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Sample records for delays pre-rrna processing

  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. 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.

  3. 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....

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

    Science.gov (United States)

    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.

  5. 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.

  6. 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.

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

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    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.

  8. 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.

  9. 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)

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

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    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

  11. 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.

  12. 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.

  13. 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...

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

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

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    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.

  3. Downregulation of rRNA transcription triggers cell differentiation.

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    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.

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

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    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.

  5. 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.

  6. 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

  7. 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.

  8. 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 .

  9. Time delay of quantum scattering processes

    International Nuclear Information System (INIS)

    Martin, P.A.

    1981-01-01

    The author presents various aspects of the theory of the time delay of scattering processes. The author mainly studies non-relativistic two-body scattering processes, first summarizing briefly the theory of simple scattering systems. (Auth.)

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

    Science.gov (United States)

    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

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. 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

  14. Practical Secure Computation with Pre-Processing

    DEFF Research Database (Denmark)

    Zakarias, Rasmus Winther

    Secure Multiparty Computation has been divided between protocols best suited for binary circuits and protocols best suited for arithmetic circuits. With their MiniMac protocol in [DZ13], Damgård and Zakarias take an important step towards bridging these worlds with an arithmetic protocol tuned...... space for pre-processing material than computing the non-linear parts online (depends on the quality of circuit of course). Surprisingly, even for our optimized AES-circuit this is not the case. We further improve the design of the pre-processing material and end up with only 10 megabyes of pre...... a protocol for small field arithmetic to do fast large integer multipli- cations. This is achieved by devising pre-processing material that allows the Toom-Cook multiplication algorithm to run between the parties with linear communication complexity. With this result computation on the CPU by the parties...

  15. 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

  16. The impact of processing delay on the exposure index value

    Science.gov (United States)

    Butler, M. L.; Brennan, P. C.; Last, J.; Rainford, L.

    2010-04-01

    Digital radiography poses the risk of unnoticed increases in patient dose. Manufacturers responded to this by offering an exposure index (EI) value to clinicians. Use of the EI value in clinical practice is encouraged by the American College of Radiology and American Association of Physicists in Medicine. This study assesses the impact of processing delay on the EI value. An anthropormorphic phantom was used to simulate three radiographic examinations; skull, pelvis and chest. For each examination, the phantom was placed in the optimal position and exposures were chosen in accordance with international guidelines. A Carestream (previously Kodak) computed radiography system was used. The imaging plate was exposed, and processing was delayed in various increments from 30 seconds to 24 hours, representing common delays in clinical practice. The EI value was recorded for each exposure. The EI value decreased considerably with increasing processing delay. The EI value decreased by 100 within 25 minutes delay for the chest, and 20 minutes for the skull and pelvis. Within 1 hour, the EI value had fallen by 180, 160 and 100 for the chest, skull and pelvis respectively. After 24 hours, the value had decreased by 370, 350 and 340 for the chest, skull and pelvis respectively, representing to the clinician more then a halving of exposure to the detector in Carestream systems. The assessment of images using EI values should be approached with caution in clinical practice when delays in processing occur. The use of EI values as a feedback mechanism is questioned.

  17. EARLINET Single Calculus Chain - technical - Part 1: Pre-processing of raw lidar data

    Science.gov (United States)

    D'Amico, Giuseppe; Amodeo, Aldo; Mattis, Ina; Freudenthaler, Volker; Pappalardo, Gelsomina

    2016-02-01

    In this paper we describe an automatic tool for the pre-processing of aerosol lidar data called ELPP (EARLINET Lidar Pre-Processor). It is one of two calculus modules of the EARLINET Single Calculus Chain (SCC), the automatic tool for the analysis of EARLINET data. ELPP is an open source module that executes instrumental corrections and data handling of the raw lidar signals, making the lidar data ready to be processed by the optical retrieval algorithms. According to the specific lidar configuration, ELPP automatically performs dead-time correction, atmospheric and electronic background subtraction, gluing of lidar signals, and trigger-delay correction. Moreover, the signal-to-noise ratio of the pre-processed signals can be improved by means of configurable time integration of the raw signals and/or spatial smoothing. ELPP delivers the statistical uncertainties of the final products by means of error propagation or Monte Carlo simulations. During the development of ELPP, particular attention has been payed to make the tool flexible enough to handle all lidar configurations currently used within the EARLINET community. Moreover, it has been designed in a modular way to allow an easy extension to lidar configurations not yet implemented. The primary goal of ELPP is to enable the application of quality-assured procedures in the lidar data analysis starting from the raw lidar data. This provides the added value of full traceability of each delivered lidar product. Several tests have been performed to check the proper functioning of ELPP. The whole SCC has been tested with the same synthetic data sets, which were used for the EARLINET algorithm inter-comparison exercise. ELPP has been successfully employed for the automatic near-real-time pre-processing of the raw lidar data measured during several EARLINET inter-comparison campaigns as well as during intense field campaigns.

  18. 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.

  19. The Effects of Test Trial and Processing Level on Immediate and Delayed Retention

    Science.gov (United States)

    Chang, Sau Hou

    2017-01-01

    The purpose of the present study was to investigate the effects of test trial and processing level on immediate and delayed retention. A 2 × 2 × 2 mixed ANOVAs was used with two between-subject factors of test trial (single test, repeated test) and processing level (shallow, deep), and one within-subject factor of final recall (immediate, delayed). Seventy-six college students were randomly assigned first to the single test (studied the stimulus words three times and took one free-recall test) and the repeated test trials (studied the stimulus words once and took three consecutive free-recall tests), and then to the shallow processing level (asked whether each stimulus word was presented in capital letter or in small letter) and the deep processing level (whether each stimulus word belonged to a particular category) to study forty stimulus words. The immediate test was administered five minutes after the trials, whereas the delayed test was administered one week later. Results showed that single test trial recalled more words than repeated test trial in immediate final free-recall test, participants in deep processing performed better than those in shallow processing in both immediate and delayed retention. However, the dominance of single test trial and deep processing did not happen in delayed retention. Additional study trials did not further enhance the delayed retention of words encoded in deep processing, but did enhance the delayed retention of words encoded in shallow processing. PMID:28344679

  20. The Effects of Test Trial and Processing Level on Immediate and Delayed Retention.

    Science.gov (United States)

    Chang, Sau Hou

    2017-03-01

    The purpose of the present study was to investigate the effects of test trial and processing level on immediate and delayed retention. A 2 × 2 × 2 mixed ANOVAs was used with two between-subject factors of test trial (single test, repeated test) and processing level (shallow, deep), and one within-subject factor of final recall (immediate, delayed). Seventy-six college students were randomly assigned first to the single test (studied the stimulus words three times and took one free-recall test) and the repeated test trials (studied the stimulus words once and took three consecutive free-recall tests), and then to the shallow processing level (asked whether each stimulus word was presented in capital letter or in small letter) and the deep processing level (whether each stimulus word belonged to a particular category) to study forty stimulus words. The immediate test was administered five minutes after the trials, whereas the delayed test was administered one week later. Results showed that single test trial recalled more words than repeated test trial in immediate final free-recall test, participants in deep processing performed better than those in shallow processing in both immediate and delayed retention. However, the dominance of single test trial and deep processing did not happen in delayed retention. Additional study trials did not further enhance the delayed retention of words encoded in deep processing, but did enhance the delayed retention of words encoded in shallow processing.

  1. The Effects of Test Trial and Processing Level on Immediate and Delayed Retention

    Directory of Open Access Journals (Sweden)

    Sau Hou Chang

    2017-03-01

    Full Text Available The purpose of the present study was to investigate the effects of test trial and processing level on immediate and delayed retention. A 2 × 2 × 2 mixed ANOVAs was used with two between-subject factors of test trial (single test, repeated test and processing level (shallow, deep, and one within-subject factor of final recall (immediate, delayed. Seventy-six college students were randomly assigned first to the single test (studied the stimulus words three times and took one free-recall test and the repeated test trials (studied the stimulus words once and took three consecutive free-recall tests, and then to the shallow processing level (asked whether each stimulus word was presented in capital letter or in small letter and the deep processing level (whether each stimulus word belonged to a particular category to study forty stimulus words. The immediate test was administered five minutes after the trials, whereas the delayed test was administered one week later. Results showed that single test trial recalled more words than repeated test trial in immediate final free-recall test, participants in deep processing performed better than those in shallow processing in both immediate and delayed retention. However, the dominance of single test trial and deep processing did not happen in delayed retention. Additional study trials did not further enhance the delayed retention of words encoded in deep processing, but did enhance the delayed retention of words encoded in shallow processing.

  2. 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

  3. 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

  4. 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

  5. Relationships between processing delay and microbial load of broiler neck skin samples.

    Science.gov (United States)

    Lucianez, A; Holmes, M A; Tucker, A W

    2010-01-01

    The measurable microbial load on poultry carcasses during processing is determined by a number of factors including farm or origin, processing hygiene, and external temperature. This study investigated associations between carcass microbial load and progressive delays to processing. A total of 30 carcasses were delayed immediately after defeathering and before evisceration in a commercial abattoir in groups of five, and were held at ambient temperature for 1, 2, 3, 4, 6, and 8 h. Delayed carcasses were reintroduced to the processing line, and quantitative assessment of total viable count, coliforms, Staphylococcus aureus, and Pseudomonas spp. was undertaken on neck skin flap samples collected after carcass chilling and then pooled for each group. Sampling was repeated on 5 separate days, and the data were combined. Significant increases in total viable count (P = 0.001) and coliforms (P = 0.004), but not for S. aureus or Pseudomonas loads, were observed across the 8-h period of delay. In line with previous studies, there was significant variation in microbiological data according to sampling day. In conclusion, there is a significant and measurable decline in microbiological status of uneviscerated but defeathered poultry carcasses after an 8-h delay, but the variability of sampling results, reflecting the wide range of factors that impact microbial load, means that it is not possible to determine maximum or minimum acceptable periods of processing delay based on this criterion alone.

  6. 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.

  7. 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.

  8. Delay oil oxidation during frying process

    International Nuclear Information System (INIS)

    Atta, N.M.M.; Shams Eldin, N.M.M.

    2010-01-01

    Blend oil (mixed of refined sunflower and soy beans oils 1:1 w/w) containing add 200 ppm of rosemary leaves methanolic extract (rosemary extract) (RE) and 3% refined rice bran oil (RRBO), were used in frying process at 1800 degree c for 5 hrs/ day, four consecutive days to delay oil oxidation during frying. Therefore, rosemary extract (methanolic extract) was analyzed by HPLC technique for identification of flavonoids compounds (as a specific active compounds; gives high protection to frying oil). Physical and chemical properties, including refractive index(RI). Red color unit (R), viscosity, acidity (FFA), peroxide value (PV), iodine value (IV) oxidized fatty acid (OFA), polymer content (PC), total polar components (TPC) and trans fatty acid (TFA) as eliadic acid were determined. The results indicated that; rosemary extract contained about eight flavonoids compounds (hypersoid, rutin, 3-OH flavon, luleotin, kempferol, sakarutin, querectrin and apeginin). Addition of RE or RRBO to frying oil caused delay oil oxidation during frying process compared with frying oil without any addition. Also, the results indicated that rosemary extract was more effective in reducing formation of PV, FFA, OFA, PC, TPC and TFA in frying oil than refined rice bran oil

  9. Opportunities for Process Monitoring Techniques at Delayed Access Facilities

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, Michael M.; Gitau, Ernest TN; Johnson, Shirley J.; Schanfein, Mark; Toomey, Christopher

    2013-09-20

    Except for specific cases where the International Atomic Energy Agency (IAEA) maintains a continuous presence at a facility (such as the Japanese Rokkasho Reprocessing Plant), there is always a period of time or delay between the moment a State is notified or aware of an upcoming inspection, and the time the inspector actually enters the material balance area or facility. Termed by the authors as “delayed access,” this period of time between inspection notice and inspector entrance to a facility poses a concern. Delayed access also has the potential to reduce the effectiveness of measures applied as part of the Safeguards Approach for a facility (such as short-notice inspections). This report investigates the feasibility of using process monitoring to address safeguards challenges posed by delayed access at a subset of facility types.

  10. 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.

  11. The 1996 ENDF pre-processing codes

    International Nuclear Information System (INIS)

    Cullen, D.E.

    1996-01-01

    The codes are named 'the Pre-processing' codes, because they are designed to pre-process ENDF/B data, for later, further processing for use in applications. This is a modular set of computer codes, each of which reads and writes evaluated nuclear data in the ENDF/B format. Each code performs one or more independent operations on the data, as described below. These codes are designed to be computer independent, and are presently operational on every type of computer from large mainframe computer to small personal computers, such as IBM-PC and Power MAC. The codes are available from the IAEA Nuclear Data Section, free of charge upon request. (author)

  12. 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…

  13. 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.

  14. Systematic identification and robust control design for uncertain time delay processes

    DEFF Research Database (Denmark)

    Huusom, Jakob Kjøbsted; Poulsen, Niels Kjølstad; Jørgensen, Sten Bay

    2011-01-01

    A systematic procedure is proposed to handle the standard process control problem. The considered standard problem involves infrequent step disturbances to processes with large delays and measurement noise. The process is modeled as an ARX model and extended with a suitable noise model in order...... to reject unmeasured step disturbances and unavoidable model errors. This controller is illustrated to perform well for both set point tracking and a disturbance rejection for a SISO process example of a furnace which has a time delay which is significantly longer than the dominating time constant....

  15. NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikatsu, Yuki [Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, Tokushima 770-8506 (Japan); Ishida, Yo-ichi; Sudo, Haruka [Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Yuasa, Keizo; Tsuji, Akihiko [Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, Tokushima 770-8506 (Japan); Nagahama, Masami, E-mail: nagahama@my-pharm.ac.jp [Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan)

    2015-08-28

    Nuclear VCP-like 2 (NVL2) is a member of the chaperone-like AAA-ATPase family and is involved in the biosynthesis of 60S ribosomal subunits in mammalian cells. We previously showed the interaction of NVL2 with a DExD/H-box RNA helicase MTR4/DOB1, which is a known cofactor for an exoribonuclease complex, the exosome. This finding implicated NVL2 in RNA metabolic processes during ribosome biogenesis. In the present study, we found that a series of mutations within the ATPase domain of NVL2 causes a defect in pre-rRNA processing into mature 28S and 5.8S rRNAs. Co-immunoprecipitation analysis showed that NVL2 was associated with the nuclear exosome complex, which includes RRP6 as a nucleus-specific catalytic subunit. This interaction was prevented by depleting either MTR4 or RRP6, indicating their essential role in mediating this interaction with NVL2. Additionally, knockdown of MPP6, another cofactor for the nuclear exosome, also prevented the interaction by causing MTR4 to dissociate from the nuclear exosome. These results suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex. - Highlights: • ATPase-deficient mutants of NVL2 have decreased pre-rRNA processing. • NVL2 associates with the nuclear exosome through interactions with MTR4 and RRP6. • MPP6 stabilizes MTR4-RRP6 interaction and allows NVL2 to interact with the complex.

  16. Stationary distributions of stochastic processes described by a linear neutral delay differential equation

    International Nuclear Information System (INIS)

    Frank, T D

    2005-01-01

    Stationary distributions of processes are derived that involve a time delay and are defined by a linear stochastic neutral delay differential equation. The distributions are Gaussian distributions. The variances of the Gaussian distributions are either monotonically increasing or decreasing functions of the time delays. The variances become infinite when fixed points of corresponding deterministic processes become unstable. (letter to the editor)

  17. NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing.

    Science.gov (United States)

    Yoshikatsu, Yuki; Ishida, Yo-ichi; Sudo, Haruka; Yuasa, Keizo; Tsuji, Akihiko; Nagahama, Masami

    2015-08-28

    Nuclear VCP-like 2 (NVL2) is a member of the chaperone-like AAA-ATPase family and is involved in the biosynthesis of 60S ribosomal subunits in mammalian cells. We previously showed the interaction of NVL2 with a DExD/H-box RNA helicase MTR4/DOB1, which is a known cofactor for an exoribonuclease complex, the exosome. This finding implicated NVL2 in RNA metabolic processes during ribosome biogenesis. In the present study, we found that a series of mutations within the ATPase domain of NVL2 causes a defect in pre-rRNA processing into mature 28S and 5.8S rRNAs. Co-immunoprecipitation analysis showed that NVL2 was associated with the nuclear exosome complex, which includes RRP6 as a nucleus-specific catalytic subunit. This interaction was prevented by depleting either MTR4 or RRP6, indicating their essential role in mediating this interaction with NVL2. Additionally, knockdown of MPP6, another cofactor for the nuclear exosome, also prevented the interaction by causing MTR4 to dissociate from the nuclear exosome. These results suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Integration Processes of Delay Differential Equation Based on Modified Laguerre Functions

    Directory of Open Access Journals (Sweden)

    Yeguo Sun

    2012-01-01

    Full Text Available We propose long-time convergent numerical integration processes for delay differential equations. We first construct an integration process based on modified Laguerre functions. Then we establish its global convergence in certain weighted Sobolev space. The proposed numerical integration processes can also be used for systems of delay differential equations. We also developed a technique for refinement of modified Laguerre-Radau interpolations. Lastly, numerical results demonstrate the spectral accuracy of the proposed method and coincide well with analysis.

  19. Time delay and noise explaining the behaviour of the cell growth in fermentation process

    Energy Technology Data Exchange (ETDEWEB)

    Ayuobi, Tawfiqullah; Rosli, Norhayati [Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang (Malaysia); Bahar, Arifah [Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor (Malaysia); Salleh, Madihah Md [Department of Biotechnology Industry, Faculty of Biosciences and Bioengineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor (Malaysia)

    2015-02-03

    This paper proposes to investigate the interplay between time delay and external noise in explaining the behaviour of the microbial growth in batch fermentation process. Time delay and noise are modelled jointly via stochastic delay differential equations (SDDEs). The typical behaviour of cell concentration in batch fermentation process under this model is investigated. Milstein scheme is applied for solving this model numerically. Simulation results illustrate the effects of time delay and external noise in explaining the lag and stationary phases, respectively for the cell growth of fermentation process.

  20. Time delay and noise explaining the behaviour of the cell growth in fermentation process

    Science.gov (United States)

    Ayuobi, Tawfiqullah; Rosli, Norhayati; Bahar, Arifah; Salleh, Madihah Md

    2015-02-01

    This paper proposes to investigate the interplay between time delay and external noise in explaining the behaviour of the microbial growth in batch fermentation process. Time delay and noise are modelled jointly via stochastic delay differential equations (SDDEs). The typical behaviour of cell concentration in batch fermentation process under this model is investigated. Milstein scheme is applied for solving this model numerically. Simulation results illustrate the effects of time delay and external noise in explaining the lag and stationary phases, respectively for the cell growth of fermentation process.

  1. Time delay and noise explaining the behaviour of the cell growth in fermentation process

    International Nuclear Information System (INIS)

    Ayuobi, Tawfiqullah; Rosli, Norhayati; Bahar, Arifah; Salleh, Madihah Md

    2015-01-01

    This paper proposes to investigate the interplay between time delay and external noise in explaining the behaviour of the microbial growth in batch fermentation process. Time delay and noise are modelled jointly via stochastic delay differential equations (SDDEs). The typical behaviour of cell concentration in batch fermentation process under this model is investigated. Milstein scheme is applied for solving this model numerically. Simulation results illustrate the effects of time delay and external noise in explaining the lag and stationary phases, respectively for the cell growth of fermentation process

  2. 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

  3. 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.

  4. 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

  5. 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...

  6. 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.

  7. Delay propagation and process management at railway stations

    NARCIS (Netherlands)

    Goverde, R.M.P.; Hansen, I.A.

    2001-01-01

    Process operators at large railway stations have the difficult task to secure a fluent train traffic flow while minimizing deviations from established timetables. Variation in actual train departure times is inevitable due to many circumstances such as arrival delays and fluctuations in alighting

  8. 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.

  9. Sulphur cement pre-composition and process for preparing such sulphur cement pre-composition

    NARCIS (Netherlands)

    2013-01-01

    The invention provides a process for the preparation of a sulphur cement pre-composition comprising reacting sulphur modifier with polysulphide-containing organosilane to obtain in the presence of sulphur the sulphur cement pre-composition, wherein the organosilane has the general molecular formula:

  10. Chloroplast RNA-Binding Protein RBD1 Promotes Chilling Tolerance through 23S rRNA Processing in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Shuai Wang

    2016-05-01

    Full Text Available Plants have varying abilities to tolerate chilling (low but not freezing temperatures, and it is largely unknown how plants such as Arabidopsis thaliana achieve chilling tolerance. Here, we describe a genome-wide screen for genes important for chilling tolerance by their putative knockout mutants in Arabidopsis thaliana. Out of 11,000 T-DNA insertion mutant lines representing half of the genome, 54 lines associated with disruption of 49 genes had a drastic chilling sensitive phenotype. Sixteen of these genes encode proteins with chloroplast localization, suggesting a critical role of chloroplast function in chilling tolerance. Study of one of these proteins RBD1 with an RNA binding domain further reveals the importance of chloroplast translation in chilling tolerance. RBD1 is expressed in the green tissues and is localized in the chloroplast nucleoid. It binds directly to 23S rRNA and the binding is stronger under chilling than at normal growth temperatures. The rbd1 mutants are defective in generating mature 23S rRNAs and deficient in chloroplast protein synthesis especially under chilling conditions. Together, our study identifies RBD1 as a regulator of 23S rRNA processing and reveals the importance of chloroplast function especially protein translation in chilling tolerance.

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

    Science.gov (United States)

    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.

  12. Superior pre-attentive auditory processing in musicians.

    Science.gov (United States)

    Koelsch, S; Schröger, E; Tervaniemi, M

    1999-04-26

    The present study focuses on influences of long-term experience on auditory processing, providing the first evidence for pre-attentively superior auditory processing in musicians. This was revealed by the brain's automatic change-detection response, which is reflected electrically as the mismatch negativity (MMN) and generated by the operation of sensoric (echoic) memory, the earliest cognitive memory system. Major chords and single tones were presented to both professional violinists and non-musicians under ignore and attend conditions. Slightly impure chords, presented among perfect major chords elicited a distinct MMN in professional musicians, but not in non-musicians. This demonstrates that compared to non-musicians, musicians are superior in pre-attentively extracting more information out of musically relevant stimuli. Since effects of long-term experience on pre-attentive auditory processing have so far been reported for language-specific phonemes only, results indicate that sensory memory mechanisms can be modulated by training on a more general level.

  13. The 1989 ENDF pre-processing codes

    International Nuclear Information System (INIS)

    Cullen, D.E.; McLaughlin, P.K.

    1989-12-01

    This document summarizes the 1989 version of the ENDF pre-processing codes which are required for processing evaluated nuclear data coded in the format ENDF-4, ENDF-5, or ENDF-6. The codes are available from the IAEA Nuclear Data Section, free of charge upon request. (author)

  14. Comparison of pre-processing methods for multiplex bead-based immunoassays.

    Science.gov (United States)

    Rausch, Tanja K; Schillert, Arne; Ziegler, Andreas; Lüking, Angelika; Zucht, Hans-Dieter; Schulz-Knappe, Peter

    2016-08-11

    High throughput protein expression studies can be performed using bead-based protein immunoassays, such as the Luminex® xMAP® technology. Technical variability is inherent to these experiments and may lead to systematic bias and reduced power. To reduce technical variability, data pre-processing is performed. However, no recommendations exist for the pre-processing of Luminex® xMAP® data. We compared 37 different data pre-processing combinations of transformation and normalization methods in 42 samples on 384 analytes obtained from a multiplex immunoassay based on the Luminex® xMAP® technology. We evaluated the performance of each pre-processing approach with 6 different performance criteria. Three performance criteria were plots. All plots were evaluated by 15 independent and blinded readers. Four different combinations of transformation and normalization methods performed well as pre-processing procedure for this bead-based protein immunoassay. The following combinations of transformation and normalization were suitable for pre-processing Luminex® xMAP® data in this study: weighted Box-Cox followed by quantile or robust spline normalization (rsn), asinh transformation followed by loess normalization and Box-Cox followed by rsn.

  15. Delay functions in trip assignment for transport planning process

    Science.gov (United States)

    Leong, Lee Vien

    2017-10-01

    In transportation planning process, volume-delay and turn-penalty functions are the functions needed in traffic assignment to determine travel time on road network links. Volume-delay function is the delay function describing speed-flow relationship while turn-penalty function is the delay function associated to making a turn at intersection. The volume-delay function used in this study is the revised Bureau of Public Roads (BPR) function with the constant parameters, α and β values of 0.8298 and 3.361 while the turn-penalty functions for signalized intersection were developed based on uniform, random and overflow delay models. Parameters such as green time, cycle time and saturation flow were used in the development of turn-penalty functions. In order to assess the accuracy of the delay functions, road network in areas of Nibong Tebal, Penang and Parit Buntar, Perak was developed and modelled using transportation demand forecasting software. In order to calibrate the models, phase times and traffic volumes at fourteen signalised intersections within the study area were collected during morning and evening peak hours. The prediction of assigned volumes using the revised BPR function and the developed turn-penalty functions show close agreement to actual recorded traffic volume with the lowest percentage of accuracy, 80.08% and the highest, 93.04% for the morning peak model. As for the evening peak model, they were 75.59% and 95.33% respectively for lowest and highest percentage of accuracy. As for the yield left-turn lanes, the lowest percentage of accuracy obtained for the morning and evening peak models were 60.94% and 69.74% respectively while the highest percentage of accuracy obtained for both models were 100%. Therefore, can be concluded that the development and utilisation of delay functions based on local road conditions are important as localised delay functions can produce better estimate of link travel times and hence better planning for future

  16. 16S rRNA gene sequencing as a tool to study microbial populations in foods and process environments

    DEFF Research Database (Denmark)

    Buschhardt, Tasja; Hansen, Tina Beck; Bahl, Martin Iain

    2015-01-01

    communities in meat and the meat process environment with special focus on the Enterobacteriaceae family as a subpopulation comprising enteropathogens including Salmonella. Samples were analyzed by a nested PCR approach combined with MiSeq® Illumina®16S DNA sequencing and standardized culture methods as cross...... reference. Results: Taxonomic assignments and abundances of sequences in the total community and in the Enterobacteriaceae subpopulation were affected by the 16S rRNA gene variable region, DNA extraction methods, and polymerases chosen. However, community compositions were very reproducible when the same...

  17. Perfluoroalkyl Acid Concentrations in Blood Samples Subjected to Transportation and Processing Delay.

    Science.gov (United States)

    Bach, Cathrine Carlsen; Henriksen, Tine Brink; Bossi, Rossana; Bech, Bodil Hammer; Fuglsang, Jens; Olsen, Jørn; Nohr, Ellen Aagaard

    2015-01-01

    In studies of perfluoroalkyl acids, the validity and comparability of measured concentrations may be affected by differences in the handling of biospecimens. We aimed to investigate whether measured plasma levels of perfluoroalkyl acids differed between blood samples subjected to delay and transportation prior to processing and samples with immediate processing and freezing. Pregnant women recruited at Aarhus University Hospital, Denmark, (n = 88) provided paired blood samples. For each pair of samples, one was immediately processed and plasma was frozen, and the other was delayed and transported as whole blood before processing and freezing of plasma (similar to the Danish National Birth Cohort). We measured 12 perfluoroalkyl acids and present results for compounds with more than 50% of samples above the lower limit of quantification. For samples taken in the winter, relative differences between the paired samples ranged between -77 and +38% for individual perfluoroalkyl acids. In most cases concentrations were lower in the delayed and transported samples, e.g. the relative difference was -29% (95% confidence interval -30; -27) for perfluorooctane sulfonate. For perfluorooctanoate there was no difference between the two setups [corresponding estimate 1% (0, 3)]. Differences were negligible in the summer for all compounds. Transport of blood samples and processing delay, similar to conditions applied in some large, population-based studies, may affect measured perfluoroalkyl acid concentrations, mainly when outdoor temperatures are low. Attention to processing conditions is needed in studies of perfluoroalkyl acid exposure in humans.

  18. Effect of delayed auditory feedback on stuttering with and without central auditory processing disorders.

    Science.gov (United States)

    Picoloto, Luana Altran; Cardoso, Ana Cláudia Vieira; Cerqueira, Amanda Venuti; Oliveira, Cristiane Moço Canhetti de

    2017-12-07

    To verify the effect of delayed auditory feedback on speech fluency of individuals who stutter with and without central auditory processing disorders. The participants were twenty individuals with stuttering from 7 to 17 years old and were divided into two groups: Stuttering Group with Auditory Processing Disorders (SGAPD): 10 individuals with central auditory processing disorders, and Stuttering Group (SG): 10 individuals without central auditory processing disorders. Procedures were: fluency assessment with non-altered auditory feedback (NAF) and delayed auditory feedback (DAF), assessment of the stuttering severity and central auditory processing (CAP). Phono Tools software was used to cause a delay of 100 milliseconds in the auditory feedback. The "Wilcoxon Signal Post" test was used in the intragroup analysis and "Mann-Whitney" test in the intergroup analysis. The DAF caused a statistically significant reduction in SG: in the frequency score of stuttering-like disfluencies in the analysis of the Stuttering Severity Instrument, in the amount of blocks and repetitions of monosyllabic words, and in the frequency of stuttering-like disfluencies of duration. Delayed auditory feedback did not cause statistically significant effects on SGAPD fluency, individuals with stuttering with auditory processing disorders. The effect of delayed auditory feedback in speech fluency of individuals who stutter was different in individuals of both groups, because there was an improvement in fluency only in individuals without auditory processing disorder.

  19. "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.

  20. Research on pre-processing of QR Code

    Science.gov (United States)

    Sun, Haixing; Xia, Haojie; Dong, Ning

    2013-10-01

    QR code encodes many kinds of information because of its advantages: large storage capacity, high reliability, full arrange of utter-high-speed reading, small printing size and high-efficient representation of Chinese characters, etc. In order to obtain the clearer binarization image from complex background, and improve the recognition rate of QR code, this paper researches on pre-processing methods of QR code (Quick Response Code), and shows algorithms and results of image pre-processing for QR code recognition. Improve the conventional method by changing the Souvola's adaptive text recognition method. Additionally, introduce the QR code Extraction which adapts to different image size, flexible image correction approach, and improve the efficiency and accuracy of QR code image processing.

  1. 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...

  2. 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.

  3. Performance of Pre-processing Schemes with Imperfect Channel State Information

    DEFF Research Database (Denmark)

    Christensen, Søren Skovgaard; Kyritsi, Persa; De Carvalho, Elisabeth

    2006-01-01

    Pre-processing techniques have several benefits when the CSI is perfect. In this work we investigate three linear pre-processing filters, assuming imperfect CSI caused by noise degradation and channel temporal variation. Results indicate, that the LMMSE filter achieves the lowest BER and the high......Pre-processing techniques have several benefits when the CSI is perfect. In this work we investigate three linear pre-processing filters, assuming imperfect CSI caused by noise degradation and channel temporal variation. Results indicate, that the LMMSE filter achieves the lowest BER...... and the highest SINR when the CSI is perfect, whereas the simple matched filter may be a good choice when the CSI is imperfect. Additionally the results give insight into the inherent trade-off between robustness against CSI imperfections and spatial focusing ability....

  4. 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...

  5. 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...

  6. 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...

  7. Effect of delayed film processing and milliamperage changes on ...

    African Journals Online (AJOL)

    Effect of delayed film processing and milliamperage changes on image quality. NO Egbe, BF Olisemeke, DU Uduwen. Abstract. No Abstract. West African Journal of Radiology Vol. 11(1) 2004: 8-13. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT.

  8. 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.

  9. Enhancing Elementary Pre-service Teachers' Plant Processes Conceptions

    Science.gov (United States)

    Thompson, Stephen L.; Lotter, Christine; Fann, Xumei; Taylor, Laurie

    2016-06-01

    Researchers examined how an inquiry-based instructional treatment emphasizing interrelated plant processes influenced 210 elementary pre-service teachers' (PTs) conceptions of three plant processes, photosynthesis, cellular respiration, and transpiration, and the interrelated nature of these processes. The instructional treatment required PTs to predict the fate of a healthy plant in a sealed terrarium (Plant-in-a-Jar), justify their predictions, observe the plant over a 5-week period, and complete guided inquiry activities centered on one of the targeted plant processes each week. Data sources included PTs' pre- and post-predictions with accompanying justifications, course artifacts such as weekly terrarium observations and science journal entries, and group models of the interrelated plant processes occurring within the sealed terraria. A subset of 33 volunteer PTs also completed interviews the week the Plant-in-a-Jar scenario was introduced and approximately 4 months after the instructional intervention ended. Pre- and post-predictions from all PTs as well as interview responses from the subgroup of PTs, were coded into categories based on key plant processes emphasized in the Next Generation Science Standards. Study findings revealed that PTs developed more accurate conceptions of plant processes and their interrelated nature as a result of the instructional intervention. Primary patterns of change in PTs' plant process conceptions included development of more accurate conceptions of how water is used by plants, more accurate conceptions of photosynthesis features, and more accurate conceptions of photosynthesis and cellular respiration as transformative processes.

  10. SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana.

    Science.gov (United States)

    Wu, Wenjuan; Liu, Sheng; Ruwe, Hannes; Zhang, Delin; Melonek, Joanna; Zhu, Yajuan; Hu, Xupeng; Gusewski, Sandra; Yin, Ping; Small, Ian D; Howell, Katharine A; Huang, Jirong

    2016-03-01

    Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5' end of the 23S-4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA 'footprint' associated with this site in sot1 mutants. We found that more than half of the 23S-4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5' and 3' ends, and that the endonucleolytic cleavage product normally released from the 5' end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5' extremity of the 23S-4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5' and 3' ends. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  11. Photonic single nonlinear-delay dynamical node for information processing

    Science.gov (United States)

    Ortín, Silvia; San-Martín, Daniel; Pesquera, Luis; Gutiérrez, José Manuel

    2012-06-01

    An electro-optical system with a delay loop based on semiconductor lasers is investigated for information processing by performing numerical simulations. This system can replace a complex network of many nonlinear elements for the implementation of Reservoir Computing. We show that a single nonlinear-delay dynamical system has the basic properties to perform as reservoir: short-term memory and separation property. The computing performance of this system is evaluated for two prediction tasks: Lorenz chaotic time series and nonlinear auto-regressive moving average (NARMA) model. We sweep the parameters of the system to find the best performance. The results achieved for the Lorenz and the NARMA-10 tasks are comparable to those obtained by other machine learning methods.

  12. 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.

  13. PI and PID controller tuning rule design for processes with delay, to achieve constant gain and phase margins for all values of delay

    OpenAIRE

    O'Dwyer, Aidan

    2001-01-01

    This paper will discuss the design of PI and PID controller tuning rules to compensate processes with delay, that are modelled in a number of ways. The rules allow the achievement of constant gain and phase margins as the delay varies.

  14. Enhancing Elementary Pre-Service Teachers' Plant Processes Conceptions

    Science.gov (United States)

    Thompson, Stephen L.; Lotter, Christine; Fann, Xumei; Taylor, Laurie

    2016-01-01

    Researchers examined how an inquiry-based instructional treatment emphasizing interrelated plant processes influenced 210 elementary pre-service teachers' (PTs) conceptions of three plant processes, photosynthesis, cellular respiration, and transpiration, and the interrelated nature of these processes. The instructional treatment required PTs to…

  15. 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.

  16. 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.

  17. Examination of Speed Contribution of Parallelization for Several Fingerprint Pre-Processing Algorithms

    Directory of Open Access Journals (Sweden)

    GORGUNOGLU, S.

    2014-05-01

    Full Text Available In analysis of minutiae based fingerprint systems, fingerprints needs to be pre-processed. The pre-processing is carried out to enhance the quality of the fingerprint and to obtain more accurate minutiae points. Reducing the pre-processing time is important for identification and verification in real time systems and especially for databases holding large fingerprints information. Parallel processing and parallel CPU computing can be considered as distribution of processes over multi core processor. This is done by using parallel programming techniques. Reducing the execution time is the main objective in parallel processing. In this study, pre-processing of minutiae based fingerprint system is implemented by parallel processing on multi core computers using OpenMP and on graphics processor using CUDA to improve execution time. The execution times and speedup ratios are compared with the one that of single core processor. The results show that by using parallel processing, execution time is substantially improved. The improvement ratios obtained for different pre-processing algorithms allowed us to make suggestions on the more suitable approaches for parallelization.

  18. 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.

  19. Parallel processing using an optical delay-based reservoir computer

    Science.gov (United States)

    Van der Sande, Guy; Nguimdo, Romain Modeste; Verschaffelt, Guy

    2016-04-01

    Delay systems subject to delayed optical feedback have recently shown great potential in solving computationally hard tasks. By implementing a neuro-inspired computational scheme relying on the transient response to optical data injection, high processing speeds have been demonstrated. However, reservoir computing systems based on delay dynamics discussed in the literature are designed by coupling many different stand-alone components which lead to bulky, lack of long-term stability, non-monolithic systems. Here we numerically investigate the possibility of implementing reservoir computing schemes based on semiconductor ring lasers. Semiconductor ring lasers are semiconductor lasers where the laser cavity consists of a ring-shaped waveguide. SRLs are highly integrable and scalable, making them ideal candidates for key components in photonic integrated circuits. SRLs can generate light in two counterpropagating directions between which bistability has been demonstrated. We demonstrate that two independent machine learning tasks , even with different nature of inputs with different input data signals can be simultaneously computed using a single photonic nonlinear node relying on the parallelism offered by photonics. We illustrate the performance on simultaneous chaotic time series prediction and a classification of the Nonlinear Channel Equalization. We take advantage of different directional modes to process individual tasks. Each directional mode processes one individual task to mitigate possible crosstalk between the tasks. Our results indicate that prediction/classification with errors comparable to the state-of-the-art performance can be obtained even with noise despite the two tasks being computed simultaneously. We also find that a good performance is obtained for both tasks for a broad range of the parameters. The results are discussed in detail in [Nguimdo et al., IEEE Trans. Neural Netw. Learn. Syst. 26, pp. 3301-3307, 2015

  20. 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.

  1. The Effects of Test Trial and Processing Level on Immediate and Delayed Retention

    OpenAIRE

    Chang, Sau Hou

    2017-01-01

    The purpose of the present study was to investigate the effects of test trial and processing level on immediate and delayed retention. A 2 × 2 × 2 mixed ANOVAs was used with two between-subject factors of test trial (single test, repeated test) and processing level (shallow, deep), and one within-subject factor of final recall (immediate, delayed). Seventy-six college students were randomly assigned first to the single test (studied the stimulus words three times and took one free-recall test...

  2. Perfluoroalkyl Acid Concentrations in Blood Samples Subjected to Transportation and Processing Delay

    DEFF Research Database (Denmark)

    Bach, Cathrine Carlsen; Henriksen, Tine Brink; Bossi, Rossana

    2015-01-01

    and transportation prior to processing and samples with immediate processing and freezing. METHODS: Pregnant women recruited at Aarhus University Hospital, Denmark, (n = 88) provided paired blood samples. For each pair of samples, one was immediately processed and plasma was frozen, and the other was delayed...... and transported as whole blood before processing and freezing of plasma (similar to the Danish National Birth Cohort). We measured 12 perfluoroalkyl acids and present results for compounds with more than 50% of samples above the lower limit of quantification. RESULTS: For samples taken in the winter, relative...... differences between the paired samples ranged between -77 and +38% for individual perfluoroalkyl acids. In most cases concentrations were lower in the delayed and transported samples, e.g. the relative difference was -29% (95% confidence interval -30; -27) for perfluorooctane sulfonate. For perfluorooctanoate...

  3. Pre-Service Teachers' Perceptions with Regard to Teaching-Learning Processes

    Science.gov (United States)

    Özdas, Faysal

    2018-01-01

    Teaching-learning process has a great important medium where pre-service teachers develop experiences and competences. Pre-service teachers are introduced to this process in a professional sense through the school experience course in teacher training. In this process, it is crucial to identify the encountered difficulties and matters. For this…

  4. American Elementary Education Pre-Service Teachers' Attitudes towards Biotechnology Processes

    Science.gov (United States)

    Chabalengula, Vivien Mweene; Mumba, Frackson; Chitiyo, Jonathan

    2011-01-01

    This study examined elementary education pre-service teachers' attitudes towards biotechnology processes. A sample comprised 88 elementary education pre-service teachers at a mid-sized university in the Midwest of the USA. Sixty and 28 of these pre-service teachers were enrolled in Introductory Science Methods course and Advance Science Methods…

  5. 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 ...

  6. A Conversation on Data Mining Strategies in LC-MS Untargeted Metabolomics: Pre-Processing and Pre-Treatment Steps

    Directory of Open Access Journals (Sweden)

    Fidele Tugizimana

    2016-11-01

    Full Text Available Untargeted metabolomic studies generate information-rich, high-dimensional, and complex datasets that remain challenging to handle and fully exploit. Despite the remarkable progress in the development of tools and algorithms, the “exhaustive” extraction of information from these metabolomic datasets is still a non-trivial undertaking. A conversation on data mining strategies for a maximal information extraction from metabolomic data is needed. Using a liquid chromatography-mass spectrometry (LC-MS-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter. Data obtained in positive mode generated from a LC-MS-based untargeted metabolomic study (sorghum plants responding dynamically to infection by a fungal pathogen were used. Raw data were pre-processed with MarkerLynxTM software (Waters Corporation, Manchester, UK. Here, two parameters were varied: the intensity threshold (50–100 counts and the mass tolerance (0.005–0.01 Da. After the pre-processing, the datasets were imported into SIMCA (Umetrics, Umea, Sweden for more data cleaning and statistical modeling. In addition, different scaling (unit variance, Pareto, etc. and data transformation (log and power methods were explored. The results showed that the pre-processing parameters (or algorithms influence the output dataset with regard to the number of defined features. Furthermore, the study demonstrates that the pre-treatment of data prior to statistical modeling affects the subspace approximation outcome: e.g., the amount of variation in X-data that the model can explain and predict. The pre-processing and pre-treatment steps subsequently influence the number of statistically significant extracted/selected features (variables. Thus, as informed by the results, to maximize the value of untargeted metabolomic data

  7. An integrated model of statistical process control and maintenance based on the delayed monitoring

    International Nuclear Information System (INIS)

    Yin, Hui; Zhang, Guojun; Zhu, Haiping; Deng, Yuhao; He, Fei

    2015-01-01

    This paper develops an integrated model of statistical process control and maintenance decision. The proposal of delayed monitoring policy postpones the sampling process till a scheduled time and contributes to ten-scenarios of the production process, where equipment failure may occur besides quality shift. The equipment failure and the control chart alert trigger the corrective maintenance and the predictive maintenance, respectively. The occurrence probability, the cycle time and the cycle cost of each scenario are obtained by integral calculation; therefore, a mathematical model is established to minimize the expected cost by using the genetic algorithm. A Monte Carlo simulation experiment is conducted and compared with the integral calculation in order to ensure the analysis of the ten-scenario model. Another ordinary integrated model without delayed monitoring is also established as comparison. The results of a numerical example indicate satisfactory economic performance of the proposed model. Finally, a sensitivity analysis is performed to investigate the effect of model parameters. - Highlights: • We develop an integrated model of statistical process control and maintenance. • We propose delayed monitoring policy and derive an economic model with 10 scenarios. • We consider two deterioration mechanisms, quality shift and equipment failure. • The delayed monitoring policy will help reduce the expected cost

  8. Are cognitive "insomnia" processes involved in the development and maintenance of delayed sleep wake phase disorder?

    Science.gov (United States)

    Richardson, Cele E; Gradisar, Michael; Barbero, Sebastian C

    2016-04-01

    Although individuals with delayed sleep wake phase disorder (DSWPD) and chronic insomnia disorder (CID) share many of the same phenomenological experiences, theories relating to the development and maintenance of these disorders are distinct in focus. Unlike CID, theory relating to DSWPD is primarily physiologically based and assumes almost no cognitive pathway. However, recent research findings suggest that individuals with DSWPD also display many of the sleep-disordered cognitive processes that were previously assumed to be unique to the insomnia experience. As such, this review aims to summarise current research findings to address the question "Could cognitive processes be involved in the development and maintenance of DSWPD?" In particular, the presence of cognitive and physiological pre-sleep arousal, sleep-related attentional bias, distorted perception of sleep and daytime functioning, dysfunctional beliefs and safety behaviours will be investigated. As this emerging area of research requires a stronger evidence base, we highlight suggestions for future investigation and provide preliminary practice points for clinicians assessing and treating "insomnia" in patients with DSWPD. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Effect of processing time delay on the dose response of Kodak EDR2 film.

    Science.gov (United States)

    Childress, Nathan L; Rosen, Isaac I

    2004-08-01

    Kodak EDR2 film is a widely used two-dimensional dosimeter for intensity modulated radiotherapy (IMRT) measurements. Our clinical use of EDR2 film for IMRT verifications revealed variations and uncertainties in dose response that were larger than expected, given that we perform film calibrations for every experimental measurement. We found that the length of time between film exposure and processing can affect the absolute dose response of EDR2 film by as much as 4%-6%. EDR2 films were exposed to 300 cGy using 6 and 18 MV 10 x 10 cm2 fields and then processed after time delays ranging from 2 min to 24 h. An ion chamber measured the relative dose for these film exposures. The ratio of optical density (OD) to dose stabilized after 3 h. Compared to its stable value, the film response was 4%-6% lower at 2 min and 1% lower at 1 h. The results of the 4 min and 1 h processing time delays were verified with a total of four different EDR2 film batches. The OD/dose response for XV2 films was consistent for time periods of 4 min and 1 h between exposure and processing. To investigate possible interactions of the processing time delay effect with dose, single EDR2 films were irradiated to eight different dose levels between 45 and 330 cGy using smaller 3 x 3 cm2 areas. These films were processed after time delays of 1, 3, and 6 h, using 6 and 18 MV photon qualities. The results at all dose levels were consistent, indicating that there is no change in the processing time delay effect for different doses. The difference in the time delay effect between the 6 and 18 MV measurements was negligible for all experiments. To rule out bias in selecting film regions for OD measurement, we compared the use of a specialized algorithm that systematically determines regions of interest inside the 10 x 10 cm2 exposure areas to manually selected regions of interest. There was a maximum difference of only 0.07% between the manually and automatically selected regions, indicating that the use of

  10. Comparative performance evaluation of transform coding in image pre-processing

    Science.gov (United States)

    Menon, Vignesh V.; NB, Harikrishnan; Narayanan, Gayathri; CK, Niveditha

    2017-07-01

    We are in the midst of a communication transmute which drives the development as largely as dissemination of pioneering communication systems with ever-increasing fidelity and resolution. Distinguishable researches have been appreciative in image processing techniques crazed by a growing thirst for faster and easier encoding, storage and transmission of visual information. In this paper, the researchers intend to throw light on many techniques which could be worn at the transmitter-end in order to ease the transmission and reconstruction of the images. The researchers investigate the performance of different image transform coding schemes used in pre-processing, their comparison, and effectiveness, the necessary and sufficient conditions, properties and complexity in implementation. Whimsical by prior advancements in image processing techniques, the researchers compare various contemporary image pre-processing frameworks- Compressed Sensing, Singular Value Decomposition, Integer Wavelet Transform on performance. The paper exposes the potential of Integer Wavelet transform to be an efficient pre-processing scheme.

  11. Effect of packaging on physicochemical characteristics of irradiated pre-processed chicken

    International Nuclear Information System (INIS)

    Jiang Xiujie; Zhang Dongjie; Zhang Dequan; Li Shurong; Gao Meixu; Wang Zhidong

    2011-01-01

    To explore the effect of modified atmosphere packaging and antioxidants on the physicochemical characteristics of irradiated pre-processed chicken, the pre-processed chicken was added antioxidants first, and then packaged in common, vacuum and gas respectively, and finally irradiated at 5 kGy dosage. All samples was stored at 4 ℃. The pH, TBA, TVB-N and color deviation were evaluated after 0, 3, 7, 10, 14, 18 and 21 d of storage. The results showed that pH value of pre-processed chicken with antioxidants and vacuum packaged increased with the storage time but not significantly among different treatments. The TBA value was also increased but not significantly (P > 0.05), which indicated that vacuum package inhibited the lipid oxidation. TVB-N value increased with storage time, TVB-N value of vacuum package samples reached 14.29 mg/100 g at 21 d storage, which did not exceeded the reference indexes of fresh meat. a * value of the pre-processed chicken of vacuum package and non-oxygen package samples increased significantly during storage (P > 0.05), and chicken color kept bright red after 21 d storage with vacuum package It is concluded that vacuum packaging of irradiated pre-processed chicken is effective on ensuring its physical and chemical properties during storage. (authors)

  12. 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.

  13. 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...

  14. 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)

  15. Optimization of Pre-Treatment Process Parameters to Generate Biodiesel from Microalga

    Directory of Open Access Journals (Sweden)

    Chukwuma Onumaegbu

    2018-03-01

    Full Text Available Cell disruption is an integral part of microalga production process, which improves the release of intracellular products that are essential for biofuel production. In this work, pre-treatment parameters that will enhance the efficiency of lipid production using high-pressure homogenizer on microalgae biomass will be investigated. The high-pressure homogenizer that is considered is a GYB40-10S/GY60-6S; with a pre-treatment pressure of 1000 psi, 2000 psi, and 3000 psi, the number of passes; 1, 2, and 3, a reaction time of 3, 3.5, and 4 h. Pressure and cavitation increase the efficiency of the pre-treatment process of the homogenizer. In addition, homogenization shear force and pressure are the basic significant factors that enhance the efficiency of microalgae cell rupture. Also, the use of modelling to simulate pre-treatment processes (Response Surface Methodology (RSM, Box-Behnken Designs (BBD, and design of experiment (DOE for process optimization will be adopted in this study. The results clearly demonstrate that high-pressure homogenization pre-treatment can effectively disrupt microalga cell walls to enhance lipid recovery efficiency, with a relatively short extraction time, both that are essential for maintaining a good quality of lipids for biofuel production. A maximum of 18% lipid yields were obtained after 3 h of HPH pre-treatment at 3000 psi.

  16. 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

  17. Pre-processing for Triangulation of Probabilistic Networks

    NARCIS (Netherlands)

    Bodlaender, H.L.; Koster, A.M.C.A.; Eijkhof, F. van den; Gaag, L.C. van der

    2001-01-01

    The currently most efficient algorithm for inference with a probabilistic network builds upon a triangulation of a networks graph. In this paper, we show that pre-processing can help in finding good triangulations for probabilistic networks, that is, triangulations with a minimal maximum

  18. 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.

  19. 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.

  20. Effect of delayed processing on nutrient composition, pH and ...

    African Journals Online (AJOL)

    Fish are a nutrient rich food but highly perishable due to its high water activity, protein content, neutral pH and presence of autolytic enzymes. This explains why fresh fish quality deteriorates rapidly if not properly stored after catch such as use of low temperature. The implication is that delayed processing of fresh fish ...

  1. Learners’ processes during pre-task planning and Working Memory Capacity

    Directory of Open Access Journals (Sweden)

    Maria da Gloria Tavares

    2016-01-01

    Full Text Available http://dx.doi.org/10.5007/2175-8026.2016v69n1p79 The present study is part of a larger scale research (Guará-Tavares, 2011, 2013 that investigates the relationship among working memory capacity, pre-task planning, and L2 speech performance. The aim of the study was to analyze 1 what processes learners engage during pre-task planning, and 2 whether higher and lower working memory spans engage in different processes during pre-task planning. Learners’ processes were accessed by means of think aloud protocols and a retrospective interview. Working memory capacity was measured by the Speaking Span Test. Results show that learners engage mainly in organization of ideas, rehearsal, lexical searches, and monitoring.. Moreover, higher spans employ significantly more metacognitive strategies during planning when compared to lower spans.

  2. 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.

  3. 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

  4. 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.

  5. Quality assessment of baby food made of different pre-processed organic raw materials under industrial processing conditions.

    Science.gov (United States)

    Seidel, Kathrin; Kahl, Johannes; Paoletti, Flavio; Birlouez, Ines; Busscher, Nicolaas; Kretzschmar, Ursula; Särkkä-Tirkkonen, Marjo; Seljåsen, Randi; Sinesio, Fiorella; Torp, Torfinn; Baiamonte, Irene

    2015-02-01

    The market for processed food is rapidly growing. The industry needs methods for "processing with care" leading to high quality products in order to meet consumers' expectations. Processing influences the quality of the finished product through various factors. In carrot baby food, these are the raw material, the pre-processing and storage treatments as well as the processing conditions. In this study, a quality assessment was performed on baby food made from different pre-processed raw materials. The experiments were carried out under industrial conditions using fresh, frozen and stored organic carrots as raw material. Statistically significant differences were found for sensory attributes among the three autoclaved puree samples (e.g. overall odour F = 90.72, p processed from frozen carrots show increased moisture content and decrease of several chemical constituents. Biocrystallization identified changes between replications of the cooking. Pre-treatment of raw material has a significant influence on the final quality of the baby food.

  6. 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.

  7. Is a pre-analytical process for urinalysis required?

    Science.gov (United States)

    Petit, Morgane; Beaudeux, Jean-Louis; Majoux, Sandrine; Hennequin, Carole

    2017-10-01

    For the reliable urinary measurement of calcium, phosphate and uric acid, a pre-analytical process by adding acid or base to urine samples at laboratory is recommended in order to dissolve precipitated solutes. Several studies on different kind of samples and analysers have previously shown that a such pre-analytical treatment is useless. The objective was to study the necessity of pre-analytical treatment of urine on samples collected using the V-Monovette ® (Sarstedt) system and measured on the analyser Architect C16000 (Abbott Diagnostics). Sixty urinary samples of hospitalized patients were selected (n=30 for calcium and phosphate, and n=30 for uric acid). After acidification of urine samples for measurement of calcium and phosphate, and alkalinisation for measurement of uric acid respectively, differences between results before and after the pre-analytical treatment were compared to acceptable limits recommended by the French society of clinical biology (SFBC). No difference in concentration between before and after pre-analytical treatment of urine samples exceeded acceptable limits from SFBC for measurement of calcium and uric acid. For phosphate, only one sample exceeded these acceptable limits, showing a result paradoxically lower after acidification. In conclusion, in agreement with previous study, our results show that acidification or alkalinisation of urine samples from 24 h urines or from urination is not a pre-analytical necessity for measurement of calcium, phosphate and uric acid.

  8. How Pre-Service Teachers' Understand and Perform Science Process Skills

    Science.gov (United States)

    Chabalengula, Vivien Mweene; Mumba, Frackson; Mbewe, Simeon

    2012-01-01

    This study explored pre-service teachers' conceptual understanding and performance on science process skills. A sample comprised 91 elementary pre-service teachers at a university in the Midwest of the USA. Participants were enrolled in two science education courses; introductory science teaching methods course and advanced science methods course.…

  9. Pre-Processing and Modeling Tools for Bigdata

    Directory of Open Access Journals (Sweden)

    Hashem Hadi

    2016-09-01

    Full Text Available Modeling tools and operators help the user / developer to identify the processing field on the top of the sequence and to send into the computing module only the data related to the requested result. The remaining data is not relevant and it will slow down the processing. The biggest challenge nowadays is to get high quality processing results with a reduced computing time and costs. To do so, we must review the processing sequence, by adding several modeling tools. The existing processing models do not take in consideration this aspect and focus on getting high calculation performances which will increase the computing time and costs. In this paper we provide a study of the main modeling tools for BigData and a new model based on pre-processing.

  10. 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

  11. Recursive Estimation for Dynamical Systems with Different Delay Rates Sensor Network and Autocorrelated Process Noises

    Directory of Open Access Journals (Sweden)

    Jianxin Feng

    2014-01-01

    Full Text Available The recursive estimation problem is studied for a class of uncertain dynamical systems with different delay rates sensor network and autocorrelated process noises. The process noises are assumed to be autocorrelated across time and the autocorrelation property is described by the covariances between different time instants. The system model under consideration is subject to multiplicative noises or stochastic uncertainties. The sensor delay phenomenon occurs in a random way and each sensor in the sensor network has an individual delay rate which is characterized by a binary switching sequence obeying a conditional probability distribution. By using the orthogonal projection theorem and an innovation analysis approach, the desired recursive robust estimators including recursive robust filter, predictor, and smoother are obtained. Simulation results are provided to demonstrate the effectiveness of the proposed approaches.

  12. A Data-Driven Air Transportation Delay Propagation Model Using Epidemic Process Models

    Directory of Open Access Journals (Sweden)

    B. Baspinar

    2016-01-01

    Full Text Available In air transport network management, in addition to defining the performance behavior of the system’s components, identification of their interaction dynamics is a delicate issue in both strategic and tactical decision-making process so as to decide which elements of the system are “controlled” and how. This paper introduces a novel delay propagation model utilizing epidemic spreading process, which enables the definition of novel performance indicators and interaction rates of the elements of the air transportation network. In order to understand the behavior of the delay propagation over the network at different levels, we have constructed two different data-driven epidemic models approximating the dynamics of the system: (a flight-based epidemic model and (b airport-based epidemic model. The flight-based epidemic model utilizing SIS epidemic model focuses on the individual flights where each flight can be in susceptible or infected states. The airport-centric epidemic model, in addition to the flight-to-flight interactions, allows us to define the collective behavior of the airports, which are modeled as metapopulations. In network model construction, we have utilized historical flight-track data of Europe and performed analysis for certain days involving certain disturbances. Through this effort, we have validated the proposed delay propagation models under disruptive events.

  13. [Variation of water DOC during the process of pre-pressure and coagulation sedimentation treatment].

    Science.gov (United States)

    Chen, Wen-Jing; Cong, Hai-Bing; Xu, Ya-Jun; Wang, Wei; Jiang, Xin-Yue; Liu, Yu-Jiao

    2014-07-01

    The aim of the study was to explore whether the pre-pressure and coagulation sedimentation process would result in algal cell disruption, leading to increased dissolved organic carbon (DOC) in water, based on which, the pressure application mode would be optimized and safe and efficient pre-pressure algae removal process would be obtained. The changes in DOC during the process of pre-pressure and preoxidation treatment, the distribution of molecular weight in water as well as the removal efficiency of algae, turbidity and DOC after coagulation and sedimentation were investigated. The results showed that the DOC in water did not increase but decreased, and the molecular weight decreased after treated with 0.5-0.8 MPa pressure. While KMnO4 and NaClO pre-oxidation both increased the DOC, in the meanwhile, the distribution of molecular weight showed no obvious change. After the pre-pressure coagulation and sedimentation process, the removal rate of algae was 96.23% and that of DOC was 29. 11%, which was by 10% - 30% higher than the rate of pre-oxidation coagulation and sedimentation process.

  14. 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 ...

  15. Multi-objective LQR with optimum weight selection to design FOPID controllers for delayed fractional order processes.

    Science.gov (United States)

    Das, Saptarshi; Pan, Indranil; Das, Shantanu

    2015-09-01

    An optimal trade-off design for fractional order (FO)-PID controller is proposed with a Linear Quadratic Regulator (LQR) based technique using two conflicting time domain objectives. A class of delayed FO systems with single non-integer order element, exhibiting both sluggish and oscillatory open loop responses, have been controlled here. The FO time delay processes are handled within a multi-objective optimization (MOO) formalism of LQR based FOPID design. A comparison is made between two contemporary approaches of stabilizing time-delay systems withinLQR. The MOO control design methodology yields the Pareto optimal trade-off solutions between the tracking performance and total variation (TV) of the control signal. Tuning rules are formed for the optimal LQR-FOPID controller parameters, using median of the non-dominated Pareto solutions to handle delayed FO processes. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

  16. 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...

  17. 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.

  18. 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.

  19. 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

  20. Zooming in on children's behavior during delay of gratification: Disentangling impulsigenic and volitional processes underlying self-regulation.

    Science.gov (United States)

    Neuenschwander, Regula; Blair, Clancy

    2017-02-01

    When delaying gratification, both motivational and regulatory processes are likely to be at play; however, the relative contributions of motivational and regulatory influences on delay behavior are unclear. By examining behavioral responses during a delay task, this study sought to examine the motivational (anticipatory behavior) and regulatory mechanisms (executive function and self-control strategies) underlying children's self-regulation. The participants, 65 5- to 9-year-old children (M age =7.19years, SD=0.89), were video-recorded during a delay procedure and later coded for anticipatory behaviors (e.g., gazing intensely at the tablet) and self-control strategies. Children also completed two executive function (EF) tasks. We found that anticipatory behavior was curvilinearly related to delay time. Children showing either very low or very high levels of anticipatory behavior were not able to wait the entire time. Furthermore, our results indicated that anticipatory behavior interacted with EF to predict delay time. Specifically, anticipatory behavior was negatively related to delay time only if EF abilities were low. Finally, self-control strategies also interacted with EF to predict children's ability to delay. Spontaneous engagement in self-control strategies such as fidgeting and engagement in alternative activities were beneficial for children with low EF but were unrelated to delay time for children with high EF. Results indicate the value of examining motivational and regulatory influences on delay behavior. Lapses in self-regulation may be due to the combination of powerful impulsigenic (i.e., anticipatory behavior) and weak volitional processes (i.e., EF, self-control strategies). Copyright © 2016. Published by Elsevier Inc.

  1. The neutron long counter NERO for studies of β-delayed neutron emission in the r-process

    International Nuclear Information System (INIS)

    Pereira, J.; Hosmer, P.; Lorusso, G.; Santi, P.; Couture, A.; Daly, J.; Del Santo, M.; Elliot, T.

    2010-01-01

    The neutron long counter NERO was built at the National Superconducting Cyclotron Laboratory (NSCL), Michigan State University, for measuring β-delayed neutron-emission probabilities. The detector was designed to work in conjunction with a β-delay implantation station, so that β decays and β-delayed neutrons emitted from implanted nuclei can be measured simultaneously. The high efficiency of about 40%, for the range of energies of interest, along with the small background, are crucial for measuring β-delayed neutron emission branchings for neutron-rich r-process nuclei produced as low intensity fragmentation beams in in-flight separator facilities.

  2. An adaptive deep-coupled GNSS/INS navigation system with hybrid pre-filter processing

    Science.gov (United States)

    Wu, Mouyan; Ding, Jicheng; Zhao, Lin; Kang, Yingyao; Luo, Zhibin

    2018-02-01

    The deep-coupling of a global navigation satellite system (GNSS) with an inertial navigation system (INS) can provide accurate and reliable navigation information. There are several kinds of deeply-coupled structures. These can be divided mainly into coherent and non-coherent pre-filter based structures, which have their own strong advantages and disadvantages, especially in accuracy and robustness. In this paper, the existing pre-filters of the deeply-coupled structures are analyzed and modified to improve them firstly. Then, an adaptive GNSS/INS deeply-coupled algorithm with hybrid pre-filters processing is proposed to combine the advantages of coherent and non-coherent structures. An adaptive hysteresis controller is designed to implement the hybrid pre-filters processing strategy. The simulation and vehicle test results show that the adaptive deeply-coupled algorithm with hybrid pre-filters processing can effectively improve navigation accuracy and robustness, especially in a GNSS-challenged environment.

  3. 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.

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

    Science.gov (United States)

    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.

  5. Study of the quality characteristics in cold-smoked salmon (Salmo salar) originating from pre- or post-rigor raw material.

    Science.gov (United States)

    Birkeland, S; Akse, L

    2010-01-01

    Improved slaughtering procedures in the salmon industry have caused a delayed onset of rigor mortis and, thus, a potential for pre-rigor secondary processing. The aim of this study was to investigate the effect of rigor status at time of processing on quality traits color, texture, sensory, microbiological, in injection salted, and cold-smoked Atlantic salmon (Salmo salar). Injection of pre-rigor fillets caused a significant (Prigor processed fillets; however, post-rigor (1477 ± 38 g) fillets had a significant (P>0.05) higher fracturability than pre-rigor fillets (1369 ± 71 g). Pre-rigor fillets were significantly (Prigor fillets (37.8 ± 0.8) and had significantly lower (Prigor processed fillets. This study showed that similar quality characteristics can be obtained in cold-smoked products processed either pre- or post-rigor when using suitable injection salting protocols and smoking techniques. © 2010 Institute of Food Technologists®

  6. Differing influence on delays in the case-finding process for tuberculosis between general physicians and specialists in Mongolia.

    Science.gov (United States)

    Enkhbat, S; Toyota, M; Yasuda, N; Ohara, H

    1997-06-01

    The objective of this study is to compare the influence on delays in the tuberculosis case-finding process according to the types of medical facilities initially visited. The subjects include 107 patients 16 years and older who were diagnosed with bacteriologically confirmed pulmonary tuberculosis at nine tuberculosis specialized facilities in Ulaanbaatar, Mongolia from May 1995 to March 1996. Patients were interviewed about their demographic and socioeconomic factors and their medical records were reviewed for measuring delays. Fifty-five patients initially consulted general physicians and the remaining 52 patients initially visited other types of facilities including tuberculosis specialized facilities. Patients who initially consulted general physicians had shorter patient's delays and longer doctor's delays than those who had visited other facilities first. Since the reduction of patient's delay outweighs the extension of doctor's delay among patients who initially consulted general physicians, their total delay was shorter than that of patients who visited other facilities first. The beneficial influence of consulting general physicians first on the total delay was observed after adjusting for patient's age, sex, residence area, family income and family history of tuberculosis. This finding indicates that general physicians play an important role in improving the passive case-finding process in Mongolia.

  7. The 1992 ENDF Pre-processing codes

    International Nuclear Information System (INIS)

    Cullen, D.E.

    1992-01-01

    This document summarizes the 1992 version of the ENDF pre-processing codes which are required for processing evaluated nuclear data coded in the format ENDF-4, ENDF-5, or ENDF-6. Included are the codes CONVERT, MERGER, LINEAR, RECENT, SIGMA1, LEGEND, FIXUP, GROUPIE, DICTION, MIXER, VIRGIN, COMPLOT, EVALPLOT, RELABEL. Some of the functions of these codes are: to calculate cross-sections from resonance parameters; to calculate angular distributions, group average, mixtures of cross-sections, etc; to produce graphical plottings and data comparisons. The codes are designed to operate on virtually any type of computer including PC's. They are available from the IAEA Nuclear Data Section, free of charge upon request, on magnetic tape or a set of HD diskettes. (author)

  8. 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.)

  9. The Effects of Test Trial and Processing Level on Immediate and Delayed Retention

    Science.gov (United States)

    Chang, Sau Hou

    2017-01-01

    The purpose of the present study was to investigate the effects of test trial and processing level on immediate and delayed retention. A 2 × 2 × 2 mixed ANOVAs was used with two between-subject factors of test trial (single test, repeated test) and processing level (shallow, deep), and one within-subject factor of final recall (immediate,…

  10. Pre-processing by data augmentation for improved ellipse fitting.

    Science.gov (United States)

    Kumar, Pankaj; Belchamber, Erika R; Miklavcic, Stanley J

    2018-01-01

    Ellipse fitting is a highly researched and mature topic. Surprisingly, however, no existing method has thus far considered the data point eccentricity in its ellipse fitting procedure. Here, we introduce the concept of eccentricity of a data point, in analogy with the idea of ellipse eccentricity. We then show empirically that, irrespective of ellipse fitting method used, the root mean square error (RMSE) of a fit increases with the eccentricity of the data point set. The main contribution of the paper is based on the hypothesis that if the data point set were pre-processed to strategically add additional data points in regions of high eccentricity, then the quality of a fit could be improved. Conditional validity of this hypothesis is demonstrated mathematically using a model scenario. Based on this confirmation we propose an algorithm that pre-processes the data so that data points with high eccentricity are replicated. The improvement of ellipse fitting is then demonstrated empirically in real-world application of 3D reconstruction of a plant root system for phenotypic analysis. The degree of improvement for different underlying ellipse fitting methods as a function of data noise level is also analysed. We show that almost every method tested, irrespective of whether it minimizes algebraic error or geometric error, shows improvement in the fit following data augmentation using the proposed pre-processing algorithm.

  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. The relaxation time of processes in a FitzHugh-Nagumo neural system with time delay

    International Nuclear Information System (INIS)

    Gong Ailing; Zeng Chunhua; Wang Hua

    2011-01-01

    In this paper, we study the relaxation time (RT) of the steady-state correlation function in a FitzHugh-Nagumo neural system under the presence of multiplicative and additive white noises and time delay. The noise correlation parameter λ can produce a critical behavior in the RT as functions of the multiplicative noise intensity D, the additive noise intensity Q and the time delay τ. That is, the RT decreases as the noise intensities D and Q increase, and increases as the time delay τ increases below the critical value of λ. However, above the critical value, the RT first increases, reaches a maximum, and then decreases as D, Q and τ increase, i.e. a noise intensity D or Q and a time delay τ exist, at which the time scales of the relaxation process are at their largest. In addition, the additive noise intensity Q can also produce a critical behavior in the RT as a function of λ. The noise correlation parameter λ first increases the RT of processes, then decreases it below the critical value of Q. Above the critical value, λ increases it.

  13. 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...

  14. Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets

    Directory of Open Access Journals (Sweden)

    Hoefsloot Huub CJ

    2009-05-01

    Full Text Available Abstract Background Mass spectrometry is increasingly being used to discover proteins or protein profiles associated with disease. Experimental design of mass-spectrometry studies has come under close scrutiny and the importance of strict protocols for sample collection is now understood. However, the question of how best to process the large quantities of data generated is still unanswered. Main challenges for the analysis are the choice of proper pre-processing and classification methods. While these two issues have been investigated in isolation, we propose to use the classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. Results Two in-house generated clinical SELDI-TOF MS datasets are used in this study as an example of high throughput mass-spectrometry data. We perform a systematic comparison of two commonly used pre-processing methods as implemented in Ciphergen ProteinChip Software and in the Cromwell package. With respect to reproducibility, Ciphergen and Cromwell pre-processing are largely comparable. We find that the overlap between peaks detected by either Ciphergen ProteinChip Software or Cromwell is large. This is especially the case for the more stringent peak detection settings. Moreover, similarity of the estimated intensities between matched peaks is high. We evaluate the pre-processing methods using five different classification methods. Classification is done in a double cross-validation protocol using repeated random sampling to obtain an unbiased estimate of classification accuracy. No pre-processing method significantly outperforms the other for all peak detection settings evaluated. Conclusion We use classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. Both pre-processing methods lead to similar classification results on an ovarian cancer and a Gaucher disease dataset. However, the settings for pre-processing

  15. Selective catalytic reduction system and process using a pre-sulfated zirconia binder

    Science.gov (United States)

    Sobolevskiy, Anatoly; Rossin, Joseph A.

    2010-06-29

    A selective catalytic reduction (SCR) process with a palladium catalyst for reducing NOx in a gas, using hydrogen as a reducing agent is provided. The process comprises contacting the gas stream with a catalyst system, the catalyst system comprising (ZrO.sub.2)SO.sub.4, palladium, and a pre-sulfated zirconia binder. The inclusion of a pre-sulfated zirconia binder substantially increases the durability of a Pd-based SCR catalyst system. A system for implementing the disclosed process is further provided.

  16. Output Information Based Fault-Tolerant Iterative Learning Control for Dual-Rate Sampling Process with Disturbances and Output Delay

    Directory of Open Access Journals (Sweden)

    Hongfeng Tao

    2018-01-01

    Full Text Available For a class of single-input single-output (SISO dual-rate sampling processes with disturbances and output delay, this paper presents a robust fault-tolerant iterative learning control algorithm based on output information. Firstly, the dual-rate sampling process with output delay is transformed into discrete system in state-space model form with slow sampling rate without time delay by using lifting technology; then output information based fault-tolerant iterative learning control scheme is designed and the control process is turned into an equivalent two-dimensional (2D repetitive process. Moreover, based on the repetitive process stability theory, the sufficient conditions for the stability of system and the design method of robust controller are given in terms of linear matrix inequalities (LMIs technique. Finally, the flow control simulations of two flow tanks in series demonstrate the feasibility and effectiveness of the proposed method.

  17. 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...

  18. 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.

  19. A review of blood sample handling and pre-processing for metabolomics studies.

    Science.gov (United States)

    Hernandes, Vinicius Veri; Barbas, Coral; Dudzik, Danuta

    2017-09-01

    Metabolomics has been found to be applicable to a wide range of clinical studies, bringing a new era for improving clinical diagnostics, early disease detection, therapy prediction and treatment efficiency monitoring. A major challenge in metabolomics, particularly untargeted studies, is the extremely diverse and complex nature of biological specimens. Despite great advances in the field there still exist fundamental needs for considering pre-analytical variability that can introduce bias to the subsequent analytical process and decrease the reliability of the results and moreover confound final research outcomes. Many researchers are mainly focused on the instrumental aspects of the biomarker discovery process, and sample related variables sometimes seem to be overlooked. To bridge the gap, critical information and standardized protocols regarding experimental design and sample handling and pre-processing are highly desired. Characterization of a range variation among sample collection methods is necessary to prevent results misinterpretation and to ensure that observed differences are not due to an experimental bias caused by inconsistencies in sample processing. Herein, a systematic discussion of pre-analytical variables affecting metabolomics studies based on blood derived samples is performed. Furthermore, we provide a set of recommendations concerning experimental design, collection, pre-processing procedures and storage conditions as a practical review that can guide and serve for the standardization of protocols and reduction of undesirable variation. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. 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.

  1. An interdisciplinary approach to study Pre-Earthquake processes

    Science.gov (United States)

    Ouzounov, D.; Pulinets, S. A.; Hattori, K.; Taylor, P. T.

    2017-12-01

    We will summarize a multi-year research effort on wide-ranging observations of pre-earthquake processes. Based on space and ground data we present some new results relevant to the existence of pre-earthquake signals. Over the past 15-20 years there has been a major revival of interest in pre-earthquake studies in Japan, Russia, China, EU, Taiwan and elsewhere. Recent large magnitude earthquakes in Asia and Europe have shown the importance of these various studies in the search for earthquake precursors either for forecasting or predictions. Some new results were obtained from modeling of the atmosphere-ionosphere connection and analyses of seismic records (foreshocks /aftershocks), geochemical, electromagnetic, and thermodynamic processes related to stress changes in the lithosphere, along with their statistical and physical validation. This cross - disciplinary approach could make an impact on our further understanding of the physics of earthquakes and the phenomena that precedes their energy release. We also present the potential impact of these interdisciplinary studies to earthquake predictability. A detail summary of our approach and that of several international researchers will be part of this session and will be subsequently published in a new AGU/Wiley volume. This book is part of the Geophysical Monograph series and is intended to show the variety of parameters seismic, atmospheric, geochemical and historical involved is this important field of research and will bring this knowledge and awareness to a broader geosciences community.

  2. 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...

  3. Domain general sequence operations contribute to pre-SMA involvement in visuo-spatial processing

    Directory of Open Access Journals (Sweden)

    E. Charles eLeek

    2016-01-01

    Full Text Available This study used 3T MRI to elucidate the functional role of supplementary motor area (SMA in relation to visuo-spatial processing. A localizer task contrasting sequential number subtraction and repetitive button pressing was used to functionally delineate non-motor sequence processing in pre-SMA, and activity in SMA-proper associated with motor sequencing. Patterns of BOLD responses in these regions were then contrasted to those from two tasks of visuo-spatial processing. In one task participants performed mental rotation in which recognition memory judgments were made to previously memorized 2D novel patterns across image-plane rotations. The other task involved abstract grid navigation in which observers computed a series of imagined location shifts in response to directional (arrow cues around a mental grid. The results showed overlapping activation in pre-SMA for sequential subtraction and both visuo-spatial tasks. These results suggest that visuo-spatial processing is supported by non-motor sequence operations that involve pre-SMA. More broadly, these data further highlight the functional heterogeneity of pre-SMA, and show that its role extends to processes beyond the planning and online control of movement.

  4. Parallel finite elements with domain decomposition and its pre-processing

    International Nuclear Information System (INIS)

    Yoshida, A.; Yagawa, G.; Hamada, S.

    1993-01-01

    This paper describes a parallel finite element analysis using a domain decomposition method, and the pre-processing for the parallel calculation. Computer simulations are about to replace experiments in various fields, and the scale of model to be simulated tends to be extremely large. On the other hand, computational environment has drastically changed in these years. Especially, parallel processing on massively parallel computers or computer networks is considered to be promising techniques. In order to achieve high efficiency on such parallel computation environment, large granularity of tasks, a well-balanced workload distribution are key issues. It is also important to reduce the cost of pre-processing in such parallel FEM. From the point of view, the authors developed the domain decomposition FEM with the automatic and dynamic task-allocation mechanism and the automatic mesh generation/domain subdivision system for it. (author)

  5. Nuclear pre-mRNA processing in plants

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, A.S.N. [Colorado State Univ., Fort Collins, CO (United States). Dept. of Biology and Program in Molecular Plant Biology; Golovkin, M. (eds.) [Thomas Jefferson Univ., Philadelphia, PA (United States). Dept. of Microbiology

    2008-07-01

    This volume of CTMI, entitled Nuclear premRNA Processing in Plants, with 16 chapters from leading scientists in this area, summarizes recent advances in nuclear pre-mRNA processing and its role in plant growth and development. It provides researchers in the field, as well as those in related areas, with an up-to-date and comprehensive, yet concise, overview of the current status and future potential of this research in understanding plant biology. The first four chapters focus on spliceosome composition, genome-wide alternative splicing, and splice site requirements for U1 and U12 introns using computational and empirical approaches. Analysis of sequenced plant genomes has revealed that 80% of all protein-coding nuclear genes contain one or more introns. The lack of an in vitro plant splicing system has made it difficult to identify general and plant-specific components of splicing machinery in plants. The next three chapters focus on serine/arginine-rich (SR) proteins, a family of highly conserved proteins, which are known to play key roles in constitutive and regulated splicing of pre-mRNA and other aspects of RNA metabolism in metazoans. These proteins engage both in RNA binding and protein.protein interactions and function as splicing regulators at multiple stages of spliceosome assembly. This family of proteins has expanded considerably in plants with several plant-specific SR proteins. Several serendipitous discoveries made using forward genetics are indicating that RNA metabolism (alternative splicing, alternative polyadenylation, mRNA transport) plays an important role in many aspects of plant growth and development and in plant responses to biotic and abiotic stresses. The next seven chapters focus on these aspects of RNA metabolism. The plant hormone abscisic acid (ABA) regulates a number of physiological processes during plant growth and development. The next chapter or A.B. Rose discusses the ways introns affect gene expression both positively and

  6. Nuclear pre-mRNA processing in plants

    International Nuclear Information System (INIS)

    Reddy, A.S.N.; Golovkin, M.

    2008-01-01

    This volume of CTMI, entitled Nuclear premRNA Processing in Plants, with 16 chapters from leading scientists in this area, summarizes recent advances in nuclear pre-mRNA processing and its role in plant growth and development. It provides researchers in the field, as well as those in related areas, with an up-to-date and comprehensive, yet concise, overview of the current status and future potential of this research in understanding plant biology. The first four chapters focus on spliceosome composition, genome-wide alternative splicing, and splice site requirements for U1 and U12 introns using computational and empirical approaches. Analysis of sequenced plant genomes has revealed that 80% of all protein-coding nuclear genes contain one or more introns. The lack of an in vitro plant splicing system has made it difficult to identify general and plant-specific components of splicing machinery in plants. The next three chapters focus on serine/arginine-rich (SR) proteins, a family of highly conserved proteins, which are known to play key roles in constitutive and regulated splicing of pre-mRNA and other aspects of RNA metabolism in metazoans. These proteins engage both in RNA binding and protein.protein interactions and function as splicing regulators at multiple stages of spliceosome assembly. This family of proteins has expanded considerably in plants with several plant-specific SR proteins. Several serendipitous discoveries made using forward genetics are indicating that RNA metabolism (alternative splicing, alternative polyadenylation, mRNA transport) plays an important role in many aspects of plant growth and development and in plant responses to biotic and abiotic stresses. The next seven chapters focus on these aspects of RNA metabolism. The plant hormone abscisic acid (ABA) regulates a number of physiological processes during plant growth and development. The next chapter or A.B. Rose discusses the ways introns affect gene expression both positively and

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Conversation on data mining strategies in LC-MS untargeted metabolomics: pre-processing and pre-treatment steps

    CSIR Research Space (South Africa)

    Tugizimana, F

    2016-11-01

    Full Text Available -MS)-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter. Data obtained in positive mode...

  12. Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides.

    Science.gov (United States)

    Hia, Fabian; Chionh, Yok Hian; Pang, Yan Ling Joy; DeMott, Michael S; McBee, Megan E; Dedon, Peter C

    2015-03-11

    A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Significance of Joint Features Derived from the Modified Group Delay Function in Speech Processing

    Directory of Open Access Journals (Sweden)

    Murthy Hema A

    2007-01-01

    Full Text Available This paper investigates the significance of combining cepstral features derived from the modified group delay function and from the short-time spectral magnitude like the MFCC. The conventional group delay function fails to capture the resonant structure and the dynamic range of the speech spectrum primarily due to pitch periodicity effects. The group delay function is modified to suppress these spikes and to restore the dynamic range of the speech spectrum. Cepstral features are derived from the modified group delay function, which are called the modified group delay feature (MODGDF. The complementarity and robustness of the MODGDF when compared to the MFCC are also analyzed using spectral reconstruction techniques. Combination of several spectral magnitude-based features and the MODGDF using feature fusion and likelihood combination is described. These features are then used for three speech processing tasks, namely, syllable, speaker, and language recognition. Results indicate that combining MODGDF with MFCC at the feature level gives significant improvements for speech recognition tasks in noise. Combining the MODGDF and the spectral magnitude-based features gives a significant increase in recognition performance of 11% at best, while combining any two features derived from the spectral magnitude does not give any significant improvement.

  14. Summary of ENDF/B pre-processing codes

    International Nuclear Information System (INIS)

    Cullen, D.E.

    1981-12-01

    This document contains the summary documentation for the ENDF/B pre-processing codes: LINEAR, RECENT, SIGMA1, GROUPIE, EVALPLOT, MERGER, DICTION, CONVERT. This summary documentation is merely a copy of the comment cards that appear at the beginning of each programme; these comment cards always reflect the latest status of input options, etc. For the latest published documentation on the methods used in these codes see UCRL-50400, Vol.17 parts A-E, Lawrence Livermore Laboratory (1979)

  15. 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 ...

  16. 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 ...

  17. 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...

  18. 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

  19. 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.

  20. 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.

  1. Pre-movement planning processes in people with congenital mirror movements.

    Science.gov (United States)

    Franz, E A; Fu, Y

    2017-10-01

    Pre-movement processes were investigated in people with Congenital mirrormovement (CMM), a rare disorder in which bilateral movement (mirroring) occurs in the upper distal extremities (primarily the hands and fingers) during intended unilateral movements. Abnormal density of ipsilateral corticospinal projections is an established hallmark of CMM. This study tested whether the Lateralised Readiness Potential (LRP), which reflects movement planning and readiness, is also abnormal in people with CMM. Twenty-eight neurologically-normal controls and 8 people with CMM were tested on a unimanual Go/No-go task while electroencephalography (EEG) was recorded to assess the LRP. No significant group differences were found in reaction time (RT). However, significantly smaller LRP amplitudes were found, on average, in the CMM group compared to Controls at central-motor (C3,C4) sites in stimulus-locked and response-locked epochs; similar group differences were also found at further frontal sites (F3,F4) during response-locked epochs. Abnormal brain activity in pre-movement processes associated with response planning and preparation is present in people with CMM. Aberrant bilateral activity during pre-movement processes is clearly implicated; whether part of the etiology of CMM, or as a mechanism of neuro-compensation, is not yet known. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

  2. Image Processing of Welding Procedure Specification and Pre-process program development for Finite Element Modelling

    International Nuclear Information System (INIS)

    Kim, K. S.; Lee, H. J.

    2009-11-01

    PRE-WELD program, which generates automatically the input file for the finite element analysis on the 2D butt welding at the dissimilar metal weld part, was developed. This program is pre-process program of the FEM code for analyzing the residual stress at the welding parts. Even if the users have not the detail knowledge for the FEM modelling, the users can make the ABAQUS INPUT easily by inputting the shape data of welding part, the weld current and voltage of welding parameters. By using PRE-WELD program, we can save the time and the effort greatly for preparing the ABAQUS INPUT for the residual stress analysis at the welding parts, and make the exact input without the human error

  3. 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...

  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. A unified approach to the design of advanced proportional-integral-derivative controllers for time-delay processes

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Moonyong [Yeungnam University, Gyeongsan (Korea, Republic of); Vu, Truong Nguyen Luan [University of Technical Education of Ho Chi Minh City, Ho Chi Minh (China)

    2013-03-15

    A unified approach for the design of proportional-integral-derivative (PID) controllers cascaded with first-order lead-lag filters is proposed for various time-delay processes. The proposed controller’s tuning rules are directly derived using the Padé approximation on the basis of internal model control (IMC) for enhanced stability against disturbances. A two-degrees-of-freedom (2DOF) control scheme is employed to cope with both regulatory and servo problems. Simulation is conducted for a broad range of stable, integrating, and unstable processes with time delays. Each simulated controller is tuned to have the same degree of robustness in terms of maximum sensitivity (Ms). The results demonstrate that the proposed controller provides superior disturbance rejection and set-point tracking when compared with recently published PID-type controllers. Controllers’ robustness is investigated through the simultaneous introduction of perturbation uncertainties to all process parameters to obtain worst-case process-model mismatch. The process-model mismatch simulation results demonstrate that the proposed method consistently affords superior robustness.

  8. 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.

  9. 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.

  10. Optimal nonlinear information processing capacity in delay-based reservoir computers

    Science.gov (United States)

    Grigoryeva, Lyudmila; Henriques, Julie; Larger, Laurent; Ortega, Juan-Pablo

    2015-09-01

    Reservoir computing is a recently introduced brain-inspired machine learning paradigm capable of excellent performances in the processing of empirical data. We focus in a particular kind of time-delay based reservoir computers that have been physically implemented using optical and electronic systems and have shown unprecedented data processing rates. Reservoir computing is well-known for the ease of the associated training scheme but also for the problematic sensitivity of its performance to architecture parameters. This article addresses the reservoir design problem, which remains the biggest challenge in the applicability of this information processing scheme. More specifically, we use the information available regarding the optimal reservoir working regimes to construct a functional link between the reservoir parameters and its performance. This function is used to explore various properties of the device and to choose the optimal reservoir architecture, thus replacing the tedious and time consuming parameter scannings used so far in the literature.

  11. 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...

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Delayed matching-to-sample: A tool to assess memory and other cognitive processes in pigeons.

    Science.gov (United States)

    Zentall, Thomas R; Smith, Aaron P

    2016-02-01

    Delayed matching-to-sample is a versatile task that has been used to assess the nature of animal memory. Although once thought to be a relatively passive process, matching research has demonstrated considerable flexibility in how animals actively represent events in memory. But delayed matching can also demonstrate how animals fail to maintain representations in memory when they are cued that they will not be tested (directed forgetting) and how the outcome expected can serve as a choice cue. When pigeons have shown divergent retention functions following training without a delay, it has been taken as evidence of the use of a single-code/default coding strategy but in many cases an alternative account may be involved. Delayed matching has also been used to investigate equivalence learning (how animals represent stimuli when they learn that the same comparison response is correct following the presentation of two different samples) and to test for metamemory (the ability of pigeons to indicate that they understand what they know) by allowing animals to decline to be tested when they are uncertain that they remember a stimulus. How animals assess the passage of time has also been studied using the matching task. And there is evidence that when memory for the sample is impaired by a delay, rather than use the probability of being correct for choice of each of the comparison stimuli, pigeons tend to choose based on the overall sample frequency (base-rate neglect). Finally, matching has been used to identify natural color categories as well as dimensional categories in pigeons. Overall, matching to sample has provided an excellent methodology for assessing an assortment of cognitive processes in animals. Copyright © 2015 Elsevier B.V. All rights reserved.

  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. Project delay analysis of HRSG

    Science.gov (United States)

    Silvianita; Novega, A. S.; Rosyid, D. M.; Suntoyo

    2017-08-01

    Completion of HRSG (Heat Recovery Steam Generator) fabrication project sometimes is not sufficient with the targeted time written on the contract. The delay on fabrication process can cause some disadvantages for fabricator, including forfeit payment, delay on HRSG construction process up until HRSG trials delay. In this paper, the author is using semi quantitative on HRSG pressure part fabrication delay with configuration plant 1 GT (Gas Turbine) + 1 HRSG + 1 STG (Steam Turbine Generator) using bow-tie analysis method. Bow-tie analysis method is a combination from FTA (Fault tree analysis) and ETA (Event tree analysis) to develop the risk matrix of HRSG. The result from FTA analysis is use as a threat for preventive measure. The result from ETA analysis is use as impact from fabrication delay.

  19. The effect of dilute acid pre-treatment process in bioethanol production from durian (Durio zibethinus) seeds waste

    Science.gov (United States)

    Ghazali, K. A.; Salleh, S. F.; Riayatsyah, T. M. I.; Aditiya, H. B.; Mahlia, T. M. I.

    2016-03-01

    Lignocellulosic biomass is one of the promising feedstocks for bioethanol production. The process starts from pre-treatment, hydrolysis, fermentation, distillation and finally obtaining the final product, ethanol. The efficiency of enzymatic hydrolysis of cellulosic biomass depends heavily on the effectiveness of the pre-treatment step which main function is to break the lignin structure of the biomass. This work aims to investigate the effects of dilute acid pre-treatment on the enzymatic hydrolysis of durian seeds waste to glucose and the subsequent bioethanol fermentation process. The yield of glucose from dilute acid pre-treated sample using 0.6% H2SO4 and 5% substrate concentration shows significant value of 23.4951 g/L. Combination of dilute acid pre-treatment and enzymatic hydrolysis using 150U of enzyme able to yield 50.0944 g/L of glucose content higher compared to normal pre-treated sample of 8.1093 g/L. Dilute acid pre-treatment sample also shows stable and efficient yeast activity during fermentation process with lowest glucose content at 2.9636 g/L compared to 14.7583g/L for normal pre-treated sample. Based on the result, it can be concluded that dilute acid pre-treatment increase the yield of ethanol from bioethanol production process.

  20. Reproducible cancer biomarker discovery in SELDI-TOF MS using different pre-processing algorithms.

    Directory of Open Access Journals (Sweden)

    Jinfeng Zou

    Full Text Available BACKGROUND: There has been much interest in differentiating diseased and normal samples using biomarkers derived from mass spectrometry (MS studies. However, biomarker identification for specific diseases has been hindered by irreproducibility. Specifically, a peak profile extracted from a dataset for biomarker identification depends on a data pre-processing algorithm. Until now, no widely accepted agreement has been reached. RESULTS: In this paper, we investigated the consistency of biomarker identification using differentially expressed (DE peaks from peak profiles produced by three widely used average spectrum-dependent pre-processing algorithms based on SELDI-TOF MS data for prostate and breast cancers. Our results revealed two important factors that affect the consistency of DE peak identification using different algorithms. One factor is that some DE peaks selected from one peak profile were not detected as peaks in other profiles, and the second factor is that the statistical power of identifying DE peaks in large peak profiles with many peaks may be low due to the large scale of the tests and small number of samples. Furthermore, we demonstrated that the DE peak detection power in large profiles could be improved by the stratified false discovery rate (FDR control approach and that the reproducibility of DE peak detection could thereby be increased. CONCLUSIONS: Comparing and evaluating pre-processing algorithms in terms of reproducibility can elucidate the relationship among different algorithms and also help in selecting a pre-processing algorithm. The DE peaks selected from small peak profiles with few peaks for a dataset tend to be reproducibly detected in large peak profiles, which suggests that a suitable pre-processing algorithm should be able to produce peaks sufficient for identifying useful and reproducible biomarkers.

  1. A unified approach for proportional-integral-derivative controller design for time delay processes

    International Nuclear Information System (INIS)

    Shamsuzzoha, Mohammad

    2015-01-01

    An analytical design method for PI/PID controller tuning is proposed for several types of processes with time delay. A single tuning formula gives enhanced disturbance rejection performance. The design method is based on the IMC approach, which has a single tuning parameter to adjust the performance and robustness of the controller. A simple tuning formula gives consistently better performance as compared to several well-known methods at the same degree of robustness for stable and integrating process. The performance of the unstable process has been compared with other recently published methods which also show significant improvement in the proposed method. Furthermore, the robustness of the controller is investigated by inserting a perturbation uncertainty in all parameters simultaneously, again showing comparable results with other methods. An analysis has been performed for the uncertainty margin in the different process parameters for the robust controller design. It gives the guidelines of the M s setting for the PI controller design based on the process parameters uncertainty. For the selection of the closed-loop time constant, (τ c ), a guideline is provided over a broad range of θ/τ ratios on the basis of the peak of maximum uncertainty (M s ). A comparison of the IAE has been conducted for the wide range of θ/τ ratio for the first order time delay process. The proposed method shows minimum IAE in compared to SIMC, while Lee et al. shows poor disturbance rejection in the lag dominant process. In the simulation study, the controllers were tuned to have the same degree of robustness by measuring the M s , to obtain a reasonable comparison

  2. Data pre-processing: a case study in predicting student's retention in ...

    African Journals Online (AJOL)

    dataset with features that are ready for data mining task. The study also proposed a process model and suggestions, which can be applied to support more comprehensible tools for educational domain who is the end user. Subsequently, the data pre-processing become more efficient for predicting student's retention in ...

  3. 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

  4. Task Difficulty Differentially Affects Two Measures of Processing Load: The Pupil Response during Sentence Processing and Delayed Cued Recall of the Sentences

    Science.gov (United States)

    Zekveld, Adriana A.; Festen, Joost M.; Kramer, Kramera

    2013-01-01

    Purpose: In this study, the authors assessed the influence of masking level (29% or 71% sentence perception) and test modality on the processing load during language perception as reflected by the pupil response. In addition, the authors administered a delayed cued stimulus recall test to examine whether processing load affected the encoding of…

  5. Summary of ENDF/B Pre-Processing Codes June 1983

    International Nuclear Information System (INIS)

    Cullen, D.E.

    1983-06-01

    This is the summary documentation for the 1983 version of the ENDF/B Pre-Processing Codes LINEAR, RECENT, SIGMA1, GROUPIE, EVALPLOT, MERGER, DICTION, COMPLOT, CONVERT. This summary documentation is merely a copy of the comment cards that appear at the beginning of each programme; these comment cards always reflect the latest status of input options, etc

  6. 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.

  7. Improvement of Haramay Fiber by Pre-treatment of Retting Process withPhosphoric Acid

    International Nuclear Information System (INIS)

    Kuntari-Sasas; Neni-Rustini Eriawati

    2000-01-01

    Haramay as bast fiber contains of cellulose fiber as the main part, mixedwith hemi cellulose, pectin, and lignin as binding material for cellulosefiber to keep it together in the bundle form. For textile material, this bastfiber has to be freed from its binding material, called as retting process,before subjecting to scouring, dyeing and finishing process in textileindustry. In the retting process the dissolve of binding material can be doneeither by using enzyme in bio technology or extraction with strong alkalinecondition in common technology. Using sodium hydroxide for dissolving thebinding material can be carried out easily with good dissolving ability, butcan render the strength retention of the cellulose fiber. Pre-treatment ofthe bast fiber with phosphoric acid (H 3 PO 4 ), is expected to hydrolyze someof the binding materials that can not be dissolved in alkaline condition,including natural pigment that colored the fiber with creamy white. In thisstudy, the pre-treatment process before retting with phosphoric acid wascarried out in various condition, such as concentration of phosphoric acid (5ml/l- 25 ml/l), time and temperature of pre-treatment (1-3 hours at 50 o C or12-24 hours at room temperature), followed by neutralization in dilutealkaline. The retting process was carried out by means of scouring in variousconcentration of sodium hydroxide (NaOH 38 o Be, 10 ml/l-30 m/l), and then wascontinued with bleaching process in hydrogen peroxide solution. Aftercarrying out those experiment, the bast fiber that called haramay wassubjected to testing for weight reduction, strength retention and degree ofwhiteness. From the testing results it is concluded that pre-treatment withphosphoric acid can increase the weight reduction, strength retention ortenacity and degree of whiteness of haramay fiber compared to the oneswithout pre-treatment with phosphoric acid. The best result was obtained bypre-treatment with 5 ml/l H 3 PO 4 at 50 o C for 2 hours, continued by

  8. Broadband true time delay for microwave signal processing, using slow light based on stimulated Brillouin scattering in optical fibers.

    Science.gov (United States)

    Chin, Sanghoon; Thévenaz, Luc; Sancho, Juan; Sales, Salvador; Capmany, José; Berger, Perrine; Bourderionnet, Jérôme; Dolfi, Daniel

    2010-10-11

    We experimentally demonstrate a novel technique to process broadband microwave signals, using all-optically tunable true time delay in optical fibers. The configuration to achieve true time delay basically consists of two main stages: photonic RF phase shifter and slow light, based on stimulated Brillouin scattering in fibers. Dispersion properties of fibers are controlled, separately at optical carrier frequency and in the vicinity of microwave signal bandwidth. This way time delay induced within the signal bandwidth can be manipulated to correctly act as true time delay with a proper phase compensation introduced to the optical carrier. We completely analyzed the generated true time delay as a promising solution to feed phased array antenna for radar systems and to develop dynamically reconfigurable microwave photonic filters.

  9. Thermally Activated Delayed Fluorescence in Polymers: A New Route toward Highly Efficient Solution Processable OLEDs.

    Science.gov (United States)

    Nikolaenko, Andrey E; Cass, Michael; Bourcet, Florence; Mohamad, David; Roberts, Matthew

    2015-11-25

    Efficient intermonomer thermally activated delayed fluorescence is demonstrated for the first time, opening a new route to achieving high-efficiency solution processable polymer light-emitting device materials. External quantum efficiency (EQE) of up to 10% is achieved in a simple fully solution-processed device structure, and routes for further EQE improvement identified. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. 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.

  11. Investigation into the effect of different fuels on ignition delay of M-type diesel combustion process

    Directory of Open Access Journals (Sweden)

    Bibić Dževad

    2008-01-01

    Full Text Available An ignition delay is a very complex process which depends on a great number of parameters. In practice, definition of the ignition delay is based on the use of correlation expressions. However, the correlation expressions have very often limited application field. This paper presents a new correlation which has been developed during the research project on the direct injection M-type diesel engine using both the diesel and biodiesel fuel, as well as different values of a static injection timing. A dynamic start of injection, as well as the ignition delay, is defined in two ways. The first approach is based on measurement of a needle lift, while the second is based on measurement of a fuel pressure before the injector. The latter approach requires calculation of pressure signals delay through the fuel injection system and the variation of a static advance injection angle changing. The start of a combustion and the end of the ignition delay is defined on the basis of measurements of an in-cylinder pressure and its point of separation from a skip-fire pressure trace. The developed correlation gives better prediction of the ignition delay definition for the M-type direct injection diesel engine in the case of diesel and biodiesel fuel use when compared with the classic expression by the other authors available in the literature.

  12. 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.

  13. Poisson pre-processing of nonstationary photonic signals: Signals with equality between mean and variance.

    Science.gov (United States)

    Poplová, Michaela; Sovka, Pavel; Cifra, Michal

    2017-01-01

    Photonic signals are broadly exploited in communication and sensing and they typically exhibit Poisson-like statistics. In a common scenario where the intensity of the photonic signals is low and one needs to remove a nonstationary trend of the signals for any further analysis, one faces an obstacle: due to the dependence between the mean and variance typical for a Poisson-like process, information about the trend remains in the variance even after the trend has been subtracted, possibly yielding artifactual results in further analyses. Commonly available detrending or normalizing methods cannot cope with this issue. To alleviate this issue we developed a suitable pre-processing method for the signals that originate from a Poisson-like process. In this paper, a Poisson pre-processing method for nonstationary time series with Poisson distribution is developed and tested on computer-generated model data and experimental data of chemiluminescence from human neutrophils and mung seeds. The presented method transforms a nonstationary Poisson signal into a stationary signal with a Poisson distribution while preserving the type of photocount distribution and phase-space structure of the signal. The importance of the suggested pre-processing method is shown in Fano factor and Hurst exponent analysis of both computer-generated model signals and experimental photonic signals. It is demonstrated that our pre-processing method is superior to standard detrending-based methods whenever further signal analysis is sensitive to variance of the signal.

  14. The Ratios of Pre-emulsified Duck Skin for Optimized Processing of Restructured Ham.

    Science.gov (United States)

    Shim, Jae-Yun; Kim, Tae-Kyung; Kim, Young-Boong; Jeon, Ki-Hong; Ahn, Kwang-Il; Paik, Hyun-Dong; Choi, Yun-Sang

    2018-02-01

    The purpose of this study was to investigate the quality of duck ham formulated with duck skin through the pre-emulsification process. The experiments to investigate the quality characteristics of duck ham were carried out to measure proximate composition, cooking loss, emulsion stability, pH, color, texture profile analysis, apparent viscosity, and sensory characteristics. Duck ham was prepared with various ratios of duck skin in pre-emulsion as follows: Control (duct skin 30%), T1 (duck skin 20% + pre-emulsified duck skin 10%), T2 (duck skin 15% + pre-emulsified duck skin 15%), T3 (duck skin 10% + pre-emulsified duck skin 20%), and T4 (pre-emulsified duck skin 30%). As the ratio of duck skin to pre-emulsified skin changed, the quality of duck ham in terms of moisture content, fat content, cooking loss, emulsion stability, lightness, textural analysis, apparent viscosity, and overall acceptability changed. The moisture content of T2 was the highest ( p ham and 1:1 ratio of duck skin and pre-emulsified skin was the proper ratio to improve the quality characteristics of duck ham.

  15. Delayed early proprioceptive information processing in schizophrenia

    DEFF Research Database (Denmark)

    Arnfred, Sidse M; Hemmingsen, RP; Parnas, Josef

    2006-01-01

    . In the patients, the early contralateral parietal activity was delayed and later central activity had increased amplitude, but gating was unaffected. The results could be understood within the "deficiency of corollary discharge" model of schizophrenia but not within the "filtering" theory. Further studies...

  16. How Do Pre-Service Teachers' Reflective Processes Differ in Relation to Different Contexts?

    Science.gov (United States)

    Kaasila, Raimo; Lauriala, Anneli

    2012-01-01

    Reflective practice represents a central theme in teacher education. The focus of this study is to look at pre-service teachers' reflection processes and their breadth and depth in four different contexts. Our research data consist of 53 pre-service teachers' mathematics portfolios, from which three were selected for closer scrutiny. The chosen…

  17. The Problem-Based Learning Process: Reflections of Pre-Service Elementary School Teachers

    Science.gov (United States)

    Baysal, Zeliha Nurdan

    2017-01-01

    This study aims to identify the benefits acquired by third-year pre-service elementary school teachers participating in a problem-based learning process in social studies education, the issues they encountered in that process and those they are likely to encounter, and their feelings about the process. Semi-structured interviews were used as one…

  18. 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...

  19. 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.

  20. 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.

  1. 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)

  2. Nonlinear delay monopoly with bounded rationality

    International Nuclear Information System (INIS)

    Matsumoto, Akio; Szidarovszky, Ferenc

    2012-01-01

    The purpose of this paper is to study the dynamics of a monopolistic firm in a continuous-time framework. The firm is assumed to be boundedly rational and to experience time delays in obtaining and implementing information on output. The dynamic adjustment process is based on the gradient of the expected profit. The paper is divided into three parts: we examine delay effects on dynamics caused by one-time delay and two-time delays in the first two parts. Global dynamics and analytical results on local dynamics are numerically confirmed in the third part. Four main results are demonstrated. First, the stability switch from stability to instability occurs only once in the case of a single delay. Second, the alternation of stability and instability can continue if two time delays are involved. Third, the occurence of Hopf bifurcation is analytically shown if stability is lost. Finally, in a bifurcation process, there are a period-doubling cascade to chaos and a period-halving cascade to the equilibrium point in the case of two time delays if the difference between the two delays is large.

  3. 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.

  4. Pre-processing data using wavelet transform and PCA based on ...

    Indian Academy of Sciences (India)

    Abazar Solgi

    2017-07-14

    Jul 14, 2017 ... Pre-processing data using wavelet transform and PCA based on support vector regression and gene expression programming for river flow simulation. Abazar Solgi1,*, Amir Pourhaghi1, Ramin Bahmani2 and Heidar Zarei3. 1. Department of Water Resources Engineering, Shahid Chamran University of ...

  5. Altered brain mechanisms of emotion processing in pre-manifest Huntington's disease.

    Science.gov (United States)

    Novak, Marianne J U; Warren, Jason D; Henley, Susie M D; Draganski, Bogdan; Frackowiak, Richard S; Tabrizi, Sarah J

    2012-04-01

    Huntington's disease is an inherited neurodegenerative disease that causes motor, cognitive and psychiatric impairment, including an early decline in ability to recognize emotional states in others. The pathophysiology underlying the earliest manifestations of the disease is not fully understood; the objective of our study was to clarify this. We used functional magnetic resonance imaging to investigate changes in brain mechanisms of emotion recognition in pre-manifest carriers of the abnormal Huntington's disease gene (subjects with pre-manifest Huntington's disease): 16 subjects with pre-manifest Huntington's disease and 14 control subjects underwent 1.5 tesla magnetic resonance scanning while viewing pictures of facial expressions from the Ekman and Friesen series. Disgust, anger and happiness were chosen as emotions of interest. Disgust is the emotion in which recognition deficits have most commonly been detected in Huntington's disease; anger is the emotion in which impaired recognition was detected in the largest behavioural study of emotion recognition in pre-manifest Huntington's disease to date; and happiness is a positive emotion to contrast with disgust and anger. Ekman facial expressions were also used to quantify emotion recognition accuracy outside the scanner and structural magnetic resonance imaging with voxel-based morphometry was used to assess the relationship between emotion recognition accuracy and regional grey matter volume. Emotion processing in pre-manifest Huntington's disease was associated with reduced neural activity for all three emotions in partially separable functional networks. Furthermore, the Huntington's disease-associated modulation of disgust and happiness processing was negatively correlated with genetic markers of pre-manifest disease progression in distributed, largely extrastriatal networks. The modulated disgust network included insulae, cingulate cortices, pre- and postcentral gyri, precunei, cunei, bilateral putamena

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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 ...

  13. Scientific data products and the data pre-processing subsystem of the Chang'e-3 mission

    International Nuclear Information System (INIS)

    Tan Xu; Liu Jian-Jun; Li Chun-Lai; Feng Jian-Qing; Ren Xin; Wang Fen-Fei; Yan Wei; Zuo Wei; Wang Xiao-Qian; Zhang Zhou-Bin

    2014-01-01

    The Chang'e-3 (CE-3) mission is China's first exploration mission on the surface of the Moon that uses a lander and a rover. Eight instruments that form the scientific payloads have the following objectives: (1) investigate the morphological features and geological structures at the landing site; (2) integrated in-situ analysis of minerals and chemical compositions; (3) integrated exploration of the structure of the lunar interior; (4) exploration of the lunar-terrestrial space environment, lunar surface environment and acquire Moon-based ultraviolet astronomical observations. The Ground Research and Application System (GRAS) is in charge of data acquisition and pre-processing, management of the payload in orbit, and managing the data products and their applications. The Data Pre-processing Subsystem (DPS) is a part of GRAS. The task of DPS is the pre-processing of raw data from the eight instruments that are part of CE-3, including channel processing, unpacking, package sorting, calibration and correction, identification of geographical location, calculation of probe azimuth angle, probe zenith angle, solar azimuth angle, and solar zenith angle and so on, and conducting quality checks. These processes produce Level 0, Level 1 and Level 2 data. The computing platform of this subsystem is comprised of a high-performance computing cluster, including a real-time subsystem used for processing Level 0 data and a post-time subsystem for generating Level 1 and Level 2 data. This paper describes the CE-3 data pre-processing method, the data pre-processing subsystem, data classification, data validity and data products that are used for scientific studies

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. Pre-writing Techniques In The Writing Process For The L2 Classroom

    OpenAIRE

    Gülşah Geyimci

    2014-01-01

    This study investigated pre-writing techniques in the learning process to improve written communication skills of learners using qualitative research methods. This study was performed in a public school, Suphi Öner Primary School in Turkey, in Mersin. Students were seventh grade class that their level was pre-intermediate. This class was made up of twenty students. It took three weeks, the students' samples, drawings and blogs were documented by the students. In order to examine the results, ...

  19. 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.

  20. 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.

  1. Discrete pre-processing step effects in registration-based pipelines, a preliminary volumetric study on T1-weighted images.

    Science.gov (United States)

    Muncy, Nathan M; Hedges-Muncy, Ariana M; Kirwan, C Brock

    2017-01-01

    Pre-processing MRI scans prior to performing volumetric analyses is common practice in MRI studies. As pre-processing steps adjust the voxel intensities, the space in which the scan exists, and the amount of data in the scan, it is possible that the steps have an effect on the volumetric output. To date, studies have compared between and not within pipelines, and so the impact of each step is unknown. This study aims to quantify the effects of pre-processing steps on volumetric measures in T1-weighted scans within a single pipeline. It was our hypothesis that pre-processing steps would significantly impact ROI volume estimations. One hundred fifteen participants from the OASIS dataset were used, where each participant contributed three scans. All scans were then pre-processed using a step-wise pipeline. Bilateral hippocampus, putamen, and middle temporal gyrus volume estimations were assessed following each successive step, and all data were processed by the same pipeline 5 times. Repeated-measures analyses tested for a main effects of pipeline step, scan-rescan (for MRI scanner consistency) and repeated pipeline runs (for algorithmic consistency). A main effect of pipeline step was detected, and interestingly an interaction between pipeline step and ROI exists. No effect for either scan-rescan or repeated pipeline run was detected. We then supply a correction for noise in the data resulting from pre-processing.

  2. 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

  3. 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.

  4. 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

  5. Learning processes of students in competence based pre-vocational secondary education

    NARCIS (Netherlands)

    Koopman, M.; Teune, P.J.; Beijaard, D.; Brok, den P.J.

    2009-01-01

    The purpose of this study was to validate a causal and hierarchical model to elaborate on the relation between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education-students. This model can be used to describe students'

  6. Learning processes of students in competence-based pre-vocational secondary education

    NARCIS (Netherlands)

    prof dr Douwe Beijaard; Dr. M. Koopman; P. den Brok; Dr P.J. Teune

    2008-01-01

    The purpose of this study was to validate a causal and hierarchical model that describes the relations between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education-students (n=719; 14 schools). Preferences of students for

  7. 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

  8. 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)

  9. 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.

  10. Pre-eruptive magmatic processes re-timed using a non-isothermal approach to magma chamber dynamics.

    Science.gov (United States)

    Petrone, Chiara Maria; Bugatti, Giuseppe; Braschi, Eleonora; Tommasini, Simone

    2016-10-05

    Constraining the timescales of pre-eruptive magmatic processes in active volcanic systems is paramount to understand magma chamber dynamics and the triggers for volcanic eruptions. Temporal information of magmatic processes is locked within the chemical zoning profiles of crystals but can be accessed by means of elemental diffusion chronometry. Mineral compositional zoning testifies to the occurrence of substantial temperature differences within magma chambers, which often bias the estimated timescales in the case of multi-stage zoned minerals. Here we propose a new Non-Isothermal Diffusion Incremental Step model to take into account the non-isothermal nature of pre-eruptive processes, deconstructing the main core-rim diffusion profiles of multi-zoned crystals into different isothermal steps. The Non-Isothermal Diffusion Incremental Step model represents a significant improvement in the reconstruction of crystal lifetime histories. Unravelling stepwise timescales at contrasting temperatures provides a novel approach to constraining pre-eruptive magmatic processes and greatly increases our understanding of magma chamber dynamics.

  11. 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...

  12. Discounting of Monetary Rewards That Are Both Delayed and Probabilistic: Delay and Probability Combine Multiplicatively, Not Additively

    Science.gov (United States)

    Vanderveldt, Ariana; Green, Leonard; Myerson, Joel

    2015-01-01

    The value of an outcome is affected both by the delay until its receipt (delay discounting) and by the likelihood of its receipt (probability discounting). Despite being well-described by the same hyperboloid function, delay and probability discounting involve fundamentally different processes, as revealed, for example, by the differential effects…

  13. Investigating Pre-service Mathematics Teachers’ Geometric Problem Solving Process in Dynamic Geometry Environment

    Directory of Open Access Journals (Sweden)

    Deniz Özen

    2013-03-01

    Full Text Available The aim of this study is to investigate pre-service elementary mathematics teachers’ open geometric problem solving process in a Dynamic Geometry Environment. With its qualitative inquiry based research design employed, the participants of the study are three pre-service teachers from 4th graders of the Department of Elementary Mathematics Teaching. In this study, clinical interviews, screencaptures of the problem solving process in the Cabri Geomery Environment, and worksheets included 2 open geometry problems have been used to collect the data. It has been investigated that all the participants passed through similar recursive phases as construction, exploration, conjecture, validate, and justification in the problem solving process. It has been thought that this study provide a new point of view to curriculum developers, teachers and researchers

  14. Learning monopolies with delayed feedback on price expectations

    Science.gov (United States)

    Matsumoto, Akio; Szidarovszky, Ferenc

    2015-11-01

    We call the intercept of the price function with the vertical axis the maximum price and the slope of the price function the marginal price. In this paper it is assumed that a monopolistic firm has full information about the marginal price and its own cost function but is uncertain on the maximum price. However, by repeated interaction with the market, the obtained price observations give a basis for an adaptive learning process of the maximum price. It is also assumed that the price observations have fixed delays, so the learning process can be described by a delayed differential equation. In the cases of one or two delays, the asymptotic behavior of the resulting dynamic process is examined, stability conditions are derived. Three main results are demonstrated in the two delay learning processes. First, it is possible to stabilize the equilibrium which is unstable in the one delay model. Second, complex dynamics involving chaos, which is impossible in the one delay model, can emerge. Third, alternations of stability and instability (i.e., stability switches) occur repeatedly.

  15. Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

    Science.gov (United States)

    Maus, Irena; Kim, Yong Sung; Wibberg, Daniel; Stolze, Yvonne; Off, Sandra; Antonczyk, Sebastian; Pühler, Alfred; Scherer, Paul; Schlüter, Andreas

    2017-02-28

    Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic autofluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality. In this study, four different BGPs were investigated. The results indicated stable process performance in the mesophilic BGPs and in the thermophilic reactor. Bacterial subcommunity characterization revealed significant differences between the four BGPs. Most remarkably, the genera Defluviitoga and Halocella dominated the thermophilic bacterial subcommunity, whereas members of another taxon, Syntrophaceticus , were found to be abundant in the mesophilic BGP. The domain Archaea was dominated by the genus Methanoculleus in all four BGPs, followed by Methanosaeta in BGP1 and BGP3. In contrast, Methanothermobacter members were highly abundant in the thermophilic BGP4. Furthermore, a high consistency between the sequencing approach and the QMF method was shown, especially for the thermophilic BGP. The differences elucidated that using this biphasic approach for mesophilic BGPs provided novel insights regarding disaggregated single cells of Methanosarcina and Methanosaeta species. Both dominated the archaeal subcommunity and replaced coccoid Methanoculleus members belonging to the same group of Methanomicrobiales that have been frequently observed in similar BGPs. This work demonstrates that combining QMF and 16S rRNA gene amplicon sequencing is a complementary strategy to describe archaeal community structures within biogas processes.

  16. Modified Firefly Algorithm based controller design for integrating and unstable delay processes

    Directory of Open Access Journals (Sweden)

    A. Gupta

    2016-03-01

    Full Text Available In this paper, Modified Firefly Algorithm has been used for optimizing the controller parameters of Smith predictor structure. The proposed algorithm modifies the position formula of the standard Firefly Algorithm in order to achieve faster convergence rate. Performance criteria Integral Square Error (ISE is optimized using this optimization technique. Simulation results show high performance for Modified Firefly Algorithm as compared to conventional Firefly Algorithm in terms of convergence rate. Integrating and unstable delay processes are taken as examples to indicate the performance of the proposed method.

  17. Enhanced IMC based PID controller design for non-minimum phase (NMP) integrating processes with time delays.

    Science.gov (United States)

    Ghousiya Begum, K; Seshagiri Rao, A; Radhakrishnan, T K

    2017-05-01

    Internal model control (IMC) with optimal H 2 minimization framework is proposed in this paper for design of proportional-integral-derivative (PID) controllers. The controller design is addressed for integrating and double integrating time delay processes with right half plane (RHP) zeros. Blaschke product is used to derive the optimal controller. There is a single adjustable closed loop tuning parameter for controller design. Systematic guidelines are provided for selection of this tuning parameter based on maximum sensitivity. Simulation studies have been carried out on various integrating time delay processes to show the advantages of the proposed method. The proposed controller provides enhanced closed loop performances when compared to recently reported methods in the literature. Quantitative comparative analysis has been carried out using the performance indices, Integral Absolute Error (IAE) and Total Variation (TV). Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  18. Analysing admission rules to a service system with two job classes and mandatory pre-emption

    DEFF Research Database (Denmark)

    Larsen, Christian

    , the pre-emptive action will cause a time delay before the server can start the service. Therefoe, the administrator might in some instances deny a class 2 job access to an idle server and instead hold it back in queue. We develop a semi-Markov decision model for this problem. In order to compute......We consider a queueing system consisting of S identical servers and two job classes, where class 1 jobs must always be processed as soon as possible. Therefore, the administrator of the system must, if neccesary, pre-empt a class 2 job and allocate the server to an arriving class 1 job. However...

  19. Effect of pre-processing on the physico-chemical properties of ...

    African Journals Online (AJOL)

    The findings indicated that the pre-processing treatments produced significant differences (p < 0.05) in protein (1.50 ± 0.18g/100g) and carbohydrate (1.09 ± 0.94g/100g) composition of the baking soda blanched milk sample. The viscosity of the baking soda blanched milk (18.91 ± 3.38cps) was significantly higher than that ...

  20. Pre-analytic process control: projecting a quality image.

    Science.gov (United States)

    Serafin, Mark D

    2006-09-26

    Within the health-care system, the term "ancillary department" often describes the laboratory. Thus, laboratories may find it difficult to define their image and with it, customer perception of department quality. Regulatory requirements give laboratories who so desire an elegant way to address image and perception issues--a comprehensive pre-analytic system solution. Since large laboratories use such systems--laboratory service manuals--I describe and illustrate the process for the benefit of smaller facilities. There exist resources to help even small laboratories produce a professional service manual--an elegant solution to image and customer perception of quality.

  1. 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.

  2. 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

  3. 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.

  4. 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

    between spliced rRNA expression levels, possibly due to changes in rRNA processing, which requires further investigation.

  5. Perturbation of Ribosome Biogenesis Drives Cells into Senescence through 5S RNP-Mediated p53 Activation

    Directory of Open Access Journals (Sweden)

    Kazuho Nishimura

    2015-03-01

    Full Text Available The 5S ribonucleoprotein particle (RNP complex, consisting of RPL11, RPL5, and 5S rRNA, is implicated in p53 regulation under ribotoxic stress. Here, we show that the 5S RNP contributes to p53 activation and promotes cellular senescence in response to oncogenic or replicative stress. Oncogenic stress accelerates rRNA transcription and replicative stress delays rRNA processing, resulting in RPL11 and RPL5 accumulation in the ribosome-free fraction, where they bind MDM2. Experimental upregulation of rRNA transcription or downregulation of rRNA processing, mimicking the nucleolus under oncogenic or replicative stress, respectively, also induces RPL11-mediated p53 activation and cellular senescence. We demonstrate that exogenous expression of certain rRNA-processing factors rescues the processing defect, attenuates p53 accumulation, and increases replicative lifespan. To summarize, the nucleolar-5S RNP-p53 pathway functions as a senescence inducer in response to oncogenic and replicative stresses.

  6. Highly efficient electroluminescence from a solution-processable thermally activated delayed fluorescence emitter

    Energy Technology Data Exchange (ETDEWEB)

    Wada, Yoshimasa; Kubo, Shosei; Suzuki, Katsuaki; Kaji, Hironori, E-mail: kaji@scl.kyoto-u.ac.jp [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Shizu, Katsuyuki [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Tanaka, Hiroyuki [Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Adachi, Chihaya [Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Japan Science and Technology Agency (JST), ERATO, Adachi Molecular Exciton Engineering Project, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan)

    2015-11-02

    We developed a thermally activated delayed fluorescence (TADF) emitter, 2,4,6-tris(4-(9,9-dimethylacridan-10-yl)phenyl)-1,3,5-triazine (3ACR-TRZ), suitable for use in solution-processed organic light-emitting diodes (OLEDs). When doped into 4,4′-bis(carbazol-9-yl)biphenyl (CBP) host at 16 wt. %, 3ACR-TRZ showed a high photoluminescence quantum yield of 98%. Transient photoluminescence decay measurements of the 16 wt. % 3ACR-TRZ:CBP film confirmed that 3ACR-TRZ exhibits efficient TADF with a triplet-to-light conversion efficiency of 96%. This high conversion efficiency makes 3ACR-TRZ attractive as an emitting dopant in OLEDs. Using 3ACR-TRZ as an emitter, we fabricated a solution-processed OLED exhibiting a maximum external quantum efficiency of 18.6%.

  7. 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.

  8. The pre-rRNA processing factor DEF is rate limiting for the pathogenesis of MYCN-driven neuroblastoma.

    Science.gov (United States)

    Tao, T; Sondalle, S B; Shi, H; Zhu, S; Perez-Atayde, A R; Peng, J; Baserga, S J; Look, A T

    2017-07-06

    The nucleolar factor, digestive organ expansion factor (DEF), has a key role in ribosome biogenesis, functioning in pre-ribosomal RNA (pre-rRNA) processing as a component of the small ribosomal subunit (SSU) processome. Here we show that the peripheral sympathetic nervous system (PSNS) is very underdeveloped in def-deficient zebrafish, and that def haploinsufficiency significantly decreases disease penetrance and tumor growth rate in a MYCN-driven transgenic zebrafish model of neuroblastoma that arises in the PSNS. Consistent with these findings, DEF is highly expressed in human neuroblastoma, and its depletion in human neuroblastoma cell lines induces apoptosis. Interestingly, overexpression of MYCN in zebrafish and in human neuroblastoma cells results in the appearance of intermediate pre-rRNAs species that reflect the processing of pre-rRNAs through Pathway 2, a pathway that processes pre-rRNAs in a different temporal order than the more often used Pathway 1. Our results indicate that DEF and possibly other components of the SSU processome provide a novel site of vulnerability in neuroblastoma cells that could be exploited for targeted therapy.

  9. Contour extraction of echocardiographic images based on pre-processing

    Energy Technology Data Exchange (ETDEWEB)

    Hussein, Zinah Rajab; Rahmat, Rahmita Wirza; Abdullah, Lili Nurliyana [Department of Multimedia, Faculty of Computer Science and Information Technology, Department of Computer and Communication Systems Engineering, Faculty of Engineering University Putra Malaysia 43400 Serdang, Selangor (Malaysia); Zamrin, D M [Department of Surgery, Faculty of Medicine, National University of Malaysia, 56000 Cheras, Kuala Lumpur (Malaysia); Saripan, M Iqbal

    2011-02-15

    In this work we present a technique to extract the heart contours from noisy echocardiograph images. Our technique is based on improving the image before applying contours detection to reduce heavy noise and get better image quality. To perform that, we combine many pre-processing techniques (filtering, morphological operations, and contrast adjustment) to avoid unclear edges and enhance low contrast of echocardiograph images, after implementing these techniques we can get legible detection for heart boundaries and valves movement by traditional edge detection methods.

  10. Contour extraction of echocardiographic images based on pre-processing

    International Nuclear Information System (INIS)

    Hussein, Zinah Rajab; Rahmat, Rahmita Wirza; Abdullah, Lili Nurliyana; Zamrin, D M; Saripan, M Iqbal

    2011-01-01

    In this work we present a technique to extract the heart contours from noisy echocardiograph images. Our technique is based on improving the image before applying contours detection to reduce heavy noise and get better image quality. To perform that, we combine many pre-processing techniques (filtering, morphological operations, and contrast adjustment) to avoid unclear edges and enhance low contrast of echocardiograph images, after implementing these techniques we can get legible detection for heart boundaries and valves movement by traditional edge detection methods.

  11. Validation of DWI pre-processing procedures for reliable differentiation between human brain gliomas.

    Science.gov (United States)

    Vellmer, Sebastian; Tonoyan, Aram S; Suter, Dieter; Pronin, Igor N; Maximov, Ivan I

    2018-02-01

    Diffusion magnetic resonance imaging (dMRI) is a powerful tool in clinical applications, in particular, in oncology screening. dMRI demonstrated its benefit and efficiency in the localisation and detection of different types of human brain tumours. Clinical dMRI data suffer from multiple artefacts such as motion and eddy-current distortions, contamination by noise, outliers etc. In order to increase the image quality of the derived diffusion scalar metrics and the accuracy of the subsequent data analysis, various pre-processing approaches are actively developed and used. In the present work we assess the effect of different pre-processing procedures such as a noise correction, different smoothing algorithms and spatial interpolation of raw diffusion data, with respect to the accuracy of brain glioma differentiation. As a set of sensitive biomarkers of the glioma malignancy grades we chose the derived scalar metrics from diffusion and kurtosis tensor imaging as well as the neurite orientation dispersion and density imaging (NODDI) biophysical model. Our results show that the application of noise correction, anisotropic diffusion filtering, and cubic-order spline interpolation resulted in the highest sensitivity and specificity for glioma malignancy grading. Thus, these pre-processing steps are recommended for the statistical analysis in brain tumour studies. Copyright © 2017. Published by Elsevier GmbH.

  12. Supervised pre-processing approaches in multiple class variables classification for fish recruitment forecasting

    KAUST Repository

    Fernandes, José Antonio

    2013-02-01

    A multi-species approach to fisheries management requires taking into account the interactions between species in order to improve recruitment forecasting of the fish species. Recent advances in Bayesian networks direct the learning of models with several interrelated variables to be forecasted simultaneously. These models are known as multi-dimensional Bayesian network classifiers (MDBNs). Pre-processing steps are critical for the posterior learning of the model in these kinds of domains. Therefore, in the present study, a set of \\'state-of-the-art\\' uni-dimensional pre-processing methods, within the categories of missing data imputation, feature discretization and feature subset selection, are adapted to be used with MDBNs. A framework that includes the proposed multi-dimensional supervised pre-processing methods, coupled with a MDBN classifier, is tested with synthetic datasets and the real domain of fish recruitment forecasting. The correctly forecasting of three fish species (anchovy, sardine and hake) simultaneously is doubled (from 17.3% to 29.5%) using the multi-dimensional approach in comparison to mono-species models. The probability assessments also show high improvement reducing the average error (estimated by means of Brier score) from 0.35 to 0.27. Finally, these differences are superior to the forecasting of species by pairs. © 2012 Elsevier Ltd.

  13. 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.

  14. 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.

  15. 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.

  16. International Best Practices for Pre-Processing and Co-Processing Municipal Solid Waste and Sewage Sludge in the Cement Industry

    Energy Technology Data Exchange (ETDEWEB)

    Hasanbeigi, Ali [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lu, Hongyou [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Williams, Christopher [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Price, Lynn [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2012-07-01

    The purpose of this report is to describe international best practices for pre-processing and coprocessing of MSW and sewage sludge in cement plants, for the benefit of countries that wish to develop co-processing capacity. The report is divided into three main sections. Section 2 describes the fundamentals of co-processing, Section 3 describes exemplary international regulatory and institutional frameworks for co-processing, and Section 4 describes international best practices related to the technological aspects of co-processing.

  17. Investigating the Representational Fluency of Pre-Service Mathematics Teachers in a Modelling Process

    Science.gov (United States)

    Delice, Ali; Kertil, Mahmut

    2015-01-01

    This article reports the results of a study that investigated pre-service mathematics teachers' modelling processes in terms of representational fluency in a modelling activity related to a cassette player. A qualitative approach was used in the data collection process. Students' individual and group written responses to the mathematical modelling…

  18. 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

  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

    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.

  20. Impact of virtual chemistry laboratory instruction on pre-service science teachers’ scientific process skills

    Directory of Open Access Journals (Sweden)

    Mutlu Ayfer

    2016-01-01

    Full Text Available This study aimed to investigate the impact of virtual chemistry laboratory instruction on pre-service science teachers’ scientific process skills. For this purpose, eight laboratory activities related to chemical kinetic, chemical equilibrium, thermochemistry, acids-bases, and electrochemistry were developed. Those activities were performed in virtual laboratory environment by the pre-service teachers in the experimental group and in the real laboratory environment by c the preservice teachers in the control group during eight weeks. Scientific process skills test developed by Burns, Okey and Wise [3], and translated into Turkish by Ateş and Bahar [2] was used before and after the instructions for data collection. According to results, while there was no significant difference between pre-test mean scores (U=133.500, p>0.05, significant difference between post-test mean scores was found in favour of experimental group (U=76.000, p<0.05. In addition, while no significant difference between pre-test mean scores for each sub-dimension was found, significant difference between post-test mean scores for designing investigation and formulating hypothesis skills was found in favour of experimental group.

  1. Development of an analogue multiplexed regulation for periodic 1. order delayed processes

    International Nuclear Information System (INIS)

    Amblard, J.C.

    1967-07-01

    The present note deals with the study regulations of the sampled type, for 1. order process with simple delay. In order to obtain a good stability in such regulations, together with acceptable performances, it is interesting to use polynomial type correctors acting directly on the sampled error signals. The active elements of these correctors can be shared by all the channels to be controlled. Furthermore, the determination of the correction parameters results from an optimal study of the system. In the second part is described the construction of a multiplexed regulation for diffusion ovens. (author) [fr

  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. Extending Practical Pre-Aggregation in On-Line Analytical Processing

    DEFF Research Database (Denmark)

    Pedersen, Torben Bach; Jensen, Christian Søndergaard; Dyreson, Curtis E.

    On-Line Analytical Processing (OLAP) based on a dimensional view of data is being used increasingly in traditional business applications as well as in applications such as health care for the purpose of analyzing very large amounts of data. Pre-aggregation, the prior materialization of aggregate...... select combinations of aggregates and then re-use these for efficiently computing other aggregates. However, this re-use of aggregates is contingent on the dimension hierarchies and the relationships between facts and dimensions satisfying stringent constraints. This severely limits the scope...

  6. Differences in metabolite profiles caused by pre-analytical blood processing procedures.

    Science.gov (United States)

    Nishiumi, Shin; Suzuki, Makoto; Kobayashi, Takashi; Yoshida, Masaru

    2018-05-01

    Recently, the use of metabolomic analysis of human serum and plasma for biomarker discovery and disease diagnosis in clinical studies has been increasing. The feasibility of using a metabolite biomarker for disease diagnosis is strongly dependent on the metabolite's stability during pre-analytical blood processing procedures, such as serum or plasma sampling and sample storage prior to centrifugation. However, the influence of blood processing procedures on the stability of metabolites has not been fully characterized. In the present study, we compared the levels of metabolites in matched human serum and plasma samples using gas chromatography coupled with mass spectrometry and liquid chromatography coupled with mass spectrometry. In addition, we evaluated the changes in plasma metabolite levels induced by storage at room temperature or at a cold temperature prior to centrifugation. As a result, it was found that 76 metabolites exhibited significant differences between their serum and plasma levels. Furthermore, the pre-centrifugation storage conditions significantly affected the plasma levels of 45 metabolites. These results highlight the importance of blood processing procedures during metabolome analysis, which should be considered during biomarker discovery and the subsequent use of biomarkers for disease diagnosis. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  7. Effects of chemical-physical pre-treatment processes on hemp fibres for reinforcement of composites and textiles

    DEFF Research Database (Denmark)

    Thomsen, Anne Belinda; Thygesen, Anders; Bohn, Vibeke

    2006-01-01

    Retted hemp fibres were treated using chemical-physical pre-treatments and the material was characterised chemically in order to evaluate the effect of the pre-treatments, respectively, wet oxidation (WO), hydrothermal treatment (HT) and steam explosion (STEX). Process variables were addition...

  8. 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.

  9. The Effect of an Instructional Intervention on Enhancement Pre-Service Science Teachers' Science Processes Skills

    Science.gov (United States)

    Durmaz, Hüsnüye

    2016-01-01

    The aim of this study is to investigate the effects of an instructional intervention on enhancement the pre-service science teachers' (PSTs) science process skills (SPSs) and to identify problems in using SPSs through Laboratory Applications in Science Education-I course (LASE-I). One group pretest-posttest pre-experimental design was employed. An…

  10. 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.

  11. Source estimation for propagation processes on complex networks with an application to delays in public transportation systems

    NARCIS (Netherlands)

    Manitz, J. (Juliane); Harbering, J. (Jonas); M.E. Schmidt (Marie); T. Kneib (Thomas); A. Schöbel (Anita)

    2017-01-01

    textabstractThe correct identification of the source of a propagation process is crucial in many research fields. As a specific application, we consider source estimation of delays in public transportation networks. We propose two approaches: an effective distance median and a backtracking method.

  12. Delay-Range-Dependent H∞ Control for Automatic Mooring Positioning System with Time-Varying Input Delay

    Directory of Open Access Journals (Sweden)

    Xiaoyu Su

    2014-01-01

    Full Text Available Aiming at the economy and security of the positioning system in semi-submersible platform, the paper presents a new scheme based on the mooring line switching strategy. Considering the input delay in switching process, H∞ control with time-varying input delay is designed to calculate the control forces to resist disturbing forces. In order to reduce the conservativeness, the information of the lower bound of delay is taken into account, and a Lyapunov function which contains the range of delay is constructed. Besides, the input constraint is considered to avoid breakage of mooring lines. The sufficient conditions for delay-range-dependent stabilization are derived in terms of LMI, and the controller is also obtained. The effectiveness of the proposed approach is illustrated by a realistic design example.

  13. 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...

  14. 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

  15. Analytical applications for delayed neutrons

    International Nuclear Information System (INIS)

    Eccleston, G.W.

    1983-01-01

    Analytical formulations that describe the time dependence of neutron populations in nuclear materials contain delayed-neutron dependent terms. These terms are important because the delayed neutrons, even though their yields in fission are small, permit control of the fission chain reaction process. Analytical applications that use delayed neutrons range from simple problems that can be solved with the point reactor kinetics equations to complex problems that can only be solved with large codes that couple fluid calculations with the neutron dynamics. Reactor safety codes, such as SIMMER, model transients of the entire reactor core using coupled space-time neutronics and comprehensive thermal-fluid dynamics. Nondestructive delayed-neutron assay instruments are designed and modeled using a three-dimensional continuous-energy Monte Carlo code. Calculations on high-burnup spent fuels and other materials that contain a mix of uranium and plutonium isotopes require accurate and complete information on the delayed-neutron periods, yields, and energy spectra. A continuing need exists for delayed-neutron parameters for all the fissioning isotopes

  16. Yeast Interacting Proteins Database: YER127W, YDR299W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available to inhibited pre-rRNA processing and reduced polysome levels; localizes primarily to the nucleolus Rows with...of 18S rRNA; depletion leads to inhibited pre-rRNA processing and reduced polysome levels; localizes primarily to the nucleolus

  17. 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

  18. Enhancing clinical effectiveness of pre-radiotherapy workflow by using multidisciplinary-cooperating e-control and e-alerts: A SQUIRE-compliant quality-improving study.

    Science.gov (United States)

    Lin, Yung-Hsiang; Hung, Shih-Kai; Lee, Moon-Sing; Chiou, Wen-Yen; Lai, Chun-Liang; Shih, Yi-Ting; Yeh, Pei-Han; Lin, Yi-An; Tsai, Wei-Ta; Hsieh, Hui-Ling; Chen, Liang-Cheng; Huang, Li-Wen; Lin, Po-Hao; Liu, Dai-Wei; Hsu, Feng-Chun; Tsai, Shiang-Jiun; Liu, Jia-Chi; Chung, En-Seu; Lin, Hon-Yi

    2017-06-01

    Radiotherapy (RT) is useful in managing cancer diseases. In clinical practice, early initiation of RT is crucial for enhancing tumor control. But, delivering precise RT requires a series of pre-RT working processes in a tight staff-cooperation manner. In this regard, using information system to conduct e-control and e-alerts has been suggested to improve practice effectiveness; however, this effect is not well defined in a real-world RT setting.We designed an information system to perform e-control and e-alerts for the whole process of pre-RT workflow to shorten processing time, to improve overall staff satisfaction, and to enhance working confidence.A quality-improving study conducted in a large RT center.Externally validated data were retrospectively analyzed for comparison before (from Sep. 2012 to Dec. 2012, n = 223) and after (from Sep. 2013 to Dec. 2013, n = 240) implementation of pre-RT e-control and e-alerts.Applying the e-control with delay-working e-alerts in pre-RT workflow was the main intervention.Nine workstations were identified in pre-RT workflow. The primary outcome measure was the processing time in each pre-RT workstations before and after implementing the e-control and e-alerts. Secondary measures were staff-working confidence and near-missing cases during the process of pre-RT workflow.After implementing e-control, overall processing time of pre-RT workflow was shortened from 12.2 days to 8.9 days (P workflow. Clinical effectiveness, staff satisfaction, and working confidence are able to be enhanced obviously.

  19. 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, ...

  20. Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases.

    Science.gov (United States)

    Tomecki, Rafal; Sikorski, Pawel J; Zakrzewska-Placzek, Monika

    2017-07-01

    Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans. © 2017 Federation of European Biochemical Societies.

  1. 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/...

  2. A Polynomial Estimate of Railway Line Delay

    DEFF Research Database (Denmark)

    Cerreto, Fabrizio; Harrod, Steven; Nielsen, Otto Anker

    2017-01-01

    Railway service may be measured by the aggregate delay over a time horizon or due to an event. Timetables for railway service may dampen aggregate delay by addition of additional process time, either supplement time or buffer time. The evaluation of these variables has previously been performed...... by numerical analysis with simulation. This paper proposes an analytical estimate of aggregate delay with a polynomial form. The function returns the aggregate delay of a railway line resulting from an initial, primary, delay. Analysis of the function demonstrates that there should be a balance between the two...

  3. 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

  4. 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.

  5. Pre-authorization processes have no effect on patients undergoing knee MRI in a pediatric setting when evaluated by specialists

    Energy Technology Data Exchange (ETDEWEB)

    Pierce, Drew; Kan, J.H.; Bisset, George S. [Texas Children' s Hospital, Department of Radiology, Houston, TX (United States); May, Megan [Texas Children' s Hospital, Department of Sports Medicine, Houston, TX (United States)

    2017-02-15

    Pre-authorization processes are often used by medical insurance companies to reduce costs by managing the utilization of advanced diagnostic imaging, and their impact on patient care is unclear. The purpose of our study is to determine if a pre-authorization process increases the rate of surgically significant abnormal knee MRI and surgical referrals compared with patients referred from pediatric orthopedic specialists who do not undergo a pre-authorization process. A retrospective study was performed; 124 patients were identified who were referred for knee MRI by a pediatric orthopedist. The study population included patients who underwent an insurance pre-authorization process and the control group consisted of those who did not. The results of the MRI and whether they were deemed surgically significant, in addition to surgical referral, were recorded and compared. The study and control groups showed no statistically significant difference in outcome with regard to surgically significant findings on MRI (p = 0.92) or whether the patient required surgery (p = 0.6). In this population, there is no difference in the likelihood of an abnormal knee MRI demonstrating surgically significant findings or referral to surgery in patients who did and those who did not undergo an insurance pre-authorization process when patients are referred from a pediatric orthopedic specialist. The insurance pre-authorization process does not appear to have an impact on patient diagnosis and treatment and may unnecessarily add bureaucracy and costs. (orig.)

  6. Textural Analysis of Fatique Crack Surfaces: Image Pre-processing

    Directory of Open Access Journals (Sweden)

    H. Lauschmann

    2000-01-01

    Full Text Available For the fatique crack history reconstitution, new methods of quantitative microfractography are beeing developed based on the image processing and textural analysis. SEM magnifications between micro- and macrofractography are used. Two image pre-processing operatins were suggested and proved to prepare the crack surface images for analytical treatment: 1. Normalization is used to transform the image to a stationary form. Compared to the generally used equalization, it conserves the shape of brightness distribution and saves the character of the texture. 2. Binarization is used to transform the grayscale image to a system of thick fibres. An objective criterion for the threshold brightness value was found as that resulting into the maximum number of objects. Both methods were succesfully applied together with the following textural analysis.

  7. The alkaline pre-filming process of the RWCU piping surface

    Energy Technology Data Exchange (ETDEWEB)

    Kao, D-Y.; Wen, T-J., E-mail: dahyukao@iner.gov.tw [Atomic Energy Council, Inst. of Nuclear Energy Research, Lungtan Taoyuan, Taiwan (China); Fong, C., E-mail: clinton@itri.org.tw [Industrial Technology Research Inst., Chutung, Hsinchu (China); Lu, J-H., E-mail: u879864@taipower.com.tw [Taiwan Power Co., Lungmen Nuclear Power Plant, Gongliao Township, Taipei County (China)

    2010-07-01

    The radiation dose rate on a BWR can cause great damage to operators and their maintenances working quality, so it is very important to lower it. The RWCU of a BWR primary system has the highest radiation dose rate and deposition of an active corrosion product because of: continually cleaning the reactor water and the repeated, acute change of temperature. The Lungmen NPP was built as an advanced BWR (ABWR) system. All new ABWRs in Japan, such as Kashiwazaki-Kariwa NPP units K6 and K7, Hamaoka NPP unit H5, and Shika NPP unit2, were given in passivation treatment in the stage of nuclear heating or flow-induced vibration (FIV) testing before each plant's initial start up. The conditions of alkaline pre-filming process include: pH, dissolve oxygen (DO) and temperature. This project had been decided by the results of earlier water loop testing. Three kinds of specimens including stainless steel AISI SS316L and carbon steel SA106 GrB, SA333 Gr6 were put into the autoclave located at a bypass system during the process of passivation treatment. The materials of these specimens have been used in RWCU piping, and during the alkaline pre-filming process they were monitored by AC impedances and electrochemical corrosion potential (ECP). Their surface analyses including SEM, EDS, ESCA and SIMS data were obtained from the initial test, and obtained every six months thereafter. From the SEM plot of first issue it was found that the specimens' surface of all three different materials presented excellent levels of oxidized pellets. They are almost completely packed, for both large and small granules, and the porosity is less than 40%. The deposition tests of cobalt ion were also completed. The material of stainless steel was nearly not affected through the passive process. However, carbon steel could reduce about 30% to 50% of deposited cobalt ion. This result follows the conclusion of Hatch Company. Based on the nominal cost of radiation protection, i.e. 10000 USD

  8. Discounting of Monetary Rewards that are Both Delayed and Probabilistic: Delay and Probability Combine Multiplicatively, not Additively

    Science.gov (United States)

    Vanderveldt, Ariana; Green, Leonard; Myerson, Joel

    2014-01-01

    The value of an outcome is affected both by the delay until its receipt (delay discounting) and by the likelihood of its receipt (probability discounting). Despite being well-described by the same hyperboloid function, delay and probability discounting involve fundamentally different processes, as revealed, for example, by the differential effects of reward amount. Previous research has focused on the discounting of delayed and probabilistic rewards separately, with little research examining more complex situations in which rewards are both delayed and probabilistic. In two experiments, participants made choices between smaller rewards that were both immediate and certain and larger rewards that were both delayed and probabilistic. Analyses revealed significant interactions between delay and probability factors inconsistent with an additive model. In contrast, a hyperboloid discounting model in which delay and probability were combined multiplicatively provided an excellent fit to the data. These results suggest that the hyperboloid is a good descriptor of decision making in complicated monetary choice situations like those people encounter in everyday life. PMID:24933696

  9. Quantification of Listeria monocytogenes in minimally processed leafy vegetables using a combined method based on enrichment and 16S rRNA real-time PCR.

    Science.gov (United States)

    Aparecida de Oliveira, Maria; Abeid Ribeiro, Eliana Guimarães; Morato Bergamini, Alzira Maria; Pereira De Martinis, Elaine Cristina

    2010-02-01

    Modern lifestyle markedly changed eating habits worldwide, with an increasing demand for ready-to-eat foods, such as minimally processed fruits and leafy greens. Packaging and storage conditions of those products may favor the growth of psychrotrophic bacteria, including the pathogen Listeria monocytogenes. In this work, minimally processed leafy vegetables samples (n = 162) from retail market from Ribeirão Preto, São Paulo, Brazil, were tested for the presence or absence of Listeria spp. by the immunoassay Listeria Rapid Test, Oxoid. Two L. monocytogenes positive and six artificially contaminated samples of minimally processed leafy vegetables were evaluated by the Most Probable Number (MPN) with detection by classical culture method and also culture method combined with real-time PCR (RTi-PCR) for 16S rRNA genes of L. monocytogenes. Positive MPN enrichment tubes were analyzed by RTi-PCR with primers specific for L. monocytogenes using the commercial preparation ABSOLUTE QPCR SYBR Green Mix (ABgene, UK). Real-time PCR assay presented good exclusivity and inclusivity results and no statistical significant difference was found in comparison with the conventional culture method (p < 0.05). Moreover, RTi-PCR was fast and easy to perform, with MPN results obtained in ca. 48 h for RTi-PCR in comparison to 7 days for conventional method.

  10. A Flexible Job Shop Scheduling Problem with Controllable Processing Times to Optimize Total Cost of Delay and Processing

    Directory of Open Access Journals (Sweden)

    Hadi Mokhtari

    2015-11-01

    Full Text Available In this paper, the flexible job shop scheduling problem with machine flexibility and controllable process times is studied. The main idea is that the processing times of operations may be controlled by consumptions of additional resources. The purpose of this paper to find the best trade-off between processing cost and delay cost in order to minimize the total costs. The proposed model, flexible job shop scheduling with controllable processing times (FJCPT, is formulated as an integer non-linear programming (INLP model and then it is converted into an integer linear programming (ILP model. Due to NP-hardness of FJCPT, conventional analytic optimization methods are not efficient. Hence, in order to solve the problem, a Scatter Search (SS, as an efficient metaheuristic method, is developed. To show the effectiveness of the proposed method, numerical experiments are conducted. The efficiency of the proposed algorithm is compared with that of a genetic algorithm (GA available in the literature for solving FJSP problem. The results showed that the proposed SS provide better solutions than the existing GA.

  11. Stochastic two-delay differential model of delayed visual feedback effects on postural dynamics.

    Science.gov (United States)

    Boulet, Jason; Balasubramaniam, Ramesh; Daffertshofer, Andreas; Longtin, André

    2010-01-28

    We report on experiments and modelling involving the 'visuo-postural control loop' in the upright stance. We experimentally manipulated an artificial delay to the visual feedback during standing, presented at delays ranging from 0 to 1 s in increments of 250 ms. Using stochastic delay differential equations, we explicitly modelled the centre-of-pressure (COP) and centre-of-mass (COM) dynamics with two independent delay terms for vision and proprioception. A novel 'drifting fixed point' hypothesis was used to describe the fluctuations of the COM with the COP being modelled as a faster, corrective process of the COM. The model was in good agreement with the data in terms of probability density functions, power spectral densities, short- and long-term correlations (Hurst exponents) as well the critical time between the two ranges. This journal is © 2010 The Royal Society

  12. 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.

  13. Status of pre-processing of waste electrical and electronic equipment in Germany and its influence on the recovery of gold.

    Science.gov (United States)

    Chancerel, Perrine; Bolland, Til; Rotter, Vera Susanne

    2011-03-01

    Waste electrical and electronic equipment (WEEE) contains gold in low but from an environmental and economic point of view relevant concentration. After collection, WEEE is pre-processed in order to generate appropriate material fractions that are sent to the subsequent end-processing stages (recovery, reuse or disposal). The goal of this research is to quantify the overall recovery rates of pre-processing technologies used in Germany for the reference year 2007. To achieve this goal, facilities operating in Germany were listed and classified according to the technology they apply. Information on their processing capacity was gathered by evaluating statistical databases. Based on a literature review of experimental results for gold recovery rates of different pre-processing technologies, the German overall recovery rate of gold at the pre-processing level was quantified depending on the characteristics of the treated WEEE. The results reveal that - depending on the equipment groups - pre-processing recovery rates of gold of 29 to 61% are achieved in Germany. Some practical recommendations to reduce the losses during pre-processing could be formulated. Defining mass-based recovery targets in the legislation does not set incentives to recover trace elements. Instead, the priorities for recycling could be defined based on other parameters like the environmental impacts of the materials. The implementation of measures to reduce the gold losses would also improve the recovery of several other non-ferrous metals like tin, nickel, and palladium.

  14. 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.

  15. Investigation of the Nature of Metaconceptual Processes of Pre-Service Biology Teachers

    Science.gov (United States)

    Yuruk, Nejla; Selvi, Meryem; Yakisan, Mehmet

    2017-01-01

    Purpose of Study: The aim of this study is to investigate the nature of pre-service biology teachers' metaconceptual processes that were active as they participated in metaconceptual teaching activities. Methods: Several instructional activities, including poster drawing, concept mapping, group and class discussions, and journal writing, were…

  16. 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...

  17. Genomic GC-content affects the accuracy of 16S rRNA gene sequencing bsed microbial profiling due to PCR bias

    DEFF Research Database (Denmark)

    Laursen, Martin F.; Dalgaard, Marlene Danner; Bahl, Martin Iain

    2017-01-01

    Profiling of microbial community composition is frequently performed by partial 16S rRNA gene sequencing on benchtop platforms following PCR amplification of specific hypervariable regions within this gene. Accuracy and reproducibility of this strategy are two key parameters to consider, which may...... be influenced during all processes from sample collection and storage, through DNA extraction and PCR based library preparation to the final sequencing. In order to evaluate both the reproducibility and accuracy of 16S rRNA gene based microbial profiling using the Ion Torrent PGM platform, we prepared libraries...... be explained partly by premature read truncation, but to larger degree their genomic GC-content, which correlated negatively with the observed relative abundances, suggesting a PCR bias against GC-rich species during library preparation. Increasing the initial denaturation time during the PCR amplification...

  18. 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....

  19. 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...

  20. PRE-LIMINAR JUDGMENT OF PROCEDENCE IN REPLICATION SUITS BY MAGISTRATES: A VIABLE ALTERNATIVE AGAINST PROCESS DELAYS IN CIVIL STATE COURTS

    OpenAIRE

    Souza, Roberta Kelly Silva; Universitá di Pisa, UNIPI, Itália; Seixas, Bernardo Silva de; Universitá di Pisa, UNIPI, Itália

    2015-01-01

    Laws 9099/95, 10259/01 and 12152/09, which respectively regulate the Special State, Federal and Fiscal Courts, were published so that access to justice in Brazil may be broadened. However, after twenty years of the establishment of State Special Civil Courts, they are so full up with suits that they have not served their function to de-bureaucratize justice and provide a fast access to justice to the Brazilian population. Current study demonstrates that the application of pre-liminar judgment...

  1. 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,

  2. 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.

  3. Logics of pre-merger decision-making processes: the case of Karolinska University Hospital.

    Science.gov (United States)

    Choi, Soki; Brommels, Mats

    2009-01-01

    The purpose of this paper is to examine how and why a decision to merge two university hospitals in a public context might occur by using an in-depth case study of the pre-merger process of Karolinska University Hospital. Based on extensive document analysis and 35 key informant interviews the paper reconstructed the pre-merger process, searched for empirical patterns, and interpreted those by applying neo-institutional theory. Spanning nearly a decade, the pre-merger process goes from idea generation through transition to decision, and took place on two arenas, political, and scientific. Both research excellence and economic efficiency are stated merger motives. By applying a neo-institutional perspective, the paper finds that the two initial phases are driven by decision rationality, which is typical for political organizations and that the final phase demonstrated action rationality, which is typical for private firms. Critical factors behind this radical change of decision logic are means convergence, uniting key stakeholder groups, and an economic and political crisis, triggering critical incidents, which ultimately legitimized the formal decision. It is evident from the paper that merger decisions in the public sector might not necessarily result from stated and/or economic drivers only. This paper suggests that a change of decision logic from decision to action rationality might promote effective decision making on large and complex issues in a public context. This is the first systematic in-depth study of a university hospital merger employing a decision-making perspective.

  4. 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).

  5. Pre- and post-processing of hydro-meteorological ensembles for the Norwegian flood forecasting system in 145 basins.

    Science.gov (United States)

    Jahr Hegdahl, Trine; Steinsland, Ingelin; Merete Tallaksen, Lena; Engeland, Kolbjørn

    2016-04-01

    Probabilistic flood forecasting has an added value for decision making. The Norwegian flood forecasting service is based on a flood forecasting model that run for 145 basins. Covering all of Norway the basins differ in both size and hydrological regime. Currently the flood forecasting is based on deterministic meteorological forecasts, and an auto-regressive procedure is used to achieve probabilistic forecasts. An alternative approach is to use meteorological and hydrological ensemble forecasts to quantify the uncertainty in forecasted streamflow. The hydrological ensembles are based on forcing a hydrological model with meteorological ensemble forecasts of precipitation and temperature. However, the ensembles of precipitation are often biased and the spread is too small, especially for the shortest lead times, i.e. they are not calibrated. These properties will, to some extent, propagate to hydrological ensembles, that most likely will be uncalibrated as well. Pre- and post-processing methods are commonly used to obtain calibrated meteorological and hydrological ensembles respectively. Quantitative studies showing the effect of the combined processing of the meteorological (pre-processing) and the hydrological (post-processing) ensembles are however few. The aim of this study is to evaluate the influence of pre- and post-processing on the skill of streamflow predictions, and we will especially investigate if the forecasting skill depends on lead-time, basin size and hydrological regime. This aim is achieved by applying the 51 medium-range ensemble forecast of precipitation and temperature provided by the European Center of Medium-Range Weather Forecast (ECMWF). These ensembles are used as input to the operational Norwegian flood forecasting model, both raw and pre-processed. Precipitation ensembles are calibrated using a zero-adjusted gamma distribution. Temperature ensembles are calibrated using a Gaussian distribution and altitude corrected by a constant gradient

  6. The effects of pre-processing strategies in sentiment analysis of online movie reviews

    Science.gov (United States)

    Zin, Harnani Mat; Mustapha, Norwati; Murad, Masrah Azrifah Azmi; Sharef, Nurfadhlina Mohd

    2017-10-01

    With the ever increasing of internet applications and social networking sites, people nowadays can easily express their feelings towards any products and services. These online reviews act as an important source for further analysis and improved decision making. These reviews are mostly unstructured by nature and thus, need processing like sentiment analysis and classification to provide a meaningful information for future uses. In text analysis tasks, the appropriate selection of words/features will have a huge impact on the effectiveness of the classifier. Thus, this paper explores the effect of the pre-processing strategies in the sentiment analysis of online movie reviews. In this paper, supervised machine learning method was used to classify the reviews. The support vector machine (SVM) with linear and non-linear kernel has been considered as classifier for the classification of the reviews. The performance of the classifier is critically examined based on the results of precision, recall, f-measure, and accuracy. Two different features representations were used which are term frequency and term frequency-inverse document frequency. Results show that the pre-processing strategies give a significant impact on the classification process.

  7. 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.

  8. Influence of pre-cure freezing of Iberian ham on proteolytic changes throughout the ripening process.

    Science.gov (United States)

    Pérez-Palacios, Trinidad; Ruiz, Jorge; Barat, Jose Manuel; Aristoy, María Concepción; Antequera, Teresa

    2010-05-01

    This work aimed to investigate the effect of pre-cure freezing Iberian hams on proteolysis phenomena throughout the ripening process. Non-protein nitrogen (NPN), peptide nitrogen (PN) and amino acid nitrogen (AN) as well as amino acid and dipeptide evolution followed the same trend in both refrigerated (R) and pre-cure frozen (F) Iberian hams during processing. At the different stages of ripening, there were no differences in the content of NPN and AN while F dry-cured hams had higher levels of PN than R hams at the final step. This seemed to be more related to the salt content (lower in F than in R hams) than to the pre-cure freezing treatment. Most amino acids and dipeptides detected showed higher concentrations in F than in R Iberian hams at the green stage, being rather similar at the intermediate phases. At the final stage, the effects of pre-cure freezing of Iberian hams were not well defined, higher levels of some amino acids and dipeptides were found in R than in F Iberian hams whereas other amino acids were lower in R than in F hams. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  9. Global Perspectives on Activated Sludge Community Composition analyzed using 16S rRNA amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Saunders, Aaron Marc; Albertsen, Mads

    communities, and in this study activated sludge sampled from 32 Wastewater Treatment Plants (WWTPs) around the world was described and compared. The top abundant bacteria in the global activated sludge ecosystem were found and the core population shared by multiple samples was investigated. The results......Activated sludge is the most commonly applied bioprocess throughout the world for wastewater treatment. Microorganisms are key to the process, yet our knowledge of their identity and function is still limited. High-througput16S rRNA amplicon sequencing can reliably characterize microbial...

  10. Perturbation of ribosome biogenesis drives cells into senescence through 5S RNP-mediated p53 activation.

    Science.gov (United States)

    Nishimura, Kazuho; Kumazawa, Takuya; Kuroda, Takao; Katagiri, Naohiro; Tsuchiya, Mai; Goto, Natsuka; Furumai, Ryohei; Murayama, Akiko; Yanagisawa, Junn; Kimura, Keiji

    2015-03-03

    The 5S ribonucleoprotein particle (RNP) complex, consisting of RPL11, RPL5, and 5S rRNA, is implicated in p53 regulation under ribotoxic stress. Here, we show that the 5S RNP contributes to p53 activation and promotes cellular senescence in response to oncogenic or replicative stress. Oncogenic stress accelerates rRNA transcription and replicative stress delays rRNA processing, resulting in RPL11 and RPL5 accumulation in the ribosome-free fraction, where they bind MDM2. Experimental upregulation of rRNA transcription or downregulation of rRNA processing, mimicking the nucleolus under oncogenic or replicative stress, respectively, also induces RPL11-mediated p53 activation and cellular senescence. We demonstrate that exogenous expression of certain rRNA-processing factors rescues the processing defect, attenuates p53 accumulation, and increases replicative lifespan. To summarize, the nucleolar-5S RNP-p53 pathway functions as a senescence inducer in response to oncogenic and replicative stresses. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  11. Learning Processes of Students in Pre-Vocational Secondary Education: Relations between Goal Orientations, Information Processing Strategies and Development of Conceptual Knowledge

    Science.gov (United States)

    Koopman, Maaike; Den Brok, Perry; Beijaard, Douwe; Teune, Peter

    2011-01-01

    The purpose of this study was to investigate relations between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education students (n = 719; 14 schools). Students' preferences for certain types of goals and information processing strategies were examined using questionnaires.…

  12. 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

  13. Constructing squares as a mathematical problem solving process in pre-school

    Directory of Open Access Journals (Sweden)

    MARIA ANGELA SHIAKALLI

    2014-06-01

    Full Text Available Could problem solving be the object of teaching in early education? Could children’s engagement in problem solving processes lead to skills and conceptual understanding development? Could appropriate teaching interventions scaffold children’s efforts? The sample consisted of 25 children attending public pre-school in Cyprus. The children were asked to construct different sized squares. Findings show that children responded positively to the problem and were successful in solving it. During the problem solving process children demonstrated development of skills and conceptual understanding. Teacher-children and children-children interactions played an important role in the positive outcome of the activity.

  14. Economical analysis of the spray drying process by pre-dehumidification of the inlet air

    Energy Technology Data Exchange (ETDEWEB)

    Madeira, A.N.; Camargo, J.R. [University of Taubate (UNITAU), SP (Brazil). Mechanical Engineering Dept.

    2009-07-01

    Spray drying is a dehumidification process by atomization in a closed chamber that aims to remove moisture of a product by heat and mass transfer from the product's contained water to the air that, in this process is previously heated. This paper presents a case study for an industry that produces food ingredients. The current process applied in the product to heat the air can uses one of these two systems: a direct heating process that burns liquid petroleum gas in contact with the inlet air or indirect heating that uses a heat exchanger which heat the air. This heating system consumes 90% of the total process energy. However, this inlet air can reach the dehumidifier with high moisture from the atmosphere condition requesting, in this case, more energy consumption according to the year's seasons. This paper promotes a utilization study of the current process through the installation of a pre-dehumidification device of the inlet air and shows a study to three different dehumidification systems that means by refrigeration, adsorption and actual comparing their performance in an energetic and economical point of view. The goals of this study are to analyze the capacity of moisture removing of each removing device, the influence of moisture variation of the inlet air in the process as well as the economic impact of each device in the global system. It concludes that the utilization of dehumidification devices can eliminate the heating system reducing this way the energy consumption. Moreover it promotes the increasing of moisture gradient between the inlet air and the product optimizing the drying process and increasing the global energy efficiency in the global system. Choosing the most appropriate system for the pre-dehumidification device depends on the desired initial and final moisture content of the product, but applying pre-dehumidifiers at the inlet air promotes an energetic optimization in the spray drying process. (author)

  15. 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 .

  16. 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

  17. Imperfect Reworking Process Consideration in Integrated Inventory Model under Permissible Delay in Payments

    Directory of Open Access Journals (Sweden)

    Ming-Cheng Lo

    2008-01-01

    Full Text Available This study develops an improved inventory model to help the enterprises to advance their profit increasing and cost reduction in a single vendor single-buyer environment with general demand curve, adjustable production rate, and imperfect reworking process under permissible delay in payments. For advancing practical use in a real world, we are concerned with the following strategy determining, which includes the buyer's optimal selling price, order quantity, and the number of shipments per production run from the vendor to the buyer. An algorithm and numerical analysis are used to illustrate the solution procedure.

  18. Reducing WI-FI handover delay using a new positioning process

    International Nuclear Information System (INIS)

    Zaidi, M.; Bhar, J.; Tourki, R.

    2011-01-01

    Mobility has now a crucial requirement for wireless communication. Handover is one of the major tasks that are used to support continuous transmission for a mobile terminal into different radio coverage area. Optimizing the existing handover protocol requires integrating new functionalities. This work focuses on presenting and optimizing handover algorithm. We analyze handover time in wireless local area networks based on the IEEE 802.11b MAC protocol. In fact, scan phase is the main contributor to the handover time. Then, we propose a handover model which replaces a scan phase by a positioning process. This model is able to select the suitable access point (AP) based on the shortest distance far from the mobile terminal (MT). Proposed Handover allows a mobile user to reacting quickly to decide about to which access point to connect. Simulation results show that the proposed model provides gains in term of delays and Handover success in various scenarios.

  19. Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene.

    Science.gov (United States)

    Schneider, Mary D; Bains, Anupinder K; Rajendra, T K; Dominski, Zbigniew; Matera, A Gregory; Simmonds, Andrew J

    2010-11-01

    MRP RNA is a noncoding RNA component of RNase mitochondrial RNA processing (MRP), a multi-protein eukaryotic endoribonuclease reported to function in multiple cellular processes, including ribosomal RNA processing, mitochondrial DNA replication, and cell cycle regulation. A recent study predicted a potential Drosophila ortholog of MRP RNA (CR33682) by computer-based genome analysis. We have confirmed the expression of this gene and characterized the phenotype associated with this locus. Flies with mutations that specifically affect MRP RNA show defects in growth and development that begin in the early larval period and end in larval death during the second instar stage. We present several lines of evidence demonstrating a role for Drosophila MRP RNA in rRNA processing. The nuclear fraction of Drosophila MRP RNA localizes to the nucleolus. Further, a mutant strain shows defects in rRNA processing that include a defect in 5.8S rRNA processing, typical of MRP RNA mutants in other species, as well as defects in early stages of rRNA processing.

  20. Infrared pre-drying and dry-dehulling of walnuts for improved processing efficiency and product quality

    Science.gov (United States)

    The walnut industry is faced with an urgent need to improve post-harvest processing efficiency, particularly drying and dehulling operations. This research investigated the feasibility of dry-dehulling and infrared (IR) pre-drying of walnuts for improved processing efficiency and dried product quali...

  1. Removal of inhibitors from pre-hydrolysis liquor of kraft-based dissolving pulp production process using adsorption and flocculation processes.

    Science.gov (United States)

    Liu, Xin; Fatehi, Pedram; Ni, Yonghao

    2012-07-01

    A process for removing inhibitors from pre-hydrolysis liquor (PHL) of a kraft-based dissolving pulp production process by adsorption and flocculation, and the characteristics of this process were studied. In this process, industrially produced PHL was treated with unmodified and oxidized activated carbon as an absorbent and polydiallyldimethylammonium chloride (PDADMAC) as a flocculant. The overall removal of lignin and furfural in the developed process was 83.3% and 100%, respectively, while that of hemicelluloses was 32.7%. These results confirmed that the developed process can remove inhibitors from PHL prior to producing value-added products, e.g. ethanol and xylitol via fermentation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. 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...

  3. 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 ...

  4. 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).

  5. Time-delay analyzer with continuous discretization

    International Nuclear Information System (INIS)

    Bayatyan, G.L.; Darbinyan, K.T.; Mkrtchyan, K.K.; Stepanyan, S.S.

    1988-01-01

    A time-delay analyzer is described which when triggered by a start pulse of adjustable duration performs continuous discretization of the analyzed signal within nearly 22 ns time intervals, the recording in a memory unit with following slow read-out of the information to the computer and its processing. The time-delay analyzer consists of four CAMAC-VECTOR systems of unit width. With its help one can separate comparatively short, small-amplitude rare signals against the background of quasistationary noise processes. 4 refs.; 3 figs

  6. Pre design processing of waste of ex-resin without materials matrix from nuclear power plant type PWR 1000 MW

    International Nuclear Information System (INIS)

    Cerdas Tarigan

    2010-01-01

    Have been done pre design processing of waste ex-resin without capacities matrix materials from nuclear power plant type PWR 1000 MW During the time radioactive waste of ex-resin processed to use process of immobilization use matrix materials like mixture cement and epoxy resin and then conditioning. This process is not effective and efficient because end result volume of end product bigger than volume early operation system and maintenance of its installation more difficult. To overcome this created a design of technology processing of waste of ex- resin without matrix materials through process of strainer, drying and conditioning represent technological innovation newly processing of radioactive waste of ex-resin. Besides this process more effective and efficient, volume of end product waste much more small from volume early and operation system and maintenance of its easier installation. Pre design is expected to be used as a basis to make conceptual of pre design installation of strainer, drying and conditioning for the processing of waste of ex-resin from nuclear power plant type PWR 1000 MW. (author)

  7. Muscle individual phospholipid classes throughout the processing of dry-cured ham: influence of pre-cure freezing.

    Science.gov (United States)

    Pérez-Palacios, Trinidad; Ruiz, Jorge; Dewettinck, Koen; Le, Thien Trung; Antequera, Teresa

    2010-03-01

    This paper aims to study the profile of phospholipid (PL) classes of Iberian ham throughout its processing and the changes it underwent due to the influence of the pre-cure freezing treatment. The general profile of each PL class did not vary during the ripening stage. Phosphatidylcholine (PC) showed the highest proportion, followed by phosphatidyletanolamine (PE) and phosphatidylserine (PS) and phosphatidylinositol (PI) being the minor PL. The four PL classes were highly hydrolysed during the salting stage and their degradation continued during the rest of the processing. Pre-cure freezing of Iberian ham influenced the levels of the four PL classes at the initial stage, all of them being higher in refrigerated (R) than in pre-cure frozen (F) hams. Moreover, the pattern of hydrolysis was not the same in these two groups. Copyright 2009 Elsevier Ltd. All rights reserved.

  8. The Cognitive, Social and Emotional Processes of Teacher Identity Construction in a Pre-Service Teacher Education Programme

    Science.gov (United States)

    Yuan, Rui; Lee, Icy

    2015-01-01

    This research investigates how three Government-funded Normal Students constructed and reconstructed their identities in a pre-service teacher education programme in China. Drawing upon data from interviews, field observation and the pre-service teachers' written reflections, the study explores the cognitive, social and emotional processes of…

  9. 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/...

  10. LAMMER kinase Kic1 is involved in pre-mRNA processing

    International Nuclear Information System (INIS)

    Tang, Zhaohua; Luca, Maria; Portillio, Jessica; Ngo, Benson; Chang, Cathey; Wen, Teresa; Murray, Johanne; Carr, Antony

    2011-01-01

    The LAMMER kinases are conserved through evolution. They play vital roles in cell growth/differentiation, development, and metabolism. One of the best known functions of the kinases in animal cells is the regulation of pre-mRNA splicing. Kic1 is the LAMMER kinase in fission yeast Schizosaccharomyces pombe. Despite the reported pleiotropic effects of kic1 + deletion/overexpression on various cellular processes the involvement of Kic1 in splicing remains elusive. In this study, we demonstrate for the first time that Kic1 not only is required for efficient splicing but also affects mRNA export, providing evidence for the conserved roles of LAMMER kinases in the unicellular context of fission yeast. Consistent with the hypothesis of its direct participation in multiple steps of pre-mRNA processing, Kic1 is predominantly present in the nucleus during interphase. In addition, the kinase activity of Kic1 plays a role in modulating its own cellular partitioning. Interestingly, Kic1 expression oscillates in a cell cycle-dependent manner and the peak level coincides with mitosis and cytokinesis, revealing a potential mechanism for controlling the kinase activity during the cell cycle. The novel information about the in vivo functions and regulation of Kic1 offers insights into the conserved biological roles fundamental to LAMMER kinases in eukaryotes.

  11. Applying Enhancement Filters in the Pre-processing of Images of Lymphoma

    International Nuclear Information System (INIS)

    Silva, Sérgio Henrique; Do Nascimento, Marcelo Zanchetta; Neves, Leandro Alves; Batista, Valério Ramos

    2015-01-01

    Lymphoma is a type of cancer that affects the immune system, and is classified as Hodgkin or non-Hodgkin. It is one of the ten types of cancer that are the most common on earth. Among all malignant neoplasms diagnosed in the world, lymphoma ranges from three to four percent of them. Our work presents a study of some filters devoted to enhancing images of lymphoma at the pre-processing step. Here the enhancement is useful for removing noise from the digital images. We have analysed the noise caused by different sources like room vibration, scraps and defocusing, and in the following classes of lymphoma: follicular, mantle cell and B-cell chronic lymphocytic leukemia. The filters Gaussian, Median and Mean-Shift were applied to different colour models (RGB, Lab and HSV). Afterwards, we performed a quantitative analysis of the images by means of the Structural Similarity Index. This was done in order to evaluate the similarity between the images. In all cases we have obtained a certainty of at least 75%, which rises to 99% if one considers only HSV. Namely, we have concluded that HSV is an important choice of colour model at pre-processing histological images of lymphoma, because in this case the resulting image will get the best enhancement

  12. Pre-engineering assessment of Enersolve Demonstration Project. Dairy processing plant. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1985-07-15

    This study involved evaluation of a dairy processing plant to demonstrate energy conservation potential and developing a strategy to realize energy savings through retrofitting and revamping. The cheese and whey making plant of Agropur Cooperative Agro-Alimentaire located in Quebec was selected as a representative Canadian dairy processing plant. The pre-engineering assessment included a review of existing facility at the plant and plant operation, identification of plant equipment or process steps where substantial economic benefits would result from retrofitting and revamping, and estimation of budgetary cost for the subsequent engineering, procurement, construction management and monitoring of the retrofitted equipment. 3 figs., 2 tabs.

  13. Time Delay of CGM Sensors

    Science.gov (United States)

    Schmelzeisen-Redeker, Günther; Schoemaker, Michael; Kirchsteiger, Harald; Freckmann, Guido; Heinemann, Lutz; del Re, Luigi

    2015-01-01

    Background: Continuous glucose monitoring (CGM) is a powerful tool to support the optimization of glucose control of patients with diabetes. However, CGM systems measure glucose in interstitial fluid but not in blood. Rapid changes in one compartment are not accompanied by similar changes in the other, but follow with some delay. Such time delays hamper detection of, for example, hypoglycemic events. Our aim is to discuss the causes and extent of time delays and approaches to compensate for these. Methods: CGM data were obtained in a clinical study with 37 patients with a prototype glucose sensor. The study was divided into 5 phases over 2 years. In all, 8 patients participated in 2 phases separated by 8 months. A total number of 108 CGM data sets including raw signals were used for data analysis and were processed by statistical methods to obtain estimates of the time delay. Results: Overall mean (SD) time delay of the raw signals with respect to blood glucose was 9.5 (3.7) min, median was 9 min (interquartile range 4 min). Analysis of time delays observed in the same patients separated by 8 months suggests a patient dependent delay. No significant correlation was observed between delay and anamnestic or anthropometric data. The use of a prediction algorithm reduced the delay by 4 minutes on average. Conclusions: Prediction algorithms should be used to provide real-time CGM readings more consistent with simultaneous measurements by SMBG. Patient specificity may play an important role in improving prediction quality. PMID:26243773

  14. 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.

  15. Time-delayed feedback control of diffusion in random walkers

    Science.gov (United States)

    Ando, Hiroyasu; Takehara, Kohta; Kobayashi, Miki U.

    2017-07-01

    Time delay in general leads to instability in some systems, while specific feedback with delay can control fluctuated motion in nonlinear deterministic systems to a stable state. In this paper, we consider a stochastic process, i.e., a random walk, and observe its diffusion phenomenon with time-delayed feedback. As a result, the diffusion coefficient decreases with increasing delay time. We analytically illustrate this suppression of diffusion by using stochastic delay differential equations and justify the feasibility of this suppression by applying time-delayed feedback to a molecular dynamics model.

  16. Delay and death-thought accessibility: a meta-analysis.

    Science.gov (United States)

    Steinman, Christopher T; Updegraff, John A

    2015-12-01

    The dual-process component of Terror Management Theory (TMT) proposes that different types of threats lead to increases in death-thought accessibility (DTA) after different delay intervals. Experimental studies of terror management threats' effect on DTA were collected and coded for their use of explicitly death-related (vs. not explicitly death-related) threats, and for their use of delay and task-switching during the delay. Results reveal that studies using death-related threats achieved larger DTA effect-sizes when they included more task-switching or a longer delay between the threat and the DTA measurement. In contrast, studies using threats that were not explicitly death-related achieved smaller DTA effect-sizes when they included more task-switching between the threat and the DTA measurement. These findings provide partial support for the dual-process component's predictions regarding delay and DTA. Limitations and future directions are discussed. © 2015 by the Society for Personality and Social Psychology, Inc.

  17. The effect of thermal pre-treatment of titanium hydride (TiH2) powder in argon condition

    Science.gov (United States)

    Franciska P., L.; Erryani, Aprilia; Annur, Dhyah; Kartika, Ika

    2018-04-01

    Titanium hydride (TiH2) powders are used to enhance the foaming process in the formation of a highly porous metallic material with a cellular structure. But, the low temperature of hydrogen release is one of its problems. The present study, different thermal pre-treatment temperatures were employed to investigate the decomposition behavior of TiH2 to retard or delay a hydrogen gas release process during foaming. As a foaming agent, TiH2 was subjected to various heat treatments prior at 450 and 500°C during 2 hours in argon condition. To study the formation mechanism, the thermal behavior of titanium hydride and hydrogen release are investigated by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The morphology of pre-treated titanium hydride powders were examined using Scanning Electron Microscope (SEM) while unsure mapping and elemental composition of the pre-treated powders processed by Energy Dispersive Spectroscopy (EDS). To study the phase formation was characterized by X-ray diffraction analysis (XRD). In accordance with the results, an increase in pre-treatment temperature of TiH2 to higher degrees are changing the process of releasing hydrogen from titanium hydride powder. DTA/TGA results showed that thermal pre-treatment TiH2 at 450°C, released the hydrogen gas at 560°C in heat treatment when foaming process. Meanwhile, thermal pre-treatment in TiH2 at 500°C, released the hydrogen gas at 670°C when foaming process. There is plenty of direct evidence for the existence of oxide layers that showed by EDS analysis obtained in SEM. As oxygen is a light element and qualitative proof shows that the higher pre-treatment temperature produces more and thicker oxygen layers on the surface of the TiH2 powder particles. It might the thickness of oxide layer are different from different pre-treatment temperatures, which leading to the differences in the decomposition temperature. But from SEM result that oxidation of the powder does not

  18. Learning processes of students pre-vocational secondary education: relations between goal orientations, information processing strategies and development of conceptual knowledge

    NARCIS (Netherlands)

    Koopman, M.; Brok, den P.J.; Beijaard, D.; Teune, P.J.

    2011-01-01

    The purpose of this study was to investigate relations between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education students (n = 719; 14 schools). Students' preferences for certain types of goals and information

  19. 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

  20. 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

  1. Improving Robustness of Hydrologic Ensemble Predictions Through Probabilistic Pre- and Post-Processing in Sequential Data Assimilation

    Science.gov (United States)

    Wang, S.; Ancell, B. C.; Huang, G. H.; Baetz, B. W.

    2018-03-01

    Data assimilation using the ensemble Kalman filter (EnKF) has been increasingly recognized as a promising tool for probabilistic hydrologic predictions. However, little effort has been made to conduct the pre- and post-processing of assimilation experiments, posing a significant challenge in achieving the best performance of hydrologic predictions. This paper presents a unified data assimilation framework for improving the robustness of hydrologic ensemble predictions. Statistical pre-processing of assimilation experiments is conducted through the factorial design and analysis to identify the best EnKF settings with maximized performance. After the data assimilation operation, statistical post-processing analysis is also performed through the factorial polynomial chaos expansion to efficiently address uncertainties in hydrologic predictions, as well as to explicitly reveal potential interactions among model parameters and their contributions to the predictive accuracy. In addition, the Gaussian anamorphosis is used to establish a seamless bridge between data assimilation and uncertainty quantification of hydrologic predictions. Both synthetic and real data assimilation experiments are carried out to demonstrate feasibility and applicability of the proposed methodology in the Guadalupe River basin, Texas. Results suggest that statistical pre- and post-processing of data assimilation experiments provide meaningful insights into the dynamic behavior of hydrologic systems and enhance robustness of hydrologic ensemble predictions.

  2. Dietary restriction delays the secretion of senescence associated secretory phenotype by reducing DNA damage response in the process of renal aging.

    Science.gov (United States)

    Wang, Wenjuan; Cai, Guangyan; Chen, Xiangmei

    2017-09-13

    Dietary restriction (DR) has multiple and essential effects in protecting against DNA damage in model organisms. Persistent DNA damage plays a central role in the process of aging. Senescence-associated secretory phenotype (SASP), as a product of cellular aging, can accelerate the process of cellular senescence as a feedback. In this study, we directly observed whether a DR of 30% for 6months in aged rats could retard SASP by delaying the progression of DNA damage and also found the specific mechanism. The results revealed that a 30% DR could significantly improve renal pathology and some metabolic characteristics. The biomarkers and products of DNA damage were decreased in the process of renal aging on a 30% DR. A series of SASP, notably cytokine, chemokine, and growth factor, were obviously reduced by DR during renal aging. The phosphorylation levels of NF-κB and IκBα in aged kidneys of DR group were markedly reduced. These findings suggest that a 30% DR for 6months can delay renal aging and reduce the accumulation of SASP by retarding the progression of DNA damage and decreasing the transcription activity of NF-κB, thus providing a target to delay renal aging. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. 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. 

  4. 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

  5. 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....

  6. A Case Study on Pre-Service Secondary School Mathematics Teachers' Cognitive-Metacognitive Behaviours in Mathematical Modelling Process

    Science.gov (United States)

    Sagirli, Meryem Özturan

    2016-01-01

    The aim of the present study is to investigate pre-service secondary mathematics teachers' cognitive-metacognitive behaviours during the mathematical problem-solving process considering class level. The study, in which the case study methodology was employed, was carried out with eight pre-service mathematics teachers, enrolled at a university in…

  7. Estimating Delays In ASIC's

    Science.gov (United States)

    Burke, Gary; Nesheiwat, Jeffrey; Su, Ling

    1994-01-01

    Verification is important aspect of process of designing application-specific integrated circuit (ASIC). Design must not only be functionally accurate, but must also maintain correct timing. IFA, Intelligent Front Annotation program, assists in verifying timing of ASIC early in design process. This program speeds design-and-verification cycle by estimating delays before layouts completed. Written in C language.

  8. ENDF/B Pre-Processing Codes: Implementing and testing on a Personal Computer

    International Nuclear Information System (INIS)

    McLaughlin, P.K.

    1987-05-01

    This document describes the contents of the diskettes containing the ENDF/B Pre-Processing codes by D.E. Cullen, and example data for use in implementing and testing these codes on a Personal Computer of the type IBM-PC/AT. Upon request the codes are available from the IAEA Nuclear Data Section, free of charge, on a series of 7 diskettes. (author)

  9. A Polynomial Estimate of Railway Line Delay

    DEFF Research Database (Denmark)

    Cerreto, Fabrizio; Harrod, Steven; Nielsen, Otto Anker

    2017-01-01

    Railway service may be measured by the aggregate delay over a time horizon or due to an event. Timetables for railway service may dampen aggregate delay by addition of additional process time, either supplement time or buffer time. The evaluation of these variables has previously been performed...

  10. Synchronization of conference presentation sequence using delay equalization approach

    Science.gov (United States)

    Godavari, Rakesh K.; Celenk, Mehmet

    2001-11-01

    In this paper, a delay equalization approach is proposed for cohesive conference presentation with minimal screen- freezing effect. The underlying screen-freezing effect is due to varying delays in the communication channels involved in broadcasting. In turn, this poses a threat to the goal of uniform delay distribution among data packets for synchronized presentation broadcast. We wish to achieve uniformity among packet arrival times to the recipients. This objective is achieved by transforming a given input delay distribution (D) to the desired output density through a delay equalization process. Considering a general case of between packet and frame delay distributions for a given input, the desired output is obtained through a delay equalization process. In case of a specific normal delay distribution, a memory-less system g(D) is determined as an approximation to the delay equalizer such that the equalizer output O(t)equalsg[D(t)] is uniformly distributed in the allowable delay limits of (a,b) assuring the specified quality of service (QoS) parameters. The corresponding delay is added at each recipient workstation, which acts as the wait period required before it begins its designated presentation.For a zero mean normal delay density case, the equalizer transfer function can be given in a closed from solution as O(t)equalsg[D(t)[equals(b-a)]0.5+eft(-D/$RO OTR(0)))[+a, where erf(x) is the standard error function. The histogram approximation is adopted as an asymptotically delay equalization means for general cases. This technique provides a means for modifying the dynamic range of data acquired by altering it into a desired distribution. In experimentation, equalizer characteristic functions are derived for a set of selected input delays to obtain the desired output. The delay equalizer system developed here is suited for deployment in a distributed hierarchical conferencing environment. To accommodate a broadcast continuity, the multimedia presentation is

  11. 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

  12. 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.

  13. Learning processes of students in competence-based pre-vocational secondary education: relations between goal orientations, information processing strategies and development of conceptual knowledge

    NARCIS (Netherlands)

    Dr. M. Koopman; prof dr Douwe Beijaard; Dr P.J. Teune; P. den Brok

    2011-01-01

    The purpose of this study was to investigate relations between goal orientations, information processing strategies and development of conceptual knowledge of pre-vocational secondary education students (n=719; 14 schools). Students' preferences for certain types of goals and information processing

  14. Cloudy Solar Software - Enhanced Capabilities for Finding, Pre-processing, and Visualizing Solar Data

    Science.gov (United States)

    Istvan Etesi, Laszlo; Tolbert, K.; Schwartz, R.; Zarro, D.; Dennis, B.; Csillaghy, A.

    2010-05-01

    In our project "Extending the Virtual Solar Observatory (VSO)” we have combined some of the features available in Solar Software (SSW) to produce an integrated environment for data analysis, supporting the complete workflow from data location, retrieval, preparation, and analysis to creating publication-quality figures. Our goal is an integrated analysis experience in IDL, easy-to-use but flexible enough to allow more sophisticated procedures such as multi-instrument analysis. To that end, we have made the transition from a locally oriented setting where all the analysis is done on the user's computer, to an extended analysis environment where IDL has access to services available on the Internet. We have implemented a form of Cloud Computing that uses the VSO search and a new data retrieval and pre-processing server (PrepServer) that provides remote execution of instrument-specific data preparation. We have incorporated the interfaces to the VSO search and the PrepServer into an IDL widget (SHOW_SYNOP) that provides user-friendly searching and downloading of raw solar data and optionally sends search results for pre-processing to the PrepServer prior to downloading the data. The raw and pre-processed data can be displayed with our plotting suite, PLOTMAN, which can handle different data types (light curves, images, and spectra) and perform basic data operations such as zooming, image overlays, solar rotation, etc. PLOTMAN is highly configurable and suited for visual data analysis and for creating publishable figures. PLOTMAN and SHOW_SYNOP work hand-in-hand for a convenient working environment. Our environment supports a growing number of solar instruments that currently includes RHESSI, SOHO/EIT, TRACE, SECCHI/EUVI, HINODE/XRT, and HINODE/EIS.

  15. Changes in cognitive control in pre-manifest Huntington's disease examined using pre-saccadic EEG potentials - a longitudinal study.

    Science.gov (United States)

    Ness, Vanessa; Bestgen, Anne-Kathrin; Saft, Carsten; Beste, Christian

    2014-01-01

    It is well-known that Huntington's disease (HD) affects saccadic processing. However, saccadic dysfunctions in HD may be seen as a result of dysfunctional processes occurring at the oculomotor level prior to the execution of saccades, i.e., at a pre-saccadic level. Virtually nothing is known about possible changes in pre-saccadic processes in HD. This study examines pre-saccadic processing in pre-manifest HD gene mutation carriers (pre-HDs) by using clinically available EEG measures. Error rates, pre-saccadic EEG potentials and saccade onset EEG potentials were measured in 14 pre-HDs and case-matched controls performing prosaccades and antisaccades in a longitudinal study over a 15-month period. The results show that pre-saccadic potentials were changed in pre-HDs, relative to controls and also revealed changes across the 15-month longitudinal period. In particular, pre-saccadic ERP in pre-HDs were characterized by lower amplitudes and longer latencies, which revealed longitudinal changes. These changes were observed for anti-saccades, but not for pro-saccades. Overt saccadic trajectories (potentials) were not different to those in controls, showing that pre-saccadic processes are sensitive to subtle changes in fronto-striatal networks in pre-HDs. Deficits in pre-saccadic processes prior the execution of an erroneous anti-saccade can be seen as an effect of dysfunctional cognitive control in HD. This may underlie saccadic abnormalities and hence a major phenotype of HD. Pre-saccadic EEG potentials preceding erroneous anti-saccades are sensitive to pre-manifest disease progression in HD.

  16. 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.

  17. Quality Measures in Pre-Analytical Phase of Tissue Processing: Understanding Its Value in Histopathology.

    Science.gov (United States)

    Rao, Shalinee; Masilamani, Suresh; Sundaram, Sandhya; Duvuru, Prathiba; Swaminathan, Rajendiran

    2016-01-01

    Quality monitoring in histopathology unit is categorized into three phases, pre-analytical, analytical and post-analytical, to cover various steps in the entire test cycle. Review of literature on quality evaluation studies pertaining to histopathology revealed that earlier reports were mainly focused on analytical aspects with limited studies on assessment of pre-analytical phase. Pre-analytical phase encompasses several processing steps and handling of specimen/sample by multiple individuals, thus allowing enough scope for errors. Due to its critical nature and limited studies in the past to assess quality in pre-analytical phase, it deserves more attention. This study was undertaken to analyse and assess the quality parameters in pre-analytical phase in a histopathology laboratory. This was a retrospective study done on pre-analytical parameters in histopathology laboratory of a tertiary care centre on 18,626 tissue specimens received in 34 months. Registers and records were checked for efficiency and errors for pre-analytical quality variables: specimen identification, specimen in appropriate fixatives, lost specimens, daily internal quality control performance on staining, performance in inter-laboratory quality assessment program {External quality assurance program (EQAS)} and evaluation of internal non-conformities (NC) for other errors. The study revealed incorrect specimen labelling in 0.04%, 0.01% and 0.01% in 2007, 2008 and 2009 respectively. About 0.04%, 0.07% and 0.18% specimens were not sent in fixatives in 2007, 2008 and 2009 respectively. There was no incidence of specimen lost. A total of 113 non-conformities were identified out of which 92.9% belonged to the pre-analytical phase. The predominant NC (any deviation from normal standard which may generate an error and result in compromising with quality standards) identified was wrong labelling of slides. Performance in EQAS for pre-analytical phase was satisfactory in 6 of 9 cycles. A low incidence

  18. Anaerobic digestion of organic by-products from meat-processing industry. The effect of pre-treatments and co-digestion

    Energy Technology Data Exchange (ETDEWEB)

    Luste, S.

    2011-07-01

    Anaerobic digestion is a multi-beneficial biological treatment during which micro-organisms degrade organic material producing biogas (i.e. methane) and stabilised end-product (i.e. digestate). Methane is a versatile renewable energy source and digestate can be used as an organic fertiliser and/or soil improver. Because of the increasing consumption and tightening environment and health legislation, production of organic wastes suitable for anaerobic digestion increases. Animal by-products (ABP) from the meat-processing industry are often rendered (contaminated material), used as feedstock (in fur breeding), or composted. However, ABPs studied could not be utilised in fodder or in animal food production and have currently been rendered or directed to composting, despite being mostly considered unsuitable for composting. Many ABPs are energy-rich, wet and pasty materials and suitable for the anaerobic digestion process. Moreover, suitable pre-treatment to hydrolyse solid materials and/or co-digestion of two or several materials may improve the anaerobic digestion with ultimate goal to increase the methane production, stabilisation and reusability of digestate. The case chosen for more detailed research was that of a middle-sized Finnish meat-processing industry. The aim of the thesis was to evaluate the feasibility of different ABPs presently available for treatment as raw material for anaerobic digestion. Another objective was to enhance the anaerobic digestion process via specific pre-treatments and co-digestion cases with the ultimate aim to increase the methane production and the quality of the digestate. The general goal was to observe the overall process from the perspective of real-circumstances in Finland to rise to needs in practice and to produce exploitable information for adopting sustainable development locally and case-specifically into practice via versatile anaerobic digestion technology. The ABPs studied were highly bio-degradable and especially

  19. Data pre-processing for web log mining: Case study of commercial bank website usage analysis

    Directory of Open Access Journals (Sweden)

    Jozef Kapusta

    2013-01-01

    Full Text Available We use data cleaning, integration, reduction and data conversion methods in the pre-processing level of data analysis. Data processing techniques improve the overall quality of the patterns mined. The paper describes using of standard pre-processing methods for preparing data of the commercial bank website in the form of the log file obtained from the web server. Data cleaning, as the simplest step of data pre-processing, is non–trivial as the analysed content is highly specific. We had to deal with the problem of frequent changes of the content and even frequent changes of the structure. Regular changes in the structure make use of the sitemap impossible. We presented approaches how to deal with this problem. We were able to create the sitemap dynamically just based on the content of the log file. In this case study, we also examined just the one part of the website over the standard analysis of an entire website, as we did not have access to all log files for the security reason. As the result, the traditional practices had to be adapted for this special case. Analysing just the small fraction of the website resulted in the short session time of regular visitors. We were not able to use recommended methods to determine the optimal value of session time. Therefore, we proposed new methods based on outliers identification for raising the accuracy of the session length in this paper.

  20. Students' goal orientations, information processing strategies and knowledge development in competence-based pre-vocational secondary education

    NARCIS (Netherlands)

    Koopman, M.

    2010-01-01

    In this study, learning processes of students in competence-based Pre-Vocational Secondary Education (PVSE; in Dutch vmbo) were investigated. The study aimed at describing the relation between goal orientations, information processing strategies and the development of knowledge of these students.

  1. The role of the amygdala during emotional processing in Huntington's disease: from pre-manifest to late stage disease.

    Science.gov (United States)

    Mason, Sarah L; Zhang, Jiaxiang; Begeti, Faye; Guzman, Natalie Valle; Lazar, Alpar S; Rowe, James B; Barker, Roger A; Hampshire, Adam

    2015-04-01

    Deficits in emotional processing can be detected in the pre-manifest stage of Huntington's disease and negative emotion recognition has been identified as a predictor of clinical diagnosis. The underlying neuropathological correlates of such deficits are typically established using correlative structural MRI studies. This approach does not take into consideration the impact of disruption to the complex interactions between multiple brain circuits on emotional processing. Therefore, exploration of the neural substrates of emotional processing in pre-manifest HD using fMRI connectivity analysis may be a useful way of evaluating the way brain regions interrelate in the period prior to diagnosis. We investigated the impact of predicted time to disease onset on brain activation when participants were exposed to pictures of faces with angry and neutral expressions, in 20 pre-manifest HD gene carriers and 23 healthy controls. On the basis of the results of this initial study went on to look at amygdala dependent cognitive performance in 79 Huntington's disease patients from a cross-section of disease stages (pre-manifest to late disease) and 26 healthy controls, using a validated theory of mind task: "the Reading the Mind in the Eyes Test" which has been previously been shown to be amygdala dependent. Psychophysiological interaction analysis identified reduced connectivity between the left amygdala and right fusiform facial area in pre-manifest HD gene carriers compared to controls when viewing angry compared to neutral faces. Change in PPI connectivity scores correlated with predicted time to disease onset (r=0.45, pneural networks underlying social cognition and emotional processing can be detected prior to clinical diagnosis in Huntington's disease. Connectivity between the amygdala and other brain regions is impacted by the disease process in pre-manifest HD and may therefore be a useful way of identifying participants who are approaching a clinical diagnosis

  2. The recursive combination filter approach of pre-processing for the estimation of standard deviation of RR series.

    Science.gov (United States)

    Mishra, Alok; Swati, D

    2015-09-01

    Variation in the interval between the R-R peaks of the electrocardiogram represents the modulation of the cardiac oscillations by the autonomic nervous system. This variation is contaminated by anomalous signals called ectopic beats, artefacts or noise which mask the true behaviour of heart rate variability. In this paper, we have proposed a combination filter of recursive impulse rejection filter and recursive 20% filter, with recursive application and preference of replacement over removal of abnormal beats to improve the pre-processing of the inter-beat intervals. We have tested this novel recursive combinational method with median method replacement to estimate the standard deviation of normal to normal (SDNN) beat intervals of congestive heart failure (CHF) and normal sinus rhythm subjects. This work discusses the improvement in pre-processing over single use of impulse rejection filter and removal of abnormal beats for heart rate variability for the estimation of SDNN and Poncaré plot descriptors (SD1, SD2, and SD1/SD2) in detail. We have found the 22 ms value of SDNN and 36 ms value of SD2 descriptor of Poincaré plot as clinical indicators in discriminating the normal cases from CHF cases. The pre-processing is also useful in calculation of Lyapunov exponent which is a nonlinear index as Lyapunov exponents calculated after proposed pre-processing modified in a way that it start following the notion of less complex behaviour of diseased states.

  3. 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

  4. Performance Comparison of Several Pre-Processing Methods in a Hand Gesture Recognition System based on Nearest Neighbor for Different Background Conditions

    Directory of Open Access Journals (Sweden)

    Iwan Setyawan

    2012-12-01

    Full Text Available This paper presents a performance analysis and comparison of several pre-processing methods used in a hand gesture recognition system. The pre-processing methods are based on the combinations of several image processing operations, namely edge detection, low pass filtering, histogram equalization, thresholding and desaturation. The hand gesture recognition system is designed to classify an input image into one of six possible classes. The input images are taken with various background conditions. Our experiments showed that the best result is achieved when the pre-processing method consists of only a desaturation operation, achieving a classification accuracy of up to 83.15%.

  5. Investigation of delayed fission gas release

    International Nuclear Information System (INIS)

    Cayet, Nicolas

    1996-05-01

    The study of the fission gas release process in the high burnup rig IFA-562 has revealed a particular fuel behaviour: a delay in the fission gas release process. It appeared that an important release of gas was measured by the pressure transducers once the power had decreased, whereas, during steady-state operation, the pressure did not increase very much. After examinations, the gap size has been concluded to be the main parameter involving this delay. However the burnup could have been a potential factor, its role is mainly to close the gap by swelling. The observations of low burnup rods have shown the same delayed fission gas release, the gap being small by design and closed essentially by thermal expansion. The study of the kinetics has demonstrated the time-independency of the phenomenon. Thus the proposed mechanism driving this delayed fission gas release would involve three consecutives stages. During steady-state, the gas is released into the interlinkage network of grain boundary bubbles and cracks. Due to the closed gap, the gas is trapped in some void volumes, unable to escape the pellet. During power reduction, the gap and some old/new cracks open, immediately providing a path for the gas to the pressure transducers and explaining this delay in the fission gas release. (author)

  6. Secondary Mathematics Pre-Service Teachers' Processes of Selection and Integration of Technology

    Science.gov (United States)

    Uzan, Erol

    2017-01-01

    This study investigated secondary mathematics pre-service teachers' (PSTs) knowledge of resources in terms of digital technologies, and explored the processes of both selection and integration of technology into their lesson plans. This study employed a case study design. Participants were six secondary mathematics PSTs who enrolled in a methods…

  7. 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.

  8. 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...

  9. 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...

  10. 3-D image pre-processing algorithms for improved automated tracing of neuronal arbors.

    Science.gov (United States)

    Narayanaswamy, Arunachalam; Wang, Yu; Roysam, Badrinath

    2011-09-01

    The accuracy and reliability of automated neurite tracing systems is ultimately limited by image quality as reflected in the signal-to-noise ratio, contrast, and image variability. This paper describes a novel combination of image processing methods that operate on images of neurites captured by confocal and widefield microscopy, and produce synthetic images that are better suited to automated tracing. The algorithms are based on the curvelet transform (for denoising curvilinear structures and local orientation estimation), perceptual grouping by scalar voting (for elimination of non-tubular structures and improvement of neurite continuity while preserving branch points), adaptive focus detection, and depth estimation (for handling widefield images without deconvolution). The proposed methods are fast, and capable of handling large images. Their ability to handle images of unlimited size derives from automated tiling of large images along the lateral dimension, and processing of 3-D images one optical slice at a time. Their speed derives in part from the fact that the core computations are formulated in terms of the Fast Fourier Transform (FFT), and in part from parallel computation on multi-core computers. The methods are simple to apply to new images since they require very few adjustable parameters, all of which are intuitive. Examples of pre-processing DIADEM Challenge images are used to illustrate improved automated tracing resulting from our pre-processing methods.

  11. Delay Estimator and Improved Proportionate Multi-Delay Adaptive Filtering Algorithm

    Directory of Open Access Journals (Sweden)

    E. Verteletskaya

    2012-04-01

    Full Text Available This paper pertains to speech and acoustic signal processing, and particularly to a determination of echo path delay and operation of echo cancellers. To cancel long echoes, the number of weights in a conventional adaptive filter must be large. The length of the adaptive filter will directly affect both the degree of accuracy and the convergence speed of the adaptation process. We present a new adaptive structure which is capable to deal with multiple dispersive echo paths. An adaptive filter according to the present invention includes means for storing an impulse response in a memory, the impulse response being indicative of the characteristics of a transmission line. It also includes a delay estimator for detecting ranges of samples within the impulse response having relatively large distribution of echo energy. These ranges of samples are being indicative of echoes on the transmission line. An adaptive filter has a plurality of weighted taps, each of the weighted taps having an associated tap weight value. A tap allocation/control circuit establishes the tap weight values in response to said detecting means so that only taps within the regions of relatively large distributions of echo energy are turned on. Thus, the convergence speed and the degree of estimation in the adaptation process can be improved.

  12. The influence of levels of processing on recall from working memory and delayed recall tasks.

    Science.gov (United States)

    Loaiza, Vanessa M; McCabe, David P; Youngblood, Jessie L; Rose, Nathan S; Myerson, Joel

    2011-09-01

    Recent research in working memory has highlighted the similarities involved in retrieval from complex span tasks and episodic memory tasks, suggesting that these tasks are influenced by similar memory processes. In the present article, the authors manipulated the level of processing engaged when studying to-be-remembered words during a reading span task (Experiment 1) and an operation span task (Experiment 2) in order to assess the role of retrieval from secondary memory during complex span tasks. Immediate recall from both span tasks was greater for items studied under deep processing instructions compared with items studied under shallow processing instructions regardless of trial length. Recall was better for deep than for shallow levels of processing on delayed recall tests as well. These data are consistent with the primary-secondary memory framework, which suggests that to-be-remembered items are displaced from primary memory (i.e., the focus of attention) during the processing phases of complex span tasks and therefore must be retrieved from secondary memory. (c) 2011 APA, all rights reserved.

  13. Process for calcium xylonate production as a concrete admixture derived from in-situ fermentation of wheat straw pre-hydrolysate.

    Science.gov (United States)

    Zhou, Xin; Zhou, Xuelian; Tang, Xiusheng; Xu, Yong

    2018-08-01

    One of the major obstacles in process of lignocellulosic biorefinery is the utilization of pre-hydrolysate from pre-treatment. Although lignocellulosic pre-hydrolysate can serve as an economic starting material for xylonic acid production, the advancement of xylonic acid or xylonate is still limited by further commercial value or applications. In the present study, xylose in the high concentration wheat straw pre-hydrolysate was first in-situ biooxidized to xylonate by Gluconobacter oxydans. To meet the needs of commercialization, crude powdered calcium xylonate was prepared by drying process and calcium xylonate content in the prepared crude product was more than 70%. Then, the calcium xylonate product was evaluated as concrete admixture without any complex purification steps and the results demonstrated that xylonate could improve the performance of concrete. Overall, the crude xylonate product directly produced from low-cost wheat straw pre-hydrolysate can potentially be developed as retarding reducer, which could subsequently benefit lignocellulosic biorefinery. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. Possibility of content change in bioethanol gasoline during pre-treatment process for using accelerator mass spectroscopy

    International Nuclear Information System (INIS)

    Saito, Masaaki; Yunoki, Shunji; Suzuki, Takashi

    2010-01-01

    We attempted to determine the bioethanol content of E3 gasoline by applying ASTM D6866 method B. In the pre-treatment process using accelerator mass spectroscopy(AMS), the graphite samples were prepared from E3 gasoline. Three portions of the same graphite sample were measured, and the contents agreed within the measurement error of AMS. The graphite samples prepared from eight portions of the same E3 gasoline sample were measured, but the accuracy was insufficient. There are many kinds of hydrocarbon compounds in the gasoline and their boiling points are different. The content of bioethanol was found to decrease with vaporization when E3 gasoline was placed in open air. A very small amount of E3 gasoline is pre-treated for AMS and the volatile loss cannot be ignored. It seems that the content change of bioethanol was caused by vaporization of E3 gasoline during the pre-treatment process. (author)

  15. 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...

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Automated Pre-processing for NMR Assignments with Reduced Tedium

    Energy Technology Data Exchange (ETDEWEB)

    2004-05-11

    An important rate-limiting step in the reasonance asignment process is accurate identification of resonance peaks in MNR spectra. NMR spectra are noisy. Hence, automatic peak-picking programs must navigate between the Scylla of reliable but incomplete picking, and the Charybdis of noisy but complete picking. Each of these extremes complicates the assignment process: incomplete peak-picking results in the loss of essential connectivities, while noisy picking conceals the true connectivities under a combinatiorial explosion of false positives. Intermediate processing can simplify the assignment process by preferentially removing false peaks from noisy peak lists. This is accomplished by requiring consensus between multiple NMR experiments, exploiting a priori information about NMR spectra, and drawing on empirical statistical distributions of chemical shift extracted from the BioMagResBank. Experienced NMR practitioners currently apply many of these techniques "by hand", which is tedious, and may appear arbitrary to the novice. To increase efficiency, we have created a systematic and automated approach to this process, known as APART. Automated pre-processing has three main advantages: reduced tedium, standardization, and pedagogy. In the hands of experienced spectroscopists, the main advantage is reduced tedium (a rapid increase in the ratio of true peaks to false peaks with minimal effort). When a project is passed from hand to hand, the main advantage is standardization. APART automatically documents the peak filtering process by archiving its original recommendations, the accompanying justifications, and whether a user accepted or overrode a given filtering recommendation. In the hands of a novice, this tool can reduce the stumbling block of learning to differentiate between real peaks and noise, by providing real-time examples of how such decisions are made.

  1. 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.

  2. Enhanced shock wave generation via pre-breakdown acceleration using water electrolysis in negative streamer pulsed spark discharges

    Science.gov (United States)

    Lee, Kern; Chung, Kyoung-Jae; Hwang, Y. S.

    2018-03-01

    This paper presents a method for enhancement of shock waves generated from underwater pulsed spark discharges with negative (anode-directed) subsonic streamers, for which the pre-breakdown process is accelerated by preconditioning a gap with water electrolysis. Hydrogen microbubbles are produced at the cathode by the electrolysis and move towards the anode during the preconditioning phase. The numbers and spatial distributions of the microbubbles vary with the amplitude and duration of each preconditioning pulse. Under our experimental conditions, the optimum pulse duration is determined to be ˜250 ms at a pulse voltage of 400 V, where the buoyancy force overwhelms the electric force and causes the microbubbles to be swept out from the water gap. When a high-voltage pulse is applied to the gap just after the preconditioning pulse, the pre-breakdown process is significantly accelerated in the presence of the microbubbles. At the optimum preconditioning pulse duration, the average breakdown delay is reduced by 87% and, more importantly, the energy consumed during the pre-breakdown period decreases by 83%. This reduced energy consumption during the pre-breakdown period, when combined with the morphological advantages of negative streamers, such as thicker and longer stalks, leads to a significant improvement in the measured peak pressure (˜40%) generated by the underwater pulsed spark discharge. This acceleration of pre-breakdown using electrolysis overcomes the biggest drawback of negative subsonic discharges, which is slow vapor bubble formation due to screening effects, and thus enhances the efficiency of the shock wave generation process using pulsed spark discharges in water.

  3. Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing.

    Science.gov (United States)

    Goldfarb, Katherine C; Cech, Thomas R

    2017-01-01

    MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR-Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor-analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing-implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation. © 2017 Goldfarb and Cech; Published by Cold Spring Harbor Laboratory Press.

  4. Delays in Building Construction Projects in Ghana

    Directory of Open Access Journals (Sweden)

    Adwoa B Agyakwah-Baah

    2010-07-01

    Full Text Available This study investigates the causes of delay of building construction projects in Ghana to determine the most important according to the key project participants; clients, consultants, and contractors. Thirty-two possible causes of delay were identified from the literature and semi-structured interviews of 15 key players in the implementation process. These delay factors were further categorised into nine major groups. The list of delay causes was subjected to a questionnaire survey for the identification of the most important causes of delay. The field survey included 130 respondents made up of 39 contractors, 37 clients and 54 consultants. The relative importance of the individual causes and the groups were calculated and ranked by their relative importance index. The overall results of the study indicate that the respondents generally agree that financial group factors ranked highest among the major factors causing delay in construction projects in Ghana. The financial group factors were delay in honouring payment certificates, difficulty in accessing credit and fluctuation in prices. Materials group factors are second followed by scheduling and controlling factors.

  5. Overcoming the Recalcitrance for the Conversion of Kenaf Pulp to Glucose via Microwave-Assisted Pre-Treatment Processes

    Directory of Open Access Journals (Sweden)

    Miguel A. Hurtado

    2011-02-01

    Full Text Available This study evaluates the pre-treatment of cellulose from kenaf plant to yield sugar precursors for the production of ethanol or butanol for use as biofuel additives. In order to convert the crystalline cellulosic form to the amorphous form that can undergo enzymatic hydrolysis of the glycosidic bond to yield sugars, kenaf pulp samples were subjected to two different pre-treatment processes. In the acid pre-treatment, the pulp samples were treated with 37.5% hydrochloric acid in the presence of FeCl3 at 50 °C or 90 °C whereas in the alkaline method, the pulp samples were treated with 25% sodium hydroxide at room temperature and with 2% or 5% sodium hydroxide at 50 °C. Microwave-assisted NaOH-treatment of the cellulose was also investigated and demonstrated to be capable of producing high glucose yield without adverse environmental impact by circumventing the use of large amounts of concentrated acids i.e., 83–85% phosphoric acid employed in most digestion processes. The treated samples were digested with the cellulase enzyme from Trichoderma reesei. The amount of glucose produced was quantified using the QuantichromTM glucose bioassay for assessing the efficiency of glucose production for each of the treatment processes. The microwave-assisted alkaline pre-treatment processes conducted at 50 °C were found to be the most effective in the conversion of the crystalline cellulose to the amorphous form based on the significantly higher yields of sugar produced by enzymatic hydrolysis compared to the untreated sample.

  6. 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

  7. 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

  8. 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

  9. 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...

  10. 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.

  11. An Integrated Monitoring System of Pre-earthquake Processes in Peloponnese, Greece

    Science.gov (United States)

    Karastathis, V. K.; Tsinganos, K.; Kafatos, M.; Eleftheriou, G.; Ouzounov, D.; Mouzakiotis, E.; Papadopoulos, G. A.; Voulgaris, N.; Bocchini, G. M.; Liakopoulos, S.; Aspiotis, T.; Gika, F.; Tselentis, A.; Moshou, A.; Psiloglou, B.

    2017-12-01

    One of the controversial issues in the contemporary seismology is the ability of radon accumulation monitoring to provide reliable earthquake forecasting. Although there are many examples in the literature showing radon increase before earthquakes, skepticism arises from instability of the measurements, false alarms, difficulties in interpretation caused by the weather influence (eg. rainfall) and difficulties on the consideration an irrefutable theoretical background of the phenomenon.We have developed and extensively tested a multi parameter network aimed for studying of the pre-earthquake processes and operating as a part of integrated monitoring system in the high seismicity area of the Western Hellenic Arc (SW Peloponnese, Greece). The prototype consists of four components: A real-time monitoring system of Radon accumulation. It consists of three gamma radiation detectors [NaI(Tl) scintillators] A nine-station seismic array to monitor the microseismicity in the offshore area of the Hellenic arc. The processing of the data is based on F-K and beam-forming techniques. Real-time weather monitoring systems for air temperature, relative humidity, precipitation and pressure. Thermal radiation emission from AVHRR/NOAA-18 polar orbit satellite observation. The project revolved around the idea of jointly studying the emission of Radon that has been proven in many cases as a reliable indicator of the possible time of an event, with the accurate location of the foreshock activity detected by the seismic array that can be a more reliable indicator of the possible position of an event. In parallel a satellite thermal anomaly detection technique has been used for monitoring of larger magnitude events (possible indicator for strong events M ≥5.0.). The first year of operations revealed a number of pre-seismic radon variation anomalies before several local earthquakes (M>3.6). The Radon increases systematically before the larger events.Details about the overall performance

  12. The reasons for delay lumbar puncture

    Directory of Open Access Journals (Sweden)

    MH. Lotfi

    2017-04-01

    Full Text Available Early diagnosis of meningitis and encephalitis and prompt initiation of appropriate therapy is vital and any delay will lead to high mortality and serious and permanent morbidity. The main purpose of this study was to evaluate the management of 220 patients with suspected central nervous system (CNS infections (meningitis and encephalitis to determine the percentage of patients’ suspected CNS infection undergo lumbar puncture in acceptable time (in accordance with conventional algorithms. In this descriptive study, patients with suspected CNS infections admitted to Bu-Ali and Qods hospitals, in the period July 2013 to December 2015 were studied. Information of 220 patients was collected. Continuous variables were summarized as means ± standard deviation and categorical variables as frequencies and percentages. Lumbar puncture (LP in patients was delayed in 200 cases (91%. Most common causes of delay in performing LP were prolongation of the process of determining patient needs to puncture, satisfying patients, CT scan delay and the delay in allowing LP by neurologist. In this study, delaying LP rate was higher than other studies. It seems certain pattern in assistants’ visits for counseling. CT requests and neurologic consultation before LP performed for all adult patients.

  13. Comparing Binaural Pre-processing Strategies II

    Directory of Open Access Journals (Sweden)

    Regina M. Baumgärtel

    2015-12-01

    Full Text Available Several binaural audio signal enhancement algorithms were evaluated with respect to their potential to improve speech intelligibility in noise for users of bilateral cochlear implants (CIs. 50% speech reception thresholds (SRT50 were assessed using an adaptive procedure in three distinct, realistic noise scenarios. All scenarios were highly nonstationary, complex, and included a significant amount of reverberation. Other aspects, such as the perfectly frontal target position, were idealized laboratory settings, allowing the algorithms to perform better than in corresponding real-world conditions. Eight bilaterally implanted CI users, wearing devices from three manufacturers, participated in the study. In all noise conditions, a substantial improvement in SRT50 compared to the unprocessed signal was observed for most of the algorithms tested, with the largest improvements generally provided by binaural minimum variance distortionless response (MVDR beamforming algorithms. The largest overall improvement in speech intelligibility was achieved by an adaptive binaural MVDR in a spatially separated, single competing talker noise scenario. A no-pre-processing condition and adaptive differential microphones without a binaural link served as the two baseline conditions. SRT50 improvements provided by the binaural MVDR beamformers surpassed the performance of the adaptive differential microphones in most cases. Speech intelligibility improvements predicted by instrumental measures were shown to account for some but not all aspects of the perceptually obtained SRT50 improvements measured in bilaterally implanted CI users.

  14. 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...

  15. 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...

  16. Area-delay trade-offs of texture decompressors for a graphics processing unit

    Science.gov (United States)

    Novoa Súñer, Emilio; Ituero, Pablo; López-Vallejo, Marisa

    2011-05-01

    Graphics Processing Units have become a booster for the microelectronics industry. However, due to intellectual property issues, there is a serious lack of information on implementation details of the hardware architecture that is behind GPUs. For instance, the way texture is handled and decompressed in a GPU to reduce bandwidth usage has never been dealt with in depth from a hardware point of view. This work addresses a comparative study on the hardware implementation of different texture decompression algorithms for both conventional (PCs and video game consoles) and mobile platforms. Circuit synthesis is performed targeting both a reconfigurable hardware platform and a 90nm standard cell library. Area-delay trade-offs have been extensively analyzed, which allows us to compare the complexity of decompressors and thus determine suitability of algorithms for systems with limited hardware resources.

  17. 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...

  18. Humans Optimize Decision-Making by Delaying Decision Onset

    Science.gov (United States)

    Teichert, Tobias; Ferrera, Vincent P.; Grinband, Jack

    2014-01-01

    Why do humans make errors on seemingly trivial perceptual decisions? It has been shown that such errors occur in part because the decision process (evidence accumulation) is initiated before selective attention has isolated the relevant sensory information from salient distractors. Nevertheless, it is typically assumed that subjects increase accuracy by prolonging the decision process rather than delaying decision onset. To date it has not been tested whether humans can strategically delay decision onset to increase response accuracy. To address this question we measured the time course of selective attention in a motion interference task using a novel variant of the response signal paradigm. Based on these measurements we estimated time-dependent drift rate and showed that subjects should in principle be able trade speed for accuracy very effectively by delaying decision onset. Using the time-dependent estimate of drift rate we show that subjects indeed delay decision onset in addition to raising response threshold when asked to stress accuracy over speed in a free reaction version of the same motion-interference task. These findings show that decision onset is a critical aspect of the decision process that can be adjusted to effectively improve decision accuracy. PMID:24599295

  19. Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors.

    Science.gov (United States)

    Pervin, Hasina M; Dennis, Paul G; Lim, Hui J; Tyson, Gene W; Batstone, Damien J; Bond, Philip L

    2013-12-01

    Temperature-phased anaerobic digestion (TPAD) is an emerging technology that facilitates improved performance and pathogen destruction in anaerobic sewage sludge digestion by optimising conditions for 1) hydrolytic and acidogenic organisms in a first-stage/pre-treatment reactor and then 2) methogenic populations in a second stage reactor. Pre-treatment reactors are typically operated at 55-65 °C and as such select for thermophilic bacterial communities. However, details of key microbial populations in hydrolytic communities and links to functionality are very limited. In this study, experimental thermophilic pre-treatment (TP) and control mesophilic pre-treatment (MP) reactors were operated as first-stages of TPAD systems treating activated sludge for 340 days. The TP system was operated sequentially at 50, 60 and 65 °C, while the MP rector was held at 35 °C for the entire period. The composition of microbial communities associated with the MP and TP pre-treatment reactors was characterised weekly using terminal-restriction fragment length polymorphism (T-RFLP) supported by clone library sequencing of 16S rRNA gene amplicons. The outcomes of this approach were confirmed using 454 pyrosequencing of gene amplicons and fluorescence in-situ hybridisation (FISH). TP associated bacterial communities were dominated by populations affiliated to the Firmicutes, Thermotogae, Proteobacteria and Chloroflexi. In particular there was a progression from Thermotogae to Lutispora and Coprothermobacter and diversity decreased as temperature and hydrolysis performance increased. While change in the composition of TP associated bacterial communities was attributable to temperature, that of MP associated bacterial communities was related to the composition of the incoming feed. This study determined processes driving the dynamics of key microbial populations that are correlated with an enhanced hydrolytic functionality of the TPAD system. Copyright © 2013 Elsevier Ltd. All rights

  20. Data assimilation of GNSS zenith total delays from a Nordic processing centre

    Science.gov (United States)

    Lindskog, Magnus; Ridal, Martin; Thorsteinsson, Sigurdur; Ning, Tong

    2017-11-01

    Atmospheric moisture-related information estimated from Global Navigation Satellite System (GNSS) ground-based receiver stations by the Nordic GNSS Analysis Centre (NGAA) have been used within a state-of-the-art kilometre-scale numerical weather prediction system. Different processing techniques have been implemented to derive the moisture-related GNSS information in the form of zenith total delays (ZTDs) and these are described and compared. In addition full-scale data assimilation and modelling experiments have been carried out to investigate the impact of utilizing moisture-related GNSS data from the NGAA processing centre on a numerical weather prediction (NWP) model initial state and on the ensuing forecast quality. The sensitivity of results to aspects of the data processing, station density, bias-correction and data assimilation have been investigated. Results show benefits to forecast quality when using GNSS ZTD as an additional observation type. The results also show a sensitivity to thinning distance applied for GNSS ZTD observations but not to modifications to the number of predictors used in the variational bias correction applied. In addition, it is demonstrated that the assimilation of GNSS ZTD can benefit from more general data assimilation enhancements and that there is an interaction of GNSS ZTD with other types of observations used in the data assimilation. Future plans include further investigation of optimal thinning distances and application of more advanced data assimilation techniques.

  1. Nuclear data for fusion: Validation of typical pre-processing methods for radiation transport calculations

    International Nuclear Information System (INIS)

    Hutton, T.; Sublet, J.C.; Morgan, L.; Leadbeater, T.W.

    2015-01-01

    Highlights: • We quantify the effect of processing nuclear data from ENDF to ACE format. • We consider the differences between fission and fusion angular distributions. • C-nat(n,el) at 2.0 MeV has a 0.6% deviation between original and processed data. • Fe-56(n,el) at 14.1 MeV has a 11.0% deviation between original and processed data. • Processed data do not accurately depict ENDF distributions for fusion energies. - Abstract: Nuclear data form the basis of the radiation transport codes used to design and simulate the behaviour of nuclear facilities, such as the ITER and DEMO fusion reactors. Typically these data and codes are biased towards fission and high-energy physics applications yet are still applied to fusion problems. With increasing interest in fusion applications, the lack of fusion specific codes and relevant data libraries is becoming increasingly apparent. Industry standard radiation transport codes require pre-processing of the evaluated data libraries prior to use in simulation. Historically these methods focus on speed of simulation at the cost of accurate data representation. For legacy applications this has not been a major concern, but current fusion needs differ significantly. Pre-processing reconstructs the differential and double differential interaction cross sections with a coarse binned structure, or more recently as a tabulated cumulative distribution function. This work looks at the validity of applying these processing methods to data used in fusion specific calculations in comparison to fission. The relative effects of applying this pre-processing mechanism, to both fission and fusion relevant reaction channels are demonstrated, and as such the poor representation of these distributions for the fusion energy regime. For the nat C(n,el) reaction at 2.0 MeV, the binned differential cross section deviates from the original data by 0.6% on average. For the 56 Fe(n,el) reaction at 14.1 MeV, the deviation increases to 11.0%. We

  2. Bayesian Optimization for Neuroimaging Pre-processing in Brain Age Classification and Prediction

    Directory of Open Access Journals (Sweden)

    Jenessa Lancaster

    2018-02-01

    Full Text Available Neuroimaging-based age prediction using machine learning is proposed as a biomarker of brain aging, relating to cognitive performance, health outcomes and progression of neurodegenerative disease. However, even leading age-prediction algorithms contain measurement error, motivating efforts to improve experimental pipelines. T1-weighted MRI is commonly used for age prediction, and the pre-processing of these scans involves normalization to a common template and resampling to a common voxel size, followed by spatial smoothing. Resampling parameters are often selected arbitrarily. Here, we sought to improve brain-age prediction accuracy by optimizing resampling parameters using Bayesian optimization. Using data on N = 2003 healthy individuals (aged 16–90 years we trained support vector machines to (i distinguish between young (<22 years and old (>50 years brains (classification and (ii predict chronological age (regression. We also evaluated generalisability of the age-regression model to an independent dataset (CamCAN, N = 648, aged 18–88 years. Bayesian optimization was used to identify optimal voxel size and smoothing kernel size for each task. This procedure adaptively samples the parameter space to evaluate accuracy across a range of possible parameters, using independent sub-samples to iteratively assess different parameter combinations to arrive at optimal values. When distinguishing between young and old brains a classification accuracy of 88.1% was achieved, (optimal voxel size = 11.5 mm3, smoothing kernel = 2.3 mm. For predicting chronological age, a mean absolute error (MAE of 5.08 years was achieved, (optimal voxel size = 3.73 mm3, smoothing kernel = 3.68 mm. This was compared to performance using default values of 1.5 mm3 and 4mm respectively, resulting in MAE = 5.48 years, though this 7.3% improvement was not statistically significant. When assessing generalisability, best performance was achieved when applying the entire Bayesian

  3. Scene matching based on non-linear pre-processing on reference image and sensed image

    Institute of Scientific and Technical Information of China (English)

    Zhong Sheng; Zhang Tianxu; Sang Nong

    2005-01-01

    To solve the heterogeneous image scene matching problem, a non-linear pre-processing method for the original images before intensity-based correlation is proposed. The result shows that the proper matching probability is raised greatly. Especially for the low S/N image pairs, the effect is more remarkable.

  4. Digital soil mapping: strategy for data pre-processing

    Directory of Open Access Journals (Sweden)

    Alexandre ten Caten

    2012-08-01

    Full Text Available The region of greatest variability on soil maps is along the edge of their polygons, causing disagreement among pedologists about the appropriate description of soil classes at these locations. The objective of this work was to propose a strategy for data pre-processing applied to digital soil mapping (DSM. Soil polygons on a training map were shrunk by 100 and 160 m. This strategy prevented the use of covariates located near the edge of the soil classes for the Decision Tree (DT models. Three DT models derived from eight predictive covariates, related to relief and organism factors sampled on the original polygons of a soil map and on polygons shrunk by 100 and 160 m were used to predict soil classes. The DT model derived from observations 160 m away from the edge of the polygons on the original map is less complex and has a better predictive performance.

  5. 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.

  6. Changes in Pre-service Science Teachers' Understandings After Being Involved in Explicit Nature of Science and Socioscientific Argumentation Processes

    Science.gov (United States)

    Kutluca, A. Y.; Aydın, A.

    2017-08-01

    The study explored the changes in pre-service science teachers' understanding of the nature of science and their opinions about the nature of science, science teaching and argumentation after their participation in explicit nature of science (NOS) and socioscientific argumentation processes. The participants were 56 third-grade pre-service science teachers studying in a state university in Turkey. The treatment group comprised 27 participants, and there were 29 participants in the comparison group. The comparison group participants were involved in a student-centred science-teaching process, and the participants of the treatment group were involved in explicit NOS and socioscientific argumentation processes. In the study, which lasted a total of 11 weeks, a NOS-as-argumentation questionnaire was administered to all the participants to determine their understanding of NOS at the beginning and end of the data collection process, and six random participants of the treatment group participated in semi-structured interview questions in order to further understand their views regarding NOS, science teaching and argumentation. Qualitative and quantitative data analysis revealed that the explicit NOS and socioscientific argumentation processes had a significant effect on pre-service science teachers' NOS understandings. Furthermore, NOS, argumentation and science teaching views of the participants in the treatment group showed a positive change. The results of this study are discussed in light of the related literature, and suggestions are made within the context of contribution to science-teaching literature, improvement of education quality and education of pre-service teachers.

  7. Statistical Downscaling Output GCM Modeling with Continuum Regression and Pre-Processing PCA Approach

    Directory of Open Access Journals (Sweden)

    Sutikno Sutikno

    2010-08-01

    Full Text Available One of the climate models used to predict the climatic conditions is Global Circulation Models (GCM. GCM is a computer-based model that consists of different equations. It uses numerical and deterministic equation which follows the physics rules. GCM is a main tool to predict climate and weather, also it uses as primary information source to review the climate change effect. Statistical Downscaling (SD technique is used to bridge the large-scale GCM with a small scale (the study area. GCM data is spatial and temporal data most likely to occur where the spatial correlation between different data on the grid in a single domain. Multicollinearity problems require the need for pre-processing of variable data X. Continuum Regression (CR and pre-processing with Principal Component Analysis (PCA methods is an alternative to SD modelling. CR is one method which was developed by Stone and Brooks (1990. This method is a generalization from Ordinary Least Square (OLS, Principal Component Regression (PCR and Partial Least Square method (PLS methods, used to overcome multicollinearity problems. Data processing for the station in Ambon, Pontianak, Losarang, Indramayu and Yuntinyuat show that the RMSEP values and R2 predict in the domain 8x8 and 12x12 by uses CR method produces results better than by PCR and PLS.

  8. 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.

  9. Mutations in 23S rRNA gene associated with decreased susceptibility to tiamulin and valnemulin in Mycoplasma gallisepticum.

    Science.gov (United States)

    Li, Bei-Bei; Shen, Jian-Zhong; Cao, Xing-Yuan; Wang, Yang; Dai, Lei; Huang, Si-Yang; Wu, Cong-Ming

    2010-07-01

    Mycoplasma gallisepticum is a major etiological agent of chronic respiratory disease (CRD) in chickens and sinusitis in turkeys. The pleuromutilin antibiotics tiamulin and valnemulin are currently used in the treatment of M. gallisepticum infection. We studied the in vitro development of pleuromutilin resistance in M. gallisepticum and investigated the molecular mechanisms involved in this process. Pleuromutilin-resistant mutants were selected by serial passages of M. gallisepticum strains PG31 and S6 in broth medium containing subinhibitory concentrations of tiamulin or valnemulin. A portion of the gene encoding 23S rRNA gene (domain V) and the gene encoding ribosome protein L3 were amplified and sequenced. No mutation could be detected in ribosome protein L3. Mutations were found at nucleotide positions 2058, 2059, 2061, 2447 and 2503 of 23S rRNA gene (Escherichia coli numbering). Although a single mutation could cause elevation of tiamulin and valnemulin MICs, combinations of two or three mutations were necessary to produce high-level resistance. All the mutants were cross-resistant to lincomycin, chloramphenicol and florfenicol. Mutants with the A2058G or the A2059G mutation exhibited cross-resistance to macrolide antibiotics erythromycin, tilmicosin and tylosin.

  10. Crystal Structure of the HEAT Domain from the Pre-mRNA Processing Factor Symplekin

    Energy Technology Data Exchange (ETDEWEB)

    Kennedy, Sarah A.; Frazier, Monica L.; Steiniger, Mindy; Mast, Ann M.; Marzluff, William F.; Redinbo, Matthew R.; (UNC)

    2010-09-30

    The majority of eukaryotic pre-mRNAs are processed by 3'-end cleavage and polyadenylation, although in metazoa the replication-dependent histone mRNAs are processed by 3'-end cleavage but not polyadenylation. The macromolecular complex responsible for processing both canonical and histone pre-mRNAs contains the {approx} 1160-residue protein Symplekin. Secondary-structural prediction algorithms identified putative HEAT domains in the 300 N-terminal residues of all Symplekins of known sequence. The structure and dynamics of this domain were investigated to begin elucidating the role Symplekin plays in mRNA maturation. The crystal structure of the Drosophila melanogaster Symplekin HEAT domain was determined to 2.4 {angstrom} resolution with single-wavelength anomalous dispersion phasing methods. The structure exhibits five canonical HEAT repeats along with an extended 31-amino-acid loop (loop 8) between the fourth and fifth repeat that is conserved within closely related Symplekin sequences. Molecular dynamics simulations of this domain show that the presence of loop 8 dampens correlated and anticorrelated motion in the HEAT domain, therefore providing a neutral surface for potential protein-protein interactions. HEAT domains are often employed for such macromolecular contacts. The Symplekin HEAT region not only structurally aligns with several established scaffolding proteins, but also has been reported to contact proteins essential for regulating 3'-end processing. Together, these data support the conclusion that the Symplekin HEAT domain serves as a scaffold for protein-protein interactions essential to the mRNA maturation process.

  11. Noise-sustained fluctuations in stochastic dynamics with a delay.

    Science.gov (United States)

    D'Odorico, Paolo; Laio, Francesco; Ridolfi, Luca

    2012-04-01

    Delayed responses to external drivers are ubiquitous in environmental, social, and biological processes. Delays may induce oscillations, Hopf bifurcations, and instabilities in deterministic systems even in the absence of nonlinearities. Despite recent advances in the study of delayed stochastic differential equations, the interaction of random drivers with delays remains poorly understood. In particular, it is unclear whether noise-induced behaviors may emerge from these interactions. Here we show that noise may enhance and sustain transient periodic oscillations inherent to deterministic delayed systems. We investigate the conditions conducive to the emergence and disappearance of these dynamics in a linear system in the presence of both additive and multiplicative noise.

  12. Automated Purification and Suspension Array Detection of 16S rRNA from Soil and Sediment Extracts by Using Tunable Surface Microparticles

    OpenAIRE

    Chandler, Darrell P.; Jarrell, Ann E.

    2004-01-01

    Autonomous, field-deployable molecular detection systems require seamless integration of complex biochemical solutions and physical or mechanical processing steps. In an attempt to simplify the fluidic requirements for integrated biodetection systems, we used tunable surface microparticles both as an rRNA affinity purification resin in a renewable microcolumn sample preparation system and as the sensor surface in a flow cytometer detector. The tunable surface detection limits in both low- and...

  13. Reliability of fully automated versus visually controlled pre- and post-processing of resting-state EEG.

    Science.gov (United States)

    Hatz, F; Hardmeier, M; Bousleiman, H; Rüegg, S; Schindler, C; Fuhr, P

    2015-02-01

    To compare the reliability of a newly developed Matlab® toolbox for the fully automated, pre- and post-processing of resting state EEG (automated analysis, AA) with the reliability of analysis involving visually controlled pre- and post-processing (VA). 34 healthy volunteers (age: median 38.2 (20-49), 82% female) had three consecutive 256-channel resting-state EEG at one year intervals. Results of frequency analysis of AA and VA were compared with Pearson correlation coefficients, and reliability over time was assessed with intraclass correlation coefficients (ICC). Mean correlation coefficient between AA and VA was 0.94±0.07, mean ICC for AA 0.83±0.05 and for VA 0.84±0.07. AA and VA yield very similar results for spectral EEG analysis and are equally reliable. AA is less time-consuming, completely standardized, and independent of raters and their training. Automated processing of EEG facilitates workflow in quantitative EEG analysis. Copyright © 2014 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  14. Musical and linguistic expertise influence pre-attentive and attentive processing of non-speech sounds.

    Science.gov (United States)

    Marie, Céline; Kujala, Teija; Besson, Mireille

    2012-04-01

    The aim of this experiment was two-fold. Our first goal was to determine whether linguistic expertise influences the pre-attentive [as reflected by the Mismatch Negativity - (MMN)] and the attentive processing (as reflected by behavioural discrimination accuracy) of non-speech, harmonic sounds. The second was to directly compare the effects of linguistic and musical expertise. To this end, we compared non-musician native speakers of a quantity language, Finnish, in which duration is a phonemically contrastive cue, with French musicians and French non-musicians. Results revealed that pre-attentive and attentive processing of duration deviants was enhanced in Finn non-musicians and French musicians compared to French non-musicians. By contrast, MMN in French musicians was larger than in both Finns and French non-musicians for frequency deviants, whereas no between-group differences were found for intensity deviants. By showing similar effects of linguistic and musical expertise, these results argue in favor of common processing of duration in music and speech. Copyright © 2010 Elsevier Srl. All rights reserved.

  15. 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

  16. 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.

  17. Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing

    Directory of Open Access Journals (Sweden)

    Miri eMichaeli

    2012-12-01

    Full Text Available High throughput sequencing (HTS yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig genes, which are variable and often highly mutated. This paper describes Ig-HTS-Cleaner (Ig High Throughput Sequencing Cleaner, a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig-Indel-Identifier (Ig Insertion – Deletion Identifier, a program for identifying legitimate and artifact insertions and/or deletions (indels. Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.

  18. Hyperspectral imaging in medicine: image pre-processing problems and solutions in Matlab.

    Science.gov (United States)

    Koprowski, Robert

    2015-11-01

    The paper presents problems and solutions related to hyperspectral image pre-processing. New methods of preliminary image analysis are proposed. The paper shows problems occurring in Matlab when trying to analyse this type of images. Moreover, new methods are discussed which provide the source code in Matlab that can be used in practice without any licensing restrictions. The proposed application and sample result of hyperspectral image analysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. 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.

  20. 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 ...

  1. Simultaneous data pre-processing and SVM classification model selection based on a parallel genetic algorithm applied to spectroscopic data of olive oils.

    Science.gov (United States)

    Devos, Olivier; Downey, Gerard; Duponchel, Ludovic

    2014-04-01

    Classification is an important task in chemometrics. For several years now, support vector machines (SVMs) have proven to be powerful for infrared spectral data classification. However such methods require optimisation of parameters in order to control the risk of overfitting and the complexity of the boundary. Furthermore, it is established that the prediction ability of classification models can be improved using pre-processing in order to remove unwanted variance in the spectra. In this paper we propose a new methodology based on genetic algorithm (GA) for the simultaneous optimisation of SVM parameters and pre-processing (GENOPT-SVM). The method has been tested for the discrimination of the geographical origin of Italian olive oil (Ligurian and non-Ligurian) on the basis of near infrared (NIR) or mid infrared (FTIR) spectra. Different classification models (PLS-DA, SVM with mean centre data, GENOPT-SVM) have been tested and statistically compared using McNemar's statistical test. For the two datasets, SVM with optimised pre-processing give models with higher accuracy than the one obtained with PLS-DA on pre-processed data. In the case of the NIR dataset, most of this accuracy improvement (86.3% compared with 82.8% for PLS-DA) occurred using only a single pre-processing step. For the FTIR dataset, three optimised pre-processing steps are required to obtain SVM model with significant accuracy improvement (82.2%) compared to the one obtained with PLS-DA (78.6%). Furthermore, this study demonstrates that even SVM models have to be developed on the basis of well-corrected spectral data in order to obtain higher classification rates. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. 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

  3. 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.

  4. RNA Processing Factor 5 is required for efficient 5' cleavage at a processing site conserved in RNAs of three different mitochondrial genes in Arabidopsis thaliana.

    Science.gov (United States)

    Hauler, Aron; Jonietz, Christian; Stoll, Birgit; Stoll, Katrin; Braun, Hans-Peter; Binder, Stefan

    2013-05-01

    The 5' ends of many mitochondrial transcripts are generated post-transcriptionally. Recently, we identified three RNA PROCESSING FACTORs required for 5' end maturation of different mitochondrial mRNAs in Arabidopsis thaliana. All of these factors are pentatricopeptide repeat proteins (PPRPs), highly similar to RESTORERs OF FERTILTY (RF), that rescue male fertility in cytoplasmic male-sterile lines from different species. Therefore, we suggested a general role of these RF-like PPRPs in mitochondrial 5' processing. We now identified RNA PROCESSING FACTOR 5, a PPRP not classified as an RF-like protein, required for the efficient 5' maturation of the nad6 and atp9 mRNAs as well as 26S rRNA. The precursor molecules of these RNAs share conserved sequence elements, approximately ranging from positions -50 to +9 relative to mature 5' mRNA termini, suggesting these sequences to be at least part of the cis elements required for processing. The knockout of RPF5 has only a moderate influence on 5' processing of atp9 mRNA, whereas the generation of the mature nad6 mRNA and 26S rRNA is almost completely abolished in the mutant. The latter leads to a 50% decrease of total 26S rRNA species, resulting in an imbalance between the large rRNA and 18S rRNA. Despite these severe changes in RNA levels and in the proportion between the 26S and 18S rRNAs, mitochondrial protein levels appear to be unaltered in the mutant, whereas seed germination capacity is markedly reduced. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  5. 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...

  6. Process performance assessment of advanced anaerobic digestion of sewage sludge including sequential ultrasound-thermal (55 °C) pre-treatment.

    Science.gov (United States)

    Neumann, Patricio; Barriga, Felipe; Álvarez, Claudia; González, Zenón; Vidal, Gladys

    2018-03-15

    The aim of this study was to evaluate the performance and digestate quality of advanced anaerobic digestion of sewage sludge including sequential ultrasound-thermal (55 °C) pre-treatment. Both stages of pre-treatment contributed to chemical oxygen demand (COD) solubilization, with an overall factor of 11.4 ± 2.2%. Pre-treatment led to 19.1, 24.0 and 29.9% increased methane yields at 30, 15 and 7.5 days solid retention times (SRT), respectively, without affecting process stability or accumulation of intermediates. Pre-treatment decreased up to 4.2% water recovery from the digestate, but SRT was a more relevant factor controlling dewatering. Advanced digestion showed 2.4-3.1 and 1.5 logarithmic removals of coliforms and coliphages, respectively, and up to a 58% increase in the concentration of inorganics in the digestate solids compared to conventional digestion. The COD balance of the process showed that the observed increase in methane production was proportional to the pre-treatment solubilization efficiency. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. 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

  8. Time delay for resonant vibrational excitation in electron--molecule collisions

    International Nuclear Information System (INIS)

    Gauyacq, J.P.

    1990-01-01

    An analysis of the time delay associated with vibrational excitation in electron--molecule collision is presented. It consists of a direct study of the time dependence of the process for three model systems. An electron wave packet, that is narrow in time, is sent on the target and the amplitudes in the different inelastic channels are studied as functions of time. The time delay is found to correspond to very different time effects: broadenings, shifts in time of the wave packet, but also complex distortions that cannot be represented by a time delay. The direct analysis of the scattered wave also provides new insights into the vibrational excitation process. It should be a useful tool to analyze complex collision processes

  9. Statistics and dimension of chaos in differential delay systems

    Energy Technology Data Exchange (ETDEWEB)

    Dorizzi, B.; Grammaticos, B.; Le Berre, M.; Pomeau, Y.; Ressayre, E.; Tallet, A.

    1987-01-01

    The chaotic solution of dissipative scalar-delay-differential equations with a nonlinear feedback periodic with respect to its argument is shown to behave as a Gaussian-Markovian process in a large time scale. The short time scale is shown to be defined by the correlation time of the delayed feedback. The dimension of the chaotic attractor is shown to be approximately equal to the number of short times that are contained inside the delay.

  10. Statistics and dimension of chaos in differential delay systems

    International Nuclear Information System (INIS)

    Dorizzi, B.; Grammaticos, B.; Le Berre, M.; Pomeau, Y.; Ressayre, E.; Tallet, A.

    1987-01-01

    The chaotic solution of dissipative scalar-delay-differential equations with a nonlinear feedback periodic with respect to its argument is shown to behave as a Gaussian-Markovian process in a large time scale. The short time scale is shown to be defined by the correlation time of the delayed feedback. The dimension of the chaotic attractor is shown to be approximately equal to the number of short times that are contained inside the delay

  11. 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.

  12. 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.

  13. Visual prediction: psychophysics and neurophysiology of compensation for time delays.

    Science.gov (United States)

    Nijhawan, Romi

    2008-04-01

    A necessary consequence of the nature of neural transmission systems is that as change in the physical state of a time-varying event takes place, delays produce error between the instantaneous registered state and the external state. Another source of delay is the transmission of internal motor commands to muscles and the inertia of the musculoskeletal system. How does the central nervous system compensate for these pervasive delays? Although it has been argued that delay compensation occurs late in the motor planning stages, even the earliest visual processes, such as phototransduction, contribute significantly to delays. I argue that compensation is not an exclusive property of the motor system, but rather, is a pervasive feature of the central nervous system (CNS) organization. Although the motor planning system may contain a highly flexible compensation mechanism, accounting not just for delays but also variability in delays (e.g., those resulting from variations in luminance contrast, internal body temperature, muscle fatigue, etc.), visual mechanisms also contribute to compensation. Previous suggestions of this notion of "visual prediction" led to a lively debate producing re-examination of previous arguments, new analyses, and review of the experiments presented here. Understanding visual prediction will inform our theories of sensory processes and visual perception, and will impact our notion of visual awareness.

  14. 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.

  15. On image pre-processing for PIV of sinlge- and two-phase flows over reflecting objects

    NARCIS (Netherlands)

    Deen, N.G.; Willems, P.; van Sint Annaland, M.; Kuipers, J.A.M.; Lammertink, Rob G.H.; Kemperman, Antonius J.B.; Wessling, Matthias; van der Meer, Walterus Gijsbertus Joseph

    2010-01-01

    A novel image pre-processing scheme for PIV of single- and two-phase flows over reflecting objects which does not require the use of additional hardware is discussed. The approach for single-phase flow consists of image normalization and intensity stretching followed by background subtraction. For

  16. 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

  17. The Absence of the Transcription Factor Yrr1p, Identified from Comparative Genome Profiling, Increased Vanillin Tolerance Due to Enhancements of ABC Transporters Expressing, rRNA Processing and Ribosome Biogenesis in Saccharomyces cerevisiae.

    Science.gov (United States)

    Wang, Xinning; Liang, Zhenzhen; Hou, Jin; Shen, Yu; Bao, Xiaoming

    2017-01-01

    Enhancing the tolerance of Saccharomyces cerevisiae to inhibitors derived from lignocellulose is conducive to producing biofuel and chemicals using abundant lignocellulosic materials. Vanillin is a major type of phenolic inhibitor in lignocellulose hydrolysates for S. cerevisiae . In the present work, the factors beneficial to vanillin resistance in yeast were identified from the vanillin-resistant strain EMV-8, which was derived from strain NAN-27 by adaptive evolution. We found 450 SNPs and 44 genes with InDels in the vanillin-tolerant strain EMV-8 by comparing the genome sequences of EMV-8 and NAN-27. To investigate the effects of InDels, InDels were deleted in BY4741, respectively. We demonstrated that the deletion of YRR1 improved vanillin tolerance of strain. In the presence of 6 mM vanillin, deleting YRR1 increase the maximum specific growth rate and the vanillin consumption rate by 142 and 51%, respectively. The subsequent transcriptome analysis revealed that deleting YRR1 resulted in changed expression of over 200 genes in the presence of 5 mM vanillin. The most marked changes were the significant up-regulation of the dehydrogenase ADH7 , several ATP-binding cassette (ABC) transporters, and dozens of genes involved in ribosome biogenesis and rRNA processing. Coincidently, the crude enzyme solution of BY4741( yrr1 Δ) exhibited higher NADPH-dependent vanillin reduction activity than control. In addition, overexpressing the ABC transporter genes PDR5, YOR1 , and SNQ2 , as well as the RNA helicase gene DBP2 , increased the vanillin tolerance of strain. Interestingly, unlike the marked changes we mentioned above, under vanillin-free conditions, there are only limited transcriptional differences between wildtype and yrr1 Δ. This indicated that vanillin might act as an effector in Yrr1p-related regulatory processes. The new findings of the relationship between YRR1 and vanillin tolerance, as well as the contribution of rRNA processing and ribosome biogenesis to

  18. Structural Studies of RNA Helicases Involved in Eukaryotic Pre-mRNA Splicing, Ribosome Biogenesis, and Translation Initiation

    DEFF Research Database (Denmark)

    He, Yangzi

    and ligates the neighbouring exons to generate mature mRNAs. Prp43 is an RNA helicase of the DEAH/RHA family. In yeast, once mRNAs are released, Prp43 catalyzes the disassembly of spliceosomes. The 18S, 5.8S and 25S rRNAs are transcribed as a single polycistronic transcript—the 35S pre......-rRNA. It is nucleolytically cleaved and chemically modified to generate mature rRNAs, which assemble with ribosomal proteins to form the ribosome. Prp43 is required for the processing of the 18S rRNA. Using X-ray crystallography, I determined a high resolution structure of Prp43 bound to ADP, the first structure of a DEAH....../RHA helicase. It defined the conserved structural features of all DEAH/RHA helicases, and unveiled a novel nucleotide binding site. Additionally a preliminary low resolution structure of a ternary complex comprising Prp43, a non-hydrolyzable ATP analogue, and a single-stranded RNA, was obtained. The ribosome...

  19. Beat processing is pre-attentive for metrically simple rhythms with clear accents: an ERP study.

    Directory of Open Access Journals (Sweden)

    Fleur L Bouwer

    Full Text Available The perception of a regular beat is fundamental to music processing. Here we examine whether the detection of a regular beat is pre-attentive for metrically simple, acoustically varying stimuli using the mismatch negativity (MMN, an ERP response elicited by violations of acoustic regularity irrespective of whether subjects are attending to the stimuli. Both musicians and non-musicians were presented with a varying rhythm with a clear accent structure in which occasionally a sound was omitted. We compared the MMN response to the omission of identical sounds in different metrical positions. Most importantly, we found that omissions in strong metrical positions, on the beat, elicited higher amplitude MMN responses than omissions in weak metrical positions, not on the beat. This suggests that the detection of a beat is pre-attentive when highly beat inducing stimuli are used. No effects of musical expertise were found. Our results suggest that for metrically simple rhythms with clear accents beat processing does not require attention or musical expertise. In addition, we discuss how the use of acoustically varying stimuli may influence ERP results when studying beat processing.

  20. Delay chemical master equation: direct and closed-form solutions.

    Science.gov (United States)

    Leier, Andre; Marquez-Lago, Tatiana T

    2015-07-08

    The stochastic simulation algorithm (SSA) describes the time evolution of a discrete nonlinear Markov process. This stochastic process has a probability density function that is the solution of a differential equation, commonly known as the chemical master equation (CME) or forward-Kolmogorov equation. In the same way that the CME gives rise to the SSA, and trajectories of the latter are exact with respect to the former, trajectories obtained from a delay SSA are exact representations of the underlying delay CME (DCME). However, in contrast to the CME, no closed-form solutions have so far been derived for any kind of DCME. In this paper, we describe for the first time direct and closed solutions of the DCME for simple reaction schemes, such as a single-delayed unimolecular reaction as well as chemical reactions for transcription and translation with delayed mRNA maturation. We also discuss the conditions that have to be met such that such solutions can be derived.

  1. Photoemission and photoionization time delays and rates

    Science.gov (United States)

    Gallmann, L.; Jordan, I.; Wörner, H. J.; Castiglioni, L.; Hengsberger, M.; Osterwalder, J.; Arrell, C. A.; Chergui, M.; Liberatore, E.; Rothlisberger, U.; Keller, U.

    2017-01-01

    Ionization and, in particular, ionization through the interaction with light play an important role in fundamental processes in physics, chemistry, and biology. In recent years, we have seen tremendous advances in our ability to measure the dynamics of photo-induced ionization in various systems in the gas, liquid, or solid phase. In this review, we will define the parameters used for quantifying these dynamics. We give a brief overview of some of the most important ionization processes and how to resolve the associated time delays and rates. With regard to time delays, we ask the question: how long does it take to remove an electron from an atom, molecule, or solid? With regard to rates, we ask the question: how many electrons are emitted in a given unit of time? We present state-of-the-art results on ionization and photoemission time delays and rates. Our review starts with the simplest physical systems: the attosecond dynamics of single-photon and tunnel ionization of atoms in the gas phase. We then extend the discussion to molecular gases and ionization of liquid targets. Finally, we present the measurements of ionization delays in femto- and attosecond photoemission from the solid–vacuum interface. PMID:29308414

  2. Photoemission and photoionization time delays and rates

    Directory of Open Access Journals (Sweden)

    L. Gallmann

    2017-11-01

    Full Text Available Ionization and, in particular, ionization through the interaction with light play an important role in fundamental processes in physics, chemistry, and biology. In recent years, we have seen tremendous advances in our ability to measure the dynamics of photo-induced ionization in various systems in the gas, liquid, or solid phase. In this review, we will define the parameters used for quantifying these dynamics. We give a brief overview of some of the most important ionization processes and how to resolve the associated time delays and rates. With regard to time delays, we ask the question: how long does it take to remove an electron from an atom, molecule, or solid? With regard to rates, we ask the question: how many electrons are emitted in a given unit of time? We present state-of-the-art results on ionization and photoemission time delays and rates. Our review starts with the simplest physical systems: the attosecond dynamics of single-photon and tunnel ionization of atoms in the gas phase. We then extend the discussion to molecular gases and ionization of liquid targets. Finally, we present the measurements of ionization delays in femto- and attosecond photoemission from the solid–vacuum interface.

  3. Pedagogical and didactical rationale of phonemic stimulation process in pre-school age children

    Directory of Open Access Journals (Sweden)

    López, Yudenia

    2010-01-01

    Full Text Available The paper describes the main results of a regional research problem dealing with education in pre-school age. It examines the effectiveness of the didactic conception of the process of phonemic stimulation in children from 3 to 5 years old. The pedagogical and didactic rationale of the process, viewed from the evolutionary, ontogeny, systemic perspective is explained. Likewise, possible scaffolding is illustrated. The suggested procedures focus the provision of support on a systematic and purposely practice which involve first the discrimination of non-verbal sounds and the discrimi-nation of verbal sound later, aiming to the creation of a phonological consciousness.

  4. 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

  5. A Fault Prognosis Strategy Based on Time-Delayed Digraph Model and Principal Component Analysis

    Directory of Open Access Journals (Sweden)

    Ningyun Lu

    2012-01-01

    Full Text Available Because of the interlinking of process equipments in process industry, event information may propagate through the plant and affect a lot of downstream process variables. Specifying the causality and estimating the time delays among process variables are critically important for data-driven fault prognosis. They are not only helpful to find the root cause when a plant-wide disturbance occurs, but to reveal the evolution of an abnormal event propagating through the plant. This paper concerns with the information flow directionality and time-delay estimation problems in process industry and presents an information synchronization technique to assist fault prognosis. Time-delayed mutual information (TDMI is used for both causality analysis and time-delay estimation. To represent causality structure of high-dimensional process variables, a time-delayed signed digraph (TD-SDG model is developed. Then, a general fault prognosis strategy is developed based on the TD-SDG model and principle component analysis (PCA. The proposed method is applied to an air separation unit and has achieved satisfying results in predicting the frequently occurred “nitrogen-block” fault.

  6. 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...

  7. Pre-processing of input files for the AZTRAN code

    International Nuclear Information System (INIS)

    Vargas E, S.; Ibarra, G.

    2017-09-01

    The AZTRAN code began to be developed in the Nuclear Engineering Department of the Escuela Superior de Fisica y Matematicas (ESFM) of the Instituto Politecnico Nacional (IPN) with the purpose of numerically solving various models arising from the physics and engineering of nuclear reactors. The code is still under development and is part of the AZTLAN platform: Development of a Mexican platform for the analysis and design of nuclear reactors. Due to the complexity to generate an input file for the code, a script based on D language is developed, with the purpose of making its elaboration easier, based on a new input file format which includes specific cards, which have been divided into two blocks, mandatory cards and optional cards, including a pre-processing of the input file to identify possible errors within it, as well as an image generator for the specific problem based on the python interpreter. (Author)

  8. 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.

  9. Road Sign Recognition with Fuzzy Adaptive Pre-Processing Models

    Science.gov (United States)

    Lin, Chien-Chuan; Wang, Ming-Shi

    2012-01-01

    A road sign recognition system based on adaptive image pre-processing models using two fuzzy inference schemes has been proposed. The first fuzzy inference scheme is to check the changes of the light illumination and rich red color of a frame image by the checking areas. The other is to check the variance of vehicle's speed and angle of steering wheel to select an adaptive size and position of the detection area. The Adaboost classifier was employed to detect the road sign candidates from an image and the support vector machine technique was employed to recognize the content of the road sign candidates. The prohibitory and warning road traffic signs are the processing targets in this research. The detection rate in the detection phase is 97.42%. In the recognition phase, the recognition rate is 93.04%. The total accuracy rate of the system is 92.47%. For video sequences, the best accuracy rate is 90.54%, and the average accuracy rate is 80.17%. The average computing time is 51.86 milliseconds per frame. The proposed system can not only overcome low illumination and rich red color around the road sign problems but also offer high detection rates and high computing performance. PMID:22778650

  10. A Fast Time-Delay Calculation Method in Through-Wall-Radar Detection Scenario

    Directory of Open Access Journals (Sweden)

    Zhang Qi

    2016-01-01

    Full Text Available In TWR (Through Wall Radar signal processing procedure, time delay estimation is one of the key steps in target localization and high resolution imaging. In time domain imaging procedure such as back projection imaging algorithm, round trip propagation time delay at the path of “transmitter-target-receiver” needs to be calculated for each pixel in imaging region. In typical TWR scenario, transmitter and receiver are at one side and targets at the other side of a wall. Based on two-dimensional searching algorithm or solving two variables equation of four times, traditional time delay calculation algorithms are complex and time consuming, and cannot be used to real-time imaging procedure. In this paper, a new fast time-delay (FTD algorithm is presented. Because of that incident angle at one side equals to refracting angle at the other side, an equation of lateral distance through the wall can be established. By solving this equation, the lateral distance can be obtained and total propagation time delay can be calculated subsequently. Through processing simulation data, the result shows that new algorithm can be applied effectively to real-time time-delay calculation in TWR signal processing.

  11. Statistical delay estimation in digital circuits using VHDL

    Directory of Open Access Journals (Sweden)

    Milić Miljana Lj.

    2014-01-01

    Full Text Available The most important feature of modern integrated circuit is the speed. It depends on circuit's delay. For the design of high-speed digital circuits, it is necessary to evaluate delays in the earliest stages of design, thus making it easy to modify and redesign a circuit if it's too slow. This paper gives an approach for efficient delay estimation in the describing phase of the circuit design. The method can statistically estimate the minimum and maximum delay of all possible paths and signal transitions in the circuit, considering the practical implementation of circuits, and information about the parameters' tolerances. The method uses a VHDL description and is verified on ISCAS85 benchmark circuits. Matlab was used for data processing.

  12. 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.

  13. 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.

  14. 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.

  15. Development of reduced crude processing technology in delayed coking units; Desenvolvimento da tecnologia de processamento de residuo atmosferico em unidade de coqueamento retardado

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Gloria Maria Gomes; Bartros, Francisco Carlos da Costa; Goncalves, Natalie Jorge; Pala, Danielle Marins; Nadolni, Aline Voigt [PETROBRAS, Rio de Janeiro, RJ (Brazil)

    2008-07-01

    Delayed Coking Technology can be described as thermal cracking of low value refinery residual streams into high-value products. This process has been applied in petroleum refining schemes in order to upgrade heavy and ultra-heavy crude oils. The typical feedstock is vacuum residue (VR). When we have an increasing medium distillates demand and refining schemes which have gas oil and VR excess, the simultaneous conversion of these streams becomes economically attractive, due mainly to the increase of diesel production. Thus, the processing of atmospheric residue (AR) in Delayed Coking Units (DCU) has fueled great interest for PETROBRAS. This work presents the results of industrial and pilot plant tests with AR and VR showing the increasing of diesel yields and decreasing of coke yields processing AR as feedstock. When we process all the AR in the DCU with high recycle rate we observe an increasing of 25% on refinery diesel production related to conventional schemes. The refining scheme of the new PETROBRAS refinery at Northeast of Brazil is based on this technology. This refinery will process heavy oils maximizing diesel production with minimum investment. (author)

  16. Close coupling of pre- and post-processing vision stations using inexact algorithms

    Science.gov (United States)

    Shih, Chi-Hsien V.; Sherkat, Nasser; Thomas, Peter D.

    1996-02-01

    Work has been reported using lasers to cut deformable materials. Although the use of laser reduces material deformation, distortion due to mechanical feed misalignment persists. Changes in the lace patten are also caused by the release of tension in the lace structure as it is cut. To tackle the problem of distortion due to material flexibility, the 2VMethod together with the Piecewise Error Compensation Algorithm incorporating the inexact algorithms, i.e., fuzzy logic, neural networks and neural fuzzy technique, are developed. A spring mounted pen is used to emulate the distortion of the lace pattern caused by tactile cutting and feed misalignment. Using pre- and post-processing vision systems, it is possible to monitor the scalloping process and generate on-line information for the artificial intelligence engines. This overcomes the problems of lace distortion due to the trimming process. Applying the algorithms developed, the system can produce excellent results, much better than a human operator.

  17. Synchronization of time-delayed systems with chaotic modulation and cryptography

    International Nuclear Information System (INIS)

    Banerjee, Santo

    2009-01-01

    This paper presents a method of synchronization between two time-delayed systems where the delay times are modulated by a common chaotic signal of the driving system. The technique is well applied to two identical autonomous continuous-time-delayed systems with numerical simulations. Finally, a new method of encryption is generated for digital messages. This method is illustrated with two different encryption processes for text as well as picture messages.

  18. Changes in Pre-Service Science Teachers' Understandings After Being Involved in Explicit Nature of Science and Socioscientific Argumentation Processes

    Science.gov (United States)

    Kutluca, A. Y.; Aydin, A.

    2017-01-01

    The study explored the changes in pre-service science teachers' understanding of the nature of science and their opinions about the nature of science, science teaching and argumentation after their participation in explicit nature of science (NOS) and socioscientific argumentation processes. The participants were 56 third-grade pre-service science…

  19. Pre-Proceedings of the 1st International Workshop on Process-oriented Information Systems in Healthcare (ProHealth'07)

    NARCIS (Netherlands)

    Reichert, M.U.; Peleg, M.; Lenz, R.

    These pre-proceedings contain the presentations given at the 1st Int'l Workshop on Process-oriented Information Systems in Healthcare (ProHealth'07). Formal proceedings will be published in Springer's LNCS series. Process-oriented information systems have been demanded for more than 20 years and

  20. 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

  1. Protein-protein interactions within late pre-40S ribosomes.

    Directory of Open Access Journals (Sweden)

    Melody G Campbell

    2011-01-01

    Full Text Available Ribosome assembly in eukaryotic organisms requires more than 200 assembly factors to facilitate and coordinate rRNA transcription, processing, and folding with the binding of the ribosomal proteins. Many of these assembly factors bind and dissociate at defined times giving rise to discrete assembly intermediates, some of which have been partially characterized with regards to their protein and RNA composition. Here, we have analyzed the protein-protein interactions between the seven assembly factors bound to late cytoplasmic pre-40S ribosomes using recombinant proteins in binding assays. Our data show that these factors form two modules: one comprising Enp1 and the export adaptor Ltv1 near the beak structure, and the second comprising the kinase Rio2, the nuclease Nob1, and a regulatory RNA binding protein Dim2/Pno1 on the front of the head. The GTPase-like Tsr1 and the universally conserved methylase Dim1 are also peripherally connected to this second module. Additionally, in an effort to further define the locations for these essential proteins, we have analyzed the interactions between these assembly factors and six ribosomal proteins: Rps0, Rps3, Rps5, Rps14, Rps15 and Rps29. Together, these results and previous RNA-protein crosslinking data allow us to propose a model for the binding sites of these seven assembly factors. Furthermore, our data show that the essential kinase Rio2 is located at the center of the pre-ribosomal particle and interacts, directly or indirectly, with every other assembly factor, as well as three ribosomal proteins required for cytoplasmic 40S maturation. These data suggest that Rio2 could play a central role in regulating cytoplasmic maturation steps.

  2. The effects of the framing of time on delay discounting.

    Science.gov (United States)

    DeHart, William Brady; Odum, Amy L

    2015-01-01

    We examined the effects of the framing of time on delay discounting. Delay discounting is the process by which delayed outcomes are devalued as a function of time. Time in a titrating delay discounting task is often framed in calendar units (e.g., as 1 week, 1 month, etc.). When time is framed as a specific date, delayed outcomes are discounted less compared to the calendar format. Other forms of framing time; however, have not been explored. All participants completed a titrating calendar unit delay-discounting task for money. Participants were also assigned to one of two delay discounting tasks: time as dates (e.g., June 1st, 2015) or time in units of days (e.g., 5000 days), using the same delay distribution as the calendar delay-discounting task. Time framed as dates resulted in less discounting compared to the calendar method, whereas time framed as days resulted in greater discounting compared to the calendar method. The hyperboloid model fit best compared to the hyperbola and exponential models. How time is framed may alter how participants attend to the delays as well as how the delayed outcome is valued. Altering how time is framed may serve to improve adherence to goals with delayed outcomes. © Society for the Experimental Analysis of Behavior.

  3. Pre-Service Mathematics Teachers’ Problem Solving Processes with Geometer’s Sketchpad: Mirror Problem

    OpenAIRE

    ÖÇAL, Mehmet Fatih; ŞİMŞEK, Mertkan

    2016-01-01

    Problem solving skill is the core of mathematics education and its importance cannot be denied. This study specifically examined 56 freshmen pre-service mathematics teachers’ problem solving processes on a specific problem with the help of Geometer’s Sketchpad (GSP). They were grouped into two-person teams to solve a problem called "the mirror problem". They were expected to solve it by means of GSP. According to their works on GSP and related reflections, there appeared two differe...

  4. 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.

  5. An Advanced Pre-Processing Pipeline to Improve Automated Photogrammetric Reconstructions of Architectural Scenes

    Directory of Open Access Journals (Sweden)

    Marco Gaiani

    2016-02-01

    Full Text Available Automated image-based 3D reconstruction methods are more and more flooding our 3D modeling applications. Fully automated solutions give the impression that from a sample of randomly acquired images we can derive quite impressive visual 3D models. Although the level of automation is reaching very high standards, image quality is a fundamental pre-requisite to produce successful and photo-realistic 3D products, in particular when dealing with large datasets of images. This article presents an efficient pipeline based on color enhancement, image denoising, color-to-gray conversion and image content enrichment. The pipeline stems from an analysis of various state-of-the-art algorithms and aims to adjust the most promising methods, giving solutions to typical failure causes. The assessment evaluation proves how an effective image pre-processing, which considers the entire image dataset, can improve the automated orientation procedure and dense 3D point cloud reconstruction, even in the case of poor texture scenarios.

  6. 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

  7. 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...

  8. lop-DWI: A Novel Scheme for Pre-Processing of Diffusion-Weighted Images in the Gradient Direction Domain.

    Science.gov (United States)

    Sepehrband, Farshid; Choupan, Jeiran; Caruyer, Emmanuel; Kurniawan, Nyoman D; Gal, Yaniv; Tieng, Quang M; McMahon, Katie L; Vegh, Viktor; Reutens, David C; Yang, Zhengyi

    2014-01-01

    We describe and evaluate a pre-processing method based on a periodic spiral sampling of diffusion-gradient directions for high angular resolution diffusion magnetic resonance imaging. Our pre-processing method incorporates prior knowledge about the acquired diffusion-weighted signal, facilitating noise reduction. Periodic spiral sampling of gradient direction encodings results in an acquired signal in each voxel that is pseudo-periodic with characteristics that allow separation of low-frequency signal from high frequency noise. Consequently, it enhances local reconstruction of the orientation distribution function used to define fiber tracks in the brain. Denoising with periodic spiral sampling was tested using synthetic data and in vivo human brain images. The level of improvement in signal-to-noise ratio and in the accuracy of local reconstruction of fiber tracks was significantly improved using our method.

  9. Effect of Processing Delay and Storage Conditions on Urine Albumin-to-Creatinine Ratio.

    Science.gov (United States)

    Herrington, William; Illingworth, Nicola; Staplin, Natalie; Kumar, Aishwarya; Storey, Ben; Hrusecka, Renata; Judge, Parminder; Mahmood, Maria; Parish, Sarah; Landray, Martin; Haynes, Richard; Baigent, Colin; Hill, Michael; Clark, Sarah

    2016-10-07

    Because there is substantial biologic intraindividual variation in albumin excretion, randomized trials of albuminuria-reducing therapies may need multiple urine samples to estimate daily urinary albumin excretion. Mailing spot urine samples could offer a convenient and cost-effective method to collect multiple samples, but urine albumin-to-creatinine ratio stability in samples stored at ambient temperatures for several days is unknown. Patients with kidney disease provided fresh urine samples in two tubes (with and without boric acid preservative). Reference aliquots from each participant were analyzed immediately, whereas remaining aliquots were subject to different handling/storage conditions before analysis, including delayed processing for up to 7 days at three different storage temperatures (4°C, 18°C, and 30°C), multiple freeze-thaw cycles, and long-term frozen storage at -80°C, -40°C, and -20°C. We calculated the mean percentage change in urine albumin-to-creatinine ratio for each condition, and we considered samples stable if the 95% confidence interval was within a ±5% threshold. Ninety-three patients provided samples with detectable albuminuria in the reference aliquot. Median (interquartile range) urine albumin-to-creatinine ratio was 87 (20-499) mg/g. The inclusion of preservative had minimal effect on fresh urine albumin-to-creatinine ratio measurements but reduced the changes in albumin and creatinine in samples subject to processing delay and storage conditions. The urine albumin-to-creatinine ratio was stable for 7 days in samples containing preservative at 4°C and 18°C and 2 days when stored at 30°C. It was also stable in samples with preservative after three freeze-thaw cycles and in frozen storage for 6 months at -80°C or -40°C but not at -20°C. Mailed urine samples collected with preservative and received within 7 days if ambient temperature is ≤18°C, or within 2 days if the temperature is higher but does not exceed 30°C, are

  10. Do Different ADHD-Related Etiological Risks Involve Specific Neuropsychological Pathways? An Analysis of Mediation Processes by Inhibitory Control and Delay Aversion

    Science.gov (United States)

    Pauli-Pott, Ursula; Dalir, Silke; Mingebach, Tanja; Roller, Alisa; Becker, Katja

    2013-01-01

    Background: Inhibitory control (IC) has been regarded as a neuropsychological basic deficit and as an endophenotype of attention deficit/hyperactivity disorder (ADHD). Implicated here are mediation processes between etiological factors and ADHD symptoms. We thus analyze whether and to what extent executive IC and delay aversion (DA; i.e.,…

  11. Resveratrol, by modulating RNA processing factor levels, can influence the alternative splicing of pre-mRNAs.

    Science.gov (United States)

    Markus, M Andrea; Marques, Francine Z; Morris, Brian J

    2011-01-01

    Alternative pre-mRNA splicing defects can contribute to, or result from, various diseases, including cancer. Aberrant mRNAs, splicing factors and other RNA processing factors have therefore become targets for new therapeutic interventions. Here we report that the natural polyphenol resveratrol can modulate alternative splicing in a target-specific manner. We transfected minigenes of several alternatively spliceable primary mRNAs into HEK293 cells in the presence or absence of 1, 5, 20 and 50 µM resveratrol and measured exon levels by semi-quantitative PCR after separation by agarose gel electrophoresis. We found that 20 µg/ml and 50 µg/ml of resveratrol affected exon inclusion of SRp20 and SMN2 pre-mRNAs, but not CD44v5 or tau pre-mRNAs. By Western blotting and immunofluorescence we showed that this effect may be due to the ability of resveratrol to change the protein level but not the localization of several RNA processing factors. The processing factors that increased significantly were ASF/SF2, hnRNPA1 and HuR, but resveratrol did not change the levels of RBM4, PTBP1 and U2AF35. By means of siRNA-mediated knockdown we depleted cells of SIRT1, regarded as a major target of resveratrol, and showed that the effect on splicing was not dependent on SIRT1. Our results suggest that resveratrol might be an attractive small molecule to treat diseases in which aberrant splicing has been implicated, and justify more extensive research on the effects of resveratrol on the splicing machinery.

  12. The effectiveness of CCDSR learning model to improve skills of creating lesson plan and worksheet science process skill (SPS) for pre-service physics teacher

    Science.gov (United States)

    Limatahu, I.; Suyatno; Wasis; Prahani, B. K.

    2018-03-01

    In the previous research, CCDSR (Condition, Construction, Development, Simulation, and Reflection) learning model has been developed to improve science process skills for pre-service physics teacher. This research is aimed to analyze the effectiveness of CCDSR learning model towards the improvement skills of creating lesson plan and worksheet of Science Process Skill (SPS) for pre-service physics teacher in academic year 2016/2017. This research used one group pre-test and post-test design on 12 pre-service physics teacher at Physics Education, University of Khairun. Data collection was conducted through test and observation. Creating lesson plan and worksheet SPS skills of pre-service physics teacher measurement were conducted through Science Process Skill Evaluation Sheet (SPSES). The data analysis technique was done by Wilcoxon t-test and n-gain. The CCDSR learning model consists of 5 phases, including (1) Condition, (2) Construction, (3) Development, (4) Simulation, and (5) Reflection. The results showed that there was a significant increase in creating lesson plan and worksheet SPS skills of pre-service physics teacher at α = 5% and n-gain average of moderate category. Thus, the CCDSR learning model is effective for improving skills of creating lesson plan and worksheet SPS for pre-service physics teacher.

  13. 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...

  14. 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...

  15. 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

  16. Pre-accidental situations highlighted by RECUPERARE method and data

    Energy Technology Data Exchange (ETDEWEB)

    Matahri, N. [Institut de Radioprotection et de Surete Nucleaire (IRSN), 92 - Fontenay-aux-Roses (France)

    2006-07-01

    RECUPERARE method has been developed for operating feedback analysis and built on the French Human Reliability Analysis (HRA) principles. It is used to study the causes of human errors or technical failures occurred in French PWRs and the recovery process of events. Based on an event classification (6 categories) model according to the nature of the link between failure and recovery, the identified and recorded data are: the causes of the defects (technical, human, organizational) and the context in which they appear; the factors of the recovery performance (depending on technical and organizational aspects); a chronological analysis, designed to collect delays between failures and their detection/recovery for each event. About 3600 events reported in French PWRs (1997-2003) had been reviewed through this model. Initially, the weight of factors and the most important factors, which influenced the detection and recovery delay, are defined. For this purpose, the regression Partial Least Square (PLS) is used. Then, to link RECUPERARE results with pre-accidental data, conditional probabilities of events linked between them by a cause and effect relationship are calculated. For this, the Bayesian method with the Bayesian network is built with the PLS obtained results and applied. This constitutes a first approach to take into account in HRA the human and organizational factors highlighted by operating feedback. (author)

  17. Pre-accidental situations highlighted by RECUPERARE method and data

    International Nuclear Information System (INIS)

    Matahri, N.

    2006-01-01

    RECUPERARE method has been developed for operating feedback analysis and built on the French Human Reliability Analysis (HRA) principles. It is used to study the causes of human errors or technical failures occurred in French PWRs and the recovery process of events. Based on an event classification (6 categories) model according to the nature of the link between failure and recovery, the identified and recorded data are: the causes of the defects (technical, human, organizational) and the context in which they appear; the factors of the recovery performance (depending on technical and organizational aspects); a chronological analysis, designed to collect delays between failures and their detection/recovery for each event. About 3600 events reported in French PWRs (1997-2003) had been reviewed through this model. Initially, the weight of factors and the most important factors, which influenced the detection and recovery delay, are defined. For this purpose, the regression Partial Least Square (PLS) is used. Then, to link RECUPERARE results with pre-accidental data, conditional probabilities of events linked between them by a cause and effect relationship are calculated. For this, the Bayesian method with the Bayesian network is built with the PLS obtained results and applied. This constitutes a first approach to take into account in HRA the human and organizational factors highlighted by operating feedback. (author)

  18. 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

  19. 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.

  20. 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.