre-embedded structure. A mathematical simulation of the linguistic input and the learning, comparing various distributional biases in AB pairs, suggests that strong distributional biases might help us to grasp the complex AnBn hierarchical structure in a later stage. This theoretical investigation might contribute to our understanding of how distributional features of the input—including those caused by semantic variation—help learning complex structures in natural languages. PMID:22688639

  11. Soil chemistry adjacent to roads treated with dust control products at Squaw Creek National Wildlife Refuge

    Science.gov (United States)

    Kunz, Bethany K.

    2016-01-01

    The health of soils along roadways is critical for maximizing habitat quality and minimizing negative ecological effects of roads. Adjacent to unpaved roads, soil chemistry may be altered by the deposition of dust, as well as by road treatment with dust suppressants or soil stabilizer products. If present in roadside soils, these product residues may be available to plants, terrestrial invertebrates, or small mammals. Unfortunately, very few studies have attempted to track the transport of dust suppressants after application. As part of a larger ongoing study on the environmental effects of dust suppressant products on roadside plants and animals, we sampled roadside soils at Squaw Creek National Wildlife Refuge (NWR). Replicated road sections at Squaw Creek NWR had been previously treated with two road products—calcium chloride-based durablend-C™ and synthetic iso-alkane EnviroKleen®. In order to quantify the effect of dust suppressant treatment on roadside soils, we took replicated composite soil samples one year after treatment at 1m and 4m from the road’s edge, and analyzed samples for a suite of soil chemistry variables (pH, conductivity, NO3-N, P, K, Ca, Mg, Na and S). We also assessed dust suppressant product residues in the soil. For durablend-C™, we used soil conductivity as an indicator. For EnviroKleen®, we developed a method for extraction and isolation, followed by analysis with gas chromatography/mass spectrometry to look for a specific EnviroKleen® signature. Surprisingly, soil conductivity was not elevated adjacent to road sections treated with durablend-C™, relative to other sections. EnviroKleen® was detectable at both 1m and 4m from treated sections at concentrations from 1 to 1500 mg/kg, and was non-detectable in soils adjacent to the untreated section. The most notable characteristic of soils across all treated and untreated sections at 1m was elevated calcium (up to 30,000 mg/kg), likely as a result of dust deposition from the

  12. Helix Geometry, Hydration, and G\\cdot A Mismatch in a B-DNA Decamer

    Science.gov (United States)

    Prive, Gilbert G.; Heinemann, Udo; Chandrasegaran, Srinivasan; Kan, Lou-Sing; Kopka, Mary L.; Dickerson, Richard E.

    1987-10-01

    The DNA double helix is not a regular, featureless barberpole molecule. Different base sequences have their own special signature, in the way that they influence groove width, helical twist, bending, and mechanical rigidity or resistance to bending. These special features probably help other molecules such as repressors to read and recognize one base sequence in preference to another. Single crystal x-ray structure analysis is beginning to show us the various structures possible in the B-DNA family. The DNA decamer C-C-A-A-G-A-T-T-G-G appears to be a better model for mixed-sequence B-DNA than was the earlier C-G-C-G-A-A-T-T-C-G-C-G, which is more akin to regions of poly (dA)\\cdot poly(dT). The G\\cdot A mismatch base pairs at the center of the decamer are in the anti-anti conformation about their bonds from base to sugar, in agreement with nuclear magnetic resonance evidence on this and other sequences, and in contrast to the anti-syn geometry reported for G\\cdot A pairs in C-G-C-G-A-A-T-T-A-G-C-G. The ordered spine of hydration seen earlier in the narrow-grooved dodecamer has its counterpart, in this wide-grooved decamer, in two strings of water molecules lining the walls of the minor groove, bridging from purine N3 or pyrimidine O2, to the following sugar O4'. The same strings of hydration are present in the phosphorothioate analog of G-C-G-C-G-C. Unlike the spine, which is broken up by the intrusion of amine groups at guanines, these water strings are found in general, mixed-sequence DNA because they can pass by unimpeded to either side of a guanine N2 amine. The spine and strings are perceived as two extremes of a general pattern of hydration of the minor groove, which probably is the dominant factor in making B-DNA the preferred form at high hydration.

  13. Mismatch negativity (MMN) in high and low noise sensitive individuals

    NARCIS (Netherlands)

    White, Kim; Meeter, Martijn

    2015-01-01

    Although noise sensitivity is known to be an important determinant of noise annoyance, its neural underpinnings are not yet well established. In the present study, high and low noise sensitive participants were selected based on their scores on the Noise Sensitivity Scale (NSS) and the Noise

  14. Effect of Bronchoconstriction-induced Ventilation-Perfusion Mismatch on Uptake and Elimination of Isoflurane and Desflurane.

    Science.gov (United States)

    Kretzschmar, Moritz; Kozian, Alf; Baumgardner, James E; Borges, Joao Batista; Hedenstierna, Göran; Larsson, Anders; Hachenberg, Thomas; Schilling, Thomas

    2017-11-01

    Increasing numbers of patients with obstructive lung diseases need anesthesia for surgery. These conditions are associated with pulmonary ventilation/perfusion (VA/Q) mismatch affecting kinetics of volatile anesthetics. Pure shunt might delay uptake of less soluble anesthetic agents but other forms of VA/Q scatter have not yet been examined. Volatile anesthetics with higher blood solubility would be less affected by VA/Q mismatch. We therefore compared uptake and elimination of higher soluble isoflurane and less soluble desflurane in a piglet model. Juvenile piglets (26.7 ± 1.5 kg) received either isoflurane (n = 7) or desflurane (n = 7). Arterial and mixed venous blood samples were obtained during wash-in and wash-out of volatile anesthetics before and during bronchoconstriction by methacholine inhalation (100 μg/ml). Total uptake and elimination were calculated based on partial pressure measurements by micropore membrane inlet mass spectrometry and literature-derived partition coefficients and assumed end-expired to arterial gradients to be negligible. VA/Q distribution was assessed by the multiple inert gas elimination technique. Before methacholine inhalation, isoflurane arterial partial pressures reached 90% of final plateau within 16 min and decreased to 10% after 28 min. By methacholine nebulization, arterial uptake and elimination delayed to 35 and 44 min. Desflurane needed 4 min during wash-in and 6 min during wash-out, but with bronchoconstriction 90% of both uptake and elimination was reached within 15 min. Inhaled methacholine induced bronchoconstriction and inhomogeneous VA/Q distribution. Solubility of inhalational anesthetics significantly influenced pharmacokinetics: higher soluble isoflurane is less affected than fairly insoluble desflurane, indicating different uptake and elimination during bronchoconstriction.

  15. Matched and mismatched appraisals of the effectiveness of communication strategies by family caregivers of persons with Alzheimer's disease.

    Science.gov (United States)

    Savundranayagam, Marie Y; Orange, J B

    2014-01-01

    Communication problems stemming from Alzheimer's disease (AD) often result in misunderstandings that can be linked with problem behaviours and increased caregiver stress. Moreover, these communication breakdowns also can result either from caregivers' use of ineffective communication strategies, which paradoxically are perceived as helpful, or can occur as a result of not using effective communication strategies that are perceived as unhelpful. The two primary aims were to determine the effectiveness of strategies used to resolve communication breakdowns and to examine whether caregivers' ratings of strategy effectiveness were consistent with evidence from video-recorded conversations and with effective communication strategies documented in the literature. Twenty-eight mealtime conversations were recorded using a sample of 15 dyads consisting of individuals with early, middle and late clinical-stage AD and their family caregivers. Conversations were analysed using the trouble-source repair paradigm to identify the communication strategies used by caregivers to resolve breakdowns. Family caregivers also rated the helpfulness of communication strategies used to resolve breakdowns. Analyses were conducted to assess the overlap or match between the use and appraisals of the helpfulness of communication strategies. Matched and mismatched appraisals of communication strategies varied across stages of AD. Matched appraisals by caregivers of persons with early-stage AD were observed for 68% of 22 communication strategies, whereas caregivers of persons with middle- and late-stage AD had matched appraisals for 45% and 55% of the strategies, respectively. Moreover, caregivers of persons with early-stage AD had matched appraisals over and above making matched appraisals by chance alone, compared with caregivers of persons in middle- and late-stage AD. Mismatches illustrate the need for communication education and training, particularly to establish empirically derived

  16. Clinicopathologic factors identify sporadic mismatch repair-defective colon cancers

    DEFF Research Database (Denmark)

    Halvarsson, Britta; Anderson, Harald; Domanska, Katarina

    2008-01-01

    were linked to MMR status based on immunostaining and BRAF mutation status.MMR defects were identified in 22.7% of the tumors, with 46 classified as sporadic. When the clinical parameters of age, sex, and proximal tumor location were combined with the morphologic features with the highest relative...... and excluded 61.5% of the tumors from MMR testing. This clinicopathologic index thus successfully selects MMR-defective colon cancers. Udgivelsesdato: 2008-Feb...

  17. Symmetry Mismatched Heterostructures: New Routes to Bandwidth Control in Oxides

    Science.gov (United States)

    2015-08-11

    Christopher Y. Li, Steven J. May. Fluorination of Epitaxial Oxides: Synthesis of Perovskite Oxyfluoride Thin Films, Journal of the American Chemical...rotations at perovskite heterointerfaces, unit cell by unit cell, ACS Nano, (07 2015): 0. doi: TOTAL: 1 Number of Papers published in non peer...meeting, Denver, CO, March 3-7, 2014. 11.*“Anion-based approaches to tunable functionality in perovskite films and superlattices” S. J. May, 21st

  18. Measuring Crowdedness between Adjacent Stations in an Urban Metro System: a Chinese Case Study

    Directory of Open Access Journals (Sweden)

    Liudan Jiao

    2017-12-01

    Full Text Available The urban metro system has been widely appreciated as the most important component in urban infrastructures. It plays a critical role in promoting urban social and economic development, and particularly in reducing the urban traffic congestion. However, there are various inherent problems with operating metro systems, which typically involve the crowdedness both at stations and inside vehicles. Both policymakers and academic researchers in China have paid little attention to the crowdedness between metro stations. In order to solve the problem of crowdedness, it is necessary to develop a method to evaluate the level of crowdedness. This work establishes a model to measure the crowdedness between adjacent stations in a metro system based on the load factor principle, passenger standing density, and other factors such as the metro operation schedule and estimations of passenger flows. The Chongqing Metro Line 3 in China is used as a case study to demonstrate the application of the evaluation model. The case study reveals that the model introduced in this study can assist with assessing the crowdedness level between adjacent stations in a metro line. The model is an effective tool for helping the metro management and administration understand the level of crowdedness, apply proper methods to mitigate the crowdedness, and thus improve the quality of the service for those utilizing the metro system.

  19. Vibration Analysis and Models of Adjacent Structures Controlled by Magnetorheological Dampers

    Directory of Open Access Journals (Sweden)

    Michela Basili

    2017-01-01

    Full Text Available This paper deals with the vibration analysis of adjacent structures controlled by a magnetorheological (MR damper and with the discussion of a numerical procedure for identification and definition of a reliable finite element model. The paper describes an extensive experimental campaign investigating the dynamic response, through shaking table tests, of a tridimensional four-story structure and a two-story structure connected by an MR device. Several base excitations and intensity levels are considered. The structures were tested in nonconnected and connected configuration, with the MR damper operating in passive or semiactive mode. Moreover, the paper illustrates a procedure for the structural identification and the definition of a reliable numerical model valid for adjacent structures connected by MR dampers. The procedure is applied in the original nonconnected configuration, which represents a linear system, and then in the connected configuration, which represents a nonlinear system due to the MR damper. In the end, the updated finite element model is reliable and suitable for all the considered configurations and the mass, damping, and stiffness matrices are derived. The experimental and numerical responses are compared and the results confirm the effectiveness of the identification procedure and the validation of the finite element model.

  20. The tiger beetles (Coleoptera, Carabidae, Cicindelinae) of Israel and adjacent lands

    Science.gov (United States)

    Matalin, Andrey V.; Chikatunov, Vladimir I.

    2016-01-01

    Abstract Based on field studies, museums collections and literature sources, the current knowledge of the tiger beetle fauna of Israel and adjacent lands is presented. In Israel eight species occur, one of them with two subspecies, while in the Sinai Peninsula nine species of tiger beetles are now known. In the combined regions seven genera from two tribes were found. The Rift Valley with six cicindelids species is the most specious region of Israel. Cylindera contorta valdenbergi and Cicindela javeti azari have localized distributions and should be considered regional endemics. A similarity analysis of the tiger beetles faunas of different regions of Israel and the Sinai Peninsula reveal two clusters of species. The first includes the Great Rift Valley and most parts of the Sinai Peninsula, and the second incorporates most regions of Israel together with Central Sinai Foothills. Five distinct adult phenological groups of tiger beetles can be distinguished in these two clusters: active all-year (three species), spring-fall (five species), summer (two species), spring-summer (one species) and spring (one species). The likely origins of the tiger beetle fauna of this area are presented. An annotated list and illustrated identification key of the Cicindelinae of Israel and adjacent lands are provided. PMID:27110198