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Sample records for strongly delays pre-rrna

  1. Characterization of 16S rRNA Processing with Pre-30S Subunit Assembly Intermediates from E. coli.

    Science.gov (United States)

    Smith, Brian A; Gupta, Neha; Denny, Kevin; Culver, Gloria M

    2018-06-08

    Ribosomal RNA (rRNA) is a major component of ribosomes and is fundamental to the process of translation. In bacteria, 16S rRNA is a component of the small ribosomal subunit and plays a critical role in mRNA decoding. rRNA maturation entails the removal of intervening spacer sequences contained within the pre-rRNA transcript by nucleolytic enzymes. Enzymatic activities involved in maturation of the 5'-end of 16S rRNA have been identified, but those involved in 3'-end maturation of 16S rRNA are more enigmatic. Here, we investigate molecular details of 16S rRNA maturation using purified in vivo-formed small subunit (SSU) assembly intermediates (pre-SSUs) from wild-type Escherichia coli that contain precursor 16S rRNA (17S rRNA). Upon incubation of pre-SSUs with E. coli S100 cell extracts or purified enzymes implicated in 16S rRNA processing, the 17S rRNA is processed into additional intermediates and mature 16S rRNA. These results illustrate that exonucleases RNase R, RNase II, PNPase, and RNase PH can process the 3'-end of pre-SSUs in vitro. However, the endonuclease YbeY did not exhibit nucleolytic activity with pre-SSUs under these conditions. Furthermore, these data demonstrate that multiple pathways facilitate 16S rRNA maturation with pre-SSUs in vitro, with the dominant pathways entailing complete processing of the 5'-end of 17S rRNA prior to 3'-end maturation or partial processing of the 5'-end with concomitant processing of the 3'-end. These results reveal the multifaceted nature of SSU biogenesis and suggest that E. coli may be able to escape inactivation of any one enzyme by using an existing complementary pathway. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Pre-45s rRNA promotes colon cancer and is associated with poor survival of CRC patients.

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    Tsoi, H; Lam, K C; Dong, Y; Zhang, X; Lee, C K; Zhang, J; Ng, S C; Ng, S S M; Zheng, S; Chen, Y; Fang, J; Yu, J

    2017-11-02

    One characteristic of cancer cells is the abnormally high rate of cell metabolism to sustain their enhanced proliferation. However, the behind mechanism of this phenomenon is still elusive. Here we find that enhanced precursor 45s ribosomal RNA (pre-45s rRNA) is one of the core mechanisms in promoting the pathogenesis of colorectal cancer (CRC). Pre-45s rRNA expression is significantly higher in primary CRC tumor tissues samples and cancer cell lines compared with the non-tumorous colon tissues, and is associated with tumor sizes. Knockdown of pre-45s rRNA inhibits G1/S cell-cycle transition by stabilizing p53 through inducing murine double minute 2 (MDM2) and ribosomal protein L11 (RpL11) interaction. In addition, we revealed that high rate of cancer cell metabolism triggers the passive release of calcium ion from endoplasmic reticulum to the cytoplasm. The elevated calcium ion in the cytoplasm activates the signaling cascade of calcium/calmodulin-dependent protein kinase II, ribosomal S6 kinase (S6K) and ribosomal S6K (CaMKII-S6K-UBF). The activated UBF promotes the transcription of rDNA, which therefore increases pre-45s rRNA. Disruption of CaMKII-S6K-UBF axis by either RNAi or pharmaceutical approaches leads to reduction of pre-45s rRNA expression, which subsequently suppresses cell proliferation in colon cancer cells by causing cell-cycle arrest. Knockdown of APC activates CaMKII-S6K-UBF cascade and thus enhances pre-45s rRNA expression. Moreover, the high expression level of pre-45s rRNA is associated with poor survival of CRC patients in two independent cohorts. Our study identifies a novel mechanism in CRC pathogenesis mediated by pre-45s rRNA and a prognostic factor of pre-45s rRNA in CRC patients.

  3. The pre-existing population of 5S rRNA effects p53 stabilization during ribosome biogenesis inhibition.

    Science.gov (United States)

    Onofrillo, Carmine; Galbiati, Alice; Montanaro, Lorenzo; Derenzini, Massimo

    2017-01-17

    Pre-ribosomal complex RPL5/RPL11/5S rRNA (5S RNP) is considered the central MDM2 inhibitory complex that control p53 stabilization during ribosome biogenesis inhibition. Despite its role is well defined, the dynamic of 5S RNP assembly still requires further characterization. In the present work, we report that MDM2 inhibition is dependent by a pre-existing population of 5S rRNA.

  4. Impulsive Choice, Alcohol Consumption, and Pre-Exposure to Delayed Rewards: II. Potential Mechanisms

    Science.gov (United States)

    Stein, Jeffrey S.; Renda, C. Renee; Hinnenkamp, Jay E.; Madden, Gregory J.

    2014-01-01

    In a prior study (Stein et al., 2013), we reported that rats pre-exposed to delayed rewards made fewer impulsive choices, but consumed more alcohol (12% wt/vol), than rats pre-exposed to immediate rewards. To understand the mechanisms that produced these findings, we again pre-exposed rats to either delayed (17.5 s; n = 32) or immediate (n = 30) rewards. In post-tests, delay-exposed rats made significantly fewer impulsive choices at both 15- and 30-s delays to a larger, later food reward than the immediacy-exposed comparison group. Behavior in an open-field test provided little evidence of differential stress exposure between groups. Further, consumption of either 12% alcohol or isocaloric sucrose in subsequent tests did not differ between groups. Because Stein et al. introduced alcohol concentration gradually (3–12%), we speculate that their group differences in 12% alcohol consumption were not determined by alcohol’s pharmacological effects, but by another variable (e.g., taste) that was preserved as an artifact from lower concentrations. We conclude that pre-exposure to delayed rewards generalizes beyond the pre-exposure delay; however, this same experimental variable does not robustly influence alcohol consumption. PMID:25418607

  5. Footprints of a trypanosomatid RNA world: pre-small subunit rRNA processing by spliced leader addition trans-splicing

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    Mario Gustavo Mayer

    2012-06-01

    Full Text Available The addition of a capped mini-exon [spliced leader (SL] through trans-splicing is essential for the maturation of RNA polymerase (pol II-transcribed polycistronic pre-mRNAs in all members of the Trypanosomatidae family. This process is an inter-molecular splicing reaction that follows the same basic rules of cis-splicing reactions. In this study, we demonstrated that mini-exons were added to precursor ribosomal RNA (pre-rRNA are transcribed by RNA pol I, including the 5' external transcribed spacer (ETS region. Additionally, we detected the SL-5'ETS molecule using three distinct methods and located the acceptor site between two known 5'ETS rRNA processing sites (A' and A1 in four different trypanosomatids. Moreover, we detected a polyadenylated 5'ETS upstream of the trans-splicing acceptor site, which also occurs in pre-mRNA trans-splicing. After treatment with an indirect trans-splicing inhibitor (sinefungin, we observed SL-5'ETS decay. However, treatment with 5-fluorouracil (a precursor of RNA synthesis that inhibits the degradation of pre-rRNA led to the accumulation of SL-5'ETS, suggesting that the molecule may play a role in rRNA degradation. The detection of trans-splicing in these molecules may indicate broad RNA-joining properties, regardless of the polymerase used for transcription.

  6. The Strong Lensing Time Delay Challenge (2014)

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    Liao, Kai; Dobler, G.; Fassnacht, C. D.; Treu, T.; Marshall, P. J.; Rumbaugh, N.; Linder, E.; Hojjati, A.

    2014-01-01

    Time delays between multiple images in strong lensing systems are a powerful probe of cosmology. At the moment the application of this technique is limited by the number of lensed quasars with measured time delays. However, the number of such systems is expected to increase dramatically in the next few years. Hundred such systems are expected within this decade, while the Large Synoptic Survey Telescope (LSST) is expected to deliver of order 1000 time delays in the 2020 decade. In order to exploit this bounty of lenses we needed to make sure the time delay determination algorithms have sufficiently high precision and accuracy. As a first step to test current algorithms and identify potential areas for improvement we have started a "Time Delay Challenge" (TDC). An "evil" team has created realistic simulated light curves, to be analyzed blindly by "good" teams. The challenge is open to all interested parties. The initial challenge consists of two steps (TDC0 and TDC1). TDC0 consists of a small number of datasets to be used as a training template. The non-mandatory deadline is December 1 2013. The "good" teams that complete TDC0 will be given access to TDC1. TDC1 consists of thousands of lightcurves, a number sufficient to test precision and accuracy at the subpercent level, necessary for time-delay cosmography. The deadline for responding to TDC1 is July 1 2014. Submissions will be analyzed and compared in terms of predefined metrics to establish the goodness-of-fit, efficiency, precision and accuracy of current algorithms. This poster describes the challenge in detail and gives instructions for participation.

  7. Pre-hospital and hospital delay in patients with non-ST elevation acute coronary syndromes in tertiary care

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    G.S. Youssef

    2017-09-01

    Conclusion: Pre-hospital delay was mainly patient-related. Hospital delay was mainly related to healthcare resources. Governmental measures to promote ambulance emergency services may reduce the pre-hospital delay, while improving the utilization of healthcare resources may reduce hospital delay.

  8. Delayed hydride cracking: alternative pre-cracking method

    International Nuclear Information System (INIS)

    Mieza, Juan I.; Ponzoni, Lucio M.E.; Vigna, Gustavo L.; Domizzi, Gladys

    2009-01-01

    The internal components of nuclear reactors built-in Zr alloys are prone to a failure mechanism known as Delayed Hydride Cracking (DHC). This situation has triggered numerous scientific studies in order to measure the crack propagation velocity and the threshold stress intensity factor associated to DHC. Tests are carried out on fatigued pre-crack samples to ensure similar test conditions and comparable results. Due to difficulties in implementing the fatigue pre-crack method it would be desirable to replace it with a pre-crack produced by the same process of DHC, for which is necessary to demonstrate equivalence of this two methods. In this work tests on samples extracted from two Zr-2.5 Nb tubes were conducted. Some of the samples were heat treated to obtain a range in their metallurgical properties as well as different DHC velocities. A comparison between velocities measured in test samples pre-cracked by fatigue and RDIH is done, demonstrating that the pre-cracking method does not affect the measured velocity value. In addition, the incubation (t inc ), which is the time between the application of the load and the first signal of crack propagation, in samples pre-cracked by RDIH, was measured. It was found that these times are sufficiently short, even in the worst cases (lower speed) and similar to the ones of fatigued pre-cracked samples. (author)

  9. Assessing the costs attributed to project delay during project pre-construction stages.

    Science.gov (United States)

    2016-03-01

    This project for the Texas Department of Transportation (TxDOT) developed a simple but sound : methodology for estimating the cost of delaying most types of highway projects. Researchers considered the : cost of delays during the pre-construction pha...

  10. Inhibition of Escherichia coli precursor-16S rRNA processing by mouse intestinal contents

    DEFF Research Database (Denmark)

    Licht, Tine Rask; Tolker-Nielsen, Tim; Holmstrøm, Kim

    1999-01-01

    . We have applied fluorescence in situ hybridization of pre-16S rRNA to Escherichia coli cells growing in vitro in extracts from two different compartments of the mouse intestine: the caecal mucus layer, where E. coli grew rapidly, and the contents of the caecum, which supported much slower bacterial...... content of pre-16S rRNA than cultures of the same strain growing rapidly in rich media. We present results suggesting that the mouse intestinal contents contain an agent that inhibits the growth of E. coli by disturbing its ability to process pre-16S rRNA....

  11. Effect of a comprehensive health education program on pre-hospital delay intentions in high-risk stroke population and caregivers.

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    Yang, Li; Zhao, Qiuli; Zhu, Xuemei; Shen, Xiaoying; Zhu, Yulan; Yang, Liu; Gao, Wei; Li, Minghui

    2017-08-01

    Many factors influence pre-hospital delays in the event of stroke. This study aimed to develop and evaluate a comprehensive educational program for decreasing pre-hospital delays in high-risk stroke population. We enrolled 220 high-risk stroke population and caregivers from six urban communities in Harbin from May 2013 to May 2015, and randomly divided them into intervention and control groups. We implemented a comprehensive educational program (intervention group), comprising public lectures, instructional brochures, case videos, simulations, and role-playing from May 2013 to May 2015. We delivered conventional oral education in the control group. We compared stroke pre-hospital delay behavioral intention (SPDBI), pre-hospital stroke symptom coping test (PSSCT), and stroke pre-symptoms alert test (SPSAT) results between the groups before and 6, 12, and 18 months after health intervention. There were significant differences between before and after intervention (P educational program was significantly effective in decreasing SPDBI, improving knowledge, enhancing stroke pre-symptoms alert, and reducing the possibility of pre-hospital delays.

  12. Charging-delay effect on longitudinal dust acoustic shock wave in strongly coupled dusty plasma

    International Nuclear Information System (INIS)

    Ghosh, Samiran; Gupta, M.R.

    2005-01-01

    Taking into account the charging-delay effect, the nonlinear propagation characteristics of longitudinal dust acoustic wave in strongly coupled collisional dusty plasma described by generalized hydrodynamic model have been investigated. In the 'hydrodynamic limit', a Korteweg-de Vries Burger (KdVB) equation with a damping term arising due to dust-neutral collision is derived in which the Burger term is proportional to the dissipation due to dust viscosity through dust-dust correlation and charging-delay-induced anomalous dissipation. On the other hand, in the 'kinetic limit', a KdVB equation with a damping term and a nonlocal nonlinear forcing term arising due to memory-dependent strong correlation effect of dust fluid is derived in which the Burger term depends only on the charging-delay-induced dissipation. Numerical solution of integrodifferential equations reveals that (i) dissipation due to dust viscosity and principally due to charging delay causes excitation of the longitudinal dust acoustic shock wave in strongly coupled dusty plasma and (ii) dust-neutral collision does not appear to play any direct role in shock formation. The condition for the generation of shock is also discussed briefly

  13. STRONG LENS TIME DELAY CHALLENGE. I. EXPERIMENTAL DESIGN

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    Dobler, Gregory [Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA 93106 (United States); Fassnacht, Christopher D.; Rumbaugh, Nicholas [Department of Physics, University of California, 1 Shields Avenue, Davis, CA 95616 (United States); Treu, Tommaso; Liao, Kai [Department of Physics, University of California, Santa Barbara, CA 93106 (United States); Marshall, Phil [Kavli Institute for Particle Astrophysics and Cosmology, P.O. Box 20450, MS29, Stanford, CA 94309 (United States); Hojjati, Alireza [Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, B.C. V6T 1Z1 (Canada); Linder, Eric, E-mail: tt@astro.ucla.edu [Lawrence Berkeley National Laboratory and University of California, Berkeley, CA 94720 (United States)

    2015-02-01

    The time delays between point-like images in gravitational lens systems can be used to measure cosmological parameters. The number of lenses with measured time delays is growing rapidly; the upcoming Large Synoptic Survey Telescope (LSST) will monitor ∼10{sup 3} strongly lensed quasars. In an effort to assess the present capabilities of the community, to accurately measure the time delays, and to provide input to dedicated monitoring campaigns and future LSST cosmology feasibility studies, we have invited the community to take part in a ''Time Delay Challenge'' (TDC). The challenge is organized as a set of ''ladders'', each containing a group of simulated data sets to be analyzed blindly by participating teams. Each rung on a ladder consists of a set of realistic mock observed lensed quasar light curves, with the rungs' data sets increasing in complexity and realism. The initial challenge described here has two ladders, TDC0 and TDC1. TDC0 has a small number of data sets, and is designed to be used as a practice set by the participating teams. The (non-mandatory) deadline for completion of TDC0 was the TDC1 launch date, 2013 December 1. The TDC1 deadline was 2014 July 1. Here we give an overview of the challenge, we introduce a set of metrics that will be used to quantify the goodness of fit, efficiency, precision, and accuracy of the algorithms, and we present the results of TDC0. Thirteen teams participated in TDC0 using 47 different methods. Seven of those teams qualified for TDC1, which is described in the companion paper.

  14. Depletion of key protein components of the RISC pathway impairs pre-ribosomal RNA processing.

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    Liang, Xue-Hai; Crooke, Stanley T

    2011-06-01

    Little is known about whether components of the RNA-induced silencing complex (RISC) mediate the biogenesis of RNAs other than miRNA. Here, we show that depletion of key proteins of the RISC pathway by antisense oligonucleotides significantly impairs pre-rRNA processing in human cells. In cells depleted of Drosha or Dicer, different precursors to 5.8S rRNA strongly accumulated, without affecting normal endonucleolytic cleavages. Moderate yet distinct processing defects were also observed in Ago2-depleted cells. Physical links between pre-rRNA and these proteins were identified by co-immunoprecipitation analyses. Interestingly, simultaneous depletion of Dicer and Drosha led to a different processing defect, causing slower production of 28S rRNA and its precursor. Both Dicer and Ago2 were detected in the nuclear fraction, and reduction of Dicer altered the structure of the nucleolus, where pre-rRNA processing occurs. Together, these results suggest that Drosha and Dicer are implicated in rRNA biogenesis.

  15. Hearing assessment in pre-school children with speech delay.

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    Psillas, George; Psifidis, Anestis; Antoniadou-Hitoglou, Magda; Kouloulas, Athanasios

    2006-09-01

    The purpose of this study was to detect any underlying hearing loss among the healthy pre-school children with speech delay. 76 children, aged from 1 to 5 years, underwent a thorough audiological examination consisting of tympanometry, free field testing, otoacoustic emission recordings and auditory brainstem responses (ABRs). If hearing was normal, then they were evaluated by a child neurologist-psychiatrist. According to our findings, the children were classified into 3 groups; those with normal hearing levels (group I, 52 children, 68.4%), sensorineural hearing loss (group II, 22 children, 28.9%) and conductive hearing loss (group III, 2 children, 2.6%). In group I, speech delay was attributed to pervasive developmental disorder (PDD), which represents high-functioning autistic children (37 cases). Other causes were specific language impairment (SLI)-expressive (3 cases), bilingualism (2 cases), and unknown etiology (10 cases). More than half (59%) of the children diagnosed with PDD evidenced significant language impairment limited to more than two words. Children with SLI-expressive and bilingualism used a maximum of two words. In group II, 13 children suffered from profound hearing loss in both ears, 3 from severe, 3 had profound hearing loss in one ear and severe in the other, 2 from moderate, and 1 had moderate in one ear and severe in the other. No child had mild sensorineural hearing loss. The children with profound hearing loss in at least one ear had total language impairment using no word at all (10 cases), or a maximum of two words (6 cases). When hearing loss was moderate to severe, then the speech vocabulary was confined to several words (more than two words-6 cases). Only two children suffering from conductive hearing loss both presented with complete lack of speech. A great number of healthy pre-school children with speech delay were found to have normal hearing. In this case, the otolaryngologist should be aware of the possible underlying clinical

  16. Strong-field Breit–Wheeler pair production in two consecutive laser pulses with variable time delay

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    Martin J.A. Jansen

    2017-03-01

    Full Text Available Photoproduction of electron–positron pairs by the strong-field Breit–Wheeler process in an intense laser field is studied. The laser field is assumed to consist of two consecutive short pulses, with a variable time delay in between. By numerical calculations within the framework of scalar quantum electrodynamics, we demonstrate that the time delay exerts a strong impact on the pair-creation probability. For the case when both pulses are identical, the effect is traced back to the relative quantum phase of the interfering S-matrix amplitudes and explained within a simplified analytical model. Conversely, when the two laser pulses differ from each other, the pair-creation probability depends not only on the time delay but, in general, also on the temporal order of the pulses.

  17. Probability distribution of wave packet delay time for strong overlapping of resonance levels

    International Nuclear Information System (INIS)

    Lyuboshits, V.L.

    1983-01-01

    Time behaviour of nuclear reactions in the case of high level densities is investigated basing on the theory of overlapping resonances. In the framework of a model of n equivalent channels an analytical expression is obtained for the probability distribution function for wave packet delay time at the compound nucleus production. It is shown that at strong overlapping of the resonance levels the relative fluctuation of the delay time is small at the stage of compound nucleus production. A possible increase in the duration of nuclear reactions with the excitation energy rise is discussed

  18. Synchronization and bidirectional communication without delay line using strong mutually coupled semiconductor lasers

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    Li, Guang-Hui; Wang, An-Bang; Feng, Ye; Wang, Yang

    2010-07-01

    This paper numerically demonstrates synchronization and bidirectional communication without delay line by using two semiconductor lasers with strong mutual injection in a face-to-face configuration. These results show that both of the two lasers' outputs synchronize with their input chaotic carriers. In addition, simulations demonstrate that this kind of synchronization can be used to realize bidirectional communications without delay line. Further studies indicate that within a small deviation in message amplitudes of two sides (±6%), the message can be extracted with signal-noise-ratio more than 10 dB; and the signal-noise-ratio is extremely sensitive to the message rates mismatch of two sides, which may be used as a key of bidirectional communication.

  19. Synchronization and bidirectional communication without delay line using strong mutually coupled semiconductor lasers

    International Nuclear Information System (INIS)

    Guang-Hui, Li; An-Bang, Wang; Ye, Feng; Yang, Wang

    2010-01-01

    This paper numerically demonstrates synchronization and bidirectional communication without delay line by using two semiconductor lasers with strong mutual injection in a face-to-face configuration. These results show that both of the two lasers' outputs synchronize with their input chaotic carriers. In addition, simulations demonstrate that this kind of synchronization can be used to realize bidirectional communications without delay line. Further studies indicate that within a small deviation in message amplitudes of two sides (±6%), the message can be extracted with signal-noise-ratio more than 10 dB; and the signal-noise-ratio is extremely sensitive to the message rates mismatch of two sides, which may be used as a key of bidirectional communication. (general)

  20. Strong delayed interactive effects of metal exposure and warming

    DEFF Research Database (Denmark)

    Debecker, Sara; Dinh, Khuong Van; Stoks, Robby

    2017-01-01

    ’ ranges could lead to an important underestimation of the risks. We addressed all three mechanisms by studying effects of larval exposure to zinc and warming before, during, and after metamorphosis in Ischnura elegans damselflies from high- and lowlatitude populations. By integrating these mechanisms...... into a single study, we could identify two novel patterns. First, during exposure zinc did not affect survival, whereas it induced mild to moderate postexposure mortality in the larval stage and at metamorphosis, and very strongly reduced adult lifespan. This severe delayed effect across metamorphosis...... was especially remarkable in high-latitude animals, as they appeared almost insensitive to zinc during the larval stage. Second, the well-known synergism between metals and warming was manifested not only during the larval stage but also after metamorphosis, yet notably only in low-latitude damselflies...

  1. Stuttering adults' lack of pre-speech auditory modulation normalizes when speaking with delayed auditory feedback.

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    Daliri, Ayoub; Max, Ludo

    2018-02-01

    Auditory modulation during speech movement planning is limited in adults who stutter (AWS), but the functional relevance of the phenomenon itself remains unknown. We investigated for AWS and adults who do not stutter (AWNS) (a) a potential relationship between pre-speech auditory modulation and auditory feedback contributions to speech motor learning and (b) the effect on pre-speech auditory modulation of real-time versus delayed auditory feedback. Experiment I used a sensorimotor adaptation paradigm to estimate auditory-motor speech learning. Using acoustic speech recordings, we quantified subjects' formant frequency adjustments across trials when continually exposed to formant-shifted auditory feedback. In Experiment II, we used electroencephalography to determine the same subjects' extent of pre-speech auditory modulation (reductions in auditory evoked potential N1 amplitude) when probe tones were delivered prior to speaking versus not speaking. To manipulate subjects' ability to monitor real-time feedback, we included speaking conditions with non-altered auditory feedback (NAF) and delayed auditory feedback (DAF). Experiment I showed that auditory-motor learning was limited for AWS versus AWNS, and the extent of learning was negatively correlated with stuttering frequency. Experiment II yielded several key findings: (a) our prior finding of limited pre-speech auditory modulation in AWS was replicated; (b) DAF caused a decrease in auditory modulation for most AWNS but an increase for most AWS; and (c) for AWS, the amount of auditory modulation when speaking with DAF was positively correlated with stuttering frequency. Lastly, AWNS showed no correlation between pre-speech auditory modulation (Experiment II) and extent of auditory-motor learning (Experiment I) whereas AWS showed a negative correlation between these measures. Thus, findings suggest that AWS show deficits in both pre-speech auditory modulation and auditory-motor learning; however, limited pre

  2. An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

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    Yih-Horng Shiao

    Full Text Available BACKGROUND: Ribosomal RNA (rRNA is a central regulator of cell growth and may control cancer development. A cis noncoding rRNA (nc-rRNA upstream from the 45S rRNA transcription start site has recently been implicated in control of rRNA transcription in mouse fibroblasts. We investigated whether a similar nc-rRNA might be expressed in human cancer epithelial cells, and related to any genomic characteristics. METHODOLOGY/PRINCIPAL FINDINGS: Using quantitative rRNA measurement, we demonstrated that a nc-rRNA is transcribed in human lung epithelial and lung cancer cells, starting from approximately -1000 nucleotides upstream of the rRNA transcription start site (+1 and extending at least to +203. This nc-rRNA was significantly more abundant in the majority of lung cancer cell lines, relative to a nontransformed lung epithelial cell line. Its abundance correlated negatively with total 45S rRNA in 12 of 13 cell lines (P = 0.014. During sequence analysis from -388 to +306, we observed diverse, frequent intercopy single nucleotide polymorphisms (SNPs in rRNA, with a frequency greater than predicted by chance at 12 sites. A SNP at +139 (U/C in the 5' leader sequence varied among the cell lines and correlated negatively with level of the nc-rRNA (P = 0.014. Modelling of the secondary structure of the rRNA 5'-leader sequence indicated a small increase in structural stability due to the +139 U/C SNP and a minor shift in local configuration occurrences. CONCLUSIONS/SIGNIFICANCE: The results demonstrate occurrence of a sense nc-rRNA in human lung epithelial and cancer cells, and imply a role in regulation of the rRNA gene, which may be affected by a +139 SNP in the 5' leader sequence of the primary rRNA transcript.

  3. The rRNA methyltransferase Bud23 shows functional interaction with components of the SSU processome and RNase MRP.

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    Sardana, Richa; White, Joshua P; Johnson, Arlen W

    2013-06-01

    Bud23 is responsible for the conserved methylation of G1575 of 18S rRNA, in the P-site of the small subunit of the ribosome. bud23Δ mutants have severely reduced small subunit levels and show a general failure in cleavage at site A2 during rRNA processing. Site A2 is the primary cleavage site for separating the precursors of 18S and 25S rRNAs. Here, we have taken a genetic approach to identify the functional environment of BUD23. We found mutations in UTP2 and UTP14, encoding components of the SSU processome, as spontaneous suppressors of a bud23Δ mutant. The suppressors improved growth and subunit balance and restored cleavage at site A2. In a directed screen of 50 ribosomal trans-acting factors, we identified strong positive and negative genetic interactions with components of the SSU processome and strong negative interactions with components of RNase MRP. RNase MRP is responsible for cleavage at site A3 in pre-rRNA, an alternative cleavage site for separating the precursor rRNAs. The strong negative genetic interaction between RNase MRP mutants and bud23Δ is likely due to the combined defects in cleavage at A2 and A3. Our results suggest that Bud23 plays a role at the time of A2 cleavage, earlier than previously thought. The genetic interaction with the SSU processome suggests that Bud23 could be involved in triggering disassembly of the SSU processome, or of particular subcomplexes of the processome.

  4. An Archaea 5S rRNA analog is stably expressed in Escherichia coli

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    Yang, Y.; Fox, G. E.

    1996-01-01

    Mini-genes for 5S-like rRNA were constructed. These genes had a sequence which largely resembles that of the naturally occurring 5S rRNA of a bacterium, Halococcus morrhuae, which phylogenetically belongs to the Archaea. Plasmids carrying the mini-genes were transformed into Escherichia coli (Ec). Ribosomal incorporation was not a prerequisite for stable accumulation of the RNA product. However, only those constructs with a well-base-paired helix I accumulated RNA product. This result strongly implies that this aspect of the structure is likely to be an important condition for stabilizing 5S rRNA-like products. The results are consistent with our current understanding of 5S rRNA processing in Ec. When used in conjunction with rRNA probe technology, the resulting chimeric RNA may be useful as a monitoring tool for genetically engineered microorganisms or naturally occurring organisms that are released into the environment.

  5. Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana.

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    Frédéric Pontvianne

    2010-11-01

    Full Text Available In eukaryotes, 45S rRNA genes are arranged in tandem arrays in copy numbers ranging from several hundred to several thousand in plants. Although it is clear that not all copies are transcribed under normal growth conditions, the molecular basis controlling the expression of specific sets of rRNA genes remains unclear. Here, we report four major rRNA gene variants in Arabidopsis thaliana. Interestingly, while transcription of one of these rRNA variants is induced, the others are either repressed or remain unaltered in A. thaliana plants with a disrupted nucleolin-like protein gene (Atnuc-L1. Remarkably, the most highly represented rRNA gene variant, which is inactive in WT plants, is reactivated in Atnuc-L1 mutants. We show that accumulated pre-rRNAs originate from RNA Pol I transcription and are processed accurately. Moreover, we show that disruption of the AtNUC-L1 gene induces loss of symmetrical DNA methylation without affecting histone epigenetic marks at rRNA genes. Collectively, these data reveal a novel mechanism for rRNA gene transcriptional regulation in which the nucleolin protein plays a major role in controlling active and repressed rRNA gene variants in Arabidopsis.

  6. Differences in symptoms, first medical contact and pre-hospital delay times between patients with ST- and non-ST-elevation myocardial infarction.

    Science.gov (United States)

    Ängerud, Karin H; Sederholm Lawesson, Sofia; Isaksson, Rose-Marie; Thylén, Ingela; Swahn, Eva

    2017-11-01

    In ST-elevation myocardial infarction, time to reperfusion is crucial for the prognosis. Symptom presentation in myocardial infarction influences pre-hospital delay times but studies about differences in symptoms between patients with ST-elevation myocardial infarction and non-ST-elevation myocardial infarction are sparse and inconclusive. The aim was to compare symptoms, first medical contact and pre-hospital delay times in patients with ST-elevation myocardial infarction and non-ST-elevation myocardial infarction. This multicentre, observational study included 694 myocardial infarction patients from five hospitals. The patients filled in a questionnaire about their pre-hospital experiences within 24 h of hospital admittance. Chest pain was the most common symptom in ST-elevation myocardial infarction and non-ST-elevation myocardial infarction (88.7 vs 87.0%, p=0.56). Patients with cold sweat (odds ratio 3.61, 95% confidence interval 2.29-5.70), jaw pain (odds ratio 2.41, 95% confidence interval 1.04-5.58), and nausea (odds ratio 1.70, 95% confidence interval 1.01-2.87) were more likely to present with ST-elevation myocardial infarction, whereas the opposite was true for symptoms that come and go (odds ratio 0.58, 95% confidence interval 0.38-0.90) or anxiety (odds ratio 0.52, 95% confidence interval 0.29-0.92). Use of emergency medical services was higher among patients admitted with ST-elevation myocardial infarction. The pre-hospital delay time from symptom onset to first medical contact was significantly longer in non-ST-elevation myocardial infarction (2:05 h vs 1:10 h, p=0.001). Patients with ST-elevation myocardial infarction differed from those with non-ST-elevation myocardial infarction regarding symptom presentation, ambulance utilisation and pre-hospital delay times. This knowledge is important to be aware of for all healthcare personnel and the general public especially in order to recognise symptoms suggestive of ST-elevation myocardial infarction and

  7. Visual stimuli in intervention approaches for pre-schoolers diagnosed with phonological delay.

    Science.gov (United States)

    Pedro, Cassandra Ferreira; Lousada, Marisa; Hall, Andreia; Jesus, Luis M T

    2018-04-01

    The aim of this study was to develop and content validate specific speech and language intervention picture cards: The Letter-Sound (L&S) cards. The present study was also focused on assessing the influence of these cards on letter-sound correspondences and speech sound production. An expert panel of six speech and language therapists analysed and discussed the L&S cards based on several criteria previously established. A Speech and Language Therapist carried out a 6-week therapeutic intervention with a group of seven Portuguese phonologically delayed pre-schoolers aged 5;3 to 6;5. The modified Bland-Altman method revealed good agreement among evaluators, that is the majority of the values was between the agreement limits. Additional outcome measures were collected before and after the therapeutic intervention process. Results indicate that the L&S cards facilitate the acquisition of letter-sound correspondences. Regarding speech sound production, some improvements were also observed at word level. The L&S cards are therefore likely to give phonetic cues, which are crucial for the correct production of therapeutic targets. These visual cues seemed to have helped children with phonological delay develop the above-mentioned skills.

  8. Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

    OpenAIRE

    Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

    2002-01-01

    The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in ...

  9. 5S rRNA and ribosome.

    Science.gov (United States)

    Gongadze, G M

    2011-12-01

    5S rRNA is an integral component of the ribosome of all living organisms. It is known that the ribosome without 5S rRNA is functionally inactive. However, the question about the specific role of this RNA in functioning of the translation apparatus is still open. This review presents a brief history of the discovery of 5S rRNA and studies of its origin and localization in the ribosome. The previously expressed hypotheses about the role of this RNA in the functioning of the ribosome are discussed considering the unique location of 5S rRNA in the ribosome and its intermolecular contacts. Based on analysis of the current data on ribosome structure and its functional complexes, the role of 5S rRNA as an intermediary between ribosome functional domains is discussed.

  10. High-resolution microscopy of active ribosomal genes and key members of the rRNA processing machinery inside nucleolus-like bodies of fully-grown mouse oocytes.

    Science.gov (United States)

    Shishova, Kseniya V; Khodarovich, Yuriy M; Lavrentyeva, Elena A; Zatsepina, Olga V

    2015-10-01

    Nucleolus-like bodies (NLBs) of fully-grown (germinal vesicle, GV) mammalian oocytes are traditionally considered as morphologically distinct entities, which, unlike normal nucleoli, contain transcribed ribosomal genes (rDNA) solely at their surface. In the current study, we for the first time showed that active ribosomal genes are present not only on the surface but also inside NLBs of the NSN-type oocytes. The "internal" rRNA synthesis was evidenced by cytoplasmic microinjections of BrUTP as precursor and by fluorescence in situ hybridization with a probe to the short-lived 5'ETS segment of the 47S pre-rRNA. We further showed that in the NLB mass of NSN-oocytes, distribution of active rDNA, RNA polymerase I (UBF) and rRNA processing (fibrillarin) protein factors, U3 snoRNA, pre-rRNAs and 18S/28S rRNAs is remarkably similar to that in somatic nucleoli capable to make pre-ribosomes. Overall, these observations support the occurrence of rDNA transcription, rRNA processing and pre-ribosome assembly in the NSN-type NLBs and so that their functional similarity to normal nucleoli. Unlike the NSN-type NLBs, the NLBs of more mature SN-oocytes do not contain transcribed rRNA genes, U3 snoRNA, pre-rRNAs, 18S and 28S rRNAs. These results favor the idea that in a process of transformation of NSN-oocytes to SN-oocytes, NLBs cease to produce pre-ribosomes and, moreover, lose their rRNAs. We also concluded that a denaturing fixative 70% ethanol used in the study to fix oocytes could be more appropriate for light microscopy analysis of nucleolar RNAs and proteins in mammalian fully-grown oocytes than a commonly used cross-linking aldehyde fixative, formalin. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Diagnosis and treatment delays among elderly breast cancer patients with pre-existing mental illness.

    Science.gov (United States)

    Iglay, Kristy; Santorelli, Melissa L; Hirshfield, Kim M; Williams, Jill M; Rhoads, George G; Lin, Yong; Demissie, Kitaw

    2017-11-01

    This study aimed to compare diagnosis and treatment delays in elderly breast cancer patients with and without pre-existing mental illness. A retrospective cohort study was conducted using the Surveillance, Epidemiology and End Results-Medicare data including 16,636 women 68+ years, who were diagnosed with stage I-IIIa breast cancer in the United States from 2005 to 2007. Mental illness was identified using International Classification of Diseases, Ninth Revision, Clinical Modification codes recorded on inpatient and outpatient claims during the 3 years prior to breast cancer diagnosis. Patients were classified as having no mental illness, anxiety, depression, anxiety and depression, or severe mental illness (bipolar disorder, schizophrenia, and other psychotic disorder). Multivariable binomial regression was used to assess the association between mental illness and delays of ≥60 and ≥90 days after adjustment for confounders. Patients with comorbid anxiety and depression had an increased risk for diagnosis delay of ≥90 days from symptom recognition (RR 1.11; 95% CI 1.00, 1.23), and those with severe mental illness had an increased risk for initial treatment delay of ≥60 days from diagnosis (RR 1.36; 95% CI 1.06, 1.74). Patients with any mental illness experienced an increased risk for adjuvant chemotherapy delay of ≥90 days from last operation (RR 1.13; 95% CI 1.01, 1.26) and each category of mental illness, except depression, showed a non-significant trend for this association. Breast cancer patients with mental illness should be closely managed by a cross-functional care team, including a psychiatrist, a primary care physician, and an oncologist, to ensure adequate care is received within an appropriate timeframe.

  12. Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda.

    Directory of Open Access Journals (Sweden)

    Shu Wu

    Full Text Available Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9 within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%; and could aid in species-level analyses, but with some limitations; 2 nearly-whole-length sequences and some partial regions (around V2, V4, and V9 of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%; 3 compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%; and 4 V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.

  13. Strong Delayed Interactive Effects of Metal Exposure and Warming: Latitude-Dependent Synergisms Persist Across Metamorphosis.

    Science.gov (United States)

    Debecker, Sara; Dinh, Khuong V; Stoks, Robby

    2017-02-21

    As contaminants are often more toxic at higher temperatures, predicting their impact under global warming remains a key challenge for ecological risk assessment. Ignoring delayed effects, synergistic interactions between contaminants and warming, and differences in sensitivity across species' ranges could lead to an important underestimation of the risks. We addressed all three mechanisms by studying effects of larval exposure to zinc and warming before, during, and after metamorphosis in Ischnura elegans damselflies from high- and low-latitude populations. By integrating these mechanisms into a single study, we could identify two novel patterns. First, during exposure zinc did not affect survival, whereas it induced mild to moderate postexposure mortality in the larval stage and at metamorphosis, and very strongly reduced adult lifespan. This severe delayed effect across metamorphosis was especially remarkable in high-latitude animals, as they appeared almost insensitive to zinc during the larval stage. Second, the well-known synergism between metals and warming was manifested not only during the larval stage but also after metamorphosis, yet notably only in low-latitude damselflies. These results highlight that a more complete life-cycle approach that incorporates the possibility of delayed interactions between contaminants and warming in a geographical context is crucial for a more realistic risk assessment in a warming world.

  14. Comparison of primary and secondary 26S rRNA structures in two Tetrahymena species: evidence for a strong evolutionary and structural constraint in expansion segments

    DEFF Research Database (Denmark)

    Engberg, J; Nielsen, Henrik; Lenaers, G

    1990-01-01

    We have determined the nucleotide sequence of the 26S large subunit (LSU) rRNA genes for two Tetrahymena species, T. thermophila and T. pyriformis. The inferred rRNA sequences are presented in their most probable secondary structures based on compensatory mutations, energy, and conservation crite...

  15. Role of Assessment Tests in the Stability of Intelligence Scoring of Pre-School Children with Uneven/Delayed Cognitive Profile

    Science.gov (United States)

    Yang, P.; Jong, Y-J.; Hsu, H-Y.; Lung, F-W.

    2011-01-01

    Background: As part of an ongoing clinical service programme for pre-school children with developmental delay in an Asian developing country, we analysed the effect of three assessment tests, that is, Bayley Scale of Infant Development-II, Leiter International Performance Scale-Revised and Wechsler Preschool and Primary Scale of…

  16. Increased 5S rRNA oxidation in Alzheimer's disease.

    Science.gov (United States)

    Ding, Qunxing; Zhu, Haiyan; Zhang, Bing; Soriano, Augusto; Burns, Roxanne; Markesbery, William R

    2012-01-01

    It is widely accepted that oxidative stress is involved in neurodegenerative disorders such as Alzheimer's disease (AD). Ribosomal RNA (rRNA) is one of the most abundant molecules in most cells and is affected by oxidative stress in the human brain. Previous data have indicated that total rRNA levels were decreased in the brains of subjects with AD and mild cognitive impairment concomitant with an increase in rRNA oxidation. In addition, level of 5S rRNA, one of the essential components of the ribosome complex, was significantly lower in the inferior parietal lobule (IP) brain area of subjects with AD compared with control subjects. To further evaluate the alteration of 5S rRNA in neurodegenerative human brains, multiple brain regions from both AD and age-matched control subjects were used in this study, including IP, superior and middle temporal gyro, temporal pole, and cerebellum. Different molecular pools including 5S rRNA integrated into ribosome complexes, free 5S rRNA, cytoplasmic 5S rRNA, and nuclear 5S rRNA were studied. Free 5S rRNA levels were significantly decreased in the temporal pole region of AD subjects and the oxidation of ribosome-integrated and free 5S rRNA was significantly increased in multiple brain regions in AD subjects compared with controls. Moreover, a greater amount of oxidized 5S rRNA was detected in the cytoplasm and nucleus of AD subjects compared with controls. These results suggest that the increased oxidation of 5S rRNA, especially the oxidation of free 5S rRNA, may be involved in the neurodegeneration observed in AD.

  17. Test of the FLRW Metric and Curvature with Strong Lens Time Delays

    International Nuclear Information System (INIS)

    Liao, Kai; Li, Zhengxiang; Wang, Guo-Jian; Fan, Xi-Long

    2017-01-01

    We present a new model-independent strategy for testing the Friedmann–Lemaître–Robertson–Walker (FLRW) metric and constraining cosmic curvature, based on future time-delay measurements of strongly lensed quasar-elliptical galaxy systems from the Large Synoptic Survey Telescope and supernova observations from the Dark Energy Survey. The test only relies on geometric optics. It is independent of the energy contents of the universe and the validity of the Einstein equation on cosmological scales. The study comprises two levels: testing the FLRW metric through the distance sum rule (DSR) and determining/constraining cosmic curvature. We propose an effective and efficient (redshift) evolution model for performing the former test, which allows us to concretely specify the violation criterion for the FLRW DSR. If the FLRW metric is consistent with the observations, then on the second level the cosmic curvature parameter will be constrained to ∼0.057 or ∼0.041 (1 σ ), depending on the availability of high-redshift supernovae, which is much more stringent than current model-independent techniques. We also show that the bias in the time-delay method might be well controlled, leading to robust results. The proposed method is a new independent tool for both testing the fundamental assumptions of homogeneity and isotropy in cosmology and for determining cosmic curvature. It is complementary to cosmic microwave background plus baryon acoustic oscillation analyses, which normally assume a cosmological model with dark energy domination in the late-time universe.

  18. Test of the FLRW Metric and Curvature with Strong Lens Time Delays

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Kai [School of Science, Wuhan University of Technology, Wuhan 430070 (China); Li, Zhengxiang; Wang, Guo-Jian [Department of Astronomy, Beijing Normal University, Beijing 100875 (China); Fan, Xi-Long, E-mail: liaokai@whut.edu.cn, E-mail: xilong.fan@glasgow.ac.uk [Department of Physics and Mechanical and Electrical Engineering, Hubei University of Education, Wuhan 430205 (China)

    2017-04-20

    We present a new model-independent strategy for testing the Friedmann–Lemaître–Robertson–Walker (FLRW) metric and constraining cosmic curvature, based on future time-delay measurements of strongly lensed quasar-elliptical galaxy systems from the Large Synoptic Survey Telescope and supernova observations from the Dark Energy Survey. The test only relies on geometric optics. It is independent of the energy contents of the universe and the validity of the Einstein equation on cosmological scales. The study comprises two levels: testing the FLRW metric through the distance sum rule (DSR) and determining/constraining cosmic curvature. We propose an effective and efficient (redshift) evolution model for performing the former test, which allows us to concretely specify the violation criterion for the FLRW DSR. If the FLRW metric is consistent with the observations, then on the second level the cosmic curvature parameter will be constrained to ∼0.057 or ∼0.041 (1 σ ), depending on the availability of high-redshift supernovae, which is much more stringent than current model-independent techniques. We also show that the bias in the time-delay method might be well controlled, leading to robust results. The proposed method is a new independent tool for both testing the fundamental assumptions of homogeneity and isotropy in cosmology and for determining cosmic curvature. It is complementary to cosmic microwave background plus baryon acoustic oscillation analyses, which normally assume a cosmological model with dark energy domination in the late-time universe.

  19. RlmCD-mediated U747 methylation promotes efficient G748 methylation by methyltransferase RlmAII in 23S rRNA in Streptococcus pneumoniae; interplay between two rRNA methylations responsible for telithromycin susceptibility.

    Science.gov (United States)

    Shoji, Tatsuma; Takaya, Akiko; Sato, Yoshiharu; Kimura, Satoshi; Suzuki, Tsutomu; Yamamoto, Tomoko

    2015-10-15

    Adenine at position 752 in a loop of helix 35 from positions 745 to 752 in domain II of 23S rRNA is involved in binding to the ribosome of telithromycin (TEL), a member of ketolides. Methylation of guanine at position 748 by the intrinsic methyltransferase RlmA(II) enhances binding of telithromycin (TEL) to A752 in Streptococcus pneumoniae. We have found that another intrinsic methylation of the adjacent uridine at position 747 enhances G748 methylation by RlmA(II), rendering TEL susceptibility. U747 and another nucleotide, U1939, were methylated by the dual-specific methyltransferase RlmCD encoded by SP_1029 in S. pneumoniae. Inactivation of RlmCD reduced N1-methylated level of G748 by RlmA(II) in vivo, leading to TEL resistance when the nucleotide A2058, located in domain V of 23S rRNA, was dimethylated by the dimethyltransferase Erm(B). In vitro methylation of rRNA showed that RlmA(II) activity was significantly enhanced by RlmCD-mediated pre-methylation of 23S rRNA. These results suggest that RlmCD-mediated U747 methylation promotes efficient G748 methylation by RlmA(II), thereby facilitating TEL binding to the ribosome. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. A Novel Association between Two Trypanosome-Specific Factors and the Conserved L5-5S rRNA Complex

    Science.gov (United States)

    Ciganda, Martin; Prohaska, Kimberly; Hellman, Kristina; Williams, Noreen

    2012-01-01

    P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are involved in and essential for ribosome biogenesis. The proteins interact with the 5S rRNA with nearly identical binding characteristics. We have shown that this interaction is achieved mainly through the LoopA region of the RNA, but P34 and P37 also protect the L5 binding site located on LoopC. We now provide evidence to show that these factors form a novel pre-ribosomal particle through interactions with both 5S rRNA and the L5 ribosomal protein. Further in silico and in vitro analysis of T. brucei L5 indicates a lower affinity for 5S rRNA than expected, based on other eukaryotic L5 proteins. We hypothesize that P34 and P37 complement L5 and bridge the interaction with 5S rRNA, stabilizing it and aiding in the early steps of ribosome biogenesis. PMID:22859981

  1. Downregulation of rRNA transcription triggers cell differentiation.

    Directory of Open Access Journals (Sweden)

    Yuki Hayashi

    Full Text Available Responding to various stimuli is indispensable for the maintenance of homeostasis. The downregulation of ribosomal RNA (rRNA transcription is one of the mechanisms involved in the response to stimuli by various cellular processes, such as cell cycle arrest and apoptosis. Cell differentiation is caused by intra- and extracellular stimuli and is associated with the downregulation of rRNA transcription as well as reduced cell growth. The downregulation of rRNA transcription during differentiation is considered to contribute to reduced cell growth. However, the downregulation of rRNA transcription can induce various cellular processes; therefore, it may positively regulate cell differentiation. To test this possibility, we specifically downregulated rRNA transcription using actinomycin D or a siRNA for Pol I-specific transcription factor IA (TIF-IA in HL-60 and THP-1 cells, both of which have differentiation potential. The inhibition of rRNA transcription induced cell differentiation in both cell lines, which was demonstrated by the expression of the common differentiation marker CD11b. Furthermore, TIF-IA knockdown in an ex vivo culture of mouse hematopoietic stem cells increased the percentage of myeloid cells and reduced the percentage of immature cells. We also evaluated whether differentiation was induced via the inhibition of cell cycle progression because rRNA transcription is tightly coupled to cell growth. We found that cell cycle arrest without affecting rRNA transcription did not induce differentiation. To the best of our knowledge, our results demonstrate the first time that the downregulation of rRNA levels could be a trigger for the induction of differentiation in mammalian cells. Furthermore, this phenomenon was not simply a reflection of cell cycle arrest. Our results provide a novel insight into the relationship between rRNA transcription and cell differentiation.

  2. A Comparison between Fixed Priority and EDF Scheduling accounting for Cache Related Pre-emption Delays

    Directory of Open Access Journals (Sweden)

    Will Lunniss

    2014-04-01

    Full Text Available In multitasking real-time systems, the choice of scheduling algorithm is an important factor to ensure that response time requirements are met while maximising limited system resources. Two popular scheduling algorithms include fixed priority (FP and earliest deadline first (EDF. While they have been studied in great detail before, they have not been compared when taking into account cache related pre-emption delays (CRPD. Memory and cache are split into a number of blocks containing instructions and data. During a pre-emption, cache blocks from the pre-empting task can evict those of the pre-empted task. When the pre-empted task is resumed, if it then has to re-load the evicted blocks, CRPD are introduced which then affect the schedulability of the task. In this paper we compare FP and EDF scheduling algorithms in the presence of CRPD using the state-of-the-art CRPD analysis. We find that when CRPD is accounted for, the performance gains offered by EDF over FP, while still notable, are diminished. Furthermore, we find that under scenarios that cause relatively high CRPD, task layout optimisation techniques can be applied to allow FP to schedule tasksets at a similar processor utilisation to EDF. Thus making the choice of the task layout in memory as important as the choice of scheduling algorithm. This is very relevant for industry, as it is much cheaper and simpler to adjust the task layout through the linker than it is to switch the scheduling algorithm.

  3. Archaeal rRNA operons, intron splicing and homing endonucleases, RNA polymerase operons and phylogeny

    DEFF Research Database (Denmark)

    Garrett, Roger Antony; Aagaard, Claus Sindbjerg; Andersen, Morten

    1994-01-01

    Over the past decade our laboratory has had a strong interest in defining the phylogenetic status of the archaea. This has involved determining and analysing the sequences of operons of both rRNAs and RNA polymerases and it led to the discovery of the first archaeal rRNA intron. What follows...

  4. "DETERMINANTS OF PREHOSPITAL DELAY IN PATIENTS WITH ACUTE MYOCARDIAL INFARCTION"

    Directory of Open Access Journals (Sweden)

    M. Alidoosti

    2004-05-01

    Full Text Available Determination of pre-hospital delay time of patients with acute myocardial infarction and seeking ways of speeding up the time for reperfusion is an important factor to lower mortality in these patients. This is a cross-sectional study to determine pre-hospital delay time, its components, and related causes and conditions, obtained in 375 patients with prolonged chest pain referred to four hospitals of Tehran University of Medical Sciences. Means of transport to hospital, reasons of ambulance disuse, decision time by the patient and finally the entire time of pre-hospital delay were specified. Suspected factors related to delays of more than 2 and 6 h were scrutinized with chi-square test. Rate of ambulance utility (18.9% directly correlated with age of patients (P<0.05. Principal motives to disuse ambulance insuccession were unrememberance (33.7%, access to private vehicle (32.8% and supposition of sufficient speed of personal reference (18.9%. Pre-hospital delay time was 8.1 ± 9.1 h (mean ± SD in whole patients and 7.6 ± 9.1 h in those with acute myocardial infarction. Delays of more than 2 and 6 hoccurred in 67.5% and 33.6% of patients, respectively. Decision time constitute three fourth of whole pre-hospital delay and was correlated with female gender, older age, history of diabetes, lower level of literacy and nocturnal onset of symptoms. In conclusion, a significant number of patients with acute myocardial infarction have pre-hospital delay of more than 2 and even 6 h, when golden time for thrombolytic therapy has already been elapsed.

  5. Patient delay is the main cause of treatment delay in acute limb ischemia: an investigation of pre- and in-hospital time delay

    DEFF Research Database (Denmark)

    Londero, Louise Skovgaard; Nørgaard, Birgitte; Houlind, Kim Christian

    2014-01-01

    Abstract BACKGROUND: The prognosis of acute limb ischemia is severe, with amputation rates of up to 25% and in-hospital mortality of 9-15%. Delay in treatment increases the risk of major amputation and may be present at different stages, including patient delay, doctors´ delay and waiting time...... in the emergency department. It is important to identify existing problems in order to reduce time delay. The aim of this study was to collect data for patients with acute limb ischemia and to evaluate the time delay between the different events from onset of symptoms to specialist evaluation and further treatment...... (median (range)) was identified. From onset of symptoms to first contact with a doctor the time for all patients were 24 (0-1200) hours. Thirty patients needed immediate intervention. In the group of fourteen patients who had immediate operation, the median time from vascular evaluation...

  6. Emergency surgery pre-operative delays - realities and economic impacts.

    Science.gov (United States)

    O'Leary, D P; Beecher, S; McLaughlin, R

    2014-12-01

    A key principle of acute surgical service provision is the establishment of a distinct patient flow process and an emergency theatre. Time-to-theatre (TTT) is a key performance indicator of theatre efficiency. The combined impacts of an aging population, increasing demands and complexity associated with centralisation of emergency and oncology services has placed pressure on emergency theatre access. We examined our institution's experience with running a designated emergency theatre for acute surgical patients. A retrospective review of an electronic prospectively maintained database was performed between 1/1/12 and 31/12/13. A cost analysis was conducted to assess the economic impact of delayed TTT, with every 24hr delay incurring the cost of an additional overnight bed. Delays and the economic effects were assessed only after the first 24 h as an in-patient had elapsed. In total, 7041 procedures were performed. Overall mean TTT was 26 h, 2 min. There were significant differences between different age groups, with those aged under 16 year and over 65 having mean TTT at 6 h, 34 min (95% C.I. 0.51-2.15, p 65 years age group had a mean TTT of 23 h, 41 min which was significantly longer than the overall mean TTT Vascular and urological emergencies are significantly disadvantaged in competition with other services for a shared emergency theatre. The economic impact of delayed TTT was calculated at €7,116,000, or €9880/day of additional costs generated from delayed TTT over a 24 month period. One third of patients waited longer than 24 h for emergency surgery, with the elderly disproportionately represented in this group. Aside from the clinical risks of delayed and out of hours surgery, such practices incur significant additional costs. New strategies must be devised to ensure efficient access to emergency theatres, investment in such services is likely to be financially and clinically beneficial. Copyright © 2014 Surgical Associates Ltd. Published by Elsevier

  7. Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion.

    Science.gov (United States)

    Zhao, Shanrong; Zhang, Ying; Gamini, Ramya; Zhang, Baohong; von Schack, David

    2018-03-19

    To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification. For blood- and colon-derived RNAs, we found that 220% and 50% more reads, respectively, would have to be sequenced to achieve the same level of exonic coverage in the rRNA depletion method compared with the polyA+ selection method. Therefore, in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing. Our evaluation revealed that a small number of lncRNAs and small RNAs made up a large fraction of the reads in the rRNA depletion RNA sequencing data. Thus, we recommend that these RNAs are specifically depleted to improve the sequencing depth of the remaining RNAs.

  8. Phylogenetic relationships of Salmonella based on rRNA sequences

    DEFF Research Database (Denmark)

    Christensen, H.; Nordentoft, Steen; Olsen, J.E.

    1998-01-01

    separated by 16S rRNA analysis and found to be closely related to the Escherichia coli and Shigella complex by both 16S and 23S rRNA analyses. The diphasic serotypes S. enterica subspp. I and VI were separated from the monophasic serotypes subspp. IIIa and IV, including S. bongori, by 23S rRNA sequence...

  9. Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

    Science.gov (United States)

    Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

    2002-12-01

    The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.

  10. rRNA maturation in yeast cells depleted of large ribosomal subunit proteins.

    Directory of Open Access Journals (Sweden)

    Gisela Pöll

    Full Text Available The structural constituents of the large eukaryotic ribosomal subunit are 3 ribosomal RNAs, namely the 25S, 5.8S and 5S rRNA and about 46 ribosomal proteins (r-proteins. They assemble and mature in a highly dynamic process that involves more than 150 proteins and 70 small RNAs. Ribosome biogenesis starts in the nucleolus, continues in the nucleoplasm and is completed after nucleo-cytoplasmic translocation of the subunits in the cytoplasm. In this work we created 26 yeast strains, each of which conditionally expresses one of the large ribosomal subunit (LSU proteins. In vivo depletion of the analysed LSU r-proteins was lethal and led to destabilisation and degradation of the LSU and/or its precursors. Detailed steady state and metabolic pulse labelling analyses of rRNA precursors in these mutant strains showed that LSU r-proteins can be grouped according to their requirement for efficient progression of different steps of large ribosomal subunit maturation. Comparative analyses of the observed phenotypes and the nature of r-protein-rRNA interactions as predicted by current atomic LSU structure models led us to discuss working hypotheses on i how individual r-proteins control the productive processing of the major 5' end of 5.8S rRNA precursors by exonucleases Rat1p and Xrn1p, and ii the nature of structural characteristics of nascent LSUs that are required for cytoplasmic accumulation of nascent subunits but are nonessential for most of the nuclear LSU pre-rRNA processing events.

  11. Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

    Science.gov (United States)

    Bodilis, Josselin; Nsigue-Meilo, Sandrine; Besaury, Ludovic; Quillet, Laurent

    2012-01-01

    Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies. PMID:22545126

  12. Choice between delayed food and immediate oxycodone in rats.

    Science.gov (United States)

    Secci, Maria E; Factor, Julie A; Schindler, Charles W; Panlilio, Leigh V

    2016-12-01

    The choice to seek immediate drug effects instead of more meaningful but delayed rewards is a defining feature of addiction. To develop a rodent model of this behavior, we allowed rats to choose between immediate intravenous delivery of the prescription opioid oxycodone (50 μg/kg) and delayed delivery of palatable food pellets. Rats preferred food at delays up to 30 s, but they chose oxycodone and food equally at 60-s delay and preferred oxycodone over food at 120-s delay. Comparison of food-drug choice, food-only, and drug-only conditions indicated that food availability decreased drug intake, but drug availability increased food intake. In the food-only condition, food was effective as a reinforcer even when delayed by 120 s. Pre-session feeding with chow slowed acquisition of food and drug self-administration, but did not affect choice. To establish procedures for testing potential anti-addiction medications, noncontingent pre-treatment with oxycodone or naltrexone (analogous to substitution and antagonist therapies, respectively) were tested on a baseline in which oxycodone was preferred over delayed food. Naltrexone pre-treatment decreased drug intake and increased food intake. Oxycodone pre-treatment decreased drug intake, but also produced extended periods with no food or drug responding. These findings show that the contingencies that induce preference for drugs over more meaningful but less immediate rewards in humans can be modeled in rodents, and they suggest that the model could be useful for assessing the therapeutic potential of treatments and exploring the underlying behavioral and neural mechanisms involved in addiction.

  13. Diversity of 23S rRNA genes within individual prokaryotic genomes.

    Directory of Open Access Journals (Sweden)

    Anna Pei

    Full Text Available BACKGROUND: The concept of ribosomal constraints on rRNA genes is deduced primarily based on the comparison of consensus rRNA sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rRNA operons. METHODOLOGY/PRINCIPAL FINDINGS: Using the 23S rRNA gene as an example, we analyzed the diversity among individual rRNA genes within a genome. Of 184 prokaryotic species containing multiple 23S rRNA genes, diversity was observed in 113 (61.4% genomes (mean 0.40%, range 0.01%-4.04%. Significant (1.17%-4.04% intragenomic variation was found in 8 species. In 5 of the 8 species, the diversity in the primary structure had only minimal effect on the secondary structure (stem versus loop transition. In the remaining 3 species, the diversity significantly altered local secondary structure, but the alteration appears minimized through complex rearrangement. Intervening sequences (IVS, ranging between 9 and 1471 nt in size, were found in 7 species. IVS in Deinococcus radiodurans and Nostoc sp. encode transposases. T. tengcongensis was the only species in which intragenomic diversity >3% was observed among 4 paralogous 23S rRNA genes. CONCLUSIONS/SIGNIFICANCE: These findings indicate tight ribosomal constraints on individual 23S rRNA genes within a genome. Although classification using primary 23S rRNA sequences could be erroneous, significant diversity among paralogous 23S rRNA genes was observed only once in the 184 species analyzed, indicating little overall impact on the mainstream of 23S rRNA gene-based prokaryotic taxonomy.

  14. Risk-factors for surgical delay following hip fracture.

    Science.gov (United States)

    Sanz-Reig, J; Salvador Marín, J; Ferrández Martínez, J; Orozco Beltrán, D; Martínez López, J F

    To identify pre-operative risk factors for surgical delay of more than 2 days after admission in patients older than 65 years with a hip fracture. A prospective observational study was conducted on 180 hip fractures in patients older than 65 years of age admitted to our hospital from January 2015 to April 2016. The data recorded included, patient demographics, day of admission, pre-fracture comorbidities, mental state, level of mobility and physical function, type of fracture, antiaggregant and anticoagulant medication, pre-operative haemoglobin value, type of treatment, and surgical delay. The mean age of the patients was 83.7 years. The mean Charlson Index was 2.8. The pre-fracture baseline co-morbidities were equal or greater than 2 in 70% of cases. Mean timing of surgery was 3.1 days. At the time of admission, 122 (67.7%) patients were fit for surgery, of which 80 (44.4%) underwent surgery within 2 days. A Charlson index greater than 2, anticoagulant therapy, and admission on Thursday to Saturday, were independently associated with a surgical delay greater than 2 days. The rate of hip fracture patients undergoing surgery within 2 days is low. Risk factors associated to surgical delay are non-modifiable. However, their knowledge should allow the development of protocols that can reduce surgical delay in this group of patients. Copyright © 2017 SECOT. Publicado por Elsevier España, S.L.U. All rights reserved.

  15. A Systematic Review of Barriers to Breast Cancer Care in Developing Countries Resulting in Delayed Patient Presentation

    Directory of Open Access Journals (Sweden)

    Ketan Sharma

    2012-01-01

    Full Text Available Background. Within the developing world, many personal, sociocultural, and economic factors cause delayed patient presentation, a prolonged interval from initial symptom discovery to provider presentation. Understanding these barriers to care is crucial to optimizing interventions that pre-empt patient delay. Methods. A systematic review was conducted querying: PubMed, Embase, Web of Science, CINAHL, Cochrane Library, J East, CAB, African Index Medicus, and LiLACS. Of 763 unique abstracts, 122 were extracted for full review and 13 included in final analysis. Results. Studies posed variable risks of bias and produced mixed results. There is strong evidence that lower education level and lesser income status contribute to patient delay. There is weaker and, sometimes, contradictory evidence that other factors may also contribute. Discussion. Poverty emerges as the underlying common denominator preventing earlier presentation in these settings. The evidence for sociocultural variables is less strong, but may reflect current paucity of high-quality research. Conflicting results may be due to heterogeneity of the developing world itself. Conclusion. Future research is required that includes patients with and without delay, utilizes a validated questionnaire, and controls for potential confounders. Current evidence suggests that interventions should primarily increase proximal and affordable healthcare access and secondarily enhance breast cancer awareness, to productively reduce patient delay.

  16. Myb-binding protein 1a (Mybbp1a) regulates levels and processing of pre-ribosomal RNA.

    Science.gov (United States)

    Hochstatter, Julia; Hölzel, Michael; Rohrmoser, Michaela; Schermelleh, Lothar; Leonhardt, Heinrich; Keough, Rebecca; Gonda, Thomas J; Imhof, Axel; Eick, Dirk; Längst, Gernot; Németh, Attila

    2012-07-13

    Ribosomal RNA gene transcription, co-transcriptional processing, and ribosome biogenesis are highly coordinated processes that are tightly regulated during cell growth. In this study we discovered that Mybbp1a is associated with both the RNA polymerase I complex and the ribosome biogenesis machinery. Using a reporter assay that uncouples transcription and RNA processing, we show that Mybbp1a represses rRNA gene transcription. In addition, overexpression of the protein reduces RNA polymerase I loading on endogenous rRNA genes as revealed by chromatin immunoprecipitation experiments. Accordingly, depletion of Mybbp1a results in an accumulation of the rRNA precursor in vivo but surprisingly also causes growth arrest of the cells. This effect can be explained by the observation that the modulation of Mybbp1a protein levels results in defects in pre-rRNA processing within the cell. Therefore, the protein may play a dual role in the rRNA metabolism, potentially linking and coordinating ribosomal DNA transcription and pre-rRNA processing to allow for the efficient synthesis of ribosomes.

  17. CRM1 and its ribosome export adaptor NMD3 localize to the nucleolus and affect rRNA synthesis.

    Science.gov (United States)

    Bai, Baoyan; Moore, Henna M; Laiho, Marikki

    2013-01-01

    CRM1 is an export factor that together with its adaptor NMD3 transports numerous cargo molecules from the nucleus to cytoplasm through the nuclear pore. Previous studies have suggested that CRM1 and NMD3 are detected in the nucleolus. However, their localization with subnucleolar domains or participation in the activities of the nucleolus are unclear. We demonstrate here biochemically and using imaging analyses that CRM1 and NMD3 co-localize with nucleolar marker proteins in the nucleolus. In particular, their nucleolar localization is markedly increased by inhibition of RNA polymerase I (Pol I) transcription by actinomycin D or by silencing Pol I catalytic subunit, RPA194. We show that CRM1 nucleolar localization is dependent on its activity and the expression of NMD3, whereas NMD3 nucleolar localization is independent of CRM1. This suggests that NMD3 provides nucleolar tethering of CRM1. While inhibition of CRM1 by leptomycin B inhibited processing of 28S ribosomal (r) RNA, depletion of NMD3 did not, suggesting that their effects on 28S rRNA processing are distinct. Markedly, depletion of NMD3 and inhibition of CRM1 reduced the rate of pre-47S rRNA synthesis. However, their inactivation did not lead to nucleolar disintegration, a hallmark of Pol I transcription stress, suggesting that they do not directly regulate transcription. These results indicate that CRM1 and NMD3 have complex functions in pathways that couple rRNA synthetic and processing engines and that the rRNA synthesis rate may be adjusted according to proficiency in rRNA processing and export.

  18. Spouses' conceptions of the pre-hospital phase when their partners suffered an acute myocardial infarction--a qualitative analysis.

    Science.gov (United States)

    Johansson, Ingela; Swahn, Eva; Strömberg, Anna

    2008-09-01

    Delay from onset of acute myocardial infarction symptoms to the delivery of medical care is a major determinant of prognosis. Although studies have explored patient reasons for delay, there are only limited data concerning experiences of the spouse. Was to describe spouses' conceptions of the pre-hospital phase when their partners suffered an acute myocardial infarction. A phenomenographic approach was applied. Fifteen spouses were interviewed rational, and consulting others. The category respecting independence contained: accepting the need for control, marital roles and experiences, restraining emotions, and seeking agreement. Our findings suggest that spouses have a strong influence on the course of events. When accepting the partner's need for control through following earlier marital roles and experiences, restraining own emotions and seeking agreement, this seemed to contribute to delay. However, when the spouse was resourceful by sharing the experience, having knowledge, understanding the severity, being rational and consulting others when needed, this seemed to have a positive influence on the pre-hospital time.

  19. A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis.

    Science.gov (United States)

    Whelan, Fiona J; Surette, Michael G

    2017-08-14

    Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses. The short-read library 16S rRNA gene sequencing pipeline (sl1p, pronounced "slip") was designed with the purpose of mitigating this lack of reproducibility by combining pre-existing tools into a computational pipeline. This pipeline automates the processing of raw 16S rRNA gene sequencing data to create human-readable tables, graphs, and figures to make the collected data more readily accessible. Data generated from mock communities were compared using eight OTU clustering algorithms, two taxon assignment approaches, and three 16S rRNA gene reference databases. While all of these algorithms and options are available to sl1p users, through testing with human-associated mock communities, AbundantOTU+, the RDP Classifier, and the Greengenes 2011 reference database were chosen as sl1p's defaults based on their ability to best represent the known input communities. sl1p promotes reproducible research by providing a comprehensive log file, and reduces the computational knowledge needed by the user to process next-generation sequencing data. sl1p is freely available at https://bitbucket.org/fwhelan/sl1p .

  20. Reperfusion delay in patients treated with primary percutaneous coronary intervention

    DEFF Research Database (Denmark)

    Schoos, Mikkel M; Sejersten, Maria; Hvelplund, Anders

    2012-01-01

    identification number to emergency medical services (EMS) and National Board of Health databases in the period of 2005-2008. Patients were stratified according to transfer distances to PPCI into zone 1 (0-25 km), zone 2 (65-100 km) and zone 3 (101-185 km) and according to referral by pre-hospital triage. System...... the local hospital (219 (171-250)). System delay was an independent predictor of mortality (ppatients. PCI-related delay exceeded European Society of Cardiology (ESC) guidelines for patients living >100 km away and for non-directly referred......BACKGROUND: Reperfusion delay in ST-segment elevation myocardial infarction (STEMI) predicts adverse outcome. We evaluated time from alarm call (system delay) and time from first medical contact (PCI-related delay), where fibrinolysis could be initiated, to balloon inflation in a pre...

  1. Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Hiraku Takada

    Full Text Available Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon, within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons

  2. Comparative analysis of the 5S rRNA and its associated proteins reveals unique primitive rather than parasitic features in Giardia lamblia.

    Science.gov (United States)

    Feng, Jin-Mei; Sun, Jun; Xin, De-Dong; Wen, Jian-Fan

    2012-01-01

    5S rRNA is a highly conserved ribosomal component. Eukaryotic 5S rRNA and its associated proteins (5S rRNA system) have become very well understood. Giardia lamblia was thought by some researchers to be the most primitive extant eukaryote while others considered it a highly evolved parasite. Previous reports have indicated that some aspects of its 5S rRNA system are simpler than that of common eukaryotes. We here explore whether this is true to its entire system, and whether this simplicity is a primitive or parasitic feature. By collecting and confirming pre-existing data and identifying new data, we obtained almost complete datasets of the system of three isolates of G. lamblia, two other parasitic excavates (Trichomonas vaginalis, Trypanosoma cruzi), and one free-living one (Naegleria gruberi). After comprehensively comparing each aspect of the system among these excavates and also with those of archaea and common eukaryotes, we found all the three Giardia isolates to harbor a same simplified 5S rRNA system, which is not only much simpler than that of common eukaryotes but also the simplest one among those of these excavates, and is surprisingly very similar to that of archaea; we also found among these excavates the system in parasitic species is not necessarily simpler than that in free-living species, conversely, the system of free-living species is even simpler in some respects than those of parasitic ones. The simplicity of Giardia 5S rRNA system should be considered a primitive rather than parasitically-degenerated feature. Therefore, Giardia 5S rRNA system might be a primitive system that is intermediate between that of archaea and the common eukaryotic model system, and it may reflect the evolutionary history of the eukaryotic 5S rRNA system from the archaeal form. Our results also imply G. lamblia might be a primitive eukaryote with secondary parasitically-degenerated features.

  3. Strong Tracking Filter for Nonlinear Systems with Randomly Delayed Measurements and Correlated Noises

    Directory of Open Access Journals (Sweden)

    Hongtao Yang

    2018-01-01

    Full Text Available This paper proposes a novel strong tracking filter (STF, which is suitable for dealing with the filtering problem of nonlinear systems when the following cases occur: that is, the constructed model does not match the actual system, the measurements have the one-step random delay, and the process and measurement noises are correlated at the same epoch. Firstly, a framework of decoupling filter (DF based on equivalent model transformation is derived. Further, according to the framework of DF, a new extended Kalman filtering (EKF algorithm via using first-order linearization approximation is developed. Secondly, the computational process of the suboptimal fading factor is derived on the basis of the extended orthogonality principle (EOP. Thirdly, the ultimate form of the proposed STF is obtained by introducing the suboptimal fading factor into the above EKF algorithm. The proposed STF can automatically tune the suboptimal fading factor on the basis of the residuals between available and predicted measurements and further the gain matrices of the proposed STF tune online to improve the filtering performance. Finally, the effectiveness of the proposed STF has been proved through numerical simulation experiments.

  4. Identification of pathogenic Nocardia species by reverse line blot hybridization targeting the 16S rRNA and 16S-23S rRNA gene spacer regions.

    Science.gov (United States)

    Xiao, Meng; Kong, Fanrong; Sorrell, Tania C; Cao, Yongyan; Lee, Ok Cha; Liu, Ying; Sintchenko, Vitali; Chen, Sharon C A

    2010-02-01

    Although 16S rRNA gene sequence analysis is employed most often for the definitive identification of Nocardia species, alternate molecular methods and polymorphisms in other gene targets have also enabled species determinations. We evaluated a combined Nocardia PCR-based reverse line blot (RLB) hybridization assay based on 16S and 16S-23S rRNA gene spacer region polymorphisms to identify 12 American Type Culture Collection and 123 clinical Nocardia isolates representing 14 species; results were compared with results from 16S rRNA gene sequencing. Thirteen 16S rRNA gene-based (two group-specific and 11 species-specific) and five 16S-23S spacer-targeted (two taxon-specific and three species-specific) probes were utilized. 16S rRNA gene-based probes correctly identified 124 of 135 isolates (sensitivity, 92%) but were unable to identify Nocardia paucivorans strains (n = 10 strains) and a Nocardia asteroides isolate with a novel 16S rRNA gene sequence. Nocardia farcinica and Nocardia cyriacigeorgica strains were identified by the sequential use of an N. farcinica-"negative" probe and a combined N. farcinica/N. cyriacigeorgica probe. The assay specificity was high (99%) except for weak cross-reactivity between the Nocardia brasiliensis probe with the Nocardia thailandica DNA product; however, cross-hybridization with closely related nontarget species may occur. The incorporation of 16S-23S rRNA gene spacer-based probes enabled the identification of all N. paucivorans strains. The overall sensitivity using both probe sets was >99%. Both N. farcinica-specific 16S-23S rRNA gene spacer-directed probes were required to identify all N. farcinica stains by using this probe set. The study demonstrates the utility of a combined PCR/RLB assay for the identification of clinically relevant Nocardia species and its potential for studying subtypes of N. farcinica. Where species assignment is ambiguous or not possible, 16S rRNA gene sequencing is recommended.

  5. Eukaryotic 5S rRNA biogenesis

    Science.gov (United States)

    Ciganda, Martin; Williams, Noreen

    2012-01-01

    The ribosome is a large complex containing both protein and RNA which must be assembled in a precise manner to allow proper functioning in the critical role of protein synthesis. 5S rRNA is the smallest of the RNA components of the ribosome, and although it has been studied for decades, we still do not have a clear understanding of its function within the complex ribosome machine. It is the only RNA species that binds ribosomal proteins prior to its assembly into the ribosome. Its transport into the nucleolus requires this interaction. Here we present an overview of some of the key findings concerning the structure and function of 5S rRNA and how its association with specific proteins impacts its localization and function. PMID:21957041

  6. Overaccumulation of the chloroplast antisense RNA AS5 is correlated with decreased abundance of 5S rRNA in vivo and inefficient 5S rRNA maturation in vitro

    Science.gov (United States)

    Sharwood, Robert E.; Hotto, Amber M.; Bollenbach, Thomas J.; Stern, David B.

    2011-01-01

    Post-transcriptional regulation in the chloroplast is exerted by nucleus-encoded ribonucleases and RNA-binding proteins. One of these ribonucleases is RNR1, a 3′-to-5′ exoribonuclease of the RNase II family. We have previously shown that Arabidopsis rnr1-null mutants exhibit specific abnormalities in the expression of the rRNA operon, including the accumulation of precursor 23S, 16S, and 4.5S species and a concomitant decrease in the mature species. 5S rRNA transcripts, however, accumulate to a very low level in both precursor and mature forms, suggesting that they are unstable in the rnr1 background. Here we demonstrate that rnr1 plants overaccumulate an antisense RNA, AS5, that is complementary to the 5S rRNA, its intergenic spacer, and the downstream trnR gene, which encodes tRNAArg, raising the possibility that AS5 destabilizes 5S rRNA or its precursor and/or blocks rRNA maturation. To investigate this, we used an in vitro system that supports 5S rRNA and trnR processing. We show that AS5 inhibits 5S rRNA maturation from a 5S-trnR precursor, and shorter versions of AS5 demonstrate that inhibition requires intergenic sequences. To test whether the sense and antisense RNAs form double-stranded regions in vitro, treatment with the single-strand-specific mung bean nuclease was used. These results suggest that 5S–AS5 duplexes interfere with a sense-strand secondary structure near the endonucleolytic cleavage site downstream from the 5S rRNA coding region. We hypothesize that these duplexes are degraded by a dsRNA-specific ribonuclease in vivo, contributing to the 5S rRNA deficiency observed in rnr1. PMID:21148395

  7. Motor skill delays in pre-school children with leukemia one year after treatment: Hematopoietic stem cell transplantation therapy as an important risk factor.

    Science.gov (United States)

    Taverna, Livia; Tremolada, Marta; Bonichini, Sabrina; Tosetto, Barbara; Basso, Giuseppe; Messina, Chiara; Pillon, Marta

    2017-01-01

    CNS-directed therapies for the treatment of leukemia can adversely affect the acquisition of new skills, such as reading/writing and math. Two years after the end of treatments, children show gross and fine motor skill delays that may persist even when patients are considered healed. The goal of the present study was to assess motor skills difficulties in pre-school children with leukemia one year after treatment. Particular attention has been paid to those patients who had undergone Hematopoietic Stem Cell Transplantation (HSCT) and to the relationship between motor delays and age bands. Participants were 60 children (median age of 5; inter quartile range: 3.07-5.76), including 31 females and 29 males, 91.7% of them were affected by acute lymphoblastic leukemia (ALL), and 8.3% by acute myeloid leukemia (AML). Five children had undergone HCST. Parents were interviewed by Vineland Adaptive Behavior Scales (VABS) on children's motor skills and filled in the Italian Temperament Questionnaire (QUIT). VABS's total scores were converted into equivalent mental age scores (EMA). A score difference of at least three months between current age and equivalent mental age was considered a developmental delay. Non-parametric analyses were run to understand if HSCT treatment and a specific age band influence children's motor skills. Significant delays were found in global motor skills (56.7%) as well as in fine and gross motor domains. Mann Whitney U tests showed that children with HSCT were reported to have lower gross motor mean ranks (U = 62; p = 0.004; Mean rank = 15.40) than peers without HSCT (Mean rank = 31.87) and lower mean rank values on motor temperament scale (U = 9; p = 0.003; HSCT Mean rank = 4.75 versus no HSCT Mean rank = 27.81). Kruskal Wallis' tests identified the high risk treatment showing that HSCT experience negatively impacted the motor skills and temperamental motor activity of pre-school children one year after the diagnosis of leukemia.

  8. Motor skill delays in pre-school children with leukemia one year after treatment: Hematopoietic stem cell transplantation therapy as an important risk factor.

    Directory of Open Access Journals (Sweden)

    Livia Taverna

    Full Text Available CNS-directed therapies for the treatment of leukemia can adversely affect the acquisition of new skills, such as reading/writing and math. Two years after the end of treatments, children show gross and fine motor skill delays that may persist even when patients are considered healed. The goal of the present study was to assess motor skills difficulties in pre-school children with leukemia one year after treatment. Particular attention has been paid to those patients who had undergone Hematopoietic Stem Cell Transplantation (HSCT and to the relationship between motor delays and age bands. Participants were 60 children (median age of 5; inter quartile range: 3.07-5.76, including 31 females and 29 males, 91.7% of them were affected by acute lymphoblastic leukemia (ALL, and 8.3% by acute myeloid leukemia (AML. Five children had undergone HCST. Parents were interviewed by Vineland Adaptive Behavior Scales (VABS on children's motor skills and filled in the Italian Temperament Questionnaire (QUIT. VABS's total scores were converted into equivalent mental age scores (EMA. A score difference of at least three months between current age and equivalent mental age was considered a developmental delay. Non-parametric analyses were run to understand if HSCT treatment and a specific age band influence children's motor skills. Significant delays were found in global motor skills (56.7% as well as in fine and gross motor domains. Mann Whitney U tests showed that children with HSCT were reported to have lower gross motor mean ranks (U = 62; p = 0.004; Mean rank = 15.40 than peers without HSCT (Mean rank = 31.87 and lower mean rank values on motor temperament scale (U = 9; p = 0.003; HSCT Mean rank = 4.75 versus no HSCT Mean rank = 27.81. Kruskal Wallis' tests identified the high risk treatment showing that HSCT experience negatively impacted the motor skills and temperamental motor activity of pre-school children one year after the diagnosis of leukemia.

  9. Motor skill delays in pre-school children with leukemia one year after treatment: Hematopoietic stem cell transplantation therapy as an important risk factor

    Science.gov (United States)

    Bonichini, Sabrina; Tosetto, Barbara; Basso, Giuseppe; Messina, Chiara; Pillon, Marta

    2017-01-01

    CNS-directed therapies for the treatment of leukemia can adversely affect the acquisition of new skills, such as reading/writing and math. Two years after the end of treatments, children show gross and fine motor skill delays that may persist even when patients are considered healed. The goal of the present study was to assess motor skills difficulties in pre-school children with leukemia one year after treatment. Particular attention has been paid to those patients who had undergone Hematopoietic Stem Cell Transplantation (HSCT) and to the relationship between motor delays and age bands. Participants were 60 children (median age of 5; inter quartile range: 3.07–5.76), including 31 females and 29 males, 91.7% of them were affected by acute lymphoblastic leukemia (ALL), and 8.3% by acute myeloid leukemia (AML). Five children had undergone HCST. Parents were interviewed by Vineland Adaptive Behavior Scales (VABS) on children’s motor skills and filled in the Italian Temperament Questionnaire (QUIT). VABS’s total scores were converted into equivalent mental age scores (EMA). A score difference of at least three months between current age and equivalent mental age was considered a developmental delay. Non-parametric analyses were run to understand if HSCT treatment and a specific age band influence children’s motor skills. Significant delays were found in global motor skills (56.7%) as well as in fine and gross motor domains. Mann Whitney U tests showed that children with HSCT were reported to have lower gross motor mean ranks (U = 62; p = 0.004; Mean rank = 15.40) than peers without HSCT (Mean rank = 31.87) and lower mean rank values on motor temperament scale (U = 9; p = 0.003; HSCT Mean rank = 4.75 versus no HSCT Mean rank = 27.81). Kruskal Wallis’ tests identified the high risk treatment showing that HSCT experience negatively impacted the motor skills and temperamental motor activity of pre-school children one year after the diagnosis of leukemia. PMID

  10. Different effects of the two types of spatial pre-cueing: what precisely is "attention" in Di Lollo's and Enns' substitution masking theory?

    Science.gov (United States)

    Luiga, I; Bachmann, T

    2007-11-01

    Enns and Di Lollo [Psychological Science, 8 (2), 135-139, 1997] have introduced the object substitution theory of visual masking. Object substitution masking occurs when focusing attention on the target is delayed. However, Posner (Quarterly Journal of Experimental Psychology, 32, 3-25, 1980) has already shown that attention can be directed to a target at least in two ways: intentionally (endogenously) and automatically (exogenously). We conducted two experiments to explore the effects of endogenous and exogenous cues on substitution masking. The results showed that when attention was shifted to the target location automatically (using a local peripheral pre-cue), masking was attenuated. A decrease in target identification dependent on a delay of mask offset, typical to substitution masking, was not observed. However, strong substitution masking occurred when the target location was not pre-cued or when attention was directed to the target location intentionally (using a symbolic pre-cue displayed centrally). The hypothesis of two different mechanisms of attentional control in substitution masking was confirmed.

  11. The importance of pre-planning for large hydrostatic test programs

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, Andrew Keith [WorleyParsons Calgary, Calgary, AB (Canada); Wong, Everett Clementi [Enbridge Pipelines Inc., Edmonton, AB (Canada)

    2010-07-01

    During the design phase of a pipeline project, large hydrostatic test programs are required to locate and secure water sources. Many companies complete hydrostatic test planning through high level desktop analysis, however this technique can result in important unplanned costs and schedule delays. The aim of this paper is to assess the cost benefits of pre-planning large hydrostatic test programs versus the costs of unplanned delays in the execution of hydrostatic testing. This comparison was based on the successful application of pre-planning of 57 mainline hydrostatic tests in the construction of the Line 4 Extension and Alberta Clipper Expansion oil pipelines by Enbridge Pipelines Inc. Results showed that costs of delays and uncertainty during construction far outweigh the costs of pre-planning. This study highlighted that pre-planning for large hydrostatic test programs should be carried out in the execution of large pipeline projects to ensure success.

  12. High throughput 16S rRNA gene amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Jørgensen, Mads Koustrup

    S rRNA gene amplicon sequencing has been developed over the past few years and is now ready to use for more comprehensive studies related to plant operation and optimization thanks to short analysis time, low cost, high throughput, and high taxonomic resolution. In this study we show how 16S r......RNA gene amplicon sequencing can be used to reveal factors of importance for the operation of full-scale nutrient removal plants related to settling problems and floc properties. Using optimized DNA extraction protocols, indexed primers and our in-house Illumina platform, we prepared multiple samples...... be correlated to the presence of the species that are regarded as “strong” and “weak” floc formers. In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling of activated sludge that in combination with multivariate statistics can be used...

  13. Prevalence of 16S rRNA methylase genes among b-lactamase ...

    African Journals Online (AJOL)

    2014-07-07

    Jul 7, 2014 ... School of Life Sciences, Pondicherry University, Pondicherry, India ... Methods: To study co existence of 16S rRNA methylases (armA, rmtA, rmtB, rmtC, rmtD, and .... Isolates positive for bla or 16S rRNA methylase genes.

  14. Modified nucleotides m2G966/m5C967 of Escherichia coli 16S rRNA are required for attenuation of tryptophan operon

    Science.gov (United States)

    Prokhorova, Irina V.; Osterman, Ilya A.; Burakovsky, Dmitry E.; Serebryakova, Marina V.; Galyamina, Maria A.; Pobeguts, Olga V.; Altukhov, Ilya; Kovalchuk, Sergey; Alexeev, Dmitry G.; Govorun, Vadim M.; Bogdanov, Alexey A.; Sergiev, Petr V.; Dontsova, Olga A.

    2013-11-01

    Ribosomes contain a number of modifications in rRNA, the function of which is unclear. Here we show - using proteomic analysis and dual fluorescence reporter in vivo assays - that m2G966 and m5C967 in 16S rRNA of Escherichia coli ribosomes are necessary for correct attenuation of tryptophan (trp) operon. Expression of trp operon is upregulated in the strain where RsmD and RsmB methyltransferases were deleted, which results in the lack of m2G966 and m5C967 modifications. The upregulation requires the trpL attenuator, but is independent of the promotor of trp operon, ribosome binding site of the trpE gene, which follows trp attenuator and even Trp codons in the trpL sequence. Suboptimal translation initiation efficiency in the rsmB/rsmD knockout strain is likely to cause a delay in translation relative to transcription which causes misregulation of attenuation control of trp operon.

  15. Isolation of temperature-sensitive mutants of 16 S rRNA in Escherichia coli

    DEFF Research Database (Denmark)

    Triman, K; Becker, E; Dammel, C

    1989-01-01

    Temperature-sensitive mutants have been isolated following hydroxylamine mutagenesis of a plasmid containing Escherichia coli rRNA genes carrying selectable markers for spectinomycin resistance (U1192 in 16 S rRNA) and erythromycin resistance (G2058 in 23 S rRNA). These antibiotic resistance....... The mutations were localized by in vitro restriction fragment replacement followed by in vivo marker rescue and were identified by DNA sequence analysis. We report here seven single-base alterations in 16 S rRNA (A146, U153, A350, A359, A538, A1292 and U1293), five of which produce temperature......-sensitive spectinomycin resistance and two that produce unconditional loss of resistance. In each case, loss of ribosomal function can be accounted for by disruption of base-pairing in the secondary structure of 16 S rRNA. For the temperature-sensitive mutants, there is a lag period of about two generations between...

  16. rRNA fragmentation induced by a yeast killer toxin.

    Science.gov (United States)

    Kast, Alene; Klassen, Roland; Meinhardt, Friedhelm

    2014-02-01

    Virus like dsDNA elements (VLE) in yeast were previously shown to encode the killer toxins PaT and zymocin, which target distinct tRNA species via specific anticodon nuclease (ACNase) activities. Here, we characterize a third member of the VLE-encoded toxins, PiT from Pichia inositovora, and identify PiOrf4 as the cytotoxic subunit by conditional expression in Saccharomyces cerevisiae. In contrast to the tRNA targeting toxins, however, neither a change of the wobble uridine modification status by introduction of elp3 or trm9 mutations nor tRNA overexpression rescued from PiOrf4 toxicity. Consistent with a distinct RNA target, expression of PiOrf4 causes specific fragmentation of the 25S and 18S rRNA. A stable cleavage product comprising the first ∼ 130 nucleotides of the 18S rRNA was purified and characterized by linker ligation and subsequent reverse transcription; 3'-termini were mapped to nucleotide 131 and 132 of the 18S rRNA sequence, a region showing some similarity to the anticodon loop of tRNA(Glu)(UUC), the zymocin target. PiOrf4 residues Glu9 and His214, corresponding to catalytic sites Glu9 and His209 in the ACNase subunit of zymocin are essential for in vivo toxicity and rRNA fragmentation, raising the possibility of functionally conserved RNase modules in both proteins. © 2013 John Wiley & Sons Ltd.

  17. Sequencing of 16S rRNA gene for id ntification of Sta h lococcus ...

    African Journals Online (AJOL)

    Asdmin

    2014-01-15

    Jan 15, 2014 ... as the type strains of a species of genus Trichoderma based on phylogenetic tree analysis together with the 18S rRNA gene sequence search in Ribosomal Database Project, small subunit rRNA and large subunit rRNA databases. The sequence was deposited in GenBank with the accession numbers.

  18. Alteration of rRNA gene copy number and expression in patients ...

    African Journals Online (AJOL)

    Background: Intellectual disability (ID) is an important medical and social problem that can be caused by different genetic and environmental factors. One such factor could be rDNA amplification and changes in rRNA expression and maturation. Aim of the study: The aim of the present study was to investigate rRNA levels in ...

  19. Prevalence of 16S rRNA methylase genes among β-lactamase ...

    African Journals Online (AJOL)

    Background: Co production of 16S rRNA methylases gene and β-Lactamase gene among Enterobacteriaceae isolates conferring resistance to both therapeutic options has serious implications for clinicians worldwide. Methods: To study co existence of 16S rRNA methylases (armA, rmtA, rmtB, rmtC, rmtD, and npmA) and ...

  20. Changes in rRNA levels during stress invalidates results from mRNA blotting: Fluorescence in situ rRNA hybridization permits renormalization for estimation of cellular mRNA levels

    DEFF Research Database (Denmark)

    Hansen, M.C.; Nielsen, A.K.; Molin, Søren

    2001-01-01

    obtained by these techniques are compared between experiments in which differences in growth rates, strains, or stress treatments occur, the normalization procedure may have a significant impact on the results. In this report we present a solution to the normalization problem in RNA slot blotting...... the relative level of rRNA per cell, and slot blotting to rRNA probes, which estimates the level of rRNA per extracted total RNA, the amount of RNA per cell was calculated in a series of heat shock experiments with the gram-positive bacterium Lactococcus lactis. It was found that the level of rRNA per cell...... decreased to 30% in the course of the heat shock. This lowered ribosome level led to a decrease in the total RNA content, resulting in a gradually increasing overestimation of the mRNA levels throughout the experiment. Using renormalized cellular mRNA levels, the HrcA-mediated regulation of the genes...

  1. Dynamic high pressure induced strong and weak hydrogen bonds enhanced by pre-resonance stimulated Raman scattering in liquid water.

    Science.gov (United States)

    Wang, Shenghan; Fang, Wenhui; Li, Fabing; Gong, Nan; Li, Zhanlong; Li, Zuowei; Sun, Chenglin; Men, Zhiwei

    2017-12-11

    355 nm pulsed laser is employed to excite pre-resonance forward stimulated Raman scattering (FSRS) of liquid water at ambient temperature. Due to the shockwave induced dynamic high pressure, the obtained Raman spectra begin to exhibit double peaks distribution at 3318 and 3373 cm -1 with the input energy of 17 mJ,which correspond with OH stretching vibration with strong and weak hydrogen (H) bonds. With laser energy rising from 17 to 27 mJ, the Stokes line at 3318 cm -1 shifts to 3255 and 3230 cm -1 because of the high pressure being enlarged. When the energy is up to 32 mJ, only 3373 cm -1 peak exists. The strong and weak H bond exhibit quite different energy dependent behaviors.

  2. How many 5S rRNA genes and pseudogenes are there in ''Aspergillus nidulans''?

    International Nuclear Information System (INIS)

    Pelczar, P.; Fiett, J.; Bartnik, E.

    1994-01-01

    We have estimated the number of 5S rRNA genes in ''Aspergillus nidulans'' using two-dimensional agarose gel electrophoresis and hybridization to appropriate probes, representing the 5'-halves, the 3'-halves of the 5S rRNA sequence and a sequence found at the 3'-end of all known. ''A. nidulans'' pseudogenes (block C). We have found 23 5S rRNA genes, 15 pseudogenes consisting of the 5'-half of the 5S rRNA sequence (of which 3 are flanked by block C) and 12 copies of block C which do not seem to be in the vicinity of 5S rRNA sequences. This number of genes is much lower than our earlier estimates, and makes our previously analyzed sample of 9 sequenced genes and 3 pseudogenes much more representative. (author). 7 refs, 1 fig

  3. Robust computational analysis of rRNA hypervariable tag datasets.

    Directory of Open Access Journals (Sweden)

    Maksim Sipos

    Full Text Available Next-generation DNA sequencing is increasingly being utilized to probe microbial communities, such as gastrointestinal microbiomes, where it is important to be able to quantify measures of abundance and diversity. The fragmented nature of the 16S rRNA datasets obtained, coupled with their unprecedented size, has led to the recognition that the results of such analyses are potentially contaminated by a variety of artifacts, both experimental and computational. Here we quantify how multiple alignment and clustering errors contribute to overestimates of abundance and diversity, reflected by incorrect OTU assignment, corrupted phylogenies, inaccurate species diversity estimators, and rank abundance distribution functions. We show that straightforward procedural optimizations, combining preexisting tools, are effective in handling large (10(5-10(6 16S rRNA datasets, and we describe metrics to measure the effectiveness and quality of the estimators obtained. We introduce two metrics to ascertain the quality of clustering of pyrosequenced rRNA data, and show that complete linkage clustering greatly outperforms other widely used methods.

  4. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales.

    Science.gov (United States)

    Jay, Zackary J; Inskeep, William P

    2015-07-09

    Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which "universal" archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

  5. The Conserved RNA Exonuclease Rexo5 Is Required for 3′ End Maturation of 28S rRNA, 5S rRNA, and snoRNAs

    Directory of Open Access Journals (Sweden)

    Stefanie Gerstberger

    2017-10-01

    Full Text Available Non-coding RNA biogenesis in higher eukaryotes has not been fully characterized. Here, we studied the Drosophila melanogaster Rexo5 (CG8368 protein, a metazoan-specific member of the DEDDh 3′-5′ single-stranded RNA exonucleases, by genetic, biochemical, and RNA-sequencing approaches. Rexo5 is required for small nucleolar RNA (snoRNA and rRNA biogenesis and is essential in D. melanogaster. Loss-of-function mutants accumulate improperly 3′ end-trimmed 28S rRNA, 5S rRNA, and snoRNA precursors in vivo. Rexo5 is ubiquitously expressed at low levels in somatic metazoan cells but extremely elevated in male and female germ cells. Loss of Rexo5 leads to increased nucleolar size, genomic instability, defective ribosome subunit export, and larval death. Loss of germline expression compromises gonadal growth and meiotic entry during germline development.

  6. Speech and language delay in two children: an unusual presentation of hyperthyroidism.

    Science.gov (United States)

    Sohal, Aman P S; Dasarathi, Madhuri; Lodh, Rajib; Cheetham, Tim; Devlin, Anita M

    2013-01-01

    Hyperthyroidism is rare in pre-school children. Untreated, it can have a profound effect on normal growth and development, particularly in the first 2 years of life. Although neurological manifestations of dysthyroid states are well known, specific expressive speech and language disorder as a presentation of hyperthyroidism is rarely documented. Case reports of two children with hyperthyroidism presenting with speech and language delay. We report two pre-school children with hyperthyroidism, who presented with expressive speech and language delay, and demonstrated a significant improvement in their language skills following treatment with anti-thyroid medication. Hyperthyroidism must be considered in all children presenting with speech and language difficulties, particularly expressive speech delay. Prompt recognition and early treatment are likely to improve outcome.

  7. MXD1 localizes in the nucleolus, binds UBF and impairs rRNA synthesis.

    Science.gov (United States)

    Lafita-Navarro, Maria Del Carmen; Blanco, Rosa; Mata-Garrido, Jorge; Liaño-Pons, Judit; Tapia, Olga; García-Gutiérrez, Lucía; García-Alegría, Eva; Berciano, María T; Lafarga, Miguel; León, Javier

    2016-10-25

    MXD1 is a protein that interacts with MAX, to form a repressive transcription factor. MXD1-MAX binds E-boxes. MXD1-MAX antagonizes the transcriptional activity of the MYC oncoprotein in most models. It has been reported that MYC overexpression leads to augmented RNA synthesis and ribosome biogenesis, which is a relevant activity in MYC-mediated tumorigenesis. Here we describe that MXD1, but not MYC or MNT, localizes to the nucleolus in a wide array of cell lines derived from different tissues (carcinoma, leukemia) as well as in embryonic stem cells. MXD1 also localizes in the nucleolus of primary tissue cells as neurons and Sertoli cells. The nucleolar localization of MXD1 was confirmed by co-localization with UBF. Co-immunoprecipitation experiments showed that MXD1 interacted with UBF and proximity ligase assays revealed that this interaction takes place in the nucleolus. Furthermore, chromatin immunoprecipitation assays showed that MXD1 was bound in the transcribed rDNA chromatin, where it co-localizes with UBF, but also in the ribosomal intergenic regions. The MXD1 involvement in rRNA synthesis was also suggested by the nucleolar segregation upon rRNA synthesis inhibition by actinomycin D. Silencing of MXD1 with siRNAs resulted in increased synthesis of pre-rRNA while enforced MXD1 expression reduces it. The results suggest a new role for MXD1, which is the control of ribosome biogenesis. This new MXD1 function would be important to curb MYC activity in tumor cells.

  8. Recognition determinants for proteins and antibiotics within 23S rRNA

    DEFF Research Database (Denmark)

    Douthwaite, Stephen Roger; Voldborg, Bjørn Gunnar Rude; Hansen, Lykke Haastrup

    1995-01-01

    Ribosomal RNAs fold into phylogenetically conserved secondary and tertiary structures that determine their function in protein synthesis. We have investigated Escherichia coli 23S rRNA to identify structural elements that interact with antibiotic and protein ligands. Using a combination of molecu......Ribosomal RNAs fold into phylogenetically conserved secondary and tertiary structures that determine their function in protein synthesis. We have investigated Escherichia coli 23S rRNA to identify structural elements that interact with antibiotic and protein ligands. Using a combination......-proteins L10.(L12)4 and L11 and is inhibited by interaction with the antibiotic thiostrepton. The peptidyltransferase center within domain V is inhibited by macrolide, lincosamide, and streptogramin B antibiotics, which interact with the rRNA around nucleotide A2058. Drug resistance is conferred by mutations...

  9. A critical role for noncoding 5S rRNA in regulating Mdmx stability.

    Science.gov (United States)

    Li, Muyang; Gu, Wei

    2011-09-16

    Both p53 and Mdmx are ubiquitinated and degraded by the same E3 ligase Mdm2; interestingly, however, while p53 is rapidly degraded by Mdm2, Mdmx is a stable protein in most cancer cells. Thus, the mechanism by which Mdmx is degraded by Mdm2 needs further elucidation. Here, we identified the noncoding 5S rRNA as a major component of Mdmx-associated complexes from human cells. We show that 5S rRNA acts as a natural inhibitor of Mdmx degradation by Mdm2. RNAi-mediated knockdown of endogenous 5S rRNA, while not affecting p53 levels, significantly induces Mdmx degradation and, subsequently, activates p53-dependent growth arrest. Notably, 5S rRNA binds the RING domain of Mdmx and blocks its ubiquitination by Mdm2, whereas Mdm2-mediated p53 ubiquitination remains intact. These results provide insights into the differential effects on p53 and Mdmx by Mdm2 in vivo and reveal a critical role for noncoding 5S rRNA in modulating the p53-Mdmx axis. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Clinical significance of DVM and its prevalence in pre-gestational diabetes cases versus normal pregnancies

    Directory of Open Access Journals (Sweden)

    Farideh Akhlaghi

    2015-06-01

    Full Text Available Pre-gestational diabetes mellitus affects less than 1% of all pregnancies and is a significant cause of fetal morbidity and mortality. It is hypothesized that impaired placental function, in the form of abnormal placental weight and/or abnormal placental histology, may be responsible for this event in such pregnancies. Delayed villous maturation of placental villi, which is one of the findings associated with pre-gestational diabetes increases the rate of perinatal mortality. There is limited literature regarding the delayed maturation of placental villous. This review included trials (randomized and non-randomized, cohort and case-control studies registered in Medline/PubMed database, from January 2001 to September 2012 that evaluated the clinical significance of delayed villous maturation and its prevalence in pre-gestational diabetic cases compared to normal pregnancies.It emphasizes that further studies with focus on possible clinical or ultrasound markers of placental delayed villous maturation, especially in a high risk-group such as women with pre-gestational diabetes mellitus are highly recommended.

  11. Frequency and spectrum of mitochondrial 12S rRNA variants in 440 Han Chinese hearing impaired pediatric subjects from two otology clinics

    Directory of Open Access Journals (Sweden)

    Zhou Jianjin

    2011-01-01

    accounted for ~30% cases of aminoglycoside-induced deafness in this cohort. Our data strongly support the idea that the mitochondrial 12S rRNA is the hot spot for mutations associated with aminoglycoside ototoxicity. These data have been providing valuable information and technology to predict which individuals are at risk for ototoxicity, to improve the safety of aminoglycoside antibiotic therapy, and eventually to decrease the incidence of deafness.

  12. Molecular evolution of the mitochondrial 12S rRNA in Ungulata (mammalia).

    Science.gov (United States)

    Douzery, E; Catzeflis, F M

    1995-11-01

    The complete 12S rRNA gene has been sequenced in 4 Ungulata (hoofed eutherians) and 1 marsupial and compared to 38 available mammalian sequences in order to investigate the molecular evolution of the mitochondrial small-subunit ribosomal RNA molecule. Ungulata were represented by one artiodactyl (the collared peccary, Tayassu tajacu, suborder Suiformes), two perissodactyls (the Grevy's zebra, Equus grevyi, suborder Hippomorpha; the white rhinoceros, Ceratotherium simum, suborder Ceratomorpha), and one hyracoid (the tree hyrax, Dendrohyrax dorsalis). The fifth species was a marsupial, the eastern gray kangaroo (Macropus giganteus). Several transition/transversion biases characterized the pattern of changes between mammalian 12S rRNA molecules. A bias toward transitions was found among 12S rRNA sequences of Ungulata, illustrating the general bias exhibited by ribosomal and protein-encoding genes of the mitochondrial genome. The derivation of a mammalian 12S rRNA secondary structure model from the comparison of 43 eutherian and marsupial sequences evidenced a pronounced bias against transversions in stems. Moreover, transversional compensatory changes were rare events within double-stranded regions of the ribosomal RNA. Evolutionary characteristics of the 12S rRNA were compared with those of the nuclear 18S and 28S rRNAs. From a phylogenetic point of view, transitions, transversions and indels in stems as well as transversional and indels events in loops gave congruent results for comparisons within orders. Some compensatory changes in double-stranded regions and some indels in single-stranded regions also constituted diagnostic events. The 12S rRNA molecule confirmed the monophyly of infraorder Pecora and order Cetacea and demonstrated the monophyly of the suborder Ruminantia was not supported and the branching pattern between Cetacea and the artiodacytyl suborders Ruminantia and Suiformes was not established. The monophyly of the order Perissodactyla was evidenced

  13. Interpreting the Strongly Lensed Supernova iPTF16geu: Time Delay Predictions, Microlensing, and Lensing Rates

    Energy Technology Data Exchange (ETDEWEB)

    More, Anupreeta; Oguri, Masamune; More, Surhud [Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU, WPI), University of Tokyo, Chiba 277-8583 (Japan); Suyu, Sherry H. [Max-Planck-Institut für Astrophysik, Karl-Schwarzschild-Str. 1, D-85748 Garching (Germany); Lee, Chien-Hsiu, E-mail: anupreeta.more@ipmu.jp [Subaru Telescope, National Astronomical Observatory of Japan, 650 North Aohoku Place, Hilo, HI 96720 (United States)

    2017-02-01

    We present predictions for time delays between multiple images of the gravitationally lensed supernova, iPTF16geu, which was recently discovered from the intermediate Palomar Transient Factory (iPTF). As the supernova is of Type Ia where the intrinsic luminosity is usually well known, accurately measured time delays of the multiple images could provide tight constraints on the Hubble constant. According to our lens mass models constrained by the Hubble Space Telescope F814W image, we expect the maximum relative time delay to be less than a day, which is consistent with the maximum of 100 hr reported by Goobar et al. but places a stringent upper limit. Furthermore, the fluxes of most of the supernova images depart from expected values suggesting that they are affected by microlensing. The microlensing timescales are small enough that they may pose significant problems to measure the time delays reliably. Our lensing rate calculation indicates that the occurrence of a lensed SN in iPTF is likely. However, the observed total magnification of iPTF16geu is larger than expected, given its redshift. This may be a further indication of ongoing microlensing in this system.

  14. Decreases in average bacterial community rRNA operon copy number during succession.

    Science.gov (United States)

    Nemergut, Diana R; Knelman, Joseph E; Ferrenberg, Scott; Bilinski, Teresa; Melbourne, Brett; Jiang, Lin; Violle, Cyrille; Darcy, John L; Prest, Tiffany; Schmidt, Steven K; Townsend, Alan R

    2016-05-01

    Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.

  15. Behavioral effects of delayed timeouts from reinforcement.

    Science.gov (United States)

    Byrne, Tom; Poling, Alan

    2017-03-01

    Timeouts are sometimes used in applied settings to reduce target responses, and in some circumstances delays are unavoidably imposed between the onset of a timeout and the offset of the response that produces it. The present study examined the effects of signaled and unsignaled timeouts in rats exposed to concurrent fixed-ratio 1 fixed-ratio 1 schedules of food delivery, where each response on one lever, the location of which changed across conditions, produced both food and a delayed 10-s timeout. Delays of 0 to 38 s were examined. Delayed timeouts often, but not always, substantially reduced the number of responses emitted on the lever that produced timeouts relative to the number emitted on the lever that did not produce timeouts. In general, greater sensitivity was observed to delayed timeouts when they were signaled. These results demonstrate that delayed timeouts, like other delayed consequences, can affect behavior, albeit less strongly than immediate consequences. © 2017 Society for the Experimental Analysis of Behavior.

  16. Implementation of Pre-Operative Checklist: An Effort to Reduce ...

    African Journals Online (AJOL)

    Implementation of Pre-Operative Checklist: An Effort to Reduce Delays in. Surgery and ... insight to develop a pre-operative checklist to ensure that patients were prepared for surgery and to minimize disruptions ... documentation audit was conducted in May 2014, showing 59% compliance in completing the checklist. Since.

  17. Recognition elements in rRNA for the tylosin resistance methyltransferase RlmA(II)

    DEFF Research Database (Denmark)

    Lebars, Isabelle; Husson, Clotilde; Yoshizawa, Satoko

    2007-01-01

    The methyltransferase RlmA(II) (formerly TlrB) is found in many Gram-positive bacteria, and methylates the N-1 position of nucleotide G748 within the loop of hairpin 35 in 23S rRNA. Methylation of the rRNA by RlmA(II) confers resistance to tylosin and other mycinosylated 16-membered ring macrolide......RNA substrate indicated that multiple contacts occur between RlmA(II) and nucleotides in stem-loops 33, 34 and 35. RlmA(II) appears to recognize its rRNA target through specific surface shape complementarity at the junction formed by these three helices. This means of recognition is highly similar...

  18. Simultaneous separation of five major ribonucleic acids by capillary electrophoresis with laser-induced fluorescence in the presence of electroosmotic flow: application to the rapid screening of 5S rRNA from ovarian cancer cells.

    Science.gov (United States)

    Shih, Ya-Chu; Liao, Ching-Ru; Chung, I-Che; Chang, Yu-Sun; Chang, Po-Ling

    2014-10-17

    RNA integrity is important in RNA studies because poor RNA quality may impact downstream methodologies. This study proposes a rapid and cost-effective method for the determination of RNA integrity based on CE-LIF in the presence of electroosmotic flow. The proposed method uses poly(ethylene) oxide (Mavg=4,000,000 Da) as a sieving matrix for total RNA separation. Ethidium bromide (μg mL(-1)) was dissolved in a polymer solution as an interchelating dye for on-column fluorescent labeling. The 28S rRNA, 18S rRNA, 5.8S rRNA, 5S rRNA and tRNA from the total human RNA extracted from the cells were fully separated using the proposed method. The lowest detectable concentration of total RNA achieved was 100 pg μL(-1) with a 6 min sample injection followed by on-column concentration. In addition, the temperature-induced degradation of total RNA was observed by CE-LIF. The electropherograms revealed more fragmentation of 28S and 18S rRNAs by temperature-induced hydrolysis compared with the 5.8S rRNA, 5S rRNA and tRNA. Therefore, the results indicated that RNA degradation should be considered for long-term, high-temperature incubations in RNA-related experiments involving RNA hybridization. The proposed method is furthermore, applied to the determination of 5S rRNA overexpressed in ovarian cancer cells as compared to the cervical cancer cells. Overall, CE-LIF is highly promising for rapid screening of ovarian cancers without tedious pre-amplification steps. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Organism-specific rRNA capture system for application in next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Sai-Kam Li

    Full Text Available RNA-sequencing is a powerful tool in studying RNomics. However, the highly abundance of ribosomal RNAs (rRNA and transfer RNA (tRNA have predominated in the sequencing reads, thereby hindering the study of lowly expressed genes. Therefore, rRNA depletion prior to sequencing is often performed in order to preserve the subtle alteration in gene expression especially those at relatively low expression levels. One of the commercially available methods is to use DNA or RNA probes to hybridize to the target RNAs. However, there is always a concern with the non-specific binding and unintended removal of messenger RNA (mRNA when the same set of probes is applied to different organisms. The degree of such unintended mRNA removal varies among organisms due to organism-specific genomic variation. We developed a computer-based method to design probes to deplete rRNA in an organism-specific manner. Based on the computation results, biotinylated-RNA-probes were produced by in vitro transcription and were used to perform rRNA depletion with subtractive hybridization. We demonstrated that the designed probes of 16S rRNAs and 23S rRNAs can efficiently remove rRNAs from Mycobacterium smegmatis. In comparison with a commercial subtractive hybridization-based rRNA removal kit, using organism-specific probes is better in preserving the RNA integrity and abundance. We believe the computer-based design approach can be used as a generic method in preparing RNA of any organisms for next-generation sequencing, particularly for the transcriptome analysis of microbes.

  20. The rRNA evolution and procaryotic phylogeny

    Science.gov (United States)

    Fox, G. E.

    1986-01-01

    Studies of ribosomal RNA primary structure allow reconstruction of phylogenetic trees for prokaryotic organisms. Such studies reveal major dichotomy among the bacteria that separates them into eubacteria and archaebacteria. Both groupings are further segmented into several major divisions. The results obtained from 5S rRNA sequences are essentially the same as those obtained with the 16S rRNA data. In the case of Gram negative bacteria the ribosomal RNA sequencing results can also be directly compared with hybridization studies and cytochrome c sequencing studies. There is again excellent agreement among the several methods. It seems likely then that the overall picture of microbial phylogeny that is emerging from the RNA sequence studies is a good approximation of the true history of these organisms. The RNA data allow examination of the evolutionary process in a semi-quantitative way. The secondary structures of these RNAs are largely established. As a result it is possible to recognize examples of local structural evolution. Evolutionary pathways accounting for these events can be proposed and their probability can be assessed.

  1. Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across marine subsurface provinces.

    Directory of Open Access Journals (Sweden)

    William Orsi

    Full Text Available The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC, nitrate, sulfide, and dissolved inorganic carbon (DIC. These correlations are supported by terminal restriction length polymorphism (TRFLP analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.

  2. Molecular phylogeny of mitochondrial cytochrome b and 12S rRNA sequences in the Felidae: ocelot and domestic cat lineages.

    Science.gov (United States)

    Masuda, R; Lopez, J V; Slattery, J P; Yuhki, N; O'Brien, S J

    1996-12-01

    Molecular phylogeny of the cat family Felidae is derived using two mitochondrial genes, cytochrome b and 12S rRNA. Phylogenetic methods of weighted maximum parsimony and minimum evolution estimated by neighbor-joining are employed to reconstruct topologies among 20 extant felid species. Sequence analyses of 363 bp of cytochrome b and 376 bp of the 12S rRNA genes yielded average pair-wise similarity values between felids ranging from 94 to 99% and from 85 to 99%, respectively. Phylogenetic reconstruction supports more recent, intralineage associations but fails to completely resolve interlineage relationships. Both genes produce a monophyletic group of Felis species but vary in the placement of the pallas cat. The ocelot lineage represents an early divergence within the Felidae, with strong associations between ocelot and margay, Geoffroy's cat and kodkod, and pampas cat and tigrina. Implications of the relative recency of felid evolution, presence of ancestral polymorphisms, and influence of outgroups in placement of the topological root are discussed.

  3. rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-Resistant Staphylococcus aureus

    Science.gov (United States)

    Jansen, M. D.; Bosch, T.; Jansen, W. T. M.; Schouls, L.; Jonker, M. J.; Boel, C. H. E.

    2016-01-01

    The distinct epidemiology of original hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) and early community-associated MRSA (CA-MRSA) is largely unexplained. S. aureus carries either five or six rRNA operon copies. Evidence is provided for a scenario in which MRSA has adapted to the hospital environment by rRNA operon loss (six to five copies) due to antibiotic pressure. Early CA-MRSA, in contrast, results from wild-type methicillin-susceptible S. aureus (MSSA) that acquired mecA without loss of an rRNA operon. Of the HA-MRSA isolates (n = 77), 67.5% had five rRNA operon copies, compared to 23.2% of the CA-MRSA isolates (n = 69) and 7.7% of MSSA isolates (n = 195) (P operon copies. For all subsets, a correlation between resistance profile and rRNA copy number was found. Furthermore, we showed that in vitro antibiotic pressure may result in rRNA operon copy loss. We also showed that without antibiotic pressure, S. aureus isolates containing six rRNA copies are more fit than isolates with five copies. We conclude that HA-MRSA and cystic fibrosis isolates most likely have adapted to an environment with high antibiotic pressure by the loss of an rRNA operon copy. This loss has facilitated resistance development, which promoted survival in these niches. However, strain fitness decreased, which explains their lack of success in the community. In contrast, CA-MRSA isolates retained six rRNA operon copies, rendering them fitter and thereby able to survive and spread in the community. PMID:27671073

  4. CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

    Directory of Open Access Journals (Sweden)

    Jeongsu Oh

    Full Text Available High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs. The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM

  5. CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

    Science.gov (United States)

    Oh, Jeongsu; Choi, Chi-Hwan; Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

    2016-01-01

    High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA

  6. CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment

    Science.gov (United States)

    Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

    2016-01-01

    High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology–a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in

  7. Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

    Science.gov (United States)

    Beauparlant, Marc A; Drouin, Guy

    2014-02-01

    Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

  8. Pre-crastination in the pigeon.

    Science.gov (United States)

    Wasserman, Edward A; Brzykcy, Stephen J

    2015-08-01

    Procrastination is the tendency to delay initiating or completing tasks. Rosenbaum et al. (Psychological Science, May 8, 2014) recently documented the opposite of procrastination: pre-crastination, the tendency to begin or to finish tasks as soon as possible. We devised a simple two-alternative forced-choice task, in which pigeons could choose to switch response location either sooner or later in a sequence of actions eventuating in food reward. Even though there was no economic advantage for doing so, pigeons chose to switch response location sooner rather than later in the sequence, showing pre-crastination to be quite general. Pre-crastination thus joins other anticipatory learning phenomena in challenging rational or optimal accounts of behavioral adaptation.

  9. Robertsonian translocation 13/14 associated with rRNA genes ...

    African Journals Online (AJOL)

    Robertsonian translocation 13/14 associated with rRNA genes overexpression and intellectual disability. Alexander A. Dolskiy, Natalya A. Lemskaya, Yulia V. Maksimova, Asia R. Shorina, Irina S. Kolesnikova, Dmitry V. Yudkin ...

  10. Utility of 16S rRNA PCR performed on clinical specimens in patient management

    Directory of Open Access Journals (Sweden)

    A. Akram

    2017-04-01

    Conclusions: Despite the low diagnostic yield, results of 16S rRNA PCR can still have a significant impact on patient management due to rationalization or cessation of the antimicrobial therapy. The yield of 16S rRNA PCR was highest for heart valves.

  11. T2 values of femoral cartilage of the knee joint: Comparison between pre-contrast and post-contrast images

    International Nuclear Information System (INIS)

    Yoon, Hyun Jung; Yoon, Young Cheol; Choe, Bong Keun

    2014-01-01

    To retrospectively evaluate the relationship between T2 values of pre- and post-contrast magnetic resonance (MR) images of femoral cartilage in patients with varying degrees of osteoarthritis. A total of 19 patients underwent delayed gadolinium-enhanced MRI of cartilage. Six regions of interest for T2 value measurement were obtained from pre- and post-contrast T2-weighted, sagittal, multi-slice, multi-echo, source images in each subject. Regions with modified Noyes classification grade 2B and 3 were excluded. Comparison of T2 values between pre- and post-contrast images and T2 values among regions with the grade 0, 1 and 2A groups were statistically analyzed. Of a total of 114 regions, 79 regions showing grade 0 (n = 46), 1 (n = 18), or 2A (n = 15) were analyzed. The overall and individual T2 values of post-contrast images were significantly lower than those of pre-contrast images (overall, 35.3 ± 9.2 [mean ± SD] vs. 29.9 ± 8.2, p < 0.01; range of individual, 28.9-37.6 vs. 27.1-36.4, p < 0.01). Pearson correlation coefficients showed a strong positive correlation between pre- and post-contrast images (rho-Pearson = 0.712-0.905). T2 values of pre- and post-contrast images of the grade 0 group were significantly lower than those of the grade 1/2A group (pre T2, p = 0.003; post T2, p = 0.006). T2 values of the femoral cartilage of the knee joint are significantly lower on post-contrast images than on pre-contrast images. Furthermore, these T2 values have a strong positive correlation between pre- and post-contrast images.

  12. T2 values of femoral cartilage of the knee joint: Comparison between pre-contrast and post-contrast images

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hyun Jung; Yoon, Young Cheol [Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Choe, Bong Keun [Department of Preventive Medicine, Kyung Hee University School of Medicine, Seoul (Korea, Republic of)

    2014-02-15

    To retrospectively evaluate the relationship between T2 values of pre- and post-contrast magnetic resonance (MR) images of femoral cartilage in patients with varying degrees of osteoarthritis. A total of 19 patients underwent delayed gadolinium-enhanced MRI of cartilage. Six regions of interest for T2 value measurement were obtained from pre- and post-contrast T2-weighted, sagittal, multi-slice, multi-echo, source images in each subject. Regions with modified Noyes classification grade 2B and 3 were excluded. Comparison of T2 values between pre- and post-contrast images and T2 values among regions with the grade 0, 1 and 2A groups were statistically analyzed. Of a total of 114 regions, 79 regions showing grade 0 (n = 46), 1 (n = 18), or 2A (n = 15) were analyzed. The overall and individual T2 values of post-contrast images were significantly lower than those of pre-contrast images (overall, 35.3 ± 9.2 [mean ± SD] vs. 29.9 ± 8.2, p < 0.01; range of individual, 28.9-37.6 vs. 27.1-36.4, p < 0.01). Pearson correlation coefficients showed a strong positive correlation between pre- and post-contrast images (rho-Pearson = 0.712-0.905). T2 values of pre- and post-contrast images of the grade 0 group were significantly lower than those of the grade 1/2A group (pre T2, p = 0.003; post T2, p = 0.006). T2 values of the femoral cartilage of the knee joint are significantly lower on post-contrast images than on pre-contrast images. Furthermore, these T2 values have a strong positive correlation between pre- and post-contrast images.

  13. 5S rRNA gene arrangements in protists: a case of nonadaptive evolution.

    Science.gov (United States)

    Drouin, Guy; Tsang, Corey

    2012-06-01

    Given their high copy number and high level of expression, one might expect that both the sequence and organization of eukaryotic ribosomal RNA genes would be conserved during evolution. Although the organization of 18S, 5.8S and 28S ribosomal RNA genes is indeed relatively well conserved, that of 5S rRNA genes is much more variable. Here, we review the different types of 5S rRNA gene arrangements which have been observed in protists. This includes linkages to the other ribosomal RNA genes as well as linkages to ubiquitin, splice-leader, snRNA and tRNA genes. Mapping these linkages to independently derived phylogenies shows that these diverse linkages have repeatedly been gained and lost during evolution. This argues against such linkages being the primitive condition not only in protists but also in other eukaryote species. Because the only characteristic the diverse genes with which 5S rRNA genes are found linked with is that they are tandemly repeated, these arrangements are unlikely to provide any selective advantage. Rather, the observed high variability in 5S rRNA genes arrangements is likely the result of the fact that 5S rRNA genes contain internal promoters, that these genes are often transposed by diverse recombination mechanisms and that these new gene arrangements are rapidly homogenized by unequal crossingovers and/or by gene conversions events in species with short generation times and frequent founder events.

  14. Transcriptional down-regulation and rRNA cleavage in Dictyostelium discoideum mitochondria during Legionella pneumophila infection.

    Directory of Open Access Journals (Sweden)

    Chenyu Zhang

    2009-05-01

    Full Text Available Bacterial pathogens employ a variety of survival strategies when they invade eukaryotic cells. The amoeba Dictyostelium discoideum is used as a model host to study the pathogenic mechanisms that Legionella pneumophila, the causative agent of Legionnaire's disease, uses to kill eukaryotic cells. Here we show that the infection of D. discoideum by L. pneumophila results in a decrease in mitochondrial messenger RNAs, beginning more than 8 hours prior to detectable host cell death. These changes can be mimicked by hydrogen peroxide treatment, but not by other cytotoxic agents. The mitochondrial large subunit ribosomal RNA (LSU rRNA is also cleaved at three specific sites during the course of infection. Two LSU rRNA fragments appear first, followed by smaller fragments produced by additional cleavage events. The initial LSU rRNA cleavage site is predicted to be on the surface of the large subunit of the mitochondrial ribosome, while two secondary sites map to the predicted interface with the small subunit. No LSU rRNA cleavage was observed after exposure of D. discoideum to hydrogen peroxide, or other cytotoxic chemicals that kill cells in a variety of ways. Functional L. pneumophila type II and type IV secretion systems are required for the cleavage, establishing a correlation between the pathogenesis of L. pneumophila and D. discoideum LSU rRNA destruction. LSU rRNA cleavage was not observed in L. pneumophila infections of Acanthamoeba castellanii or human U937 cells, suggesting that L. pneumophila uses distinct mechanisms to interrupt metabolism in different hosts. Thus, L. pneumophila infection of D. discoideum results in dramatic decrease of mitochondrial RNAs, and in the specific cleavage of mitochondrial rRNA. The predicted location of the cleavage sites on the mitochondrial ribosome suggests that rRNA destruction is initiated by a specific sequence of events. These findings suggest that L. pneumophila specifically disrupts mitochondrial

  15. Pre-cementation of deep shaft

    Science.gov (United States)

    Heinz, W. F.

    1988-12-01

    Pre-cementation or pre-grouting of deep shafts in South Africa is an established technique to improve safety and reduce water ingress during shaft sinking. The recent completion of several pre-cementation projects for shafts deeper than 1000m has once again highlighted the effectiveness of pre-grouting of shafts utilizing deep slimline boreholes and incorporating wireline technique for drilling and conventional deep borehole grouting techniques for pre-cementation. Pre-cementation of deep shaft will: (i) Increase the safety of shaft sinking operation (ii) Minimize water and gas inflow during shaft sinking (iii) Minimize the time lost due to additional grouting operations during sinking of the shaft and hence minimize costly delays and standing time of shaft sinking crews and equipment. (iv) Provide detailed information of the geology of the proposed shaft site. Informations on anomalies, dykes, faults as well as reef (gold bearing conglomerates) intersections can be obtained from the evaluation of cores of the pre-cementation boreholes. (v) Provide improved rock strength for excavations in the immediate vicinity of the shaft area. The paper describes pre-cementation techniques recently applied successfully from surface and some conclusions drawn for further considerations.

  16. Temporal trends and associated factors for pre-hospital and in-hospital delays of stroke patients over a 16-year period: the Athens study.

    Science.gov (United States)

    Papapanagiotou, Panagiotis; Iacovidou, Nicoletta; Spengos, Konstantinos; Xanthos, Theodoros; Zaganas, Ioannis; Aggelina, Afrodite; Alegakis, Athanasios; Vemmos, Konstantinos

    2011-01-01

    The management and outcome of acute ischemic stroke changed dramatically after the introduction of intravenous thrombolysis. However, relatively few patients have received thrombolytic treatment, mainly due to pre-hospital and/or in-hospital delays. Although the causes of these delays have been adequately studied, their change over a long period has not. All acute first-ever stroke patients (n = 2,746) presenting to our academic center from 1993 to 2008 were prospectively documented in a computerized stroke data bank. The time from symptoms onset to presentation at the emergency room and to acquisition of a brain CT was calculated. Time trends over this period as well as the factors affecting them were analyzed. The final study cohort consisted of 2,326 acute stroke patients after excluding 302 patients with an unknown time of stroke onset and 118 who suffered a stroke during hospitalization for another illness. Over the 16-year period, the median time from stroke onset to presentation at the emergency room decreased significantly from 3.15 h (interquartile range 1.30-10.30) to 2.00 h (range 1.00-4.00) (p best early management of acute stroke patients. Copyright © 2010 S. Karger AG, Basel.

  17. Cracking chaos-based encryption systems ruled by nonlinear time delay differential equations

    International Nuclear Information System (INIS)

    Udaltsov, Vladimir S.; Goedgebuer, Jean-Pierre; Larger, Laurent; Cuenot, Jean-Baptiste; Levy, Pascal; Rhodes, William T.

    2003-01-01

    We report that signal encoding with high-dimensional chaos produced by delayed feedback systems with a strong nonlinearity can be broken. We describe the procedure and illustrate the method with chaotic waveforms obtained from a strongly nonlinear optical system that we used previously to demonstrate signal encryption/decryption with chaos in wavelength. The method can be extended to any systems ruled by nonlinear time-delayed differential equations

  18. Robust convergence of Cohen-Grossberg neural networks with time-varying delays

    International Nuclear Information System (INIS)

    Xiong Wenjun; Ma Deyi; Liang Jinling

    2009-01-01

    In this paper, robust convergence is studied for the Cohen-Grossberg neural networks (CGNNs) with time-varying delays. By applying the differential inequality and the Lyapunov method, some delay-independent conditions are derived ensuring the robust CGNNs to converge, globally, uniformly and exponentially, to a ball in the state space with a pre-specified convergence rate. Finally, the effectiveness of our results are verified by an illustrative example.

  19. Impaired rRNA synthesis triggers homeostatic responses in hippocampal neurons

    Directory of Open Access Journals (Sweden)

    Anna eKiryk

    2013-11-01

    Full Text Available Decreased rRNA synthesis and nucleolar disruption, known as nucleolar stress, are primary signs of cellular stress associated with aging and neurodegenerative disorders. Silencing of rDNA occurs during early stages of Alzheimer´s disease (AD and may play a role in dementia. Moreover aberrant regulation of the protein synthesis machinery is present in the brain of suicide victims and implicates the epigenetic modulation of rRNA. Recently, we developed unique mouse models characterized by nucleolar stress in neurons. We inhibited RNA polymerase I by genetic ablation of the basal transcription factor TIF-IA in adult hippocampal neurons. Nucleolar stress resulted in progressive neurodegeneration, although with a differential vulnerability within the CA1, CA3 and dentate gyrus. Here, we investigate the consequences of nucleolar stress on learning and memory. The mutant mice show normal performance in the Morris water maze and in other behavioral tests, suggesting the activation of adaptive mechanisms. In fact, we observe a significantly enhanced learning and re-learning corresponding to the initial inhibition of rRNA transcription. This phenomenon is accompanied by aberrant synaptic plasticity. By the analysis of nucleolar function and integrity, we find that the synthesis of rRNA is later restored. Gene expression profiling shows that thirty-six transcripts are differentially expressed in comparison to the control group in absence of neurodegeneration. Additionally, we observe a significant enrichment of the putative serum response factor (SRF binding sites in the promoters of the genes with changed expression, indicating potential adaptive mechanisms mediated by the mitogen-activated protein kinase pathway. In the dentate gyrus a neurogenetic response might compensate the initial molecular deficits. These results underscore the role of nucleolar stress in neuronal homeostasis and open a new ground for therapeutic strategies aiming at preserving

  20. Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18

    Science.gov (United States)

    Smirnov, Alexandre; Entelis, Nina; Martin, Robert P.; Tarassov, Ivan

    2011-01-01

    5S rRNA is an essential component of ribosomes of all living organisms, the only known exceptions being mitochondrial ribosomes of fungi, animals, and some protists. An intriguing situation distinguishes mammalian cells: Although the mitochondrial genome contains no 5S rRNA genes, abundant import of the nuclear DNA-encoded 5S rRNA into mitochondria was reported. Neither the detailed mechanism of this pathway nor its rationale was clarified to date. In this study, we describe an elegant molecular conveyor composed of a previously identified human 5S rRNA import factor, rhodanese, and mitochondrial ribosomal protein L18, thanks to which 5S rRNA molecules can be specifically withdrawn from the cytosolic pool and redirected to mitochondria, bypassing the classic nucleolar reimport pathway. Inside mitochondria, the cytosolic 5S rRNA is shown to be associated with mitochondrial ribosomes. PMID:21685364

  1. The reduction of radiation-induced mitotic delay by caffeine: a test of the cyclic AMP hypothesis

    International Nuclear Information System (INIS)

    Oleinick, N.L.; Brewer, E.N.; Rustad, R.C.

    1978-01-01

    A study has been made of the reduction in γ-radiation-induced mitotic delay by caffeine in the naturally-synchronous plasmodial slime mould. Physarum polycephalum during late G 2 and early prophase, and the results compared with those obtained with other compounds of similar structure and/or physiological function. The reduction of radiation-induced mitotic delay was related to increasing concentrations of caffeine over at least two orders of magnitude. Pre-irradiation treatment with caffeine had no detectable effect. Caffeine had to be present for most, if not all, of the post-irradiation pre-mitotic period. Other chemicals which are reported to inhibit cyclic AMP phosphodiesterase either reduce or increase radiation-induced mitotic delay. The results therefore indicate that the reduction of mitotic delay by caffeine is not a result of altered cyclic AMP levels. (UK)

  2. RNase MRP is required for entry of 35S precursor rRNA into the canonical processing pathway.

    Science.gov (United States)

    Lindahl, Lasse; Bommankanti, Ananth; Li, Xing; Hayden, Lauren; Jones, Adrienne; Khan, Miriam; Oni, Tolulope; Zengel, Janice M

    2009-07-01

    RNase MRP is a nucleolar RNA-protein enzyme that participates in the processing of rRNA during ribosome biogenesis. Previous experiments suggested that RNase MRP makes a nonessential cleavage in the first internal transcribed spacer. Here we report experiments with new temperature-sensitive RNase MRP mutants in Saccharomyces cerevisiae that show that the abundance of all early intermediates in the processing pathway is severely reduced upon inactivation of RNase MRP. Transcription of rRNA continues unabated as determined by RNA polymerase run-on transcription, but the precursor rRNA transcript does not accumulate, and appears to be unstable. Taken together, these observations suggest that inactivation of RNase MRP blocks cleavage at sites A0, A1, A2, and A3, which in turn, prevents precursor rRNA from entering the canonical processing pathway (35S > 20S + 27S > 18S + 25S + 5.8S rRNA). Nevertheless, at least some cleavage at the processing site in the second internal transcribed spacer takes place to form an unusual 24S intermediate, suggesting that cleavage at C2 is not blocked. Furthermore, the long form of 5.8S rRNA is made in the absence of RNase MRP activity, but only in the presence of Xrn1p (exonuclease 1), an enzyme not required for the canonical pathway. We conclude that RNase MRP is a key enzyme for initiating the canonical processing of precursor rRNA transcripts, but alternative pathway(s) might provide a backup for production of small amounts of rRNA.

  3. Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes.

    Science.gov (United States)

    Erales, Jenny; Marchand, Virginie; Panthu, Baptiste; Gillot, Sandra; Belin, Stéphane; Ghayad, Sandra E; Garcia, Maxime; Laforêts, Florian; Marcel, Virginie; Baudin-Baillieu, Agnès; Bertin, Pierre; Couté, Yohann; Adrait, Annie; Meyer, Mélanie; Therizols, Gabriel; Yusupov, Marat; Namy, Olivier; Ohlmann, Théophile; Motorin, Yuri; Catez, Frédéric; Diaz, Jean-Jacques

    2017-12-05

    Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.

  4. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians

    Directory of Open Access Journals (Sweden)

    Chiari Ylenia

    2005-03-01

    Full Text Available Abstract Background Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI has been proposed as universal marker for this purpose among animals. Results Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1–17%, with low degrees of pairwise haplotype divergence within populations (0–1%. Conclusion We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.

  5. AMPK agonist AICAR delays the initial decline in lifetime-apex V̇o2 peak, while voluntary wheel running fails to delay its initial decline in female rats.

    Science.gov (United States)

    Toedebusch, Ryan G; Ruegsegger, Gregory N; Braselton, Joshua F; Heese, Alexander J; Hofheins, John C; Childs, Tom E; Thyfault, John P; Booth, Frank W

    2016-02-01

    There has never been an outcome measure for human health more important than peak oxygen consumption (V̇o2 peak), yet little is known regarding the molecular triggers for its lifetime decline with aging. We examined the ability of physical activity or 5 wk of 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR) administration to delay the initial aging-induced decline in lifetime-apex V̇o2 peak and potential underlying molecular mechanisms. Experiment 1 consisted of female rats with (RUN) and without (NO RUN) running wheels, while experiment 2 consisted of female nonrunning rats getting the AMPK agonist AICAR (0.5 mg/g/day) subcutaneously for 5 wk beginning at 17 wk of age. All rats underwent frequent, weekly or biweekly V̇o2 peak tests beginning at 10 wk of age. In experiment 1, lifetime-apex V̇o2 peak occurred at 19 wk of age in both RUN and NO RUN and decreased thereafter. V̇o2 peak measured across experiment 1 was ∼25% higher in RUN than in NO RUN. In experiment 2, AICAR delayed the chronological age observed in experiment 1 by 1 wk, from 19 wk to 20 wk of age. RUN and NO RUN showed different skeletal muscle transcriptomic profiles both pre- and postapex. Additionally, growth and development pathways are differentially regulated between RUN and NO RUN. Angiomotin mRNA was downregulated postapex in RUN and NO RUN. Furthermore, strong significant correlations to V̇o2 peak and trends for decreased protein concentration supports angiomotin's potential importance in our model. Contrary to our primary hypothesis, wheel running was not sufficient to delay the chronological age of lifetime-apex V̇o2 peak decline, whereas AICAR delayed it 1 wk. Copyright © 2016 the American Physiological Society.

  6. Truncated predictor feedback for time-delay systems

    CERN Document Server

    Zhou, Bin

    2014-01-01

    This book provides a systematic approach to the design of predictor based controllers for (time-varying) linear systems with either (time-varying) input or state delays. Differently from those traditional predictor based controllers, which are infinite-dimensional static feedback laws and may cause difficulties in their practical implementation, this book develops a truncated predictor feedback (TPF) which involves only finite dimensional static state feedback. Features and topics: A novel approach referred to as truncated predictor feedback for the stabilization of (time-varying) time-delay systems in both the continuous-time setting and the discrete-time setting is built systematically Semi-global and global stabilization problems of linear time-delay systems subject to either magnitude saturation or energy constraints are solved in a systematic manner Both stabilization of a single system and consensus of a group of systems (multi-agent systems) are treated in a unified manner by applying the truncated pre...

  7. Pre-operative urinary tract infection: is it a risk factor for early surgical site infection with hip fracture surgery? A retrospective analysis.

    Science.gov (United States)

    Yassa, Rafik Rd; Khalfaoui, Mahdi Y; Veravalli, Karunakar; Evans, D Alun

    2017-03-01

    The aims of the current study were to determine whether pre-operative urinary tract infections in patients presenting acutely with neck of femur fractures resulted in a delay to surgery and whether such patients were at increased risk of developing post-operative surgical site infections. A retrospective review of all patients presenting with a neck of femur fracture, at a single centre over a one-year period. The hospital hip fracture database was used as the main source of data. UK University Teaching Hospital. All patients ( n  = 460) presenting across a single year study period with a confirmed hip fracture. The presence of pre-operative urinary tract infection, the timing of surgical intervention, the occurrence of post-operative surgical site infection and the pathogens identified. A total of 367 patients were operated upon within 24 hours of admission. Urinary infections were the least common cause of delay. A total of 99 patients (21.5%) had pre-operative urinary tract infection. Post-operatively, a total of 57 (12.4%) patients developed a surgical site infection. Among the latter, 31 (54.4%) did not have a pre-operative urinary infection, 23 (40.4%) patients had a pre-operative urinary tract infection, 2 had chronic leg ulcers and one patient had a pre-operative chest infection. Statistically, there was a strong relationship between pre-operative urinary tract infection and the development of post-operative surgical site infection ( p -value: 0.0005). The results of our study indicate that pre-operative urinary tract infection has a high prevalence amongst those presenting with neck of femur fractures, and this is a risk factor for the later development of post-operative surgical site infection.

  8. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jiemin [National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhou, Xuemei; Li, Yuguang [101 Institute, Ministry of Civil Affairs, Beijing 100070 (China); Xing, Jianmin, E-mail: jmxing@ipe.ac.cn [National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190 (China)

    2015-09-15

    Highlights: • Bacterial communities of haloalkaliphilic bioreactors were investigated. • MiSeq was first used in analysis of communities of haloalkaliphilic bioreactors. • Electron donors had significant effect on bacterial communities. - Abstract: Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities.

  9. Transcription analysis of the Streptomyces coelicolor A3(2) rrnA operon

    DEFF Research Database (Denmark)

    van Wezel, G P; Krab, I M; Douthwaite, S

    1994-01-01

    Transcription start sites and processing sites of the Streptomyces coelicolor A3(2) rrnA operon have been investigated by a combination of in vivo and in vitro transcription analyses. The data from these approaches are consistent with the existence of four in vivo transcription sites, corresponding...... to the promoters P1-P4. The transcription start sites are located at -597, -416, -334 and -254 relative to the start of the 16S rRNA gene. Two putative processing sites were identified, one of which is similar to a sequence reported earlier in S. coelicolor and other eubacteria. The P1 promoter is likely...... common to P2, P3 and P4 is not similar to any other known consensus promoter sequence. In fast-growing mycelium, P2 appears to be the most frequently used promoter. Transcription from all of the rrnA promoters decreased during the transition from exponential to stationary phase, although transcription...

  10. Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome

    DEFF Research Database (Denmark)

    Santos, Susana S.; Nunes, Ines Marques; Nielsen, Tue K.

    2017-01-01

    Advances in sequencing technologies allow deeper studies of the soil protist diversity and function. However, little attention has been given to the impact of the chosen soil DNA extraction procedure to the overall results. We examined the effect of three acknowledged DNA recovery methods, two...... manual methods (ISOm-11063, GnS-GII) and one commercial kit (MoBio), on soil protist community structures obtained from different sites with different land uses. Results from 18S rRNA gene amplicon sequencing suggest that DNA extraction method significantly affect the replicate homogeneity, the total...... number of operational taxonomic units (OTUs) recovered and the overall taxonomic structure and diversity of soil protist communities. However, DNA extraction effects did not overwhelm the natural variation among samples, as the community data still strongly grouped by geographical location...

  11. Study of Relationship Between Illness Perception and Delay in Seeking Help for Breast Cancer Patients Based on Leventhal's Self-Regulation Model.

    Science.gov (United States)

    Attari, Seyedeh Maryam; Ozgoli, Giti; Solhi, Mahnaz; Alavi Majd, Hamid

    2016-01-01

    One of the major causes of morbidity and mortality in breast cancer patients is delay in seeking help. Leventhal's self-regulation model provides an appropriate framework to assess delay in seeking help. The aim of this study was to investigate the relationship between "illness perception" and "help seeking delay" in breast cancer patients based on Leventhal's self-regulation model. In this correlational descriptive study with convenience sampling conducted in 2013, participants were 120 women with breast cancer who were diagnosed in the last year and referred to chemotherapy and radiotherapy centers in Rasht, Iran. Data collection scales included demographic data, Revised Illness Perception Questionnaire (IPQ-R)and a researcher made questionnaire to measure the delay in seeking help. Pre-hospital delay (help seeking delay) was evaluated in 3 phases (assessment, disease, behavior). The data were analyzed using SPSS-19. The mean (SD) age calculated for the patients was 47.3±10.2. Some 43% of the patients had a high school or higher education level and 82% were married. The "pre-hospital delay" was reported ≥3 months. Logistic regression analysis showed that none of the illness perception components were correlated with appraisal and behavioral delay phases. In the illness delay phase, "time line" (p-value =0.04) and "risk factors"(p-value=0.03) had significant effects on reducing and "psychological attributions" had significant effects on increasing the delay (p-value =0.01). "Illness coherence" was correlated with decreased pre-hospital patient delay (p-valueperceptions of breast cancer influences delay in seeking help. In addition to verifying the validity of Leventhal's self-regulation model in explaining delay in seeking help, the results signify the importance of the "illness delay phase" (decision to seek help) and educational interventions-counseling for women in the community.

  12. Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria.

    Directory of Open Access Journals (Sweden)

    Jeffrey R Johansen

    Full Text Available A highly divergent 16S rRNA gene was found in one of the five ribosomal operons present in a species complex currently circumscribed as Scytonema hyalinum (Nostocales, Cyanobacteria using clone libraries. If 16S rRNA sequence macroheterogeneity among ribosomal operons due to insertions, deletions or truncation is excluded, the sequence heterogeneity observed in S. hyalinum was the highest observed in any prokaryotic species thus far (7.3-9.0%. The secondary structure of the 16S rRNA molecules encoded by the two divergent operons was nearly identical, indicating possible functionality. The 23S rRNA gene was examined for a few strains in this complex, and it was also found to be highly divergent from the gene in Type 2 operons (8.7%, and likewise had nearly identical secondary structure between the Type 1 and Type 2 operons. Furthermore, the 16S-23S ITS showed marked differences consistent between operons among numerous strains. Both operons have promoter sequences that satisfy consensus requirements for functional prokaryotic transcription initiation. Horizontal gene transfer from another unknown heterocytous cyanobacterium is considered the most likely explanation for the origin of this molecule, but does not explain the ultimate origin of this sequence, which is very divergent from all 16S rRNA sequences found thus far in cyanobacteria. The divergent sequence is highly conserved among numerous strains of S. hyalinum, suggesting adaptive advantage and selective constraint of the divergent sequence.

  13. Numeracy Predicts Risk of Pre-Hospital Decision Delay: a Retrospective Study of Acute Coronary Syndrome Survival.

    Science.gov (United States)

    Petrova, Dafina; Garcia-Retamero, Rocio; Catena, Andrés; Cokely, Edward; Heredia Carrasco, Ana; Arrebola Moreno, Antonio; Ramírez Hernández, José Antonio

    2017-04-01

    Many patients delay seeking medical attention during acute coronary syndromes (ACS), profoundly increasing their risk for death and major disability. Although research has identified several risk factors, efforts to improve patient decision making have generally been unsuccessful, prompting a call for more research into psychological factors. The purpose of this study is to estimate the relationship between ACS decision delay and numeracy, a factor closely related to general decision making skill and risk literacy. About 5 days after experiencing ACS, 102 survivors (mean age = 58, 32-74) completed a questionnaire including measures of numeracy, decision delay, and other relevant factors (e.g., anxiety, depression, symptom severity, knowledge, demographics). Low patient numeracy was related to longer decision delay, OR = 0.64 [95 % confidence interval (CI) 0.44, 0.92], which was in turn related to higher odds of positive troponin on arrival at the hospital, OR = 1.37 [95 % CI 1.01, 2.01]. Independent of the influence of all other assessed factors, a patient with high (vs. low) numeracy was about four times more likely to seek medical attention within the critical first hour after symptom onset (i.e., OR high-low  = 3.84 [1.127, 11.65]). Numeracy may be one of the largest decision delay risk factors identified to date. Results accord with theories emphasizing potentially pivotal roles of patient deliberation, denial, and outcome understanding during decision making. Findings suggest that brief numeracy assessments may predict which patients are at greater risk for life-threatening decision delay and may also facilitate the design of risk communications that are appropriate for diverse patients who vary in risk literacy.

  14. Nucleation by rRNA Dictates the Precision of Nucleolus Assembly.

    Science.gov (United States)

    Falahati, Hanieh; Pelham-Webb, Bobbie; Blythe, Shelby; Wieschaus, Eric

    2016-02-08

    Membrane-less organelles are intracellular compartments specialized to carry out specific cellular functions. There is growing evidence supporting the possibility that such organelles form as a new phase, separating from cytoplasm or nucleoplasm. However, a main challenge to such phase separation models is that the initial assembly, or nucleation, of the new phase is typically a highly stochastic process and does not allow for the spatiotemporal precision observed in biological systems. Here, we investigate the initial assembly of the nucleolus, a membrane-less organelle involved in different cellular functions including ribosomal biogenesis. We demonstrate that the nucleolus formation is precisely timed in D. melanogaster embryos and follows the transcription of rRNA. We provide evidence that transcription of rRNA is necessary for overcoming the highly stochastic nucleation step in the formation of the nucleolus, through a seeding mechanism. In the absence of rDNA, the nucleolar proteins studied are able to form high-concentration assemblies. However, unlike the nucleolus, these assemblies are highly variable in number, location, and time at which they form. In addition, quantitative study of the changes in the nucleoplasmic concentration and distribution of these nucleolar proteins in the wild-type embryos is consistent with the role of rRNA in seeding the nucleolus formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Delayed luminescence in a multiparameter approach to evaluation and reduction of radiobiological risks

    Science.gov (United States)

    Grasso, Rosaria; Cammarata, Francesco Paolo; Minafra, Luigi; Marchese, Valentina; Russo, Giorgio; Manti, Lorenzo; Musumeci, Francesco; Scordino, Agata

    2017-07-01

    In the framework of the research project ETHICS "Pre-clinical experimental and theoretical studies to improve treatment and protection by charged particles" funded by the National Nuclear Physics Institute, Italy, we studied the phenomenon called delayed luminescence emitted by non-tumorigenic breast epithelial MCF10A cell line after proton irradiation at different doses (0.5, 2, 6, 9 Gy). The aim is to found possible correlations between delayed luminescence and in vitro damaging induced by ion irradiation. The first results of this research show that the delayed luminescence kinetics is proton dose dependent. An interesting correlation between delayed luminescence and clonogenic potential was observed.

  16. Local Stability of AIDS Epidemic Model Through Treatment and Vertical Transmission with Time Delay

    Science.gov (United States)

    Novi W, Cascarilla; Lestari, Dwi

    2016-02-01

    This study aims to explain stability of the spread of AIDS through treatment and vertical transmission model. Human with HIV need a time to positively suffer AIDS. The existence of a time, human with HIV until positively suffer AIDS can be delayed for a time so that the model acquired is the model with time delay. The model form is a nonlinear differential equation with time delay, SIPTA (susceptible-infected-pre AIDS-treatment-AIDS). Based on SIPTA model analysis results the disease free equilibrium point and the endemic equilibrium point. The disease free equilibrium point with and without time delay are local asymptotically stable if the basic reproduction number is less than one. The endemic equilibrium point will be local asymptotically stable if the time delay is less than the critical value of delay, unstable if the time delay is more than the critical value of delay, and bifurcation occurs if the time delay is equal to the critical value of delay.

  17. The probability distribution of the delay time of a wave packet in strong overlap of resonance levels

    International Nuclear Information System (INIS)

    Lyuboshitz, V.L.

    1982-01-01

    The time development of nuclear reactions at a large density of levels is investigated using the theory of overlapping resonances. The analytical expression for the function describing the time delay probability distribution of a wave packet is obtained in the framework of the model of n equi - valent channels. It is shown that a relative fluctuation of the time delay at the stage of the compound nucleus is snall. The possibility is discussed of increasing the duration of nuclear raactions with rising excitation energy

  18. Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.

    Science.gov (United States)

    Santiago-Rodriguez, Tasha M; Fornaciari, Gino; Luciani, Stefania; Dowd, Scot E; Toranzos, Gary A; Marota, Isolina; Cano, Raul J

    2016-11-01

    Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Methyltransferase That Modifies Guanine 966 of the 16 S rRNA: FUNCTIONAL IDENTIFICATION AND TERTIARY STRUCTURE*

    Science.gov (United States)

    Lesnyak, Dmitry V.; Osipiuk, Jerzy; Skarina, Tatiana; Sergiev, Petr V.; Bogdanov, Alexey A.; Edwards, Aled; Savchenko, Alexei; Joachimiak, Andrzej; Dontsova, Olga A.

    2010-01-01

    N2-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m2G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m2G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m2G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05 Å. The structure closely resembles RsmC rRNA methyltransferase, specific for m2G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m2G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed. PMID:17189261

  20. Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.

    Science.gov (United States)

    Lesnyak, Dmitry V; Osipiuk, Jerzy; Skarina, Tatiana; Sergiev, Petr V; Bogdanov, Alexey A; Edwards, Aled; Savchenko, Alexei; Joachimiak, Andrzej; Dontsova, Olga A

    2007-02-23

    N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.

  1. Time delays across saddles as a test of modified gravity

    International Nuclear Information System (INIS)

    Magueijo, João; Mozaffari, Ali

    2013-01-01

    Modified gravity theories can produce strong signals in the vicinity of the saddles of the total gravitational potential. In a sub-class of these models, this translates into diverging time delays for echoes crossing the saddles. Such models arise from the possibility that gravity might be infrared divergent or confined, and if suitably designed they are very difficult to rule out. We show that Lunar Laser Ranging during an eclipse could probe the time-delay effect within metres of the saddle, thereby proving or excluding these models. Very Large Baseline Interferometry, instead, could target delays across the Jupiter–Sun saddle. Such experiments would shed light on the infrared behaviour of gravity and examine the puzzling possibility that there might be well-hidden regions of strong gravity and even singularities inside the solar system. (fast track communication)

  2. A renaissance for the pioneering 16S rRNA gene

    Energy Technology Data Exchange (ETDEWEB)

    Tringe, Susannah; Hugenholtz, Philip

    2008-09-07

    Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the last quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene is making a comeback in its own right thanks to a number of methodological advancements including higher resolution (more sequences), analysis of multiple related samples (e.g. spatial and temporal series) and improved metadata and use of metadata. The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene.

  3. A renaissance for the pioneering 16S rRNA gene.

    Science.gov (United States)

    Tringe, Susannah G; Hugenholtz, Philip

    2008-10-01

    Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the past quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene is making a comeback in its own right thanks to a number of methodological advancements including higher resolution (more sequences), analysis of multiple related samples (e.g. spatial and temporal series) and improved metadata, and use of metadata. The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene.

  4. Robertsonian translocation 13/14 associated with rRNA genes ...

    African Journals Online (AJOL)

    Alexander A. Dolskiy

    2017-12-01

    Dec 1, 2017 ... Results: We describe a family case of a translocation rob (13; 14) and elevated rRNA expression in the proband with ..... Clin Genet 2010;78:299–309. ... [9] Bertini V, Fogli A, Bruno R, Azzarà A, Michelucci A, Mattina T, et al.

  5. Variable Delay Element For Jitter Control In High Speed Data Links

    Science.gov (United States)

    Livolsi, Robert R.

    2002-06-11

    A circuit and method for decreasing the amount of jitter present at the receiver input of high speed data links which uses a driver circuit for input from a high speed data link which comprises a logic circuit having a first section (1) which provides data latches, a second section (2) which provides a circuit generates a pre-destorted output and for compensating for level dependent jitter having an OR function element and a NOR function element each of which is coupled to two inputs and to a variable delay element as an input which provides a bi-modal delay for pulse width pre-distortion, a third section (3) which provides a muxing circuit, and a forth section (4) for clock distribution in the driver circuit. A fifth section is used for logic testing the driver circuit.

  6. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments

    DEFF Research Database (Denmark)

    Ravenschlag, K.; Sahm, K.; Knoblauch, C.

    2000-01-01

    The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburg-fjorden, Svalbard) a-as characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes...... that FISH and rRNA slot blot hybridization gave comparable results. Furthermore, a combination of the two methods allowed us to calculate specific cellular rRNA contents with respect to localization in the sediment profile. The rRNA contents of Desulfosarcina-Desulfococcus cells were highest in the first 5...... mm of the sediment (0.9 and 1.4 fg, respectively) and decreased steeply with depth, indicating that maximal metabolic activity occurred close to the surface, Based on SRB cell numbers, cellular sulfate reduction rates were calculated. The rates were highest in the surface layer (0.14 fmol cell(-1...

  7. Mortality associated with delays between clinic entry and ART initiation in resource-limited-settings: results of a transition-state model

    Science.gov (United States)

    HOFFMANN, Christopher J; LEWIS, James J; DOWDY, David W; FIELDING, Katherine L; GRANT, Alison D; MARTINSON, Neil A; CHURCHYARD, Gavin J; CHAISSON, Richard E

    2013-01-01

    Objective Estimate the mortality impact of delay in antiretroviral therapy (ART) initiation from the time of entry-into-care. Design A state-transition Markov process model. This technique allows for assessing mortality before and after ART initiation associated with delays in ART initiation among a general population of ART eligible patients without conducting a randomized trial. Methods We used patient-level data from three South African cohorts to determine transition probabilities for pre-ART CD4 count changes and pre-ART and on-ART mortality. For each parameter we generated probabilities and distributions for Monte Carlo simulations with one week cycles to estimate mortality 52 weeks from clinic entry. Results We estimated an increase in mortality from 11.0% to 14.7% (relative increase of 34%) with a 10 week delay in ART for patients entering care with our pre-ART cohort CD4 distribution. When we examined low CD4 ranges, the relative increase in mortality delays remained similar; however, the absolute increase in mortality rose. For example, among patients entering with CD4 count 50–99 cells/mm3, 12 month mortality increased from 13.3% with no delay compared to 17.0% with a 10 week delay and 22.9% with a 6 month delay. Conclusions Delays in ART initiation, common in routine HIV programs, can lead to important increases in mortality. Prompt ART initiation for patients entering clinical care and eligible for ART, especially those with lower CD4 counts, could be a relatively low cost approach with a potential marked impact on mortality. PMID:23392457

  8. Mortality associated with delays between clinic entry and ART initiation in resource-limited settings: results of a transition-state model.

    Science.gov (United States)

    Hoffmann, Christopher J; Lewis, James J; Dowdy, David W; Fielding, Katherine L; Grant, Alison D; Martinson, Neil A; Churchyard, Gavin J; Chaisson, Richard E

    2013-05-01

    To estimate the mortality impact of delay in antiretroviral therapy (ART) initiation from the time of entry into care. A state-transition Markov process model. This technique allows for assessing mortality before and after ART initiation associated with delays in ART initiation among a general population of ART-eligible patients without conducting a randomized trial. We used patient-level data from 3 South African cohorts to determine transition probabilities for pre-ART CD4 count changes and pre-ART and on-ART mortality. For each parameter, we generated probabilities and distributions for Monte Carlo simulations with 1-week cycles to estimate mortality 52 weeks from clinic entry. We estimated an increase in mortality from 11.0% to 14.7% (relative increase of 34%) with a 10-week delay in ART for patients entering care with our pre-ART cohort CD4 distribution. When we examined low CD4 ranges, the relative increase in mortality delays remained similar; however, the absolute increase in mortality rose. For example, among patients entering with CD4 count 50-99 cells per cubic millimeter, 12-month mortality increased from 13.3% with no delay compared with 17.0% with a 10-week delay and 22.9% with a 6-month delay. Delays in ART initiation, common in routine HIV programs, can lead to important increases in mortality. Prompt ART initiation for patients entering clinical care and eligible for ART, especially those with lower CD4 counts, could be a relatively low-cost approach with a potential marked impact on mortality.

  9. Patients and acute coronary syndrome - Prehospital delay and mental and emotional delaying responses - a qualitative study

    DEFF Research Database (Denmark)

    Lorentzen, Vibeke; Larsen, Birte Hedegaard

    2016-01-01

    to identify and discuss patient’s mental and emotional responses, including interpretations and delaying strategies concerning Acute Coronary Syndrome symptoms, with a view to elucidating patterns in the pre-hospital decision-making process of female and male persons to contact medical services...... cardinal. Male participants often used expletives and expressed symptoms in concrete terms. Women expressed symptoms in vaguer terms. Both genders used linguistic metaphors. The implications for nursing emphasised the impact of prodromal symptoms, mental and emotional withdrawal, and linguistic...

  10. Patients and acute coronary syndrome - Prehospital delay and mental and emotional delaying responses - a qualitative study

    DEFF Research Database (Denmark)

    Lorentzen, Vibeke; Larsen, Birte Hedegaard

    2016-01-01

    cardinal. Male participants often used expletives and expressed symptoms in concrete terms. Women expressed symptoms in vaguer terms. Both genders used linguistic metaphors. The implications for nursing emphasised the impact of prodromal symptoms, mental and emotional withdrawal, and linguistic...... to identify and discuss patient’s mental and emotional responses, including interpretations and delaying strategies concerning Acute Coronary Syndrome symptoms, with a view to elucidating patterns in the pre-hospital decision-making process of female and male persons to contact medical services...

  11. On the performance of data receivers with a restricted detection delay

    NARCIS (Netherlands)

    Bergmans, J.W.M.; Willems, F.M.J.; Kerpen, G.S.M.

    1994-01-01

    It is well known that the performance of a data receiver for an intersymbol interference (ISI) channel can depend strongly on the detection delay d. For a discrete-time communication system, this paper derives a lower bound on the bit-error probability as a function of d. This "restricted delay

  12. Microbial Dark Matter: Unusual intervening sequences in 16S rRNA genes of candidate phyla from the deep subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Jarett, Jessica; Stepanauskas, Ramunas; Kieft, Thomas; Onstott, Tullis; Woyke, Tanja

    2014-03-17

    The Microbial Dark Matter project has sequenced genomes from over 200 single cells from candidate phyla, greatly expanding our knowledge of the ecology, inferred metabolism, and evolution of these widely distributed, yet poorly understood lineages. The second phase of this project aims to sequence an additional 800 single cells from known as well as potentially novel candidate phyla derived from a variety of environments. In order to identify whole genome amplified single cells, screening based on phylogenetic placement of 16S rRNA gene sequences is being conducted. Briefly, derived 16S rRNA gene sequences are aligned to a custom version of the Greengenes reference database and added to a reference tree in ARB using parsimony. In multiple samples from deep subsurface habitats but not from other habitats, a large number of sequences proved difficult to align and therefore to place in the tree. Based on comparisons to reference sequences and structural alignments using SSU-ALIGN, many of these ?difficult? sequences appear to originate from candidate phyla, and contain intervening sequences (IVSs) within the 16S rRNA genes. These IVSs are short (39 - 79 nt) and do not appear to be self-splicing or to contain open reading frames. IVSs were found in the loop regions of stem-loop structures in several different taxonomic groups. Phylogenetic placement of sequences is strongly affected by IVSs; two out of three groups investigated were classified as different phyla after their removal. Based on data from samples screened in this project, IVSs appear to be more common in microbes occurring in deep subsurface habitats, although the reasons for this remain elusive.

  13. Evolution of primary and secondary structures in 5S and 5.8S rRNA

    International Nuclear Information System (INIS)

    Curtiss, W.C.

    1986-01-01

    The secondary structure of Bombyx mori 5S rRNA was studied using the sing-strand specific S1 nuclease and the base pair specific cobra venom ribonuclease. The RNA was end-labeled with [ 32 P] at either the 5' or 3' end and sequenced using enzymatic digestion techniques. These enzymatic data coupled with thermodynamic structure prediction were used to generate a secondary structure for 5S rRNA. A computer algorithm has been implemented to aid in the comparison of a large set of homologous RNAs. Eukaryotic 5S rRNA sequences from thirty four diverse species were compared by (1) alignment or the sequences, (2) the positions of substitutions were located with respect to the aligned sequence and secondary structure, and (3) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. Eukaryotic 5S rRNA was found to have significant sequence variation throughout much of the molecule while maintaining a relatively constant secondary structure. A detailed analysis of the sequence and structure variability in each region of the molecule is presented

  14. Effects of shading and covering material application for delaying ...

    African Journals Online (AJOL)

    To delay the harvest of Sultani Cekirdeksiz grape variety and to reduce pre and post-harvest botrytis bunch rot severity, shading and covering material application were tested in 2009 to 2010 growing periods. In this study, grape vines were shaded with shading materials which had three different shading densities (35, 55, ...

  15. Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins.

    OpenAIRE

    ARCURI, P.B.; THONNEY, M.L.; SCHOFIELD, P.; PELL, A.N.

    2003-01-01

    In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA) probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG) and polyvinylpirrolidone (PVP) on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/...

  16. Mitochondrial 12S rRNA A827G mutation is involved in the genetic susceptibility to aminoglycoside ototoxicity

    International Nuclear Information System (INIS)

    Xing Guangqian; Chen Zhibin; Wei Qinjun; Tian Huiqin; Li Xiaolu; Zhou Aidong; Bu Xingkuan; Cao Xin

    2006-01-01

    We have analyzed the clinical and molecular characterization of a Chinese family with aminoglycoside-induced and non-syndromic hearing impairment. Clinical evaluations revealed that only those family members who had a history of exposure to aminoglycoside antibiotics subsequently developed hearing loss, suggesting mitochondrial genome involvement. Sequence analysis of the mitochondrial 12S rRNA and tRNA Ser(UCN) genes led to the identification of a homoplasmic A827G mutation in all maternal relatives, a mutation that was identified previously in a few sporadic patients and in another Chinese family with non-syndromic deafness. The pathogenicity of the A827G mutation is strongly supported by the occurrence of the same mutation in two independent families and several genetically unrelated subjects. The A827G mutation is located at the A-site of the mitochondrial 12S rRNA gene which is highly conserved in mammals. It is possible that the alteration of the tertiary or quaternary structure of this rRNA by the A827G mutation may lead to mitochondrial dysfunction, thereby playing a role in the pathogenesis of hearing loss and aminoglycoside hypersensitivity. However, incomplete penetrance of hearing impairment indicates that the A827G mutation itself is not sufficient to produce clinical phenotype but requires the involvement of modifier factors for the phenotypic expression. Indeed, aminoglycosides may contribute to the phenotypic manifestation of the A827G mutation in this family. In contrast with the congenital or early-onset hearing impairment in another Chinese family carrying the A827G mutation, three patients in this pedigree developed hearing loss only after use of aminoglycosides. This discrepancy likely reflects the difference of genetic backgrounds, either mitochondrial haplotypes or nuclear modifier genes, between two families

  17. Pre-Irradiation Chemotherapy in High Risk Medulloblastoma

    International Nuclear Information System (INIS)

    Abd-El-Aal, H.

    2006-01-01

    Rationale: The present study evaluates the effect of pre-irradiation chemotherapy in pediatric patients with high risk medulloblastoma. Twenty-four (24) pediatric patients attended the pediatric unit of Kasr-EI-Aini Center of Radiation Oncology and Nuclear Medicine (NEMROCK) from January 2000 to January 2003. Patients and Methods: Our patients were 13 boys and II girls aged 3-12 years with a median of 6.5 years. According to Chang staging system 6 cases had T2, 14 cases had T3 A and 4 cases had T3 B, 20 cases were M0, 3 cases were M I and I case was M2. All patients were treated by initial surgery, 2 cycles of pre-irradiation chemotherapy followed by craniospinal radiation then by 4 cycles of post-radiation chemotherapy. Results: Fifteen out of the 20 patients with M0 had objective response (10CR + 5PR) and no one had disease progression after pre-irradiation chemotherapy. Among 4 patients with M0 disease, 2 patients had PR and 2 had S.D. There was no disease progression among patients who received pre-irradiation chemotherapy. The 3-year overall survival and 3-year progression-free survival; (PFS) were 50% and 51 %, respectively, Myelosuppression was the main toxic effect observed during pre-irradiation chemotherapy; however, there was no delay or interruption of craniospinal irradiation. Conclusion: Pre-irradiation chemotherapy is effective in high risk medulloblastoma and is associated with acceptable side effects. The delay in craniospinal irradiation (CSI) for about 5 weeks to receive 2 courses of chemotherapy will not significantly increase disease progression. Multiple cycles of post-irradiation chemotherapy can be given safely after C51. A larger number of patients and longer follow-up is needed to confirm the results

  18. Nucleolar TRF2 attenuated nucleolus stress-induced HCC cell-cycle arrest by altering rRNA synthesis.

    Science.gov (United States)

    Yuan, Fuwen; Xu, Chenzhong; Li, Guodong; Tong, Tanjun

    2018-05-03

    The nucleolus is an important organelle that is responsible for the biogenesis of ribosome RNA (rRNA) and ribosomal subunits assembly. It is also deemed to be the center of metabolic control, considering the critical role of ribosomes in protein translation. Perturbations of rRNA synthesis are closely related to cell proliferation and tumor progression. Telomeric repeat-binding factor 2 (TRF2) is a member of shelterin complex that is responsible for telomere DNA protection. Interestingly, it was recently reported to localize in the nucleolus of human cells in a cell-cycle-dependent manner, while the underlying mechanism and its role on the nucleolus remained unclear. In this study, we found that nucleolar and coiled-body phosphoprotein 1 (NOLC1), a nucleolar protein that is responsible for the nucleolus construction and rRNA synthesis, interacted with TRF2 and mediated the shuttle of TRF2 between the nucleolus and nucleus. Abating the expression of NOLC1 decreased the nucleolar-resident TRF2. Besides, the nucleolar TRF2 could bind rDNA and promoted rRNA transcription. Furthermore, in hepatocellular carcinoma (HCC) cell lines HepG2 and SMMC7721, TRF2 overexpression participated in the nucleolus stress-induced rRNA inhibition and cell-cycle arrest.

  19. GEOM/GEOM[a]/1/ queue with late arrival system with delayed access and delayed multiple working vacations

    Directory of Open Access Journals (Sweden)

    Cheng Jiang

    2014-01-01

    Full Text Available This paper considers a discrete-time bulk-service queue with infinite buffer space and delay multiple working vacations. Considering a late arrival system with delayed access (LAS-AD, it is assumed that the inter-arrival times, service times, vacation times are all geometrically distributed. The server does not take a vacation immediately at service complete epoch but keeps idle period. According to a bulk-service rule, at least one customer is needed to start a service with a maximum serving capacity 'a'. Using probability analysis method and displacement operator method, the queue length and the probability generating function of waiting time at pre-arrival epochs are obtained. Furthermore, the outside observer’s observation epoch queue length distributions are given. Finally, computational examples with numerical results in the form of graphs and tables are discussed.

  20. An approach to constitutional delay of growth and puberty

    Directory of Open Access Journals (Sweden)

    Ashraf T Soliman

    2012-01-01

    Full Text Available Constitutional delay of growth and puberty is a transient state of hypogonadotropic hypogonadism associated with prolongation of childhood phase of growth, delayed skeletal maturation, delayed and attenuated pubertal growth spurt, and relatively low insulin-like growth factor-1 secretion. In a considerable number of cases, the final adult height (Ht does not reach the mid-parental or the predicted adult Ht for the individual, with some degree of disproportionately short trunk. In the pre-pubertal male, testosterone (T replacement therapy can be used to induce pubertal development, accelerate growth and relieve the psychosocial complaints of the adolescents. However, some issues in the management are still unresolved. These include type, optimal timing, dose and duration of sex steroid treatment and the possible use of adjunctive or alternate therapy including: oxandrolone, aromatase inhibitors and human growth hormone.

  1. Solving the pre-marshalling problem to optimality with A* and IDA*

    DEFF Research Database (Denmark)

    Tierney, Kevin; Pacino, Dario; Voß, Stefan

    2017-01-01

    We present a novel solution approach to the container pre-marshalling problem using the A* and IDA* algorithms combined with several novel branching and symmetry breaking rules that significantly increases the number of pre-marshalling instances that can be solved to optimality. A* and IDA......* are graph search algorithms that use heuristics combined with a complete graph search to find optimal solutions to problems. The container pre-marshalling problem is a key problem for container terminals seeking to reduce delays of inter-modal container transports. The goal of the container pre...

  2. Beta-delayed neutron decay of $^{33}$Na

    CERN Document Server

    Radivojevic, Z; Caurier, E; Cederkäll, J; Courtin, S; Dessagne, P; Jokinen, A; Knipper, A; Le Scornet, G; Lyapin, V G; Miehé, C; Nowacki, F; Nummela, S; Oinonen, M; Poirier, E; Ramdhane, M; Trzaska, W H; Walter, G; Äystö, J

    2002-01-01

    Beta-delayed neutron decay of /sup 33/Na has been studied using the on-line mass separator ISOLDE. The delayed neutron spectra were measured by time-of-flight technique using fast scintillators. Two main neutron groups at 800(60) and 1020(80) keV were assigned to the /sup 33/Na decay, showing evidence for strong feeding of states at about 4 MeV in /sup 33/Mg. By simultaneous beta - gamma -n counting the delayed neutron emission probabilities P/sub 1n/ = 47(6)% and P /sub 2n/ = 13(3)% were determined. The half-life value for /sup 33 /Na, T/sub 1/2/ = 8.0(3) ms, was measured by three different techniques, one employing identifying gamma transitions and two employing beta and neutron counting. (21 refs).

  3. Assembly of proteins and 5 S rRNA to transcripts of the major structural domains of 23 S rRNA

    DEFF Research Database (Denmark)

    Ostergaard, P; Phan, H; Johansen, L B

    1998-01-01

    The six major structural domains of 23 S rRNA from Escherichia coli, and all combinations thereof, were synthesized as separate T7 transcripts and reconstituted with total 50 S subunit proteins. Analysis by one and two-dimensional gel electrophoresis demonstrated the presence of at least one prim...... approach was used to map the putative binding regions on domain V of protein L9 and the 5 S RNA-L5-L18 complex....

  4. Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life

    DEFF Research Database (Denmark)

    Karst, Soeren M; Dueholm, Morten S; McIlroy, Simon J

    2016-01-01

    Ribosomal RNA (rRNA) genes are the consensus marker for determination of microbial diversity on the planet, invaluable in studies of evolution and, for the past decade, high-throughput sequencing of variable regions of ribosomal RNA genes has become the backbone of most microbial ecology studies...... (SSU) rRNA genes and synthetic long read sequencing by molecular tagging, to generate primer-free, full-length SSU rRNA gene sequences from all domains of life, with a median raw error rate of 0.17%. We generated thousands of full-length SSU rRNA sequences from five well-studied ecosystems (soil, human...... gut, fresh water, anaerobic digestion, and activated sludge) and obtained sequences covering all domains of life and the majority of all described phyla. Interestingly, 30% of all bacterial operational taxonomic units were novel, compared to the SILVA database (less than 97% similarity...

  5. A mathematical model of a crocodilian population using delay-differential equations.

    Science.gov (United States)

    Gallegos, Angela; Plummer, Tenecia; Uminsky, David; Vega, Cinthia; Wickman, Clare; Zawoiski, Michael

    2008-11-01

    The crocodilia have multiple interesting characteristics that affect their population dynamics. They are among several reptile species which exhibit temperature-dependent sex determination (TSD) in which the temperature of egg incubation determines the sex of the hatchlings. Their life parameters, specifically birth and death rates, exhibit strong age-dependence. We develop delay-differential equation (DDE) models describing the evolution of a crocodilian population. In using the delay formulation, we are able to account for both the TSD and the age-dependence of the life parameters while maintaining some analytical tractability. In our single-delay model we also find an equilibrium point and prove its local asymptotic stability. We numerically solve the different models and investigate the effects of multiple delays on the age structure of the population as well as the sex ratio of the population. For all models we obtain very strong agreement with the age structure of crocodilian population data as reported in Smith and Webb (Aust. Wild. Res. 12, 541-554, 1985). We also obtain reasonable values for the sex ratio of the simulated population.

  6. Linking Maternal and Somatic 5S rRNA types with Different Sequence-Specific Non-LTR Retrotransposons

    NARCIS (Netherlands)

    Locati, M.D.; Pagano, J.F.B.; Ensink, W.A.; van Olst, M.; van Leeuwen, S.; Nehrdich, U.; Zhu, K.; Spaink, H.P.; Girard, G.; Rauwerda, H.; Jonker, M.J.; Dekker, R.J.; Breit, T.M.

    5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo and adult tissue,

  7. Transcript levels, alternative splicing and proteolytic cleavage of TFIIIA control 5S rRNA accumulation during Arabidopsis thaliana development.

    Science.gov (United States)

    Layat, Elodie; Cotterell, Sylviane; Vaillant, Isabelle; Yukawa, Yasushi; Tutois, Sylvie; Tourmente, Sylvette

    2012-07-01

    Ribosome biogenesis is critical for eukaryotic cells and requires coordinated synthesis of the protein and rRNA moieties of the ribosome, which are therefore highly regulated. 5S ribosomal RNA, an essential component of the large ribosomal subunit, is transcribed by RNA polymerase III and specifically requires transcription factor IIIA (TFIIIA). To obtain insight into the regulation of 5S rRNA transcription, we have investigated the expression of 5S rRNA and the exon-skipped (ES) and exon-including (EI) TFIIIA transcripts, two transcript isoforms that result from alternative splicing of the TFIIIA gene, and TFIIIA protein amounts with respect to requirements for 5S rRNA during development. We show that 5S rRNA quantities are regulated through distinct but complementary mechanisms operating through transcriptional and post-transcriptional control of TFIIIA transcripts as well as at the post-translational level through proteolytic cleavage of the TFIIIA protein. During the reproductive phase, high expression of the TFIIIA gene together with low proteolytic cleavage contributes to accumulation of functional, full-length TFIIIA protein, and results in 5S rRNA accumulation in the seed. In contrast, just after germination, the levels of TFIIIA-encoding transcripts are low and stable. Full-length TFIIIA protein is undetectable, and the level of 5S rRNA stored in the embryo progressively decreases. After day 4, in correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length TFIIIA protein with transcriptional activity accumulates and permits de novo transcription of 5S rRNA. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  8. Detection and characterization of Pasteuria 16S rRNA gene sequences from nematodes and soils.

    Science.gov (United States)

    Duan, Y P; Castro, H F; Hewlett, T E; White, J H; Ogram, A V

    2003-01-01

    Various bacterial species in the genus Pasteuria have great potential as biocontrol agents against plant-parasitic nematodes, although study of this important genus is hampered by the current inability to cultivate Pasteuria species outside their host. To aid in the study of this genus, an extensive 16S rRNA gene sequence phylogeny was constructed and this information was used to develop cultivation-independent methods for detection of Pasteuria in soils and nematodes. Thirty new clones of Pasteuria 16S rRNA genes were obtained directly from nematodes and soil samples. These were sequenced and used to construct an extensive phylogeny of this genus. These sequences were divided into two deeply branching clades within the low-G + C, Gram-positive division; some sequences appear to represent novel species within the genus Pasteuria. In addition, a surprising degree of 16S rRNA gene sequence diversity was observed within what had previously been designated a single strain of Pasteuria penetrans (P-20). PCR primers specific to Pasteuria 16S rRNA for detection of Pasteuria in soils were also designed and evaluated. Detection limits for soil DNA were 100-10,000 Pasteuria endospores (g soil)(-1).

  9. Presence of Helicobacter pylori in a Mexican Pre-Columbian Mummy

    Directory of Open Access Journals (Sweden)

    Cerbón Marco A

    2008-07-01

    Full Text Available Abstract Background Recent studies showed that Helicobacter pylori existed in the New World prior to the arrival of Columbus. The purpose of the present study was to detect the presence of Helicobacter pylori in pre-Columbian mummies from Northern Mexico. Methods Six samples were studied (four samples of gastric remains, tongue-soft palate, and brain remained as negative controls from two of the six naturally mummified corpses studied (adult male and infant male. Samples were taken from tissues suitable for DNA amplification by Polymerase chain reaction (PCR. DNA was extracted and H. pylori detection was carried out by PCR and hybridized with the pHp probe from 16S rRNA gene. The purified PCR products were cloned and sequenced in both directions. DNA sequences were analyzed with ALIGN and BLAST software. A second amplification was performed using ureB gene by real-time PCR. Results From four samples of gastric remnant, only two were H. pylori-positive for amplification of a 109 bp DNA fragment; the remaining two were negative, as were the tongue-soft palate and the brain biopsies as well. These PCR products were hybridized with a pHp probe. Nucleotide sequence analysis showed homology with H. pylori in 98 of 99% when compared with the gene bank nucleotide sequence. Only one sample of gastric remnant H. pylori-positive with 16S rRNA gene was also positive for ureB gene from H. pylori. Conclusion This data supported infection with H. pylori in Mexican pre-Columbian mummies dating from approximately 1,350 AC.

  10. Common 5S rRNA variants are likely to be accepted in many sequence contexts

    Science.gov (United States)

    Zhang, Zhengdong; D'Souza, Lisa M.; Lee, Youn-Hyung; Fox, George E.

    2003-01-01

    Over evolutionary time RNA sequences which are successfully fixed in a population are selected from among those that satisfy the structural and chemical requirements imposed by the function of the RNA. These sequences together comprise the structure space of the RNA. In principle, a comprehensive understanding of RNA structure and function would make it possible to enumerate which specific RNA sequences belong to a particular structure space and which do not. We are using bacterial 5S rRNA as a model system to attempt to identify principles that can be used to predict which sequences do or do not belong to the 5S rRNA structure space. One promising idea is the very intuitive notion that frequently seen sequence changes in an aligned data set of naturally occurring 5S rRNAs would be widely accepted in many other 5S rRNA sequence contexts. To test this hypothesis, we first developed well-defined operational definitions for a Vibrio region of the 5S rRNA structure space and what is meant by a highly variable position. Fourteen sequence variants (10 point changes and 4 base-pair changes) were identified in this way, which, by the hypothesis, would be expected to incorporate successfully in any of the known sequences in the Vibrio region. All 14 of these changes were constructed and separately introduced into the Vibrio proteolyticus 5S rRNA sequence where they are not normally found. Each variant was evaluated for its ability to function as a valid 5S rRNA in an E. coli cellular context. It was found that 93% (13/14) of the variants tested are likely valid 5S rRNAs in this context. In addition, seven variants were constructed that, although present in the Vibrio region, did not meet the stringent criteria for a highly variable position. In this case, 86% (6/7) are likely valid. As a control we also examined seven variants that are seldom or never seen in the Vibrio region of 5S rRNA sequence space. In this case only two of seven were found to be potentially valid. The

  11. Airport Flight Departure Delay Model on Improved BN Structure Learning

    Science.gov (United States)

    Cao, Weidong; Fang, Xiangnong

    An high score prior genetic simulated annealing Bayesian network structure learning algorithm (HSPGSA) by combining genetic algorithm(GA) with simulated annealing algorithm(SAA) is developed. The new algorithm provides not only with strong global search capability of GA, but also with strong local hill climb search capability of SAA. The structure with the highest score is prior selected. In the mean time, structures with lower score are also could be choice. It can avoid efficiently prematurity problem by higher score individual wrong direct growing population. Algorithm is applied to flight departure delays analysis in a large hub airport. Based on the flight data a BN model is created. Experiments show that parameters learning can reflect departure delay.

  12. Punctual mutations in 23S rRNA gene of clarithromycin-resistant Helicobacter pylori in Colombian populations.

    Science.gov (United States)

    Matta, Andrés Jenuer; Zambrano, Diana Carolina; Pazos, Alvaro Jairo

    2018-04-14

    To characterize punctual mutations in 23S rRNA gene of clarithromycin-resistant Helicobacter pylori ( H. pylori ) and determine their association with therapeutic failure. PCR products of 23S rRNA gene V domain of 74 H. pylori isolates; 34 resistant to clarithromycin (29 from a low-risk gastric cancer (GC) population: Tumaco-Colombia, and 5 from a high-risk population: Tuquerres-Colombia) and 40 from a susceptible population (28 from Tumaco and 12 from Túquerres) were sequenced using capillary electrophoresis. The concordance between mutations of V domain 23S rRNA gene of H. pylori and therapeutic failure was determined using the Kappa coefficient and McNemar's test was performed to determine the relationship between H. pylori mutations and clarithromycin resistance. 23S rRNA gene from H. pylori was amplified in 56/74 isolates, of which 25 were resistant to clarithromycin (20 from Tumaco and 5 from Túquerres, respectively). In 17 resistant isolates (13 from Tumaco and 4 from Túquerres) the following mutations were found: A1593T1, A1653G2, C1770T, C1954T1, and G1827C in isolates from Tumaco, and A2144G from Túquerres. The mutations T2183C, A2144G and C2196T in H. pylori isolates resistant to clarithromycin from Colombia are reported for the first time. No association between the H. pylori mutations and in vitro clarithromycin resistance was found. However, therapeutic failure of eradication treatment was associated with mutations of 23S rRNA gene in clarithromycin-resistant H. pylori ( κ = 0.71). The therapeutic failure of eradication treatment in the two populations from Colombia was associated with mutations of the 23S rRNA gene in clarithromycin-resistant H. pylori .

  13. Pre-scission 4He multiplicity in the 19F+197Au reaction

    International Nuclear Information System (INIS)

    Ikezoe, H.; Shikazono, N.; Nagame, Y.; Sugiyama, Y.; Tomita, Y.; Ideno, K.; Iwamoto, A.; Ohtsuki, T.

    1990-01-01

    Pre- and post-scission 4 He particle multiplicities for the 19 F+ 197 Au reaction in the excitation energy range of 43 to 90 MeV have been measured in coincidence with fission fragments. The coincident 4 He particles measured at backward angles are accounted for by evaporation from a compound nucleus and fission fragments. The most probable center-of-mass energy of the 4 He particles measured at backward angles is shifted towards lower energies by ∼2 MeV compared to a statistical model calculation performed by assuming 4 He emission from a spherical compound nucleus. The observed pre-scission 4 He multiplicity as a function of excitation energy is compared to a set of statistical-model calculations which also included the delayed onset of fission. The comparison shows that the observed energy dependence of the pre-scission 4 He multiplicity is reproduced by the calculation without taking into account the delayed onset of fission if the reduced emission barrier for 4 He is assumed in the calculation. The emission mechanism of the pre-scission 4 He is discussed

  14. Fission delay and GDR γ-ray from very heavy system

    International Nuclear Information System (INIS)

    Shen, W.Q.; Wang, J.S.; Ye, W.; Cai, Y.H.; Ma, Y.G.; Feng, J.; Fang, D.Q.; Cai, X.Z.

    1999-01-01

    The study of the fission delay in reaction of 84 Kr+ 27 Al at 10.6 Mev/u and the systematics of fission delay are described. Authors also discussed the possibility to study the GDR γ rays emitted from the super-heavy compound system on the basis of the strong increasing of the GDR γ rays duo to the fission delay. The calculation results of the GDR γ rays from the super-heavy compound system via microscopic semi-classical Vlasov equation and the experimental data analysis for searching the super-heavy compound system via GDR γ were given

  15. Human TRMU encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase is a putative nuclear modifier gene for the phenotypic expression of the deafness-associated 12S rRNA mutations

    International Nuclear Information System (INIS)

    Yan Qingfeng; Bykhovskaya, Yelena; Li Ronghua; Mengesha, Emebet; Shohat, Mordechai; Estivill, Xavier; Fischel-Ghodsian, Nathan; Guan Minxin

    2006-01-01

    Nuclear modifier genes have been proposed to modulate the phenotypic manifestation of human mitochondrial 12S rRNA A1491G mutation associated with deafness in many families world-wide. Here we identified and characterized the putative nuclear modifier gene TRMU encoding a highly conserved mitochondrial protein related to tRNA modification. A 1937 bp TRMU cDNA has been isolated and the genomic organization of TRMU has been elucidated. The human TRMU gene containing 11 exons encodes a 421 residue protein with a strong homology to the TRMU-like proteins of bacteria and other homologs. TRMU is ubiquitously expressed in various tissues, but abundantly in tissues with high metabolic rates including heart, liver, kidney, and brain. Immunofluorescence analysis of human 143B cells expressing TRMU-GFP fusion protein demonstrated that the human Trmu localizes and functions in mitochondrion. Furthermore, we show that in families with the deafness-associated 12S rRNA A1491G mutation there is highly suggestive linkage and linkage disequilibrium between microsatellite markers adjacent to TRMU and the presence of deafness. These observations suggest that human TRMU may modulate the phenotypic manifestation of the deafness-associated mitochondrial 12S rRNA mutations

  16. Domain V of 23S rRNA contains all the structural elements necessary for recognition by the ErmE methyltransferase

    DEFF Research Database (Denmark)

    Vester, B; Douthwaite, S

    1994-01-01

    investigated what structural elements in 23S rRNA are required for specific recognition by the ErmE methyltransferase. The ermE gene was cloned into R1 plasmid derivatives, providing a means of inducible expression in Escherichia coli. Expression of the methyltransferase in vivo confers resistance......, and the enzyme efficiently modifies 23S rRNA in vitro. Removal of most of the 23S rRNA structure, so that only domain V (nucleotides 2000 to 2624) remains, does not affect the efficiency of modification by the methyltransferase. In addition, modification still occurs after the rRNA tertiary structure has been...

  17. Imitation of contrastive lexical stress in children with speech delay

    Science.gov (United States)

    Vick, Jennell C.; Moore, Christopher A.

    2005-09-01

    This study examined the relationship between acoustic correlates of stress in trochaic (strong-weak), spondaic (strong-strong), and iambic (weak-strong) nonword bisyllables produced by children (30-50) with normal speech acquisition and children with speech delay. Ratios comparing the acoustic measures (vowel duration, rms, and f0) of the first syllable to the second syllable were calculated to evaluate the extent to which each phonetic parameter was used to mark stress. In addition, a calculation of the variability of jaw movement in each bisyllable was made. Finally, perceptual judgments of accuracy of stress production were made. Analysis of perceptual judgments indicated a robust difference between groups: While both groups of children produced errors in imitating the contrastive lexical stress models (~40%), the children with normal speech acquisition tended to produce trochaic forms in substitution for other stress types, whereas children with speech delay showed no preference for trochees. The relationship between segmental acoustic parameters, kinematic variability, and the ratings of stress by trained listeners will be presented.

  18. On the linearity of cross-correlation delay times

    Science.gov (United States)

    Mercerat, E. D.; Nolet, G.

    2012-12-01

    major contributor to deviation from linearity. The strong velocity contrast of 10% and the regularity of the anomalous structure generate strong reverberations. The test thus provides a worst-case scenario. The results scale up to regional (upper mantle) seismology if times and distances are multiplied by 10(4) . We conclude that in all but the most extreme cases, P-wave delay times depend quasi-linearly on the model perturbations.

  19. Alteration of rRNA gene copy number and expression in patients ...

    African Journals Online (AJOL)

    Irina S. Kolesnikova

    2017-09-01

    Sep 1, 2017 ... Asia R. Shorina d, Alexander S. Graphodatsky a, Ekaterina M. Galanina b, Dmitry V. Yudkin a,b,* ... rRNA gene copy numbers on affected acrocentric chromosomes in .... estimated using MS Excel software (Microsoft, USA).

  20. Shear Wave Splitting analysis of borehole microseismic reveals weak azimuthal anisotropy hidden behind strong VTI fabric of Lower Paleozoic shales in northern Poland

    Science.gov (United States)

    Gajek, Wojciech; Verdon, James; Malinowski, Michał; Trojanowski, Jacek

    2017-04-01

    Azimuthal anisotropy plays a key-role in hydraulic fracturing experiments, since it provides information on stress orientation and pre-existing fracture system presence. The Lower Paleozoic shale plays in northern Poland are characterized by a strong (15-18%) Vertical Transverse Isotropy (VTI) fabric which dominates weak azimuthal anisotropy being of order of 1-2%. A shear wave travelling in the subsurface after entering an anisotropic medium splits into two orthogonally polarized waves travelling with different velocities. Splitting parameters which can be assessed using a microseismic array are polarization of the fast shear wave and time delay between two modes. Polarization of the fast wave characterizes the anisotropic system on the wave path while the time delay is proportional to the magnitude of anisotropy. We employ Shear Wave Splitting (SWS) technique using a borehole microseismic dataset collected during a hydraulic stimulation treatment located in northern Poland, to image fracture strike masked by a strong VTI signature. During the inversion part, the VTI background parameters were kept constant using information from 3D seismic (VTI model used for pre-stack depth migration). Obtained fracture azimuths averaged over fracturing stages are consistent with the available XRMI imager logs from the nearby vertical well, however they are different from the large-scale maximum stress direction (by 40-45 degrees). Inverted Hudson's crack density (ca. 2%) are compatible with the low shear-wave anisotropy observed in the cross-dipole sonic logs (1-2%). This work has been funded by the Polish National Centre for Research and Development within the Blue Gas project (No BG2/SHALEMECH/14). Data were provided by the PGNiG SA. Collaboration with University of Bristol was supported within TIDES COST Action ES1401.

  1. Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins Efeito de polietilenoglicol e polivinilpirrolidona na extração e hibridização de rRNA bacteriano de células expostas a taninos

    OpenAIRE

    Pedro Braga Arcuri; Michael Larry Thonney; Peter Schofield; Alice Nelson Pell

    2003-01-01

    In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA) probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG) and polyvinylpirrolidone (PVP) on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/...

  2. Temporal-contextual processing in working memory: evidence from delayed cued recall and delayed free recall tests.

    Science.gov (United States)

    Loaiza, Vanessa M; McCabe, David P

    2012-02-01

    Three experiments are reported that addressed the nature of processing in working memory by investigating patterns of delayed cued recall and free recall of items initially studied during complex and simple span tasks. In Experiment 1, items initially studied during a complex span task (i.e., operation span) were more likely to be recalled after a delay in response to temporal-contextual cues, relative to items from subspan and supraspan list lengths in a simple span task (i.e., word span). In Experiment 2, items initially studied during operation span were more likely to be recalled from neighboring serial positions during delayed free recall than were items studied during word span trials. Experiment 3 demonstrated that the number of attentional refreshing opportunities strongly predicts episodic memory performance, regardless of whether the information is presented in a spaced or massed format in a modified operation span task. The results indicate that the content-context bindings created during complex span trials reflect attentional refreshing opportunities that are used to maintain items in working memory.

  3. Strongly seasonal Proterozoic glacial climate in low palaeolatitudes: Radically different climate system on the pre-Ediacaran Earth

    Directory of Open Access Journals (Sweden)

    George E. Williams

    2016-07-01

    Full Text Available Proterozoic (pre-Ediacaran glaciations occurred under strongly seasonal climates near sea level in low palaeolatitudes. Metre-scale primary sand wedges in Cryogenian periglacial deposits are identical to those actively forming, through the infilling of seasonal (winter thermal contraction-cracks in permafrost by windblown sand, in present-day polar regions with a mean monthly air temperature range of 40 °C and mean annual air temperatures of −20 °C or lower. Varve-like rhythmites with dropstones in Proterozoic glacial successions are consistent with an active seasonal freeze–thaw cycle. The seasonal (annual oscillation of sea level recorded by tidal rhythmites in Cryogenian glacial successions indicates a significant seasonal cycle and extensive open seas. Palaeomagnetic data determined directly for Proterozoic glacial deposits and closely associated rocks indicate low palaeolatitudes: Cryogenian deposits in South Australia accumulated at ≤10°, most other Cryogenian deposits at 54° during Proterozoic low-latitude glaciations, whereby the equator would be cooler than the poles, on average, and global seasonality would be greatly amplified.

  4. Methanosarcina acetivorans 16S rRNA and transcription factor nucleotide fluctuation with implications in exobiology and pathology

    Science.gov (United States)

    Holden, Todd; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Sullivan, R.; Schneider, P.; Flamholz, A.; Marchese, P.; Hiciano, O.; Yao, H.; Lieberman, D.; Cheung, T.

    2008-08-01

    Cultures of the methane-producing archaea Methanosarcina, have recently been isolated from Alaskan sediments. It has been proposed that methanogens are strong candidates for exobiological life in extreme conditions. The spatial environmental gradients, such as those associated with the polygons on Mars' surface, could have been produced by past methanogenesis activity. The 16S rRNA gene has been used routinely to classify phenotypes. Using the fractal dimension of nucleotide fluctuation, a comparative study of the 16S rRNA nucleotide fluctuation in Methanosarcina acetivorans C2A, Deinococcus radiodurans, and E. coli was conducted. The results suggest that Methanosarcina acetivorans has the lowest fractal dimension, consistent with its ancestral position in evolution. Variation in fluctuation complexity was also detected in the transcription factors. The transcription factor B (TFB) was found to have a higher fractal dimension as compared to transcription factor E (TFE), consistent with the fact that a single TFB in Methanosarcina acetivorans can code three different TATA box proteins. The average nucleotide pair-wise free energy of the DNA repair genes was found to be highest for Methanosarcina acetivorans, suggesting a relatively weak bonding, which is consistent with its low prevalence in pathology. Multitasking capacity comparison of type-I and type-II topoisomerases has been shown to correlate with fractal dimension using the methicillin-resistant strain MRSA 252. The analysis suggests that gene adaptation in a changing chemical environment can be measured in terms of bioinformatics. Given that the radiation resistant Deinococcus radiodurans is a strong candidate for an extraterrestrial origin and that the cold temperature Psychrobacter cryohalolentis K5 can function in Siberian permafrost, the fractal dimension comparison in this study suggests that a chemical resistant methanogen could exist in extremely cold conditions (such as that which existed on early

  5. Individual development of preschool children-prevalences and determinants of delays in Germany: a cross-sectional study in Southern Bavaria

    Directory of Open Access Journals (Sweden)

    Stich Heribert L

    2012-12-01

    Full Text Available Abstract Background Even minor abnormalities of early child development may have dramatic long term consequences. Accurate prevalence rates for a range of developmental impairments have been difficult to establish. Since related studies have used different methodological approaches, direct comparisons of the prevalence of developmental delays are difficult. The understanding of the key factors affecting child development, especially in preschool aged children remains limited. We used data from school entry examinations in Bavaria to measure the prevalence of developmental impairments in pre-school children beginning primary school in 1997–2009. Methods The developmental impairments of all school beginners in the district of Dingolfing- Landau, Bavaria were assessed using modified “Bavarian School Entry Model” examination from 1997 to 2009 (N=13,182. The children were assessed for motor, cognitive, language and psychosocial impairments using a standardised medical protocol. Prevalence rates of impairments in twelve domains of development were estimated. Using uni- and multivariable logistic regression models, association between selected factors and development delays were assessed. Results The highest prevalence existed for impairments of pronunciation (13.8% followed by fine motor impairments (12.2%, and impairments of memory and concentration (11.3% and the lowest for impairments of rhythm of speech (3.1%. Younger children displayed more developmental delays. Male gender was strongly associated with all developmental impairments (highest risk for fine motor impairments = OR 3.22, 95% confidence interval 2.86-3.63. Preschool children with siblings (vs. children without any siblings were at higher risk of having impairments in pronunciation (OR 1.31, 1.14-1.50. The influence of the non-German nationality was strong, with a maximum risk increase for the subareas of grammar and psychosocial development. Although children with non

  6. Individual development of preschool children-prevalences and determinants of delays in Germany: a cross-sectional study in Southern Bavaria.

    Science.gov (United States)

    Stich, Heribert L; Baune, Bernhard Th; Caniato, Riccardo N; Mikolajczyk, Rafael T; Krämer, Alexander

    2012-12-05

    Even minor abnormalities of early child development may have dramatic long term consequences. Accurate prevalence rates for a range of developmental impairments have been difficult to establish. Since related studies have used different methodological approaches, direct comparisons of the prevalence of developmental delays are difficult. The understanding of the key factors affecting child development, especially in preschool aged children remains limited. We used data from school entry examinations in Bavaria to measure the prevalence of developmental impairments in pre-school children beginning primary school in 1997-2009. The developmental impairments of all school beginners in the district of Dingolfing-Landau, Bavaria were assessed using modified "Bavarian School Entry Model" examination from 1997 to 2009 (N=13,182). The children were assessed for motor, cognitive, language and psychosocial impairments using a standardised medical protocol. Prevalence rates of impairments in twelve domains of development were estimated. Using uni- and multivariable logistic regression models, association between selected factors and development delays were assessed. The highest prevalence existed for impairments of pronunciation (13.8%) followed by fine motor impairments (12.2%), and impairments of memory and concentration (11.3%) and the lowest for impairments of rhythm of speech (3.1%). Younger children displayed more developmental delays. Male gender was strongly associated with all developmental impairments (highest risk for fine motor impairments = OR 3.22, 95% confidence interval 2.86-3.63). Preschool children with siblings (vs. children without any siblings) were at higher risk of having impairments in pronunciation (OR 1.31, 1.14-1.50). The influence of the non-German nationality was strong, with a maximum risk increase for the subareas of grammar and psychosocial development. Although children with non-German nationality had a reduced risk of disorders for the rhythm

  7. Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria.

    Science.gov (United States)

    Sagova-Mareckova, Marketa; Ulanova, Dana; Sanderova, Petra; Omelka, Marek; Kamenik, Zdenek; Olsovska, Jana; Kopecky, Jan

    2015-04-01

    Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite

  8. Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.

    Directory of Open Access Journals (Sweden)

    Manal Helal

    Full Text Available BACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. METHODS: A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. RESULTS: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52% corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578. CONCLUSION: The identification of centroids of 16S rRNA gene sequence clusters using novel distance matrix clustering enables the identification of the most representative sequences for each individual species of Nocardia and allows the quantitation of inter- and intra

  9. SPEECH DELAY IN THE PRACTICE OF A PAEDIATRICIAN AND CHILD’S NEUROLOGIST

    Directory of Open Access Journals (Sweden)

    N. N. Zavadenko

    2015-01-01

    Full Text Available The article describes the main clinical forms and causes of speech delay in children. It presents modern data on the role of neurobiological factors in the speech delay pathogenesis, including early organic damage to the central nervous system due to the pregnancy and childbirth pathology, as well as genetic mechanisms. For early and accurate diagnosis of speech disorders in children, you need to consider normal patterns of speech development. The article presents indicators of pre-speech and speech development in children and describes the screening method for determining the speech delay. The main areas of complex correction are speech therapy, psycho-pedagogical and psychotherapeutic assistance, as well as pharmaceutical treatment. The capabilities of drug therapy for dysphasia (alalia are shown. 

  10. Characterization of a Novel Association between Two Trypanosome-Specific Proteins and 5S rRNA

    Science.gov (United States)

    Ciganda, Martin; Williams, Noreen

    2012-01-01

    P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are essential and are involved in ribosome biogenesis. Here, we show that these proteins interact in vitro with the 5S rRNA with nearly identical binding characteristics in the absence of other cellular factors. The T. brucei 5S rRNA has a complex secondary structure and presents four accessible loops (A to D) for interactions with RNA-binding proteins. In other eukaryotes, loop C is bound by the L5 ribosomal protein and loop A mainly by TFIIIA. The binding of P34 and P37 to T. brucei 5S rRNA involves the LoopA region of the RNA, but these proteins also protect the L5 binding site located on LoopC. PMID:22253864

  11. DNA sequencing reveals limited heterogeneity in the 16S rRNA gene from the rrnB operon among five Mycoplasma hominis isolates

    DEFF Research Database (Denmark)

    Mygind, T; Birkelund, Svend; Christiansen, Gunna

    1998-01-01

    To investigate the intraspecies heterogeneity within the 16S rRNA gene of Mycoplasma hominis, five isolates with diverse antigenic profiles, variable/identical P120 hypervariable domains, and different 16S rRNA gene RFLP patterns were analysed. The 16S rRNA gene from the rrnB operon was amplified...... by PCR and the PCR products were sequenced. Three isolates had identical 16S rRNA sequences and two isolates had sequences that differed from the others by only one nucleotide....

  12. Pre-K as School Turnaround Strategy

    Science.gov (United States)

    Buenafe, Anthony Q.

    2011-01-01

    Both state and local school systems, recognizing the strong and growing evidence of pre-kindergarten's effectiveness in closing achievement gaps, are implementing early learning programs as part of their education reform efforts. In low-performing districts, pre-k has emerged as a promising turnaround strategy, reaching children before they become…

  13. International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

    Science.gov (United States)

    Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

    2015-01-01

    This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

  14. International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

    Directory of Open Access Journals (Sweden)

    Nathan D. Olson

    2015-03-01

    Full Text Available This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1 identity of biologically conserved position, (2 ratio of 16S rRNA gene copies featuring identified variants, and (3 the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

  15. Modeling delay in genetic networks: from delay birth-death processes to delay stochastic differential equations.

    Science.gov (United States)

    Gupta, Chinmaya; López, José Manuel; Azencott, Robert; Bennett, Matthew R; Josić, Krešimir; Ott, William

    2014-05-28

    Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein. Genetic regulatory networks are therefore frequently modeled as stochastic birth-death processes with delay. Here, we examine the relationship between delay birth-death processes and their appropriate approximating delay chemical Langevin equations. We prove a quantitative bound on the error between the pathwise realizations of these two processes. Our results hold for both fixed delay and distributed delay. Simulations demonstrate that the delay chemical Langevin approximation is accurate even at moderate system sizes. It captures dynamical features such as the oscillatory behavior in negative feedback circuits, cross-correlations between nodes in a network, and spatial and temporal information in two commonly studied motifs of metastability in biochemical systems. Overall, these results provide a foundation for using delay stochastic differential equations to approximate the dynamics of birth-death processes with delay.

  16. Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Chinmaya; López, José Manuel; Azencott, Robert; Ott, William [Department of Mathematics, University of Houston, Houston, Texas 77004 (United States); Bennett, Matthew R. [Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77204, USA and Institute of Biosciences and Bioengineering, Rice University, Houston, Texas 77005 (United States); Josić, Krešimir [Department of Mathematics, University of Houston, Houston, Texas 77004 (United States); Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204 (United States)

    2014-05-28

    Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein. Genetic regulatory networks are therefore frequently modeled as stochastic birth-death processes with delay. Here, we examine the relationship between delay birth-death processes and their appropriate approximating delay chemical Langevin equations. We prove a quantitative bound on the error between the pathwise realizations of these two processes. Our results hold for both fixed delay and distributed delay. Simulations demonstrate that the delay chemical Langevin approximation is accurate even at moderate system sizes. It captures dynamical features such as the oscillatory behavior in negative feedback circuits, cross-correlations between nodes in a network, and spatial and temporal information in two commonly studied motifs of metastability in biochemical systems. Overall, these results provide a foundation for using delay stochastic differential equations to approximate the dynamics of birth-death processes with delay.

  17. Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations

    International Nuclear Information System (INIS)

    Gupta, Chinmaya; López, José Manuel; Azencott, Robert; Ott, William; Bennett, Matthew R.; Josić, Krešimir

    2014-01-01

    Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein. Genetic regulatory networks are therefore frequently modeled as stochastic birth-death processes with delay. Here, we examine the relationship between delay birth-death processes and their appropriate approximating delay chemical Langevin equations. We prove a quantitative bound on the error between the pathwise realizations of these two processes. Our results hold for both fixed delay and distributed delay. Simulations demonstrate that the delay chemical Langevin approximation is accurate even at moderate system sizes. It captures dynamical features such as the oscillatory behavior in negative feedback circuits, cross-correlations between nodes in a network, and spatial and temporal information in two commonly studied motifs of metastability in biochemical systems. Overall, these results provide a foundation for using delay stochastic differential equations to approximate the dynamics of birth-death processes with delay

  18. Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.

    Science.gov (United States)

    Ceuppens, Siele; De Coninck, Dieter; Bottledoorn, Nadine; Van Nieuwerburgh, Filip; Uyttendaele, Mieke

    2017-09-18

    Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results. Copyright © 2017 Elsevier B

  19. Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses.

    Science.gov (United States)

    Chen, Jiazhen; Miao, Xinyu; Xu, Meng; He, Junlin; Xie, Yi; Wu, Xingwen; Chen, Gang; Yu, Liying; Zhang, Wenhong

    2015-01-01

    Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3-100%. However, the inter-species similarities were

  20. 5S rRNA and accompanying proteins in gonads: powerful markers to identify sex and reproductive endocrine disruption in fish.

    Science.gov (United States)

    Diaz de Cerio, Oihane; Rojo-Bartolomé, Iratxe; Bizarro, Cristina; Ortiz-Zarragoitia, Maren; Cancio, Ibon

    2012-07-17

    In anuran ovaries, 5S rDNA is regulated transcriptionally by transcription factor IIIA (TFIIIA), which upon transcription, binds 5S rRNA, forming 7S RNP. 5S rRNA can be stockpiled also in the form of 42S RNP bound to 42sp43. The aim of the present study was to assess the differential transcriptional regulation of 5S rRNA and associated proteins in thicklip gray mullet (Chelon labrosus) gonads. Up to 75% of the total RNA from mullet ovaries was 5S rRNA. qPCR quantification of 5S rRNA expression, in gonads of histologically sexed individuals from different geographical areas, successfully sexed animals. All males had expression levels that were orders of magnitude below expression levels in females, throughout an annual reproductive cycle, with the exception of two individuals: one in November and one in December. Moreover, intersex mullets from a polluted harbor had expression levels between both sexes. TFIIIA and 42sp43 were also very active transcriptionally in gonads of female and intersex mullets, in comparison to males. Nucleocytoplasmatic transport is important in this context and we also analyzed transcriptional levels of importins-α1, -α2, and -β2 and different exportins. Importin-αs behaved similarly to 5S rRNA. Thus, 5S rRNA and associated proteins constitute very powerful molecular markers of sex and effects of xenosterogens in fish gonads, with potential technological applications in the analysis of fish stock dynamics and reproduction as well as in environmental health assessment.

  1. Effect of pre-analytical handling on haematological variables in minipigs

    DEFF Research Database (Denmark)

    Olsen, A K; Bladbjerg, E-M; Jensen, A L

    2001-01-01

    Pre-analytical handling may be an important determinant of haematological variables, if analysis is delayed. We investigated the effect of anticoagulants, i.e. tripotassium ethylenediamine-tetraacetic acid (EDTA) and citric acid, theophylline, adenosine, dipyridamole (CTAD), storage time (0.5, 1......, the samples must be stored in a refrigerator until analysis. Our studies underline that time delay before analysis of haematological variables can cause increased variation, and should therefore be limited as far as possible in order to reduce the number of animals needed to make reliable conclusions...

  2. DNA sequencing reveals limited heterogeneity in the 16S rRNA gene from the rrnB operon among five Mycoplasma hominis isolates

    DEFF Research Database (Denmark)

    Mygind, T; Birkelund, Svend; Christiansen, Gunna

    1998-01-01

    To investigate the intraspecies heterogeneity within the 16S rRNA gene of Mycoplasma hominis, five isolates with diverse antigenic profiles, variable/identical P120 hypervariable domains, and different 16S rRNA gene RFLP patterns were analysed. The 16S rRNA gene from the rrnB operon was amplified...

  3. Selective inhibition of precursor incorporation into ribosomal RNA in gamma-irradiated Tetrahymena pyriformis

    International Nuclear Information System (INIS)

    Ernst, S.G.; Oleinick, N.L.; Rustad, R.C.; Greenblatt, R.M.

    1979-01-01

    Sublethal doses of γ radiation are known to inhibit total RNA synthesis in the ciliate protozoan Tetrahymena. To determine if the synthesis of a particular class of RNA is preferentially inhibited, pulse-labeled RNA was isolated from normal exponentially growing cells, irradiated cells, and cells in which total RNA synthesis had recovered to the pre-irradiation level. The RNAs were analyzed by SDS-polyacrylamide gel electrphoresis and oligo(dT)-cellulose column chromatography. Inhibition of RNA synthesis primarily involves ribosomal RNA. However, radiation does not cause a delay in the processing of precursor rRNA or a preferential loss of either of the mature rRNAs. Following irradiation, poly(A)-containing RNA [poly(A+)RNA] is synthesized at a rate up to three times greater than the control rate. The elevated poly(A+)RNA synthesis occurs during the period of depressed rRNA synthesis and even after rRNA synthesis has recovered to its pre-irradiation rate. While the sizes of the total cellular ribonucleoside triphosphate pools are depressed in the irradiated cells, these pools probably do not represent the actual compartments containing the precursors for RNA synthesis, and the observed changes cannot explain the modifications in macromolecular synthesis in irradiated Tetrahymena. (Auth.)

  4. Engineering fluidic delays in paper-based devices using laser direct-writing.

    Science.gov (United States)

    He, P J W; Katis, I N; Eason, R W; Sones, C L

    2015-10-21

    We report the use of a new laser-based direct-write technique that allows programmable and timed fluid delivery in channels within a paper substrate which enables implementation of multi-step analytical assays. The technique is based on laser-induced photo-polymerisation, and through adjustment of the laser writing parameters such as the laser power and scan speed we can control the depth and/or the porosity of hydrophobic barriers which, when fabricated in the fluid path, produce controllable fluid delay. We have patterned these flow delaying barriers at pre-defined locations in the fluidic channels using either a continuous wave laser at 405 nm, or a pulsed laser operating at 266 nm. Using this delay patterning protocol we generated flow delays spanning from a few minutes to over half an hour. Since the channels and flow delay barriers can be written via a common laser-writing process, this is a distinct improvement over other methods that require specialist operating environments, or custom-designed equipment. This technique can therefore be used for rapid fabrication of paper-based microfluidic devices that can perform single or multistep analytical assays.

  5. Importance of delayed neutron data in transmutation system

    International Nuclear Information System (INIS)

    Tsujimoto, Kazufumi

    1999-01-01

    The accelerator-driven transmutation system has been studied at the Japan Atomic Energy Research Institute. This system is a hybrid system which consists of a high intensity accelerator, a spallation target and a subcritical core region. The subcritical core is driven by neutrons generated by spallation reaction in the target region. There is no control rod in this system, so the power is controlled only by proton beam current. The beam current to keep constant power change with effective multiplication factor of subcritical core. So, the evaluation of delayed neutron fraction which is strongly connected to the measurement of subcritical level is important factor in operation of accelerator-driven system. In this paper, important nuclides for the delayed neutron fraction of ADS will be discussed, moreover, present state of delayed neutron data in evaluated nuclear data library is presented. (author)

  6. Delaying information search

    Directory of Open Access Journals (Sweden)

    Yaniv Shani

    2012-11-01

    Full Text Available In three studies, we examined factors that may temporarily attenuate information search. People are generally curious and dislike uncertainty, which typically encourages them to look for relevant information. Despite these strong forces that promote information search, people sometimes deliberately delay obtaining valuable information. We find they may do so when they are concerned that the information might interfere with future pleasurable activities. Interestingly, the decision to search or to postpone searching for information is influenced not only by the value and importance of the information itself but also by well-being maintenance goals related to possible detrimental effects that negative knowledge may have on unrelated future plans.

  7. Processing of the 17-S Escherichia coli precursor RNA in the 27-S pre-ribosomal particle

    Energy Technology Data Exchange (ETDEWEB)

    Hayes, F; Vasseur, M [Institut de Biologie Physico-Chimique, 75 - Paris (France)

    1976-01-01

    An RNase activity probably involved in the maturation of 16-S pre-ribosomal RNA in Escherichia coli has been partially purified from crude cell extracts. When 27-S ribosome precursor particles are incubated with this enzyme preparation in vitro, their 17-S RNA is converted to a product with the same electrophoretic mobility as mature 16-S rRNA. FingerprS rRNA. Generation of the normal 5'-P terminus seems to require a factor present in cell extracts since incubation of the 27-S precursor particle in an extract obtained after centrifugation at 30,000 x g causes conversion of the 17-S RNA to a 16-S species containing both termini of mature 16-S rRNS. Preliminary experiments suggest that correct maturation of the 5' end of the 17-S precursor RNA requires a system in which protein synthesis can take place.

  8. Pseudoknot in domain II of 23 S rRNA is essential for ribosome function

    DEFF Research Database (Denmark)

    Rosendahl, G; Hansen, L H; Douthwaite, S

    1995-01-01

    The structure of domain II in all 23 S (and 23 S-like) rRNAs is constrained by a pseudoknot formed between nucleotides 1005 and 1138, and between 1006 and 1137 (Escherichia coli numbering). These nucleotides are exclusively conserved as 1005C.1138G and 1006C.1137G pairs in all Bacteria, Archaea...... increased accessibility in the rRNA structure close to the sites of the mutations. The degree to which the mutations increase rRNA accessibility correlates with the severity of their phenotypic effects. Nucleotide 1131G is extremely reactive to dimethyl sulphate modification in wild-type subunits...

  9. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons.

    Science.gov (United States)

    Locati, Mauro D; Pagano, Johanna F B; Ensink, Wim A; van Olst, Marina; van Leeuwen, Selina; Nehrdich, Ulrike; Zhu, Kongju; Spaink, Herman P; Girard, Geneviève; Rauwerda, Han; Jonker, Martijs J; Dekker, Rob J; Breit, Timo M

    2017-04-01

    5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci. © 2017 Locati et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  10. Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

    Science.gov (United States)

    Nakashima, T; Yao, M; Kawamura, S; Iwasaki, K; Kimura, M; Tanaka, I

    2001-05-01

    Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and plays an essential role in the promotion of a particular conformation of 5S rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stearothermophilus has been determined at 1.8 A resolution. The molecule consists of a five-stranded antiparallel beta-sheet and four alpha-helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. The molecular shape and electrostatic representation suggest that the concave surface and loop regions are involved in 5S rRNA binding. To identify amino acid residues responsible for 5S rRNA binding, we made use of Ala-scanning mutagenesis of evolutionarily conserved amino acids occurring in the beta-strands and loop regions. The mutations of Asn37 at the beta1-strand and Gln63 at the loop between helix 2 and beta3-strand as well as that of Phe77 at the tip of the loop structure between the beta2- and beta3-strands caused a significant reduction in 5S rRNA binding. In addition, the mutations of Thr90 on the beta3-strand and Ile141 and Asp144 at the loop between beta4- and beta5-strands moderately reduced the 5S rRNA-binding affinity. Comparison of these results with the more recently analyzed structure of the 50S subunit from Haloarcula marismortui suggests that there are significant differences in the structure at N- and C-terminal regions and probably in the 5S rRNA binding.

  11. Tomato (Solanum lycopersicum) variety discrimination and hybridization analysis based on the 5S rRNA region.

    Science.gov (United States)

    Sun, Yan-Lin; Kang, Ho-Min; Kim, Young-Sik; Baek, Jun-Pill; Zheng, Shi-Lin; Xiang, Jin-Jun; Hong, Soon-Kwan

    2014-05-04

    The tomato ( Solanum lycopersicum ) is a major vegetable crop worldwide. To satisfy popular demand, more than 500 tomato varieties have been bred. However, a clear variety identification has not been found. Thorough understanding of the phylogenetic relationship and hybridization information of tomato varieties is very important for further variety breeding. Thus, in this study, we collected 26 tomato varieties and attempted to distinguish them based on the 5S rRNA region, which is widely used in the determination of phylogenetic relations. Sequence analysis of the 5S rRNA region suggested that a large number of nucleotide variations exist among tomato varieties. These variable nucleotide sites were also informative regarding hybridization. Chromas sequencing of Yellow Mountain View and Seuwiteuking varieties indicated three and one variable nucleotide sites in the non-transcribed spacer (NTS) of the 5S rRNA region showing hybridization, respectively. Based on a phylogenetic tree constructed using the 5S rRNA sequences, we observed that 16 tomato varieties were divided into three groups at 95% similarity. Rubiking and Sseommeoking, Lang Selection Procedure and Seuwiteuking, and Acorn Gold and Yellow Mountain View exhibited very high identity with their partners. This work will aid variety authentication and provides a basis for further tomato variety breeding.

  12. Fractal analysis of intraflow unidirectional delay over w-lan and w-wan environments

    OpenAIRE

    Pezaros, D. P.; Sifalakis, M.; Mathy, Laurent

    2007-01-01

    We have analysed unidirectional delay traces of a diverse set of IPv6 microflows routed over W-LAN and W-WAN environments. Using a number of time-domain and frequency-domain estimators we have examined the existence and intensity of long-range dependence in packet delay when viewed as time-series data. The correlation structures of packet delay on bulk TCP data path and UDP flows follow asymptotic decay while Hurst exponent estimates suggest from moderate to strong intensity(H->1).

  13. When good pigeons make bad decisions: Choice with probabilistic delays and outcomes.

    Science.gov (United States)

    Pisklak, Jeffrey M; McDevitt, Margaret A; Dunn, Roger M; Spetch, Marcia L

    2015-11-01

    Pigeons chose between an (optimal) alternative that sometimes provided food after a 10-s delay and other times after a 40-s delay and another (suboptimal) alternative that sometimes provided food after 10 s but other times no food after 40 s. When outcomes were not signaled during the delays, pigeons strongly preferred the optimal alternative. When outcomes were signaled, choices of the suboptimal alternative increased and most pigeons preferred the alternative that provided no food after the long delay despite the cost in terms of obtained food. The pattern of results was similar whether the short delays occurred on 25% or 50% of the trials. Shortening the 40-s delay to food sharply reduced suboptimal choices, but shortening the delay to no food had little effect. The results suggest that a signaled delay to no food does not punish responding in probabilistic choice procedures. The findings are discussed in terms of conditioned reinforcement by signals for good news. © Society for the Experimental Analysis of Behavior.

  14. Reducing time delays in the management of ischemic stroke patients in Northern Italy.

    Science.gov (United States)

    Vidale, Simone; Arnaboldi, Marco; Bezzi, Giacomo; Bono, Giorgio; Grampa, Giampiero; Guidotti, Mario; Perrone, Patrizia; Salmaggi, Andrea; Zarcone, Davide; Zoli, Alberto; Agostoni, Elio

    2016-07-15

    Thrombolysis represents the best therapy for ischemic stroke but the main limitation of its administration is time. The avoidable delay is a concept reflecting the effectiveness of management pathway. For this reason, we projected a study concerning the detection of main delays with following introduction of corrective factors. In this paper we describe the results after these corrections. Consecutive patients admitted for ischemic stroke during a 3-months period to 35 hospitals of a macro-area of Northern Italy were enrolled. Each time of management was registered, identifying three main intervals: pre-hospital, in-hospital and total times. Previous corrective interventions were: 1.increasing of population awareness to use the Emergency Medical Service (EMS); 2.pre-notification of Emergency Department; 3.use of high urgency codes; 4.use of standardised operational algorithm. Statistical analysis was conducted using time-to-event analysis and Cox proportional hazard regression. 1084 patients were enrolled. EMS was alerted for 56.3% of subjects, mainly in females and severe strokes (ptimes were 113 and 105min, while total time was 240. High urgency codes at transport contributed to reduce pre-hospital and in-hospital time (p<0.05). EMS use and high urgency codes promoted thrombolysis. Treatment within 4.5hours from symptom onset was performed in 14% of patients more than the first phase of study. The implementation of an organizational system based on EMS and concomitant high urgency codes use was effective to reduce avoidable delay and to increase thrombolysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  15. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

    Science.gov (United States)

    Ziesemer, Kirsten A; Mann, Allison E; Sankaranarayanan, Krithivasan; Schroeder, Hannes; Ozga, Andrew T; Brandt, Bernd W; Zaura, Egija; Waters-Rist, Andrea; Hoogland, Menno; Salazar-García, Domingo C; Aldenderfer, Mark; Speller, Camilla; Hendy, Jessica; Weston, Darlene A; MacDonald, Sandy J; Thomas, Gavin H; Collins, Matthew J; Lewis, Cecil M; Hofman, Corinne; Warinner, Christina

    2015-11-13

    To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

  16. Lack of WDR36 leads to preimplantation embryonic lethality in mice and delays the formation of small subunit ribosomal RNA in human cells in vitro.

    Science.gov (United States)

    Gallenberger, Martin; Meinel, Dominik M; Kroeber, Markus; Wegner, Michael; Milkereit, Philipp; Bösl, Michael R; Tamm, Ernst R

    2011-02-01

    Mutations in WD repeat domain 36 gene (WDR36) play a causative role in some forms of primary open-angle glaucoma, a leading cause of blindness worldwide. WDR36 is characterized by the presence of multiple WD40 repeats and shows homology to Utp21, an essential protein component of the yeast small subunit (SSU) processome required for maturation of 18S rRNA. To clarify the functional role of WDR36 in the mammalian organism, we generated and investigated mutant mice with a targeted deletion of Wdr36. In parallel experiments, we used RNA interference to deplete WDR36 mRNA in mouse embryos and cultured human trabecular meshwork (HTM-N) cells. Deletion of Wdr36 in the mouse caused preimplantation embryonic lethality, and essentially similar effects were observed when WDR36 mRNA was depleted in mouse embryos by RNA interference. Depletion of WDR36 mRNA in HTM-N cells caused apoptotic cell death and upregulation of mRNA for BAX, TP53 and CDKN1A. By immunocytochemistry, staining for WDR36 was observed in the nucleolus of cells, which co-localized with that of nucleolar proteins such as nucleophosmin and PWP2. In addition, recombinant and epitope-tagged WDR36 localized to the nucleolus of HTM-N cells. By northern blot analysis, a substantial decrease in 21S rRNA, the precursor of 18S rRNA, was observed following knockdown of WDR36. In addition, metabolic-labeling experiments consistently showed a delay of 18S rRNA maturation in WDR36-depleted cells. Our results provide evidence that WDR36 is an essential protein in mammalian cells which is involved in the nucleolar processing of SSU 18S rRNA.

  17. Delayed hepatobiliary imaging in the diagnosis of hepatocellular carcinoma

    International Nuclear Information System (INIS)

    Chen, S.; Ma, Z.; Tang, Z.

    2000-01-01

    In recent years, the use of ultrasonography (US), X-CT and MRI has reduced the employment of isotopic explorations in the detection of hepatocellular carcinoma (HCC). But sometime the results of US, X-CT or MRI were different and diagnosis was very difficult. This present investigation was aimed to assess the usefulness of delayed hepatobiliary imaging in the diagnosis of HCC in these patients. Forty-eight patients consisting of 33 males and 15 females were entered into the research protocol. The mean age was 46 yr old (range 12-71 yr old). All of the patients were performed by surgery and verified histologically after nuclear examination. The subject was in a supine position under a gamma camera (Elscint, Apex Ap-6) and 555 MBq of Tc-99m-PMT were injected intravenously. The initial scinphotos obtained within 1 min after injection were used to image the blood pool phase. Subsequently, hepatic scans were obtained at 5 min, 1,2 and 5 hr. Anterior, right lateral and posterior hepatic images were recorded. According to the radioactive uptake by the lesion in delayed phase, the negative (no or minor uptake), positive (equal or greater uptake) or very strong positive (almost equal to the activity, of gallbladder) were judged. The positive were considered as diagnostic of HCC. And the very strong positive, were considered as diagnostic of benign hepatoma, such as adenoma or FNH. Thirty-seven of the forty-eight patients were HCC based on histology. Delayed imaging revealed increased or equilibrated uptake of radioactivity by the tumors in 22 of 37 patients with hepatocellular carcinoma. The sensitivity was 59.5%. One patient final diagnosis based on histology was focal nodular regenerative hyperplasia, and only the diagnosis with delayed hepatobiliary imaging before surgery was correct. Compared with US, X-CT and MRI, delayed hepatobiliary imaging had the highest specificity for diagnosis of hepatocellular carcinoma. In recent group, the specificity of Tc-99m-PMT delayed

  18. Folate deficiency facilitates recruitment of upstream binding factor to hot spots of DNA double-strand breaks of rRNA genes and promotes its transcription.

    Science.gov (United States)

    Xie, Qiu; Li, Caihua; Song, Xiaozhen; Wu, Lihua; Jiang, Qian; Qiu, Zhiyong; Cao, Haiyan; Yu, Kaihui; Wan, Chunlei; Li, Jianting; Yang, Feng; Huang, Zebing; Niu, Bo; Jiang, Zhengwen; Zhang, Ting

    2017-03-17

    The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) landscape in mouse embryonic stem cells. A significant DSB enhancement was detected in the genome of these cells and a large majority of these DSBs were found in rRNA genes. Furthermore, spontaneous DSBs in cells under folate deficiency conditions were located exclusively within the rRNA gene units, representing a H3K4me1 hallmark. Enrichment H3K4me1 at the hot spots of DSB regions enhanced the recruitment of upstream binding factor (UBF) to rRNA genes, resulting in the increment of rRNA genes transcription. Supplement of folate resulted in a restored UBF binding across DNA breakage sites of rRNA genes, and normal rRNA gene transcription. In samples from neural tube defects (NTDs) with low folate level, up-regulation of rRNA gene transcription was observed, along with aberrant UBF level. Our results present a new view by which alterations in folate levels affects DNA breakage through epigenetic control leading to the regulation of rRNA gene transcription during the early stage of development. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Effect of bacterial contamination on the incorporation of radioactive phosphate in plant r-RNA

    Energy Technology Data Exchange (ETDEWEB)

    Koleva, S; Khanymova, T; Marinova, E; Varadinova, S

    1974-01-01

    It is ascertained that the amount of bacterial colonies in root tips of maize seedlings (Wisconsin 641 AA) constitutes approximately 4.5x10/sup 7/ per gram of fresh weight, 90% of the bacterial colonies being various pseudomonas. In the case when plant RNA is labelled with /sup 32/P, the bacteria take up a large amount of phosphate. Owing to this, the RNA isolated from the root tips and fractionated in agar gel, in addition to 25S and 18S r-RNA of the plant cell cytoplasma contains also 23S and 16S of the bacterial r-RNA. Chloramphenicol at a concentration of 50/cm/sup 3/ does not suppress the incorporation of /sup 32/P by the bacteria. The pseudomonas strains isolated are almost insensitive to chloramphenicol and a number of other antibiotics, such as penicyllin, erythromycin, neomycin and oxacylin. This results, as well as the results, obtained by other researchers, indicate that antibiotics do not suppress effectively the action of bacterial contamination if plant RNA is labelled. Furtheremore, some of them, as streptomycin, for instance, if employed at higher concentrations inhibit the growth of the plant cell. Of all asceptic agents (hypochlorite, ethanol, sulphuric acid, etc.), used for surface sterilization, best results in the elimination of bacterial infection on maize seeds have been obtained with 0.1% HgCl/sub 2/ after treatment for 2 min. In spite of the elimination of the bacterial contamination with HgCl/sub 2/,the RNA from the elongated cells, labelled with /sup 32/P for an hour, is distributed into four fractions in the agar gel conversely to the RNA isolated from dividing cells, where only the two 25S and 18S fractions of plant cytoplasmic r-RNA are observed. An assumption is made that the two more fast-moving r-RNA fractions, as compared with 25S and 18S of plant r-RNA, isolated from elongating cells, originate from subcellular organelles, since the mitochondria and the proplstids are fully differentiated during the phase of the elongation of the

  20. Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins Efeito de polietilenoglicol e polivinilpirrolidona na extração e hibridização de rRNA bacteriano de células expostas a taninos

    Directory of Open Access Journals (Sweden)

    Pedro Braga Arcuri

    2003-09-01

    Full Text Available In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG and polyvinylpirrolidone (PVP on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/L condensed tannins extracted from Acacia angustissima, banana (Musa sp. skin, Desmodium ovalifolium, red grape (Vitis vinifera skin and Inga edulis, or no tannins. Cells were rinsed with Tris buffer pH 7 containing either 8% PEG or 6% PVP prior to cell lysis. Total RNA samples rinsed with either PEG or PVP migrated through denaturing agarose gels. The 16S rRNA bands successfully hybridized with a R. albus species-specific oligonucleotide probe, regardless of tannin source. The effect of rinsing buffers on the density of 16S rRNA bands, as well as on the hybridization signals was compared. There were significant effects (PA recuperação de RNA ribossômico (rRNA intacto é necessária para a detecção de flutuações na população microbiana ruminal decorrentes dos taninos de forrageiras, utilizando-se sondas para 16S rRNA. O objetivo deste trabalho foi avaliar o efeito de polietilenoglicol (PEG e polivinilpirrolidona (PVP na extração de rRNA bacteriano, em presença de taninos de leguminosas forrageiras tropicais e de outras fontes, que possa ser hibridizado com sondas de oligonucleotídeos. Culturas de Ruminococcus albus 8 foram expostas ou não a 8 g/L de ácido tânico ou a 1 g/L de taninos condensados, extraídos de Acacia angustissima, casca de banana (Musa sp., Desmodium ovalifolium, cascas de uvas vermelhas (Vitis vinifera e Inga edulis. As culturas foram lavadas com tampão Tris pH 7 contendo 8% PEG ou 6% PVP antes do rompimento das c

  1. The nucleotide sequence and organization of nuclear 5S rRNA genes in yellow lupine

    International Nuclear Information System (INIS)

    Nuc, K.; Nuc, P.; Pawelkiewicz, J.

    1993-01-01

    We have isolated a genomic clone containing 'Lupinus luteus' 5S ribosomal RNA genes by screening with 5S rDNA probe clones that were hybridized previously with the initiator methionine tRNA preparation (contaminated) with traces of rRNA or its degradation products). The clone isolated contains ten repeat units of 342 bp with 119 bp fragment showing 100% homology to the 5S rRNA from yellow lupine. Sequence analysis indicates only point heterogeneities among the flanking regions of the genes. (author). 6 refs, 3 figs

  2. The secondary structure of large-subunit rRNA divergent domains, a marker for protist evolution

    DEFF Research Database (Denmark)

    Lenaers, G; Nielsen, Henrik; Engberg, J

    1988-01-01

    The secondary structure of the large-subunit ribosomal RNA (24-26S rRNA) has been studied with emphasis on comparative analysis of the folding patterns of the divergent domains in the available protist sequences, that is Prorocentrum micans (dinoflagellate), Saccharomyces carlsbergensis (yeast......), Tetrahymena thermophila (ciliate), Physarum polycephalum and Dictyostelium discoideum (slime moulds), Crithidia fasciculata and Giardia lamblia (parasitic flagellates). The folding for the D3, D7a and D10 divergent domains has been refined and a consensus model for the protist 24-26S rRNA structure...

  3. Anomalous delayed loss of trapped D-D fusion products in TFTR

    International Nuclear Information System (INIS)

    Zweben, S.J.; Darrow, D.S.; Fredrickson, E.D.; Mynick, H.E.

    1993-02-01

    A new anomalous delayed loss of D-D fusion products has been measured at the bottom of the TFRR vessel. This loss is delayed by ∼ 0.2 sec with respect to the usual prompt first-orbit loss, and has a correspondingly lower energy, i.e. about half the fusion product birth energy. This loss process dominates the total fusion product loss measured 90 degrees below the midplane for plasma currents. I≥ 1.8 MA and major radii near R=2.45 m, e.g. for recent TFTR supershots. This delayed feature can occur without large coherent MED activity, although it can be strongly modulated by such activity. Several possible causes for this phenomenon are discussed, but no clear explanation for this delayed loss has yet been found

  4. Rapid identification of probiotic Lactobacillus species by multiplex PCR using species-specific primers based on the region extending from 16S rRNA through 23S rRNA.

    Science.gov (United States)

    Kwon, Hyuk-Sang; Yang, Eun-Hee; Yeon, Seung-Woo; Kang, Byoung-Hwa; Kim, Tae-Yong

    2004-10-15

    This study aimed to develop a novel multiplex polymerase chain reaction (PCR) primer set for the identification of seven probiotic Lactobacillus species such as Lactobacillus acidophilus, Lactobacillus delbrueckii, Lactobacillus casei, Lactobacillus gasseri, Lactobacillus plantarum, Lactobacillus reuteri and Lactobacillus rhamnosus. The primer set, comprising of seven specific and two conserved primers, was derived from the integrated sequences of 16S and 23S rRNA genes and their rRNA intergenic spacer region of each species. It was able to identify the seven target species with 93.6% accuracy, which exceeds that of the general biochemical methods. The phylogenetic analyses, using 16S rDNA sequences of the probiotic isolates, also provided further support that the results from the multiplex PCR assay were trustworthy. Taken together, we suggest that the multiplex primer set is an efficient tool for simple, rapid and reliable identification of seven Lactobacillus species.

  5. Delayed electron emission in strong-field driven tunnelling from a metallic nanotip in the multi-electron regime

    Science.gov (United States)

    Yanagisawa, Hirofumi; Schnepp, Sascha; Hafner, Christian; Hengsberger, Matthias; Kim, Dong Eon; Kling, Matthias F.; Landsman, Alexandra; Gallmann, Lukas; Osterwalder, Jürg

    2016-01-01

    Illuminating a nano-sized metallic tip with ultrashort laser pulses leads to the emission of electrons due to multiphoton excitations. As optical fields become stronger, tunnelling emission directly from the Fermi level becomes prevalent. This can generate coherent electron waves in vacuum leading to a variety of attosecond phenomena. Working at high emission currents where multi-electron effects are significant, we were able to characterize the transition from one regime to the other. Specifically, we found that the onset of laser-driven tunnelling emission is heralded by the appearance of a peculiar delayed emission channel. In this channel, the electrons emitted via laser-driven tunnelling emission are driven back into the metal, and some of the electrons reappear in the vacuum with some delay time after undergoing inelastic scattering and cascading processes inside the metal. Our understanding of these processes gives insights on attosecond tunnelling emission from solids and should prove useful in designing new types of pulsed electron sources. PMID:27786287

  6. China vs. USA: energy consumption of the two giants markets in 2010. Very strong growth in energy consumption in China and USA in 2010 which is well beyond the pre-crisis trend; this allows anticipation of a very strong global growth in 2010; China surpasses 10% of U.S.A's Energy consumption in 2010 - March 2011

    International Nuclear Information System (INIS)

    Lapillonne, Bruno

    2011-01-01

    Enerdata compares 2010 energy consumption between China and USA: China surpasses 10% of U.S.A's Energy consumption in 2010; Very strong growth in energy consumption in China and USA in 2010 which is well beyond the pre-crisis trend; this allows anticipation of a very strong global growth in 2010. (authors)

  7. Patient delay and associated factors among breast cancer patients

    International Nuclear Information System (INIS)

    Khan, M.A.; Khan, M.I.; Andleeb, U.

    2015-01-01

    Objectives: To stratify patients into various stages, calculate average patient delay and study various causes of delay to presentation. Methodology: This was a one year hospital based cross sectional study at Khyber Teaching Hospital, using non probability consecutive sampling. A simplified staging was used for this study; Early (Stage I), Intermediate (Stage II, III), and Late (Stage IV). A patient was labelled delay when >3 months had elapsed between first symptom perception and first doctor consultation. Results: 80 patients were included with age 21-80 years (mean 45.28+-13.15). 80% of the patients were married, 76.3% (n=61/80) were poor with annual income of <500 US $, 85% of patients were illiterate. The participants from Rural and Urban areas were similar (37 % vs 31%); 15% were from Afghanistan. 80% patients presented with a delay of >3 months. Most common cause of delay was false symptom interpretation in 25.3% (n=17) patients. Conclusion: Late clinical presentation is because of lack of health education, unawareness, misconceptions about treatment and strong belief in traditional medicine resulting in advanced disease. This is worsened by poverty and unavailability of health care services especially in rural areas. (author)

  8. The conformation of 23S rRNA nucleotide A2058 determines its recognition by the ErmE methyltransferase

    DEFF Research Database (Denmark)

    Vester, B; Hansen, L H; Douthwaite, S

    1995-01-01

    the effects of mutations around position A2058 on methylation. Mutagenizing A2058 (to G or U) completely abolishes methylation of 23S rRNA by ErmE. No methylation occurred at other sites in the rRNA, demonstrating the fidelity of ErmE for A2058. Breaking the neighboring G2057-C2611 Watson-Crick base pair...... by introducing either an A2057 or a U2611 mutation, greatly reduces the rate of methylation at A2058. Methylation remains impaired after these mutations have been combined to create a new A2057-U2611 Watson-Crick base interaction. The conformation of this region in 23S rRNA was probed with chemical reagents...

  9. 16S rRNA gene sequence and phylogenetic tree of lactobacillus ...

    African Journals Online (AJOL)

    ... processed by denaturing gradient gel electrophoresis (DGGE). Phylogenetic tree was constructed with the sequences of the V2-V3 region of 16S rRNA gene. Results show two distinct divisions among the Lactobacillus species. The study presents a new understanding of the nature of the Lactobacillus vaginal microbiota ...

  10. Pre-analytical factors influencing the stability of cerebrospinal fluid proteins

    DEFF Research Database (Denmark)

    Simonsen, Anja H; Bahl, Justyna M C; Danborg, Pia B

    2013-01-01

    Cerebrospinal fluid (CSF) is a potential source for new biomarkers due to its proximity to the brain. This study aimed to clarify the stability of the CSF proteome when undergoing pre-analytical factors. We investigated the effects of repeated freeze/thaw cycles, protease inhibitors and delayed s...

  11. Optimal Joint Expected Delay Forwarding in Delay Tolerant Networks

    OpenAIRE

    Jia Xu; Xin Feng; Wen Jun Yang; Ru Chuan Wang; Bing Qing Han

    2013-01-01

    Multicopy forwarding schemes have been employed in delay tolerant network (DTN) to improve the delivery delay and delivery rate. Much effort has been focused on reducing the routing cost while retaining high performance. This paper aims to provide an optimal joint expected delay forwarding (OJEDF) protocol which minimizes the expected delay while satisfying a certain constant on the number of forwardings per message. We propose a comprehensive forwarding metric called joint expected delay (JE...

  12. Analytical approximate solutions for a general class of nonlinear delay differential equations.

    Science.gov (United States)

    Căruntu, Bogdan; Bota, Constantin

    2014-01-01

    We use the polynomial least squares method (PLSM), which allows us to compute analytical approximate polynomial solutions for a very general class of strongly nonlinear delay differential equations. The method is tested by computing approximate solutions for several applications including the pantograph equations and a nonlinear time-delay model from biology. The accuracy of the method is illustrated by a comparison with approximate solutions previously computed using other methods.

  13. Fractal analysis of intraflow unidirectional\\ud delay over W-LAN and W-WAN environments

    OpenAIRE

    Pezaros, D.; Sifalakis, M.; Mathy, L.

    2007-01-01

    We have analysed unidirectional delay traces of a diverse\\ud set of IPv6 microflows routed over W-LAN and W-WAN\\ud environments. Using a number of time-domain and frequency-domain estimators we have examined the existence and intensity of long-range dependence in packet delay when viewed as time-series data. The correlation structures of packet delay on bulk TCP data path and UDP flows follow asymptotic decay while Hurst exponent estimates suggest from moderate to strong intensity(H->1).

  14. Suppression of cocaine self-administration in monkeys: effects of delayed punishment.

    Science.gov (United States)

    Woolverton, William L; Freeman, Kevin B; Myerson, Joel; Green, Leonard

    2012-04-01

    Delaying presentation of a drug can decrease its effectiveness as a reinforcer, but the effect of delaying punishment of drug self-administration is unknown. This study examined whether a histamine injection could punish cocaine self-administration in a drug-drug choice, whether delaying histamine would decrease its effectiveness, and whether the effects of delay could be described within a delay discounting framework. Monkeys were implanted with double-lumen catheters to allow separate injection of cocaine and histamine. In discrete trials, subjects first chose between cocaine (50 or 100 μg/kg/inj) alone and an injection of the same dose of cocaine followed immediately by an injection of histamine (0.37-50 μg/kg). Next, they chose between cocaine followed immediately by histamine and cocaine followed by an equal but delayed dose of histamine. When choosing between cocaine alone and cocaine followed immediately by histamine, preference increased with histamine dose from indifference to >80% choice of cocaine alone. When choosing between cocaine followed by immediate histamine and cocaine followed by delayed histamine, monkeys showed strong position preferences. When delayed histamine was associated with the nonpreferred position, preference for that option increased with delay from ≤30% to >85%. The corresponding decrease in choice of the preferred position was well described by a hyperboloid discounting function. Histamine can function as a punisher in the choice between injections of cocaine and delay can decrease its effectiveness as a punisher. The effects of delaying punishment of drug self-administration can be conceptualized within the delay discounting framework.

  15. A New CMOS Posicast Pre-shaper for Vibration Reduction of CMOS Op-Amps

    Science.gov (United States)

    Rasoulzadeh, M.; Ghaznavi-Ghoushchi, M. B.

    2010-06-01

    Posicast-based control is a widely used method in vibration reduction of lightly damped oscillatory systems especially in mechanical fields. The target systems to apply Posicast method are the systems which are excited by pulse inputs. Using the Posicast idea, the input pulse is reshaped into a new pulse, which is called Posicast pulse. Applying the generated Posicast pulse reduces the undesired oscillatory manner of under-test systems. In this paper, a fully CMOS Pulse pre-shaper circuit for realization of Posicast command is proposed. Our design is based on delay-and-add approach for the incoming pulses. The delay is done via a modified Schmitt Trigger-like circuit. The adder circuit is implemented by a simple non-binary analog adder terminated by a passive element. Our proposed design has a reasonable flexibility in configuration of time delay and amplitude of the desired pulse-like shapes. The delay is controlled via the delay unit and the pre-shaped pulse's amplitudes are controlled by an analog adder unit. The overall system has 18 MOS transistors, one small capacitor, and one resistor. To verify the effectiveness of the recommended method, it is experienced on a real CMOS Op-Amp. HSPICE simulation results, on 0.25u technology, show a significant reduction on overshoot and settling time of the under-test Op-Amp. The mentioned reduction is more than 95% in overshoot and more than 60% in settling time of the system.

  16. Identification of clinical biomarkers for pre-analytical quality control of blood samples.

    Science.gov (United States)

    Kang, Hyun Ju; Jeon, Soon Young; Park, Jae-Sun; Yun, Ji Young; Kil, Han Na; Hong, Won Kyung; Lee, Mee-Hee; Kim, Jun-Woo; Jeon, Jae-Pil; Han, Bok Ghee

    2013-04-01

    Pre-analytical conditions are key factors in maintaining the high quality of biospecimens. They are necessary for accurate reproducibility of experiments in the field of biomarker discovery as well as achieving optimal specificity of laboratory tests for clinical diagnosis. In research at the National Biobank of Korea, we evaluated the impact of pre-analytical conditions on the stability of biobanked blood samples by measuring biochemical analytes commonly used in clinical laboratory tests. We measured 10 routine laboratory analytes in serum and plasma samples from healthy donors (n = 50) with a chemistry autoanalyzer (Hitachi 7600-110). The analyte measurements were made at different time courses based on delay of blood fractionation, freezing delay of fractionated serum and plasma samples, and at different cycles (0, 1, 3, 6, 9) of freeze-thawing. Statistically significant changes from the reference sample mean were determined using the repeated-measures ANOVA and the significant change limit (SCL). The serum levels of GGT and LDH were changed significantly depending on both the time interval between blood collection and fractionation and the time interval between fractionation and freezing of serum and plasma samples. The glucose level was most sensitive only to the elapsed time between blood collection and centrifugation for blood fractionation. Based on these findings, a simple formula (glucose decrease by 1.387 mg/dL per hour) was derived to estimate the length of time delay after blood collection. In addition, AST, BUN, GGT, and LDH showed sensitive responses to repeated freeze-thaw cycles of serum and plasma samples. These results suggest that GGT and LDH measurements can be used as quality control markers for certain pre-analytical conditions (eg, delayed processing or repeated freeze-thawing) of blood samples which are either directly used in the laboratory tests or stored for future research in the biobank.

  17. Strong seismic wave scattering beneath Kanto region derived from dense K-NET/KiK-net strong motion network and numerical simulation

    Science.gov (United States)

    Takemura, S.; Yoshimoto, K.

    2013-12-01

    Observed seismograms, which consist of the high-frequency body waves through the low-velocity (LV) region at depth of 20-40 km beneath northwestern Chiba in Kanto, show strong peak delay and spindle shape of S waves. By analyzing dense seismic records from K-NET/KiK-net, such spindle-shape S waves are clearly observed in the frequency range of 1-8 Hz. In order to investigate a specific heterogeneous structure to generate such observations, we conduct 3-D finite-difference method (FDM) simulation using realistic heterogeneous models and compare the simulation results with dense strong motion array observations. Our 3-D simulation model is covering the zone 150 km by 64 km in horizontal directions and 75 km in vertical direction, which has been discretized with uniform grid size 0.05 km. We assume a layered background velocity structure, which includes basin structure, crust, mantle and subducting oceanic plate, base on the model proposed by Koketsu et al. (2008). In order to introduce the effect of seismic wave scattering, we assume a stochastic random velocity fluctuation in each layer. Random velocity fluctuations are characterized by exponential-type auto-correlation function (ACF) with correlation distance a = 3 km and rms value of fluctuation e = 0.05 in the upper crust, a = 3 km and e = 0.07 in the lower crust, a = 10 km and e = 0.02 in the mantle. In the subducting oceanic plate, we assume an anisotropic random velocity fluctuation characterized by exponential-type ACF with aH = 10 km in horizontal direction, aZ = 0.5 km in vertical direction and e = 0.02 (e.g., Furumura and Kennett, 2005). In addition, we assume a LV zone at northeastern part of Chiba with depth of 20-40 km (e.g., Matsubara et al., 2004). In the LV zone, random velocity fluctuation characterized by Gaussian-type ACF with a = 1 km and e = 0.07 is superposed on exponential-type ACF with a = 3 km and e = 0.07, in order to modulate the S-wave propagation in the dominant frequency range of

  18. Salinity inhibits post transcriptional processing of chloroplast 16S rRNA in shoot cultures of jojoba (Simmondsia chinesis).

    Science.gov (United States)

    Mizrahi-Aviv, Ela; Mills, David; Benzioni, Aliza; Bar-Zvi, Dudy

    2005-03-01

    Chloroplast metabolism is rapidly affected by salt stress. Photosynthesis is one of the first processes known to be affected by salinity. Here, we report that salinity inhibits chloroplast post-transcriptional RNA processing. A differentially expressed 680-bp cDNA, containing the 3' sequence of 16S rRNA, transcribed intergenic spacer, exon 1 and intron of tRNA(Ile), was isolated by differential display reverse transcriptase PCR from salt-grown jojoba (Simmondsia chinesis) shoot cultures. Northern blot analysis indicated that although most rRNA appears to be fully processed, partially processed chloroplast 16S rRNA accumulates in salt-grown cultures. Thus, salinity appears to decrease the processing of the rrn transcript. The possible effect of this decreased processing on physiological processes is, as yet, unknown.

  19. Crystal Structure of the 23S rRNA Fragment Specific to r-Protein L1 and Designed Model of the Ribosomal L1 Stalk from Haloarcula marismortui

    Directory of Open Access Journals (Sweden)

    Azat Gabdulkhakov

    2017-02-01

    Full Text Available The crystal structure of the 92-nucleotide L1-specific fragment of 23S rRNA from Haloarcula marismortui (Hma has been determined at 3.3 Å resolution. Similar to the corresponding bacterial rRNA fragments, this structure contains joined helix 76-77 topped by an approximately globular structure formed by the residual part of the L1 stalk rRNA. The position of HmaL1 relative to the rRNA was found by its docking to the rRNA fragment using the L1-rRNA complex from Thermus thermophilus as a guide model. In spite of the anomalous negative charge of the halophilic archaeal protein, the conformation of the HmaL1-rRNA interface appeared to be very close to that observed in all known L1-rRNA complexes. The designed structure of the L1 stalk was incorporated into the H. marismortui 50S ribosomal subunit. Comparison of relative positions of L1 stalks in 50S subunits from H. marismortui and T. thermophilus made it possible to reveal the site of inflection of rRNA during the ribosome function.

  20. The predictive value of MR diffusion weighted imaging on the delayed encephalopathy after carbon monoxide poisoning

    International Nuclear Information System (INIS)

    Xiao Xinlan; Fu Lihui; Xi Weimin; Yin Jianhua; Gong Liangeng; Yuan Aimei; Yang Xinyue; Liu Zhiyong

    2007-01-01

    Objective: To investigate the value of diffusion weighted imaging (DWI)in predicting delayed encephalopathy of the rabbits brain after carbon monoxide (CO)poisoning. Methods: Sixty healthy rabbits were put into self-made poisoning cabinet and were poisoned by inhalation of CO. Aeration of CO was stopped when the rabbits became comatous, and the cabinet was kept airpoof for 6 h. The rabbits underwent MRI before poisoning , at 1 h, 3 d, 5 d, 7 d, 15 d, 30 d ,45 d, and 60 d after poisoning respectively. Axial and sagittal T 2 WI, axial T 1 WI and DWI were performed. In the rabbits that did not show symptoms of delayed encephalopathy, the observation was discontinued on the 60th day. In the rabbit that showed the symptoms, the observation was discontinued on the 30th-45th day. The changing pattern of cortical ADC values before and after CO poisoning was observed and its relationship with delayed encephalopathy was investigated. Results: In the group without delayed encephalopathy (15 rabbits), the ADC value at 1 h after poisoning [(7.58±0.36) x 10 -4 mm 2 /s] decreased significantly compared with the pre- poisoning value [(8.02±0.35) x 10 -4 mm 2 /s] (q=0.4441, P -4 mm 2 /s], and maintained at the same level as pre- poisoning at 60 d after poisoning (P >0.05). In the group with delayed encephalopathy (15 rabbits), the ADC value at 1 h after poisoning [(7.40±0.32) x 10 -4 mm 2 /s] decreased significantly compared with the pre- poisoning value [(8.08± 0.32) x 10 -4 mm 2 /s] (q=0.6728, P -4 mm 2 /s], secondly significantly decreased at 15 d [(7.29±0.93) x 10 -4 mm 2 /s] without further recovery. The ADC value decrease at 15d alter poisoning [(7.29±0.93) x 10 -4 mm 2 /s] was significant compared with the prepoisoning ADC value (q=0.7850, P<0.01). Conclusions: There is a correlation between the decrease of the ADC value and the degree of tissue damage. The decrease of the ADC value in acute stage can predict the delayed encephalopathy. The second significant decrease

  1. Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068 (Italy); Department of Mathematics, University of Trento (Italy); Zunino, Roberto, E-mail: roberto.zunino@unitn.it [Department of Mathematics, University of Trento (Italy)

    2014-10-07

    We propose a new exact stochastic rejection-based simulation algorithm for biochemical reactions and extend it to systems with delays. Our algorithm accelerates the simulation by pre-computing reaction propensity bounds to select the next reaction to perform. Exploiting such bounds, we are able to avoid recomputing propensities every time a (delayed) reaction is initiated or finished, as is typically necessary in standard approaches. Propensity updates in our approach are still performed, but only infrequently and limited for a small number of reactions, saving computation time and without sacrificing exactness. We evaluate the performance improvement of our algorithm by experimenting with concrete biological models.

  2. Location of rRNA transcription to the nucleolar components: disappearance of the fibrillar centers in nucleoli of regenerating rat hepatocytes.

    Science.gov (United States)

    Montanaro, Lorenzo; Govoni, Marzia; Orrico, Catia; Treré, Davide; Derenzini, Massimo

    2011-01-01

    The precise location of rDNA transcription to the components of mammalian cell nucleolus is still debated. This was due to the fact that all the molecules necessary for rRNA synthesis are located in two of the three components, the fibrillar centers (FCs) and the dense fibrillar component (DFC), which together with the granular component (GC) are considered to be constantly present in mammalian cell nucleoli. In the present study we demonstrated that in nucleoli of many regenerating rat hepatocytes at 15 h after partial hepatectomy the FCs were no longer present, only the DFC and the GC being detected. At this time of regeneration the rRNA transcriptional activity was three fold that of resting hepatocytes, while the synthesis of DNA was not yet significantly increased, indicating that these nucleolar changes were due to the rRNA synthesis up-regulation. The DFC appeared to be organized in numerous, small, roundish tufts of fibrils. The silver staining procedure for AgNOR proteins, which are associated with the ribosomal genes, selectively and homogeneously stained these fibrillar tufts. Immuno-gold visualization of the Upstream Binding Factor (UBF), which is associated with the promoter region and the transcribed portion of the rRNA 45S gene, demonstrated that UBF was selectively located in the fibrillar tufts. We concluded that in proliferating rat hepatocytes the increased synthesis of rRNA induced an activation of the rRNA transcription machinery located in the fibrillar centers which, by becoming associated with the ribonucleoprotein transcripts, assumed the morphological pattern of the DFC.

  3. A Systematic Evaluation of Blood Serum and Plasma Pre-Analytics for Metabolomics Cohort Studies

    Directory of Open Access Journals (Sweden)

    Elodie Jobard

    2016-12-01

    Full Text Available The recent thriving development of biobanks and associated high-throughput phenotyping studies requires the elaboration of large-scale approaches for monitoring biological sample quality and compliance with standard protocols. We present a metabolomic investigation of human blood samples that delineates pitfalls and guidelines for the collection, storage and handling procedures for serum and plasma. A series of eight pre-processing technical parameters is systematically investigated along variable ranges commonly encountered across clinical studies. While metabolic fingerprints, as assessed by nuclear magnetic resonance, are not significantly affected by altered centrifugation parameters or delays between sample pre-processing (blood centrifugation and storage, our metabolomic investigation highlights that both the delay and storage temperature between blood draw and centrifugation are the primary parameters impacting serum and plasma metabolic profiles. Storing the blood drawn at 4 °C is shown to be a reliable routine to confine variability associated with idle time prior to sample pre-processing. Based on their fine sensitivity to pre-analytical parameters and protocol variations, metabolic fingerprints could be exploited as valuable ways to determine compliance with standard procedures and quality assessment of blood samples within large multi-omic clinical and translational cohort studies.

  4. An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

    Directory of Open Access Journals (Sweden)

    Shenkar Noa

    2009-08-01

    Full Text Available Abstract Background Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. Results Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1 Phlebobranchia + Thaliacea + Aplousobranchia, 2 Appendicularia, and 3 Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models

  5. Phylogenetic analysis of 23S rRNA gene sequences of some ...

    African Journals Online (AJOL)

    ... glycol plus control. All isolates exhibited good drought-tolerant efficiencies at 10% PEG. While most of the isolates could not tolerate up to 20% PEG, isolates of Rlv6, Rlv9, Rlv12 and Rlv13 tolerated up to 20% PEG. Keywords: Rhizobium leguminosarum, 23S rRNA gene, phylogenetic tree, diversity and drought tolerance ...

  6. The mass-sheet degeneracy and time-delay cosmography: analysis of the strong lens RXJ1131-1231

    International Nuclear Information System (INIS)

    Birrer, Simon; Amara, Adam; Refregier, Alexandre

    2016-01-01

    We present extended modelling of the strong lens system RXJ1131-1231 with archival data in two HST bands in combination with existing line-of-sight contribution and velocity dispersion estimates. Our focus is on source size and its influence on time-delay cosmography. We therefore examine the impact of mass-sheet degeneracy and especially the degeneracy pointed out by Schneider and Sluse (2013) [1] using the source reconstruction scale. We also extend on previous work by further exploring the effects of priors on the kinematics of the lens and the external convergence in the environment of the lensing system. Our results coming from RXJ1131-1231 are given in a simple analytic form so that they can be easily combined with constraints coming from other cosmological probes. We find that the choice of priors on lens model parameters and source size are subdominant for the statistical errors for H 0 measurements of this systems. The choice of prior for the source is sub-dominant at present (2% uncertainty on H 0 ) but may be relevant for future studies. More importantly, we find that the priors on the kinematic anisotropy of the lens galaxy have a significant impact on our cosmological inference. When incorporating all the above modeling uncertainties, we find H 0 = 86.6 +6.8 -6.9 km s -1 Mpc -1 , when using kinematic priors similar to other studies. When we use a different kinematic prior motivated by Barnabè et al. (2012) [2] but covering the same anisotropic range, we find H 0 = 74.5 +8.0 -7.8 km s -1 Mpc -1 . This means that the choice of kinematic modeling and priors have a significant impact on cosmographic inferences. The way forward is either to get better velocity dispersion measures which would down weight the impact of the priors or to construct physically motivated priors for the velocity dispersion model.

  7. Delay discounting, treatment motivation and treatment retention among substance-dependent individuals attending an in inpatient detoxification program

    NARCIS (Netherlands)

    Stevens, Laura; Verdejo-García, Antonio; Roeyers, Herbert; Goudriaan, Anna E.; Vanderplasschen, Wouter

    2015-01-01

    Recent studies consistently indicate high rates of delay discounting in drug users, which refers to a strong tendency to devaluate delayed rewards. Many addiction treatment programs however, place high demands on the ability to postpone immediate gratification. Therefore, these programs may be

  8. Trading Later Rewards for Current Pleasure: Pornography Consumption and Delay Discounting.

    Science.gov (United States)

    Negash, Sesen; Sheppard, Nicole Van Ness; Lambert, Nathaniel M; Fincham, Frank D

    2016-01-01

    Internet pornography is a multi-billion-dollar industry that has grown increasingly accessible. Delay discounting involves devaluing larger, later rewards in favor of smaller, more immediate rewards. The constant novelty and primacy of sexual stimuli as particularly strong natural rewards make Internet pornography a unique activator of the brain's reward system, thereby having implications for decision-making processes. Based on theoretical studies of evolutionary psychology and neuroeconomics, two studies tested the hypothesis that consuming Internet pornography would relate to higher rates of delay discounting. Study 1 used a longitudinal design. Participants completed a pornography use questionnaire and a delay discounting task at Time 1 and then again four weeks later. Participants reporting higher initial pornography use demonstrated a higher delay discounting rate at Time 2, controlling for initial delay discounting. Study 2 tested for causality with an experimental design. Participants were randomly assigned to abstain from either their favorite food or pornography for three weeks. Participants who abstained from pornography use demonstrated lower delay discounting than participants who abstained from their favorite food. The finding suggests that Internet pornography is a sexual reward that contributes to delay discounting differently than other natural rewards. Theoretical and clinical implications of these studies are highlighted.

  9. A normalized PID controller in networked control systems with varying time delays.

    Science.gov (United States)

    Tran, Hoang-Dung; Guan, Zhi-Hong; Dang, Xuan-Kien; Cheng, Xin-Ming; Yuan, Fu-Shun

    2013-09-01

    It requires not only simplicity and flexibility but also high specified stability and robustness of system to design a PI/PID controller in such complicated networked control systems (NCSs) with delays. By gain and phase margins approach, this paper proposes a novel normalized PI/PID controller for NCSs based on analyzing the stability and robustness of system under the effect of network-induced delays. Specifically, We take into account the total measured network delays to formulate the gain and phase margins of the closed-loop system in the form of a set of equations. With pre-specified values of gain and phase margins, this set of equations is then solved for calculating the closed forms of control parameters which enable us to propose the normalized PI/PID controller simultaneously satisfying the following two requirements: (1) simplicity without re-solving the optimization problem for a new process, (2) high flexibility to cope with large scale of random delays and deal with many different processes in different conditions of network. Furthermore, in our method, the upper bound of random delay can be estimated to indicate the operating domain of proposed PI/PID controller. Finally, simulation results are shown to demonstrate the advantages of our proposed controller in many situations of network-induced delays. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

  10. Deletion analysis of the expression of rRNA genes and associated tRNA genes carried by a lambda transducing bacteriophage

    International Nuclear Information System (INIS)

    Morgan, E.A.; Nomura, M.

    1979-01-01

    Transducing phage lambda ilv5 carries genes for rRNA's, spacer tRNA's (tRNA 1 /sup Ile/ and tRNA/sub 1B//sup Ala/), and two other tRNA's (tRNA 1 /sup Asp/ and tRNA/sup Trp/). We have isolated a mutant of lambda ilv5, lambda ilv5su7, which carries an amber suppressor mutation in the tRNA/sup Trp/ gene. A series of deletion mutants were isolated from the lambda ilv5su7 phage. Genetic and biochemical analyses of these deletion mutants have confirmed our previous conclusion that the genes for tRNA 1 /sup Asp/ and tRNA/sup Trp/ located at the distal end of the rRNA operon (rrnC) are cotranscribed with other rRNA genes in that operon. In addition, these deletions were used to define roughly the physical location of the promoter(s) of the rRNA operon carried by the lambda ilv5su7 transducing phage

  11. Stability and delay sensitivity of neutral fractional-delay systems.

    Science.gov (United States)

    Xu, Qi; Shi, Min; Wang, Zaihua

    2016-08-01

    This paper generalizes the stability test method via integral estimation for integer-order neutral time-delay systems to neutral fractional-delay systems. The key step in stability test is the calculation of the number of unstable characteristic roots that is described by a definite integral over an interval from zero to a sufficient large upper limit. Algorithms for correctly estimating the upper limits of the integral are given in two concise ways, parameter dependent or independent. A special feature of the proposed method is that it judges the stability of fractional-delay systems simply by using rough integral estimation. Meanwhile, the paper shows that for some neutral fractional-delay systems, the stability is extremely sensitive to the change of time delays. Examples are given for demonstrating the proposed method as well as the delay sensitivity.

  12. Wigner-Smith delay times and the non-Hermitian Hamiltonian for the HOCl molecule

    International Nuclear Information System (INIS)

    Barr, A.M.; Reichl, L.E.

    2013-01-01

    We construct the scattering matrix for a two-dimensional model of a Cl atom scattering from an OH dimer. We show that the scattering matrix can be written in terms of a non-Hermitian Hamiltonian whose complex energy eigenvalues can be used to compute Wigner-Smith delay times for the Cl-OH scattering process. We compute the delay times for a range of energies, and show that the scattering states with the longest delay times are strongly influenced by unstable periodic orbits in the classical dynamics. (Copyright copyright 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment

    DEFF Research Database (Denmark)

    Sahm, K.; MacGregor, BJ; Jørgensen, BB

    1999-01-01

    In the past, enumeration of sulphate-reducing bacteria (SRB) by cultivation-based methods generally contradicted measurements of sulphate reduction, suggesting unrealistically high respiration rates per cell. Here, we report evidence that quantification of SRB rRNA by slot-blot hybridization...... between 18% and 25% to the prokaryotic rRNA pool. The dominant SRB were related to complete oxidizing genera (Desulphococcus, Desulphosarcina and Desulphobacterium), while Desulpho-bacter could not be detected. The vertical profile and quantity of rRNA from SRB was compared with sulphate reduction rates......, directly above the sulphate reduction maximum. Cell numbers calculated by converting the relative contribution of SRB rRNA to the percentage of DAPI-stained cells indicated a population size for SRB of 2.4-6.1 x 10(8) cells cm(-3) wet sediment. Cellular sulphate reduction rates calculated on the basis...

  14. Validation of a PCR Assay for Chlamydophila abortus rRNA gene detection in a murine model

    Directory of Open Access Journals (Sweden)

    Francielle Gibson da Silva-Zacarias

    2009-11-01

    Full Text Available Chlamydophila abortus (C. abortus is associated with reproductive problems in cattle, sheep, and goats. Diagnosis of C. abortus using embryonated chicken eggs or immortalized cell lines has a very low sensitivity. Polymerase chain reaction (PCR assays have been used to detect C. abortus infection in clinical specimens and organ fragments, such as placenta, fetal organs, vaginal secretions, and semen. The aim of this study was to develop a PCR assay for the amplification of an 856-bp fragment of the rRNA gene of the Chlamydiaceae family. The PCR assay was evaluated using organs from 15 mice experimentally infected with the S26/3 reference strain of C. abortus. The results of the rRNA PCR were compared to the results from another PCR system (Omp2 PCR that has been previously described for the Omp2 (outer major protein gene from the Chlamydiaceae family. From the 15 C. abortus-inoculated mice, 13 (K=0.84, standard error =0.20 tested positive using the rRNA PCR assay and 9 (K=0.55, standard error=0.18 tested positive using the Omp2 PCR assay. The detection limit, measured using inclusion-forming units (IFU, for C. abortus with the rRNA PCR (1.05 IFU was 100-fold lower than for the Omp2 PCR (105 IFU. The higher sensitivity of the rRNA PCR, as compared to the previously described PCR assay, and the specificity of the assay, demonstrated using different pathogenic microorganisms of the bovine reproductive system, suggest that the new PCR assay developed in this study can be used for the molecular diagnosis of C. abortus in abortion and other reproductive failures in bovines, caprines, and ovines.Chlamydophila abortus (C. abortus é frequentemente associada a distúrbios reprodutivos em bovinos, ovinos e caprinos. Para o diagnóstico, os métodos de cultivo em ovo embrionado de galinha e em células de linhagem contínua apresentam baixa sensibilidade. A reação em cadeia da polimerase (PCR tem sido utilizada em placenta, órgãos fetais, secre

  15. Evaluation of 5.8S rRNA to identify Penaeus semisulcatus and its subspecies, Penaeus semisulcatus persicus (Penaeidae and some Decapoda species

    Directory of Open Access Journals (Sweden)

    Zahra Noroozi

    2015-10-01

    Full Text Available The green tiger prawn, Penaeus semisulcatus is one of the most important members of the family Penaeidae in the Persian Gulf. Based on the morphological characteristics, two groups, including P. semisulcatus and its subspecies viz. P. s. persicus are recognized. This study was conducted to investigate the genetic distance between P. semisulcatus and P. s. persicus by analyzing partial sequence of 5.8S rRNA. Another objective of this study is to evaluate the ability of 5.8S rRNA to identify the species of Decapoda. The results indicated that the 5.8S rRNA gene of both P. semisulcatus and P. s. persicus were exactly identical, and sequence variation was not observed. The results also indicated that 5.8S rRNA sequences between species of the same genus of analysed species of Decapoda are conserved, and no genetic distance was observed in species level. The low evolutionary rate and efficient conservation of the 5.8S rRNA can be attributed to its role in the translation process.

  16. PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

    Directory of Open Access Journals (Sweden)

    Leyla Esfandiari

    2016-07-01

    Full Text Available A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli 16S rRNA at 10 fM, which corresponds to ~100–1000 colony forming units/mL (CFU/mL depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids.

  17. Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing.

    Directory of Open Access Journals (Sweden)

    Heather P McLaughlin

    Full Text Available Coxiella burnetii is a human pathogen that causes the serious zoonotic disease Q fever. It is ubiquitous in the environment and due to its wide host range, long-range dispersal potential and classification as a bioterrorism agent, this microorganism is considered an HHS Select Agent. In the event of an outbreak or intentional release, laboratory strain typing methods can contribute to epidemiological investigations, law enforcement investigation and the public health response by providing critical information about the relatedness between C. burnetii isolates collected from different sources. Laboratory cultivation of C. burnetii is both time-consuming and challenging. Availability of strain collections is often limited and while several strain typing methods have been described over the years, a true gold-standard method is still elusive. Building upon epidemiological knowledge from limited, historical strain collections and typing data is essential to more accurately infer C. burnetii phylogeny. Harmonization of auspicious high-resolution laboratory typing techniques is critical to support epidemiological and law enforcement investigation. The single nucleotide polymorphism (SNP -based genotyping approach offers simplicity, rapidity and robustness. Herein, we demonstrate SNPs identified within 16S rRNA gene sequences can differentiate C. burnetii strains. Using this method, 55 isolates were assigned to six groups based on six polymorphisms. These 16S rRNA SNP-based genotyping results were largely congruent with those obtained by analyzing restriction-endonuclease (RE-digested DNA separated by SDS-PAGE and by the high-resolution approach based on SNPs within multispacer sequence typing (MST loci. The SNPs identified within the 16S rRNA gene can be used as targets for the development of additional SNP-based genotyping assays for C. burnetii.

  18. Alteration of rRNA gene copy number and expression in patients ...

    African Journals Online (AJOL)

    Irina S. Kolesnikova

    2017-09-01

    Sep 1, 2017 ... conjugated avidin and anti-avidin antibody (both from New Eng- land Biolabs ... performed using an Aurum Total RNA Mini Kit (BioRad, USA) or .... 5.8S rRNA in CPG148 are 19.60 ± 0.82 and 20.09 ± 0.13 times the .... Science + Business Media Dordrecht; 2011. p. ... New York: Academic Press; 1977. p.

  19. Strong field gravitational lensing by a charged Galileon black hole

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Shan-Shan; Xie, Yi, E-mail: clefairy035@163.com, E-mail: yixie@nju.edu.cn [School of Astronomy and Space Science, Nanjing University, Nanjing 210093 (China)

    2016-07-01

    Strong field gravitational lensings are dramatically disparate from those in the weak field by representing relativistic images due to light winds one to infinity loops around a lens before escaping. We study such a lensing caused by a charged Galileon black hole, which is expected to have possibility to evade no-hair theorem. We calculate the angular separations and time delays between different relativistic images of the charged Galileon black hole. All these observables can potentially be used to discriminate a charged Galileon black hole from others. We estimate the magnitudes of these observables for the closest supermassive black hole Sgr A*. The strong field lensing observables of the charged Galileon black hole can be close to those of a tidal Reissner-Nordström black hole or those of a Reissner-Nordström black hole. It will be helpful to distinguish these black holes if we can separate the outermost relativistic images and determine their angular separation, brightness difference and time delay, although it requires techniques beyond the current limit.

  20. Parents' and speech and language therapists' explanatory models of language development, language delay and intervention.

    Science.gov (United States)

    Marshall, Julie; Goldbart, Juliet; Phillips, Julie

    2007-01-01

    Parental and speech and language therapist (SLT) explanatory models may affect engagement with speech and language therapy, but there has been dearth of research in this area. This study investigated parents' and SLTs' views about language development, delay and intervention in pre-school children with language delay. The aims were to describe, explore and explain the thoughts, understandings, perceptions, beliefs, knowledge and feelings held by: a group of parents from East Manchester, UK, whose pre-school children had been referred with suspected language delay; and SLTs working in the same area, in relation to language development, language delay and language intervention. A total of 24 unstructured interviews were carried out: 15 with parents whose children had been referred for speech and language therapy and nine with SLTs who worked with pre-school children. The interviews were transcribed verbatim and coded using Atlas/ti. The data were analysed, subjected to respondent validation, and grounded theories and principled descriptions developed to explain and describe parents' and SLTs' beliefs and views. Parent and SLT data are presented separately. There are commonalities and differences between the parents and the SLTs. Both groups believe that language development and delay are influenced by both external and internal factors. Parents give more weight to the role of gender, imitation and personality and value television and videos, whereas the SLTs value the 'right environment' and listening skills and consider that health/disability and socio-economic factors are important. Parents see themselves as experts on their child and have varied ideas about the role of SLTs, which do not always accord with SLTs' views. The parents and SLTs differ in their views of the roles of imitation and play in intervention. Parents typically try strategies before seeing an SLT. These data suggest that parents' ideas vary and that, although parents and SLTs may share some

  1. Grape berry ripening delay induced by a pre-véraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene-related genes.

    Science.gov (United States)

    Ziliotto, Fiorenza; Corso, Massimiliano; Rizzini, Fabio Massimo; Rasori, Angela; Botton, Alessandro; Bonghi, Claudio

    2012-10-09

    Auxins act as repressors of ripening inception in grape (véraison), while ethylene and abscisic acid (ABA) play a positive role as inducers of the syndrome. Despite the increasing amount of information made available on this topic, the complex network of interactions among these hormones remains elusive. In order to shed light on these aspects, a holistic approach was adopted to evaluate, at the transcriptomic level, the crosstalk between hormones in grape berries, whose ripening progression was delayed by applying naphtalenacetic acid (NAA) one week before véraison. The NAA treatment caused significant changes in the transcription rate of about 1,500 genes, indicating that auxin delayed grape berry ripening also at the transcriptional level, along with the recovery of a steady state of its intracellular concentration. Hormone indices analysis carried out with the HORMONOMETER tool suggests that biologically active concentrations of auxins were achieved throughout a homeostatic recovery. This occurred within 7 days after the treatment, during which the physiological response was mainly unspecific and due to a likely pharmacological effect of NAA. This hypothesis is strongly supported by the up-regulation of genes involved in auxin conjugation (GH3-like) and action (IAA4- and IAA31-like). A strong antagonistic effect between auxin and ethylene was also observed, along with a substantial 'synergism' between auxins and ABA, although to a lesser extent. This study suggests that, in presence of altered levels of auxins, the crosstalk between hormones involves diverse mechanisms, acting at both the hormone response and biosynthesis levels, creating a complex response network.

  2. Improving operating room first start efficiency - value of both checklist and a pre-operative facilitator.

    Science.gov (United States)

    Panni, M K; Shah, S J; Chavarro, C; Rawl, M; Wojnarwsky, P K; Panni, J K

    2013-10-01

    There are multiple components leading to improved operating room efficiency. We undertook a project focusing on first case starts; accounting for each delay component on a global basis. Our hypothesis was there would be a reduction in first start delays after we implemented strategies to address the issues identified through this accounting process. An orange sheet checklist was implemented, with specific items that needed to be clear prior to roll back to the operating room (OR), and an OR facilitator was employed to intervene whenever there were any missing items needed for a specific patient. We present the data from this quality improvement project over an 18-month period. Initially, 10.07 (± 0.73) delayed first starts occurred per day but declined steadily over time to a low of 4.95 (± 0.38) per day after 6 months (-49.2 %, P < 0.001). By the end of the project, the most common reasons for delay still included late surgical attending (19%), schedule changes (14%) as well as 'other reasons' (13%), but with an overall reduction per day of each. Total anaesthesia delay initially totalled 11% of the first start delays, but was negligible (< 1%) at the project's completion. While we have a challenging operating room environment based on our patient population, multiple trainees in both the surgery and anaesthesiology teams: an orange sheet - pre-operative checklist in addition to a dedicated pre-operative facilitator; allowed us to make a substantial improvement in our first start on time starts. © 2013 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  3. Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

    Czech Academy of Sciences Publication Activity Database

    Ságová-Marečková, M.; Ulanová, Dana; Šanderová, P.; Omelka, M.; Kameník, Zdeněk; Olšovská, J.; Kopecký, J.

    2015-01-01

    Roč. 15, APR 2015 (2015) ISSN 1471-2180 Institutional support: RVO:61388971 Keywords : Actinobacteria * 16S rRNA diversity * Resistance genes Subject RIV: EH - Ecology, Behaviour Impact factor: 2.581, year: 2015

  4. Effect of mutations in the A site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction

    DEFF Research Database (Denmark)

    Recht, M I; Douthwaite, S; Dahlquist, K D

    1999-01-01

    antibiotics, which also interact with this region of rRNA. Mutations of certain nucleotides in rRNA reduce aminoglycoside binding affinity, as previously demonstrated using a model RNA oligonucleotide system. Here, predictions from the oligonucleotide system were tested in the ribosome by mutation...... for the aminoglycoside paromomycin, whereas no discernible reduction in affinity was observed with 1406 mutant ribosomes. These data are consistent with prior NMR structural determination of aminoglycoside interaction with the decoding region, and further our understanding of how aminoglycoside resistance can...

  5. Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Cébron, Aurélie; Murrell, J Colin

    2007-11-01

    Active methanotrophs in a landfill soil were revealed by detecting the 16S rRNA of methanotrophs and the mRNA transcripts of key genes involved in methane oxidation. New 16S rRNA primers targeting type I and type II methanotrophs were designed and optimized for analysis by denaturing gradient gel electrophoresis. Direct extraction of RNA from soil enabled the analysis of the expression of the functional genes: mmoX, pmoA and mxaF, which encode subunits of soluble methane monooxygenase, particulate methane monooxygenase and methanol dehydrogenase respectively. The 16S rRNA polymerase chain reaction (PCR) primers for type I methanotrophs detected Methylomonas, Methylosarcina and Methylobacter sequences from both soil DNA and cDNA which was generated from RNA extracted directly from the landfill cover soil. The 16S rRNA primers for type II methanotrophs detected primarily Methylocella and some Methylocystis 16S rRNA genes. Phylogenetic analysis of mRNA recovered from the soil indicated that Methylobacter, Methylosarcina, Methylomonas, Methylocystis and Methylocella were actively expressing genes involved in methane and methanol oxidation. Transcripts of pmoA but not mmoX were readily detected by reverse transcription polymerase chain reaction (RT-PCR), indicating that particulate methane monooxygenase may be largely responsible for methane oxidation in situ.

  6. Radio and Gamma-Ray Monitoring of Strongly Lensed Quasars and Blazars

    NARCIS (Netherlands)

    Rumbaugh, Nick; Fassnacht, Chris; McKean, John; Koopmans, Leon; Auger, Matthew; Suyu, Sherry; Marshall, Philip J.

    2015-01-01

    We observed six strongly lensed, radio-loud quasars (MG 0414+0534, CLASS B0712+472, JVAS B1030+074, CLASS B1127+385, CLASS B1152+199, and JVAS B1938+666) in order to identify systems suitable for measuring cosmological parameters using time delays between their multiple images. Two separate

  7. Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies.

    Science.gov (United States)

    van der Kuyl, A C; Kuiken, C L; Dekker, J T; Perizonius, W R; Goudsmit, J

    1995-06-01

    Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.

  8. Neuronal model with distributed delay: analysis and simulation study for gamma distribution memory kernel.

    Science.gov (United States)

    Karmeshu; Gupta, Varun; Kadambari, K V

    2011-06-01

    A single neuronal model incorporating distributed delay (memory)is proposed. The stochastic model has been formulated as a Stochastic Integro-Differential Equation (SIDE) which results in the underlying process being non-Markovian. A detailed analysis of the model when the distributed delay kernel has exponential form (weak delay) has been carried out. The selection of exponential kernel has enabled the transformation of the non-Markovian model to a Markovian model in an extended state space. For the study of First Passage Time (FPT) with exponential delay kernel, the model has been transformed to a system of coupled Stochastic Differential Equations (SDEs) in two-dimensional state space. Simulation studies of the SDEs provide insight into the effect of weak delay kernel on the Inter-Spike Interval(ISI) distribution. A measure based on Jensen-Shannon divergence is proposed which can be used to make a choice between two competing models viz. distributed delay model vis-á-vis LIF model. An interesting feature of the model is that the behavior of (CV(t))((ISI)) (Coefficient of Variation) of the ISI distribution with respect to memory kernel time constant parameter η reveals that neuron can switch from a bursting state to non-bursting state as the noise intensity parameter changes. The membrane potential exhibits decaying auto-correlation structure with or without damped oscillatory behavior depending on the choice of parameters. This behavior is in agreement with empirically observed pattern of spike count in a fixed time window. The power spectral density derived from the auto-correlation function is found to exhibit single and double peaks. The model is also examined for the case of strong delay with memory kernel having the form of Gamma distribution. In contrast to fast decay of damped oscillations of the ISI distribution for the model with weak delay kernel, the decay of damped oscillations is found to be slower for the model with strong delay kernel.

  9. Delays in the diagnosis and treatment of tuberculosis patients in Vietnam: a cross-sectional study

    Directory of Open Access Journals (Sweden)

    Khanh Vu T

    2007-06-01

    Full Text Available Abstract Background Treatment delay is an important indicator of access to tuberculosis diagnosis and treatment. Analyses of patient delay (i.e. time interval between onset of symptoms and first consultation of a health care provider and health care delay (i.e. time interval between first consultation and start of treatment can inform policies to improve access. This study assesses the patient, health care provider and total delay in diagnosis and treatment of new smear-positive pulmonary tuberculosis patients, and the risk factors for long delay, in Vietnam. Methods A cross-sectional survey of new patients treated by the National Tuberculosis Control Programme was conducted in 70 randomly selected districts in Vietnam. All consecutively registered patients in one quarter of 2002 were interviewed using a pre-coded structured questionnaire. Results Median (range delay was 4 weeks (1–48 for total, 3 (1–48 weeks for patient and 1 (0–25 week for health care delay. Patients with long total delay (≥ 12 weeks, 15% accounted for 49% of the cumulative number of delay-weeks. Independent risk factors (p 5 km distance from a health facility or in the northern area. For long health care delay (≥ 6 weeks this was urban setting, residence in the central area and initial visit to a communal health post, TB hospital or the private sector. Conclusion Analyses of patient and treatment delays can indicate target groups and areas for health education and strengthening of the referral system, in particular between the private sector and the NTP.

  10. The Human Microbiome and Understanding the 16S rRNA Gene in Translational Nursing Science.

    Science.gov (United States)

    Ames, Nancy J; Ranucci, Alexandra; Moriyama, Brad; Wallen, Gwenyth R

    As more is understood regarding the human microbiome, it is increasingly important for nurse scientists and healthcare practitioners to analyze these microbial communities and their role in health and disease. 16S rRNA sequencing is a key methodology in identifying these bacterial populations that has recently transitioned from use primarily in research to having increased utility in clinical settings. The objectives of this review are to (a) describe 16S rRNA sequencing and its role in answering research questions important to nursing science; (b) provide an overview of the oral, lung, and gut microbiomes and relevant research; and (c) identify future implications for microbiome research and 16S sequencing in translational nursing science. Sequencing using the 16S rRNA gene has revolutionized research and allowed scientists to easily and reliably characterize complex bacterial communities. This type of research has recently entered the clinical setting, one of the best examples involving the use of 16S sequencing to identify resistant pathogens, thereby improving the accuracy of bacterial identification in infection control. Clinical microbiota research and related requisite methods are of particular relevance to nurse scientists-individuals uniquely positioned to utilize these techniques in future studies in clinical settings.

  11. Pre-exposure rabies prophylaxis: a systematic review

    Science.gov (United States)

    Recuenco, Sergio; Navarro-Vela, Ana Maria; Deray, Raffy; Vigilato, Marco; Ertl, Hildegund; Durrheim, David; Rees, Helen; Nel, Louis H; Abela-Ridder, Bernadette; Briggs, Deborah

    2017-01-01

    Abstract Objective To review the safety and immunogenicity of pre-exposure rabies prophylaxis (including accelerated schedules, co-administration with other vaccines and booster doses), its cost–effectiveness and recommendations for use, particularly in high-risk settings. Methods We searched the PubMed, Centre for Agriculture and Biosciences International, Cochrane Library and Web of Science databases for papers on pre-exposure rabies prophylaxis published between 2007 and 29 January 2016. We reviewed field data from pre-exposure prophylaxis campaigns in Peru and the Philippines. Findings Pre-exposure rabies prophylaxis was safe and immunogenic in children and adults, also when co-administered with routine childhood vaccinations and the Japanese encephalitis vaccine. The evidence available indicates that shorter regimens and regimens involving fewer doses are safe and immunogenic and that booster intervals could be extended up to 10 years. The few studies on cost suggest that, at current vaccine and delivery costs, pre-exposure prophylaxis campaigns would not be cost-effective in most situations. Although pre-exposure prophylaxis has been advocated for high-risk populations, only Peru and the Philippines have implemented appropriate national programmes. In the future, accelerated regimens and novel vaccines could simplify delivery and increase affordability. Conclusion Pre-exposure rabies prophylaxis is safe and immunogenic and should be considered: (i) where access to postexposure prophylaxis is limited or delayed; (ii) where the risk of exposure is high and may go unrecognized; and (iii) where controlling rabies in the animal reservoir is difficult. Pre-exposure prophylaxis should not distract from canine vaccination efforts, provision of postexposure prophylaxis or education to increase rabies awareness in local communities. PMID:28250534

  12. Stimulated adiabatic passage in a dissipative ensemble of atoms with strong Rydberg-state interactions

    DEFF Research Database (Denmark)

    Petrosyan, David; Molmer, Klaus

    2013-01-01

    We study two-photon excitation of Rydberg states of atoms under stimulated adiabatic passage with delayed laser pulses. We find that the combination of strong interaction between the atoms in Rydberg state and the spontaneous decay of the intermediate exited atomic state leads to the Rydberg exci...... for deterministic creation and, possibly, extraction of Rydberg atoms or ions one at a time. The sympathetic monitoring via decay of ancilla particles may find wider applications for state preparation and probing of interactions in dissipative many-body systems.......We study two-photon excitation of Rydberg states of atoms under stimulated adiabatic passage with delayed laser pulses. We find that the combination of strong interaction between the atoms in Rydberg state and the spontaneous decay of the intermediate exited atomic state leads to the Rydberg...

  13. Attosecond Time Delay in Photoionization of Noble-Gas and Halogen Atoms

    Directory of Open Access Journals (Sweden)

    Liang-Wen Pi

    2018-02-01

    Full Text Available Ultrafast processes are now accessible on the attosecond time scale due to the availability of ultrashort XUV laser pulses. Noble-gas and halogen atoms remain important targets due to their giant dipole resonance and Cooper minimum. Here, we calculate photoionization cross section, asymmetry parameter and Wigner time delay using the time-dependent local-density approximation (TDLDA, which includes the electron correlation effects. Our results are consistent with experimental data and other theoretical calculations. The asymmetry parameter provides an extra layer of access to the phase information of the photoionization processes. We find that halogen atoms bear a strong resemblance on cross section, asymmetry parameter and time delay to their noble-gas neighbors. Our predicted time delay should provide a guidance for future experiments on those atoms and related molecules.

  14. Terrestrial Sagnac delay constraining modified gravity models

    Science.gov (United States)

    Karimov, R. Kh.; Izmailov, R. N.; Potapov, A. A.; Nandi, K. K.

    2018-04-01

    Modified gravity theories include f(R)-gravity models that are usually constrained by the cosmological evolutionary scenario. However, it has been recently shown that they can also be constrained by the signatures of accretion disk around constant Ricci curvature Kerr-f(R0) stellar sized black holes. Our aim here is to use another experimental fact, viz., the terrestrial Sagnac delay to constrain the parameters of specific f(R)-gravity prescriptions. We shall assume that a Kerr-f(R0) solution asymptotically describes Earth's weak gravity near its surface. In this spacetime, we shall study oppositely directed light beams from source/observer moving on non-geodesic and geodesic circular trajectories and calculate the time gap, when the beams re-unite. We obtain the exact time gap called Sagnac delay in both cases and expand it to show how the flat space value is corrected by the Ricci curvature, the mass and the spin of the gravitating source. Under the assumption that the magnitude of corrections are of the order of residual uncertainties in the delay measurement, we derive the allowed intervals for Ricci curvature. We conclude that the terrestrial Sagnac delay can be used to constrain the parameters of specific f(R) prescriptions. Despite using the weak field gravity near Earth's surface, it turns out that the model parameter ranges still remain the same as those obtained from the strong field accretion disk phenomenon.

  15. A novel femtosecond-gated, high-resolution, frequency-shifted shearing interferometry technique for probing pre-plasma expansion in ultra-intense laser experiments

    Energy Technology Data Exchange (ETDEWEB)

    Feister, S., E-mail: feister.7@osu.edu; Orban, C. [Department of Physics, The Ohio State University, Columbus, Ohio 43210 (United States); Innovative Scientific Solutions, Inc., Dayton, Ohio 45459 (United States); Nees, J. A. [Innovative Scientific Solutions, Inc., Dayton, Ohio 45459 (United States); Center for Ultra-Fast Optical Science, University of Michigan, Ann Arbor, Michigan 48109 (United States); Morrison, J. T. [Fellow, National Research Council, Washington, D.C. 20001 (United States); Frische, K. D. [Innovative Scientific Solutions, Inc., Dayton, Ohio 45459 (United States); Chowdhury, E. A. [Department of Physics, The Ohio State University, Columbus, Ohio 43210 (United States); Intense Energy Solutions, LLC., Plain City, Ohio 43064 (United States); Roquemore, W. M. [Air Force Research Laboratory, Dayton, Ohio 45433 (United States)

    2014-11-15

    Ultra-intense laser-matter interaction experiments (>10{sup 18} W/cm{sup 2}) with dense targets are highly sensitive to the effect of laser “noise” (in the form of pre-pulses) preceding the main ultra-intense pulse. These system-dependent pre-pulses in the nanosecond and/or picosecond regimes are often intense enough to modify the target significantly by ionizing and forming a plasma layer in front of the target before the arrival of the main pulse. Time resolved interferometry offers a robust way to characterize the expanding plasma during this period. We have developed a novel pump-probe interferometry system for an ultra-intense laser experiment that uses two short-pulse amplifiers synchronized by one ultra-fast seed oscillator to achieve 40-fs time resolution over hundreds of nanoseconds, using a variable delay line and other techniques. The first of these amplifiers acts as the pump and delivers maximal energy to the interaction region. The second amplifier is frequency shifted and then frequency doubled to generate the femtosecond probe pulse. After passing through the laser-target interaction region, the probe pulse is split and recombined in a laterally sheared Michelson interferometer. Importantly, the frequency shift in the probe allows strong plasma self-emission at the second harmonic of the pump to be filtered out, allowing plasma expansion near the critical surface and elsewhere to be clearly visible in the interferograms. To aid in the reconstruction of phase dependent imagery from fringe shifts, three separate 120° phase-shifted (temporally sheared) interferograms are acquired for each probe delay. Three-phase reconstructions of the electron densities are then inferred by Abel inversion. This interferometric system delivers precise measurements of pre-plasma expansion that can identify the condition of the target at the moment that the ultra-intense pulse arrives. Such measurements are indispensable for correlating laser pre-pulse measurements

  16. Examining the psychosocial determinants of women's decisions to delay childbearing.

    Science.gov (United States)

    Kearney, Allison L; White, Katherine M

    2016-08-01

    What are the psychosocial determinants of women's intentions to delay childbearing until after 35 years? Attitudes, pressure from important others, perceived self-confidence and anticipated regret all influence the decision-making process of women aged 18-30 years to defer their attempts to conceive their first child until 35+ years. Research has consistently demonstrated that, for many women, the decision to delay childbearing can lead to 'unintentional childlessness' due to a failure to consider the impact of age-related fertility decline. A large body of literature has also found strong links between age-related involuntary infertility and negative psychological impacts, including an increased prevalence of anxiety, depression, guilt, stigma and poor mental health. The study initially conducted focus groups designed to ascertain important beliefs informing participants' intentions to delay childbearing. A subsequent larger-scale quantitative questionnaire followed. Participants (n = 358) were female, aged between 18 and 30 years, lived in Australia, identified as being open to the idea of having children, were heterosexual, had not already had children, were not already pregnant, and had not received a diagnosis of medical infertility prior to participating. Hierarchical multiple regression analyses showed strong support for psychosocial predictors of attitude, pressure from others and perceived self-confidence as predictors of women's intentions to delay childbearing, accounting for 59% of total variance. The extended model that included anticipated regret, accounted for a significant additional 4.4% variance in intention to delay childbearing past the age of 35 years. Proportionally more participants were younger, Caucasian, and were university students, thus limiting the generalizability of results to the wider Australian community. Future research in this domain is recommended to adopt a prospective design and incorporate a measure of behaviour to

  17. Fuzzy delay model based fault simulator for crosstalk delay fault test ...

    Indian Academy of Sciences (India)

    In this paper, a fuzzy delay model based crosstalk delay fault simulator is proposed. As design trends move towards nanometer technologies, more number of new parameters affects the delay of the component. Fuzzy delay models are ideal for modelling the uncertainty found in the design and manufacturing steps.

  18. Does delaying the first mowing date benefit biodiversity in meadowland?

    Directory of Open Access Journals (Sweden)

    Humbert Jean-Yves

    2012-07-01

    Full Text Available Abstract Background Meadows are regularly mown in order to provide fodder or litter for livestock and to prevent vegetation succession. However, the time of year at which meadows should be first mown in order to maximize biological diversity remains controversial and may vary with respect to context and focal taxa. We carried out a systematic review and meta-analysis on the effects of delaying the first mowing date upon plants and invertebrates in European meadowlands. Methods Following a CEE protocol, ISI Web of Science, Science Direct, JSTOR, Google and Google Scholar were searched. We recorded all studies that compared the species richness of plants, or the species richness or abundance of invertebrates, between grassland plots mown at a postponed date (treatment vs plots mown earlier (control. In order to be included in the meta-analysis, compared plots had to be similar in all management respects, except the date of the first cut that was (mostly experimentally manipulated. They were also to be located in the same meadow type. Meta-analyses applying Hedges’d statistic were performed. Results Plant species richness responded differently to the date to which mowing was postponed. Delaying mowing from spring to summer had a positive effect, while delaying either from spring to fall, or from early summer to later in the season had a negative effect. Invertebrates were expected to show a strong response to delayed mowing due to their dependence on sward structure, but only species richness showed a clearly significant positive response. Invertebrate abundance was positively influenced in only a few studies. Conclusions The present meta-analysis shows that in general delaying the first mowing date in European meadowlands has either positive or neutral effects on plant and invertebrate biodiversity (except for plant species richness when delaying from spring to fall or from early summer to later. Overall, there was also strong between

  19. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

    NARCIS (Netherlands)

    Ziesemer, K.A.; Mann, A.E.; Sankaranarayanan, K.; Schroeder, H.; Ozga, A.T.; Brandt, B.W.; Zaura, E.; Waters-Rist, A.; Hoogland, M.; Salazar-García, D.C.; Aldenderfer, M.; Speller, C.; Hendy, J.; Weston, D.A.; MacDonald, S.J.; Thomas, G.H.; Collins, M.J.; Lewis, C.M.; Hofman, C.; Warinner, C.

    2015-01-01

    To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this

  20. Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

    DEFF Research Database (Denmark)

    Karst, Søren Michael; Dueholm, Morten Simonsen; McIlroy, Simon Jon

    2018-01-01

    Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied e...

  1. Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications

    DEFF Research Database (Denmark)

    Harrington, C.S.; On, Stephen L.W.

    1999-01-01

    Phylogenetic relationships of Campylobacter hyointestinalis subspecies were examined by means of 16S rRNA gene sequencing. Sequence similarities among C. hyointestinalis subsp. lawsonii strains exceeded 99.0 %, but values among C. hyointestinalis subsp. hyointestinalis strains ranged from 96...... of the genus Campylobacter, emphasizing the need for multiple strain analysis when using 16S rRNA gene sequence comparisons for taxonomic investigations........4 to 100 %. Sequence similarites between strains representing the two different subspecies ranged from 95.7 to 99.0 %. An intervening sequence was identified in certain of the C. hyointestinalis subsp. lawsonii strains. C. hyointestinalis strains occupied two distinct branches in a phylogenetic analysis...

  2. YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407

    DEFF Research Database (Denmark)

    Andersen, Niels Møller; Douthwaite, Stephen

    2006-01-01

    generally require specific enzymes, and only one m5C rRNA methyltransferase, RsmB (formerly Fmu) that methylates nucleotide C967, has previously been identified. BLAST searches of the E.coli genome revealed a single gene, yebU, with sufficient similarity to rsmB to encode a putative m5C RNA...... methyltransferase. This suggested that the yebU gene product modifies C1407 and/or C1962. Here, we analysed the E.coli rRNAs by matrix assisted laser desorption/ionization mass spectrometry and show that inactivation of the yebU gene leads to loss of methylation at C1407 in 16 S rRNA, but does not interfere...

  3. Pre- and post-diagnosis costs of tuberculosis to patients on Directly Observed Treatment Short course in districts of southwestern Ethiopia: a longitudinal study.

    Science.gov (United States)

    Asres, Abyot; Jerene, Degu; Deressa, Wakgari

    2018-05-21

    Financial burden on tuberculosis (TB) patients results in delayed treatment and poor compliance. We assessed pre- and post-diagnosis costs to TB patients. A longitudinal study among 735 new TB cases was conducted from January 2015 through June 2016 in 10 woredas (districts) of southwestern Ethiopia. Direct out-of-pocket, payments, and lost income (indirect cost) were solicited from patients during the first 2 months and at the end of treatment. Thus, we ascertained direct medical, nonmedical, and indirect costs incurred by patients during pre- and post-diagnosis periods. We categorized costs incurred from onset of illness until TB diagnosis as pre-diagnosis and that incurred after diagnosis through treatment completion as post-diagnosis. Pre- and post-diagnosis costs constitute total cost incurred by the patients. We fitted linear regression model to identify predictors of cost. Between onset of illness and anti-TB treatment course, patients incurred a median (inter-quartile range (IQR)) of US$201.48 (136.7-318.94). Of the total cost, the indirect and direct costs respectively constituted 70.6 and 29.4%. TB patients incurred a median (IQR) of US$97.62 (6.43-184.22) and US$93.75 (56.91-141.54) during the pre- and post-diagnosis periods, respectively. Thus, patients incurred 53.6% of the total cost during the pre-diagnosis period. Direct out-of-pocket expenses during the pre- and post-diagnosis periods respectively amount to median (IQR) of US$21.64 (10.23-48.31) and US$35.02 (0-70.04). Patient delay days (p < 0.001), provider delay days (p < 0.001), number of healthcare facilities visited until TB diagnosis (p < 0.001), and TB diagnosis at private facilities (p = 0.02) independently predicted increased pre-diagnosis cost. Similarly, rural residence (p < 0.001), hospitalization during anti-TB treatment (p < 0.001), patient delay days (p < 0.001), and provider delay days (p < 0.001) predicted increased post-diagnosis costs. TB patients

  4. Mutational analysis of the mitochondrial 12S rRNA and tRNASer(UCN) genes in Tunisian patients with nonsyndromic hearing loss

    International Nuclear Information System (INIS)

    Mkaouar-Rebai, Emna; Tlili, Abdelaziz; Masmoudi, Saber; Louhichi, Nacim; Charfeddine, Ilhem; Amor, Mohamed Ben; Lahmar, Imed; Driss, Nabil; Drira, Mohamed; Ayadi, Hammadi; Fakhfakh, Faiza

    2006-01-01

    We explored the mitochondrial 12S rRNA and the tRNA Ser(UCN) genes in 100 Tunisian families affected with NSHL and in 100 control individuals. We identified the mitochondrial A1555G mutation in one out of these 100 families and not in the 100 control individuals. Members of this family harbouring the A1555G mutation showed phenotypic heterogeneity which could be explained by an eventual nuclear-mitochondrial interaction. So, we have screened three nuclear genes: GJB2, GJB3, and GJB6 but we have not found correlation between the phenotypic heterogeneity and variants detected in these genes. We explored also the entire mitochondrial 12S rRNA and the tRNA Ser(UCN) genes. We detected five novel polymorphisms: T742C, T794A, A813G, C868T, and C954T, and 12 known polymorphisms in the mitochondrial 12S rRNA gene. None of the 100 families or the 100 controls were found to carry mutations in the tRNA Ser(UCN) gene. We report here First mutational screening of the mitochondrial 12S rRNA and the tRNA Ser(UCN) genes in the Tunisian population which describes the second family harbouring the A1555G mutation in Africa and reveals novel polymorphisms in the mitochondrial 12S rRNA gene

  5. Characterization of Hydrocortisone Biometabolites and 18S rRNA Gene in Chlamydomonas reinhardtii Cultures

    Directory of Open Access Journals (Sweden)

    Seyed Bagher Mosavi-Azam

    2008-10-01

    Full Text Available A unicellular microalga, Chlamydomonas reinhardtii, was isolated from rice paddy-field soil and water samples and used in the biotransformation of hydrocortisone (1. This strain has not been previously tested for steroid bioconversion. Fermentation was carried out in BG-11 medium supplemented with 0.05% substrate at 25ºC for 14 days of incubation. The products obtained were chromatographically purified and characterized using spectroscopic methods. 11b,17b-Dihydroxyandrost-4-en-3-one (2, 11b-hydroxyandrost-4-en-3,17-dione (3, 11b,17a,20b,21-tetrahydroxypregn-4-en-3-one (4 and prednisolone (5 were the main products of the bioconversion. The observed bioreaction features were the side chain degradation of the substrate to give compounds 2 and 3 and the 20-ketone reduction and 1,2-dehydrogenation affording compounds 4 and 5, respectively. A time course study showed the accumulation of product 2 from the second day of the fermentation and of compounds 3, 4 and 5 from the third day. All the metabolites reached their maximum concentration in seven days. Microalgal 18S rRNA gene was also amplified by PCR. PCR products were sequenced to confirm their authenticity as 18S rRNA gene of microalgae. The result of PCR blasted with other sequenced microalgae in NCBI showed 100% homology to the 18S small subunit rRNA of two Chlamydomonas reinhardtii spp.

  6. Characterization of hydrocortisone biometabolites and 18S rRNA gene in Chlamydomonas reinhardtii cultures.

    Science.gov (United States)

    Ghasemi, Younes; Rasoul-Amini, Sara; Morowvat, Mohammad Hossein; Raee, Mohammad Javad; Ghoshoon, Mohammad Bagher; Nouri, Fatemeh; Negintaji, Narges; Parvizi, Rezvan; Mosavi-Azam, Seyed Bagher

    2008-10-31

    A unicellular microalga, Chlamydomonas reinhardtii, was isolated from rice paddy-field soil and water samples and used in the biotransformation of hydrocortisone (1). This strain has not been previously tested for steroid bioconversion. Fermentation was carried out in BG-11 medium supplemented with 0.05% substrate at 25 degrees C for 14 days of incubation. The products obtained were chromatographically purified and characterized using spectroscopic methods. 11b,17 beta-Dihydroxyandrost-4-en-3-one (2), 11 beta-hydroxyandrost-4-en-3,17-dione (3), 11 beta,17 alpha,20 beta,21-tetrahydroxypregn-4-en-3-one (4) and prednisolone (5) were the main products of the bioconversion. The observed bioreaction features were the side chain degradation of the substrate to give compounds 2 and 3 and the 20-ketone reduction and 1,2-dehydrogenation affording compounds 4 and 5, respectively. A time course study showed the accumulation of product 2 from the second day of the fermentation and of compounds 3, 4 and 5 from the third day. All the metabolites reached their maximum concentration in seven days. Microalgal 18S rRNA gene was also amplified by PCR. PCR products were sequenced to confirm their authenticity as 18S rRNA gene of microalgae. The result of PCR blasted with other sequenced microalgae in NCBI showed 100% homology to the 18S small subunit rRNA of two Chlamydomonas reinhardtii spp.

  7. Phylogenetic analysis of Fusobacterium prausnitzii based upon the 16S rRNA gene sequence and PCR confirmation.

    Science.gov (United States)

    Wang, R F; Cao, W W; Cerniglia, C E

    1996-01-01

    In order to develop a PCR method to detect Fusobacterium prausnitzii in human feces and to clarify the phylogenetic position of this species, its 16S rRNA gene sequence was determined. The sequence described in this paper is different from the 16S rRNA gene sequence is specific for F. prausnitzii, and the results of this assay confirmed that F. prausnitzii is the most common species in human feces. However, a PCR assay based on the original GenBank sequence was negative when it was performed with two strains of F. prausnitzii obtained from the American Type Culture Collection. A phylogenetic tree based on the new 16S rRNA gene sequence was constructed. On this tree F. prausnitzii was not a member of the Fusobacterium group but was closer to some Eubacterium spp. and located between Clostridium "clusters III and IV" (M.D. Collins, P.A. Lawson, A. Willems, J.J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J.A.E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994).

  8. On the cost/delay tradeoff of wireless delay tolerant geographic routing

    OpenAIRE

    Tasiopoulos, Argyrios; Tsiaras, Christos; Toumpis, Stavros

    2012-01-01

    In Delay Tolerant Networks (DTNs), there is a fundamental tradeoff between the aggregate transport cost of a packet and the delay in its delivery. We study this tradeoff in the context of geographical routing in wireless DTNs.We ?rst specify the optimal cost/delay tradeoff, i.e., the tradeoff under optimal network operation, using a dynamic network construction termed the Cost/Delay Evolving Graph (C/DEG) and the Optimal Cost/Delay Curve (OC/DC), a function that gives the minimum possible agg...

  9. Short-course radiotherapy, with elective delay prior to surgery, in patients with unresectable rectal cancer who have poor performance status or significant co-morbidity

    International Nuclear Information System (INIS)

    Hatfield, Paul; Hingorani, Mohan; Radhakrishna, Ganesh; Cooper, Rachel; Melcher, Alan; Crellin, Adrian; Kwok-Williams, Michelle; Sebag-Montefiore, David

    2009-01-01

    Background and purpose: Standard treatment for rectal cancer which threatens the expected plane of resection on MRI imaging is long-course, pre-operative chemoradiotherapy (1.8-2 Gy, 25-28 fractions). Not all patients are suitable for this because of age, poor performance status or co-morbidities. We describe our experience of short-course (5 x 5 Gy) pre-operative radiotherapy with planned, delayed surgery (SCPRT-delay) in this patient group. Materials and methods: Between April 2001 and October 2007, 43 patients were selected for SCPRT-delay. The clinical records were retrospectively evaluated. Results: Median age was 82 (range 58-87). Forty-one patients had radiotherapy of which 26 (61%) were subsequently able to have surgery. Of these, R0, R1 and R2 resections were performed in 22, 2 and 2 patients, respectively. Treatment was well tolerated, although two patients required hospital admission for management of diarrhoea and one developed significant late small bowel toxicity, attributable to radiotherapy. In those undergoing R0 or R1 resection there have been no local recurrences (median follow-up 18 months). Median survival for the whole group was 23 months, although this was 44 months in those undergoing surgery. Conclusions: SCPRT-delay appears to be a useful alternative to long-course pre-operative chemoradiotherapy in this high-risk group of patients.

  10. Leveraging delay discounting for health: Can time delays influence food choice?

    Science.gov (United States)

    Appelhans, Bradley M; French, Simone A; Olinger, Tamara; Bogucki, Michael; Janssen, Imke; Avery-Mamer, Elizabeth F; Powell, Lisa M

    2018-03-15

    Delay discounting, the tendency to choose smaller immediate rewards over larger delayed rewards, is theorized to promote consumption of immediately rewarding but unhealthy foods at the expense of long-term weight maintenance and nutritional health. An untested implication of delay discounting models of decision-making is that selectively delaying access to less healthy foods may promote selection of healthier (immediately available) alternatives, even if they may be less desirable. The current study tested this hypothesis by measuring healthy versus regular vending machine snack purchasing before and during the implementation of a 25-s time delay on the delivery of regular snacks. Purchasing was also examined under a $0.25 discount on healthy snacks, a $0.25 tax on regular snacks, and the combination of both pricing interventions with the 25-s time delay. Across 32,019 vending sales from three separate vending locations, the 25-s time delay increased healthy snack purchasing from 40.1% to 42.5%, which was comparable to the impact of a $0.25 discount (43.0%). Combining the delay and the discount had a roughly additive effect (46.0%). However, the strongest effects were seen under the $0.25 tax on regular snacks (53.7%) and the combination of the delay and the tax (50.2%). Intervention effects varied substantially between vending locations. Importantly, time delays did not harm overall vending sales or revenue, which is relevant to the real-world feasibility of this intervention. More investigation is needed to better understand how the impact of time delays on food choice varies across populations, evaluate the effects of time delays on beverage vending choices, and extend this approach to food choices in contexts other than vending machines. ClinicalTrials.gov, NCT02359916. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data.

    Science.gov (United States)

    Wei, Yulong; Silke, Jordan R; Xia, Xuhua

    2017-12-15

    Bacterial translation initiation is influenced by base pairing between the Shine-Dalgarno (SD) sequence in the 5' UTR of mRNA and the anti-SD (aSD) sequence at the free 3' end of the 16S rRNA (3' TAIL) due to: 1) the SD/aSD sequence binding location and 2) SD/aSD binding affinity. In order to understand what makes an SD/aSD interaction optimal, we must define: 1) terminus of the 3' TAIL and 2) extent of the core aSD sequence within the 3' TAIL. Our approach to characterize these components in Escherichia coli and Bacillus subtilis involves 1) mapping the 3' boundary of the mature 16S rRNA using high-throughput RNA sequencing (RNA-Seq), and 2) identifying the segment within the 3' TAIL that is strongly preferred in SD/aSD pairing. Using RNA-Seq data, we resolve previous discrepancies in the reported 3' TAIL in B. subtilis and recovered the established 3' TAIL in E. coli. Furthermore, we extend previous studies to suggest that both highly and lowly expressed genes favor SD sequences with intermediate binding affinity, but this trend is exclusive to SD sequences that complement the core aSD sequences defined herein.

  12. Prediction of biodiesel ignition delay in a diesel engine using artificial neural networks

    International Nuclear Information System (INIS)

    Piloto-Rodríguez, Ramón; Sánchez-Borroto, Yisel

    2017-01-01

    Ignition delay is one of the most important parameters of the combustion process and have a strong influence in exhaust emissions and engines performance. In the present work, the results of the mathematical modeling of ignition delay through artificial neural networks are shown. The modeling starts from input values that cover thermodynamic variables, engines parameters and biodiesel properties. The model obtained is only useful for biodiesel samples and several neural network algorithms were applied in order to predict the ignition delay. From its correlation coefficient, prediction capability and lowest absolute error, the best model was selected. Among other network’s input parameters, the cetane number was taken into account, also previously predicted by the use of ANN. (author)

  13. Comparison of COBAS AMPLICOR Neissefia gonorrhoeae PCR, including confirmation with N-gonorrhoeae-specific 16S rRNA PCR, with traditional culture

    NARCIS (Netherlands)

    Luijt, DS; Bos, PAJ; van Zwet, AA; Vader, PCV; Schirm, J

    A total of 3,023 clinical specimens were tested for Neisseria gonorrhoeae by using COBAS AMPLICOR (CA) PCR and confirmation of positives by N. gonorrhoeae-specific 16S rRNA PCR. The sensitivity of CA plus 16S rRNA PCR was 98.8%, compared to 68.2% for culture. Confirmation of CA positives increased

  14. Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria)

    Czech Academy of Sciences Publication Activity Database

    Johansen, J. R.; Mareš, Jan; Pietrasiak, N.; Bohunická, M.; Zima Jr., J.; Štenclová, Lenka; Hauer, T.

    2017-01-01

    Roč. 12, č. 10 (2017), č. článku e0186393. E-ISSN 1932-6203 Institutional support: RVO:60077344 Keywords : rRNA operon * heterogenita * Scytonema hyalinum Subject RIV: EF - Botanics OBOR OECD: Microbiology Impact factor: 2.806, year: 2016

  15. Representing delayed force feedback as a combination of current and delayed states.

    Science.gov (United States)

    Avraham, Guy; Mawase, Firas; Karniel, Amir; Shmuelof, Lior; Donchin, Opher; Mussa-Ivaldi, Ferdinando A; Nisky, Ilana

    2017-10-01

    To adapt to deterministic force perturbations that depend on the current state of the hand, internal representations are formed to capture the relationships between forces experienced and motion. However, information from multiple modalities travels at different rates, resulting in intermodal delays that require compensation for these internal representations to develop. To understand how these delays are represented by the brain, we presented participants with delayed velocity-dependent force fields, i.e., forces that depend on hand velocity either 70 or 100 ms beforehand. We probed the internal representation of these delayed forces by examining the forces the participants applied to cope with the perturbations. The findings showed that for both delayed forces, the best model of internal representation consisted of a delayed velocity and current position and velocity. We show that participants relied initially on the current state, but with adaptation, the contribution of the delayed representation to adaptation increased. After adaptation, when the participants were asked to make movements with a higher velocity for which they had not previously experienced with the delayed force field, they applied forces that were consistent with current position and velocity as well as delayed velocity representations. This suggests that the sensorimotor system represents delayed force feedback using current and delayed state information and that it uses this representation when generalizing to faster movements. NEW & NOTEWORTHY The brain compensates for forces in the body and the environment to control movements, but it is unclear how it does so given the inherent delays in information transmission and processing. We examined how participants cope with delayed forces that depend on their arm velocity 70 or 100 ms beforehand. After adaptation, participants applied opposing forces that revealed a partially correct representation of the perturbation using the current and the

  16. Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

    OpenAIRE

    Nakashima, T; Yao, M; Kawamura, S; Iwasaki, K; Kimura, M; Tanaka, I

    2001-01-01

    Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and plays an essential role in the promotion of a particular conformation of 5S rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stearothermophilus has been determined at 1.8 A resolution. The molecule consists of a five-stranded antiparallel beta-sheet and four alpha-helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. The molecular shape and electrostatic ...

  17. Delay Insensitive Ternary CMOS Logic for Secure Hardware

    Directory of Open Access Journals (Sweden)

    Ravi S. P. Nair

    2015-09-01

    Full Text Available As digital circuit design continues to evolve due to progress of semiconductor processes well into the sub 100 nm range, clocked architectures face limitations in a number of cases where clockless asynchronous architectures generate less noise and produce less electro-magnetic interference (EMI. This paper develops the Delay-Insensitive Ternary Logic (DITL asynchronous design paradigm that combines design aspects of similar dual-rail asynchronous paradigms and Boolean logic to create a single wire per bit, three voltage signaling and logic scheme. DITL is compared with other delay insensitive paradigms, such as Pre-Charge Half-Buffers (PCHB and NULL Convention Logic (NCL on which it is based. An application of DITL is discussed in designing secure digital circuits resistant to side channel attacks based on measurement of timing, power, and EMI signatures. A Secure DITL Adder circuit is designed at the transistor level, and several variance parameters are measured to validate the efficiency of DITL in resisting side channel attacks. The DITL design methodology is then applied to design a secure 8051 ALU.

  18. Mutations in domain II of 23 S rRNA facilitate translation of a 23 S rRNA-encoded pentapeptide conferring erythromycin resistance

    DEFF Research Database (Denmark)

    Dam, M; Douthwaite, S; Tenson, T

    1996-01-01

    Mutations in domain II of Escherichia coli 23 S rRNA that cause resistance to erythromycin do so in a manner fundamentally different from mutations at the drug binding site in domain V of the 23 S rRNA. The domain II mutations are located in a hairpin structure between nucleotides 1198 and 1247...... this hypothesis, a range of point mutations was generated in domain II of 23 S rRNA in the vicinity of the E-peptide open reading frame. We find a correlation between erythromycin resistance of the mutant clones and increased accessibility of the ribosome binding site of the E-peptide gene. Furthermore......, the erythromycin resistance determinant in the mutants was shown to be confined to a small 23 S rRNA segment containing the coding region and the ribosome binding site of the E-peptide open reading frame. It thus appears that the domain II mutations mediate erythromycin resistance by increasing expression...

  19. Accuracy Assessment of Immediate and Delayed Implant Placements Using CAD/CAM Surgical Guides.

    Science.gov (United States)

    Alzoubi, Fawaz; Massoomi, Nima; Nattestad, Anders

    2016-10-01

    The aim of this study is to assess the accuracy of immediately placed implants using Anatomage Invivo5 computer-assisted design/computer-assisted manufacturing (CAD/CAM) surgical guides and compare the accuracy to delayed implant placement protocol. Patients who had implants placed using Anatomage Invivo5 CAD/CAM surgical guides during the period of 2012-2015 were evaluated retrospectively. Patients who received immediate implant placements and/or delayed implant placements replacing 1-2 teeth were included in this study. Pre- and postsurgical images were superimposed to evaluate deviations at the crest, apex, and angle. A total of 40 implants placed in 29 patients were included in this study. The overall mean deviations measured at the crest, apex, and angle were 0.86 mm, 1.25 mm, and 3.79°, respectively. The means for the immediate group deviations were: crest = 0.85 mm, apex = 1.10, and angle = 3.49°. The means for the delayed group deviations were: crest = 0.88 mm, apex = 1.59, and angle = 4.29°. No statistically significant difference was found at the crest and angle; however, there was a statistically significant difference between the immediate and delayed group at the apex, with the immediate group presenting more accurate placements at the apical point than the delayed group. CAD/CAM surgical guides can be reliable tools to accurately place implants immediately and/or in a delayed fashion. No statistically significant differences were found between the delayed and the immediate group at the crest and angle, however apical position was more accurate in the immediate group.

  20. Development of a strong electromagnet wiggler

    International Nuclear Information System (INIS)

    Burns, M.J.; Deis, G.A.; Holmes, R.H.; Van Maren, R.D.; Halbach, K.

    1987-01-01

    The Strong Electromagnet (SEM) wiggler is a permanent magnet-assisted electromagnet under development at the Lawrence Livermore National Laboratory (LLNL) as part of the Induction Linac Free-Electron-Laser (IFEL) program. This concept uses permanent magnets within the wiggler to provide a reverse bias flux in the iron and thus delay the onset of magnetic saturation. The electromagnet coils determine the wiggler field and operate at low current densities by virtue of their placement away from the midplane. We describe here the design approach used and test data from a 7-period wiggler prototype that includes curved pole tips to provide wiggle-plane focusing. 7 refs

  1. Relativistic effects in photoionization time delay near the Cooper minimum of noble-gas atoms

    Science.gov (United States)

    Saha, Soumyajit; Mandal, Ankur; Jose, Jobin; Varma, Hari R.; Deshmukh, P. C.; Kheifets, A. S.; Dolmatov, V. K.; Manson, S. T.

    2014-11-01

    Time delay of photoemission from valence n s , n p3 /2 , and n p1 /2 subshells of noble-gas atoms is theoretically scrutinized within the framework of the dipole relativistic random phase approximation. The focus is on the variation of time delay in the vicinity of the Cooper minima in photoionization of the outer subshells of neon, argon, krypton, and xenon, where the corresponding dipole matrix element changes its sign while passing through a node. It is revealed that the presence of the Cooper minimum in one photoionization channel has a strong effect on time delay in other channels. This is shown to be due to interchannel coupling.

  2. Toward heterogeneity in feedforward network with synaptic delays based on FitzHugh-Nagumo model

    Science.gov (United States)

    Qin, Ying-Mei; Men, Cong; Zhao, Jia; Han, Chun-Xiao; Che, Yan-Qiu

    2018-01-01

    We focus on the role of heterogeneity on the propagation of firing patterns in feedforward network (FFN). Effects of heterogeneities both in parameters of neuronal excitability and synaptic delays are investigated systematically. Neuronal heterogeneity is found to modulate firing rates and spiking regularity by changing the excitability of the network. Synaptic delays are strongly related with desynchronized and synchronized firing patterns of the FFN, which indicate that synaptic delays may play a significant role in bridging rate coding and temporal coding. Furthermore, quasi-coherence resonance (quasi-CR) phenomenon is observed in the parameter domain of connection probability and delay-heterogeneity. All these phenomena above enable a detailed characterization of neuronal heterogeneity in FFN, which may play an indispensable role in reproducing the important properties of in vivo experiments.

  3. Duration of the first steps of the human rRNA processing

    Czech Academy of Sciences Publication Activity Database

    Popov, A.; Smirnov, E.; Kováčik, L.; Raška, O.; Hagen, G.; Stixová, Lenka; Raška, I.

    2013-01-01

    Roč. 4, č. 2 (2013), s. 134-141 ISSN 1949-1034 R&D Projects: GA ČR(CZ) GBP302/12/G157; GA MŠk(CZ) EE2.3.30.0030 Grant - others:GA ČR(CZ) GAP302/12/1885 Institutional research plan: CEZ:AV0Z50040702 Institutional support: RVO:68081707 Keywords : rRNA processing * cleavage * half-life time Subject RIV: BO - Biophysics Impact factor: 3.148, year: 2013

  4. Asymptotic Delay Analysis for Cross-Layer Delay-Based Routing in Ad Hoc Networks

    Directory of Open Access Journals (Sweden)

    Philippe Jacquet

    2007-01-01

    Full Text Available This paper addresses the problem of the evaluation of the delay distribution via analytical means in IEEE 802.11 wireless ad hoc networks. We show that the asymptotic delay distribution can be expressed as a power law. Based on the latter result, we present a cross-layer delay estimation protocol and we derive new delay-distribution-based routing algorithms, which are well adapted to the QoS requirements of real-time multimedia applications. In fact, multimedia services are not sensitive to average delays, but rather to the asymptotic delay distributions. Indeed, video streaming applications drop frames when they are received beyond a delay threshold, determined by the buffer size. Although delay-distribution-based routing is an NP-hard problem, we show that it can be solved in polynomial time when the delay threshold is large, because of the asymptotic power law distribution of the link delays.

  5. Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer.

    Science.gov (United States)

    Karahan, Gurbet; Sayar, Nilufer; Gozum, Gokcen; Bozkurt, Betul; Konu, Ozlen; Yulug, Isik G

    2015-06-01

    Ribosomal RNA (rRNA) expression, one of the most important factors regulating ribosome production, is primarily controlled by a CG-rich 45 S rDNA promoter. However, the DNA methylation state of the 45 S rDNA promoter, as well as its effect on rRNA gene expression in types of human cancers is controversial. In the present study we analyzed the methylation status of the rDNA promoter (-380 to +53 bp) as well as associated rRNA expression levels in breast cancer cell lines and breast tumor-normal tissue pairs. We found that the aforementioned regulatory region was extensively methylated (74-96%) in all cell lines and in 68% (13/19 tumor-normal pairs) of the tumors. Expression levels of rRNA transcripts 18 S, 28 S, 5.8 S and 45 S external transcribed spacer (45 S ETS) greatly varied in the breast cancer cell lines regardless of their methylation status. Analyses of rRNA transcript expression levels in the breast tumor and normal matched tissues showed no significant difference when normalized with TBP. On the other hand, using the geometric mean of the rRNA expression values (GM-rRNA) as reference enabled us to identify significant changes in the relative expression of rRNAs in the tissue samples. We propose GM-rRNA normalization as a novel strategy to analyze expression differences between rRNA transcripts. Accordingly, the 18S rRNA/GM-rRNA ratio was significantly higher whereas the 5.8S rRNA/GM-rRNA ratio was significantly lower in breast tumor samples than this ratio in the matched normal samples. Moreover, the 18S rRNA/GM-rRNA ratio was negatively correlated with the 45 S rDNA promoter methylation level in the normal breast tissue samples, yet not in the breast tumors. Significant correlations observed between the expression levels of rRNA transcripts in the normal samples were lost in the tumor samples. We showed that the expression of rRNA transcripts may not be based solely on promoter methylation. Carcinogenesis may cause dysregulation of the correlation

  6. Changes in the Composition of Drinking Water Bacterial Clone Libraries Introduced by Using Two Different 16S rRNA Gene PCR Primers

    Science.gov (United States)

    Sequence analysis of 16S rRNA gene clone libraries is a popular tool used to describe the composition of natural microbial communities. Commonly, clone libraries are developed by direct cloning of 16S rRNA gene PCR products. Different primers are often employed in the initial amp...

  7. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

    KAUST Repository

    Arrigoni, Roberto; Vacherie, Benoî t; Benzoni, Francesca; Stefani, Fabrizio; Karsenti, Eric; Jaillon, Olivier; Not, Fabrice; Nunes, Flavia; Payri, Claude; Wincker, Patrick; Barbe, Valé rie

    2016-01-01

    Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.

  8. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

    KAUST Repository

    Arrigoni, Roberto

    2016-11-27

    Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time-calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.

  9. Pre-service teachers’ awareness of child abuse

    Directory of Open Access Journals (Sweden)

    Nihal TUNCA

    2015-12-01

    Full Text Available The purpose of this study is to determine the awareness of pre-service teachers from different departments related to the concept of child abuse. This study aims to determine pre-service teachers’ awareness of child abuse as a qualitative study, conducted in line with phenomenological design. In the study, one of the purposeful sampling methods, maximum diversity sampling method, was employed. The participants of the study are 15 pre-service teachers attending the departments of Psychological Counseling and Guidance, Teacher Education for the Intellectually Disabled, Pre-school Teacher Education, Social Studies, Art Teaching, Computer and Instructional Technologies, German Language Teaching, French Language Teaching, and Teacher Education for the Hearing Impaired, all within the Education Faculty of Anatolian University, Turkey. The data of the study was collected through the focus-group interview technique. The data collected from two different focus-group interviews were analyzed by content analysis technique using the NVivo 8 data analysis program. As a result of the analysis of the data, it was concluded that the pre-service teachers explained the concept of child abuse by most strongly emphasizing emotional abuse and least strongly by emphasizing economic abuse. In light of the pre-service teachers’ opinions, it was also concluded that the culture constructed by society through the meanings attached to genders, society’s view of sexuality, child marriage, proverbs and idioms specific to the local society and superstitions lead to incidences of child abuse. The current study revealed that child abuse can be prevented by providing training to raise the awareness of child abuse primarily for families then children, teachers and other concerned people. It was also found that the majority of pre-service teachers do not have enough information about how to act in the face of an incidence of child abuse.

  10. rRNA and Poly-β-Hydroxybutyrate Dynamics in Bioreactors Subjected to Feast and Famine Cycles

    Science.gov (United States)

    Frigon, Dominic; Muyzer, Gerard; van Loosdrecht, Mark; Raskin, Lutgarde

    2006-01-01

    Feast and famine cycles are common in activated sludge wastewater treatment systems, and they select for bacteria that accumulate storage compounds, such as poly-β-hydroxybutyrate (PHB). Previous studies have shown that variations in influent substrate concentrations force bacteria to accumulate high levels of rRNA compared to the levels in bacteria grown in chemostats. Therefore, it can be hypothesized that bacteria accumulate more rRNA when they are subjected to feast and famine cycles. However, PHB-accumulating bacteria can form biomass (grow) throughout a feast and famine cycle and thus have a lower peak biomass formation rate during the cycle. Consequently, PHB-accumulating bacteria may accumulate less rRNA when they are subjected to feast and famine cycles than bacteria that are not capable of PHB accumulation. These hypotheses were tested with Wautersia eutropha H16 (wild type) and W. eutropha PHB-4 (a mutant not capable of accumulating PHB) grown in chemostat and semibatch reactors. For both strains, the cellular RNA level was higher when the organism was grown in semibatch reactors than when it was grown in chemostats, and the specific biomass formation rates during the feast phase were linearly related to the cellular RNA levels for cultures. Although the two strains exhibited maximum uptake rates when they were grown in semibatch reactors, the wild-type strain responded much more rapidly to the addition of fresh medium than the mutant responded. Furthermore, the chemostat-grown mutant culture was unable to exhibit maximum substrate uptake rates when it was subjected to pulse-wise addition of fresh medium. These data show that the ability to accumulate PHB does not prevent bacteria from accumulating high levels of rRNA when they are subjected to feast and famine cycles. Our results also demonstrate that the ability to accumulate PHB makes the bacteria more responsive to sudden increases in substrate concentrations, which explains their ecological

  11. rRNA and poly-beta-hydroxybutyrate dynamics in bioreactors subjected to feast and famine cycles.

    Science.gov (United States)

    Frigon, Dominic; Muyzer, Gerard; van Loosdrecht, Mark; Raskin, Lutgarde

    2006-04-01

    Feast and famine cycles are common in activated sludge wastewater treatment systems, and they select for bacteria that accumulate storage compounds, such as poly-beta-hydroxybutyrate (PHB). Previous studies have shown that variations in influent substrate concentrations force bacteria to accumulate high levels of rRNA compared to the levels in bacteria grown in chemostats. Therefore, it can be hypothesized that bacteria accumulate more rRNA when they are subjected to feast and famine cycles. However, PHB-accumulating bacteria can form biomass (grow) throughout a feast and famine cycle and thus have a lower peak biomass formation rate during the cycle. Consequently, PHB-accumulating bacteria may accumulate less rRNA when they are subjected to feast and famine cycles than bacteria that are not capable of PHB accumulation. These hypotheses were tested with Wautersia eutropha H16 (wild type) and W. eutropha PHB-4 (a mutant not capable of accumulating PHB) grown in chemostat and semibatch reactors. For both strains, the cellular RNA level was higher when the organism was grown in semibatch reactors than when it was grown in chemostats, and the specific biomass formation rates during the feast phase were linearly related to the cellular RNA levels for cultures. Although the two strains exhibited maximum uptake rates when they were grown in semibatch reactors, the wild-type strain responded much more rapidly to the addition of fresh medium than the mutant responded. Furthermore, the chemostat-grown mutant culture was unable to exhibit maximum substrate uptake rates when it was subjected to pulse-wise addition of fresh medium. These data show that the ability to accumulate PHB does not prevent bacteria from accumulating high levels of rRNA when they are subjected to feast and famine cycles. Our results also demonstrate that the ability to accumulate PHB makes the bacteria more responsive to sudden increases in substrate concentrations, which explains their ecological

  12. Overexpression of a natural chloroplast-encoded antisense RNA in tobacco destabilizes 5S rRNA and retards plant growth

    Directory of Open Access Journals (Sweden)

    Stern David B

    2010-09-01

    Full Text Available Abstract Background The roles of non-coding RNAs in regulating gene expression have been extensively studied in both prokaryotes and eukaryotes, however few reports exist as to their roles in organellar gene regulation. Evidence for accumulation of natural antisense RNAs (asRNAs in chloroplasts comes from the expressed sequence tag database and cDNA libraries, while functional data have been largely obtained from artificial asRNAs. In this study, we used Nicotiana tabacum to investigate the effect on sense strand transcripts of overexpressing a natural chloroplast asRNA, AS5, which is complementary to the region which encodes the 5S rRNA and tRNAArg. Results AS5-overexpressing (AS5ox plants obtained by chloroplast transformation exhibited slower growth and slightly pale green leaves. Analysis of AS5 transcripts revealed four distinct species in wild-type (WT and AS5ox plants, and additional AS5ox-specific products. Of the corresponding sense strand transcripts, tRNAArg overaccumulated several-fold in transgenic plants whereas 5S rRNA was unaffected. However, run-on transcription showed that the 5S-trnR region was transcribed four-fold more in the AS5ox plants compared to WT, indicating that overexpression of AS5 was associated with decreased stability of 5S rRNA. In addition, polysome analysis of the transformants showed less 5S rRNA and rbcL mRNA associated with ribosomes. Conclusions Our results suggest that AS5 can modulate 5S rRNA levels, giving it the potential to affect Chloroplast translation and plant growth. More globally, overexpression of asRNAs via chloroplast transformation may be a useful strategy for defining their functions.

  13. Delayed fission

    Energy Technology Data Exchange (ETDEWEB)

    Hatsukawa, Yuichi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1997-07-01

    Delayed fission is a nuclear decay process that couples {beta} decay and fission. In the delayed fission process, a parent nucleus undergoes {beta} decay and thereby populates excited states in the daughter. If these states are of energies comparable to or greater than the fission barrier of the daughter, then fission may compete with other decay modes of the excited states in the daughter. In this paper, mechanism and some experiments of the delayed fission will be discussed. (author)

  14. Detection of coupling delay: A problem not yet solved

    Science.gov (United States)

    Coufal, David; Jakubík, Jozef; Jajcay, Nikola; Hlinka, Jaroslav; Krakovská, Anna; Paluš, Milan

    2017-08-01

    Nonparametric detection of coupling delay in unidirectionally and bidirectionally coupled nonlinear dynamical systems is examined. Both continuous and discrete-time systems are considered. Two methods of detection are assessed—the method based on conditional mutual information—the CMI method (also known as the transfer entropy method) and the method of convergent cross mapping—the CCM method. Computer simulations show that neither method is generally reliable in the detection of coupling delays. For continuous-time chaotic systems, the CMI method appears to be more sensitive and applicable in a broader range of coupling parameters than the CCM method. In the case of tested discrete-time dynamical systems, the CCM method has been found to be more sensitive, while the CMI method required much stronger coupling strength in order to bring correct results. However, when studied systems contain a strong oscillatory component in their dynamics, results of both methods become ambiguous. The presented study suggests that results of the tested algorithms should be interpreted with utmost care and the nonparametric detection of coupling delay, in general, is a problem not yet solved.

  15. Strong expectations cancel locality effects: evidence from Hindi.

    Directory of Open Access Journals (Sweden)

    Samar Husain

    Full Text Available Expectation-driven facilitation (Hale, 2001; Levy, 2008 and locality-driven retrieval difficulty (Gibson, 1998, 2000; Lewis & Vasishth, 2005 are widely recognized to be two critical factors in incremental sentence processing; there is accumulating evidence that both can influence processing difficulty. However, it is unclear whether and how expectations and memory interact. We first confirm a key prediction of the expectation account: a Hindi self-paced reading study shows that when an expectation for an upcoming part of speech is dashed, building a rarer structure consumes more processing time than building a less rare structure. This is a strong validation of the expectation-based account. In a second study, we show that when expectation is strong, i.e., when a particular verb is predicted, strong facilitation effects are seen when the appearance of the verb is delayed; however, when expectation is weak, i.e., when only the part of speech "verb" is predicted but a particular verb is not predicted, the facilitation disappears and a tendency towards a locality effect is seen. The interaction seen between expectation strength and distance shows that strong expectations cancel locality effects, and that weak expectations allow locality effects to emerge.

  16. Strong expectations cancel locality effects: evidence from Hindi.

    Science.gov (United States)

    Husain, Samar; Vasishth, Shravan; Srinivasan, Narayanan

    2014-01-01

    Expectation-driven facilitation (Hale, 2001; Levy, 2008) and locality-driven retrieval difficulty (Gibson, 1998, 2000; Lewis & Vasishth, 2005) are widely recognized to be two critical factors in incremental sentence processing; there is accumulating evidence that both can influence processing difficulty. However, it is unclear whether and how expectations and memory interact. We first confirm a key prediction of the expectation account: a Hindi self-paced reading study shows that when an expectation for an upcoming part of speech is dashed, building a rarer structure consumes more processing time than building a less rare structure. This is a strong validation of the expectation-based account. In a second study, we show that when expectation is strong, i.e., when a particular verb is predicted, strong facilitation effects are seen when the appearance of the verb is delayed; however, when expectation is weak, i.e., when only the part of speech "verb" is predicted but a particular verb is not predicted, the facilitation disappears and a tendency towards a locality effect is seen. The interaction seen between expectation strength and distance shows that strong expectations cancel locality effects, and that weak expectations allow locality effects to emerge.

  17. A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates.

    Science.gov (United States)

    Helbling, Damian E; Johnson, David R; Lee, Tae Kwon; Scheidegger, Andreas; Fenner, Kathrin

    2015-03-01

    The rates at which wastewater treatment plant (WWTP) microbial communities biotransform specific substrates can differ by orders of magnitude among WWTP communities. Differences in taxonomic compositions among WWTP communities may predict differences in the rates of some types of biotransformations. In this work, we present a novel framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates. We selected ten WWTPs with substantial variation in their environmental and operational metrics and measured the in situ ammonia biotransformation rate constants in nine of them. We isolated total RNA from samples from each WWTP and analyzed 16S rRNA sequence reads. We then developed multivariate models between the measured abundances of specific bacterial 16S rRNA sequence reads and the ammonia biotransformation rate constants. We constructed model scenarios that systematically explored the effects of model regularization, model linearity and non-linearity, and aggregation of 16S rRNA sequences into operational taxonomic units (OTUs) as a function of sequence dissimilarity threshold (SDT). A large percentage (greater than 80%) of model scenarios resulted in well-performing and significant models at intermediate SDTs of 0.13-0.14 and 0.26. The 16S rRNA sequences consistently selected into the well-performing and significant models at those SDTs were classified as Nitrosomonas and Nitrospira groups. We then extend the framework by applying it to the biotransformation rate constants of ten micropollutants measured in batch reactors seeded with the ten WWTP communities. We identified phylogenetic groups that were robustly selected into all well-performing and significant models constructed with biotransformation rates of isoproturon, propachlor, ranitidine, and venlafaxine. These phylogenetic groups can be used as predictive biomarkers of WWTP microbial community activity towards these specific

  18. Enhancing endogenous stem cells in the newbornvia delayed umbilical cord clamping

    Institute of Scientific and Technical Information of China (English)

    Christopher Lawton; Sandra Acosta; Nate Watson; Chiara Gonzales-Portillo; hTeo Diamandis; Naoki Tajiri; Yuji Kaneko; Paul R. Sanberg; Cesar V. Borlongan

    2015-01-01

    There is currently no consensus among clinicians and scientists over the appropriate or optimal timing for umbilical cord clamping. However, many clinical studies have suggested that delayed cord clamping is associated with various neonatal beneifts including increased blood volume, reduced need for blood transfusion, increased cerebral oxygenation in pre-term infants, and decreased frequency of iron deifciency anemia in term infants. Human umbilical cord blood con-tains signiifcant amounts of stem and progenitor cells and is currently used in the treatment of several life-threatening diseases. We propose that delayed cord clamping be encouraged as it en-hances blood lfow from the placenta to the neonate, which is accompanied by an increase supply of valuable stem and progenitor cells, as well as may improve blood oxygenation and increase blood volume, altogether reducing the infant’s susceptibility to both neonatal and age-related diseases.

  19. Exploring internal features of 16S rRNA gene for identification of clinically relevant species of the genus Streptococcus

    Science.gov (United States)

    2011-01-01

    Background Streptococcus is an economically important genus as a number of species belonging to this genus are human and animal pathogens. The genus has been divided into different groups based on 16S rRNA gene sequence similarity. The variability observed among the members of these groups is low and it is difficult to distinguish them. The present study was taken up to explore 16S rRNA gene sequence to develop methods that can be used for preliminary identification and can supplement the existing methods for identification of clinically-relevant isolates of the genus Streptococcus. Methods 16S rRNA gene sequences belonging to the isolates of S. dysgalactiae, S. equi, S. pyogenes, S. agalactiae, S. bovis, S. gallolyticus, S. mutans, S. sobrinus, S. mitis, S. pneumoniae, S. thermophilus and S. anginosus were analyzed with the purpose to define genetic variability within each species to generate a phylogenetic framework, to identify species-specific signatures and in-silico restriction enzyme analysis. Results The framework based analysis was used to segregate Streptococcus spp. previously identified upto genus level. This segregation was validated using species-specific signatures and in-silico restriction enzyme analysis. 43 uncharacterized Streptococcus spp. could be identified using this approach. Conclusions The markers generated exploring 16S rRNA gene sequences provided useful tool that can be further used for identification of different species of the genus Streptococcus. PMID:21702978

  20. Detecting 16S rRNA Methyltransferases in Enterobacteriaceae by Use of Arbekacin.

    Science.gov (United States)

    McGann, Patrick; Chahine, Sarah; Okafor, Darius; Ong, Ana C; Maybank, Rosslyn; Kwak, Yoon I; Wilson, Kerry; Zapor, Michael; Lesho, Emil; Hinkle, Mary

    2016-01-01

    16S rRNA methyltransferases confer resistance to most aminoglycosides, but discriminating their activity from that of aminoglycoside-modifying enzymes (AMEs) is challenging using phenotypic methods. We demonstrate that arbekacin, an aminoglycoside refractory to most AMEs, can rapidly detect 16S methyltransferase activity in Enterobacteriaceae with high specificity using the standard disk susceptibility test. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. Transcription and translation of the rpsJ, rplN and rRNA operons of the tubercle bacillus.

    Science.gov (United States)

    Cortes, Teresa; Cox, Robert Ashley

    2015-04-01

    Several species of the genus Mycobacterium are human pathogens, notably the tubercle bacillus (Mycobacterium tuberculosis). The rate of proliferation of a bacterium is reflected in the rate of ribosome synthesis. This report describes a quantitative analysis of the early stages of the synthesis of ribosomes of M. tuberculosis. Specifically, the roles of three large operons, namely: the rrn operon (1.7 microns) encoding rrs (16S rRNA), rrl (23S rRNA) and rrf (5S rRNA); the rpsJ operon (1.93 microns), which encodes 11 ribosomal proteins; and the rplN operon (1.45 microns), which encodes 10 ribosomal proteins. A mathematical framework based on properties of population-average cells was developed to identify the number of transcripts of the rpsJ and rplN operons needed to maintain exponential growth. The values obtained were supported by RNaseq data. The motif 5'-gcagac-3' was found close to 5' end of transcripts of mycobacterial rplN operons, suggesting it may form part of the RpsH feedback binding site because the same motif is present in the ribosome within the region of rrs that forms the binding site for RpsH. Medical Research Council.

  2. 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia.

    Science.gov (United States)

    Schönmann, Susan; Loy, Alexander; Wimmersberger, Céline; Sobek, Jens; Aquino, Catharine; Vandamme, Peter; Frey, Beat; Rehrauer, Hubert; Eberl, Leo

    2009-04-01

    For cultivation-independent and highly parallel analysis of members of the genus Burkholderia, an oligonucleotide microarray (phylochip) consisting of 131 hierarchically nested 16S rRNA gene-targeted oligonucleotide probes was developed. A novel primer pair was designed for selective amplification of a 1.3 kb 16S rRNA gene fragment of Burkholderia species prior to microarray analysis. The diagnostic performance of the microarray for identification and differentiation of Burkholderia species was tested with 44 reference strains of the genera Burkholderia, Pandoraea, Ralstonia and Limnobacter. Hybridization patterns based on presence/absence of probe signals were interpreted semi-automatically using the novel likelihood-based strategy of the web-tool Phylo- Detect. Eighty-eight per cent of the reference strains were correctly identified at the species level. The evaluated microarray was applied to investigate shifts in the Burkholderia community structure in acidic forest soil upon addition of cadmium, a condition that selected for Burkholderia species. The microarray results were in agreement with those obtained from phylogenetic analysis of Burkholderia 16S rRNA gene sequences recovered from the same cadmiumcontaminated soil, demonstrating the value of the Burkholderia phylochip for determinative and environmental studies.

  3. Fuzzy delay model based fault simulator for crosstalk delay fault test ...

    Indian Academy of Sciences (India)

    In this paper, a fuzzy delay model based crosstalk delay fault simulator is proposed. As design .... To find the quality of non-robust tests, a fuzzy delay ..... Dubois D and Prade H 1989 Processing Fuzzy temporal knowledge. IEEE Transactions ...

  4. Delayed power analysis

    International Nuclear Information System (INIS)

    Adamovich, L.A.; Azarov, V.V.

    1999-01-01

    Time dependent core power behavior in a nuclear reactor is described with well-known neutron kinetics equations. At the same time, two portions are distinguished in energy released from uranium nuclei fission; one released directly at fission and another delayed (residual) portion produced during radioactive decay of fission products. While prompt power is definitely described with kinetics equations, the delayed power presentation still remains outstanding. Since in operation the delayed power part is relatively small (about 6%) operation, it can be neglected for small reactivity disturbances assuming that entire power obeys neutron kinetics equations. In case of a high negative reactivity rapidly inserted in core (e.g. reactor scram initiation) the prompt and delayed components can be calculated separately with practically no impact on each other, employing kinetics equations for prompt power and known approximation formulas for delayed portion, named residual in this specific case. Under substantial disturbances the prompt component in the dynamic process becomes commensurable with delayed portion, thus making necessary to take into account their cross impact. A system of differential equations to describe time-dependent behavior of delayed power is presented. Specific NPP analysis shows a way to significantly simplify the task formulation. (author)

  5. dq-Frame Cascaded Delayed Signal Cancellation-Based PLL

    DEFF Research Database (Denmark)

    Golestan, Saeed; Ramezani, Malek; Guerrero, Josep M.

    2015-01-01

    on their position in the PLL structure. Inspired from the concept of delayed signal cancellation (DSC), the idea of cascaded DSC (CDSC) has recently been introduced as an effective solution to improve the performance of the PLL under adverse grid conditions. However, the focus has been on the application of CDSC...... operator as the pre-filtering stage of PLL, and little work has been conducted on its application as the in-loop filtering stage of PLL. This paper provides a detailed analysis and design of dqCDSC-PLL (PLL with in-loop dq-frame CDSC operator). The study is started with an overview of this PLL...

  6. Delayed postoperative gastric emptying following intrathecal morphine and intrathecal bupivacaine.

    LENUS (Irish Health Repository)

    Lydon, A M

    2012-02-03

    PURPOSE: A decrease in the rate of gastric emptying can delay resumption of enteral feeding, alter bioavailability of orally administered drugs, and result in larger residual gastric volumes, increasing the risk of nausea and vomiting. We compared the effects of 1) intrathecal bupivacaine (17.5 mg) and 2) the combination of intrathecal morphine (0.6 mg) and intrathecal bupivacaine (17.5 mg) on the rate of gastric emptying in patients undergoing elective hip arthroplasty. METHODS: Twenty four fasting ASA 1-3 patients were randomly assigned, in a double blind manner, to receive intrathecal hyperbaric bupivacaine (17.5 mg), either alone (group 1), or followed by intrathecal morphine (0.6 mg) (group 2). Gastric emptying was measured (using an acetaminophen absorption technique), twice in each patient; preoperatively, and approximately one hour postoperatively. Gastric emptying parameters are: AUC (area under the plasma acetaminophen concentration time curve), maximum plasma acetaminophen concentration (Cmax), and time to Cmax (tCmax), analyzed using paired Student\\'s t tests. RESULTS: Gastric emptying rates were reduced in both group 1 (AUC = 14.98 (3.8) and 11.05 (4.6) pre- and postoperatively, respectively) and group 2 (AUC = 13.93 (3.59) and 6.4 (3.42) pre- and postoperatively, respectively); the magnitude of the reduction was greater in group 2 [AUC (P = 0.04), Cmax (P = 0.05), tCmax (P = 0.13)]. CONCLUSION: The combination of intrathecal morphine (0.6 mg) and intrathecal bupivacaine (17.5 mg) delays gastric emptying postoperatively.

  7. Managing Pre-Construction and Construction Risks on Project Sites in Abuja-Nigeria

    Directory of Open Access Journals (Sweden)

    Jimoh R.A.

    2016-03-01

    Full Text Available Managing risks in construction projects has been acknowledged as a key direction process for the purposes of attaining the project goal in terms of time, cost, quality, safety, and environmental sustainability. Hence, the paper evaluated pre-construction and construction risks on active project sites in Abuja-Nigeria. This was achieved using survey method through the self-administration of 35 questionnaires to the professionals handling the 35 identified projects being undertaking at that time. Results showed that errors and omissions in design and improperly defined project scope had mean score values of 3.03 and 2.54, respectively, were the construction risks most experienced by the professionals during pre-construction. On the other hand, fluctuation in market prices and delays with mean score values of 3.14 and 2.74, respectively, were the construction risks experienced by the professionals during the construction phase of the projects. It is recommended that procurement methods such as construction management should be adopted and stakeholders should keep to their own side of the bargain to avoid unnecessary delays.

  8. A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming.

    Science.gov (United States)

    Lin, Geng-Ming; Lai, Yu-Heng; Audira, Gilbert; Hsiao, Chung-Der

    2017-11-06

    Green algae, Chlorella ellipsoidea , Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5-0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

  9. Patient Delay, Diagnosis Delay and Treatment Delay for Breast Cancer: Comparison of the Pattern between Patients in Public and Private Health Sectors

    Directory of Open Access Journals (Sweden)

    Iraj Harirchi

    2015-05-01

    Full Text Available Background: The purpose of this study was to compare patient delay, diagnosis delay and treatment delay in breast cancer patients of selected public and private health centers in Tehran, Iran.Methods: In this cross-sectional study, female patients with newly diagnosed breast cancer in a public medical complex and a private breast clinic within one year were included. Patient delay was considered positive, if the interval between the detection of the first symptom by the patient and the first visit to a health care provider took longer than one month. Delay in diagnosis was defined as the period of more than one week between the first medical visit for the symptoms and the diagnosis of breast cancer. Following the confirmed diagnosis of breast malignancy, if the medical treatment was initiated later than one week, treatment delay had occurred. The potential reasons for patient, diagnosis and treatment delay according to the patients’ reports were also recorded.Results: Overall, 385 patients were included of whom 52.7% were recruited from the public hospitals and 47.3% from a private clinic. The prevalence of patient delay, diagnosis delay and treatment delay were 31.7%, 17.9% and 28.3%, respectively. Patient delay was significantly more common among patients with lower socio-economic status and those recruited from the public hospitals. All the patients with diagnosis delay were in the group recruited from the public hospitals.Conclusions: Gaps between women of different socio-economic levels of the society need to be addressed in order to decrease patient, diagnosis and treatment delay.

  10. Speech and Language Delay

    Science.gov (United States)

    ... OTC Relief for Diarrhea Home Diseases and Conditions Speech and Language Delay Condition Speech and Language Delay Share Print Table of Contents1. ... Treatment6. Everyday Life7. Questions8. Resources What is a speech and language delay? A speech and language delay ...

  11. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

    2004-01-01

    for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......  FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

  12. Can the attention training technique turn one marshmallow into two? Improving children's ability to delay gratification.

    Science.gov (United States)

    Murray, Joanne; Theakston, Anna; Wells, Adrian

    2016-02-01

    The seminal Marshmallow Test (Mischel & Ebbesen, 1970) has reliably demonstrated that children who can delay gratification are more likely to be emotionally stable and successful later in life. However, this is not good news for those children who can't delay. Therefore, this study aimed to explore whether a metacognitive therapy technique, Attention Training (ATT: Wells, 1990) can improve young children's ability to delay gratification. One hundred children participated. Classes of 5-6 year olds were randomly allocated to either the ATT or a no-intervention condition and were tested pre and post-intervention on ability to delay gratification, verbal inhibition (executive control), and measures of mood. The ATT intervention significantly increased (2.64 times) delay of gratification compared to the no-intervention condition. After controlling for age and months in school, the ATT intervention and verbal inhibition task performance were significant independent predictors of delay of gratification. These results provide evidence that ATT can improve children's self-regulatory abilities with the implication that this might reduce psychological vulnerability later in life. The findings highlight the potential contribution that the Self-Regulatory Executive Function (S-REF) model could make to designing techniques to enhance children's self-regulatory processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Electron-capture delayed fission properties of neutron-deficient einsteinium nuclei

    International Nuclear Information System (INIS)

    Shaughnessy, Dawn A.

    2000-01-01

    Electron-capture delayed fission (ECDF) properties of neutron-deficient einsteinium isotopes were investigated using a combination of chemical separations and on-line radiation detection methods. 242 Es was produced via the 233 U( 14 N,5n) 242 Es reaction at a beam energy of 87 MeV (on target) in the lab system, and was found to decay with a half-life of 11 ± 3 seconds. The ECDF of 242 Es showed a highly asymmetric mass distribution with an average pre-neutron emission total kinetic energy (TKE) of 183 ± 18 MeV. The probability of delayed fission (P DF ) was measured to be 0.006 ± 0.002. In conjunction with this experiment, the excitation functions of the 233 U( 14 N,xn) 247-x Es and 233 U( 15 N,xn) 248-x Es reactions were measured for 243 Es, 244 Es and 245 Es at projectile energies between 80 MeV and 100 MeV

  14. The influences of delay time on the stability of a market model with stochastic volatility

    Science.gov (United States)

    Li, Jiang-Cheng; Mei, Dong-Cheng

    2013-02-01

    The effects of the delay time on the stability of a market model are investigated, by using a modified Heston model with a cubic nonlinearity and cross-correlated noise sources. These results indicate that: (i) There is an optimal delay time τo which maximally enhances the stability of the stock price under strong demand elasticity of stock price, and maximally reduces the stability of the stock price under weak demand elasticity of stock price; (ii) The cross correlation coefficient of noises and the delay time play an opposite role on the stability for the case of the delay time τo. Moreover, the probability density function of the escape time of stock price returns, the probability density function of the returns and the correlation function of the returns are compared with other literatures.

  15. Delay of Gratification, Delay Discounting and their Associations with Age, Episodic Future Thinking, and Future Time Perspective.

    Science.gov (United States)

    Göllner, Lars M; Ballhausen, Nicola; Kliegel, Matthias; Forstmeier, Simon

    2017-01-01

    The delay of gratification (DoG) in children is widely investigated with an experimental procedure originally called the "marshmallow test," whereas the studies on self-regulation (SR) in adolescents and adults usually use self-report questionnaires. Delay discounting (DD) measures simplify the DoG procedure and focus on monetary rewards. The aim of this study was to investigate age differences in DoG and DD from childhood to old age using a test that is suitable for both children and adults. Furthermore, investigations were conducted on the association between DoG/DD and two future orientation constructs [future time perspective (FTP) and episodic future thinking (EFT)] as well as age differences in these constructs. Participants from five age groups (9-14, 18-25, 35-55, 65-80, 80+) participated in the study ( N = 96). While we found no age difference for DoG, DD was the lowest [i.e., self-control (SC) was the highest] in young/middle adults; however, it was the highest (i.e., SC was the lowest) in children and old/oldest adults. Furthermore, we found significant age differences for DD and FTP. As predicted, there were strong correlations between DoG and FTP and between DD and FTP, but not between DoG/DD and EFT. These results indicate that age differences in SR vary across the measures used. Individuals who generally think and act in a future-oriented manner have a stronger ability to delay gratification.

  16. Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes.

    Science.gov (United States)

    Chen, Jing; Zhou, Zhichao; Gu, Ji-Dong

    2015-02-01

    In the present work, both 16S rRNA and pmoA gene-based PCR primers were employed successfully to study the diversity and distribution of n-damo bacteria in the surface and lower layer sediments at the coastal Mai Po wetland. The occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity was confirmed in this study. Unlike the two other known n-damo communities from coastal areas, the pmoA gene-amplified sequences in the present work clustered not only with some freshwater subclusters but also within three newly erected marine subclusters mostly, indicating the unique niche specificity of n-damo bacteria in this wetland. Results suggested vegetation affected the distribution and community structures of n-damo bacteria in the sediments and n-damo could coexist with sulfate-reducing methanotrophs in the coastal ecosystem. Community structures of the Mai Po n-damo bacteria based on 16S rRNA gene were different from those of either the freshwater or the marine. In contrast, structures of the Mai Po n-damo communities based on pmoA gene grouped with the marine ones and were clearly distinguished from the freshwater ones. The abundance of n-damo bacteria at this wetland was quantified using 16S rRNA gene PCR primers to be 2.65-6.71 × 10(5) copies/g dry sediment. Ammonium and nitrite strongly affected the community structures and distribution of n-damo bacteria in the coastal Mai Po wetland sediments.

  17. Electro convulsive therapy in a pre-pubertal child with severe depression.

    Directory of Open Access Journals (Sweden)

    Russell P

    2002-10-01

    Full Text Available Electro Convulsive Therapy (ECT in pre-pubertal children is a controversial and underreported treatment. Even though the effectiveness and side effects of ECT in adolescents are comparable with those in adults, there is a pervasive reluctance to use ECT in children and adolescents. We report the case of a pre-pubertal child in an episode of severe depression with catatonic features, where a protracted course of ECT proved life-saving in spite of prolonged duration of seizures and delayed response to treatment. The case illustrates the safety and efficacy of ECT in children. Relevant literature is also reviewed along with the case report.

  18. Pre-ART levels of inflammation and coagulation markers are strong predictors of death in a South African cohort with advanced HIV disease.

    Science.gov (United States)

    Ledwaba, Lotty; Tavel, Jorge A; Khabo, Paul; Maja, Patrick; Qin, Jing; Sangweni, Phumele; Liu, Xiao; Follmann, Dean; Metcalf, Julia A; Orsega, Susan; Baseler, Beth; Neaton, James D; Lane, H Clifford

    2012-01-01

    Levels of high-sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), and D-dimer predict mortality in HIV patients on antiretroviral therapy (ART) with relatively preserved CD4+ T cell counts. We hypothesized that elevated pre-ART levels of these markers among patients with advanced HIV would be associated with an increased risk of death following the initiation of ART. Pre-ART plasma from patients with advanced HIV in South Africa was used to measure hsCRP, IL-6 and D-dimer. Using a nested case-control study design, the biomarkers were measured for 187 deaths and two controls matched on age, sex, clinical site, follow-up time and CD4+ cell counts. Odds ratios were estimated using conditional logistic regression. In addition, for a random sample of 100 patients, biomarkers were measured at baseline and 6 months following randomization to determine whether ART altered their levels. Median baseline biomarkers levels for cases and controls, respectively, were 11.25 vs. 3.6 mg/L for hsCRP, 1.41 vs. 0.98 mg/L for D-dimer, and 9.02 vs. 4.20 pg/mL for IL-6 (all pART compared to baseline (pART levels of hsCRP, IL-6 and D-dimer are strongly associated with early mortality after commencing ART. Elevated levels of inflammatory and coagulation biomarkers may identify patients who may benefit from aggressive clinical monitoring after commencing ART. Further investigation of strategies to reduce biomarkers of inflammation and coagulation in patients with advanced HIV disease is warranted. Parent study: ClinicalTrials.gov NCT00342355.

  19. Geometric pre-patterning based tuning of the period doubling onset strain during thin film wrinkling

    Energy Technology Data Exchange (ETDEWEB)

    Saha, Sourabh K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-16

    Wrinkling of supported thin films is an easy-to-implement and low-cost fabrication technique for generation of stretch-tunable periodic micro and nano-scale structures. However, the tunability of such structures is often limited by the emergence of an undesirable period doubled mode at high strains. Predictively tuning the onset strain for period doubling via existing techniques requires one to have extensive knowledge about the nonlinear pattern formation behavior. Herein, a geometric pre-patterning based technique is introduced to delay the onset of period doubling that can be implemented to predictively tune the onset strain even with limited system knowledge. The technique comprises pre-patterning the film/base bilayer with a sinusoidal pattern that has the same period as the natural wrinkle period of the system. The effectiveness of this technique has been verified via physical and computational experiments on the polydimethylsiloxane/glass bilayer system. It is observed that the period doubling onset strain can be increased from the typical value of 20% for flat films to greater than 30% with a modest pre-pattern aspect ratio (2∙amplitude/period) of 0.15. In addition, finite element simulations reveal that (i) the onset strain can be increased up to a limit by increasing the amplitude of the pre-patterns and (ii) the delaying effect can be captured entirely by the pre-pattern geometry. As a result, one can implement this technique even with limited system knowledge, such as material properties or film thickness, by simply replicating pre-existing wrinkled patterns to generate prepatterned bilayers. Thus, geometric pre-patterning is a practical scheme to suppress period doubling that can increase the operating range of stretch-tunable wrinkle-based devices by at least 50%.

  20. Methyltransferase Erm(37) Slips on rRNA to Confer Atypical Resistance in Mycobacterium tuberculosis

    Czech Academy of Sciences Publication Activity Database

    Madsen, Ch. T.; Jakobsen, L.; Buriánková, Karolína; Doucet-Populaire, F.; Perdonet, J. L.; Douthwaite, S.

    2005-01-01

    Roč. 280, č. 47 (2005), s. 38942-38947 ISSN 0021-9258 R&D Projects: GA ČR GA310/03/0292 Institutional research plan: CEZ:AV0Z50200510 Keywords : methyltransferase erm * mycobacterium tuberculosis * rRNA Subject RIV: EE - Microbiology, Virology Impact factor: 5.854, year: 2005

  1. Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

    Science.gov (United States)

    Viscogliosi, E.; Edgcomb, V. P.; Gerbod, D.; Noel, C.; Delgado-Viscogliosi, P.; Sogin, M. L. (Principal Investigator)

    1999-01-01

    The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.

  2. High prevalence of plasmid-mediated 16S rRNA methylase gene rmtB among Escherichia coli clinical isolates from a Chinese teaching hospital

    Directory of Open Access Journals (Sweden)

    Zhang Xue-qing

    2010-06-01

    Full Text Available Abstract Background Recently, production of 16S rRNA methylases by Gram-negative bacilli has emerged as a novel mechanism for high-level resistance to aminoglycosides by these organisms in a variety of geographic locations. Therefore, the spread of high-level aminoglycoside resistance determinants has become a great concern. Methods Between January 2006 and July 2008, 680 distinct Escherichia coli clinical isolates were collected from a teaching hospital in Wenzhou, China. PCR and DNA sequencing were used to identify 16S rRNA methylase and extended-spectrum β-lactamase (ESBL genes, including armA and rmtB, and in situ hybridization was performed to determine the location of 16S rRNA methylase genes. Conjugation experiments were subsequently performed to determine whether aminoglycoside resistance was transferable from the E. coli isolates via 16S rRNA methylase-bearing plasmids. Homology of the isolates harboring 16S rRNA methylase genes was determined using pulse-field gel electrophoresis (PFGE. Results Among the 680 E. coli isolates, 357 (52.5%, 346 (50.9% and 44 (6.5% isolates were resistant to gentamicin, tobramycin and amikacin, respectively. Thirty-seven of 44 amikacin-resistant isolates harbored 16S rRNA methylase genes, with 36 of 37 harboring the rmtB gene and only one harboring armA. The positive rates of 16S rRNA methylase genes among all isolates and amikacin-resistant isolates were 5.4% (37/680 and 84.1% (37/44, respectively. Thirty-one isolates harboring 16S rRNA methylase genes also produced ESBLs. In addition, high-level aminoglycoside resistance could be transferred by conjugation from four rmtB-positive donors. The plasmids of incompatibility groups IncF, IncK and IncN were detected in 34, 3 and 3 isolates, respectively. Upstream regions of the armA gene contained ISCR1 and tnpU, the latter a putative transposase gene,. Another putative transposase gene, tnpD, was located within a region downstream of armA. Moreover, a

  3. Persistent Language Delay Versus Late Language Emergence in Children With Early Cochlear Implantation

    Science.gov (United States)

    Nicholas, Johanna; Tobey, Emily; Davidson, Lisa

    2016-01-01

    Purpose The purpose of the present investigation is to differentiate children using cochlear implants (CIs) who did or did not achieve age-appropriate language scores by midelementary grades and to identify risk factors for persistent language delay following early cochlear implantation. Materials and Method Children receiving unilateral CIs at young ages (12–38 months) were tested longitudinally and classified with normal language emergence (n = 19), late language emergence (n = 22), or persistent language delay (n = 19) on the basis of their test scores at 4.5 and 10.5 years of age. Relative effects of demographic, audiological, linguistic, and academic characteristics on language emergence were determined. Results Age at CI was associated with normal language emergence but did not differentiate late emergence from persistent delay. Children with persistent delay were more likely to use left-ear implants and older speech processor technology. They experienced higher aided thresholds and lower speech perception scores. Persistent delay was foreshadowed by low morphosyntactic and phonological diversity in preschool. Logistic regression analysis predicted normal language emergence with 84% accuracy and persistent language delay with 74% accuracy. Conclusion CI characteristics had a strong effect on persistent versus resolving language delay, suggesting that right-ear (or bilateral) devices, technology upgrades, and improved audibility may positively influence long-term language outcomes. PMID:26501740

  4. Speed of Gravitational Waves from Strongly Lensed Gravitational Waves and Electromagnetic Signals.

    Science.gov (United States)

    Fan, Xi-Long; Liao, Kai; Biesiada, Marek; Piórkowska-Kurpas, Aleksandra; Zhu, Zong-Hong

    2017-03-03

    We propose a new model-independent measurement strategy for the propagation speed of gravitational waves (GWs) based on strongly lensed GWs and their electromagnetic (EM) counterparts. This can be done in two ways: by comparing arrival times of GWs and their EM counterparts and by comparing the time delays between images seen in GWs and their EM counterparts. The lensed GW-EM event is perhaps the best way to identify an EM counterpart. Conceptually, this method does not rely on any specific theory of massive gravitons or modified gravity. Its differential setting (i.e., measuring the difference between time delays in GW and EM domains) makes it robust against lens modeling details (photons and GWs travel in the same lensing potential) and against internal time delays between GW and EM emission acts. It requires, however, that the theory of gravity is metric and predicts gravitational lensing similar to general relativity. We expect that such a test will become possible in the era of third-generation gravitational-wave detectors, when about 10 lensed GW events would be observed each year. The power of this method is mainly limited by the timing accuracy of the EM counterpart, which for kilonovae is around 10^{4}  s. This uncertainty can be suppressed by a factor of ∼10^{10}, if strongly lensed transients of much shorter duration associated with the GW event can be identified. Candidates for such short transients include short γ-ray bursts and fast radio bursts.

  5. Synchronization of delayed systems in the presence of delay time modulation

    International Nuclear Information System (INIS)

    Kye, Won-Ho; Choi, Muhan; Kim, Myung-Woon; Lee, Soo-Young; Rim, Sunghwan; Kim, Chil-Min; Park, Young-Jai

    2004-01-01

    We investigate synchronization in the presence of delay time modulation for application to communication. We have observed that the robust synchronization is established by a common delay signal and its threshold is presented using Lyapunov exponents analysis. The influence of the delay time modulation in chaotic oscillators is also discussed

  6. A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number

    Science.gov (United States)

    Tadmor, Arbel

    2009-03-01

    In this work a biophysical model of Escherichia coli is presented that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential steady-state growth, growing in a temporally and spatially constant environment, rich in resources. We apply this model to a series of past measurements, where the growth rate and rRNA-to-protein ratio have been measured for seven E. coli strains with an rRNA operon copy number ranging from one to seven (the wild-type copy number). These experiments show that growth rate markedly decreases for strains with fewer than six copies. Using the model, we were able to reproduce these measurements. We show that the model that best fits these data suggests that the volume fraction of macromolecules inside E. coli is not fixed when the rRNA operon copy number is varied. Moreover, the model predicts that increasing the copy number beyond seven results in a cytoplasm densely packed with ribosomes and proteins. Assuming that under such overcrowded conditions prolonged diffusion times tend to weaken binding affinities, the model predicts that growth rate will not increase substantially beyond the wild-type growth rate, as indicated by other experiments. Our model therefore suggests that changing the rRNA operon copy number of wild-type E. coli cells growing in a constant rich environment does not substantially increase their growth rate. Other observations regarding strains with an altered rRNA operon copy number, such as nucleoid compaction and the rRNA operon feedback response, appear to be qualitatively consistent with this model. In addition, we discuss possible design principles suggested by the model and propose further experiments to test its validity.

  7. Rats bred for high alcohol drinking are more sensitive to delayed and probabilistic outcomes.

    Science.gov (United States)

    Wilhelm, C J; Mitchell, S H

    2008-10-01

    Alcoholics and heavy drinkers score higher on measures of impulsivity than nonalcoholics and light drinkers. This may be because of factors that predate drug exposure (e.g. genetics). This study examined the role of genetics by comparing impulsivity measures in ethanol-naive rats selectively bred based on their high [high alcohol drinking (HAD)] or low [low alcohol drinking (LAD)] consumption of ethanol. Replicates 1 and 2 of the HAD and LAD rats, developed by the University of Indiana Alcohol Research Center, completed two different discounting tasks. Delay discounting examines sensitivity to rewards that are delayed in time and is commonly used to assess 'choice' impulsivity. Probability discounting examines sensitivity to the uncertain delivery of rewards and has been used to assess risk taking and risk assessment. High alcohol drinking rats discounted delayed and probabilistic rewards more steeply than LAD rats. Discount rates associated with probabilistic and delayed rewards were weakly correlated, while bias was strongly correlated with discount rate in both delay and probability discounting. The results suggest that selective breeding for high alcohol consumption selects for animals that are more sensitive to delayed and probabilistic outcomes. Sensitivity to delayed or probabilistic outcomes may be predictive of future drinking in genetically predisposed individuals.

  8. Earth system commitments due to delayed mitigation

    International Nuclear Information System (INIS)

    Pfister, Patrik L; Stocker, Thomas F

    2016-01-01

    As long as global CO 2 emissions continue to increase annually, long-term committed Earth system changes grow much faster than current observations. A novel metric linking this future growth to policy decisions today is the mitigation delay sensitivity (MDS), but MDS estimates for Earth system variables other than peak temperature (ΔT max ) are missing. Using an Earth System Model of Intermediate Complexity, we show that the current emission increase rate causes a ΔT max increase roughly 3–7.5 times as fast as observed warming, and a millenial steric sea level rise (SSLR) 7–25 times as fast as observed SSLR, depending on the achievable rate of emission reductions after the peak of emissions. These ranges are only slightly affected by the uncertainty range in equilibrium climate sensitivity, which is included in the above values. The extent of ocean acidification at the end of the century is also strongly dependent on the starting time and rate of emission reductions. The preservable surface ocean area with sufficient aragonite supersaturation for coral reef growth is diminished globally at an MDS of roughly 25%–80% per decade. A near-complete loss of this area becomes unavoidable if mitigation is delayed for a few years to decades. Also with respect to aragonite, 12%–18% of the Southern Ocean surface become undersaturated per decade, if emission reductions are delayed beyond 2015–2040. We conclude that the consequences of delaying global emission reductions are much better captured if the MDS of relevant Earth system variables is communicated in addition to current trends and total projected future changes. (letter)

  9. Can Early Years Professionals Determine Which Preschoolers Have Comprehension Delays? A Comparison of Two Screening Tools

    Science.gov (United States)

    Seager, Emily; Abbot-Smith, Kirsten

    2017-01-01

    Language comprehension delays in pre-schoolers are predictive of difficulties in a range of developmental domains. In England, early years practitioners are required to assess the language comprehension of 2-year-olds in their care. Many use a format based on the Early Years Foundation Stage Unique Child Communication Sheet (EYFS:UCCS) in which…

  10. Chaos synchronization in time-delayed systems with parameter mismatches and variable delay times

    International Nuclear Information System (INIS)

    Shahverdiev, E.M.; Nuriev, R.A.; Hashimov, R.H.; Shore, K.A.

    2004-06-01

    We investigate synchronization between two undirectionally linearly coupled chaotic nonidentical time-delayed systems and show that parameter mismatches are of crucial importance to achieve synchronization. We establish that independent of the relation between the delay time in the coupled systems and the coupling delay time, only retarded synchronization with the coupling delay time is obtained. We show that with parameter mismatch or without it neither complete nor anticipating synchronization occurs. We derive existence and stability conditions for the retarded synchronization manifold. We demonstrate our approach using examples of the Ikeda and Mackey Glass models. Also for the first time we investigate chaos synchronization in time-delayed systems with variable delay time and find both existence and sufficient stability conditions for the retarded synchronization manifold with the coupling-delay lag time. (author)

  11. 31 CFR 205.17 - Are funds transfers delayed by automated payment systems restrictions based on the size and...

    Science.gov (United States)

    2010-07-01

    ... automated payment systems restrictions based on the size and timing of the drawdown request subject to this... Treasury-State Agreement § 205.17 Are funds transfers delayed by automated payment systems restrictions... to payment processes that automatically reject drawdown requests that fall outside a pre-determined...

  12. Identificación de Yarrowia lipolytica (Ascomycota: Hemiascomycetes como contaminante en la obtención de amplificados del gen 28S rRNA de moluscos

    Directory of Open Access Journals (Sweden)

    Jenny Chirinos

    2011-05-01

    Full Text Available En el presente trabajo se identifica una secuencia de DNA no esperada proveniente de los amplificados del gen 28S rRNA de moluscos terrestres. Las extracciones de DNA se realizaron del tejido del pie de caracoles terrestres por el método del CTAB modificado. Las PCRs fueron llevadas a cabo con primers universales para el gen COI e iniciadores diseñados para moluscos, para el marcador 16S rRNA, 28S rRNA y la región ITS-2. Los tamaños aproximados de las bandas de los amplificados de moluscos fueron de 706 pb para el COI, 330 pb para el 16S rRNA, 900 pb para el ITS-2 y 583 pb para el 28S rRNA; un amplificado del último marcador fue de una longitud inesperada, ~340 pb. Las secuencias de DNA fueron comparadas con la base de datos del GenBank mediante el programa BLASTn y la muestra con la banda de tamaño inesperado resultó en un 100% de identidad y cobertura del 99% con el gen 26S rRNA de la levadura Yarrowia lipolytica. El análisis filogenético con Neighbour-Joining y los valores de divergencia confirmaron la identificación, proporcionando resultados que apoyan la ubicación taxonómica de la especie dentro del clado de los Hemiascomycetes.

  13. Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge.

    Science.gov (United States)

    Pervin, Hasina M; Batstone, Damien J; Bond, Philip L

    2013-06-01

    Thermophilic biological pre-treatment enables enhanced anaerobic digestion for treatment of wastewater sludges but, at present, there is limited understanding of the hydrolytic-acidogenic microbial composition and its contribution to this process. In this study, the process was assessed by comparing the microbiology of thermophilic (50-65 °C) and mesophilic (35 °C) pre-treatment reactors treating primary sludge. A full-cycle approach for the 16S rRNA genes was applied in order to monitor the diversity of bacteria and their abundance in a thermophilic pre-treatment reactor treating primary sludge. For the thermophilic pre-treatment (TP), over 90% of the sequences were previously undetected and these had less than 97% sequence similarity to cultured organisms. During the first 83 days, members of the Betaproteobacteria dominated the community sequences and a newly designed probe was used to monitor a previously unknown bacterium affiliated with the genus Brachymonas. Between days 85 and 183, three phylotypes that affiliated with the genera Comamonas, Clostridium and Lysobacter were persistently dominant in the TP community, as revealed by terminal-restriction fragment length polymorphism (T-RFLP). Hydrolytic and fermentative functions have been speculated for these bacteria. Mesophilic pre-treatment (MP) and TP communities were different but they were both relatively dynamic. Statistical correlation analysis and the function of closely allied reference organisms indicated that previously unclassified bacteria dominated the TP community and may have been functionally involved in the enhanced hydrolytic performance of thermophilic anaerobic pre-treatment. This study is the first to reveal the diversity and dynamics of bacteria during anaerobic digestion of primary sludge. Copyright © 2013 Elsevier GmbH. All rights reserved.

  14. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction

    Science.gov (United States)

    Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.

    1989-01-01

    Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

  15. Controlling chaos in RCL-shunted Josephson junction by delayed linear feedback

    International Nuclear Information System (INIS)

    Feng Yuling; Shen Ke

    2008-01-01

    The resistively-capacitively-inductively-shunted (RCL-shunted) Josephson junction (RCLSJJ) shows chaotic behaviour under some parameter conditions. Here a scheme for controlling chaos in the RCLSJJ is presented based on the linear feedback theory. Numerical simulations show that this scheme can be effectively used to control chaotic states in this junction into stable periodic states. Moreover, the different stable period states with different period numbers can be obtained by appropriately adjusting the feedback intensity and delay time without any pre-knowledge of this system required

  16. A behavioral economic analysis of texting while driving: Delay discounting processes.

    Science.gov (United States)

    Hayashi, Yusuke; Miller, Kimberly; Foreman, Anne M; Wirth, Oliver

    2016-12-01

    The purpose of the present study was to examine an impulsive decision-making process underlying texting while driving from a behavioral economic perspective. A sample of 108 college students completed a novel discounting task that presented participants with a hypothetical scenario in which, after receiving a text message while driving, they rated the likelihood of replying to a text message immediately versus waiting to reply for a specific period of time. Participants also completed a delay discounting task in which they made repeated hypothetical choices between obtaining a larger amount of money available after a delay and an equal or lesser amount of money available immediately. The results show that the duration of the delay is a critical variable that strongly determines whether participants choose to wait to reply to a text message, and that the decrease in the likelihood of waiting as a function of delay is best described by a hyperbolic delay discounting function. The results also show that participants who self-reported higher frequency of texting while driving discounted the opportunity to reply to a text message at greater rates, whereas there was no relation between the rates of discounting of hypothetical monetary rewards and the frequency of texting while driving. The results support the conclusion that texting while driving is fundamentally an impulsive choice. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Assessing hog lagoon waste contamination in the Cape Fear Watershed using Bacteroidetes 16S rRNA gene pyrosequencing.

    Science.gov (United States)

    Arfken, Ann M; Song, Bongkeun; Mallin, Michael A

    2015-09-01

    Hog lagoons can be major sources of waste and nutrient contamination to watersheds adjacent to pig farms. Fecal source tracking methods targeting Bacteroidetes 16S rRNA genes in pig fecal matter may underestimate or fail to detect hog lagoon contamination in riverine environments. In order to detect hog lagoon wastewater contamination in the Cape Fear Watershed, where a large number of hog farms are present, we conducted pyrosequencing analyses of Bacteroidetes 16S rRNA genes in hog lagoon waste and identified new hog lagoon-specific marker sequences. Additional pyrosequencing analyses of Bacteroidetes 16S rRNA genes were conducted with surface water samples collected at 4 sites during 5 months in the Cape Fear Watershed. Using an operational taxonomic unit (OTU) identity cutoff value of 97 %, these newly identified hog lagoon markers were found in 3 of the river samples, while only 1 sample contained the pig fecal marker. In the sample containing the pig fecal marker, there was a relatively high percentage (14.1 %) of the hog lagoon markers and a low pig fecal marker relative abundance of 0.4 % in the Bacteroidetes 16S rRNA gene sequences. This suggests that hog lagoon contamination must be somewhat significant in order for pig fecal markers to be detected, and low levels of hog lagoon contamination cannot be detected targeting only pig-specific fecal markers. Thus, new hog lagoon markers have a better detection capacity for lagoon waste contamination, and in conjunction with a pig fecal marker, provide a more comprehensive and accurate detection of hog lagoon waste contamination in susceptible watersheds.

  18. Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.

    Directory of Open Access Journals (Sweden)

    Hideyuki Tamaki

    Full Text Available BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform METHODOLOGY/PRINCIPAL FINDINGS: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1, after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies.

  19. Diagnostic and treatment delay among pulmonary tuberculosis patients in Ethiopia: a cross sectional study

    Directory of Open Access Journals (Sweden)

    Yimer Solomon

    2005-12-01

    Full Text Available Abstract Background Delayed diagnosis and treatment of tuberculosis (TB results in severe disease and a higher mortality. It also leads to an increased period of infectivity in the community. The objective of this study was to determine the length of delays, and analyze the factors affecting the delay from onset of symptoms of pulmonary tuberculosis (PTB until the commencement of treatment. Methods In randomly selected TB management units (TBMUs, i.e. government health institutions which have diagnosing and treatment facilities for TB in Amhara Region, we conducted a cross sectional study from September 1-December 31/2003. Delay was analyzed from two perspectives, 1. Period between onset of TB symptoms to first visit to any health provider (health seeking period, and from the first health provider visit to initiation of treatment (health providers' delay, and 2. Period between onset of TB symptoms to first visit to a medical provider (patients' delay, and from this visit to commencement of anti-TB treatment (health systems' delay. Patients were interviewed on the same date of diagnosis using a semi-structured questionnaire. Logistics regression analysis was applied to analyze the risk factors of delays. Results A total of 384 new smear positive PTB patients participated in the study. The median total delay was 80 days. The median health-seeking period and health providers' delays were 15 and 61 days, respectively. Conversely, the median patients' and health systems' delays were 30 and 21 days, respectively. Taking medical providers as a reference point, we found that forty eight percent of the subjects delayed for more than one month. Patients' delays were strongly associated with first visit to non-formal health providers and self treatment (P Conclusion Delay in the diagnosis and treatment of PTB is unacceptably high in Amhara region. Health providers' and health systems' delays represent the major portion of the total delay. Accessing a

  20. Classic conditioning in aged rabbits: delay, trace, and long-delay conditioning.

    Science.gov (United States)

    Solomon, P R; Groccia-Ellison, M E

    1996-06-01

    Young (0.5 years) and aged (2+, 3+, and 4+ years) rabbits underwent acquisition of the classically conditioned nictitating membrane response in a delay (500-ms conditioned stimulus [CS], 400-ms interstimulus interval [ISI]), long-delay (1,000-ms CS, 900-ms ISI), or trace (500-ms CS, 400-ms stimulus-free period) paradigm. Collapsing across age groups, there is a general tendency for animals to acquire trace conditioning more slowly than delay conditioning. Collapsing across conditioning paradigms, there is a general tendency for aged animals to acquire more slowly than younger animals. Of greater significance, however, are the age differences in the different conditioning paradigms. In the delay and long-delay paradigms, significant conditioning deficits first appeared in the 4(+)-year-old group. In the trace conditioning paradigm, significant conditioning deficits became apparent in the 2(+)-year-old animals.

  1. Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

    Directory of Open Access Journals (Sweden)

    Bryan E. Dutton

    2002-12-01

    Full Text Available We have developed a ten-week curriculum for molecular biology that uses 16S ribosomal RNA genes to characterize and compare novel bacteria from hot spring communities in Yellowstone National Park. The 16S rRNA approach bypasses selective culture-based methods. Our molecular biology course offered the opportunity for students to learn broadly applicable methods while contributing to a long-term research project. Specifically, students isolated and characterized clones that contained novel 16S rRNA inserts using restriction enzyme, DNA sequencing, and computer-based phylogenetic methods. In both classes, students retrieved novel bacterial 16S rRNA genes, several of which were most similar to Green Nonsulfur bacterial isolates. During class, we evaluated student performance and mastery of skills and concepts using quizzes, formal lab notebooks, and a broad project assignment. For this report, we also assessed student performance alongside data quality and discussed the significance, our goal being to improve both research and teaching methods.

  2. Energy decay in a Timoshenko-type system for thermoelasticity of type III with distributed delay and past history

    Directory of Open Access Journals (Sweden)

    Jianghao Hao

    2018-03-01

    Full Text Available In this work, we consider a one-dimensional Timoshenko system of thermoelasticity of type III with past history and distributive delay. It is known that an arbitrarily small delay may be the source of instability. We establish the well-posedness and the stability of the system for the cases of equal and nonequal speeds of wave propagation respectively. Our results show that the damping effect is strong enough to uniformly stabilize the system even in the presence of time delay under suitable conditions and improve the related results.

  3. Bipartite consensus for multi-agent systems with antagonistic interactions and communication delays

    Science.gov (United States)

    Guo, Xing; Lu, Jianquan; Alsaedi, Ahmed; Alsaadi, Fuad E.

    2018-04-01

    This paper studies the consensus problems over signed digraphs with arbitrary finite communication delays. For the considered system, the information flow is directed and only locally delayed information can be used for each node. We derive that bipartite consensus of this system can be realized when the associated signed digraph is strongly connected. Furthermore, for structurally balanced networks, this paper studies the pinning partite consensus for the considered system. we design a pinning scheme to pin any one agent in the signed network, and obtain that the network achieves pinning bipartite consensus with any initial conditions. Finally, two examples are provided to demonstrate the effectiveness of our main results.

  4. Controllability of nonlocal second-order impulsive neutral stochastic functional integro-differential equations with delay and Poisson jumps

    Directory of Open Access Journals (Sweden)

    Diem Dang Huan

    2015-12-01

    Full Text Available The current paper is concerned with the controllability of nonlocal second-order impulsive neutral stochastic functional integro-differential equations with infinite delay and Poisson jumps in Hilbert spaces. Using the theory of a strongly continuous cosine family of bounded linear operators, stochastic analysis theory and with the help of the Banach fixed point theorem, we derive a new set of sufficient conditions for the controllability of nonlocal second-order impulsive neutral stochastic functional integro-differential equations with infinite delay and Poisson jumps. Finally, an application to the stochastic nonlinear wave equation with infinite delay and Poisson jumps is given.

  5. A novel approach to delayed-start analyses for demonstrating disease-modifying effects in Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Hong Liu-Seifert

    Full Text Available One method for demonstrating disease modification is a delayed-start design, consisting of a placebo-controlled period followed by a delayed-start period wherein all patients receive active treatment. To address methodological issues in previous delayed-start approaches, we propose a new method that is robust across conditions of drug effect, discontinuation rates, and missing data mechanisms. We propose a modeling approach and test procedure to test the hypothesis of noninferiority, comparing the treatment difference at the end of the delayed-start period with that at the end of the placebo-controlled period. We conducted simulations to identify the optimal noninferiority testing procedure to ensure the method was robust across scenarios and assumptions, and to evaluate the appropriate modeling approach for analyzing the delayed-start period. We then applied this methodology to Phase 3 solanezumab clinical trial data for mild Alzheimer's disease patients. Simulation results showed a testing procedure using a proportional noninferiority margin was robust for detecting disease-modifying effects; conditions of high and moderate discontinuations; and with various missing data mechanisms. Using all data from all randomized patients in a single model over both the placebo-controlled and delayed-start study periods demonstrated good statistical performance. In analysis of solanezumab data using this methodology, the noninferiority criterion was met, indicating the treatment difference at the end of the placebo-controlled studies was preserved at the end of the delayed-start period within a pre-defined margin. The proposed noninferiority method for delayed-start analysis controls Type I error rate well and addresses many challenges posed by previous approaches. Delayed-start studies employing the proposed analysis approach could be used to provide evidence of a disease-modifying effect. This method has been communicated with FDA and has been

  6. Dynamics of Time Delay-Induced Multiple Synchronous Behaviors in Inhibitory Coupled Neurons

    Science.gov (United States)

    Gu, Huaguang; Zhao, Zhiguo

    2015-01-01

    The inhibitory synapse can induce synchronous behaviors different from the anti-phase synchronous behaviors, which have been reported in recent studies. In the present paper, synchronous behaviors are investigated in the motif model composed of reciprocal inhibitory coupled neurons with endogenous bursting and time delay. When coupling strength is weak, synchronous behavior appears at a single interval of time delay within a bursting period. When coupling strength is strong, multiple synchronous behaviors appear at different intervals of time delay within a bursting period. The different bursting patterns of synchronous behaviors, and time delays and coupling strengths that can induce the synchronous bursting patterns can be well interpreted by the dynamics of the endogenous bursting pattern of isolated neuron, which is acquired by the fast-slow dissection method, combined with the inhibitory coupling current. For an isolated neuron, when a negative impulsive current with suitable strength is applied at different phases of the bursting, multiple different bursting patterns can be induced. For a neuron in the motif, the inhibitory coupling current, of which the application time and strength is modulated by time delay and coupling strength, can cause single or multiple synchronous firing patterns like the negative impulsive current when time delay and coupling strength is suitable. The difference compared to the previously reported multiple synchronous behaviors that appear at time delays wider than a period of the endogenous firing is discussed. The results present novel examples of synchronous behaviors in the neuronal network with inhibitory synapses and provide a reasonable explanation. PMID:26394224

  7. Evaluation of focused ultrasound algorithms: Issues for reducing pre-focal heating and treatment time.

    Science.gov (United States)

    Yiannakou, Marinos; Trimikliniotis, Michael; Yiallouras, Christos; Damianou, Christakis

    2016-02-01

    Due to the heating in the pre-focal field the delay between successive movements in high intensity focused ultrasound (HIFU) are sometimes as long as 60s, resulting to treatment time in the order of 2-3h. Because there is generally a requirement to reduce treatment time, we were motivated to explore alternative transducer motion algorithms in order to reduce pre-focal heating and treatment time. A 1 MHz single element transducer with 4 cm diameter and 10 cm focal length was used. A simulation model was developed that estimates the temperature, thermal dose and lesion development in the pre-focal field. The simulated temperature history that was combined with the motion algorithms produced thermal maps in the pre-focal region. Polyacrylimde gel phantom was used to evaluate the induced pre-focal heating for each motion algorithm used, and also was used to assess the accuracy of the simulation model. Three out of the six algorithms having successive steps close to each other, exhibited severe heating in the pre-focal field. Minimal heating was produced with the algorithms having successive steps apart from each other (square, square spiral and random). The last three algorithms were improved further (with small cost in time), thus eliminating completely the pre-focal heating and reducing substantially the treatment time as compared to traditional algorithms. Out of the six algorithms, 3 were successful in eliminating the pre-focal heating completely. Because these 3 algorithms required no delay between successive movements (except in the last part of the motion), the treatment time was reduced by 93%. Therefore, it will be possible in the future, to achieve treatment time of focused ultrasound therapies shorter than 30 min. The rate of ablated volume achieved with one of the proposed algorithms was 71 cm(3)/h. The intention of this pilot study was to demonstrate that the navigation algorithms play the most important role in reducing pre-focal heating. By evaluating in

  8. Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma'.

    Science.gov (United States)

    Hodgetts, Jennifer; Boonham, Neil; Mumford, Rick; Harrison, Nigel; Dickinson, Matthew

    2008-08-01

    Phytoplasma phylogenetics has focused primarily on sequences of the non-coding 16S rRNA gene and the 16S-23S rRNA intergenic spacer region (16-23S ISR), and primers that enable amplification of these regions from all phytoplasmas by PCR are well established. In this study, primers based on the secA gene have been developed into a semi-nested PCR assay that results in a sequence of the expected size (about 480 bp) from all 34 phytoplasmas examined, including strains representative of 12 16Sr groups. Phylogenetic analysis of secA gene sequences showed similar clustering of phytoplasmas when compared with clusters resolved by similar sequence analyses of a 16-23S ISR-23S rRNA gene contig or of the 16S rRNA gene alone. The main differences between trees were in the branch lengths, which were elongated in the 16-23S ISR-23S rRNA gene tree when compared with the 16S rRNA gene tree and elongated still further in the secA gene tree, despite this being a shorter sequence. The improved resolution in the secA gene-derived phylogenetic tree resulted in the 16SrII group splitting into two distinct clusters, while phytoplasmas associated with coconut lethal yellowing-type diseases split into three distinct groups, thereby supporting past proposals that they represent different candidate species within 'Candidatus Phytoplasma'. The ability to differentiate 16Sr groups and subgroups by virtual RFLP analysis of secA gene sequences suggests that this gene may provide an informative alternative molecular marker for pathogen identification and diagnosis of phytoplasma diseases.

  9. Aggregation of Ribosomal Protein S6 at Nucleolus Is Cell Cycle-Controlled and Its Function in Pre-rRNA Processing Is Phosphorylation Dependent.

    Science.gov (United States)

    Zhang, Duo; Chen, Hui-Peng; Duan, Hai-Feng; Gao, Li-Hua; Shao, Yong; Chen, Ke-Yan; Wang, You-Liang; Lan, Feng-Hua; Hu, Xian-Wen

    2016-07-01

    Ribosomal protein S6 (rpS6) has long been regarded as one of the primary r-proteins that functions in the early stage of 40S subunit assembly, but its actual role is still obscure. The correct forming of 18S rRNA is a key step in the nuclear synthesis of 40S subunit. In this study, we demonstrate that rpS6 participates in the processing of 30S pre-rRNA to 18S rRNA only when its C-terminal five serines are phosphorylated, however, the process of entering the nucleus and then targeting the nucleolus does not dependent its phosphorylation. Remarkably, we also find that the aggregation of rpS6 at the nucleolus correlates to the phasing of cell cycle, beginning to concentrate in the nucleolus at later S phase and disaggregate at M phase. J. Cell. Biochem. 117: 1649-1657, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  10. NoRC Recruitment by H2A.X Deposition at rRNA Gene Promoter Limits Embryonic Stem Cell Proliferation

    Directory of Open Access Journals (Sweden)

    Boris Eleuteri

    2018-05-01

    Full Text Available Summary: Embryonic stem cells (ESCs display an abbreviated cell cycle, resulting in a short doubling time and rapid proliferation. The histone variant H2A.X is critical for proliferation of stem cells, although mechanistic insights have remained obscure. Here, we show that H2A.X defines the rate of mouse ESC proliferation independently of the DNA damage response pathway, and it associates with three major chromatin-modifying complexes. Our functional and biochemical analyses demonstrate that H2A.X-associated factors mediate the H2A.X-dependent effect on ESC proliferation and involve the nucleolar remodeling complex (NoRC. A specific H2A.X deposition at rDNA promoters determines the chromatin recruitment of the NoRC, histone modifications, the rRNA transcription, and the rate of proliferation. Collectively, our results suggest that NoRC assembly by H2A.X deposition at rRNA promoters silences transcription, and this represents an important regulatory component for ESC proliferation. : Histone variant H2A.X defines the rate of embryonic stem cell proliferation. Eleuteri et al. identify H2A.X-interacting proteins, and they show that H2A.X deposition at rDNA promoters assembles the NoRC, which represses rRNA transcription and determines the rate of self-renewal. Keywords: ribosomal biogenesis, rRNA, rDNA, stem cells, TIP5, SNF2H, SPT16, BRG1, H2A.X, G1, cell cycle, cell cycle arrest, proliferation

  11. Global synchronization criteria with channel time-delay for chaotic time-delay system

    International Nuclear Information System (INIS)

    Sun Jitao

    2004-01-01

    Based on the Lyapunov stabilization theory, matrix measure, and linear matrix inequality (LMIs), this paper studies the chaos synchronization of time-delay system using the unidirectional linear error feedback coupling with time-delay. Some generic conditions of chaos synchronization with time-delay in the transmission channel is established. The chaotic Chua's circuit is used for illustration, where the coupling parameters are determined according to the criteria under which the global chaos synchronization of the time-delay coupled systems is achieved

  12. Ignition delay and soot oxidative reactivity of MTBE blended diesel fuel

    KAUST Repository

    Yang, Seung Yeon; Naser, Nimal; Chung, Suk-Ho; Al-Qurashi, Khalid

    2014-01-01

    Methyl tert-butyl ether (MTBE) was added to diesel fuel to investigate the effect on ignition delay and soot oxidative reactivity. An ignition quality tester (IQT) was used to study the ignition propensity of MTBE blended diesel fuels in a reactive spray environment. The IQT data showed that ignition delay increases linearly as the MTBE fraction increases in the fuel. A four-stroke single cylinder diesel engine was used to generate soot samples for a soot oxidation study. Soot samples were pre-treated using a tube furnace in a nitrogen environment to remove any soluble organic fractions and moisture content. Non-isothermal oxidation of soot samples was conducted using a thermogravimetric analyzer (TGA). It was observed that oxidation of 'MTBE soot' started began at a lower temperature and had higher reaction rate than 'diesel soot' across a range of temperatures. Several kinetic analyses including an isoconversional method and a combined model fitting method were carried out to evaluate kinetic parameters. The results showed that Diesel and MTBE soot samples had similar activation energy but the pre-exponential factor of MTBE soot was much higher than that of the Diesel soot. This may explain why MTBE soot was more reactive than Diesel soot. It is suggested that adding MTBE to diesel fuel is better for DPF regeneration since an MTBE blend can significantly influence the ignition characteristics and, consequently, the oxidative reactivity of soot. Copyright © 2014 SAE International.

  13. Ignition delay and soot oxidative reactivity of MTBE blended diesel fuel

    KAUST Repository

    Yang, Seung Yeon

    2014-04-01

    Methyl tert-butyl ether (MTBE) was added to diesel fuel to investigate the effect on ignition delay and soot oxidative reactivity. An ignition quality tester (IQT) was used to study the ignition propensity of MTBE blended diesel fuels in a reactive spray environment. The IQT data showed that ignition delay increases linearly as the MTBE fraction increases in the fuel. A four-stroke single cylinder diesel engine was used to generate soot samples for a soot oxidation study. Soot samples were pre-treated using a tube furnace in a nitrogen environment to remove any soluble organic fractions and moisture content. Non-isothermal oxidation of soot samples was conducted using a thermogravimetric analyzer (TGA). It was observed that oxidation of \\'MTBE soot\\' started began at a lower temperature and had higher reaction rate than \\'diesel soot\\' across a range of temperatures. Several kinetic analyses including an isoconversional method and a combined model fitting method were carried out to evaluate kinetic parameters. The results showed that Diesel and MTBE soot samples had similar activation energy but the pre-exponential factor of MTBE soot was much higher than that of the Diesel soot. This may explain why MTBE soot was more reactive than Diesel soot. It is suggested that adding MTBE to diesel fuel is better for DPF regeneration since an MTBE blend can significantly influence the ignition characteristics and, consequently, the oxidative reactivity of soot. Copyright © 2014 SAE International.

  14. Emotions delay care-seeking in patients with an acute myocardial infarction.

    Science.gov (United States)

    Nymark, Carolin; Mattiasson, Anne-Cathrine; Henriksson, Peter; Kiessling, Anna

    2014-02-01

    In acute myocardial infarction the risk of death and loss of myocardial tissue is at its highest during the first few hours. However, the process from symptom onset to the decision to seek medical care can take time. To comprehend patients' pre-hospital delay, attention must be focused on the circumstances preceding the decision to seek medical care. To add a deeper understanding of patients' thoughts, feelings and actions that preceded the decision to seek medical care when afflicted by an acute myocardial infarction. Fourteen men and women with a first or second acute myocardial infarction were interviewed individually in semi-structured interviews. Data were analysed by qualitative content analysis. Four themes were conceptualized: 'being incapacitated by fear, anguish and powerlessness', 'being ashamed of oneself', 'fear of losing a healthy identity' and 'striving to avoid fear by not interacting with others'. Patients were torn between feelings such as anguish, fear, shame and powerlessness. They made an effort to uphold their self-image as being a healthy person thus affected by an unrecognized discomfort. This combined with a struggle to protect others from involvement, strengthened the barriers to seeking care. The present study indicates that emotional reactions are important and influence patients' pre-hospital behaviour. Being ashamed of oneself stood out as a novel finding. Emotions might be an important explanation of undesired and persisting patient delays. However, our findings have to and should be evaluated quantitatively. Such a study is in progress.

  15. Delayed minocycline but not delayed mild hypothermia protects against embolic stroke

    Directory of Open Access Journals (Sweden)

    Noor Raza

    2002-04-01

    Full Text Available Abstract Background Inflammatory reactions occurring in the brain after ischemia may contribute to secondary damage. In the present study, effects of minocycline, an anti-inflammatory agent, alone or in combination with mild hypothermia on focal embolic cerebral ischemia have been examined. Methods Focal ischemic injury was induced by embolizing a preformed clot into the middle cerebral artery (MCA. Infarction volume was measured at 48 h after the injury. Mortality was also recorded. Results Delayed administration of minocycline alone or delayed minocycline plus delayed mild hypothermia reduced the infarction volume significantly. However, delayed mild hypothermia alone was not protective and delayed mild hypothermia in combination with minocycline did not show any additive effect. Conclusions These results suggest that minocycline is beneficial in focal ischemic brain injury, and the lack of the enhanced neuroprotection may be due to the brief exposure to hypothermia.

  16. Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria)

    Czech Academy of Sciences Publication Activity Database

    Johansen, J. R.; Mareš, Jan; Pietrasiak, N.; Bohunická, Markéta; Zima, Jan; Štenclová, L.; Hauer, Tomáš

    2017-01-01

    Roč. 12, č. 10 (2017), č. článku e0186393. E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GA15-11912S Institutional support: RVO:67985939 Keywords : rRNA operon * heterogenita * Scytonema hyalinum Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 2.806, year: 2016

  17. Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota.

    Directory of Open Access Journals (Sweden)

    Lance B Price

    Full Text Available BACKGROUND: Bacterial colonization is hypothesized to play a pathogenic role in the non-healing state of chronic wounds. We characterized wound bacteria from a cohort of chronic wound patients using a 16S rRNA gene-based pyrosequencing approach and assessed the impact of diabetes and antibiotics on chronic wound microbiota. METHODOLOGY/PRINCIPAL FINDINGS: We prospectively enrolled 24 patients at a referral wound center in Baltimore, MD; sampled patients' wounds by curette; cultured samples under aerobic and anaerobic conditions; and pyrosequenced the 16S rRNA V3 hypervariable region. The 16S rRNA gene-based analyses revealed an average of 10 different bacterial families in wounds--approximately 4 times more than estimated by culture-based analyses. Fastidious anaerobic bacteria belonging to the Clostridiales family XI were among the most prevalent bacteria identified exclusively by 16S rRNA gene-based analyses. Community-scale analyses showed that wound microbiota from antibiotic treated patients were significantly different from untreated patients (p = 0.007 and were characterized by increased Pseudomonadaceae abundance. These analyses also revealed that antibiotic use was associated with decreased Streptococcaceae among diabetics and that Streptococcaceae was more abundant among diabetics as compared to non-diabetics. CONCLUSIONS/SIGNIFICANCE: The 16S rRNA gene-based analyses revealed complex bacterial communities including anaerobic bacteria that may play causative roles in the non-healing state of some chronic wounds. Our data suggest that antimicrobial therapy alters community structure--reducing some bacteria while selecting for others.

  18. Delay of Gratification, Delay Discounting and their Associations with Age, Episodic Future Thinking, and Future Time Perspective

    Directory of Open Access Journals (Sweden)

    Lars M. Göllner

    2018-01-01

    Full Text Available The delay of gratification (DoG in children is widely investigated with an experimental procedure originally called the “marshmallow test,” whereas the studies on self-regulation (SR in adolescents and adults usually use self-report questionnaires. Delay discounting (DD measures simplify the DoG procedure and focus on monetary rewards. The aim of this study was to investigate age differences in DoG and DD from childhood to old age using a test that is suitable for both children and adults. Furthermore, investigations were conducted on the association between DoG/DD and two future orientation constructs [future time perspective (FTP and episodic future thinking (EFT] as well as age differences in these constructs. Participants from five age groups (9–14, 18–25, 35–55, 65–80, 80+ participated in the study (N = 96. While we found no age difference for DoG, DD was the lowest [i.e., self-control (SC was the highest] in young/middle adults; however, it was the highest (i.e., SC was the lowest in children and old/oldest adults. Furthermore, we found significant age differences for DD and FTP. As predicted, there were strong correlations between DoG and FTP and between DD and FTP, but not between DoG/DD and EFT. These results indicate that age differences in SR vary across the measures used. Individuals who generally think and act in a future-oriented manner have a stronger ability to delay gratification.

  19. Investigation of histone H4 hyperacetylation dynamics in the 5S rRNA genes family by chromatin immunoprecipitation assay.

    Science.gov (United States)

    Burlibașa, Liliana; Suciu, Ilinca

    2015-12-01

    Oogenesis is a critical event in the formation of female gamete, whose role in development is to transfer genomic information to the next generation. During this process, the gene expression pattern changes dramatically concomitant with genome remodelling, while genomic information is stably maintained. The aim of the present study was to investigate the presence of H4 acetylation of the oocyte and somatic 5S rRNA genes in Triturus cristatus, using chromatin immunoprecipitation assay (ChIP). Our findings suggest that some epigenetic mechanisms such as histone acetylation could be involved in the transcriptional regulation of 5S rRNA gene families.

  20. Strong deflection gravitational lensing by a modified Hayward black hole

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Shan-Shan; Xie, Yi [Nanjing University, School of Astronomy and Space Science, Nanjing (China); Nanjing University, Ministry of Education, Key Laboratory of Modern Astronomy and Astrophysics, Nanjing (China)

    2017-05-15

    A modified Hayward black hole is a nonsingular black hole. It is proposed that it would form when the pressure generated by quantum gravity can stop matter's collapse as the matter reaches the Planck density. Strong deflection gravitational lensing occurring nearby its event horizon might provide some clues of these quantum effects in its central core. We investigate observables of the strong deflection lensing, including angular separations, brightness differences and time delays between its relativistic images, and we estimate their values for the supermassive black hole in the Galactic center. We find that it is possible to distinguish the modified Hayward black hole from a Schwarzschild one, but it demands a very high resolution, beyond current stage. (orig.)

  1. Delayed puberty in girls

    Science.gov (United States)

    ... sexual development - girls; Pubertal delay - girls; Constitutional delayed puberty ... In most cases of delayed puberty, growth changes just begin later than usual, sometimes called a late bloomer. Once puberty begins, it progresses normally. This pattern runs ...

  2. A mitochondrial tRNA(Met) mutation causing developmental delay, exercise intolerance and limb girdle phenotype with onset in early childhood

    DEFF Research Database (Denmark)

    Born, Alfred Peter; Duno, Morten; Rafiq, Jabin

    2015-01-01

    A 10-year-old girl presented with exercise intolerance, learning difficulty, and muscle weakness in a limb girdle distribution. She had delayed achievement of motor milestones and difficulties with social interaction at pre-school age. Muscle biopsy showed no myopathic or dystrophic features...

  3. Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications

    DEFF Research Database (Denmark)

    Monshupanee, Tanakarn; Gregory, Steven T; Douthwaite, Stephen

    2008-01-01

    of previously reported capreomycin resistance base substitutions. Capreomycin resistance in other bacteria has been shown to result from inactivation of the TlyA methyltransferase which 2'-O methylates C1920 of 23S rRNA. Inactivation of the tlyA gene in T. thermophilus does not affect its sensitivity...... for resistance to the tuberactinomycin antibiotic capreomycin. Two base substitutions, A1913U and mU1915G, and a single base deletion, DeltamU1915, were identified in helix 69 of 23S rRNA, a structural element that forms part of an interribosomal subunit bridge with the decoding center of 16S rRNA, the site...... to capreomycin. Finally, none of the mutations in helix 69 interferes with methylation at C1920 or with pseudouridylation at positions 1911 and 1917. We conclude that the resistance phenotype is a consequence of structural changes introduced by the mutations....

  4. Delayed Puberty (For Teens)

    Science.gov (United States)

    ... Safe Videos for Educators Search English Español Delayed Puberty KidsHealth / For Teens / Delayed Puberty What's in this ... wonder if there's anything wrong. What Is Delayed Puberty? Puberty is the time when your body grows ...

  5. Distribution of 16S rRNA Methylases Among Different Species of Aminoglycoside-Resistant Enterobacteriaceae in a Tertiary Care Hospital in Poland.

    Science.gov (United States)

    Piekarska, Katarzyna; Zacharczuk, Katarzyna; Wołkowicz, Tomasz; Rzeczkowska, Magdalena; Bareja, Elżbieta; Olak, Monika; Gierczyński, Rafał

    2016-01-01

    Aminoglycosides are a group of antimicrobial agents still the most commonly used in the treatment of life-threatening bacterial infections in human and animals. The emergence and spread of 16S rRNA methylases, which confer high-level resistance to the majority of clinically relevant aminoglycosides, constitute a major public health concern. Our goal was to evaluate the distribution of 16S rRNA methylases among different species of Enterobacteriaceae during a five month-long survey in a tertiary hospital in Warszawa, Poland. In the survey, a total of 1770 non-duplicate clinical isolates were collected from all hospital wards in a tertiary hospital in Warszawa, Poland. The survey was conducted between 19 April and 19 September 2010. The ability to produce 16S rRNA methylase was examined by determining MICs for gentamicin, kanamycin, amikacin by means of the agar dilution method. The isolates resistant to high concentration of aminoglycosides were PCR tested for genes: armA, rmtA, rmtB and rmtC. PCR products were subjected to DNA sequencing by the Sanger method. The genetic similarity of the ArmA-producing isolates was analysed by pulsed-filed gel electrophoresis (PFGE). ArmA was the only 16S rRNA methylase detected in 20 of 1770 tested isolates. The overall prevalence rate of ArmA was 1.13%. In K. pneumoniae (n = 742), P. mirabilis (n = 130), and E. cloacae (n = 253) collected in the survey, the prevalence of ArmA was 0.4%, 0.8% and 5.9%, respectively. The PFGE revealed both horizontal and clonal spread of the armA gene in the hospital. The prevalence of 16S rRNA methylase ArmA reported in this study is significantly higher than observed in other countries in Europe.

  6. Delayed percutaneous coronary intervention in patients with acute myocardial infarction

    International Nuclear Information System (INIS)

    Zhu Weiming; Tian Fang; Shi Li; Lan Xi

    2004-01-01

    Objective: To observe the clinical effects, safeness and prognosis of delayed percutaneous coronary intervention (PCI) for infarct related artery (IRA) in post-infarct patients. Methods: In total 53 patients with acute myocardial infarction (AMI) underwent delayed PCI within 5-15 days after the acute event. Conventional treatment (including thrombolytic therapy) was given in all patients as they were admitted. Results: Intervention was performed in 68 branches of IRA were, including 64 cases of PTCA followed by stent implantation and 4 cases of direct stent implantation. In total 68 stents were implanted. The TIMI classification was improved from the pre-PCI 0-2 to post-PCI 3. No patient died during the treatment. No repeated AMI, post-infarct angina and repeated recanalization happened in the hospitalization. A 5-48 month follow up showed there was 1 death (1.9%), 1 case of repeated myocardial infarction (1.9%), 3 cases of unstable angina (5.7%), 2 cases of repeated PCI and 1 case of CABG. The rate of repeated recanalization was 5.7%. Seven patients (13.2%) were admitted for the second time, who survived 6-48 months after the intervention. Conclusion: Delayed PCT can obviously improve the short and long term prognosis as well as the life quality of patients with AMI, which is a safe interventional procedure

  7. Detection of a Mixed Infection in a Culture-Negative Brain Abscess by Broad-Spectrum Bacterial 16S rRNA Gene PCR ▿ †

    Science.gov (United States)

    Keller, Peter M.; Rampini, Silvana K.; Bloemberg, Guido V.

    2010-01-01

    We describe the identification of two bacterial pathogens from a culture-negative brain abscess by the use of broad-spectrum 16S rRNA gene PCR. Simultaneous detection of Fusobacterium nucleatum and Porphyromonas endodontalis was possible due to a 24-bp length difference of their partially amplified 16S rRNA genes, which allowed separation by high-resolution polyacrylamide gel electrophoresis. PMID:20392909

  8. UV-induced modifications in the peptidyl transferase loop of 23S rRNA dependent on binding of the streptogramin B antibiotic, pristinamycin IA

    DEFF Research Database (Denmark)

    Porse, B T; Kirillov, S V; Awayez, M J

    1999-01-01

    The naturally occurring streptogramin B antibiotic, pristinamycin IA, which inhibits peptide elongation, can produce two modifications in 23S rRNA when bound to the Escherichia coli 70S ribosome and irradiated at 365 nm. Both drug-induced effects map to highly conserved nucleotides within...... in the latter modification to A2062/C2063. Pristinamycin IA can also produce a modification on binding to deproteinized, mature 23S rRNA, at position U2500/C2501. The same modification occurs on an approximately 37-nt fragment, encompassing positions approximately 2496-2532 of the peptidyl transferase loop...... the sequence Cm-C-U-C-G-m2A-psi-G2505 are important for pristinamycin IA binding and/or the antibiotic-dependent modification of 23S rRNA....

  9. Delays in initiation of acyclovir therapy in herpes simplex encephalitis.

    Science.gov (United States)

    Hughes, Peter S; Jackson, Alan C

    2012-09-01

    Diagnosis of herpes simplex encephalitis (HSE) is based on clinical findings, MRI, and detection of herpes simplex virus (HSV) DNA in cerebrospinal fluid (CSF) using polymerase chain reaction amplification. Delays in starting treatment are associated with poorer clinical outcomes. We assessed the timing of initiation of acyclovir therapy in HSE. Inpatient databases from seven hospitals in Winnipeg, Manitoba were used to identify individuals diagnosed with encephalitis and HSE from 2004 to 2009. The time taken to initiate therapy with acyclovir and the reasons for delays were determined. Seventy-seven patients were identified; 69 (90%) received acyclovir; in the others a non-HSV infection was strongly suspected. Thirteen patients were subsequently confirmed to have HSE. Acyclovir was initiated a median of 21 hours (3-407) after presentation in encephalitis cases, and a median of 11 hours (3-118) in HSE. The most common reason for delay was a failure to consider HSE in the differential diagnosis, despite suggestive clinical features. Where therapy was delayed in HSE patients, the decision to begin acyclovir was prompted by transfer of the patient to a different service (55%), recommendations by consultants (18%), imaging results (18%), and CSF pleocytosis (9%). Delays in initiating acyclovir for HSE are common, and are most often due to a failure to consider HSE in a timely fashion on presentation. In order to improve patient outcomes, physicians should be more vigilant for HSE, and begin acyclovir therapy expeditiously on the basis of clinical suspicion rather than waiting for confirmatory tests.

  10. Dynamic contrast-enhanced MR imaging of endometrial cancer. Optimizing the imaging delay for tumour-myometrium contrast

    International Nuclear Information System (INIS)

    Park, Sung Bin; Moon, Min Hoan; Sung, Chang Kyu; Oh, Sohee; Lee, Young Ho

    2014-01-01

    To investigate the optimal imaging delay time of dynamic contrast-enhanced magnetic resonance (MR) imaging in women with endometrial cancer. This prospective single-institution study was approved by the institutional review board, and informed consent was obtained from the participants. Thirty-five women (mean age, 54 years; age range, 29-66 years) underwent dynamic contrast-enhanced MR imaging with a temporal resolution of 25-40 seconds. The signal intensity difference ratios between the myometrium and endometrial cancer were analyzed to investigate the optimal imaging delay time using single change-point analysis. The optimal imaging delay time for appropriate tumour-myometrium contrast ranged from 31.7 to 268.1 seconds. The median optimal imaging delay time was 91.3 seconds, with an interquartile range of 46.2 to 119.5 seconds. The median signal intensity difference ratios between the myometrium and endometrial cancer were 0.03, with an interquartile range of -0.01 to 0.06, on the pre-contrast MR imaging and 0.20, with an interquartile range of 0.15 to 0.25, on the post-contrast MR imaging. An imaging delay of approximately 90 seconds after initiating contrast material injection may be optimal for obtaining appropriate tumour-myometrium contrast in women with endometrial cancer. (orig.)

  11. Stochastic resonance in a bistable system subject to multi-time-delayed feedback and aperiodic signal

    International Nuclear Information System (INIS)

    Li Jianlong; Zeng Lingzao

    2010-01-01

    We discuss in detail the effects of the multi-time-delayed feedback driven by an aperiodic signal on the output of a stochastic resonance (SR) system. The effective potential function and dynamical probability density function (PDF) are derived. To measure the performance of the SR system in the presence of a binary random signal, the bit error rate (BER) defined by the dynamical PDF is employed, as is commonly used in digital communications. We find that the delay time, strength of the feedback, and number of time-delayed terms can change the effective potential function and the effective amplitude of the signal, and then affect the BER of the SR system. The numerical simulations strongly support the theoretical results. The goal of this investigation is to explore the effects of the multi-time-delayed feedback on SR and give a guidance to nonlinear systems in the application of information processing.

  12. Autonomic Recovery Is Delayed in Chinese Compared with Caucasian following Treadmill Exercise.

    Directory of Open Access Journals (Sweden)

    Peng Sun

    Full Text Available Caucasian populations have a higher prevalence of cardiovascular disease (CVD when compared with their Chinese counterparts and CVD is associated with autonomic function. It is unknown whether autonomic function during exercise recovery differs between Caucasians and Chinese. The present study investigated autonomic recovery following an acute bout of treadmill exercise in healthy Caucasians and Chinese. Sixty-two participants (30 Caucasian and 32 Chinese, 50% male performed an acute bout of treadmill exercise at 70% of heart rate reserve. Heart rate variability (HRV and baroreflex sensitivity (BRS were obtained during 5-min epochs at pre-exercise, 30-min, and 60-min post-exercise. HRV was assessed using frequency [natural logarithm of high (LnHF and low frequency (LnLF powers, normalized high (nHF and low frequency (nLF powers, and LF/HF ratio] and time domains [Root mean square of successive differences (RMSSD, natural logarithm of RMSSD (LnRMSSD and R-R interval (RRI]. Spontaneous BRS included both up-up and down-down sequences. At pre-exercise, no group differences were observed for any HR, HRV and BRS parameters. During exercise recovery, significant race-by-time interactions were observed for LnHF, nHF, nLF, LF/HF, LnRMSSD, RRI, HR, and BRS (up-up. The declines in LnHF, nHF, RMSSD, RRI and BRS (up-up and the increases in LF/HF, nLF and HR were blunted in Chinese when compared to Caucasians from pre-exercise to 30-min to 60-min post-exercise. Chinese exhibited delayed autonomic recovery following an acute bout of treadmill exercise. This delayed autonomic recovery may result from greater sympathetic dominance and extended vagal withdrawal in Chinese.Chinese Clinical Trial Register ChiCTR-IPR-15006684.

  13. Autonomic Recovery Is Delayed in Chinese Compared with Caucasian following Treadmill Exercise.

    Science.gov (United States)

    Sun, Peng; Yan, Huimin; Ranadive, Sushant M; Lane, Abbi D; Kappus, Rebecca M; Bunsawat, Kanokwan; Baynard, Tracy; Hu, Min; Li, Shichang; Fernhall, Bo

    2016-01-01

    Caucasian populations have a higher prevalence of cardiovascular disease (CVD) when compared with their Chinese counterparts and CVD is associated with autonomic function. It is unknown whether autonomic function during exercise recovery differs between Caucasians and Chinese. The present study investigated autonomic recovery following an acute bout of treadmill exercise in healthy Caucasians and Chinese. Sixty-two participants (30 Caucasian and 32 Chinese, 50% male) performed an acute bout of treadmill exercise at 70% of heart rate reserve. Heart rate variability (HRV) and baroreflex sensitivity (BRS) were obtained during 5-min epochs at pre-exercise, 30-min, and 60-min post-exercise. HRV was assessed using frequency [natural logarithm of high (LnHF) and low frequency (LnLF) powers, normalized high (nHF) and low frequency (nLF) powers, and LF/HF ratio] and time domains [Root mean square of successive differences (RMSSD), natural logarithm of RMSSD (LnRMSSD) and R-R interval (RRI)]. Spontaneous BRS included both up-up and down-down sequences. At pre-exercise, no group differences were observed for any HR, HRV and BRS parameters. During exercise recovery, significant race-by-time interactions were observed for LnHF, nHF, nLF, LF/HF, LnRMSSD, RRI, HR, and BRS (up-up). The declines in LnHF, nHF, RMSSD, RRI and BRS (up-up) and the increases in LF/HF, nLF and HR were blunted in Chinese when compared to Caucasians from pre-exercise to 30-min to 60-min post-exercise. Chinese exhibited delayed autonomic recovery following an acute bout of treadmill exercise. This delayed autonomic recovery may result from greater sympathetic dominance and extended vagal withdrawal in Chinese. Chinese Clinical Trial Register ChiCTR-IPR-15006684.

  14. TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels

    Directory of Open Access Journals (Sweden)

    Eric W. Triplett

    2010-07-01

    Full Text Available The high level of conservation of 16S ribosomal RNA gene (16S rRNA in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org.

  15. Enhancing endogenous stem cells in the newborn via delayed umbilical cord clamping

    Directory of Open Access Journals (Sweden)

    Christopher Lawton

    2015-01-01

    Full Text Available There is currently no consensus among clinicians and scientists over the appropriate or optimal timing for umbilical cord clamping. However, many clinical studies have suggested that delayed cord clamping is associated with various neonatal benefits including increased blood volume, reduced need for blood transfusion, increased cerebral oxygenation in pre-term infants, and decreased frequency of iron deficiency anemia in term infants. Human umbilical cord blood contains significant amounts of stem and progenitor cells and is currently used in the treatment of several life-threatening diseases. We propose that delayed cord clamping be encouraged as it enhances blood flow from the placenta to the neonate, which is accompanied by an increase supply of valuable stem and progenitor cells, as well as may improve blood oxygenation and increase blood volume, altogether reducing the infant′s susceptibility to both neonatal and age-related diseases.

  16. Effects of delayed nonlinear response on wave packet dynamics in one-dimensional generalized Fibonacci chains

    International Nuclear Information System (INIS)

    Zhang, Jianxin; Zhang, Zhenjun; Tong, Peiqing

    2013-01-01

    We investigate the spreading of an initially localized wave packet in one-dimensional generalized Fibonacci (GF) lattices by solving numerically the discrete nonlinear Schrödinger equation (DNLSE) with a delayed cubic nonlinear term. It is found that for short delay time, the wave packet is self-trapping in first class of GF lattices, that is, the second moment grows with time, but the corresponding participation number does not grow. However, both the second moment and the participation number grow with time for large delay time. This illuminates that the wave packet is delocalized. For the second class of GF lattices, the dynamic behaviors of wave packet depend on the strength of on-site potential. For a weak on-site potential, the results are similar to the case of the first class. For a strong on-site potential, both the second moment and the participation number does not grow with time in the regime of short delay time. In the regime of large delay time, both the second moment and the participation number exhibit stair-like growth

  17. Effects of delayed nonlinear response on wave packet dynamics in one-dimensional generalized Fibonacci chains

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jianxin; Zhang, Zhenjun [Department of Physics and Institute of Theoretical Physics, Nanjing Normal University, Nanjing 210023 (China); Tong, Peiqing, E-mail: pqtong@njnu.edu.cn [Department of Physics and Institute of Theoretical Physics, Nanjing Normal University, Nanjing 210023 (China); Jiangsu Key Laboratory for Numerical Simulation of Large Scale Complex Systems, Nanjing Normal University, Nanjing 210023 (China)

    2013-07-15

    We investigate the spreading of an initially localized wave packet in one-dimensional generalized Fibonacci (GF) lattices by solving numerically the discrete nonlinear Schrödinger equation (DNLSE) with a delayed cubic nonlinear term. It is found that for short delay time, the wave packet is self-trapping in first class of GF lattices, that is, the second moment grows with time, but the corresponding participation number does not grow. However, both the second moment and the participation number grow with time for large delay time. This illuminates that the wave packet is delocalized. For the second class of GF lattices, the dynamic behaviors of wave packet depend on the strength of on-site potential. For a weak on-site potential, the results are similar to the case of the first class. For a strong on-site potential, both the second moment and the participation number does not grow with time in the regime of short delay time. In the regime of large delay time, both the second moment and the participation number exhibit stair-like growth.

  18. Attosecond Electron Wave Packet Dynamics in Strong Laser Fields

    International Nuclear Information System (INIS)

    Johnsson, P.; Remetter, T.; Varju, K.; L'Huillier, A.; Lopez-Martens, R.; Valentin, C.; Balcou, Ph.; Kazamias, S.; Mauritsson, J.; Gaarde, M. B.; Schafer, K. J.; Mairesse, Y.; Wabnitz, H.; Salieres, P.

    2005-01-01

    We use a train of sub-200 attosecond extreme ultraviolet (XUV) pulses with energies just above the ionization threshold in argon to create a train of temporally localized electron wave packets. We study the energy transfer from a strong infrared (IR) laser field to the ionized electrons as a function of the delay between the XUV and IR fields. When the wave packets are born at the zero crossings of the IR field, a significant amount of energy (∼20 eV) is transferred from the field to the electrons. This results in dramatically enhanced above-threshold ionization in conditions where the IR field alone does not induce any significant ionization. Because both the energy and duration of the wave packets can be varied independently of the IR laser, they are valuable tools for studying and controlling strong-field processes

  19. Delay Mitigation in the Malaysian Housing Industry: A Structural Equation Modelling Approach

    Directory of Open Access Journals (Sweden)

    Chang Saar Chai

    2015-01-01

    Full Text Available The housing industry is one of the major contributors to the economy in Malaysia due to the constantly high housing demand. The housing demand has increased due to the rapid growth in population and urbanisation in the country. One of the major challenges in the housing industry is the late delivery of housing supply, which in some instances leads to sick and abandoned housing projects. Despite being extensively investigated, th in a negative impact, there is a strong need to review the housing delay mitigation measures practised in Malaysia. This paper aims to evaluate the current delay mitigation measures and its main objective is to explore the relationship between the mitigation measures and delay in housing via a Structural Equation Modelling (SEM approach. A questionnaire survey through an online survey tool was conducted across 13 states and three Federal Territories in Malaysia. The target respondents are the local authorities, developers, consultants (principal submitting persons and contractors. The findings show that 17 predictive, preventive, organisational or corrective. This paper demonstrates that preventive measures are the most influential mitigation measures for housing delivery delay.

  20. Pre-Service Secondary Mathematics Teachers' Reflections on Good and Bad Mathematics Teaching

    Science.gov (United States)

    Dayal, Hem Chand

    2013-01-01

    Researchers suggest that teachers' beliefs about teaching are strongly influenced by their personal experiences with mathematics. This study aimed to explore Pacific Island pre-service secondary mathematics teachers' perceptions about good and bad mathematics teachers. Thirty pre-service teachers, enrolled in a mathematics teaching methods course…

  1. Reward acts as a signal to control delay-period activity in delayed-response tasks.

    Science.gov (United States)

    Ichihara-Takeda, Satoe; Takeda, Kazuyoshi; Funahashi, Shintaro

    2010-03-31

    Prefrontal delay-period activity represents a neural mechanism for the active maintenance of information and needs to be controlled by some signal to appropriately operate working memory. To examine whether reward-delivery acts as this signal, the effects of delay-period activity in response to unexpected reward-delivery were examined by analyzing single-neuron activity recorded in the primate dorsolateral prefrontal cortex. Among neurons that showed delay-period activity, 34% showed inhibition of this activity in response to unexpected reward-delivery. The delay-period activity of these neurons was affected by the expectation of reward-delivery. The strength of the reward signal in controlling the delay-period activity is related to the strength of the effect of reward information on the delay-period activity. These results indicate that reward-delivery acts as a signal to control delay-period activity.

  2. Delay-dependent exponential stability of cellular neural networks with time-varying delays

    International Nuclear Information System (INIS)

    Zhang Qiang; Wei Xiaopeng; Xu Jin

    2005-01-01

    The global exponential stability of cellular neural networks (CNNs) with time-varying delays is analyzed. Two new sufficient conditions ensuring global exponential stability for delayed CNNs are obtained. The conditions presented here are related to the size of delay. The stability results improve the earlier publications. Two examples are given to demonstrate the effectiveness of the obtained results

  3. Development of an education campaign to reduce delays in pre-hospital response to stroke.

    Science.gov (United States)

    Caminiti, Caterina; Schulz, Peter; Marcomini, Barbara; Iezzi, Elisa; Riva, Silvia; Scoditti, Umberto; Zini, Andrea; Malferrari, Giovanni; Zedde, Maria Luisa; Guidetti, Donata; Montanari, Enrico; Baratti, Mario; Denti, Licia

    2017-06-24

    Systematic reviews call for well-designed trials with clearly described intervention components to support the effectiveness of educational campaigns to reduce patient delay in stroke presentation. We herein describe the systematic development process of a campaign aimed to increase stroke awareness and preparedness. Campaign development followed Intervention Mapping (IM), a theory- and evidence-based tool, and was articulated in two phases: needs assessment and intervention development. In phase 1, two cross-sectional surveys were performed, one aiming to measure stroke awareness in the target population and the other to analyze the behavioral determinants of prehospital delay. In phase 2, a matrix of proximal program objectives was developed, theory-based intervention methods and practical strategies were selected and program components and materials produced. In phase 1, the survey on 202 citizens highlighted underestimation of symptom severity, as in only 44% of stroke situations respondents would choose to call the emergency service (EMS). In the survey on 393 consecutive patients, 55% presented over 2 hours after symptom onset; major determinants were deciding to call the general practitioner first and the reaction of the first person the patient called. In phase 2, adult individuals were identified as the target of the intervention, both as potential "patients" and witnesses of stroke. The low educational level found in the patient survey called for a narrative approach in cartoon form. The family setting was chosen for the message because 42% of patients who presented within 2 hours had been advised by a family member to call EMS. To act on people's tendency to view stroke as an untreatable disease, it was decided to avoid fear-arousal appeals and use a positive message providing instructions and hope. Focus groups were used to test educational products and identify the most suitable sites for message dissemination. The IM approach allowed to develop a

  4. Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Xiao Li Shi

    Full Text Available The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX, which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.

  5. Theta burst magnetic stimulation over the pre-supplementary motor area improves motor inhibition.

    Science.gov (United States)

    Obeso, Ignacio; Wilkinson, Leonora; Teo, James T; Talelli, Penelope; Rothwell, John C; Jahanshahi, Marjan

    Stopping an ongoing motor response or resolving conflict induced by conflicting stimuli are associated with activation of a right-lateralized network of inferior frontal gyrus (IFG), pre-supplementary motor area (pre-SMA) and subthalamic nucleus (STN). However, the roles of the right IFG and pre-SMA in stopping a movement and in conflict resolution remain unclear. We used continuous theta burst stimulation (cTBS) to examine the involvement of the right IFG and pre-SMA in inhibition and conflict resolution using the conditional stop signal task. We measured stop signal reaction time (SSRT, measure of reactive inhibition), response delay effect (RDE, measure of proactive action restraint) and conflict induced slowing (CIS, measure of conflict resolution). Stimulation over the pre-SMA resulted in significantly shorter SSRTs (improved inhibition) compared to sham cTBS. This effect was not observed for CIS, RDE, or any other measures. cTBS over the right IFG had no effect on SSRT, CIS, RDE or on any other measure. The improvement of SSRT with cTBS over the pre-SMA suggests its critical contribution to stopping ongoing movements. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Effect of Phase Response Curve Skew on Synchronization with and without Conduction Delays

    Directory of Open Access Journals (Sweden)

    Carmen eCanavier

    2013-12-01

    Full Text Available A central problem in cortical processing including sensory binding and attentional gating is how neurons can synchronize their responses with zero or near-zero time lag. For a spontaneously firing neuron, an input from another neuron can delay or advance the next spike by different amounts depending upon the timing of the input relative to the previous spike. This information constitutes the phase response curve (PRC. We present a simple graphical method for determining the effect of PRC shape on synchronization tendencies and illustrate it using type 1 PRCs, which consist entirely of advances (delays in response to excitation (inhibition. We obtained the following generic solutions for type 1 PRCs, which include the pulse coupled leaky integrate and fire model. For pairs with mutual excitation, exact synchrony can be stable for strong coupling because of the stabilizing effect of the causal limit region of the PRC in which an input triggers a spike immediately upon arrival. However, synchrony is unstable for short delays, because delayed inputs arrive during a refractory period and cannot trigger an immediate spike. Right skew destabilizes antiphase and enables modes with time lags that grow as the conduction delay is increased. Therefore, right skew favors near-synchrony at short conduction delays and a gradual transition between synchrony and antiphase for pairs coupled by mutual excitation. For pairs with mutual inhibition, zero time lag synchrony is stable for conduction delays ranging from zero to a substantial fraction of the period for pairs. However, for right skew there is a preferred antiphase mode at short delays. In contrast to mutual excitation, left skew destabilizes antiphase for mutual inhibition so that synchrony dominates at short delays as well. These pairwise synchronization tendencies constrain the synchronization properties of neurons embedded in larger networks.

  7. The rates and time-delay distribution of multiply imaged supernovae behind lensing clusters

    Science.gov (United States)

    Li, Xue; Hjorth, Jens; Richard, Johan

    2012-11-01

    Time delays of gravitationally lensed sources can be used to constrain the mass model of a deflector and determine cosmological parameters. We here present an analysis of the time-delay distribution of multiply imaged sources behind 17 strong lensing galaxy clusters with well-calibrated mass models. We find that for time delays less than 1000 days, at z = 3.0, their logarithmic probability distribution functions are well represented by P(log Δt) = 5.3 × 10-4Δttilde beta/M2502tilde beta, with tilde beta = 0.77, where M250 is the projected cluster mass inside 250 kpc (in 1014M⊙), and tilde beta is the power-law slope of the distribution. The resultant probability distribution function enables us to estimate the time-delay distribution in a lensing cluster of known mass. For a cluster with M250 = 2 × 1014M⊙, the fraction of time delays less than 1000 days is approximately 3%. Taking Abell 1689 as an example, its dark halo and brightest galaxies, with central velocity dispersions σ>=500kms-1, mainly produce large time delays, while galaxy-scale mass clumps are responsible for generating smaller time delays. We estimate the probability of observing multiple images of a supernova in the known images of Abell 1689. A two-component model of estimating the supernova rate is applied in this work. For a magnitude threshold of mAB = 26.5, the yearly rate of Type Ia (core-collapse) supernovae with time delays less than 1000 days is 0.004±0.002 (0.029±0.001). If the magnitude threshold is lowered to mAB ~ 27.0, the rate of core-collapse supernovae suitable for time delay observation is 0.044±0.015 per year.

  8. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA

    DEFF Research Database (Denmark)

    Purta, Elzbieta; O'Connor, Michelle; Bujnicki, Janusz M

    2009-01-01

    The rRNAs of Escherichia coli contain four 2'-O-methylated nucleotides. Similar to other bacterial species and in contrast with Archaea and Eukaryota, the E. coli rRNA modifications are catalysed by specific methyltransferases that find their nucleotide targets without being guided by small...... complementary RNAs. We show here that the ygdE gene encodes the methyltransferase that catalyses 2'-O-methylation at nucleotide C2498 in the peptidyl transferase loop of E. coli 23S rRNA. Analyses of rRNAs using MALDI mass spectrometry showed that inactivation of the ygdE gene leads to loss of methylation...... at nucleotide C2498. The loss of ygdE function causes a slight reduction in bacterial fitness. Methylation at C2498 was restored by complementing the knock-out strain with a recombinant copy of ygdE. The recombinant YgdE methyltransferase modifies C2498 in naked 23S rRNA, but not in assembled 50S subunits...

  9. Pre-treatment with antibiotics and Escherichia coli to equalize the gut microbiota in conventional mice.

    Science.gov (United States)

    Linninge, Caroline; Ahrné, Siv; Molin, Göran

    2015-01-01

    The composition of the gut microbiota can vary widely between individual mice of the same batch and thereby affect the resulting outcome in experimental studies. Therefore, an efficient method is needed to equalize the gut microbiota prior to the start of critical experiments. In order to minimize variations in gut microbiota between animals and provide the animals with a Gram-negative flora exposing lipopolysaccharides in the cell-walls, C57BL/6 mice were given a mixture of ampicillin, metronidazole and clindamycin in the drinking water for 3 days and then Escherichia coli for two additional days. Treatment with antibiotics alone or with antibiotics in combination with E. coli was well tolerated by all animals. Body weight and liver weight were not affected, although higher hepatic fat content was found in treated animals (p antibiotics and antibiotics in combination with E. coli (p < 0.01), without affecting the total amount of bacteria. Cloned and sequenced 16S rRNA genes showed high presence of Enterobacteriaceae and Porphymonadaceae in the treated animals. Analysis with Principal Component Analysis gave a clear separation of the composition in microbiota between different treatment groups. The described treatment efficiently equalized the gut microbiota and provided the animals with a strong abundance of Enterobacteriaceae without changing the total load of bacteria. This is a straightforward, lenient and efficient method of pre-treatment to equalize the gut microbiota of mice as a starting procedure of animal studies.

  10. Parenting Practices and Associations with Development Delays among Young Children in Dominican Republic.

    Science.gov (United States)

    Uwemedimo, Omolara Thomas; Howlader, Afrin; Pierret, Giselina

    According to the World Health Organization, >200 million children in low- and middle-income countries experience developmental delays. However, household structure and parenting practices have been minimally explored as potential correlates of developmental delay in low- and middle-income countries, despite potential as areas for intervention. The objective of the study was to examine associations of developmental delays with use of World Health Organization-recommended parenting practices among a clinic-based cohort of children aged 6-60 months attending in La Romana, Dominican Republic. This study was conducted among 74 caregiver-child pairs attending the growth-monitoring clinic at Hospital Francisco Gonzalvo in June 2015. The Malawi Developmental Assessment Tool was adapted and performed on each child to assess socioadaptive, fine motor, gross motor, and language development. The IMCI Household Level Survey Questionnaire was used to assess parenting practices. Fisher's exact test was used to determine associations significant at P children had a delay in at least 1 developmental domain. Most caregivers used scolding (43.2%) or spanking (44%) for child discipline. Children who were disciplined by spanking and scolding were more likely to have language delay (P = .007) and socioadaptive delay (P = .077), respectively. On regression analysis, children with younger primary caregivers had 7 times higher odds of language delay (adjusted odds ratio [AOR]: 7.35, 95% confidence interval [CI]: 1.52-35.61) and 4 times greater odds of any delay (AOR: 4.72, 95% CI: 1.01-22.22). In addition, children punished by spanking had 5 times higher odds of having language delay (AOR: 5.04, 95% CI: 1.13-22.39). Parenting practices such as harsh punishment and lack of positive parental reinforcement were found to have strong associations with language and socioadaptive delays. Likewise, delays were also more common among children with younger caregivers. Copyright © 2017 Icahn

  11. Prosthetic joint infection due to Lysobacter thermophilus diagnosed by 16S rRNA gene sequencing

    OpenAIRE

    B Dhawan; S Sebastian; R Malhotra; A Kapil; D Gautam

    2016-01-01

    We report the first case of prosthetic joint infection caused by Lysobacter thermophilus which was identified by 16S rRNA gene sequencing. Removal of prosthesis followed by antibiotic treatment resulted in good clinical outcome. This case illustrates the use of molecular diagnostics to detect uncommon organisms in suspected prosthetic infections.

  12. Delayed recall, hippocampal volume and Alzheimer neuropathology: findings from the Nun Study.

    Science.gov (United States)

    Mortimer, J A; Gosche, K M; Riley, K P; Markesbery, W R; Snowdon, D A

    2004-02-10

    To examine the associations of hippocampal volume and the severity of neurofibrillary lesions determined at autopsy with delayed verbal recall performance evaluated an average of 1 year prior to death. Hippocampal volumes were computed using postmortem brain MRI from the first 56 scanned participants of the Nun Study. Quantitative neuropathologic studies included lesion counts, Braak staging, and determination of whether neuropathologic criteria for Alzheimer disease (AD) were met. Multiple regression was used to assess the association of hippocampal volume and neuropathologic lesions with the number of words (out of 10) recalled on the Consortium to Establish a Registry for Alzheimer's Disease Delayed Word Recall Test administered an average of 1 year prior to death. When entered separately, hippocampal volume, Braak stage, and the mean neurofibrillary tangle counts in the CA-1 region of the hippocampus and the subiculum were strongly associated with the number of words recalled after a delay, adjusting for age and education. When hippocampal volume was entered together with each neuropathologic index, only hippocampal volume retained a significant association with the delayed recall measure. The association between hippocampal volume and the number of words recalled was present in both demented and nondemented individuals as well as in those with and without substantial AD neurofibrillary pathology. The association of neurofibrillary tangles with delayed verbal recall may reflect associated hippocampal atrophy.

  13. The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing.

    Directory of Open Access Journals (Sweden)

    Luis G Morello

    Full Text Available NIP7 is one of the many trans-acting factors required for eukaryotic ribosome biogenesis, which interacts with nascent pre-ribosomal particles and dissociates as they complete maturation and are exported to the cytoplasm. By using conditional knockdown, we have shown previously that yeast Nip7p is required primarily for 60S subunit synthesis while human NIP7 is involved in the biogenesis of 40S subunit. This raised the possibility that human NIP7 interacts with a different set of proteins as compared to the yeast protein. By using the yeast two-hybrid system we identified FTSJ3, a putative ortholog of yeast Spb1p, as a human NIP7-interacting protein. A functional association between NIP7 and FTSJ3 is further supported by colocalization and coimmunoprecipitation analyses. Conditional knockdown revealed that depletion of FTSJ3 affects cell proliferation and causes pre-rRNA processing defects. The major pre-rRNA processing defect involves accumulation of the 34S pre-rRNA encompassing from site A' to site 2b. Accumulation of this pre-rRNA indicates that processing of sites A0, 1 and 2 are slower in cells depleted of FTSJ3 and implicates FTSJ3 in the pathway leading to 18S rRNA maturation as observed previously for NIP7. The results presented in this work indicate a close functional interaction between NIP7 and FTSJ3 during pre-rRNA processing and show that FTSJ3 participates in ribosome synthesis in human cells.

  14. Assessing delay discounting in mice

    OpenAIRE

    Mitchell, Suzanne H.

    2014-01-01

    Delay discounting (also intertemporal choice or impulsive choice) is the process by which delayed outcomes, such as delayed food delivery, are valued less than the same outcomes delivered immediately or with a shorter delay. This process is of interest because many psychopathologies, including substance dependence, pathological gambling, attention deficit hyperactivity disorder and conduct disorder, are characterized by heightened levels of delay discounting. Some of these disorders are herit...

  15. 16S rRNA gene sequencing in routine identification of anaerobic bacteria isolated from blood cultures

    DEFF Research Database (Denmark)

    Justesen, Ulrik Stenz; Skov, Marianne Nielsine; Knudsen, Elisa

    2010-01-01

    A comparison between conventional identification and 16S rRNA gene sequencing of anaerobic bacteria isolated from blood cultures in a routine setting was performed (n = 127). With sequencing, 89% were identified to the species level, versus 52% with conventional identification. The times...

  16. Modelling delays in pharmacokinetics

    International Nuclear Information System (INIS)

    Farooqi, Z.H.; Lambrecht, R.M.

    1990-01-01

    Linear system analysis has come to form the backbone of pharmacokinetics. Natural systems usually involve time delays, thus models incorporating them would be an order closer approximation to the real world compared to those that do not. Delays may be modelled in several ways. The approach considered in this study is to have a discrete-time delay dependent rate with the delay respresenting the duration between the entry of a drug into a compartment and its release in some form (may be as a metabolite) from the compartment. Such a delay may be because of one or more of several physiological reasons, like, formation of a reservoir, slow metabolism, or receptor binding. The mathematical structure this gives rise to is a system of delay-differential equations. Examples are given of simple one and two compartment systems with drugs like bumetanide, carbamazepine, and quinolone-caffeine interaction. In these examples generally a good fit is obtained and the suggested models form a good approximation. 21 refs., 6 figs

  17. Analysis of rRNA gene methylation in Arabidopsis thaliana by CHEF-Conventional 2D gel electrophoresis

    Science.gov (United States)

    Mohannath, Gireesha; Pikaard, Craig S.

    2017-01-01

    Summary Contour-clamped homogenous electric field (CHEF) gel electrophoresis, a variant of Pulsed-field gel electrophoresis (PFGE), is a powerful technique for resolving large fragments of DNA (10 kb to 9 Mb). CHEF has many applications including the physical mapping of chromosomes, artificial chromosomes and sub-chromosomal DNA fragments, etc. Here we describe the use of CHEF and two-dimensional gel electrophoresis to analyze rRNA gene methylation patterns within the two ~ 4 million base pair nucleolus organizer regions (NORs) of Arabidopsis thaliana. The method involves CHEF gel electrophoresis of agarose-embedded DNA following restriction endonuclease digestion to cut the NORs into large but resolvable segments, followed by digestion with methylation-sensitive restriction endonucleases and conventional (or CHEF) gel electrophoresis, in a second dimension. Resulting products are then detected by Southern blotting or PCR analyses capable of discriminating rRNA gene subtypes. PMID:27576719

  18. [Determinants of patient and health system delays for women with breast cancer in Morocco, 2013].

    Science.gov (United States)

    Benbakhta, B; Tazi, M; Benjaafar, N; Khattabi, A; Maaroufi, A

    2015-06-01

    In Morocco, breast cancer is the first most common cancer in women. It is diagnosed in most cases at an advanced stage. Delay in diagnosis and access to treatment for breast cancer increases morbidity and mortality. The objective of this study was to determine the consultation delay (patient delay), diagnosis delay and access to treatment delay (health system delays) of women with breast cancer admitted at the National Institute of Oncology in Rabat. Factors associated with these delays were analyzed. We conducted a cross-sectional study from December 2012 to May 2013 at the National Institute of Oncology in Rabat. Two hundred eligible and consenting women were interviewed using a structured and pre-tested questionnaire. Stages I and II were identified as "early stages" and III and IV as "advanced stages". In our population, 54% were diagnosed at an early stage of breast cancer and 46% at an advanced stage. The median total delay was 120 days (interquartile interval [IIQ]=81-202 days). The patient delay (median=65 days, IIQ=31-121) was longer than the health system delay (median=50 days, IIQ=29-77). High risk for a long total delay (more than 4 months) was observed for women who were aged over 65 years (OR=1.30, 95% CI 1.10-4.20), illiterate (OR=4.50, 95% CI 2.10-6.20), rural residents (OR=3.40, 95% CI 1.23-8.13), in a lower socioeconomic category (OR=4.75, 95% CI 1.45-15.60), without knowledge about breast self-examination (OR=5.67, 95% CI 2.65-12.15) and seen more than 2 times before diagnosis (OR=7.70, 95% CI 2.88-20.50). A long total delay increased the risk of being diagnosed at an advanced stage (OR=5.62, 95% CI 3.03-10.45). Efforts should be directed to providing good information to the population at risk, better access to screening and continuing medical training to enable diagnosis and early treatment. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  19. Single Cell Analysis Linking Ribosomal (r)DNA and rRNA Copy Numbers to Cell Size and Growth Rate Provides Insights into Molecular Protistan Ecology.

    Science.gov (United States)

    Fu, Rao; Gong, Jun

    2017-11-01

    Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)-based characteristics are linked with diversity, abundance, and activity of protist populations and communities observed at organismal levels. Here, we applied a single-cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per-cell rDNA and rRNA CNs scaled with cell volume (CV) to 0.44 and 0.58 powers, respectively. The modeled rDNA and rRNA concentrations thus appear to be much higher in smaller than in larger cells. The observed rRNA:rDNA ratio scaled with CV 0.14 . The maximum growth rate could be well predicted by a combination of per-cell ribotype CN and temperature. Our empirical data and modeling on single-cell ribotype scaling are in agreement with both the metabolic theory of ecology and the growth rate hypothesis, providing a quantitative framework for linking cellular rDNA and rRNA CNs with body size, growth (activity), and biomass stoichiometry. This study also demonstrates that the expression rate of rRNA genes is constrained by cell size, and favors biomass rather than abundance-based interpretation of quantitative ribotype data in population and community ecology of protists. © 2017 The Authors. Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

  20. Response to Competitive Entry: A Rationale for Delayed Defensive Reaction

    OpenAIRE

    Ajay Kalra; Surendra Rajiv; Kannan Srinivasan

    1998-01-01

    Empirical studies examining responses to new product entries come to the puzzling conclusion that, in general, an incumbent reacts to a new entrant after a significant delay. Even easy-to-implement price cuts are observed after significant lag following entry. These findings seem to contradict the existing literature that either implicitly assumes or strongly advocates immediate defensive responses to limit competitive encroachment. When a competing firm enters the market, consumers may be un...

  1. Delayed Rebleeding of Cerebral Aneurysm Misdiagnosed as Traumatic Subarachnoid Hemorrhage

    OpenAIRE

    Song, Seung-Yoon; Kim, Dae-Won; Park, Jong-Tae; Kang, Sung-Don

    2016-01-01

    An intracranial saccular aneurysm is uncommonly diagnosed in a patient with closed head trauma. We herein present a patient with delayed rebleeding of a cerebral aneurysm misdiagnosed as traumatic subarachnoid hemorrhage (SAH). A 26-year-old female visited our emergency department because of headache after a motorcycle accident. Brain computed tomography (CT) showed a right-side dominant SAH in Sylvian fissure. Although traumatic SAH was strongly suggested because of the history of head traum...

  2. Problems created on delayed supply of feedstock for the HDPE plant of Jam Petrochemical Complex (JPC) in Iran : a case study[The 1. international construction specialty conference

    Energy Technology Data Exchange (ETDEWEB)

    Etemadzadeh, S.; Mortaheb, M. [Sharif Univ. of Technology, Tehran (Iran, Islamic Republic of). Dept. of Civil Engineering; Beigi, H. [Jam Petrochemical Co., Assaluyeh, Bushehr (Iran, Islamic Republic of)

    2006-07-01

    The total loss incurred due to delays in supply of feedstock and utilities over the past 2 years during Iran's construction boom in petrochemical plants was evaluated. The problems associated with the delay of feedstock supply and its impact on the final stages of a petrochemical project were discussed and the factors that affect the financial viability of a project were identified. In particular, the paper reviewed issues regarding equipment warranty and their pre-mature expiration; unavoidable rework prior to pre-commissioning; preservation and maintenance cost of equipment in a humid and hot environment; changes in technology and market demands; and, additional fixed costs covering salaries and maintenance costs. Remedial action plans addressing these issues were proposed in order to reduce the costs and any further delays of a project. The importance of technical audits at the feasibility stage of a project was emphasized along with the need to verify the accuracy of initial data for proper design and completion of a project.

  3. Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers.

    Science.gov (United States)

    Biderre-Petit, Corinne; Boucher, Delphine; Kuever, Jan; Alberic, Patrick; Jézéquel, Didier; Chebance, Brigitte; Borrel, Guillaume; Fonty, Gérard; Peyret, Pierre

    2011-02-01

    Geochemical researches at Lake Pavin, a low-sulfate-containing freshwater lake, suggest that the dominant biogeochemical processes are iron and sulfate reduction, and methanogenesis. Although the sulfur cycle is one of the main active element cycles in this lake, little is known about the sulfate-reducer and sulfur-oxidizing bacteria. The aim of this study was to assess the vertical distribution of these microbes and their diversities and to test the hypothesis suggesting that only few SRP populations are involved in dissimilatory sulfate reduction and that Epsilonproteobacteria are the likely key players in the oxidative phase of sulfur cycle by using a PCR aprA gene-based approach in comparison with a 16S rRNA gene-based analysis. The results support this hypothesis. Finally, this preliminary work points strongly the likelihood of novel metabolic processes upon the availability of sulfate and other electron acceptors.

  4. REASONS FOR PATIENT DELAYS & HEALTH SYSTEM DELAYS FOR TUBERCULOSIS IN SOUTH INDIA

    Directory of Open Access Journals (Sweden)

    Kapil Goel

    2011-12-01

    Full Text Available Background: Globally, the burden of Tuberculosis is escalating. Early diagnosis and prompt initiation of tuberculosis treatment is essential for an effective tuberculosis control programme. Objectives: To study the self reported reasons for patient and health system (diagnosis & treatment delays in Tuberculosis patients. Methods: A community based cross sectional study was conducted among 98 new sputum positive TB cases aged > 15 years registered under RNTCP from Oct 2006 to June 2007 & receiving treatment under DOTS in Udupi taluk by interviewing them. Results: Total 98 patients were recruited and 68% were males. Out of 17 patients with patient delays, 82% felt that their symptoms were not severe, 71% felt that patient delay was due to lack of awareness and 71% did not take it seriously. Out of 86 patients with health system delays, 82.6% of patients mentioned that doctor has not advised for sputum examination, 76.7% of patients told that they first consulted a private doctor, 21% of them mentioned that doctor was unaware to diagnose TB. Conclusion: Symptoms not severe is the main reason for the patient delay and doctor didn’t advise for sputum examination is the main reason for health system delays.

  5. Pre-Equilibrium Cluster Emission with Pickup and Knockout

    International Nuclear Information System (INIS)

    Betak, E.

    2005-01-01

    We present a generalization of the Iwamoto-Harada-Bisplinghoff pre-equilibrium model of light cluster formation and emission, which is enhanced by allowing for possible admixtures of knockout for strongly coupled ejectiles, like α's. The model is able to attain the Weisskopf-Ewing formula for compound-nucleus decay at long-time limit; it keeps the philosophy of pre-equilibrium decay during the equilibration stage and it describes the initial phase of a reaction as direct process(es) expressed using the language of the exciton model

  6. Decreasing delays in urgent and expedited surgery in a university teaching hospital through audit and communication between peri-operative and surgical directorates.

    Science.gov (United States)

    Cosgrove, J F; Gaughan, M; Snowden, C P; Lees, T

    2008-06-01

    National Confidential Enquiry into Patient Outcome and Death guidelines for urgent surgery recommend a fully staffed emergency operating theatre and restriction of 'after-midnight' operating to immediate life-, limb- or organ-threatening conditions. Audit performed in our institution demonstrated significant decreases in waiting times for urgent surgery and an increased seniority of medical care associated with overnight pre-operative assessment of patients by anaesthetic trainees. Nevertheless, urgent cases continued to be delayed unnecessarily. A classification of delays was developed from existing guidelines and their incidence was audited. The results were disseminated to involved directorates. A repeat of the audit demonstrated a significant decrease in delays (p = 0.001), a significant increase in the availability of surgeons (p = 0.001) and a significant decrease in the median waiting time for urgent surgery compared to the first audit cycle and a previous standard (p auditing delays and disseminating the results of the audit significantly decreases delays and median waiting times for urgent surgery because of improved surgical availability.

  7. Delayed high school start times later than 8:30am and impact on graduation rates and attendance rates.

    Science.gov (United States)

    McKeever, Pamela Malaspina; Clark, Linda

    2017-04-01

    The first purpose of this study was to investigate changes in high school graduation rates with a delayed school start time of later than 8:30am. The second aim of the study was to analyze the association between a delayed high school start time later than 8:30am and attendance rates. In the current study, a pre-post design using a repeated-measures analysis of variance was used to examine changes in attendance and graduation rates 2 years after a delayed start was implemented. Public high schools from 8 school districts (n=29 high schools) located throughout 7 different states. Schools were identified using previous research from the Children's National Medical Center's Division of Sleep Medicine Research Team. A total membership of more than 30,000 high school students enrolled in the 29 schools identified by the Children's National Medical Center's Research Team. A pre-post design was used for a within-subject design, controlling for any school-to-school difference in the calculation of the response variable. This is the recommended technique for a study that may include data with potential measurement error. Findings from this study linked a start time of later than 8:30am to improved attendance rates and graduation rates. Attendance rates and graduation rates significantly improved in schools with delayed start times of 8:30am or later. School officials need to take special notice that this investigation also raises questions about whether later start times are a mechanism for closing the achievement gap due to improved graduation rates. Copyright © 2017 National Sleep Foundation. Published by Elsevier Inc. All rights reserved.

  8. Rrsm: The European Rapid Raw Strong-Motion Database

    Science.gov (United States)

    Cauzzi, C.; Clinton, J. F.; Sleeman, R.; Domingo Ballesta, J.; Kaestli, P.; Galanis, O.

    2014-12-01

    We introduce the European Rapid Raw Strong-Motion database (RRSM), a Europe-wide system that provides parameterised strong motion information, as well as access to waveform data, within minutes of the occurrence of strong earthquakes. The RRSM significantly differs from traditional earthquake strong motion dissemination in Europe, which has focused on providing reviewed, processed strong motion parameters, typically with significant delays. As the RRSM provides rapid open access to raw waveform data and metadata and does not rely on external manual waveform processing, RRSM information is tailored to seismologists and strong-motion data analysts, earthquake and geotechnical engineers, international earthquake response agencies and the educated general public. Access to the RRSM database is via a portal at http://www.orfeus-eu.org/rrsm/ that allows users to query earthquake information, peak ground motion parameters and amplitudes of spectral response; and to select and download earthquake waveforms. All information is available within minutes of any earthquake with magnitude ≥ 3.5 occurring in the Euro-Mediterranean region. Waveform processing and database population are performed using the waveform processing module scwfparam, which is integrated in SeisComP3 (SC3; http://www.seiscomp3.org/). Earthquake information is provided by the EMSC (http://www.emsc-csem.org/) and all the seismic waveform data is accessed at the European Integrated waveform Data Archive (EIDA) at ORFEUS (http://www.orfeus-eu.org/index.html), where all on-scale data is used in the fully automated processing. As the EIDA community is continually growing, the already significant number of strong motion stations is also increasing and the importance of this product is expected to also increase. Real-time RRSM processing started in June 2014, while past events have been processed in order to provide a complete database back to 2005.

  9. Delayed orgasm and anorgasmia.

    Science.gov (United States)

    Jenkins, Lawrence C; Mulhall, John P

    2015-11-01

    Delayed orgasm/anorgasmia defined as the persistent or recurrent difficulty, delay in, or absence of attaining orgasm after sufficient sexual stimulation, which causes personal distress. Delayed orgasm and anorgasmia are associated with significant sexual dissatisfaction. A focused medical history can shed light on the potential etiologies, which include medications, penile sensation loss, endocrinopathies, penile hyperstimulation, and psychological etiologies. Unfortunately, there are no excellent pharmacotherapies for delayed orgasm/anorgasmia, and treatment revolves largely around addressing potential causative factors and psychotherapy. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  10. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

    NARCIS (Netherlands)

    Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; Vos, de Willem M.

    2015-01-01

    Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to

  11. Greengenes: Chimera-checked 16S rRNA gene database and workbenchcompatible in ARB

    Energy Technology Data Exchange (ETDEWEB)

    DeSantis, T.Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie,E.L; Keller, K.; Huber, T.; Dalevi, D.; Hu, P.; Andersen, G.L.

    2006-02-01

    A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that incongruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3% of environmental sequences and 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.

  12. Globicatella sanguinis bacteraemia identified by partial 16S rRNA gene sequencing

    DEFF Research Database (Denmark)

    Abdul-Redha, Rawaa Jalil; Balslew, Ulla; Christensen, Jens Jørgen

    2007-01-01

    Globicatella sanguinis is a gram-positive coccus, resembling non-haemolytic streptococci. The organism has been isolated infrequently from normally sterile sites of humans. Three isolates obtained by blood culture could not be identified by Rapid 32 ID Strep, but partial sequencing of the 16S r......RNA gene revealed the identity of the isolated bacteria, and supplementary biochemical tests confirmed the species identification. The cases histories illustrate the dilemma of finding relevant, newly recognized, opportunistic pathogens and the identification achievement (s) that can be obtained by using...

  13. Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling.

    Directory of Open Access Journals (Sweden)

    Luís França

    Full Text Available Over a period of ten months a total of 5618 cord blood units (CBU were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.

  14. Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling.

    Science.gov (United States)

    França, Luís; Simões, Catarina; Taborda, Marco; Diogo, Catarina; da Costa, Milton S

    2015-01-01

    Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.

  15. Dominant obligate anaerobes revealed in lower respiratory tract infection in horses by 16S rRNA gene sequencing.

    Science.gov (United States)

    Kinoshita, Yuta; Niwa, Hidekazu; Katayama, Yoshinari; Hariu, Kazuhisa

    2014-04-01

    Obligate anaerobes are important etiological agents in pneumonia or pleuropneumonia in horses, because they are isolated more commonly from ill horses that have died or been euthanized than from those that survive. We performed bacterial identification and antimicrobial susceptibility testing for obligate anaerobes to establish effective antimicrobial therapy. We used 16S rRNA gene sequencing to identify 58 obligate anaerobes and compared the results with those from a phenotypic identification kit. The identification results of 16S rRNA gene sequencing were more reliable than those of the commercial kit. We concluded that genera Bacteroides and Prevotella-especially B. fragilis and P. heparinolytica-are dominant anaerobes in lower respiratory tract infection in horses; these organisms were susceptible to metronidazole, imipenem and clindamycin.

  16. Differential contributions of specimen types, culturing, and 16S rRNA sequencing in diagnosis of prosthetic joint infections

    DEFF Research Database (Denmark)

    Larsen, Lone Heimann; Khalid, Vesal; Xu, Yijuan

    2018-01-01

    Prosthetic joint failure is mainly caused by infection, aseptic failure (AF), and mechanical problems. Infection detection has been improved with modified culture methods and molecular diagnostics. However, comparisons between modified and conventional microbiology methods are difficult due...... to variations in specimen sampling. In this prospective, multidisciplinary study of hip or knee prosthetic failures, we assessed the contributions of different specimen types, extended culture incubations, and 16S rRNA sequencing for diagnosing prosthetic joint infections (PJI). Project specimens included joint...... fluid (JF), bone biopsy specimens (BB), soft-tissue biopsy specimens (STB), and swabs (SW) from the prosthesis, collected in situ, and sonication fluid collected from prosthetic components (PC). Specimens were cultured for 6 (conventional) or 14 days, and 16S rRNA sequencing was performed at study...

  17. Comparison of two approaches for the classification of 16S rRNA gene sequences.

    Science.gov (United States)

    Chatellier, Sonia; Mugnier, Nathalie; Allard, Françoise; Bonnaud, Bertrand; Collin, Valérie; van Belkum, Alex; Veyrieras, Jean-Baptiste; Emler, Stefan

    2014-10-01

    The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods. © 2014 The Authors.

  18. A pre-FFT equalizer design for application to Hiperlan/2

    OpenAIRE

    Armour, SMD; Nix, AR; Bull, David

    2000-01-01

    Use of a pre-FFT Equaliser (PFE) has been previously proposed as a method for either improving the efficiency of OFDM radio modems or increasing the excess delay spread that they are capable of operating under. In this paper, application of the PFE to the Hiperlad/2 standard is considered. Key features of the physical layer specification of the Hiperlad/2 standard are summarised and those aspects that are particularly relevant when considering the use of the PFE are highlighted. A Hiperlad/2 ...

  19. Spectral pulsed-wave tissue Doppler imaging lateral-to-septal delay fails to predict clinical or echocardiographic outcome after cardiac resynchronization therapy

    NARCIS (Netherlands)

    O.I.I. Soliman (Osama Ibrahim Ibrahim); D.A.M.J. Theuns (Dominic); M.L. Geleijnse (Marcel); A. Nemes (Attila); K. Caliskan (Kadir); W.B. Vletter (Wim); L.J.L.M. Jordaens (Luc); F.J. ten Cate (Folkert)

    2007-01-01

    textabstractAims: The current study sought to assess if pre-implantation lateral-to-septal delay (LSD) ≥60 ms assessed by spectral pulsed-wave myocardial tissue Doppler imaging (PW-TDI) could predict successful long-term outcome after cardiac resynchronization therapy (CRT). Methods and results

  20. Exploiting selective excitation of strongly coupled modes to reduce DMGD in multi-mode transmission systems

    NARCIS (Netherlands)

    van Weerdenburg, J.J.A.; Antonio-Lopez, J.E.; Alvarado-Zacarias, J.; Molin, D.; Bigot-Astruc, M.; van Uden, R.; de Waardt, H.; Koonen, A.M.J.; Amezcua-Correa, R.; Sillard, P.; Okonkwo, C.M.

    2016-01-01

    By exploiting strong coupling in higher-order modes, we experimentally demonstrate reduced differential mode group delay by a factor of 3. Comparing LP02+LP21 with respect to LP01+LP11 3-mode transmission, a 27% reduction in equalizer length is shown after 53.4km MMF transmission.

  1. A New Design Strategy for Efficient Thermally Activated Delayed Fluorescence Organic Emitters: From Twisted to Planar Structures

    KAUST Repository

    Chen, Xiankai; Tsuchiya, Youichi; Ishikawa, Yuma; Zhong, Cheng; Adachi, Chihaya; Bredas, Jean-Luc

    2017-01-01

    In the traditional molecular design of thermally activated delayed fluorescence (TADF) emitters composed of electron-donor and electron-acceptor moieties, achieving a small singlet-triplet energy gap (ΔEST ) in strongly twisted structures usually

  2. Partial Sequencing of 16S rRNA Gene of Selected Staphylococcus aureus Isolates and its Antibiotic Resistance

    Directory of Open Access Journals (Sweden)

    Harsi Dewantari Kusumaningrum

    2016-08-01

    Full Text Available The choice of primer used in 16S rRNA sequencing for identification of Staphylococcus species found in food is important. This study aimed to characterize Staphylococcus aureus isolates by partial sequencing based on 16S rRNA gene employing primers 16sF, 63F or 1387R. The isolates were isolated from milk, egg dishes and chicken dishes and selected based on the presence of sea gene that responsible for formation of enterotoxin-A. Antibiotic susceptibility of the isolates towards six antibiotics was also tested. The use of 16sF resulted generally in higher identity percentage and query coverage compared to the sequencing by 63F or 1387R. BLAST results of all isolates, sequenced by 16sF, showed 99% homology to complete genome of four S. aureus strains, with different characteristics on enterotoxin production and antibiotic resistance. Considering that all isolates were carrying sea gene, indicated by the occurence of 120 bp amplicon after PCR amplification using primer SEA1/SEA2,  the isolates were most in agreeing to S. aureus subsp. aureus ST288. This study indicated that 4 out of 8 selected isolates were resistant towards streptomycin. The 16S rRNA gene sequencing using 16sF is useful for identification of S. aureus. However, additional analysis such as PCR employing specific gene target, should give a valuable supplementary information, when specific characteristic is expected.

  3. Big bang nucleosynthesis: The strong nuclear force meets the weak anthropic principle

    International Nuclear Information System (INIS)

    MacDonald, J.; Mullan, D. J.

    2009-01-01

    Contrary to a common argument that a small increase in the strength of the strong force would lead to destruction of all hydrogen in the big bang due to binding of the diproton and the dineutron with a catastrophic impact on life as we know it, we show that provided the increase in strong force coupling constant is less than about 50% substantial amounts of hydrogen remain. The reason is that an increase in strong force strength leads to tighter binding of the deuteron, permitting nucleosynthesis to occur earlier in the big bang at higher temperature than in the standard big bang. Photodestruction of the less tightly bound diproton and dineutron delays their production to after the bulk of nucleosynthesis is complete. The decay of the diproton can, however, lead to relatively large abundances of deuterium.

  4. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment

    DEFF Research Database (Denmark)

    Sahm, K.; MacGregor, BJ; Jørgensen, BB

    1999-01-01

    In the past, enumeration of sulphate-reducing bacteria (SRB) by cultivation-based methods generally contradicted measurements of sulphate reduction, suggesting unrealistically high respiration rates per cell. Here, we report evidence that quantification of SRB rRNA by slot-blot hybridization......, directly above the sulphate reduction maximum. Cell numbers calculated by converting the relative contribution of SRB rRNA to the percentage of DAPI-stained cells indicated a population size for SRB of 2.4-6.1 x 10(8) cells cm(-3) wet sediment. Cellular sulphate reduction rates calculated on the basis...

  5. Prosthetic joint infection due to Lysobacter thermophilus diagnosed by 16S rRNA gene sequencing

    Directory of Open Access Journals (Sweden)

    B Dhawan

    2016-01-01

    Full Text Available We report the first case of prosthetic joint infection caused by Lysobacter thermophilus which was identified by 16S rRNA gene sequencing. Removal of prosthesis followed by antibiotic treatment resulted in good clinical outcome. This case illustrates the use of molecular diagnostics to detect uncommon organisms in suspected prosthetic infections.

  6. Strong-Field Control of Laser Filamentation Mechanisms

    Science.gov (United States)

    Levis, Robert; Romanov, Dmitri; Filin, Aleskey; Compton, Ryan

    2008-05-01

    The propagation of short strong-file laser pulses in gas and solution phases often result in formation of filaments. This phenomenon involves many nonlinear processes including Kerr lensing, group velocity dispersion, multi-photon ionization, plasma defocusing, intensity clamping, and self-steepening. Of these, formation and dynamics of pencil-shape plasma areas plays a crucial role. The fundamental understanding of these laser-induced plasmas requires additional effort, because the process is highly nonlinear and complex. We studied the ultrafast laser-generated plasma dynamics both experimentally and theoretically. Ultrafast plasma dynamics was probed using Coherent Anti-Stokes Raman Scattering. The measurements were made in a room temperature gas maintained at 1 atm in a flowing cell. The time dependent scattering was measured by delaying the CARS probe with respect to the intense laser excitation pulse. A general trend is observed between the spacing of the ground state and the first allowed excited state with the rise time for the noble gas series and the molecular gases. This trend is consistent with our theoretical model, which considers the ultrafast dynamics of the strong field generated plasma as a three-step process; (i) strong-field ionization followed by the electron gaining considerable kinetic energy during the pulse; (ii) immediate post-pulse dynamics: fast thermalization, impact-ionization-driven electron multiplication and cooling; (iii) ensuing relaxation: evolution to electron-ion equilibrium and eventual recombination.

  7. Phylogenetic relationships between Sarcocystis species from reindeer and other Sarcocystidae deduced from ssu rRNA gene sequences

    DEFF Research Database (Denmark)

    Dahlgren, S.S.; Oliveira, Rodrigo Gouveia; Gjerde, B.

    2008-01-01

    any effect on previously inferred phylogenetic relationships within the Sarcocystidae. The complete small subunit (ssu) rRNA gene sequences of all six Sarcocystis species from reindeer were used in the phylogenetic analyses along with ssu rRNA gene sequences of 85 other members of the Coccidea. Trees...... the six species in phylogenetic analyses of the Sarcocystidae, and also to investigate the phylogenetic relationships between the species from reindeer and those from other hosts. The study also aimed at revealing whether the inclusion of six Sarcocystis species from the same intermediate host would have....... tarandivulpes, formed a sister group to other Sarcocystis species with a canine definitive host. The position of S. hardangeri on the tree suggested that it uses another type of definitive host than the other Sarcocystis species in this clade. Considering the geographical distribution and infection intensity...

  8. The Cfr rRNA methyltransferase confers resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibiotics

    DEFF Research Database (Denmark)

    Long, K. S.; Poehlsgaard, Jacob; Kehrenberg, C.

    2006-01-01

    to overlapping sites at the peptidyl transferase center that abut nucleotide A2503, is perturbed upon Cfr-mediated methylation. Decreased drug binding to Cfr-methylated ribosomes has been confirmed by footprinting analysis. No other rRNA methyltransferase is known to confer resistance to five chemically distinct...

  9. Polybacterial community analysis in human conjunctiva through 16S rRNA gene libraries.

    Science.gov (United States)

    Deepthi, KrishnanNair Geetha; Jayasudha, Rajagopalaboopathi; Girish, Rameshan Nair; Manikandan, Palanisamy; Ram, Rammohan; Narendran, Venkatapathy; Prabagaran, Solai Ramatchandirane

    2018-05-14

    The conjunctival sac of healthy human harbours a variety of microorganisms. When the eye is compromised, an occasional inadvertent spread happens to the adjacent tissue, resulting in bacterial ocular infections. Microbiological investigation of the conjunctival swab is one of the broadly used modality to study the aetiological agent of conjunctiva. However, most of the time such methods yield unsatisfactory results. Hence, the present study intends to identify the bacterial community in human conjunctiva of pre-operative subjects through 16S rRNA gene libraries. Out of 45 samples collected from preoperative patients undergoing cataract surgery, 36 libraries were constructed with bacterial nested-PCR-positive samples. The representative clones with unique restriction pattern were generated through Amplified Ribosomal DNA Restriction Analysis (ARDRA) which were sequenced for phylogenetic affiliation. A total of 211 representative clones were obtained which were distributed in phyla Actinobacteria, Firmicutes, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, and Deinococcus-Thermus. Findings revealed the presence of polybacterial community, especially in some cases even though no bacterium or a single bacterium alone was identified through cultivable method. Remarkably, we identified 17 species which have never been reported in any ocular infections. The sequencing data reported 6 unidentified bacteria suggesting the possibility of novel organisms in the sample. Since, polybacterial community has been identified consisting of both gram positive and gram negative bacteria, a broad spectrum antibiotic therapy is advisable to the patients who are undergoing cataract surgery. Consolidated effort would significantly improve a clear understanding of the nature of microbial community in the human conjunctiva which will promote administration of appropriate antibiotic regimen and also help in the development of oligonucleotide probes to screen the

  10. Time and decision making: differential contribution of the posterior insular cortex and the striatum during a delay discounting task.

    Science.gov (United States)

    Wittmann, Marc; Leland, David S; Paulus, Martin P

    2007-06-01

    Delay discounting refers to the fact that an immediate reward is valued more than the same reward if it occurs some time in the future. To examine the neural substrates underlying this process, we studied 13 healthy volunteers who repeatedly had to decide between an immediate and parametrically varied delayed hypothetical reward using a delay discounting task during event-related functional magnetic resonance imaging. Subject's preference judgments resulted in different discounting slopes for shorter ( or =1 year) delays. Neural activation associated with the shorter delays relative to the longer delays was associated with increased activation in the head of the left caudate nucleus and putamen. When individuals selected the delayed relative to the immediate reward, a strong activation was found in bilateral posterior insular cortex. Several brain areas including the left caudate nucleus showed a correlation between the behaviorally determined discounting and brain activation for the contrast of intervals with delays or =1 year. These results suggest that (1) the posterior insula, which is a critical component of the decision-making neural network, is involved in delaying gratification and (2) the degree of neural activation in the striatum, which plays a fundamental role in reward prediction and in time estimation, may code for the time delay.

  11. Expressive language of two year-old pre-term and full-term children.

    Science.gov (United States)

    Isotani, Selma Mie; Azevedo, Marisa Frasson de; Chiari, Brasília Maria; Perissinoto, Jacy

    2009-01-01

    expressive language of pre-term children. to compare the expressive vocabulary of two year-old children born prematurely, to that of those born at term. the study sample was composed by 118 speech-language assessment protocols, divided in two groups: the pre-term group (PTG) composed by 58 underweight premature children followed by a multi-professional team at the Casa do Prematuro (House of Premature Children) at Unifesp, and the full-term group (FTG) composed by 60 full-term born children. In order to evaluate the expressive language of these children, the Lave - Lista de Avaliação do Vocabulário Expressivo (Assessment List of the Expressive Vocabulary) was used. The Lave is an adaptation of the LDS - Language Development Survey - for the Brazilian Portuguese Language. The Lave investigates the expressive language and detects delays in oral language. children born underweight and prematurely present a greater occurrence of expressive language delay, 27.6%. These pre-term children present significantly lower expressive vocabulary and phrasal extension than children of the same age born at full-term in all semantic categories. Family income proved to be positively associated to phrasal extension, as well as to gestational age and weight at birth; thus indicating the effect of these adverse conditions still during the third year of age. The audiological status was associated to word utterances in the PTG. children born prematurely and underweight are at risk in terms of vocabulary development; this determines the need for speech-therapy intervention programs.

  12. [Phylogeny of protostome moulting animals (Ecdysozoa) inferred from 18 and 28S rRNA gene sequences].

    Science.gov (United States)

    Petrov, N B; Vladychenskaia, N S

    2005-01-01

    Reliability of reconstruction of phylogenetic relationships within a group of protostome moulting animals was evaluated by means of comparison of 18 and 28S rRNA gene sequences sets both taken separately and combined. Reliability of reconstructions was evaluated by values of the bootstrap support of major phylogenetic tree nodes and by degree of congruence of phylogenetic trees inferred by various methods. By both criteria, phylogenetic trees reconstructed from the combined 18 and 28S rRNA gene sequences were better than those inferred from 18 and 28S sequences taken separately. Results obtained are consistent with phylogenetic hypothesis separating protostome animals into two major clades, moulting Ecdysozoa (Priapulida + Kinorhyncha, Nematoda + Nematomorpha, Onychophora + Tardigrada, Myriapoda + Chelicerata, Crustacea + Hexapoda) and unmoulting Lophotrochozoa (Plathelminthes, Nemertini, Annelida, Mollusca, Echiura, Sipuncula). Clade Cephalorhyncha does not include nematomorphs (Nematomorpha). Conclusion was taken that it is necessary to use combined 18 and 28S data in phylogenetic studies.

  13. Delay-dependent stability of neural networks of neutral type with time delay in the leakage term

    International Nuclear Information System (INIS)

    Li, Xiaodi; Cao, Jinde

    2010-01-01

    This paper studies the global asymptotic stability of neural networks of neutral type with mixed delays. The mixed delays include constant delay in the leakage term (i.e. 'leakage delay'), time-varying delays and continuously distributed delays. Based on the topological degree theory, Lyapunov method and linear matrix inequality (LMI) approach, some sufficient conditions are derived ensuring the existence, uniqueness and global asymptotic stability of the equilibrium point, which are dependent on both the discrete and distributed time delays. These conditions are expressed in terms of LMI and can be easily checked by the MATLAB LMI toolbox. Even if there is no leakage delay, the obtained results are less restrictive than some recent works. It can be applied to neural networks of neutral type with activation functions without assuming their boundedness, monotonicity or differentiability. Moreover, the differentiability of the time-varying delay in the non-neutral term is removed. Finally, two numerical examples are given to show the effectiveness of the proposed method

  14. Direct 16S rRNA gene sequencing of polymicrobial culture-negative samples with analysis of mixed chromatograms

    DEFF Research Database (Denmark)

    Hartmeyer, Gitte N; Justesen, Ulrik S

    2010-01-01

    Two cases involving polymicrobial culture-negative samples were investigated by 16S rRNA gene sequencing, with analysis of mixed chromatograms. Fusobacterium necrophorum, Prevotella intermedia and Streptococcus constellatus were identified from pleural fluid in a patient with Lemierre's syndrome...

  15. Prices, wages and fertility in pre-industrial England

    DEFF Research Database (Denmark)

    Klemp, Marc Patrick Brag

    2012-01-01

    and relative prices to affect fertility. The model is estimated using new data for the pre-industrial period in England, and the analysis reveals a strong, positive effect of agricultural wages as well as a nonnegative effect of real agricultural prices on fertility. Furthermore, it is demonstrated......To shed light on the economic-demographic mechanisms operating in the epoch of pre-industrial economic stagnation, a two-sector Malthusian model is formulated in terms of a cointegrated vector autoregressive model on error correction form. The model allows for both agricultural product wages...

  16. Me, Myself, and Money II: Relative Deprivation Predicts Disordered Gambling Severity via Delay Discounting, Especially Among Gamblers Who Have a Financially Focused Self-Concept.

    Science.gov (United States)

    Tabri, Nassim; Will Shead, N; Wohl, Michael J A

    2017-12-01

    In the current research, we examined whether the known link between relative deprivation and disordered gambling (via delay discounting; i.e., preferences for immediate smaller rewards relative to delayed larger rewards) is moderated by the extent to which gamblers have a financially focused self-concept. Specifically, we hypothesized that delay discounting would be a strong predictor of disordered gambling among those who base their self-worth on their financial success. To test this moderated-mediation model, a community sample of gamblers (N = 239) completed measures that assessed relative deprivation, delay discounting, financially focused self-concept, and disordered gambling severity. As predicted, people who felt more relative deprivation reported more severe symptoms of disordered gambling and this association was mediated by delay discounting. Importantly, this mediated relationship was moderated by the extent to which participants' self-concept was focused on financial success. Among participants whose self-concept was high in financial focus, greater delay discounting (stemming from relative deprivation) was a strong predictor of disordered gambling. Among people whose self-concept was low in financial focus, delay discounting (stemming from relative deprivation) was a weak predictor of disordered gambling. Thus, the magnitude of the indirect effect of relative deprivation on disordered gambling severity was larger among people with a more financially focused self-concept-an effect mediated by delay discounting. These findings suggest that targeting gamblers' financial focus in prevention and treatment interventions may be instrumental in curtailing the development and maintenance of disordered gambling.

  17. American Dream Delayed

    DEFF Research Database (Denmark)

    Khorunzhina, Natalia; Miller, Robert A.

    This paper investigates the delay in homeownership and a subsequent reduction in homeownership rate observed over the past decades. We focus on the delay in giving birth to children and increased labor market participation as contributing factors to homeownership dynamics for prime-age female hou...

  18. Delayed Orgasm and Anorgasmia

    OpenAIRE

    Jenkins, Lawrence C.; Mulhall, John P.

    2015-01-01

    Delayed orgasm/anorgasmia defined as the persistent or recurrent difficulty, delay in, or absence of attaining orgasm after sufficient sexual stimulation, which causes personal distress. Delayed orgasm and anorgasmia are associated with significant sexual dissatisfaction. A focused medical history can shed light on the potential etiologies; which include: medications, penile sensation loss, endocrinopathies, penile hyperstimulation and psychological etiologies, amongst others. Unfortunately, ...

  19. Evaluation of performance of distributed delay model for chemotherapy-induced myelosuppression.

    Science.gov (United States)

    Krzyzanski, Wojciech; Hu, Shuhua; Dunlavey, Michael

    2018-04-01

    The distributed delay model has been introduced that replaces the transit compartments in the classic model of chemotherapy-induced myelosuppression with a convolution integral. The maturation of granulocyte precursors in the bone marrow is described by the gamma probability density function with the shape parameter (ν). If ν is a positive integer, the distributed delay model coincides with the classic model with ν transit compartments. The purpose of this work was to evaluate performance of the distributed delay model with particular focus on model deterministic identifiability in the presence of the shape parameter. The classic model served as a reference for comparison. Previously published white blood cell (WBC) count data in rats receiving bolus doses of 5-fluorouracil were fitted by both models. The negative two log-likelihood objective function (-2LL) and running times were used as major markers of performance. Local sensitivity analysis was done to evaluate the impact of ν on the pharmacodynamics response WBC. The ν estimate was 1.46 with 16.1% CV% compared to ν = 3 for the classic model. The difference of 6.78 in - 2LL between classic model and the distributed delay model implied that the latter performed significantly better than former according to the log-likelihood ratio test (P = 0.009), although the overall performance was modestly better. The running times were 1 s and 66.2 min, respectively. The long running time of the distributed delay model was attributed to computationally intensive evaluation of the convolution integral. The sensitivity analysis revealed that ν strongly influences the WBC response by controlling cell proliferation and elimination of WBCs from the circulation. In conclusion, the distributed delay model was deterministically identifiable from typical cytotoxic data. Its performance was modestly better than the classic model with significantly longer running time.

  20. A review of literature on delays in seeking care for tuberculosis in different Indian states

    Directory of Open Access Journals (Sweden)

    Janmejaya Samal

    2017-01-01

    Full Text Available The passive case-finding approach of Revised National Tuberculosis (TB Control Programme in India strongly affects the health-seeking behavior of TB patients, the timing of help seeking as well as the subsequent delays associated with the same. Studies carried out in different parts of India reveal a host of several factors for delay in seeking help and the reasons for not seeking help at all. Important reasons for delayed health-seeking behavior include financial constraint, symptoms are not severe (as perceived by the patients, work pressure, lack of awareness, first consulted nonpublic sector, inaccessibility to health facility, home remedy, social stigma, self-medication, transport problem, and dissatisfaction with health facility. Similarly, the median patient delay ranged from 7 to 56 days as reported by various studies. Health-seeking behavior and related delays are of utmost importance in TB care from two important perspectives; first, TB requires timely treatment, and second, it requires protracted treatment. Required level of knowledge and a positive health behavior helps the patients in taking timely help from an appropriate health facility. Moreover, timely help-seeking prevents further spread of the disease and helps in establishing a TB-free society.

  1. Derivation and computation of discrete-delay and continuous-delay SDEs in mathematical biology.

    Science.gov (United States)

    Allen, Edward J

    2014-06-01

    Stochastic versions of several discrete-delay and continuous-delay differential equations, useful in mathematical biology, are derived from basic principles carefully taking into account the demographic, environmental, or physiological randomness in the dynamic processes. In particular, stochastic delay differential equation (SDDE) models are derived and studied for Nicholson's blowflies equation, Hutchinson's equation, an SIS epidemic model with delay, bacteria/phage dynamics, and glucose/insulin levels. Computational methods for approximating the SDDE models are described. Comparisons between computational solutions of the SDDEs and independently formulated Monte Carlo calculations support the accuracy of the derivations and of the computational methods.

  2. Acute gallbladder torsion - a continued pre-operative diagnostic dilemma

    Directory of Open Access Journals (Sweden)

    Desrochers Randal

    2011-04-01

    Full Text Available Abstract Acute gallbladder volvulus continues to remain a relatively uncommon process, manifesting itself usually during exploration for an acute surgical abdomen with a presumptive diagnosis of acute cholecystitis. The pathophysiology is that of mechanical organo-axial torsion along the gallbladder's longitudinal axis involving the cystic duct and cystic artery, and with a pre-requisite of local mesenteric redundancy. The demographic tendency is septua- and octo-genarians of the female sex, and its overall incidence is increasing, this being attributed to increasing life expectancy. We discuss two cases of elderly, fragile women presenting to the emergency department complaining of sudden onset right upper quadrant abdominal pain. Their subsequent evaluation suggested acute cholecystitis. Ultimately both were taken to the operating room where the correct diagnosis of gallbladder torsion was made. Pre-operative diagnosis continues to be a major challenge with only 4 cases reported in the literature diagnosed with pre-operative imaging; the remainder were found intra-operatively. Consequently, a delay in diagnosis can have devastating patient outcomes. Herein we propose a necessary high index of suspicion for gallbladder volvulus in the outlined patient demographic with symptoms and signs mimicking acute cholecystitis.

  3. Rapid detection of rRNA group I pseudomonads in contaminated metalworking fluids and biofilm formation by fluorescent in situ hybridization.

    Science.gov (United States)

    Saha, Ratul; Donofrio, Robert S; Goeres, Darla M; Bagley, Susan T

    2012-05-01

    Metalworking fluids (MWFs), used in different machining operations, are highly prone to microbial degradation. Microbial communities present in MWFs lead to biofilm formation in the MWF systems, which act as a continuous source of contamination. Species of rRNA group I Pseudomonas dominate in contaminated MWFs. However, their actual distribution is typically underestimated when using standard culturing techniques as most fail to grow on the commonly used Pseudomonas Isolation Agar. To overcome this, fluorescent in situ hybridization (FISH) was used to study their abundance along with biofilm formation by two species recovered from MWFs, Pseudomonas fluorescens MWF-1 and the newly described Pseudomonas oleovorans subsp. lubricantis. Based on 16S rRNA sequences, a unique fluorescent molecular probe (Pseudo120) was designed targeting a conserved signature sequence common to all rRNA group I Pseudomonas. The specificity of the probe was evaluated using hybridization experiments with whole cells of different Pseudomonas species. The probe's sensitivity was determined to be 10(3) cells/ml. It successfully detected and enumerated the abundance and distribution of Pseudomonas indicating levels between 3.2 (± 1.1) × 10(6) and 5.0 (± 2.3) × 10(6) cells/ml in four different industrial MWF samples collected from three different locations. Biofilm formation was visualized under stagnant conditions using high and low concentrations of cells for both P. fluorescens MWF-1 and P. oleovorans subsp. lubricantis stained with methylene blue and Pseudo120. On the basis of these observations, this molecular probe can be successfully be used in the management of MWF systems to monitor the levels and biofilm formation of rRNA group I pseudomonads.

  4. Attosecond Delays in Molecular Photoionization.

    Science.gov (United States)

    Huppert, Martin; Jordan, Inga; Baykusheva, Denitsa; von Conta, Aaron; Wörner, Hans Jakob

    2016-08-26

    We report measurements of energy-dependent photoionization delays between the two outermost valence shells of N_{2}O and H_{2}O. The combination of single-shot signal referencing with the use of different metal foils to filter the attosecond pulse train enables us to extract delays from congested spectra. Remarkably large delays up to 160 as are observed in N_{2}O, whereas the delays in H_{2}O are all smaller than 50 as in the photon-energy range of 20-40 eV. These results are interpreted by developing a theory of molecular photoionization delays. The long delays measured in N_{2}O are shown to reflect the population of molecular shape resonances that trap the photoelectron for a duration of up to ∼110 as. The unstructured continua of H_{2}O result in much smaller delays at the same photon energies. Our experimental and theoretical methods make the study of molecular attosecond photoionization dynamics accessible.

  5. Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay.

    Directory of Open Access Journals (Sweden)

    Jun Yang

    Full Text Available Ribosomes are large ribonucleoprotein complexes that are fundamental for protein synthesis. Ribosomes are ribozymes because their catalytic functions such as peptidyl transferase and peptidyl-tRNA hydrolysis depend on the rRNA. rRNA is a heterogeneous biopolymer comprising of at least 112 chemically modified residues that are believed to expand its topological potential. In the present study, we established a comprehensive modification profile of Saccharomyces cerevisiae's 18S and 25S rRNA using a high resolution Reversed-Phase High Performance Liquid Chromatography (RP-HPLC. A combination of mung bean nuclease assay, rDNA point mutants and snoRNA deletions allowed us to systematically map all ribose and base modifications on both rRNAs to a single nucleotide resolution. We also calculated approximate molar levels for each modification using their UV (254nm molar response factors, showing sub-stoichiometric amount of modifications at certain residues. The chemical nature, their precise location and identification of partial modification will facilitate understanding the precise role of these chemical modifications, and provide further evidence for ribosome heterogeneity in eukaryotes.

  6. Virtual unit delay for digital frequency adaptive T/4 delay phase-locked loop system

    DEFF Research Database (Denmark)

    Yang, Yongheng; Zhou, Keliang; Blaabjerg, Frede

    2016-01-01

    /processor with a fixed sampling rate considering the cost and complexity, where the number of unit delays that have been adopted should be an integer. For instance, in conventional digital control systems, a single-phase T/4 Delay Phase-Locked Loop (PLL) system takes 50 unit delays (i.e., in a 50-Hz system...... Delay PLL system should be done in its implementation. This process will result in performance degradation in the digital control system, as the exactly required number of delays is not realized. Hence, in this paper, a Virtual Unit Delay (VUD) has been proposed to address such challenges to the digital......Digital micro-controllers/processors enable the cost-effective control of grid-connected power converter systems in terms of system monitoring, signal processing (e.g., grid synchronization), control (e.g., grid current and voltage control), etc. Normally, the control is implemented in a micro-controller...

  7. Anti-replicative recombinant 5S rRNA molecules can modulate the mtDNA heteroplasmy in a glucose-dependent manner.

    Science.gov (United States)

    Loutre, Romuald; Heckel, Anne-Marie; Jeandard, Damien; Tarassov, Ivan; Entelis, Nina

    2018-01-01

    Mutations in mitochondrial DNA are an important source of severe and incurable human diseases. The vast majority of these mutations are heteroplasmic, meaning that mutant and wild-type genomes are present simultaneously in the same cell. Only a very high proportion of mutant mitochondrial DNA (heteroplasmy level) leads to pathological consequences. We previously demonstrated that mitochondrial targeting of small RNAs designed to anneal with mutant mtDNA can decrease the heteroplasmy level by specific inhibition of mutant mtDNA replication, thus representing a potential therapy. We have also shown that 5S ribosomal RNA, partially imported into human mitochondria, can be used as a vector to deliver anti-replicative oligoribonucleotides into human mitochondria. So far, the efficiency of cellular expression of recombinant 5S rRNA molecules bearing therapeutic insertions remained very low. In the present study, we designed new versions of anti-replicative recombinant 5S rRNA targeting a large deletion in mitochondrial DNA which causes the KSS syndrome, analyzed their specific annealing to KSS mitochondrial DNA and demonstrated their import into mitochondria of cultured human cells. To obtain an increased level of the recombinant 5S rRNA stable expression, we created transmitochondrial cybrid cell line bearing a site for Flp-recombinase and used this system for the recombinase-mediated integration of genes coding for the anti-replicative recombinant 5S rRNAs into nuclear genome. We demonstrated that stable expression of anti-replicative 5S rRNA versions in human transmitochondrial cybrid cells can induce a shift in heteroplasmy level of KSS mutation in mtDNA. This shift was directly dependent on the level of the recombinant 5S rRNA expression and the sequence of the anti-replicative insertion. Quantification of mtDNA copy number in transfected cells revealed the absence of a non-specific effect on wild type mtDNA replication, indicating that the decreased proportion

  8. Information transfer via implicit encoding with delay time modulation in a time-delay system

    Energy Technology Data Exchange (ETDEWEB)

    Kye, Won-Ho, E-mail: whkye@kipo.go.kr [Korean Intellectual Property Office, Government Complex Daejeon Building 4, 189, Cheongsa-ro, Seo-gu, Daejeon 302-701 (Korea, Republic of)

    2012-08-20

    A new encoding scheme for information transfer with modulated delay time in a time-delay system is proposed. In the scheme, the message is implicitly encoded into the modulated delay time. The information transfer rate as a function of encoding redundancy in various noise scales is presented and it is analyzed that the implicit encoding scheme (IES) has stronger resistance against channel noise than the explicit encoding scheme (EES). In addition, its advantages in terms of secure communication and feasible applications are discussed. -- Highlights: ► We propose new encoding scheme with delay time modulation. ► The message is implicitly encoded with modulated delay time. ► The proposed scheme shows stronger resistance against channel noise.

  9. Diversity, Dynamics, and Activity of Bacterial Communities during Production of an Artisanal Sicilian Cheese as Evaluated by 16S rRNA Analysis†

    OpenAIRE

    Randazzo, Cinzia L.; Torriani, Sandra; Akkermans, Antoon D. L.; de Vos, Willem M.; Vaughan, Elaine E.

    2002-01-01

    The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes (rDNA). Bacterial and Lactobacillus group-specific primers were used to amplify the V6 to V8 and V1 to V3 regions of the 16S rRNA gene...

  10. Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples.

    Directory of Open Access Journals (Sweden)

    Jennifer J Barb

    Full Text Available There is much speculation on which hypervariable region provides the highest bacterial specificity in 16S rRNA sequencing. The optimum solution to prevent bias and to obtain a comprehensive view of complex bacterial communities would be to sequence the entire 16S rRNA gene; however, this is not possible with second generation standard library design and short-read next-generation sequencing technology.This paper examines a new process using seven hypervariable or V regions of the 16S rRNA (six amplicons: V2, V3, V4, V6-7, V8, and V9 processed simultaneously on the Ion Torrent Personal Genome Machine (Life Technologies, Grand Island, NY. Four mock samples were amplified using the 16S Ion Metagenomics Kit™ (Life Technologies and their sequencing data is subjected to a novel analytical pipeline.Results are presented at family and genus level. The Kullback-Leibler divergence (DKL, a measure of the departure of the computed from the nominal bacterial distribution in the mock samples, was used to infer which region performed best at the family and genus levels. Three different hypervariable regions, V2, V4, and V6-7, produced the lowest divergence compared to the known mock sample. The V9 region gave the highest (worst average DKL while the V4 gave the lowest (best average DKL. In addition to having a high DKL, the V9 region in both the forward and reverse directions performed the worst finding only 17% and 53% of the known family level and 12% and 47% of the genus level bacteria, while results from the forward and reverse V4 region identified all 17 family level bacteria.The results of our analysis have shown that our sequencing methods using 6 hypervariable regions of the 16S rRNA and subsequent analysis is valid. This method also allowed for the assessment of how well each of the variable regions might perform simultaneously. Our findings will provide the basis for future work intended to assess microbial abundance at different time points

  11. High-speed Imaging of Vocal Fold Vibration Onset Delay: Normal Versus Abnormal.

    Science.gov (United States)

    Woo, Peak

    2017-05-01

    Vocal fold vibration onset delay (VFVOD) is heard frequently in spasmodic dysphonia and in muscle tension dysphonia. VFVOD changes due to other vocal pathologies have not been investigated. VFVOD during sustained vowel production was estimated with high-speed video in 10 normal and 40 pathologic subjects (scars, vocal fold paralysis, vocal fold nodules, and polyps). Analysis of high-speed video was done using digital kymography. VFVOD can be divided into two portions. Pre-phonation delay (PPD) is the duration when the vocal folds are nearly approximated to the time of first observed oscillation. Steady state delay (SSD) is the time when vocal folds are observed to come into oscillation until steady state of oscillation is observed. Normal subjects have almost zero PPD with vocal fold oscillation observed before full vocal fold adduction. Pathologic cases showed prolonged PPD because of (1) false cord adduction, (2) prolonged true vocal fold adduction, and (3) delay to onset of vocal fold vibration. Normal subjects have SSD of three to five cycles before steady state. Pathologic states result in increased SSD. Causes for increased SSD include (1) slow ramping up to steady state, (2) partial vibration of vocal folds, and (3) diplophonia with alternating beats before achieving steady state. There are significant differences between normal and pathology groups in both PPD and SSD. VFVOD is elevated in pathologic states. This can be due to increase in PPD or SSD. VFVOD is an under-recognized phenomenon that may contribute to complaints of vocal fatigue and dysphonia. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  12. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

    Directory of Open Access Journals (Sweden)

    Robert C. Edgar

    2018-04-01

    Full Text Available Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%, all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. Accuracy was found to fall rapidly with identity; for example, better methods were found to have V4 genus prediction accuracy of ∼100% at 100% identity but ∼50% at 97% identity. The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal.

  13. Exploiting Pre-rRNA Processing in Diamond Blackfan Anemia Gene Discovery and Diagnosis

    Science.gov (United States)

    Farrar, Jason E.; Quarello, Paola; Fisher, Ross; O’Brien, Kelly A.; Aspesi, Anna; Parrella, Sara; Henson, Adrianna L.; Seidel, Nancy E.; Atsidaftos, Eva; Prakash, Supraja; Bari, Shahla; Garelli, Emanuela; Arceci, Robert J.; Dianzani, Irma; Ramenghi, Ugo; Vlachos, Adrianna; Lipton, Jeffrey M.; Bodine, David M.; Ellis, Steven R.

    2014-01-01

    Diamond Blackfan anemia (DBA), a syndrome primarily characterized by anemia and physical abnormalities, is one among a group of related inherited bone marrow failure syndromes (IBMFS) which share overlapping clinical features. Heterozygous mutations or single-copy deletions have been identified in 12 ribosomal protein genes in approximately 60% of DBA cases, with the genetic etiology unexplained in most remaining patients. Unlike many IBMFS, for which functional screening assays complement clinical and genetic findings, suspected DBA in the absence of typical alterations of the known genes must frequently be diagnosed after exclusion of other IBMFS. We report here a novel deletion in a child that presented such a diagnostic challenge and prompted development of a novel functional assay that can assist in the diagnosis of a significant fraction of patients with DBA. The ribosomal proteins affected in DBA are required for pre-rRNA processing, a process which can be interrogated to monitor steps in the maturation of 40S and 60S ribosomal subunits. In contrast to prior methods used to assess pre-rRNA processing, the assay reported here, based on capillary electrophoresis measurement of the maturation of rRNA in pre-60S ribosomal subunits, would be readily amenable to use in diagnostic laboratories. In addition to utility as a diagnostic tool, we applied this technique to gene discovery in DBA, resulting in the identification of RPL31 as a novel DBA gene. PMID:25042156

  14. The Effects of Combinations of Cognitive Impairment and Pre-frailty on Adverse Outcomes from a Prospective Community-Based Cohort Study of Older Chinese People

    Directory of Open Access Journals (Sweden)

    Ruby Yu

    2018-03-01

    Full Text Available ObjectivesTo examine how various combinations of cognitive impairment (overall performance and specific domains and pre-frailty predict risks of adverse outcomes; and to determine whether cognitive frailty may be defined as the combination of cognitive impairment and the presence of pre-frailty.DesignCommunity-based cohort study.ParticipantsChinese men and women (n = 3,491 aged 65+ without dementia, Parkinson’s disease and/or frailty at baseline.MeasurementsFrailty was characterized using the Cardiovascular Health Study criteria. Overall cognitive impairment was defined by a Cantonese Mini-Mental Status Examination (CMMSE total score (<21/24/27, depending on participants’ educational levels; delayed recall impairment by a CMMSE delayed recall score (<3; and language and praxis impairment by a CMMSE language and praxis score (<9. Adverse outcomes included poor quality of life, physical limitation, increased cumulative hospital stay, and mortality.ResultsCompared to those who were robust and cognitively intact at baseline, those who were robust but cognitively impaired were more likely to develop pre-frailty/frailty after 4 years (P < 0.01. Compared to participants who were robust and cognitively intact at baseline, those who were pre-frail and with overall cognitive impairment had lower grip strength (P < 0.05, lower gait speed (P < 0.01, poorer lower limb strength (P < 0.01, and poorer delayed recall at year 4 [OR, 1.6; 95% confidence interval (CI, 1.2–2.3]. They were also associated with increased risks of poor quality of life (OR, 1.5; 95% CI, 1.1–2.2 and incident physical limitation at year 4 (OR, 1.8; 95% CI, 1.3–2.5, increased cumulative hospital stay at year 7 (OR, 1.5; 95% CI, 1.1–2.1, and mortality over an average of 12 years (OR, 1.5; 95% CI, 1.0–2.1 after adjustment for covariates. There was no significant difference in risks of adverse outcomes between participants who were pre-frail, with

  15. SSU rRNA reveals a sequential increase in shell complexity among the euglyphid testate amoebae (Rhizaria: Euglyphida)

    DEFF Research Database (Denmark)

    Lara, Enrique; Heger, Thierry J; Mitchell, Edward A D

    2007-01-01

    The existing data on the molecular phylogeny of filose testate amoebae from order Euglyphida has revealed contradictions between traditional morphological classification and SSU rRNA phylogeny and, moreover, the position of several important genera remained unknown. We therefore carried out a stu...

  16. Recognition of Potentially Novel Human Disease-Associated Pathogens by Implementation of Systematic 16S rRNA Gene Sequencing in the Diagnostic Laboratory▿ †

    Science.gov (United States)

    Keller, Peter M.; Rampini, Silvana K.; Büchler, Andrea C.; Eich, Gerhard; Wanner, Roger M.; Speck, Roberto F.; Böttger, Erik C.; Bloemberg, Guido V.

    2010-01-01

    Clinical isolates that are difficult to identify by conventional means form a valuable source of novel human pathogens. We report on a 5-year study based on systematic 16S rRNA gene sequence analysis. We found 60 previously unknown 16S rRNA sequences corresponding to potentially novel bacterial taxa. For 30 of 60 isolates, clinical relevance was evaluated; 18 of the 30 isolates analyzed were considered to be associated with human disease. PMID:20631113

  17. Impulsive control of time-delay systems using delayed impulse and its application to impulsive master-slave synchronization

    International Nuclear Information System (INIS)

    Sun Jitao; Han Qinglong; Jiang Xiefu

    2008-01-01

    This Letter is concerned with impulsive control of a class of nonlinear time-delay systems. Some uniform stability criteria for the closed-loop time-delay system under delayed impulsive control are derived by using piecewise Lyapunov functions. Then the criteria are applied to impulsive master-slave synchronization of some secure communication systems with transmission delays and sample delays under delayed impulsive control. Two numerical examples are given to illustrate the effectiveness of the derived results

  18. Delayed hydrogen cracking test design for pressure tubes

    International Nuclear Information System (INIS)

    Haddad, Roberto; Loberse, Antonio N.; Yawny, Alejandro A.; Riquelme, Pablo

    1999-01-01

    CANDU nuclear power stations pressure tubes of alloy Zr-2,5 % Nb present a cracking phenomenon known as delayed hydrogen cracking (DHC). This is a brittle fracture of zirconium hydrides that are developed by hydrogen due to aqueous corrosion on the metal surface. This hydrogen diffuses to the crack tip where brittle zirconium hydrides develops and promotes the crack propagation. A direct current potential decay (DCPD) technique has been developed to measure crack propagation rates on compact test (CT) samples machined from a non irradiated pressure tube. Those test samples were hydrogen charged by cathodic polarization in an acid solution and then pre cracked in a fatigue machine. This technique proved to be useful to measure crack propagation rates with at least 1% accuracy for DHC in pressure tubes. (author)

  19. SHARP - III. First use of adaptive-optics imaging to constrain cosmology with gravitational lens time delays

    NARCIS (Netherlands)

    Chen, Geoff C. -F; Suyu, Sherry H.; Wong, Kenneth C.; Fassnacht, Christopher D.; Chiueh, Tzihong; Halkola, Aleksi; Hu, I. Shing; Auger, Matthew W.; Koopmans, Léon V. E.; Lagattuta, David J.; McKean, John P.; Vegetti, Simona

    2016-01-01

    Accurate and precise measurements of the Hubble constant are critical for testing our current standard cosmological model and revealing possibly new physics. With Hubble Space Telescope (HST) imaging, each strong gravitational lens system with measured time delays can allow one to determine the

  20. Prehospital delay in acute coronary syndrome--an analysis of the components of delay

    DEFF Research Database (Denmark)

    Ottesen, Michael Mundt; Dixen, Ulrik; Torp-Pedersen, Christian

    2004-01-01

    BACKGROUND: Prompt hospital admission is essential when treating acute coronary syndrome. Delay prior to admission is unnecessarily long. Therefore, a thorough scrutiny of the influence of characteristics, circumstantial and subjective variables on elements of prehospital delay among patients...... admitted with acute coronary syndrome is warranted. METHODS: A structured interview was conducted on 250 consecutive patients admitted alive with acute coronary syndrome. RESULTS: Median prehospital, decision, physician and transportation delays were 107, 74, 25 and 22 min, respectively. Women (n=77) had...... of acute coronary syndrome among women, and thereby contributes to unnecessary long delay to treatment. The patient's prior experience and interpretation has a significant influence on behaviour....

  1. Communication key using delay times in time-delayed chaos synchronization

    International Nuclear Information System (INIS)

    Kim, Chil-Min; Kye, Won-Ho; Rim, Sunghwan; Lee, Soo-Young

    2004-01-01

    We propose an efficient key scheme, which can generate a great number of communication keys, for communication using chaos synchronization. We have attained the keys from delay times of time-delay coupled chaotic systems. We explain the scheme and the efficiency by coupling Henon and logistic maps and illustrate them by coupling Navier-Stokes and Lorenz equations as a continuous system

  2. Severe hyperparathyroidism in a pre-dialysis chronic kidney disease patient treated with a very low protein diet.

    Science.gov (United States)

    Ohta, Eriko; Akazawa, Masanobu; Noda, Yumi; Mandai, Shintaro; Naito, Shotaro; Ohta, Akihito; Sohara, Eisei; Okado, Tomokazu; Rai, Tatemitsu; Uchida, Shinichi; Sasaki, Sei

    2012-03-01

    The present report describes a case of a 64-year-old pre-dialysis woman with chronic kidney disease (CKD) stage 5, who developed severe hyperparathyroidism. This patient had been on a very low protein diet (VLPD) to delay the progression of CKD and the need for renal replacement therapy (RRT). Her serum calcium levels were high-normal to slightly high during this time. However, her serum intact parathyroid hormone (PTH) levels increased from 400 to 1160 pg/ml rapidly over a period of 3 months. Serum 1,25-(OH)2D levels were low, and ultrasound of the neck showed three markedly enlarged parathyroid glands exceeding 2 cm. Parathyroidectomy was performed, and all glands showed nodular hyperplasia, which indicated severe secondary hyperparathyroidism leading to tertiary. Severe secondary hyperparathyroidism requiring surgical intervention is usually observed in patients with long-term RRT and is relatively rare in the pre-dialysis patient. In this case, extension of the pre-dialysis period by VLPD may have predisposed this patient to develop severe secondary hyperparathyroidism. Thus, careful monitoring of calcium, phosphorus, and PTH may be necessary in patients treated with VLPD even before renal replacement therapy. Furthermore, initiation of dialysis should not be excessively delayed by strict protein restriction dietary therapy.

  3. Interaction of the tylosin-resistance methyltransferase RlmA II at its rRNA target differs from the orthologue RlmA I

    DEFF Research Database (Denmark)

    Douthwaite, Stephen; Jakobsen, Lene; Yoshizawa, Satoko

    2008-01-01

    of Gram-positive bacteria, including the tylosin-producer Streptomyces fradiae and the pathogen Streptococcus pneumoniae. Recombinant S. pneumoniae RlmA(II) was purified and shown to retain its activity and specificity in vitro when tested on unmethylated 23 S rRNA substrates. RlmA(II) makes multiple......RlmA(II) methylates the N1-position of nucleotide G748 in hairpin 35 of 23 S rRNA. The resultant methyl group extends into the peptide channel of the 50 S ribosomal subunit and confers resistance to tylosin and other mycinosylated macrolide antibiotics. Methylation at G748 occurs in several groups...

  4. Identification of Bacillus Probiotics Isolated from Soil Rhizosphere Using 16S rRNA, recA, rpoB Gene Sequencing and RAPD-PCR.

    Science.gov (United States)

    Mohkam, Milad; Nezafat, Navid; Berenjian, Aydin; Mobasher, Mohammad Ali; Ghasemi, Younes

    2016-03-01

    Some Bacillus species, especially Bacillus subtilis and Bacillus pumilus groups, have highly similar 16S rRNA gene sequences, which are hard to identify based on 16S rDNA sequence analysis. To conquer this drawback, rpoB, recA sequence analysis along with randomly amplified polymorphic (RAPD) fingerprinting was examined as an alternative method for differentiating Bacillus species. The 16S rRNA, rpoB and recA genes were amplified via a polymerase chain reaction using their specific primers. The resulted PCR amplicons were sequenced, and phylogenetic analysis was employed by MEGA 6 software. Identification based on 16S rRNA gene sequencing was underpinned by rpoB and recA gene sequencing as well as RAPD-PCR technique. Subsequently, concatenation and phylogenetic analysis showed that extent of diversity and similarity were better obtained by rpoB and recA primers, which are also reinforced by RAPD-PCR methods. However, in one case, these approaches failed to identify one isolate, which in combination with the phenotypical method offsets this issue. Overall, RAPD fingerprinting, rpoB and recA along with concatenated genes sequence analysis discriminated closely related Bacillus species, which highlights the significance of the multigenic method in more precisely distinguishing Bacillus strains. This research emphasizes the benefit of RAPD fingerprinting, rpoB and recA sequence analysis superior to 16S rRNA gene sequence analysis for suitable and effective identification of Bacillus species as recommended for probiotic products.

  5. Variation in secondary structure of the 16S rRNA molecule in cyanobacteria with implications for phylogenetic analysis

    Czech Academy of Sciences Publication Activity Database

    Řeháková, Klára; Johansen, J. R.; Bowen, M.B.; Martin, M.P.; Sheil, C.A.

    2014-01-01

    Roč. 14, č. 2 (2014), s. 161-178 ISSN 1802-5439 Institutional support: RVO:60077344 Keywords : 16S rRNA secondary structure * cyanobacteria * phylogeny Subject RIV: EE - Microbiology, Virology Impact factor: 1.930, year: 2014

  6. Influence of pre-infarction angina, collateral flow, and pre-procedural TIMI flow on myocardial salvage index by cardiac magnetic resonance in patients with ST-segment elevation myocardial infarction.

    Science.gov (United States)

    Lønborg, Jacob; Kelbæk, Henning; Vejlstrup, Niels; Bøtker, Hans Erik; Kim, Won Yong; Holmvang, Lene; Jørgensen, Erik; Helqvist, Steffen; Saunamäki, Kari; Thuesen, Leif; Krusell, Lars Romer; Clemmensen, Peter; Engstrøm, Thomas

    2012-05-01

    In patients with ST-segment elevation myocardial infarction (STEMI) pre-infarction angina, pre-procedural TIMI flow and collateral flow to the myocardium supplied by the infarct related artery are suggested to be cardioprotective. We evaluated the effect of these factors on myocardial salvage index (MSI) and infarct size adjusting for area at risk in patients with STEMI treated with primary percutaneous coronary intervention. Cardiac magnetic resonance (CMR) was used to measure myocardial area at risk within 1-7 days and final infarct size 90 ± 21 days after the STEMI in 200 patients. MSI was calculated as (area-at-risk infarct size) / area-at-risk. Patients with pre-infarction angina had a median MSI of 0.80 (IQR 0.67 to 0.86) versus 0.72 (0.61 to 0.80) in those without pre-infarction angina, P = 0.004). In a regression analysis of the infarct size plotted against the area-at-risk there was a strong trend that the line for the pre-infarction angina group was below the one for the non-angina group (P = 0.05). Patients with pre-procedural TIMI flow 0/1, 2 and 3 had a median MSI of (0.69 (IQR 0.59 to 0.76), 0.78 (0.68 to 0.86) and 0.85 (0.77 to 0.91), respectively (PCollateral flow did not change MSI (P = 0.45) nor area-at-risk (P = 0.40) and no significant difference in infarct size adjusted for area at risk (P = 0.25) was observed. Pre-infarction angina increases MSI in patients with STEMI supporting the theory that pre-infarction angina leads to ischemic preconditioning. As opposed to the presence of angiographically visible collateral flow to the infarct area pre-procedural TIMI flow is strongly associated with MSI.

  7. Pre-service teachers’ challenges in presenting mathematical problems

    Science.gov (United States)

    Desfitri, R.

    2018-01-01

    The purpose of this study was to analyzed how pre-service teachers prepare and assigned tasks or assignments in teaching practice situations. This study was also intended to discuss about kind of tasks or assignments they gave to students. Participants of this study were 15 selected pre-service mathematics teachers from mathematics education department who took part on microteaching class as part of teaching preparation program. Based on data obtained, it was occasionally found that there were hidden errors on questions or tasks assigned by pre-service teachers which might lead their students not to be able to reach a logical or correct answer. Although some answers might seem to be true, they were illogical or unfavourable. It is strongly recommended that pre-service teachers be more careful when posing mathematical problems so that students do not misunderstand the problems or the concepts, since both teachers and students were sometimes unaware of errors in problems being worked on.

  8. Mitochondrial respiratory complex I probed by delayed luminescence spectroscopy

    Science.gov (United States)

    Baran, Irina; Ionescu, Diana; Privitera, Simona; Scordino, Agata; Mocanu, Maria Magdalena; Musumeci, Francesco; Grasso, Rosaria; Gulino, Marisa; Iftime, Adrian; Tofolean, Ioana Teodora; Garaiman, Alexandru; Goicea, Alexandru; Irimia, Ruxandra; Dimancea, Alexandru; Ganea, Constanta

    2013-12-01

    The role of mitochondrial complex I in ultraweak photon-induced delayed photon emission [delayed luminescence (DL)] of human leukemia Jurkat T cells was probed by using complex I targeting agents like rotenone, menadione, and quercetin. Rotenone, a complex I-specific inhibitor, dose-dependently increased the mitochondrial level of reduced nicotinamide adenine dinucleotide (NADH), decreased clonogenic survival, and induced apoptosis. A strong correlation was found between the mitochondrial levels of NADH and oxidized flavin mononucleotide (FMNox) in rotenone-, menadione- and quercetin-treated cells. Rotenone enhanced DL dose-dependently, whereas quercetin and menadione inhibited DL as well as NADH or FMNox. Collectively, the data suggest that DL of Jurkat cells originates mainly from mitochondrial complex I, which functions predominantly as a dimer and less frequently as a tetramer. In individual monomers, both pairs of pyridine nucleotide (NADH/reduced nicotinamide adenine dinucleotide phosphate) sites and flavin (FMN-a/FMN-b) sites appear to bind cooperatively their specific ligands. Enhancement of delayed red-light emission by rotenone suggests that the mean time for one-electron reduction of ubiquinone or FMN-a by the terminal Fe/S center (N2) is 20 or 284 μs, respectively. All these findings suggest that DL spectroscopy could be used as a reliable, sensitive, and robust technique to probe electron flow within complex I in situ.

  9. The Effects of Combinations of Cognitive Impairment and Pre-frailty on Adverse Outcomes from a Prospective Community-Based Cohort Study of Older Chinese People.

    Science.gov (United States)

    Yu, Ruby; Morley, John E; Kwok, Timothy; Leung, Jason; Cheung, Osbert; Woo, Jean

    2018-01-01

    To examine how various combinations of cognitive impairment (overall performance and specific domains) and pre-frailty predict risks of adverse outcomes; and to determine whether cognitive frailty may be defined as the combination of cognitive impairment and the presence of pre-frailty. Community-based cohort study. Chinese men and women ( n  = 3,491) aged 65+ without dementia, Parkinson's disease and/or frailty at baseline. Frailty was characterized using the Cardiovascular Health Study criteria. Overall cognitive impairment was defined by a Cantonese Mini-Mental Status Examination (CMMSE) total score (impairment by a CMMSE delayed recall score (impairment by a CMMSE language and praxis score (impaired were more likely to develop pre-frailty/frailty after 4 years ( P  impairment had lower grip strength ( P  without cognitive impairment at baseline. Similar results were obtained with delayed recall and language and praxis impairments. Robust and cognitively impaired participants had higher risks of becoming pre-frail/frail over 4 years compared with those with normal cognition. Cognitive impairment characterized by the CMMSE overall score or its individual domain score improved the predictive power of pre-frailty for poor quality of life, incident physical limitation, increased cumulative hospital stay, and mortality. Our findings support to the concept that cognitive frailty may be defined as the occurrence of both cognitive impairment and pre-frailty, not necessarily progressing to dementia.

  10. Electron-capture delayed fission properties of neutron-deficient einsteinium nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Shaughnessy, Dawn A. [Univ. of California, Berkeley, CA (United States)

    2000-01-01

    Electron-capture delayed fission (ECDF) properties of neutron-deficient einsteinium isotopes were investigated using a combination of chemical separations and on-line radiation detection methods. 242Es was produced via the 233U(14N,5n)242Es reaction at a beam energy of 87 MeV (on target) in the lab system, and was found to decay with a half-life of 11 ± 3 seconds. The ECDF of 242Es showed a highly asymmetric mass distribution with an average pre-neutron emission total kinetic energy (TKE) of 183 ± 18 MeV. The probability of delayed fission (PDF) was measured to be 0.006 ± 0.002. In conjunction with this experiment, the excitation functions of the 233U(14N,xn)247-xEs and 233U(15N,xn)248-xEs reactions were measured for 243Es, 244Es and 245Es at projectile energies between 80 MeV and 100 MeV.

  11. Vehicle barrier with access delay

    Science.gov (United States)

    Swahlan, David J; Wilke, Jason

    2013-09-03

    An access delay vehicle barrier for stopping unauthorized entry into secure areas by a vehicle ramming attack includes access delay features for preventing and/or delaying an adversary from defeating or compromising the barrier. A horizontally deployed barrier member can include an exterior steel casing, an interior steel reinforcing member and access delay members disposed within the casing and between the casing and the interior reinforcing member. Access delay members can include wooden structural lumber, concrete and/or polymeric members that in combination with the exterior casing and interior reinforcing member act cooperatively to impair an adversarial attach by thermal, mechanical and/or explosive tools.

  12. rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-Resistant Staphylococcus aureus

    NARCIS (Netherlands)

    Fluit, A.C.; Jansen, M.D.; Bosch, T.; Jansen, W.T.M.; Schouls, L.; Jonker, M.J.; Boel, C.H.E.

    2016-01-01

    The distinct epidemiology of original hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) and early community-associated MRSA (CA-MRSA) is largely unexplained. S. aureus carries either five or six rRNA operon copies. Evidence is provided for a scenario in which MRSA has adapted

  13. Precise delay measurement through combinatorial logic

    Science.gov (United States)

    Burke, Gary R. (Inventor); Chen, Yuan (Inventor); Sheldon, Douglas J. (Inventor)

    2010-01-01

    A high resolution circuit and method for facilitating precise measurement of on-chip delays for FPGAs for reliability studies. The circuit embeds a pulse generator on an FPGA chip having one or more groups of LUTS (the "LUT delay chain"), also on-chip. The circuit also embeds a pulse width measurement circuit on-chip, and measures the duration of the generated pulse through the delay chain. The pulse width of the output pulse represents the delay through the delay chain without any I/O delay. The pulse width measurement circuit uses an additional asynchronous clock autonomous from the main clock and the FPGA propagation delay can be displayed on a hex display continuously for testing purposes.

  14. Improving Delay-Range-Dependent Stability Condition for Systems with Interval Time-Varying Delay

    Directory of Open Access Journals (Sweden)

    Wei Qian

    2013-01-01

    Full Text Available This paper discusses the delay-range-dependent stability for systems with interval time-varying delay. Through defining the new Lyapunov-Krasovskii functional and estimating the derivative of the LKF by introducing new vectors, using free matrices and reciprocally convex approach, the new delay-range-dependent stability conditions are obtained. Two well-known examples are given to illustrate the less conservatism of the proposed theoretical results.

  15. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David; Stingl, Ulrich

    2012-01-01

    that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While

  16. Observation of the Avalanche of Runaway Electrons in Air in a Strong Electric Field

    Science.gov (United States)

    Gurevich, A. V.; Mesyats, G. A.; Zybin, K. P.; Yalandin, M. I.; Reutova, A. G.; Shpak, V. G.; Shunailov, S. A.

    2012-08-01

    The generation of an avalanche of runaway electrons is demonstrated for the first time in a laboratory experiment. Two flows of runaway electrons are formed sequentially in an extended air discharge gap at the stage of delay of a pulsed breakdown. The first, picosecond, runaway electron flow is emitted in the cathode region where the field is enhanced. Being accelerated in the gap, this beam generates electrons due to impact ionization. These secondary electrons form a delayed avalanche of runaway electrons if the field is strong enough. The properties of the avalanche correspond to the existing notions about the runaway breakdown in air. The measured current of the avalanche exceeds up to an order the current of the initiating electron beam.

  17. Modeling of delays in PKPD: classical approaches and a tutorial for delay differential equations.

    Science.gov (United States)

    Koch, Gilbert; Krzyzanski, Wojciech; Pérez-Ruixo, Juan Jose; Schropp, Johannes

    2014-08-01

    In pharmacokinetics/pharmacodynamics (PKPD) the measured response is often delayed relative to drug administration, individuals in a population have a certain lifespan until they maturate or the change of biomarkers does not immediately affects the primary endpoint. The classical approach in PKPD is to apply transit compartment models (TCM) based on ordinary differential equations to handle such delays. However, an alternative approach to deal with delays are delay differential equations (DDE). DDEs feature additional flexibility and properties, realize more complex dynamics and can complementary be used together with TCMs. We introduce several delay based PKPD models and investigate mathematical properties of general DDE based models, which serve as subunits in order to build larger PKPD models. Finally, we review current PKPD software with respect to the implementation of DDEs for PKPD analysis.

  18. A delay fractioning approach to global synchronization of delayed complex networks with stochastic disturbances

    International Nuclear Information System (INIS)

    Wang Yao; Wang Zidong; Liang Jinling

    2008-01-01

    In this Letter, the synchronization problem is investigated for a class of stochastic complex networks with time delays. By utilizing a new Lyapunov functional form based on the idea of 'delay fractioning', we employ the stochastic analysis techniques and the properties of Kronecker product to establish delay-dependent synchronization criteria that guarantee the globally asymptotically mean-square synchronization of the addressed delayed networks with stochastic disturbances. These sufficient conditions, which are formulated in terms of linear matrix inequalities (LMIs), can be solved efficiently by the LMI toolbox in Matlab. The main results are proved to be much less conservative and the conservatism could be reduced further as the number of delay fractioning gets bigger. A simulation example is exploited to demonstrate the advantage and applicability of the proposed result

  19. A distributed delay approach for modeling delayed outcomes in pharmacokinetics and pharmacodynamics studies.

    Science.gov (United States)

    Hu, Shuhua; Dunlavey, Michael; Guzy, Serge; Teuscher, Nathan

    2018-04-01

    A distributed delay approach was proposed in this paper to model delayed outcomes in pharmacokinetics and pharmacodynamics studies. This approach was shown to be general enough to incorporate a wide array of pharmacokinetic and pharmacodynamic models as special cases including transit compartment models, effect compartment models, typical absorption models (either zero-order or first-order absorption), and a number of atypical (or irregular) absorption models (e.g., parallel first-order, mixed first-order and zero-order, inverse Gaussian, and Weibull absorption models). Real-life examples were given to demonstrate how to implement distributed delays in Phoenix ® NLME™ 8.0, and to numerically show the advantages of the distributed delay approach over the traditional methods.

  20. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing.

    Science.gov (United States)

    Chan, Chia Sing; Chan, Kok-Gan; Tay, Yea-Ling; Chua, Yi-Heng; Goh, Kian Mau

    2015-01-01

    The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0-9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.