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Sample records for a-to-i editing detects

  1. A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: De Novo Detection in Human Spinal Cord Tissue

    Science.gov (United States)

    Picardi, Ernesto; Gallo, Angela; Galeano, Federica; Tomaselli, Sara; Pesole, Graziano

    2012-01-01

    RNA editing is a post-transcriptional process occurring in a wide range of organisms. In human brain, the A-to-I RNA editing, in which individual adenosine (A) bases in pre-mRNA are modified to yield inosine (I), is the most frequent event. Modulating gene expression, RNA editing is essential for cellular homeostasis. Indeed, its deregulation has been linked to several neurological and neurodegenerative diseases. To date, many RNA editing sites have been identified by next generation sequencing technologies employing massive transcriptome sequencing together with whole genome or exome sequencing. While genome and transcriptome reads are not always available for single individuals, RNA-Seq data are widespread through public databases and represent a relevant source of yet unexplored RNA editing sites. In this context, we propose a simple computational strategy to identify genomic positions enriched in novel hypothetical RNA editing events by means of a new two-steps mapping procedure requiring only RNA-Seq data and no a priori knowledge of RNA editing characteristics and genomic reads. We assessed the suitability of our procedure by confirming A-to-I candidates using conventional Sanger sequencing and performing RNA-Seq as well as whole exome sequencing of human spinal cord tissue from a single individual. PMID:22957051

  2. Altered A-to-I RNA Editing in Human Embryogenesis

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    Mandel, Rachel; Ziskind, Anna; Nahor, Irit; Safran, Michal; Osenberg, Sivan; Sherf, Ofra; Rechavi, Gideon; Itskovitz-Eldor, Joseph

    2012-01-01

    Post-transcriptional events play an important role in human development. The question arises as to whether Adenosine to Inosine RNA editing, catalyzed by the ADAR (Adenosine Deaminase acting on RNA) enzymes, differs in human embryogenesis and in adulthood. We tested the editing of various target genes in coding (FLNA, BLCAP, CYFIP2) and non-coding sequences at their Alu elements (BRCA1, CARD11, RBBP9, MDM4, FNACC), as well as the transcriptional levels of the ADAR1 enzymes. This analysis was performed on five fetal and adult human tissues: brain, heart, liver, kidney, and spleen, as well as on human embryonic stem cells (hESCs), which represent the blastocyst stage in early human development. Our results show substantially greater editing activity for most adult tissue samples relative to fetal ones, in six of the eight genes tested. To test the effect of reduced A-to-I RNA editing activity in early human development we used human embryonic stem cells (hESCs) as a model and tried to generate hESC clones that overexpress the ADAR1–p110 isoform. We were unable to achieve overexpression of ADAR1–p110 by either transfection or lentiviral infection, though we easily generated hESC clones that expressed the GFP transgene and overexpressed ADAR1-p110 in 293T cells and in primary human foreskin fibroblast (HFF) cells. Moreover, in contrast to the expected overexpression of ADAR1-p110 protein following its introduction into hESCs, the expression levels of this protein decreased dramatically 24–48 hr post infection. Similar results were obtained when we tried to overexpress ADAR1-p110 in pluripotent embryonal carcinoma cells. This suggests that ADAR1 protein is substantially regulated in undifferentiated pluripotent hESCs. Overall, our data suggest that A-to-I RNA editing plays a critical role during early human development. PMID:22859999

  3. Altered A-to-I RNA editing in human embryogenesis.

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    Ronit Shtrichman

    Full Text Available Post-transcriptional events play an important role in human development. The question arises as to whether Adenosine to Inosine RNA editing, catalyzed by the ADAR (Adenosine Deaminase acting on RNA enzymes, differs in human embryogenesis and in adulthood. We tested the editing of various target genes in coding (FLNA, BLCAP, CYFIP2 and non-coding sequences at their Alu elements (BRCA1, CARD11, RBBP9, MDM4, FNACC, as well as the transcriptional levels of the ADAR1 enzymes. This analysis was performed on five fetal and adult human tissues: brain, heart, liver, kidney, and spleen, as well as on human embryonic stem cells (hESCs, which represent the blastocyst stage in early human development. Our results show substantially greater editing activity for most adult tissue samples relative to fetal ones, in six of the eight genes tested. To test the effect of reduced A-to-I RNA editing activity in early human development we used human embryonic stem cells (hESCs as a model and tried to generate hESC clones that overexpress the ADAR1-p110 isoform. We were unable to achieve overexpression of ADAR1-p110 by either transfection or lentiviral infection, though we easily generated hESC clones that expressed the GFP transgene and overexpressed ADAR1-p110 in 293T cells and in primary human foreskin fibroblast (HFF cells. Moreover, in contrast to the expected overexpression of ADAR1-p110 protein following its introduction into hESCs, the expression levels of this protein decreased dramatically 24-48 hr post infection. Similar results were obtained when we tried to overexpress ADAR1-p110 in pluripotent embryonal carcinoma cells. This suggests that ADAR1 protein is substantially regulated in undifferentiated pluripotent hESCs. Overall, our data suggest that A-to-I RNA editing plays a critical role during early human development.

  4. Small RNA and A-to-I Editing in Autism Spectrum Disorders

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    Eran, Alal

    One in every 88 children is diagnosed with Autism Spectrum Disorders (ASDs), a set of neurodevelopmental conditions characterized by social impairments, communication deficits, and repetitive behavior. ASDs have a substantial genetic component, but the specific cause of most cases remains unknown. Understanding gene-environment interactions underlying ASD is essential for improving early diagnosis and identifying critical targets for intervention and prevention. Towards this goal, we surveyed adenosine-to-inosine (A-to-I) RNA editing in autistic brains. A-to-I editing is an epigenetic mechanism that fine-tunes synaptic function in response to environmental stimuli, shown to modulate complex behavior in animals. We used ultradeep sequencing to quantify A-to-I receding of candidate synaptic genes in postmortem cerebella from individuals with ASD and neurotypical controls. We found unexpectedly wide distributions of human A-to-I editing levels, whose extremes were consistently populated by individuals with ASD. We correlated A-to-I editing with isoform usage, identified clusters of correlated sites, and examined differential editing patterns. Importantly, we found that individuals with ASD commonly use a dysfunctional form of the editing enzyme ADARB1. We next profiled small RNAs thought to regulate A-to-I editing, which originate from one of the most commonly altered loci in ASD, 15q11. Deep targeted sequencing of SNORD115 and SNORD116 transcripts enabled their high-resolution detection in human brains, and revealed a strong gender bias underlying their expression. The consistent 2-fold upregulation of 15q11 small RNAs in male vs. female cerebella could be important in delineating the role of this locus in ASD, a male dominant disorder. Overall, these studies provide an accurate population-level view of small RNA and A-to-I editing in human cerebella, and suggest that A-to-I editing of synaptic genes may be informative for assessing the epigenetic risk for autism

  5. Perturbing A-to-I RNA editing using genetics and homologous recombination.

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    Staber, Cynthia J; Gell, Selena; Jepson, James E C; Reenan, Robert A

    2011-01-01

    Evidence for the chemical conversion of adenosine-to-inosine (A-to-I) in messenger RNA (mRNA) has been detected in numerous metazoans, especially those "most successful" phyla: Arthropoda, Mollusca, and Chordata. The requisite enzymes for A-to-I editing, ADARs (adenosine deaminases acting on RNA) are highly conserved and are present in every higher metazoan genome sequenced to date. The fruit fly, Drosophila melanogaster, represents an ideal model organism for studying A-to-I editing, both in terms of fundamental biochemistry and in relation to determining adaptive downstream effects on physiology and behavior. The Drosophila genome contains a single structural gene for ADAR (dAdar), yet the fruit fly transcriptome has the widest range of conserved and validated ADAR targets in coding mRNAs of any known organism. In addition, many of the genes targeted by dADAR have been genetically identified as playing a role in nervous system function, providing a rich source of material to investigate the biological relevance of this intriguing process. Here, we discuss how recent advances in the use of ends-out homologous recombination (HR) in Drosophila make possible both the precise control of the editing status for defined adenosine residues and the engineering of flies with globally altered RNA editing of the fly transcriptome. These new approaches promise to significantly improve our understanding of how mRNA modification contributes to insect physiology and ethology.

  6. A-to-I RNA editing: A new mechanism of genomic information modification

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A-to-I RNA editing, the important event of gene modification, which takes place at post-transcriptional level, was firstly reported in 1991. The molecular mechanism of A-to-I RNA editing involves site-selective deamination of adenosine to inosine in pre-mRNA, which leads to altering translation codons and splicing in nuclear transcripts, thereby functionally distinct proteins can be produced from a single gene. The mammalian editing enzymes ADARs (adenosine deaminases acting on RNA) are widely expressed in brain and other tissues, however, up to date their substrates are mainly found in the central nervous system. It has recently been noticed that imperfect editing of these RNA substrates play critical roles in corresponding diseases, indicating that A-to-I RNA editing may be quite important in physiological or pathophysiological processes. Finding more new substrates of ADARs, especially in peripheral tissues, and performing functional research on new genes will be helpful to elucidate the biological significance of A-to-I RNA editing.

  7. The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers | Office of Cancer Genomics

    Science.gov (United States)

    Adenosine-to-inosine (A-to-I) RNA editing is a widespread post-transcriptional mechanism, but its genomic landscape and clinical relevance in cancer have not been investigated systematically. We characterized the global A-to-I RNA editing profiles of 6,236 patient samples of 17 cancer types from The Cancer Genome Atlas and revealed a striking diversity of altered RNA-editing patterns in tumors relative to normal tissues. We identified an appreciable number of clinically relevant editing events, many of which are in noncoding regions.

  8. Reciprocal regulation of A-to-I RNA editing and the vertebrate nervous system

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    Andrew Charles Penn

    2013-04-01

    Full Text Available The fine control of molecules mediating communication in the nervous system is key to adjusting neuronal responsiveness during development and in maintaining the stability of established networks in the face of altered sensory input. To prevent culmination of pathological recurrent network excitation or debilitating periods of quiescence, adaptive alterations occur in the signalling molecules and ion channels that control membrane excitability and synaptic transmission. However, rather than encoding (and thus ‘hardwiring’ modified gene copies, the nervous systems of metazoa have opted for expanding on post-transcriptional pre-mRNA splicing by altering key encoded amino acids using a conserved mechanism of A-to-I RNA editing: the enzymatic deamination of adenosine resulting in a change in the nucleotide to inosine. Inosine exhibits similar base-pairing properties to guanosine with respect to tRNA codon recognition, replication by polymerases and RNA secondary structure forming capacity. In addition to recoding within the open reading frame, adenosine deamination also occurs with high frequency throughout the non-coding transcriptome, where it affects multiple aspects of RNA metabolism and gene expression. We will describe here the recoding function of key RNA editing targets in the mammalian central nervous system (CNS and their potential to be regulated. We will then discuss how interactions of A-to-I editing with gene expression and alternative splicing could play a wider role in regulating the neuronal transcriptome. Finally, we will highlight the increasing complexity of this multifaceted control hub by summarising new findings from high-throughput studies.

  9. Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing.

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    Sivan Osenberg

    Full Text Available Adenosine to Inosine (A-to-I RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3'UTRs, 5'UTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs. We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, we speculate that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions.

  10. Alu Sequences in Undifferentiated Human Embryonic Stem Cells Display High Levels of A-to-I RNA Editing

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    Osenberg, Sivan; Paz Yaacov, Nurit; Safran, Michal; Moshkovitz, Sharon; Shtrichman, Ronit; Sherf, Ofra; Jacob-Hirsch, Jasmine; Keshet, Gilmor; Amariglio, Ninette; Itskovitz-Eldor, Joseph; Rechavi, Gideon

    2010-01-01

    Adenosine to Inosine (A-to-I) RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA) protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3′UTRs, 5′UTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs). We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, we speculate that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions. PMID:20574523

  11. Consistent levels of A-to-I RNA editing across individuals in coding sequences and non-conserved Alu repeats

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    Osenberg Sivan

    2010-10-01

    Full Text Available Abstract Background Adenosine to inosine (A-to-I RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consistent levels of editing across individuals in a few targets in the human brain and altered in several human pathologies. However, the variability across human individuals of editing levels in other tissues has not been studied so far. Results Here, we analyzed 32 skin samples, looking at A-to-I editing level in three genes within coding sequences and in the Alu repeats of six different genes. We observed highly consistent editing levels across different individuals as well as across tissues, not only in coding targets but, surprisingly, also in the non evolutionary conserved Alu repeats. Conclusions Our findings suggest that A-to-I RNA-editing of Alu elements is a tightly regulated process and, as such, might have been recruited in the course of primate evolution for post-transcriptional regulatory mechanisms.

  12. A-to-I editing of protein coding and noncoding RNAs.

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    Mallela, Arka; Nishikura, Kazuko

    2012-01-01

    Adenosine deaminase acting on RNA (ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) substrates. Inosine pairs preferentially with cytidine, as opposed to uridine; therefore, ADAR editing alters the sequence and base pairing properties of both protein-coding and non-coding RNA. Editing can directly alter the sequence of protein-coding transcripts and modify splicing, or affect a variety of non-coding targets, including microRNA, small interfering RNA, viral transcripts, and repeat elements such as Alu and LINE. Such editing has a wide range of physiological effects, including modification of targets in the brain and in disease states.

  13. Region-specific alterations of A-to-I RNA editing of serotonin 2c receptor in the cortex of suicides with major depression.

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    Weissmann, D; van der Laan, S; Underwood, M D; Salvetat, N; Cavarec, L; Vincent, L; Molina, F; Mann, J J; Arango, V; Pujol, J F

    2016-01-01

    Brain region-specific abnormalities in serotonergic transmission appear to underlie suicidal behavior. Alterations of RNA editing on the serotonin receptor 2C (HTR2C) pre-mRNA in the brain of suicides produce transcripts that attenuate 5-HT2CR signaling by impairing intracellular G-protein coupling and subsequent intracellular signal transduction. In brain, the distribution of RNA-editing enzymes catalyzing deamination (A-to-I modification) shows regional variation, including within the cerebral cortex. We tested the hypothesis that altered pre-mRNA 5-HT2CR receptor editing in suicide is region-specific. To this end, we investigated the complete 5-HT2CR mRNA-editing profile in two architectonically distinct cortical areas involved in mood regulation and decision-making in a clinically well-characterized cohort of age- and sex-matched non-psychiatric drug-free controls and depressed suicides. By using an original biochemical detection method, that is, capillary electrophoresis single-stranded conformational polymorphism (CE-SSCP), we corroborated the 5-HT2CR mRNA-editing profile previously described in the dorsolateral prefrontal cortex (Brodmann area 9 (BA9)). Editing of 5-HT2CR mRNA displayed clear regional difference when comparing dorsolateral prefrontal cortex (BA9) and anterior cingulate cortex (BA24). Compared with non-psychiatric control individuals, alterations of editing levels of 5-HT2CR mRNA were detected in both cortical areas of depressed suicides. A marked increase in editing on 5-HT2CR was especially observed in the anterior cingulate cortex in suicides, implicating this cortical area in suicide risk. The results suggest that region-specific changes in RNA editing of 5-HT2CR mRNA and deficient receptor function likely contribute to the etiology of major depressive disorder or suicide. PMID:27576167

  14. Canonical A-to-I and C-to-U RNA editing is enriched at 3'UTRs and microRNA target sites in multiple mouse tissues.

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    Tongjun Gu

    Full Text Available RNA editing is a process that modifies RNA nucleotides and changes the efficiency and fidelity of the central dogma. Enzymes that catalyze RNA editing are required for life, and defects in RNA editing are associated with many diseases. Recent advances in sequencing have enabled the genome-wide identification of RNA editing sites in mammalian transcriptomes. Here, we demonstrate that canonical RNA editing (A-to-I and C-to-U occurs in liver, white adipose, and bone tissues of the laboratory mouse, and we show that apparent non-canonical editing (all other possible base substitutions is an artifact of current high-throughput sequencing technology. Further, we report that high-confidence canonical RNA editing sites can cause non-synonymous amino acid changes and are significantly enriched in 3' UTRs, specifically at microRNA target sites, suggesting both regulatory and functional consequences for RNA editing.

  15. Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

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    Eisenberg Eli

    2010-07-01

    Full Text Available Abstract Background Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identified weak sequence motifs characterizing the editing sites, but these alone do not account for the large diversity observed. Results Here we build a dataset of 29,971 editing sites and use it to characterize editing preferences. We focus on structural aspects, studying the double-stranded RNA structure of the Alu repeats, and show the editing frequency of a given site to depend strongly on the micro-structure it resides in. Surprisingly, we find that interior loops, and especially the nucleotides at their edges, are more likely to be edited than helices. In addition, the sequence motifs characterizing editing sites vary with the micro-structure. Finally, we show that thermodynamic stability of the site is important for its editing. Conclusions Analysis of a large dataset of editing events reveals more information on sequence and structural motifs characterizing the A-to-I editing process

  16. Detecting Single-Nucleotide Substitutions Induced by Genome Editing.

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    Miyaoka, Yuichiro; Chan, Amanda H; Conklin, Bruce R

    2016-01-01

    The detection of genome editing is critical in evaluating genome-editing tools or conditions, but it is not an easy task to detect genome-editing events-especially single-nucleotide substitutions-without a surrogate marker. Here we introduce a procedure that significantly contributes to the advancement of genome-editing technologies. It uses droplet digital polymerase chain reaction (ddPCR) and allele-specific hydrolysis probes to detect single-nucleotide substitutions generated by genome editing (via homology-directed repair, or HDR). HDR events that introduce substitutions using donor DNA are generally infrequent, even with genome-editing tools, and the outcome is only one base pair difference in 3 billion base pairs of the human genome. This task is particularly difficult in induced pluripotent stem (iPS) cells, in which editing events can be very rare. Therefore, the technological advances described here have implications for therapeutic genome editing and experimental approaches to disease modeling with iPS cells.

  17. Using REDItools to Detect RNA Editing Events in NGS Datasets.

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    Picardi, Ernesto; D'Erchia, Anna Maria; Montalvo, Antonio; Pesole, Graziano

    2015-03-09

    RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine-tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA-Seq and DNA-Seq data or RNA-Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts.

  18. Special-effect edit detection using VideoTrails: a comparison with existing techniques

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    Kobla, Vikrant; DeMenthon, Daniel; Doermann, David S.

    1998-12-01

    Video segmentation plays an integral role in many multimedia applications, such as digital libraries, content management systems, and various other video browsing, indexing, and retrieval systems. Many algorithms for segmentation of video have appeared within the past few years. Most of these algorithms perform well on cuts, but yield poor performance on gradual transitions or special effects edits. A complete video segmentation system must also achieve good performance on special effect edit detection. In this paper, we discuss the performance of our Video Trails-based algorithms, with other existing special effect edit-detection algorithms within the literature. Results from experiments testing for the ability to detect edits from TV programs, ranging from commercials to news magazine programs, including diverse special effect edits, which we have introduced.

  19. Proton observed phosphorus editing (POPE) for in vivo detection of phospholipid metabolites.

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    Wijnen, Jannie P; Klomp, Dennis W J; Nabuurs, Christine I H C; de Graaf, Robin A; van Kalleveen, Irene M L; van der Kemp, Wybe J M; Luijten, Peter R; Kruit, Mark C; Webb, Andrew; Kan, Hermien E; Boer, Vincent O

    2016-09-01

    The purpose of this article was to compare the sensitivity of proton observed phosphorus editing (POPE) with direct (31) P MRS with Ernst angle excitation for (1) H-(31) P coupled metabolites at 7 T. POPE sequences were developed for detecting phosphocholine (PC), phosphoethanolamine (PE), glycerophosphocholine (GPC), and glycerophosphoethanolamine (GPE) on the (1) H channel, thereby using the enhanced sensitivity of the (1) H nuclei over (31) P detection. Five healthy volunteers were examined with POPE and (31) P-MRS. POPE editing showed a more than doubled sensitivity in an ideal phantom experiment as compared with direct (31) P MRS with Ernst angle excitation. In vivo, despite increased relaxation losses, significant gains in signal-to-noise ratio (SNR) of 30-40% were shown for PE and GPE + PC levels in the human brain. The SNR of GPC was lower in the POPE measurement compared with the (31) P-MRS measurement. Furthermore, selective narrowband editing on the (31) P channel showed the ability to separate the overlapping GPE and PE signals in the (1) H spectrum. POPE can be used for enhanced detection of (1) H-(31) P coupled metabolites in vivo. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26601921

  20. Enhanced Fault Detection of Rolling Element Bearing Based on Cepstrum Editing and Stochastic Resonance

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    Zhang, Xiaofei; Hu, Niaoqing; Hu, Lei; Fan, Bin; Cheng, Zhe

    2012-05-01

    By signal pre-whitening based on cepstrum editing,the envelope analysis can be done over the full bandwidth of the pre-whitened signal, and this enhances the bearing characteristic frequencies. The bearing faults detection could be enhanced without knowledge of the optimum frequency bands to demodulate, however, envelope analysis over full bandwidth brings more noise interference. Stochastic resonance (SR), which is now often used in weak signal detection, is an important nonlinear effect. By normalized scale transform, SR can be applied in weak signal detection of machinery system. In this paper, signal pre-whitening based on cepstrum editing and SR theory are combined to enhance the detection of bearing fault. The envelope spectrum kurtosis of bearing fault characteristic components is used as indicators of bearing faults. Detection results of planted bearing inner race faults on a test rig show the enhanced detecting effects of the proposed method. And the indicators of bearing inner race faults enhanced by SR are compared to the ones without enhancement to validate the proposed method.

  1. The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

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    Kong, Yimeng; Pan, Bohu; Chen, Longxian; Wang, Hongbing; Hao, Pei; Li, Xuan

    2016-01-01

    The hydrolytic deamination of adenosine to inosine (A-to-I editing) in precursor mRNA induces variable gene products at the post-transcription level. How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution, and very little is known about the selective constraints that drive the evolution of RNA editing events. Here we present a study on A-to-I RNA editing, by generating a global profile of A-to-I editing for a phylogeny of seven Drosophila species, a model system spanning an evolutionary timeframe of approximately 45 million years. Of totally 9281 editing events identified, 5150 (55.5%) are located in the coding sequences (CDS) of 2734 genes. Phylogenetic analysis places these genes into 1,526 homologous families, about 5% of total gene families in the fly lineages. Based on conservation of the editing sites, the editing events in CDS are categorized into three distinct types, representing events on singleton genes (type I), and events not conserved (type II) or conserved (type III) within multi-gene families. While both type I and II events are subject to purifying selection, notably type III events are positively selected, and highly enriched in the components and functions of the nervous system. The tissue profiles are documented for three editing types, and their critical roles are further implicated by their shifting patterns during holometabolous development and in post-mating response. In conclusion, three A-to-I RNA editing types are found to have distinct evolutionary dynamics. It appears that nervous system functions are mainly tested to determine if an A-to-I editing is beneficial for an organism. The coding plasticity enabled by A-to-I editing creates a new class of binary variations, which is a superior alternative to maintain heterozygosity of expressed genes in a diploid mating system. PMID:27467689

  2. News Editing. Second Edition.

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    Westley, Bruce H.

    A revision of the first edition of "News Editing," this is a textbook for the newspaper editor. The duties of the editor are detailed, as are those of other newspaper employees. Among the basic editing skills the author includes suggestions for sentence structure, word usage, and vocabulary. Examples are given of editing for objectivity, handling…

  3. Edit wars in Wikipedia

    CERN Document Server

    Sumi, Róbert; Rung, András; Kornai, András; Kertész, János

    2011-01-01

    We present a new, efficient method for automatically detecting severe conflicts `edit wars' in Wikipedia and evaluate this method on six different language WPs. We discuss how the number of edits, reverts, the length of discussions, the burstiness of edits and reverts deviate in such pages from those following the general workflow, and argue that earlier work has significantly over-estimated the contentiousness of the Wikipedia editing process.

  4. Genetic Architectures of Quantitative Variation in RNA Editing Pathways.

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    Gu, Tongjun; Gatti, Daniel M; Srivastava, Anuj; Snyder, Elizabeth M; Raghupathy, Narayanan; Simecek, Petr; Svenson, Karen L; Dotu, Ivan; Chuang, Jeffrey H; Keller, Mark P; Attie, Alan D; Braun, Robert E; Churchill, Gary A

    2016-02-01

    RNA editing refers to post-transcriptional processes that alter the base sequence of RNA. Recently, hundreds of new RNA editing targets have been reported. However, the mechanisms that determine the specificity and degree of editing are not well understood. We examined quantitative variation of site-specific editing in a genetically diverse multiparent population, Diversity Outbred mice, and mapped polymorphic loci that alter editing ratios globally for C-to-U editing and at specific sites for A-to-I editing. An allelic series in the C-to-U editing enzyme Apobec1 influences the editing efficiency of Apob and 58 additional C-to-U editing targets. We identified 49 A-to-I editing sites with polymorphisms in the edited transcript that alter editing efficiency. In contrast to the shared genetic control of C-to-U editing, most of the variable A-to-I editing sites were determined by local nucleotide polymorphisms in proximity to the editing site in the RNA secondary structure. Our results indicate that RNA editing is a quantitative trait subject to genetic variation and that evolutionary constraints have given rise to distinct genetic architectures in the two canonical types of RNA editing.

  5. Spectral Editing Technique for the in Vitroand in VivoDetection of Taurine

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    Hardy, D. L.; Norwood, T. J.

    1998-07-01

    In vivo1H NMR spectroscopy has proven to be a useful noninvasive tool for the investigation of numerous metabolic and physiological states. Taurine is potentially a useful indicator in neonate development and is involved in a number of physiological processes. However, it could not previously be observed in thein vivo1H spectrum because of overlap with adjacent resonances. We have developed a spectral editing technique based upon double quantum filtration which allows the taurine resonances to be resolved from adjacent peaks. The experiment is demonstrated both on perchloric acid rodent brain extract and on rodent brain homogenate.

  6. Detection of an antioxidant profile in the human brain in vivo via double editing with MEGA-PRESS.

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    Terpstra, Melissa; Marjanska, Malgorzata; Henry, Pierre-Gilles; Tkác, Ivan; Gruetter, Rolf

    2006-12-01

    Vitamin C (ascorbate) and glutathione (GSH) are the two most concentrated non-enzymatic antioxidants in the human brain. Double editing with (DEW) MEGA-PRESS at 4T was designed in this study to measure both antioxidants in the same amount of time previously required to measure one. In the occipital lobe of four human subjects, resolved ascorbate (Asc) and GSH resonances were detected repeatedly and simultaneously using DEW MEGA-PRESS. The Asc and GSH concentrations measured using LCModel analysis of DEW MEGA-PRESS spectra were 0.8 +/- 0.1 and 1.0 +/- 0.1 micromol/g (mean +/- SD), with average Cramer-Rao lower bounds (CRLB) of 10% and 7%, respectively. Aside from the effects of J-modulation at a common echo time (TE), double editing did not compromise sensitivity. To determine the extent to which the oxidized forms of Asc and GSH contribute to DEW MEGA-PRESS spectra in vivo, chemical shifts and coupling constants for dehydroascorbate (DHA) and oxidized glutathione (GSSG) were measured at physiologic pH and temperature. DHA does not contribute to the 3.73 ppm DEW MEGA-PRESS Asc resonance. GSSG contributions to the DEW MEGA-PRESS GSH resonance (3.0 ppm) are negligible under physiologic conditions, and would be evidenced by a distinct GSSG resonance (3.3 ppm) at exceptionally high concentrations. PMID:17089366

  7. Transfer Rate Edited experiment for the selective detection of Chemical Exchange via Saturation Transfer (TRE-CEST)

    Science.gov (United States)

    Friedman, Joshua I.; Xia, Ding; Regatte, Ravinder R.; Jerschow, Alexej

    2015-07-01

    Chemical Exchange Saturation Transfer (CEST) magnetic resonance experiments have become valuable tools in magnetic resonance for the detection of low concentration solutes with far greater sensitivity than direct detection methods. Accurate measures of rates of chemical exchange provided by CEST are of particular interest to biomedical imaging communities where variations in chemical exchange can be related to subtle variations in biomarker concentration, temperature and pH within tissues using MRI. Despite their name, however, traditional CEST methods are not truly selective for chemical exchange and instead detect all forms of magnetization transfer including through-space NOE. This ambiguity crowds CEST spectra and greatly complicates subsequent data analysis. We have developed a Transfer Rate Edited CEST experiment (TRE-CEST) that uses two different types of solute labeling in order to selectively amplify signals of rapidly exchanging proton species while simultaneously suppressing 'slower' NOE-dominated magnetization transfer processes. This approach is demonstrated in the context of both NMR and MRI, where it is used to detect the labile amide protons of proteins undergoing chemical exchange (at rates ⩾ 30 s-1) while simultaneously eliminating signals originating from slower (∼5 s-1) NOE-mediated magnetization transfer processes. TRE-CEST greatly expands the utility of CEST experiments in complex systems, and in-vivo, in particular, where it is expected to improve the quantification of chemical exchange and magnetization transfer rates while enabling new forms of imaging contrast.

  8. Studies on the influence of a TO I RNA editing on protein evolution

    OpenAIRE

    Ribeiro, Diogo de Abreu Marques, 1988-

    2012-01-01

    Tese de mestrado [versão pública]. Bioinformática e Biologia Computacional. Universidade de Lisboa, Faculdade de Ciências, 2012 A edição de ARN é um processo que altera as propriedades de moléculas de ARN – incluindo ARN transportadores, ARN mensagueiros e micro-ARNs. A edição de ARN ocorre em eucariotas e abrange vários tipos, como inserção ou remoção de nucleótidos (uracilos) e dois tipos de desaminação de nucleótidos: de citosina para uracilo e de adenosina para inosina. A edição de ARN...

  9. In vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI) : [3,4-(CH2)-C-13] glutamate/glutamine tomography in rat brain

    NARCIS (Netherlands)

    Hyder, F; Renken, R; Rothman, DL

    1999-01-01

    A method for in vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI) is described. This method is composed of an echo-planar based acquisition implemented with C-13-H-1 J editing spectroscopy and is intended for high temporal and spatial resolution in vivo spectros

  10. To edit or not to edit: regulation of ADAR editing specificity and efficiency.

    Science.gov (United States)

    Deffit, Sarah N; Hundley, Heather A

    2016-01-01

    Hundreds to millions of adenosine (A)-to-inosine (I) modifications are present in eukaryotic transcriptomes and play an essential role in the creation of proteomic and phenotypic diversity. As adenosine and inosine have different base-pairing properties, the functional consequences of these modifications or 'edits' include altering coding potential, splicing, and miRNA-mediated gene silencing of transcripts. However, rather than serving as a static control of gene expression, A-to-I editing provides a means to dynamically rewire the genetic code during development and in a cell-type specific manner. Interestingly, during normal development, in specific cells, and in both neuropathological diseases and cancers, the extent of RNA editing does not directly correlate with levels of the substrate mRNA or the adenosine deaminase that act on RNA (ADAR) editing enzymes, implying that cellular factors are required for spatiotemporal regulation of A-to-I editing. The factors that affect the specificity and extent of ADAR activity have been thoroughly dissected in vitro. Yet, we still lack a complete understanding of how specific ADAR family members can selectively deaminate certain adenosines while others cannot. Additionally, in the cellular environment, ADAR specificity and editing efficiency is likely to be influenced by cellular factors, which is currently an area of intense investigation. Data from many groups have suggested two main mechanisms for controlling A-to-I editing in the cell: (1) regulating ADAR accessibility to target RNAs and (2) protein-protein interactions that directly alter ADAR enzymatic activity. Recent studies suggest cis- and trans-acting RNA elements, heterodimerization and RNA-binding proteins play important roles in regulating RNA editing levels in vivo. WIREs RNA 2016, 7:113-127. doi: 10.1002/wrna.1319. PMID:26612708

  11. Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates

    Science.gov (United States)

    Frésard, Laure; Leroux, Sophie; Roux, Pierre-François; Klopp, Christophe; Fabre, Stéphane; Esquerré, Diane; Dehais, Patrice; Djari, Anis; Gourichon, David

    2015-01-01

    RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome. PMID:26024316

  12. Exploring the RNA editing potential of RNA-Seq data by ExpEdit.

    Science.gov (United States)

    D'Antonio, Mattia; Picardi, Ernesto; Castrignanò, Tiziana; D'Erchia, Anna Maria; Pesole, Graziano

    2015-01-01

    Revealing the impact of A-to-I RNA editing in RNA-Seq experiments is relevant in humans because RNA editing can influence gene expression. In addition, its deregulation has been linked to a variety of human diseases. Exploiting the RNA editing potential in complete RNA-Seq datasets, however, is a challenging task. Indeed, no dedicated software is available, and sometimes deep computational skills and appropriate hardware resources are required. To explore the impact of known RNA editing events in massive transcriptome sequencing experiments, we developed the ExpEdit web service application. In the present work, we provide an overview of ExpEdit as well as methodologies to investigate known RNA editing in human RNA-Seq datasets.

  13. REDIdb: the RNA editing database.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

    2007-01-01

    The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

  14. Cluster editing

    DEFF Research Database (Denmark)

    Böcker, S.; Baumbach, Jan

    2013-01-01

    The Cluster Editing problem asks to transform a graph into a disjoint union of cliques using a minimum number of edge modifications. Although the problem has been proven NP-complete several times, it has nevertheless attracted much research both from the theoretical and the applied side. The...... algorithms for biological problems. © 2013 Springer-Verlag....... problem has been the inspiration for numerous algorithms in bioinformatics, aiming at clustering entities such as genes, proteins, phenotypes, or patients. In this paper, we review exact and heuristic methods that have been proposed for the Cluster Editing problem, and also applications of these...

  15. Adenosine to Inosine editing frequency controlled by splicing efficiency.

    Science.gov (United States)

    Licht, Konstantin; Kapoor, Utkarsh; Mayrhofer, Elisa; Jantsch, Michael F

    2016-07-27

    Alternative splicing and adenosine to inosine (A to I) RNA-editing are major factors leading to co- and post-transcriptional modification of genetic information. Both, A to I editing and splicing occur in the nucleus. As editing sites are frequently defined by exon-intron basepairing, mRNA splicing efficiency should affect editing levels. Moreover, splicing rates affect nuclear retention and will therefore also influence the exposure of pre-mRNAs to the editing-competent nuclear environment. Here, we systematically test the influence of splice rates on RNA-editing using reporter genes but also endogenous substrates. We demonstrate for the first time that the extent of editing is controlled by splicing kinetics when editing is guided by intronic elements. In contrast, editing sites that are exclusively defined by exonic structures are almost unaffected by the splicing efficiency of nearby introns. In addition, we show that editing levels in pre- and mature mRNAs do not match. This phenomenon can in part be explained by the editing state of an RNA influencing its splicing rate but also by the binding of the editing enzyme ADAR that interferes with splicing. PMID:27112566

  16. Multilinguals and Wikipedia Editing

    CERN Document Server

    Hale, Scott A

    2013-01-01

    This article analyzes one month of edits to Wikipedia in order to examine the role of users editing multiple language editions (referred to as multilingual users). Such multilingual users may serve an important function in diffusing information across different language editions of the project, and prior work has suggested this could reduce the level of self-focus bias in each edition. This study finds multilingual users are much more active than their single-edition (monolingual) counterparts. They are found in all language editions, but smaller-sized editions with fewer users have a higher percentage of multilingual users than larger-sized editions. About a quarter of multilingual users always edit the same articles in multiple languages, while just over 40% of multilingual users edit different articles in different languages. When non-English users do edit a second language edition, that edition is most frequently English. Nonetheless, several regional and linguistic cross-editing patterns are also present...

  17. A distant cis acting intronic element induces site-selective RNA editing

    DEFF Research Database (Denmark)

    Daniel, Chammiran; Venø, Morten Trillingsgaard; Ekdahl, Ylva;

    2012-01-01

    Transcripts have been found to be site selectively edited from adenosine-to-inosine (A-to-I) in the mammalian brain, mostly in genes involved in neurotransmission. While A-to-I editing occurs at double-stranded structures, other structural requirements are largely unknown. We have investigated th...

  18. Editing modifies the GABA(A) receptor subunit alpha3

    DEFF Research Database (Denmark)

    Ohlson, Johan; Pedersen, Jakob Skou; Haussler, David;

    2007-01-01

    to find selectively edited sites and combined it with bioinformatic techniques that find stem-loop structures suitable for editing. We present here the first verified editing candidate detected by this screening procedure. We show that Gabra-3, which codes for the alpha3 subunit of the GABA...

  19. The levels of edit, second edition

    Science.gov (United States)

    Vanburen, R.; Buehler, M. F.

    1980-01-01

    The editorial process is analyzed, and five levels of edit are identified. These levels represent cumulative combinations of nine types of edit: Coordination, Policy, Integrity, Screening, Copy Clarification, Format, Mechanical Style, Language, and Substantive. The levels and types of edit, although developed for specific use with external reports at the Jet Propulsion Laboratory, cover the general range of technical editing, especially as it applies to an in-house technical publications organization. Each type of edit is set forth in terms of groups of actions to be performed by editor. The edit-level concept has enhanced understanding and communication among editors, authors, and publications managers concerning the specific editorial work to be done on each manuscript. It has also proved useful as a management tool for estimating and monitoring cost.

  20. Isotope-edited infrared spectroscopy.

    Science.gov (United States)

    Buchner, Ginka S; Kubelka, Jan

    2012-01-01

    Isotope-edited infrared (IR) spectroscopy is a powerful tool for studying structural and dynamical properties of peptides and proteins with site-specific resolution. Labeling of selected amide carbonyls with (13)C results in detectable sidebands of amide I' vibrations, which provide information about local conformation and/or solvent exposure without structural perturbation to the protein. Incorporation of isotopically labeled amino acids at specific positions is achieved by the chemical synthesis of the studied proteins. We describe the basic procedures for synthesis of (13)C isotopically edited protein samples, experimental IR spectroscopic measurements, and analysis of the site-specific structural changes from the thermal unfolding IR data.

  1. Wikipedia editing dynamics

    Science.gov (United States)

    Gandica, Y.; Carvalho, J.; Sampaio dos Aidos, F.

    2015-01-01

    A model for the probabilistic function followed in editing Wikipedia is presented and compared with simulations and real data. It is argued that the probability of editing is proportional to the editor's number of previous edits (preferential attachment), to the editor's fitness, and to an aging factor. Using these simple ingredients, it is possible to reproduce the results obtained for Wikipedia editing dynamics for a collection of single pages as well as the averaged results. Using a stochastic process framework, a recursive equation was obtained for the average of the number of edits per editor that seems to describe the editing behavior in Wikipedia.

  2. Wikipedia edition dynamics

    CERN Document Server

    Gandica, Y; Carvalho, J

    2014-01-01

    A model for the probabilistic function followed in Wikipedia edition is presented and compared with simulations and real data. It is argued that the probability to edit is proportional to the editor's number of previous editions (preferential attachment), to the editor's fitness and to an ageing factor. Using these simple ingredients, it is possible to reproduce the results obtained for Wikipedia edition dynamics for a collection of single pages as well as the averaged results. Using a stochastic process framework, a recursive equation was obtained for the average of the number of editions per editor that seems to describe the editing behaviour in Wikipedia.

  3. Malware Detection Based on Graph Edit Distance%基于图编辑距离的恶意代码检测

    Institute of Scientific and Technical Information of China (English)

    杨帆; 张焕国; 傅建明; 沈志东

    2013-01-01

    To overcome the disadvantages of traditional malware detection with high false negative rate and low running efficiency,we abstract function call graphs from candidate malware by static analysis.Graph edit distance is taken as the evaluation criteria of the malware similarity,and therefore the malware classification and identification is transformed into the problem of searching the nearest neighbors in the existing malware graph database.To improve the detection speed,we introduce the assembly instruction sets of functions and the multi-way vantage point tree as high dimensional indexing algorithm.Experiments show that our method has good performance in both accuracy and efficiency of malware detection.%传统的恶意代码检测方法漏报率高且运行效率低,很大程度的依赖于人工检测.为解决该问题,基于恶意代码自身的函数调用顺序及程序结构特征,通过静态分析技术将恶意代码抽象为函数调用图,采用图的编辑距离作为恶意代码间相似度的评估标准,将恶意代码的分类识别转化为在已建立的恶意代码图数据库中搜索最小编辑距离邻居图的问题,在此基础上实现了用户检测未知文件恶意性的系统.为了提高检测速度,引入了函数对应的汇编指令集和多路优势点树的高维索引算法.实验证明,该方案兼顾了恶意代码检测的准确性和运行效率.

  4. Oligophrenin-1 (OPHN1, a gene involved in X-linked intellectual disability, undergoes RNA editing and alternative splicing during human brain development.

    Directory of Open Access Journals (Sweden)

    Sabina Barresi

    Full Text Available Oligophrenin-1 (OPHN1 encodes for a Rho-GTPase-activating protein, important for dendritic morphogenesis and synaptic function. Mutations in this gene have been identified in patients with X-linked intellectual disability associated with cerebellar hypoplasia. ADAR enzymes are responsible for A-to-I RNA editing, an essential post-transcriptional RNA modification contributing to transcriptome and proteome diversification. Specifically, ADAR2 activity is essential for brain development and function. Herein, we show that the OPHN1 transcript undergoes post-transcriptional modifications such as A-to-I RNA editing and alternative splicing in human brain and other tissues. We found that OPHN1 editing is detectable already at the 18th week of gestation in human brain with a boost of editing at weeks 20 to 33, concomitantly with OPHN1 expression increase and the appearance of a novel OPHN1 splicing isoform. Our results demonstrate that multiple post-transcriptional events occur on OPHN1, a gene playing an important role in brain function and development.

  5. 肿瘤中GLI1RNA编辑的下调及其潜在功能分析%Down-regulation of RNA editing of GLI1 in tumors and analysis of its potential function

    Institute of Scientific and Technical Information of China (English)

    张颖; 胡亚欧; 何涛; 侯小强; 汪莉; 张部昌; 王玉民

    2012-01-01

    Objective To detect the A-to-[ RNA editing in the coding region of cancer associated gene GUI, compare the difference in the editing level between tumor and normal cell lines , and to analyze the potential effect of this editing event in the hope of discovering the role of the RNA editing in the occurrence and progression of cancer . Methods The identification of the A-to-[ RNA editing event and the comparison of the editing level were carried out by comparing the cDNA sequences with their corresponding genomic templates based on PCR , RT-PCR and sequencing methods. The potential functional implications of RNA editing were analyzed by multiple bioinformatics tools . Results An A-to-I RNA editing site mapped to chr 12: 56150891 changed the arginine residue at position 701 of the GUI protein to a glutamine residue, which was detected in the human brain , breast, small intestine tissues and multiple cell lines. Compared with normal controls, the editing level of this site decreased in the hepatoma and breast cancer cell lines . By bioinformatics analysis, this editing event altered amino acid residue and was predicted to destroy putative exonic splicing enhancers ( ESE) and affect putative protein tertiary structure. Conclusion This A-to-I RNA editing event in the coding region of GUI occurs in many diverse human tissues and cell lines. Down^-egulation of RNA editing of GUI in hepatoma and breast cancer cell lines may be associated with the occurrence and progression of cancer .%目的 检测癌相关基因GLI1编码区发生的A-to-I RNA编辑,比较编辑水平在肿瘤与正常细胞系中的差异,并分析编辑事件的潜在影响,以期揭示其与癌症发生发展的关联.方法 通过PCR、RT-PCR及测序的方法检测GLI1编码区DNA和RNA序列上的差异,以此来识别该区域上的A-to-I RNA编辑事件和比较肿瘤与正常细胞系中编辑位点的编辑水平差异.使用多种生物信息学工具分析编辑事

  6. A distant cis acting intronic element induces site-selective RNA editing.

    Science.gov (United States)

    Daniel, Chammiran; Venø, Morten T; Ekdahl, Ylva; Kjems, Jørgen; Öhman, Marie

    2012-10-01

    Transcripts have been found to be site selectively edited from adenosine-to-inosine (A-to-I) in the mammalian brain, mostly in genes involved in neurotransmission. While A-to-I editing occurs at double-stranded structures, other structural requirements are largely unknown. We have investigated the requirements for editing at the I/M site in the Gabra-3 transcript of the GABA(A) receptor. We identify an evolutionarily conserved intronic duplex, 150 nt downstream of the exonic hairpin where the I/M site resides, which is required for its editing. This is the first time a distant RNA structure has been shown to be important for A-to-I editing. We demonstrate that the element also can induce editing in related but normally not edited RNA sequences. In human, thousands of genes are edited in duplexes formed by inverted repeats in non-coding regions. It is likely that numerous such duplexes can induce editing of coding regions throughout the transcriptome. PMID:22848101

  7. Multiplex editing system

    DEFF Research Database (Denmark)

    2015-01-01

    The present invention relates to a multiplex editing system. The system allows multiple editing of nucleic acid sequences such as genomic sequences, such as knockins of genes of interest in a genome, knockouts of genomic sequences and/or allele replacement. Also provided herein are a method...

  8. Quality text editing

    Directory of Open Access Journals (Sweden)

    Gyöngyi Bujdosó

    2009-10-01

    Full Text Available Text editing is more than the knowledge of word processing techniques. Originally typographers, printers, text editors were the ones qualified to edit texts, which were well structured, legible, easily understandable, clear, and were able to emphasize the coreof the text. Time has changed, and nowadays everyone has access to computers as well as to text editing software and most users believe that having these tools is enough to edit texts. However, text editing requires more skills. Texts appearing either in printed or inelectronic form reveal that most of the users do not realize that they are not qualified to edit and publish their works. Analyzing the ‘text-products’ of the last decade a tendency can clearly be drawn. More and more documents appear, which instead of emphasizingthe subject matter, are lost in the maze of unstructured text slices. Without further thoughts different font types, colors, sizes, strange arrangements of objects, etc. are applied. We present examples with the most common typographic and text editing errors. Our aim is to call the attention to these mistakes and persuadeusers to spend time to educate themselves in text editing. They have to realize that a well-structured text is able to strengthen the effect on the reader, thus the original message will reach the target group.

  9. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

    DEFF Research Database (Denmark)

    Peng, Zhiyu; Cheng, Yanbing; Tan, Bertrand Chin-Ming;

    2012-01-01

    a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual. We identified 22,688 RNA editing events in noncoding genes and introns, untranslated regions and coding sequences of protein-coding genes. Most...... changes (∼93%) converted A to I(G), consistent with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). We also found evidence of other types of nucleotide changes; however, these were validated at lower rates. We found 44 editing sites in microRNAs (miRNAs), suggesting a potential...

  10. CRISPR Genome Editing

    Science.gov (United States)

    A research article about a technique for gene editing known as CRISPR-Cas9. The technique has made it much easier and faster for cancer researchers to study mutations and test new therapeutic targets.

  11. Comprehensive high-resolution analysis of the role of an Arabidopsis gene family in RNA editing.

    Science.gov (United States)

    Bentolila, Stéphane; Oh, Julyun; Hanson, Maureen R; Bukowski, Robert

    2013-06-01

    In flowering plants, mitochondrial and chloroplast mRNAs are edited by C-to-U base modification. In plant organelles, RNA editing appears to be generally a correcting mechanism that restores the proper function of the encoded product. Members of the Arabidopsis RNA editing-Interacting Protein (RIP) family have been recently shown to be essential components of the plant editing machinery. We report the use of a strand- and transcript-specific RNA-seq method (STS-PCRseq) to explore the effect of mutation or silencing of every RIP gene on plant organelle editing. We confirm RIP1 to be a major editing factor that controls the editing extent of 75% of the mitochondrial sites and 20% of the plastid C targets of editing. The quantitative nature of RNA sequencing allows the precise determination of overlapping effects of RIP factors on RNA editing. Over 85% of the sites under the influence of RIP3 and RIP8, two moderately important mitochondrial factors, are also controlled by RIP1. Previously uncharacterized RIP family members were found to have only a slight effect on RNA editing. The preferential location of editing sites controlled by RIP7 on some transcripts suggests an RNA metabolism function for this factor other than editing. In addition to a complete characterization of the RIP factors for their effect on RNA editing, our study highlights the potential of RNA-seq for studying plant organelle editing. Unlike previous attempts to use RNA-seq to analyze RNA editing extent, our methodology focuses on sequencing of organelle cDNAs corresponding to known transcripts. As a result, the depth of coverage of each editing site reaches unprecedented values, assuring a reliable measurement of editing extent and the detection of numerous new sites. This strategy can be applied to the study of RNA editing in any organism.

  12. Comprehensive high-resolution analysis of the role of an Arabidopsis gene family in RNA editing.

    Directory of Open Access Journals (Sweden)

    Stéphane Bentolila

    2013-06-01

    Full Text Available In flowering plants, mitochondrial and chloroplast mRNAs are edited by C-to-U base modification. In plant organelles, RNA editing appears to be generally a correcting mechanism that restores the proper function of the encoded product. Members of the Arabidopsis RNA editing-Interacting Protein (RIP family have been recently shown to be essential components of the plant editing machinery. We report the use of a strand- and transcript-specific RNA-seq method (STS-PCRseq to explore the effect of mutation or silencing of every RIP gene on plant organelle editing. We confirm RIP1 to be a major editing factor that controls the editing extent of 75% of the mitochondrial sites and 20% of the plastid C targets of editing. The quantitative nature of RNA sequencing allows the precise determination of overlapping effects of RIP factors on RNA editing. Over 85% of the sites under the influence of RIP3 and RIP8, two moderately important mitochondrial factors, are also controlled by RIP1. Previously uncharacterized RIP family members were found to have only a slight effect on RNA editing. The preferential location of editing sites controlled by RIP7 on some transcripts suggests an RNA metabolism function for this factor other than editing. In addition to a complete characterization of the RIP factors for their effect on RNA editing, our study highlights the potential of RNA-seq for studying plant organelle editing. Unlike previous attempts to use RNA-seq to analyze RNA editing extent, our methodology focuses on sequencing of organelle cDNAs corresponding to known transcripts. As a result, the depth of coverage of each editing site reaches unprecedented values, assuring a reliable measurement of editing extent and the detection of numerous new sites. This strategy can be applied to the study of RNA editing in any organism.

  13. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    the previously available DNA binding templates, zinc fingers and meganucleases. Recently, the area experimented a quantum leap because of the introduction of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system (clustered regularly interspaced short palindromic...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR......-Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human...

  14. Precision genome editing

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Bennett, Eric P; Schjoldager, Katrine Ter-Borch Gram;

    2014-01-01

    of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption...... by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene...

  15. Edit Distance for Timed Automata

    OpenAIRE

    Chatterjee, Krishnendu; Ibsen-Jensen, Rasmus; Majumdar, Rupak

    2013-01-01

    The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define ...

  16. Editing graphs for maximum effect

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, P.W.; Rhiner, R.W.

    1991-01-08

    The paper contains over eighty rules for editing graphs, arranged under nine major headings in a logical sequence for editing all the graphs in a manuscript. It is excerpted from a monograph used at the Lawrence Livermore National Laboratory to train beginning technical editors in editing graphs; a corresponding Hypercard stack is also used in this training. 6 refs., 4 figs.

  17. Beginning to edit physics

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, P.W.

    1995-02-01

    A physicist-turned-editor shows you the basics required for copyediting physics papers (physical quantities, symbols, units, scientific notation, the structure of mathematical expressions, the nature of graphs), and points the way to learning enough ``editorial physics`` to begin substantive editing.

  18. The Craft of Editing

    DEFF Research Database (Denmark)

    Moeran, Brian

    To edit is to make a choice, or series of choices. Will I write a rough draft of this essay in longhand, or hammer it out on my computer? If the latter, what font shall I use? Times New Roman, Book Antiqua, or Garamond? Once I get started, what style shall I adopt: realistic, confessional or impr...

  19. Edit Distance for Pushdown Automata

    OpenAIRE

    Chatterjee, Krishnendu; Henzinger, Thomas A.; Ibsen-Jensen, Rasmus; Otop, Jan

    2015-01-01

    The edit distance between two words $w_1, w_2$ is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform $w_1$ to $w_2$. The edit distance generalizes to languages ${\\cal L}_1, {\\cal L}_2$, where the edit distance is the minimal number $k$ such that for every word from ${\\cal L}_1$ there exists a word in ${\\cal L}_2$ with edit distance at most $k$. We study the edit distance computation problem between pushdown automata and their subclas...

  20. Application of binomial-edited CPMG to shale characterization

    Science.gov (United States)

    Washburn, Kathryn E.; Birdwell, Justin E.

    2014-01-01

    Unconventional shale resources may contain a significant amount of hydrogen in organic solids such as kerogen, but it is not possible to directly detect these solids with many NMR systems. Binomial-edited pulse sequences capitalize on magnetization transfer between solids, semi-solids, and liquids to provide an indirect method of detecting solid organic materials in shales. When the organic solids can be directly measured, binomial-editing helps distinguish between different phases. We applied a binomial-edited CPMG pulse sequence to a range of natural and experimentally-altered shale samples. The most substantial signal loss is seen in shales rich in organic solids while fluids associated with inorganic pores seem essentially unaffected. This suggests that binomial-editing is a potential method for determining fluid locations, solid organic content, and kerogen–bitumen discrimination.

  1. Psychology. 5th edition

    OpenAIRE

    Martin, G. Neil; Carlson, Neil R.; Buskist, William

    2013-01-01

    A comprehensive, lively and engaging introduction to the fascinating study of the subject. The fifth edition of the best-selling Psychology is a contemporary text that will captivate all psychology students. The authors describe and explore every major area of psychology and present the latest findings, along with clear evaluation of controversial theories and models, to give a rigorous and critical grounding in the subject. Over 420 new references in this thoroughly updated fifth editi...

  2. Interactive Metro Map Editing.

    Science.gov (United States)

    Wang, Yu-Shuen; Peng, Wan-Yu

    2016-02-01

    Manual editing of a metro map is essential because many aesthetic and readability demands in map generation cannot be achieved by using a fully automatic method. In addition, a metro map should be updated when new metro lines are developed in a city. Considering that manually designing a metro map is time-consuming and requires expert skills, we present an interactive editing system that considers human knowledge and adjusts the layout to make it consistent with user expectations. In other words, only a few stations are controlled and the remaining stations are relocated by our system. Our system supports both curvilinear and octilinear layouts when creating metro maps. It solves an optimization problem, in which even spaces, route straightness, and maximum included angles at junctions are considered to obtain a curvilinear result. The system then rotates each edge to extend either vertically, horizontally, or diagonally while approximating the station positions provided by users to generate an octilinear layout. Experimental results, quantitative and qualitative evaluations, and user studies show that our editing system is easy to use and allows even non-professionals to design a metro map.

  3. An RNA editing fingerprint of cancer stem cell reprogramming

    OpenAIRE

    Crews, Leslie A; Jiang, Qingfei; Zipeto, Maria A; de Lazzari, Elisa; Court, Angela C.; Ali, Shawn; Barrett, Christian L.; Frazer, Kelly A; Jamieson, Catriona HM

    2015-01-01

    Background Deregulation of RNA editing by adenosine deaminases acting on dsRNA (ADARs) has been implicated in the progression of diverse human cancers including hematopoietic malignancies such as chronic myeloid leukemia (CML). Inflammation-associated activation of ADAR1 occurs in leukemia stem cells specifically in the advanced, often drug-resistant stage of CML known as blast crisis. However, detection of cancer stem cell-associated RNA editing by RNA sequencing in these rare cell populatio...

  4. Revising and editing for translators

    CERN Document Server

    Mossop, Brian

    2014-01-01

    Revising and Editing for Translators provides guidance and learning materials for translation students learning to edit texts written by others, and professional translators wishing to improve their self-revision ability or learning to revise the work of others. Editing is understood as making corrections and improvements to texts, with particular attention to tailoring them to the given readership. Revising is this same task applied to draft translations. The linguistic work of editors and revisers is related to the professional situations in which they work. Mossop offers in-depth coverage of a wide range of topics, including copyediting, style editing, structural editing, checking for consistency, revising procedures and principles, and translation quality assessment. This third edition provides extended coverage of computer aids for revisers, and of the different degrees of revision suited to different texts. The inclusion of suggested activities and exercises, numerous real-world examples, a proposed gra...

  5. Edit Distance with Block Deletions

    OpenAIRE

    Dana Shapira; Storer, James A.

    2011-01-01

    Several variants of the edit distance problem with block deletions are considered. Polynomial time optimal algorithms are presented for the edit distance with block deletions allowing character insertions and character moves, but without block moves. We show that the edit distance with block moves and block deletions is NP-complete (Nondeterministic Polynomial time problems in which any given solution to such problem can be verified in polynomial time, and any NP problem can be converted into...

  6. A contextual normalised edit distance

    OpenAIRE

    Higuera, Colin de la; Micó Andrés, Luisa

    2008-01-01

    In order to better fit a variety of pattern recognition problems over strings, using a normalised version of the edit or Levenshtein distance is considered to be an appropriate approach. The goal of normalisation is to take into account the lengths of the strings. We define a new normalisation, contextual, where each edit operation is divided by the length of the string on which the edit operation takes place. We prove that this contextual edit distance is a metric and that it can be...

  7. Nanoparticles for Site Specific Genome Editing

    Science.gov (United States)

    McNeer, Nicole Ali

    Triplex-forming peptide nucleic acids (PNAs) can be used to coordinate the recombination of short 50-60 by "donor DNA" fragments into genomic DNA, resulting in site-specific correction of genetic mutations or the introduction of advantageous genetic modifications. Site-specific gene editing in hematopoietic stem and progenitor cells (HSPCs) could result in treatment or cure of inherited disorders of the blood such as beta-thalassemia. Gene editing in HSPCs and differentiated T cells could help combat HIV/AIDs by modifying receptors, such as CCR5, necessary for R5-tropic HIV entry. However, translation of genome modification technologies to clinical practice is limited by challenges in intracellular delivery, especially in difficult-to-transfect hematolymphoid cells. In vivo gene editing could also provide novel treatment for systemic monogenic disorders such as cystic fibrosis, an autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane receptor. Here, we have engineered biodegradable nanoparticles to deliver oligonucleotides for site-specific genome editing of disease-relevant genes in human cells, with high efficiency, low toxicity, and editing of clinically relevant cell types. We designed nanoparticles to edit the human beta-globin and CCR5 genes in hematopoietic cells. We show that poly(lactic-co-glycolic acid) (PLGA) nanoparticles can delivery PNA and donor DNA for site-specific gene modification in human hematopoietic cells in vitro and in vivo in NOD-scid IL2rgammanull mice. Nanoparticles delivered by tail vein localized to hematopoietic compartments in the spleen and bone marrow of humanized mice, resulting in modification of the beta-globin and CCR5 genes. Modification frequencies ranged from 0.005 to 20% of cells depending on the organ and cell type, without detectable toxicity. This project developed highly versatile methods for delivery of therapeutics to hematolymphoid cells and hematopoietic stem cells, and will help to

  8. Regulation of gene expression in neuronal tissue by RNA interference and editing

    DEFF Research Database (Denmark)

    Venø, Morten Trillingsgaard

    No tissue in the mammalian organism is more complex than the brain. This complexity is in part the result of precise timing and interplay of a large number mechanisms modulating gene expression post-transcriptionally. Fine-tuning mechanisms such as A-to-I editing of RNA transcripts and regulation...... mediated by microRNAs are crucial for the correct function of the mammalian brain. We are addressing A-to-I editing and regulation by microRNAs with spatio-temporal resolution in the embryonic porcine brain by Solexa sequencing of microRNAs and 454 sequencing of edited neuronal messenger RNAs, resulting......RNAs, causing these transgenic mice to be less prone to cocaine addictive behavior. Another study demonstrated that abolishing the expression of histone methylases, GLP and G9a, increases the expression level of a large number of miRNAs. A possible feed-back mechanism is suggested, since a subset of these mi...

  9. A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans.

    Science.gov (United States)

    Kim, Heesun; Ishidate, Takao; Ghanta, Krishna S; Seth, Meetu; Conte, Darryl; Shirayama, Masaki; Mello, Craig C

    2014-08-01

    Genome editing based on CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease (Cas9) has been successfully applied in dozens of diverse plant and animal species, including the nematode Caenorhabditis elegans. The rapid life cycle and easy access to the ovary by micro-injection make C. elegans an ideal organism both for applying CRISPR-Cas9 genome editing technology and for optimizing genome-editing protocols. Here we report efficient and straightforward CRISPR-Cas9 genome-editing methods for C. elegans, including a Co-CRISPR strategy that facilitates detection of genome-editing events. We describe methods for detecting homologous recombination (HR) events, including direct screening methods as well as new selection/counterselection strategies. Our findings reveal a surprisingly high frequency of HR-mediated gene conversion, making it possible to rapidly and precisely edit the C. elegans genome both with and without the use of co-inserted marker genes.

  10. Video summarization and semantics editing tools

    Science.gov (United States)

    Xu, Li-Qun; Zhu, Jian; Stentiford, Fred

    2001-01-01

    This paper describes a video summarization and semantics editing tool that is suited for content-based video indexing and retrieval with appropriate human operator assistance. The whole system has been designed with a clear focus on the extraction and exploitation of motion information inherent in the dynamic video scene. The dominant motion information has ben used explicitly for shot boundary detection, camera motion characterization, visual content variations description, and for key frame extraction. Various contributions have been made to ensure that the system works robustly with complex scenes and across different media types. A window-based graphical user interface has been designed to make the task very easy for interactive analysis and editing of semantic events and episode where appropriate.

  11. Natural Hazards, Second Edition

    Science.gov (United States)

    Rouhban, Badaoui

    Natural disaster loss is on the rise, and the vulnerability of the human and physical environment to the violent forces of nature is increasing. In many parts of the world, disasters caused by natural hazards such as earthquakes, floods, landslides, drought, wildfires, intense windstorms, tsunami, and volcanic eruptions have caused the loss of human lives, injury, homelessness, and the destruction of economic and social infrastructure. Over the last few years, there has been an increase in the occurrence, severity, and intensity of disasters, culminating with the devastating tsunami of 26 December 2004 in South East Asia.Natural hazards are often unexpected or uncontrollable natural events of varying magnitude. Understanding their mechanisms and assessing their distribution in time and space are necessary for refining risk mitigation measures. This second edition of Natural Hazards, (following a first edition published in 1991 by Cambridge University Press), written by Edward Bryant, associate dean of science at Wollongong University, Australia, grapples with this crucial issue, aspects of hazard prediction, and other issues. The book presents a comprehensive analysis of different categories of hazards of climatic and geological origin.

  12. A new strategy for in vivo spectral editing. Application to GABA editing using selective homonuclear polarization transfer spectroscopy

    Science.gov (United States)

    Shen, Jun; Yang, Jehoon; Choi, In-Young; Li, Shizhe Steve; Chen, Zhengguang

    2004-10-01

    A novel single-shot in vivo spectral editing method is proposed in which the signal to be detected, is regenerated anew from the thermal equilibrium magnetization of a source to which it is J-coupled. The thermal equilibrium magnetization of the signal to be detected together with those of overlapping signals are suppressed by single-shot gradient dephasing prior to the signal regeneration process. Application of this new strategy to in vivo GABA editing using selective homonuclear polarization transfer allows complete suppression of overlapping creatine and glutathione while detecting the GABA-4 methylene resonance at 3.02 ppm with an editing yield similar to that of conventional editing methods. The NAA methyl group at 2.02 ppm was simultaneously detected and can be used as an internal navigator echo for correcting the zero order phase and frequency shifts and as an internal reference for concentration. This new method has been demonstrated for robust in vivo GABA editing in the rat brain and for study of GABA synthesis after acute vigabatrin administration.

  13. Introduction to Surgical Technology. Third Edition. Teacher Edition [and] Student Edition.

    Science.gov (United States)

    Bushey, Vicki; Hildebrand, Bob; Hildebrand, Dinah; Johnson, Dave; Sikes, John; Tahah, Ann; Walker, Susan; Zielsdorf, Lani

    These teacher and student editions provide instructional materials for an introduction to surgical technology course. Introductory materials in the teacher edition include information on use, instructional/task analysis, academic and workplace skill classifications and definitions, related academic and workplace skill list, and crosswalk to…

  14. Residential and Light Commercial HVAC. Teacher Edition and Student Edition. Second Edition.

    Science.gov (United States)

    Stephenson, David

    This package contains teacher and student editions of a residential and light commercial heating, ventilation, and air conditioning (HVAC) course of study. The teacher edition contains information on the following: using the publication; national competencies; competency profile; related academic and workplace skills list; tools, equipment, and…

  15. Oxyacetylene Welding and Oxyfuel Cutting. Third Edition. Teacher Edition [and] Student Edition [and] Student Workbook.

    Science.gov (United States)

    Knapp, John; Harper, Eddie

    This Oklahoma curriculum guide, which includes a teacher edition, a student edition, and a student workbook, provides three units for a course on oxyacetylene welding, oxyfuel cutting, and cutting done with alternative fuels such as MAPP, propane, and natural gas. The three units are: "Oxyacetylene Welding"; "Oxyfuel Cutting"; and "Oxyacetylene…

  16. Fundamentals of Welding. Teacher Edition [and] Student Edition [and] Student Workbook. Second Edition.

    Science.gov (United States)

    Fortney, Clarence; Gregory, Mike; New, Larry

    Teacher and student editions and a student workbook for fundamentals of welding comprise the first of six in a series of competency-based instructional materials for welding programs. Introductory pages in the teacher edition are training and competency profile, instructional/task analysis, basic skills icons and classifications, basic skills…

  17. Map Edit Distance vs Graph Edit Distance for Matching Images

    OpenAIRE

    Combier, Camille; Damiand, Guillaume; Solnon, Christine

    2013-01-01

    Generalized maps are widely used to model the topology of nD objects (such as 2D or 3D images) by means of incidence and adjacency relationships between cells (0D vertices, 1D edges, 2D faces, 3D volumes, ...). Recently, we have introduced a map edit distance. This distance compares maps by means of a minimum cost sequence of edit operations that should be performed to transform a map into another map. In this paper, we introduce labelled maps and we show how the map edit distance may be exte...

  18. Edit while watching: home video editing made easy

    Science.gov (United States)

    Campanella, Marco; Weda, Hans; Barbieri, Mauro

    2007-01-01

    In recent years, more and more people capture their experiences in home videos. However, home video editing still is a difficult and time-consuming task. We present the Edit While Watching system that allows users to automatically create and change a summary of a home video in an easy, intuitive and lean-back way. Based on content analysis, video is indexed, segmented, and combined with proper music and editing effects. The result is an automatically generated home video summary that is shown to the user. While watching it, users can indicate whether they like certain content, so that the system will adapt the summary to contain more content that is similar or related to the displayed content. During the video playback users can also modify and enrich the content, seeing immediately the effects of their changes. Edit While Watching does not require a complex user interface: a TV and a few keys of a remote control are sufficient. A user study has shown that it is easy to learn and to use, even if users expressed the need for more control in the editing operations and in the editing process.

  19. Learning Stochastic Tree Edit Distance

    OpenAIRE

    Bernard, Marc; Habrard, Amaury; Sebban, Marc

    2006-01-01

    Trees provide a suited structural representation to deal with complex tasks such as web information extraction, RNA secondary structure prediction, or conversion of tree structured documents. In this context, many applications require the calculation of similarities between tree pairs. The most studied distance is likely the tree edit distance for which improvements in terms of complexity have been achieved during the last decade. However, this classic edit distance usually uses a priori fixe...

  20. Marine botany. Second edition

    Energy Technology Data Exchange (ETDEWEB)

    Dawes, C.J. [Univ. of South Florida, Tampa, FL (United States)

    1998-12-01

    Marine plants are a diverse group that include unicellular algae, seaweeds, seagrasses, salt marshes, and mangrove forests. They carry out a variety of ecological functions and serve as the primary producers in coastal wetlands and oceanic waters. The theme that connects such a wide variety of plants is their ecology, which was also emphasized in the 1981 edition. The goal of this revision is to present taxonomic, physiological, chemical, and ecological aspects of marine plants, their adaptations, and how abiotic and biotic factors interact in their communities. The data are presented in a concise, comparative manner in order to identify similarities and differences between communities such as salt marsh and mangroves or subtidal seaweeds and seagrasses. To accomplish this, the text is organized into five chapters that introduce the marine habitats, consider abiotic and biotic factors, and anthropogenic influences on the communities followed by seven chapters that deal with microalgae, seaweeds, salt marshes, mangroves, seagrasses, and coral reefs. Two appendixes are included; one presents simple field techniques and the other is a summary of seaweed uses.

  1. A plant mitochondrial sequence transcribed in transgenic tobacco chloroplasts is not edited

    Energy Technology Data Exchange (ETDEWEB)

    Sutton, C.A.; Hanson, M.R. [Cornell Univ., Ithaca, NY (United States); Zoubenko, O.V.; Maliga, P. [State Univ. of New Jersey, Piscataway, NJ (United States)

    1995-03-01

    RNA editing occurs in two higher-plant organelles, chloroplasts, and mitochondria. Because chloroplasts and mitochondria exhibit some similarity in editing site selection, we investigated whether mitochondrial RNA sequences could be edited in chloroplasts. We produced transgenic tobacco plants that contained chimeric genes in which the second exon of a Petunia hybrida mitochondrial coxII gene was under the control of chloroplast gene regulatory sequences. coxII transcripts accumulated to low or high levels in transgenic chloroplasts containing chimeric genes with the plastid ribosomal protein gene rps16 or the rRNA operon promoter, respectively. Exon 2 of coxII was chosen because it carries seven editing sites and is edited in petunia mitochondria even when located in an abnormal context in an aberrant recombined gene. When editing of the coxII transcripts in transgenic chloroplasts was examined, no RNA editing at any of the usual sites was detected, nor was there any novel editing at any other sites. These results indicate that the RNA editing mechanisms of chloroplasts and mitochondria are not identical but must have at least some organelle-specific components. 33 refs., 5 figs.

  2. Connectivity editing for quadrilateral meshes

    KAUST Repository

    Peng, Chihan

    2011-12-12

    We propose new connectivity editing operations for quadrilateral meshes with the unique ability to explicitly control the location, orientation, type, and number of the irregular vertices (valence not equal to four) in the mesh while preserving sharp edges. We provide theoretical analysis on what editing operations are possible and impossible and introduce three fundamental operations to move and re-orient a pair of irregular vertices. We argue that our editing operations are fundamental, because they only change the quad mesh in the smallest possible region and involve the fewest irregular vertices (i.e., two). The irregular vertex movement operations are supplemented by operations for the splitting, merging, canceling, and aligning of irregular vertices. We explain how the proposed highlevel operations are realized through graph-level editing operations such as quad collapses, edge flips, and edge splits. The utility of these mesh editing operations are demonstrated by improving the connectivity of quad meshes generated from state-of-art quadrangulation techniques. © 2011 ACM.

  3. Connectivity editing for quadrilateral meshes

    KAUST Repository

    Peng, Chihan

    2011-12-01

    We propose new connectivity editing operations for quadrilateral meshes with the unique ability to explicitly control the location, orientation, type, and number of the irregular vertices (valence not equal to four) in the mesh while preserving sharp edges. We provide theoretical analysis on what editing operations are possible and impossible and introduce three fundamental operations to move and re-orient a pair of irregular vertices. We argue that our editing operations are fundamental, because they only change the quad mesh in the smallest possible region and involve the fewest irregular vertices (i.e., two). The irregular vertex movement operations are supplemented by operations for the splitting, merging, canceling, and aligning of irregular vertices. We explain how the proposed high-level operations are realized through graph-level editing operations such as quad collapses, edge flips, and edge splits. The utility of these mesh editing operations are demonstrated by improving the connectivity of quad meshes generated from state-of-art quadrangulation techniques.

  4. CTD writing and editing standards

    Science.gov (United States)

    Caruthers, C. M.

    1991-03-01

    The Computer and Telecommunication Division (CTD) recognizes that the communication of clear, accurate, reasonably complete information is essential to the success of its Laboratory mission. CTD therefore encourages all Division personnel to adhere to the principles of good writing and to the standards for grammar, usage, style, formats, and publication procedures that are described in CTD Writing and Editing Standards. We encourage CTD personnel to read CTD Writing and Editing Standards and to use it continually as a desktop reference. It will help CTD writers to produce better documents consistent with CTD standards in less time. Applying the principles specified in this document on how to write and organize technical information will speed up the editing, review, and revision processes. CTD Writing and Editing Standards complements the Argonne National Laboratory Technical Publications Guide, which serves as the basic Argonne documentation reference on issues concerning DOE orders and guidelines, NRC directives, and other sponsor requirements. However, this Laboratory-wide document does not address matters of grammar or style. Documents recommended in CTD Writing and Editing Standards are usually available for purchase at the Document Distribution Counter (Building 221, Room A-134) or through the mail (by calling extension 2-5405 and ordering copies).

  5. 3D Surface Editing Based on Level-Sets

    Institute of Scientific and Technical Information of China (English)

    Lin Maosong; Zhang Dianhua

    2005-01-01

    A novel method which integrates the topological flexibility of the level-set approach and the simphcity of point-sampled surfaces is proposed. The grid structure resulted from the level-set approach not only offers a wide range of powerful surface editing techniques for the point set surface editing, but also facilitates the topological change with ease. With the aid of point-based resampling,the method updates the surface shape of the point-based geometry quickly without worrying about point connectivity at all. The point set surface can also change its topology properly whenever a collision with other parts of itself is detected. The experiment demonstrates their effectiveness on several scanned objects and scan-converted models. Four examples of surface editing operations: smoothing, tapering, deforming, and Boolean operations, are presented.

  6. Understanding Editing Behaviors in Multilingual Wikipedia.

    Science.gov (United States)

    Kim, Suin; Park, Sungjoon; Hale, Scott A; Kim, Sooyoung; Byun, Jeongmin; Oh, Alice H

    2016-01-01

    Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest user-generated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary) languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language. PMID:27171158

  7. Understanding Editing Behaviors in Multilingual Wikipedia

    Science.gov (United States)

    Hale, Scott A.; Kim, Sooyoung; Byun, Jeongmin; Oh, Alice H.

    2016-01-01

    Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest user-generated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary) languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language. PMID:27171158

  8. Understanding Editing Behaviors in Multilingual Wikipedia.

    Directory of Open Access Journals (Sweden)

    Suin Kim

    Full Text Available Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest user-generated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language.

  9. Understanding Editing Behaviors in Multilingual Wikipedia.

    Science.gov (United States)

    Kim, Suin; Park, Sungjoon; Hale, Scott A; Kim, Sooyoung; Byun, Jeongmin; Oh, Alice H

    2016-01-01

    Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest user-generated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary) languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language.

  10. Description scheme for video editing work

    Science.gov (United States)

    Ruiloba, Rosa I.; Joly, Philippe

    2001-03-01

    This article presents a Description Scheme (DS) to describe the audio-visual documents from the video editing work point of view. This DS is based on edition techniques used in the video edition domain. The main objective of this DS is to provide a complete, modular and extensible description of the structure of the video documents based on editing process. This VideoEditing DS is generic in the sense that it may be used in a large number of applications such as video document indexing and analysis, description of Edit Decision List and elaboration of editing patterns. It is based on accurate and complete definitions of shots and transition effects required for video document analysis applications. The VideoEditing DS allows three levels of description : analytic, synthetic and semantic. In the DS, the higher (resp. the lower) is the element of description, the more analytic (resp. synthetic) is the information. %Phil This DS allows describing the editing work made by editing boards, using more detailed descriptors of Shots and Transition DSs. These elements are provided to define editing patterns that allow several possible reconstructions of movies depending on, for example, the target audience. A part of the video description made with this DS may be automatically produced by the video to shots segmentation algorithms (analytic DSs ) or by editing software, at the same time the edition work is made. This DS gives an answer to the needs related to the exchange of editing work descriptions between editing softwares. At the same time, the same DS provide an analytic description of editing work which is complementary to existing standards for Edit Decision Lists like SMPTE or AAF.

  11. A structural determinant required for RNA editing

    Science.gov (United States)

    Tian, Nan; Yang, Yun; Sachsenmaier, Nora; Muggenhumer, Dominik; Bi, Jingpei; Waldsich, Christina; Jantsch, Michael F.; Jin, Yongfeng

    2011-01-01

    RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence and structural context. However, the detailed mechanisms underlying these preferences are not fully understood. Here, we show that duplex structures mimicking an editing site in the Gabra3 pre-mRNA unexpectedly fail to support RNA editing at the Gabra3 I/M site, although phylogenetic analysis suggest an evolutionarily conserved duplex structure essential for efficient RNA editing. These unusual results led us to revisit the structural requirement for this editing by mutagenesis analysis. In vivo nuclear injection experiments of mutated editing substrates demonstrate that a non-conserved structure is a determinant for editing. This structure contains bulges either on the same or the strand opposing the edited adenosine. The position of these bulges and the distance to the edited base regulate editing. Moreover, elevated folding temperature can lead to a switch in RNA editing suggesting an RNA structural change. Our results indicate the importance of RNA tertiary structure in determining RNA editing. PMID:21427087

  12. Boneless Pose Editing and Animation

    DEFF Research Database (Denmark)

    Bærentzen, Jakob Andreas; Hansen, Kristian Evers; Erleben, Kenny

    2007-01-01

    In this paper, we propose a pose editing and animation method for triangulated surfaces based on a user controlled partitioning of the model into deformable parts and rigid parts which are denoted handles. In our pose editing system, the user can sculpt a set of poses simply by transforming...... the handles for each pose. Using Laplacian editing, the deformable parts are deformed to match the handles. In our animation system the user can constrain one or several handles in order to define a new pose. New poses are interpolated from the examples poses, by solving a small non-linear optimization...... problem in order to obtain the interpolation weights. While the system can be used simply for building poses, it is also an animation system. The user can specify a path for a given constraint and the model is animated correspondingly....

  13. Beginning XML, 5th Edition

    CERN Document Server

    Fawcett, Joe; Quin, Liam R E

    2012-01-01

    A complete update covering the many advances to the XML language The XML language has become the standard for writing documents on the Internet and is constantly improving and evolving. This new edition covers all the many new XML-based technologies that have appeared since the previous edition four years ago, providing you with an up-to-date introductory guide and reference. Packed with real-world code examples, best practices, and in-depth coverage of the most important and relevant topics, this authoritative resource explores both the advantages and disadvantages of XML and addresses the mo

  14. Introducing ZBrush 3rd Edition

    CERN Document Server

    Keller, Eric

    2012-01-01

    Learn ZBrush inside and out with this updated new edition Get totally comfortable sculpting in a digital environment with the latest edition of this bestselling beginner's guide to ZBrush. Fully updated for the newest version of the software, ZBrush 4R3, this book dispels any fears you might have about the difficulty of using ZBrush and soon has you creating realistic, cartoon, and organic models with flair. Learn all the essentials, as you complete fun tutorials on painting, meshes, organic scripting, hard surface sculpting, lighting, rendering, and more. Introduces you to ZBrush, the sculpt

  15. Medical writing, revising and editing

    DEFF Research Database (Denmark)

    Pilegaard, Morten

    2006-01-01

    The globalization of science makes medical writing, editing and revision a rapidly growing field of linguistic study and practice. Medical science texts are written according to uniform, general guidelines and medical genres have become highly conventionalized in terms of structure and linguistic...... form. Medical editing often takes the form of peer review and mainly addresses issues of contents and overall validity. Medical revision incorporates the checking of the macrostructure and the microstructure of the text, its language and style and its suitability for the target reader or client...

  16. Genome editing comes of age.

    Science.gov (United States)

    Kim, Jin-Soo

    2016-09-01

    Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster of regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) RNA-guided endonucleases (RGENs). I specifically highlight the key advances that set the foundation for the rapid and widespread implementation of CRISPR-Cas9 genome editing approaches that has revolutionized the field. PMID:27490630

  17. Gas Metal Arc Welding and Flux-Cored Arc Welding. Third Edition. Teacher Edition [and] Student Edition [and] Student Workbook.

    Science.gov (United States)

    Knapp, John; Harper, Eddie

    This packet, containing a teacher's edition, a student edition, and a student workbook, introduces students to high deposition welding and processes for "shielding" a weld. In addition to general information, the teacher edition consists of introductory pages and teacher pages, as well as unit information that corresponds to the materials in the…

  18. Civil Technology Applications. Teacher Edition [and] Student Edition.

    Science.gov (United States)

    Schertz, Karen

    Teacher and student editions of Civil Technology Applications are one in a series of competency-based instructional materials for drafting and civil technology programs. It includes the technical content and tasks necessary for a student to be employed as a drafter or civil technician in a civil engineering firm. Introductory pages in the teacher…

  19. Investigating RNA editing factors from trypanosome mitochondria

    Science.gov (United States)

    Aphasizheva, Inna; Zhang, Liye; Aphasizhev, Ruslan

    2016-01-01

    Mitochondrial U-insertion/deletion mRNA editing is carried out by two principal multiprotein assemblies, enzymatic RNA editing core (RECC) and RNA editing substrate binding (RESC) complexes, and a plethora of auxiliary factors. An integral part of mitochondrial gene expression, editing receives inputs from primary mRNA and gRNA precursor processing pathways, and generates substrates for mRNA polyadenylation and translation. Although nearly all RECC-embedded enzymes have been implicated in specific editing reactions, the majority of proteins that populate the RESC are also essential for generating edited mRNAs. However, lack of recognizable motifs in RESC subunits limits the prowess of bioinformatics in guiding biochemical experiments and elucidating their specific biological functions. In this chapter, we describe a generic workflow for investigating mitochondrial mRNA editing in Trypanosoma brucei and focus on several methods that proved instrumental is assigning definitive functions to editing factors lacking known signature sequences. PMID:27020893

  20. ADAR2 editing activity in newly diagnosed versus relapsed pediatric high-grade astrocytomas

    International Nuclear Information System (INIS)

    High-grade (WHO grade III and IV) astrocytomas are aggressive malignant brain tumors affecting humans with a high risk of recurrence in both children and adults. To date, limited information is available on the genetic and molecular alterations important in the onset and progression of pediatric high-grade astrocytomas and, even less, on the prognostic factors that influence long-term outcome in children with recurrence. A-to-I RNA editing is an essential post-transcriptional mechanism that can alter the nucleotide sequence of several RNAs and is mediated by the ADAR enzymes. ADAR2 editing activity is particularly important in mammalian brain and is impaired in both adult and pediatric high-grade astrocytomas. Moreover, we have recently shown that the recovered ADAR2 activity in high-grade astrocytomas inhibits in vivo tumor growth. The aim of the present study is to investigate whether changes may occur in ADAR2-mediated RNA editing profiles of relapsed high-grade astrocytomas compared to their respective specimens collected at diagnosis, in four pediatric patients. Total RNAs extracted from all tumor samples and controls were tested for RNA editing levels (by direct sequencing on cDNA pools) and for ADAR2 mRNA expression (by qRT-PCR). A significant loss of ADAR2-editing activity was observed in the newly diagnosed and recurrent astrocytomas in comparison to normal brain. Surprisingly, we found a substantial rescue of ADAR2 editing activity in the relapsed tumor of the only patient showing prolonged survival. High-grade astrocytomas display a generalized loss of ADAR2-mediated RNA editing at both diagnosis and relapse. However, a peculiar Case, in complete remission of disease, displayed a total rescue of RNA editing at relapse, intriguingly suggesting ADAR2 activity/expression as a possible marker for long-term survival of patients with high-grade astrocytomas

  1. Controlled flexibility in technical editing - The levels-of-edit concept at JPL

    Science.gov (United States)

    Buehler, M. F.

    1977-01-01

    The levels-of-edit concept, which can be used to specify the amount of editorial effort involved in the preparation of a manuscript for publication, is discussed. Nine types of editing are identified and described. These include coordination edit (preparing estimates, gathering cost data, monitoring production processes), policy edit, integrity edit (making sure that parts of a publication match in a physical or numerical sense), screening edit (ensuring that the quality of camera-ready copy is sufficient for external publication), copy clarification edit, format edit, mechanical style edit, language edit, and substantive edit (reviewing the manuscript for content coherence, emphasis, subordination and parallelism). These functions are grouped into five levels of edit. An edit-level number is assigned to each manuscript, providing a quantitative and qualitative indicator of the editing to be done which is clearly understood by authors, managers, and editors alike. In addition, clear boundaries are drawn between normal and extraordinary editing tasks. Individual organizations will group various edits in different ways to reflect their needs and priorities; the essential element of the system is unambiguous definition and coding of the types and amount of work to be done.

  2. Parameter-Free Extended Edit Distance

    OpenAIRE

    Muhammad Fuad, Muhammad Marwan

    2014-01-01

    The edit distance is the most famous distance to compute the similarity between two strings of characters. The main drawback of the edit distance is that it is based on local procedures which reflect only a local view of similarity. To remedy this problem we presented in a previous work the extended edit distance, which adds a global view of similarity between two strings. However, the extended edit distance includes a parameter whose computation requires a long training time. In this paper w...

  3. [An introduction on the editions of Zhang Gao's Yi shuo (Medical Narrations)].

    Science.gov (United States)

    Wang, Xuguang; Lu, Xiang

    2014-11-01

    Zhang Gao's Yi shuo (Medical Narrations) of the Southern Song Dynasty had 2 kinds of editions: domestic editions and foreign editions. The former includes 1 Song edition, 14 Ming editions, 3 Qing editions and 25 editions after the Republic of China. The latter, mainly 2 classes, the Japanese edition and Korean printing type edition. In the Ming Dynasty, the editions of Yi shuo generated 2 branches: inherited edition and supplementary edition. The inherited editions include Gu Dingfang's edition, Zhang Yaode's edition, Wu Mianxue's edition, Wu Zhongheng's edition, Wang Kentang's edition, editions from Si ku quan shu (Imperial Collection of Four), stereotype edition of the 3th year of Xuantong reign (1911) from Shanghai Civilization Bookstore, edition of the 2(nd) year of Manji of Japan etc. The supplemental editions include Zhang Zili's edition, Shen Fan's edition, Fu Feng'ao's edition, transcript of the late Ming Dynasty preserved in the Library of Peking University, and Korean printing type edition etc.

  4. [An introduction on the editions of Zhang Gao's Yi shuo (Medical Narrations)].

    Science.gov (United States)

    Wang, Xuguang; Lu, Xiang

    2014-11-01

    Zhang Gao's Yi shuo (Medical Narrations) of the Southern Song Dynasty had 2 kinds of editions: domestic editions and foreign editions. The former includes 1 Song edition, 14 Ming editions, 3 Qing editions and 25 editions after the Republic of China. The latter, mainly 2 classes, the Japanese edition and Korean printing type edition. In the Ming Dynasty, the editions of Yi shuo generated 2 branches: inherited edition and supplementary edition. The inherited editions include Gu Dingfang's edition, Zhang Yaode's edition, Wu Mianxue's edition, Wu Zhongheng's edition, Wang Kentang's edition, editions from Si ku quan shu (Imperial Collection of Four), stereotype edition of the 3th year of Xuantong reign (1911) from Shanghai Civilization Bookstore, edition of the 2(nd) year of Manji of Japan etc. The supplemental editions include Zhang Zili's edition, Shen Fan's edition, Fu Feng'ao's edition, transcript of the late Ming Dynasty preserved in the Library of Peking University, and Korean printing type edition etc. PMID:25620361

  5. Strategies of Qualitative Inquiry. Third Edition

    Science.gov (United States)

    Denzin, Norman K., Ed.; Lincoln, Yvonna S., Ed.

    2007-01-01

    "Strategies of Qualitative Inquiry, Third Edition," the second volume in the paperback version of "The SAGE Handbook of Qualitative Research, 3rd Edition," consists of Part III of the handbook ("Strategies of Inquiry"). "Strategies of Qualitative Inquiry, Third Edition" presents the major tactics--historically, the research methods--that…

  6. Teaching Students to Self-Edit.

    Science.gov (United States)

    Ferris, Dana

    1995-01-01

    Emphasizes the need for students to develop their editing skills. This article suggests that teachers and students should concentrate on major error patterns, and teachers should personalize editing instruction. Attention should also be given to the most frequent and glaring errors. Students who followed this editing approach significantly reduced…

  7. Testing post-editing guidelines

    DEFF Research Database (Denmark)

    Flanagan, Marian; Christensen, Tina Paulsen

    2014-01-01

    There is a growing interest in machine translation (MT) and post-editing (PE). MT has been around for decades, but the use of the technology has grown significantly in the language industry in recent years, while PE is still a relatively new task. Consequently, there are currently no standard PE...

  8. Veterinary Microbiology, 3rd Edition

    Science.gov (United States)

    Veterinary Microbiology, Third Edition is organized into four sections and begins with an updated and expanded introductory section on infectious disease pathogenesis, diagnosis and clinical management. The second section covers bacterial and fungal pathogens, and the third section describes viral d...

  9. Money and Schools. Fifth Edition

    Science.gov (United States)

    Thompson, David C.; Crampton, Faith E.; Wood, R. Craig

    2012-01-01

    In the new edition of this essential, all-inclusive text, the authors provide more important research for future principals and others enrolled in graduate-level school finance courses. Written in a style that is highly readable, the book offers strong connections to real-world experiences. Readers get both a broad overview of funding concepts and…

  10. Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection

    Science.gov (United States)

    Doria, Margherita; Neri, Francesca; Gallo, Angela; Farace, Maria Giulia; Michienzi, Alessandro

    2009-01-01

    Adenosine deaminases that act on dsRNA (ADARs) are enzymes that target double-stranded regions of RNA converting adenosines into inosines (A-to-I editing) thus contributing to genome complexity and fine regulation of gene expression. It has been described that a member of the ADAR family, ADAR1, can target viruses and affect their replication process. Here we report evidence showing that ADAR1 stimulates human immuno deficiency virus type 1 (HIV-1) replication by using both editing-dependent and editing-independent mechanisms. We show that over-expression of ADAR1 in HIV-1 producer cells increases viral protein accumulation in an editing-independent manner. Moreover, HIV-1 virions generated in the presence of over-expressed ADAR1 but not an editing-inactive ADAR1 mutant are released more efficiently and display enhanced infectivity, as demonstrated by challenge assays performed with T cell lines and primary CD4+ T lymphocytes. Finally, we report that ADAR1 associates with HIV-1 RNAs and edits adenosines in the 5′ untranslated region (UTR) and the Rev and Tat coding sequence. Overall these results suggest that HIV-1 has evolved mechanisms to take advantage of specific RNA editing activity of the host cell and disclose a stimulatory function of ADAR1 in the spread of HIV-1. PMID:19651874

  11. Statistical Physics Approaches to RNA Editing

    Science.gov (United States)

    Bundschuh, Ralf

    2012-02-01

    The central dogma of molecular Biology states that DNA is transcribed base by base into RNA which is in turn translated into proteins. However, some organisms edit their RNA before translation by inserting, deleting, or substituting individual or short stretches of bases. In many instances the mechanisms by which an organism recognizes the positions at which to edit or by which it performs the actual editing are unknown. One model system that stands out by its very high rate of on average one out of 25 bases being edited are the Myxomycetes, a class of slime molds. In this talk we will show how the computational methods and concepts from statistical Physics can be used to analyze DNA and protein sequence data to predict editing sites in these slime molds and to guide experiments that identified previously unknown types of editing as well as the complete set of editing events in the slime mold Physarum polycephalum.

  12. Edition des Corpus areopagiticum slavicum

    Directory of Open Access Journals (Sweden)

    Dieter Fahl

    2005-12-01

    Full Text Available An Edition of the Corpus areopagiticum slavicum In the fourteenth century, the monk Isaiah of the holy Mount Athos translated the writings of pseudo-Dionysius the Areopagite (c. end of the 5th century, core texts for Eastern and Western European theological and philosophical thought, from Greek into Church Slavonic. This first Slavic translation of Dionysius’ oeuvre (“De Coelesti Hierarchia,” “De Ecclesiastica Hierarchia,” “De Divinis Nominibus,” “De Mystica Theologia,” the epistles and scholia, which played a significant role in the development of Slavic culture, Orthodox Slavic socio-political theory and praxis, is still central to the study of Slavia Orthodoxa. A working group of German and Russian scholars has completed an edition of the translator’s Church Slavonic autograph with an en face reconstruction of the Greek text used by the translator and philological commentary. A Church Slavonic-Greek and Greek-Church Slavonic dictionary of this edition, currently in preparation, plans to make the terminology used in this influential translation accessible to interdisciplinary researchers. For the first time, the Church Slavonic lexica of this corpus, a substantial part of which was coined by the translator, will be registered in an index of words and forms.

  13. Linked Edit Rules: A Web Friendly Way of Checking Quality of RDF Data Cubes

    OpenAIRE

    Meroño-Peñuela, A.; Guéret, Christophe Dominique Marie; Schlobach, S.; Capadisli, Sarvan; Cotton, Franck; Haller, Armin; Kalampokis, Evangelos; Scannapieco, Monica; Troncy, Raphael

    2015-01-01

    Statistical data often comes with inconsistencies: records of people with negative ages, pregnant males, and underaged car drivers often populate statistical databases. National Statistical Offices (NSO) encode knowledge to detect these inconsistencies in so-called edit rules. These days, there is an increasing number of statistical data being published and linked on the Web using the RDF Data Cube vocabulary. However, edit rules are hardly ever published together with data cubes on the Web. ...

  14. Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection

    OpenAIRE

    Doria, Margherita; Neri, Francesca; Gallo, Angela; Farace, Maria Giulia; Michienzi, Alessandro

    2009-01-01

    Adenosine deaminases that act on dsRNA (ADARs) are enzymes that target double-stranded regions of RNA converting adenosines into inosines (A-to-I editing) thus contributing to genome complexity and fine regulation of gene expression. It has been described that a member of the ADAR family, ADAR1, can target viruses and affect their replication process. Here we report evidence showing that ADAR1 stimulates human immuno deficiency virus type 1 (HIV-1) replication by using both editing-dependent ...

  15. Connectivity editing for quad-dominant meshes

    KAUST Repository

    Peng, Chihan

    2013-08-01

    We propose a connectivity editing framework for quad-dominant meshes. In our framework, the user can edit the mesh connectivity to control the location, type, and number of irregular vertices (with more or fewer than four neighbors) and irregular faces (non-quads). We provide a theoretical analysis of the problem, discuss what edits are possible and impossible, and describe how to implement an editing framework that realizes all possible editing operations. In the results, we show example edits and illustrate the advantages and disadvantages of different strategies for quad-dominant mesh design. © 2013 The Author(s) Computer Graphics Forum © 2013 The Eurographics Association and John Wiley & Sons Ltd.

  16. Operational Transformation In Co-Operative Editing

    Directory of Open Access Journals (Sweden)

    Mandeep Kaur

    2015-08-01

    Full Text Available Cooperative Editing Systems in real-time allows a virtual team to view and edit a shared document at the same time. The document shared must be synchronized in order to ensure consistency for all the participants. This paper describes the Operational Transformation the evolution of its techniques its various applications major issues and achievements. In addition this paper will present working of a platform where two users can edit a code programming file at the same time.

  17. Edit Distance between Unlabeled Ordered Trees

    OpenAIRE

    Micheli, Anne; Rossin, Dominique

    2005-01-01

    There exists a bijection between one stack sortable permutations --permutations which avoid the pattern $231$-- and planar trees. We define an edit distance between permutations which is coherent with the standard edit distance between trees. This one-to-one correspondence yields a polynomial algorithm for the subpermutation problem for $(231)$ avoiding permutations. Moreover, we obtain the generating function of the edit distance between ordered trees and some special ones. For the general c...

  18. RNA Editing Dynamically Rewrites the Cancer Code

    Science.gov (United States)

    Rayon-Estrada, Violeta; Papavasiliou, F. Nina; Harjanto, Dewi

    2016-01-01

    Global analyses of cancer transcriptomes demonstrate that ADAR (adenosine deaminase, RNA-specific)-mediated RNA editing dynamically contributes to genetic alterations in cancer, and directly correlates with progression and prognosis. RNA editing is abundant and frequently elevated in cancer, and affects functionally and clinically relevant sites in both coding and non-coding regions of the transcriptome. Therefore, ADAR and differentially edited transcripts may be promising biomarkers or targets for therapy.

  19. Electronic editions – possibilities, limitations, perspectives

    OpenAIRE

    Mertens, Martin

    2010-01-01

    The thesis "Electronic Editions – Possibilities, Limitations, Perspectives" presents concepts and technologies for electronic editions in the field of German language and literature. The thesis focuses on describing forms of information contained by written texts that extend beyond the literal information content, and on the possibilities that exist for encoding this information in electronic editions and thus opening it up to electronic evaluation. It begins with a survey of existing electro...

  20. A potential role for NF1 mRNA editing in the pathogenesis of NF1 tumors

    Energy Technology Data Exchange (ETDEWEB)

    Cappione, A.J.; French, B.L.; Skuse, G.R. [Univ. of Rochester School of Medicine and Dentistry, NY (United States)

    1997-02-01

    Neurofibromatosis type I (NF1) is a common disorder that predisposes to neoplasia in tissues derived from the embryonic neural crest. The NF1 gene encodes a tumor suppressor that most likely acts through the interaction of its GTPase-activating protein (GAP)-related domain (GRD) with the product of the ras protooncogene. We have previously identified a site in the NF1 mRNA, within the first half of the NF1 GRD, which undergoes base-modification editing. Editing at that site changes a C to a U, thereby introducing an in-frame stop codon. NF1 RNA editing has been detected in all cell types studied, to date. In order to investigate the role played by editing in NF1 tumorigenesis, we analyzed RNA from 19 NF1 and 4 non-NF1 tumors. We observed varying levels of NF1 mRNA editing in different tumors, with a higher range of editing levels in more malignant tumors (e.g., neurofibrosarcomas) compared to benign tumors (cutaneous neurofibromas). Plexiform neurofibromas have an intermediate range of levels of NF1 mRNA editing. We also compared tumor and nontumor tissues from several NF1 individuals, to determine the extent of variability present in the constitutional levels of NF1 mRNA editing and to determine whether higher levels are present in tumors. The constitutional levels of NF1 mRNA editing varied slightly but were consistent with the levels observed in non-NF1 individuals. In every case, there was a greater level of NF1 mRNA editing in the tumor than in the nontumor tissue from the same patient. These results suggest that inappropriately high levels of NF1 mRNA editing does play a role in NF1 tumorigenesis and that editing may result in the functional equivalent of biallelic inactivation of the NF1 tumor suppressor. 24 refs., 4 figs., 2 tabs.

  1. Fuel Cell Handbook, Fourth Edition

    Energy Technology Data Exchange (ETDEWEB)

    Stauffer, D.B; Hirschenhofer, J.H.; Klett, M.G.; Engleman, R.R.

    1998-11-01

    Robust progress has been made in fuel cell technology since the previous edition of the Fuel Cell Handbook was published in January 1994. This Handbook provides a foundation in fuel cells for persons wanting a better understanding of the technology, its benefits, and the systems issues that influence its application. Trends in technology are discussed, including next-generation concepts that promise ultra high efficiency and low cost, while providing exceptionally clean power plant systems. Section 1 summarizes fuel cell progress since the last edition and includes existing power plant nameplate data. Section 2 addresses the thermodynamics of fuel cells to provide an understanding of fuel cell operation at two levels (basic and advanced). Sections 3 through 6 describe the four major fuel cell types and their performance based on cell operating conditions. The section on polymer electrolyte membrane fuel cells has been added to reflect their emergence as a significant fuel cell technology. Phosphoric acid, molten carbonate, and solid oxide fuel cell technology description sections have been updated from the previous edition. New information indicates that manufacturers have stayed with proven cell designs, focusing instead on advancing the system surrounding the fuel cell to lower life cycle costs. Section 7, Fuel Cell Systems, has been significantly revised to characterize near-term and next-generation fuel cell power plant systems at a conceptual level of detail. Section 8 provides examples of practical fuel cell system calculations. A list of fuel cell URLs is included in the Appendix. A new index assists the reader in locating specific information quickly.

  2. Biocommunication and natural genome editing

    Institute of Scientific and Technical Information of China (English)

    Guenther; Witzany

    2010-01-01

    The biocommunicative approach investigates communication processes within and among cells,tissues,organs and organisms as sign-mediated interactions,and nucleotide sequences as code,i.e.language-like text,which follows in parallel three kinds of rules:combinatorial (syntactic),context-sensitive(pragmatic),and contentspecific(semantic).Natural genome editing from a bio-communicative perspective is competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements and the ability to(re-)combine and(re-)regulate them according to context-dependent(i.e.adaptational) purposes of the host organism.

  3. APP Snrinn Edition Kicks Off

    Institute of Scientific and Technical Information of China (English)

    Tang Rong

    2012-01-01

    When European textile insiders still take delight in talking about the last apparel sourcing show in September 2011, the debut of APP Spring edition bring people back to the Le Bourget Expo Center, with entire passion. The 7th APP Show, sponsored by China National Textile and Apparel Council (CNTAC), organized by the Sub-Council of Textile Industry, China Council for the Promotion of International Trade (CCPIT TEX), China National Garment Association and Messe Frankfurt French Subsidiary, was on display from Feb 13th to 16th 2012,

  4. 6. Electronic Editions for Everyone

    OpenAIRE

    Robinson, Peter

    2013-01-01

    1. Books Defy the Digital Revolution In January 2004, I gave a lecture on electronic scholarly editing at the University of Virginia. At the beginning of the lecture I asked the audience, of around 60 people, three questions. The first question was: who among them had bought a movie on DVD in the last year; who had bought a piece of music on CD-ROM or by download in the last year; who had taken digital photographs? Almost everyone in the audience had done all three. The second question: who i...

  5. GPU Computing Gems Emerald Edition

    CERN Document Server

    Hwu, Wen-mei W

    2011-01-01

    ".the perfect companion to Programming Massively Parallel Processors by Hwu & Kirk." -Nicolas Pinto, Research Scientist at Harvard & MIT, NVIDIA Fellow 2009-2010 Graphics processing units (GPUs) can do much more than render graphics. Scientists and researchers increasingly look to GPUs to improve the efficiency and performance of computationally-intensive experiments across a range of disciplines. GPU Computing Gems: Emerald Edition brings their techniques to you, showcasing GPU-based solutions including: Black hole simulations with CUDA GPU-accelerated computation and interactive display of

  6. Parallel Evolution and Lineage-Specific Expansion of RNA Editing in Ctenophores.

    Science.gov (United States)

    Kohn, Andrea B; Sanford, Rachel S; Yoshida, Masa-aki; Moroz, Leonid L

    2015-12-01

    RNA editing is a process of targeted alterations of nucleotides in all types of RNA molecules (e.g., rRNA, tRNA, mRNA, and miRNA). As a result, the transcriptional output differs from its genomic DNA template. RNA editing can be defined both by biochemical mechanisms and by enzymes that perform these reactions. There are high levels of RNA editing detected in the mammalian nervous system, suggesting that nervous systems use this mechanism to increase protein diversity, because the post-transcription modifications lead to new gene products with novel functions. By re-annotating the ctenophore genomes, we found that the number of predicted RNA-editing enzymes is comparable to the numbers in mammals, but much greater than in other non-bilaterian basal metazoans. However, the overall molecular diversity of RNA-editing enzymes in ctenophores is lower, suggesting a possible "compensation" by an expansion of the ADAT1-like subfamily in this lineage. In two genera of ctenophores, Pleurobrachia and Mnemiopsis, there are high levels of expression for RNA-editing enzymes in their aboral organs, the integrative center involved in control of locomotion and geotaxis. This finding supports the hypothesis that RNA editing is correlated with the complexity of tissues and behaviors. Smaller numbers of RNA-editing enzymes in Porifera and Placozoa also correlates with the primary absence of neural and muscular systems in these lineages. In ctenophores, the expansion of the RNA-editing machinery can also provide mechanisms that support the remarkable capacity for regeneration in these animals. In summary, despite their compact genomes, a wide variety of epigenomic mechanisms employed by ctenophores and other non-bilaterian basal metazoans can provide novel insights into the evolutionary origins of biological novelties. PMID:26089435

  7. Parallel Evolution and Lineage-Specific Expansion of RNA Editing in Ctenophores.

    Science.gov (United States)

    Kohn, Andrea B; Sanford, Rachel S; Yoshida, Masa-aki; Moroz, Leonid L

    2015-12-01

    RNA editing is a process of targeted alterations of nucleotides in all types of RNA molecules (e.g., rRNA, tRNA, mRNA, and miRNA). As a result, the transcriptional output differs from its genomic DNA template. RNA editing can be defined both by biochemical mechanisms and by enzymes that perform these reactions. There are high levels of RNA editing detected in the mammalian nervous system, suggesting that nervous systems use this mechanism to increase protein diversity, because the post-transcription modifications lead to new gene products with novel functions. By re-annotating the ctenophore genomes, we found that the number of predicted RNA-editing enzymes is comparable to the numbers in mammals, but much greater than in other non-bilaterian basal metazoans. However, the overall molecular diversity of RNA-editing enzymes in ctenophores is lower, suggesting a possible "compensation" by an expansion of the ADAT1-like subfamily in this lineage. In two genera of ctenophores, Pleurobrachia and Mnemiopsis, there are high levels of expression for RNA-editing enzymes in their aboral organs, the integrative center involved in control of locomotion and geotaxis. This finding supports the hypothesis that RNA editing is correlated with the complexity of tissues and behaviors. Smaller numbers of RNA-editing enzymes in Porifera and Placozoa also correlates with the primary absence of neural and muscular systems in these lineages. In ctenophores, the expansion of the RNA-editing machinery can also provide mechanisms that support the remarkable capacity for regeneration in these animals. In summary, despite their compact genomes, a wide variety of epigenomic mechanisms employed by ctenophores and other non-bilaterian basal metazoans can provide novel insights into the evolutionary origins of biological novelties.

  8. Repfinder: Finding approximately repeated scene elements for image editing

    KAUST Repository

    Cheng, Ming-Ming

    2010-07-26

    Repeated elements are ubiquitous and abundant in both manmade and natural scenes. Editing such images while preserving the repetitions and their relations is nontrivial due to overlap, missing parts, deformation across instances, illumination variation, etc. Manually enforcing such relations is laborious and error-prone. We propose a novel framework where user scribbles are used to guide detection and extraction of such repeated elements. Our detection process, which is based on a novel boundary band method, robustly extracts the repetitions along with their deformations. The algorithm only considers the shape of the elements, and ignores similarity based on color, texture, etc. We then use topological sorting to establish a partial depth ordering of overlapping repeated instances. Missing parts on occluded instances are completed using information from other instances. The extracted repeated instances can then be seamlessly edited and manipulated for a variety of high level tasks that are otherwise difficult to perform. We demonstrate the versatility of our framework on a large set of inputs of varying complexity, showing applications to image rearrangement, edit transfer, deformation propagation, and instance replacement. © 2010 ACM.

  9. Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity.

    Science.gov (United States)

    Tycko, Josh; Myer, Vic E; Hsu, Patrick D

    2016-08-01

    Advances in the development of delivery, repair, and specificity strategies for the CRISPR-Cas9 genome engineering toolbox are helping researchers understand gene function with unprecedented precision and sensitivity. CRISPR-Cas9 also holds enormous therapeutic potential for the treatment of genetic disorders by directly correcting disease-causing mutations. Although the Cas9 protein has been shown to bind and cleave DNA at off-target sites, the field of Cas9 specificity is rapidly progressing, with marked improvements in guide RNA selection, protein and guide engineering, novel enzymes, and off-target detection methods. We review important challenges and breakthroughs in the field as a comprehensive practical guide to interested users of genome editing technologies, highlighting key tools and strategies for optimizing specificity. The genome editing community should now strive to standardize such methods for measuring and reporting off-target activity, while keeping in mind that the goal for specificity should be continued improvement and vigilance. PMID:27494557

  10. Sex Differences in Cognitive Abilities. Fourth Edition

    Science.gov (United States)

    Halpern, Diane F.

    2011-01-01

    The fourth edition of "Sex Differences in Cognitive Abilities" critically examines the breadth of research on this complex and controversial topic, with the principal aim of helping the reader to understand where sex differences are found--and where they are not. Since the publication of the third edition, there have been many exciting and…

  11. Edit Distance to Monotonicity in Sliding Windows

    DEFF Research Database (Denmark)

    Chan, Ho-Leung; Lam, Tak-Wah; Lee, Lap Kei;

    2011-01-01

    Given a stream of items each associated with a numerical value, its edit distance to monotonicity is the minimum number of items to remove so that the remaining items are non-decreasing with respect to the numerical value. The space complexity of estimating the edit distance to monotonicity of a ...

  12. Non-GMO genetically edited crop plants.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Velasco, Riccardo; Kim, Jin-Soo; Viola, Roberto

    2015-09-01

    Direct delivery of purified Cas9 protein with guide RNA into plant cells, as opposed to plasmid-mediated delivery, displays high efficiency and reduced off-target effects. Following regeneration from edited cells, the ensuing plant is also likely to bypass genetically modified organism (GMO) legislation as the genome editing complex is degraded in the recipient cells.

  13. Books in Action: The Armed Services Editions.

    Science.gov (United States)

    Cole, John Y., Ed.

    In an effort to reach a wide audience, the Center for the Book in the Library of Congress presents this book in honor of the 40th anniversary celebration of the Armed Services Editions (ASE), the paperback books distributed during World War II. The titles of the essays and their authors are as follows: "The Armed Services Editions: An…

  14. Non-GMO genetically edited crop plants.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Velasco, Riccardo; Kim, Jin-Soo; Viola, Roberto

    2015-09-01

    Direct delivery of purified Cas9 protein with guide RNA into plant cells, as opposed to plasmid-mediated delivery, displays high efficiency and reduced off-target effects. Following regeneration from edited cells, the ensuing plant is also likely to bypass genetically modified organism (GMO) legislation as the genome editing complex is degraded in the recipient cells. PMID:25978870

  15. Applications of genome editing in insects

    Science.gov (United States)

    Insect genome editing was first reported 1991 in Drosophila melanogaster but the technology used was not portable to other species. Not until the recent development of facile, engineered DNA endonuclease systems has gene editing become widely available to insect scientists. Most applications in inse...

  16. Profs, Professionals Agree about Students' Editing Skills.

    Science.gov (United States)

    Fee, Frank; Russial, John; Auman Ann

    2003-01-01

    Considers where journalism educators should focus when they design editing curriculum. Examines what professors say is important for students to know about editing. Compares what professors at accredited programs say about necessary skills with what professional copy editors say is important. Concludes that professors and professionals are largely…

  17. Accounting for Independent Schools. Second Edition.

    Science.gov (United States)

    National Association of Independent Schools, Boston, MA.

    This is a thoroughly revised edition of the 1969 publication, "Accounting for Independent Schools," a guide that attempted to codify basic accounting principles and practices for specific application to independent schools. The focus of the second edition is more on refining practices than on initiating them, and more on extending the managerial…

  18. The Aldine Edition of Aristotle's De Sensu

    DEFF Research Database (Denmark)

    Bloch, David Kristian

    2006-01-01

    This small article examines the quality of and the textual foundation for the først printed edition ever of Aristotle's De Sensu et Sensibilibus, that is, Aldus Manutius' (1497).......This small article examines the quality of and the textual foundation for the først printed edition ever of Aristotle's De Sensu et Sensibilibus, that is, Aldus Manutius' (1497)....

  19. Editing Technical Proposals (The Friendly Editor).

    Science.gov (United States)

    Bush, Don

    1994-01-01

    Makes suggestions for editing technical proposals. Discusses the marketeers, the hierarchy of hype, how to save days, managing story boards, expediting a laborious process, teaching engineers to write, writing incrementally, the art group, and the editing task. Argues that the best proposals come from starting to write early. (SR)

  20. Efficient Communication Protocols for Deciding Edit Distance

    DEFF Research Database (Denmark)

    Jowhari, Hossein

    2012-01-01

    Parsing method of [5,6] in combination with the Karp-Rabin fingerprints. In addition to yielding non-trivial bounds for the edit distance problem, this paper suggest a new conceptual framework and raises new questions regarding the embeddability of edit distance into the Hamming cube which might...

  1. Adaptive sampling for mesh spectrum editing

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiang-jun; ZHANG Hong-xin; BAO Hu-jun

    2006-01-01

    A mesh editing framework is presented in this paper, which integrates Free-Form Deformation (FFD) and geometry signal processing. By using simplified model from original mesh, the editing task can be accomplished with a few operations. We take the deformation of the proxy and the position coordinates of the mesh models as geometry signal. Wavelet analysis is employed to separate local detail information gracefully. The crucial innovation of this paper is a new adaptive regular sampling approach for our signal analysis based editing framework. In our approach, an original mesh is resampled and then refined iteratively which reflects optimization of our proposed spectrum preserving energy. As an extension of our spectrum editing scheme,the editing principle is applied to geometry details transferring, which brings satisfying results.

  2. Fuel Cell Handbook, Fifth Edition

    Energy Technology Data Exchange (ETDEWEB)

    Energy and Environmental Solutions

    2000-10-31

    Progress continues in fuel cell technology since the previous edition of the Fuel Cell Handbook was published in November 1998. Uppermost, polymer electrolyte fuel cells, molten carbonate fuel cells, and solid oxide fuel cells have been demonstrated at commercial size in power plants. The previously demonstrated phosphoric acid fuel cells have entered the marketplace with more than 220 power plants delivered. Highlighting this commercial entry, the phosphoric acid power plant fleet has demonstrated 95+% availability and several units have passed 40,000 hours of operation. One unit has operated over 49,000 hours. Early expectations of very low emissions and relatively high efficiencies have been met in power plants with each type of fuel cell. Fuel flexibility has been demonstrated using natural gas, propane, landfill gas, anaerobic digester gas, military logistic fuels, and coal gas, greatly expanding market opportunities. Transportation markets worldwide have shown remarkable interest in fuel cells; nearly every major vehicle manufacturer in the U.S., Europe, and the Far East is supporting development. This Handbook provides a foundation in fuel cells for persons wanting a better understanding of the technology, its benefits, and the systems issues that influence its application. Trends in technology are discussed, including next-generation concepts that promise ultrahigh efficiency and low cost, while providing exceptionally clean power plant systems. Section 1 summarizes fuel cell progress since the last edition and includes existing power plant nameplate data. Section 2 addresses the thermodynamics of fuel cells to provide an understanding of fuel cell operation at two levels (basic and advanced). Sections 3 through 8 describe the six major fuel cell types and their performance based on cell operating conditions. Alkaline and intermediate solid state fuel cells were added to this edition of the Handbook. New information indicates that manufacturers have stayed

  3. AAO Observer - August 2011 Edition

    CERN Document Server

    Brough, Sarah

    2011-01-01

    This edition of the Australian Astronomical Observatory Observer contains articles on the commissioning of the new SAMI instrument giving the first hexabundle galaxy spectra; galaxy parameter variations across and through the 6dFGS Fundamental Plane; an introduction to the new Dragonfly stellar interferometer; an update on the RAdial VElocity (RAVE) survey at half a million spectra; the Magellanic Quasars Survey; the Integrated Photonic Spectrograph's first look at the heart of the Scorpion; using AAOMega to measure the age of the young open cluster IC2602; making MANIFEST fibres for the Giant Magellan Telescope and a Voyage through Filaments of Galaxies. The Observer also contains thoughts on diversity in the astronomy community and reports on the recent Supernovae and their Host Galaxies conference and the 2011 Science Meets Parliament. In addition there are the usual features of the AUSGO Corner, Epping News and Letter from Coona.

  4. 基于转录组测序数据识别黑猩猩RNA编辑位点%Identification of RNA Editing Sites in Chimpanzee by Transcriptome-wide Sequencing Data

    Institute of Scientific and Technical Information of China (English)

    王端青; 何涛; 汪莉; 王玉民; 邵卫东

    2012-01-01

    RNA editing is a widespread post-transcriptional modification mechanism that alters genetic information at the RNA level by nucleotide insertions, deletions or substitutions, which can contribute to the diversification of the transcriptome and proteome. Although tens of thousands of A-to-I RNA editing events have been found in humans, there is limited knowledge of RNA editing in other nonhuman primates. For exploring the mechanism as well as potential functions of the RNA editing events in chimpanzee, we identified RNA editing sites based on chimpanzee RNA-Seq data here. By aligning between RNA-Seq data and chimpanzee genome sequences with TopHat software, all RNA-DNA mismatch sites were regarded as a candidate set. Low quality sites were filtered out by using both genome and transcriptome sequencing quality scores. The other filters containing uncertainty of sequencing at 3'-terminial positions, read coverage, SNP sites and estimated editing level were also applied on the candidate set. Statistical tests based on the Binomial distribution and Bonferroni multiple testing correction were performed on each candidate site to remove random errors between genome and transcriptome. Then, we detected tissue- and sex-specific RNA editing sites using bioinformatics approaches based on the Fisher's exact test and the Bonferroni multiple testing correction. The Two Sample Logo software was used to analyze the feature of the sequences surrounding the RNA editing site. A total of 8 334 RNA editing sites were identified in chimpanzee transcriptome and all 12 possible categories of discordances were observed. The top four distributions were A-to-G, U-to-C, G-to-A and C-to-U editing sites, which contained 1 995, 1 452, 1 293 and 1 101 sites, respectively. Forty-one editing sites alter amino acid residues, one of them creates a new stop codon which may shorten the KRT31 protein and affect its activity. Three editing sites damage the binding of microRNA potentially. Six hundred and

  5. BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment.

    Science.gov (United States)

    Boel, Annekatrien; Steyaert, Woutert; De Rocker, Nina; Menten, Björn; Callewaert, Bert; De Paepe, Anne; Coucke, Paul; Willaert, Andy

    2016-01-01

    Targeted mutagenesis by the CRISPR/Cas9 system is currently revolutionizing genetics. The ease of this technique has enabled genome engineering in-vitro and in a range of model organisms and has pushed experimental dimensions to unprecedented proportions. Due to its tremendous progress in terms of speed, read length, throughput and cost, Next-Generation Sequencing (NGS) has been increasingly used for the analysis of CRISPR/Cas9 genome editing experiments. However, the current tools for genome editing assessment lack flexibility and fall short in the analysis of large amounts of NGS data. Therefore, we designed BATCH-GE, an easy-to-use bioinformatics tool for batch analysis of NGS-generated genome editing data, available from https://github.com/WouterSteyaert/BATCH-GE.git. BATCH-GE detects and reports indel mutations and other precise genome editing events and calculates the corresponding mutagenesis efficiencies for a large number of samples in parallel. Furthermore, this new tool provides flexibility by allowing the user to adapt a number of input variables. The performance of BATCH-GE was evaluated in two genome editing experiments, aiming to generate knock-out and knock-in zebrafish mutants. This tool will not only contribute to the evaluation of CRISPR/Cas9-based experiments, but will be of use in any genome editing experiment and has the ability to analyze data from every organism with a sequenced genome. PMID:27461955

  6. BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment

    Science.gov (United States)

    Boel, Annekatrien; Steyaert, Woutert; De Rocker, Nina; Menten, Björn; Callewaert, Bert; De Paepe, Anne; Coucke, Paul; Willaert, Andy

    2016-01-01

    Targeted mutagenesis by the CRISPR/Cas9 system is currently revolutionizing genetics. The ease of this technique has enabled genome engineering in-vitro and in a range of model organisms and has pushed experimental dimensions to unprecedented proportions. Due to its tremendous progress in terms of speed, read length, throughput and cost, Next-Generation Sequencing (NGS) has been increasingly used for the analysis of CRISPR/Cas9 genome editing experiments. However, the current tools for genome editing assessment lack flexibility and fall short in the analysis of large amounts of NGS data. Therefore, we designed BATCH-GE, an easy-to-use bioinformatics tool for batch analysis of NGS-generated genome editing data, available from https://github.com/WouterSteyaert/BATCH-GE.git. BATCH-GE detects and reports indel mutations and other precise genome editing events and calculates the corresponding mutagenesis efficiencies for a large number of samples in parallel. Furthermore, this new tool provides flexibility by allowing the user to adapt a number of input variables. The performance of BATCH-GE was evaluated in two genome editing experiments, aiming to generate knock-out and knock-in zebrafish mutants. This tool will not only contribute to the evaluation of CRISPR/Cas9-based experiments, but will be of use in any genome editing experiment and has the ability to analyze data from every organism with a sequenced genome. PMID:27461955

  7. NRP 7th Edition: Are You Prepared?

    Science.gov (United States)

    Zaichkin, Jeanette; Mccarney, Linda; Weiner, Gary

    2016-01-01

    The seventh edition of the American Academy of Pediatrics/American Heart Association Neonatal Resuscitation Program (NRP) materials must be in use by January 1, 2017. As in previous editions, changes in resuscitation science are based on an international review and consensus of current resuscitation science. The seventh edition NRP materials also include enhancements to training materials aimed at improving the quality of NRP instruction and providing the opportunity for ongoing education. A standardized approach to instructor training, an online Instructor Toolkit, eSim cases, and a new learning management system are among the new resources. PMID:27461196

  8. Graph edit distance from spectral seriation

    OpenAIRE

    Robles-Kelly, A; Hancock, E.R.

    2005-01-01

    This paper is concerned with computing graph edit distance. One of the criticisms that can be leveled at existing methods for computing graph edit distance is that they lack some of the formality and rigor of the computation of string edit distance. Hence, our aim is to convert graphs to string sequences so that string matching techniques can be used. To do this, we use a graph spectral seriation method to convert the adjacency matrix into a string or sequence order. We show how the serial or...

  9. On the computation of edit distance functions

    OpenAIRE

    Martin, Ryan R.

    2010-01-01

    The edit distance between two graphs on the same labeled vertex set is the size of the symmetric difference of the edge sets. The edit distance function of the hereditary property, $\\mathcal{H}$, is a function of $p\\in[0,1]$ and is the limit of the maximum normalized distance between a graph of density $p$ and $\\mathcal{H}$. This paper uses the symmetrization method of Sidorenko in order to compute the edit distance function of various hereditary properties. For any graph $H$, ${\\rm Forb}(H)$...

  10. Tethers in space handbook, second edition

    Science.gov (United States)

    Penzo, Paul A. (Editor); Ammann, Paul W. (Editor)

    1989-01-01

    The Tethers in Space Handbook, Second Edition represents an update to the initial volume issued in September 1986. As originally intended, this handbook is designed to serve as a reference manual for policy makers, program managers, educators, engineers, and scientists alike. It contains information for the uninitiated, providing insight into the fundamental behavior of tethers in space. For those familiar with space tethers, it includes a summary of past and ongoing studies and programs, a complete bibliography of tether publications, and names, addresses, and phone numbers of workers in the field. Perhaps its most valuable asset is the brief description of nearly 50 tether applications which have been proposed and analyzed over the past 10 years. The great variety of these applications, from energy generation to boosting satellites to gravity wave detection is an indication that tethers will play a significant part in the future of space development. This edition of the handbook preserves the major characteristics of the original; however, some significant rearrangements and additions have been made. The first section on Tether Programs has been brought up to date, and now includes a description of TSS-2, the aerodynamic NASA/Italian Space Agency (ASI) mission. Tether Applications follows, and this section has been substantially rearranged. First, the index and cross-reference for the applications have been simplified. Also, the categories have changed slightly, with Technology and Test changed to Aerodynamics, and the Constellations category removed. In reality, tether constellations may be applicable to many of the other categories, since it is simply a different way of using tethers. Finally, to separate out those applications which are obviously in the future, a Concepts category has been added. A new section included here on Conference Summaries recognizes the fact that the tether community is growing internationally, and that meetings provide a means of

  11. Getting Started with Isabelle/jEdit

    OpenAIRE

    Sternagel, Christian

    2012-01-01

    We give a beginner-oriented introduction to Isabelle/jEdit, providing motivation for using it as well as pointing at some differences to the traditional Proof General interface and current limitations.

  12. Specification Editing and Discovery Assistant Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The project will prototype a specification editing and discovery tool (SPEEDY) for C/C++ that will assist software developers with modular formal verification tasks...

  13. Prescott’s Microbiology, Eighth Edition

    OpenAIRE

    Joanne J. Dobbins

    2010-01-01

    Review of: Prescott’s Microbiology, Eighth Edition. Joanne M. Willey, Linda M. Sherwood, and Christopher J. Woolverton. 2011. McGraw-Hill Higher Education, NewYork, NY. 1070 pages. ISBN- 978-0-07-337526-7.

  14. KWIC Index of nuclear codes (1975 edition)

    International Nuclear Information System (INIS)

    It is a KWIC Index for 254 nuclear codes in the Nuclear Code Abstracts (1975 edition). The classification of nuclear codes and the form of index are the same as those in the Computer Programme Library at Ispra, Italy. (auth.)

  15. LabVIEW 8 student edition

    CERN Document Server

    Bishop, Robert H

    2007-01-01

    For courses in Measurement and Instrumentation, Electrical Engineering lab, and Physics and Chemistry lab. This revised printing has been updated to include new LabVIEW 8.2 Student Edition. National Instruments' LabVIEW is the defacto industry standard for test, measurement, and automation software solutions. With the Student Edition of LabVIEW, students can design graphical programming solutions to their classroom problems and laboratory experiments with software that delivers the graphical programming capabilites of the LabVIEW professional version. . The Student Edition is also compatible with all National Instruments data acquisition and instrument control hardware. Note: The LabVIEW Student Edition is available to students, faculty, and staff for personal educational use only. It is not intended for research, institutional, or commercial use. For more information about these licensing options, please visit the National Instruments website at (http:www.ni.com/academic/)

  16. Fine-Tuning Next-Generation Genome Editing Tools.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala; Maffei, Massimo; Malnoy, Mickael; Velasco, Riccardo; Kim, Jin-Soo

    2016-07-01

    The availability of genome sequences of numerous organisms and the revolution brought about by genome editing tools (e.g., ZFNs, TALENs, and CRISPR/Cas9 or RGENs) has provided a breakthrough in introducing targeted genetic changes both to explore emergent phenotypes and to introduce new functionalities. However, the wider application of these tools in biology, agriculture, medicine, and biotechnology is limited by off-target mutation effects. In this review, we compare available methods for detecting, measuring, and analyzing off-target mutations. Furthermore, we particularly focus on CRISPR/Cas9 regarding various methods, tweaks, and software tools available to nullify off-target effects. PMID:27167723

  17. Radar principles for the nonspecialist, 3rd edition

    CERN Document Server

    Toomay, John

    2004-01-01

    Radar Principles for the Non-specialist, Third Edition continues its popular tradition: to distill the very complex technology of radar into its fundamentals, tying them to the laws of nature on one end and to the most modern and complex systems on the other. It starts with electromagnetic propagation, describes a radar of the utmost simplicity, and derives the radar range equation from that simple radar. Once the range equation is available, the book attacks the meaning of each term in it, moving through antennas, detection and tracking, radar cross-section, waveforms andsignal proces

  18. Good edit similarity learning by loss minimization

    OpenAIRE

    Bellet, Aurélien; Habrard, Amaury; Sebban, Marc

    2012-01-01

    Similarity functions are a fundamental component of many learning algorithms. When dealing with string or tree-structured data, edit distancebased measures are widely used, and there exists a few methods for learning them from data. However, these methods offer no theoretical guarantee as to the generalization ability and discriminative power of the learned similarities. In this paper, we propose a loss minimization-based edit similarity learning approach, called GESL. It is driven by the not...

  19. Nuclear electronics laboratory manual 1989 edition

    International Nuclear Information System (INIS)

    This manual is a joint product of several electronics experts who have been associated with IAEA activity in this field for many years. It is based on the experience of conducting twenty-three training courses on nuclear electronics. Compared with the first edition, published 1984, this edition contains many new experiments, mainly on the advanced technical level. The total number of experiments and special projects is 58. Tabs and figs

  20. Applications of genome editing in insects.

    Science.gov (United States)

    Reid, William; O'Brochta, David A

    2016-02-01

    Insect genome editing was first reported 1991 in Drosophila melanogaster but the technology used was not portable to other species. Not until the recent development of facile, engineered DNA endonuclease systems has gene editing become widely available to insect scientists. Most applications in insects to date have been technical in nature but this is rapidly changing. Functional genomics and genetics-based insect control efforts will be major beneficiaries of the application of contemporary gene editing technologies. Engineered endonucleases like Cas9 make it possible to create powerful and effective gene drive systems that could be used to reduce or even eradicate specific insect populations. 'Best practices' for using Cas9-based editing are beginning to emerge making it easier and more effective to design and use but gene editing technologies still require traditional means of delivery in order to introduce them into somatic and germ cells of insects-microinjection of developing embryos. This constrains the use of these technologies by insect scientists. Insects created using editing technologies challenge existing governmental regulatory structures designed to manage genetically modified organisms. PMID:27436552

  1. [Textual research on the edition of WU Kun's books].

    Science.gov (United States)

    Wang, Xu-Guang; Lu, Xiang

    2013-03-01

    WU Kun is a famous physician of the Xin'an School. He wrote a 6-volume Yi fang kao (Textual Research on Recipes) in 1584, a 24-volume Wu zhu su wen (Wu's Annotation of Plain Questions) in 1594, a 6-volume Zhen fang liu ji (Six Collections of Acupuncture and Prescription) in 1618 block-printed and funded by CHENG Biao, and a 2-volume Mai yu (Language of Pulse) with writing date unknown. For Yi fang kao, there were 4 editions, including Ming-dynasty block-printed edition, Japanese and Korean block-printed edition, old hand-copied edition and modern printing edition. For Wu zhu su wen, there were 5 editions, Ming-Qing-dynasty block-printed edition, Japanese block-printed edition, old hand-copied edition, photocopy and modern edition. For Zhen fang liu ji, there were Ming-dynasty block-printed edition, hand-copied edition, photocopy and modern edition. Mai yu always was printed together with Yi fang kao, and its editions were same as those of Yi fang kao, except some modern printing edition with Mai yu excluded. PMID:24135480

  2. Statistical theory of signal detection

    CERN Document Server

    Helstrom, Carl Wilhelm; Costrell, L; Kandiah, K

    1968-01-01

    Statistical Theory of Signal Detection, Second Edition provides an elementary introduction to the theory of statistical testing of hypotheses that is related to the detection of signals in radar and communications technology. This book presents a comprehensive survey of digital communication systems. Organized into 11 chapters, this edition begins with an overview of the theory of signal detection and the typical detection problem. This text then examines the goals of the detection system, which are defined through an analogy with the testing of statistical hypotheses. Other chapters consider

  3. Book Review: New Perspectives on Technical Editing

    Science.gov (United States)

    Murphy, A. J. (Ed.); Sterken, Christiaan

    2012-08-01

    New Perspectives on Technical Editing by Avon J. Murphy (ed.) ISBN : 978-0895033949 (2010) Baywood Publishing Company Inc, Hardcover, 210 pages, 35.5 GBP This book presents a collection of 10 chapters dealing with diverse aspects of technical editing (ie, editorial planning, and analysis and structural changes made to other people's technological documents): research in technical editing, trends and teaching of technical editing, copyediting, and technical journal editing. The role and function of the modern journal and book editor is also dealt with in detail. Each chapter is written by an expert in the field: senior editors, university professors in technical communication, technical writers and linguists. The ever-evolving role of the editor is clearly elucidated in several historical reviews, and in the descriptions of the expectations for the future. A very striking aspect of this book is its extensive collection of bibliographic resources: every chapter lists dozens of very useful references, and the closing chapter, and annotated bibliography, contain many not so well known references, and are most useful. All in all, the book is a treasure trove listing more than 400 references, in addition to numerous webpage URLs embedded in the texts. The book is designed to help the reader to understand current practices and norms in technical editing, and to help to take action in editing as well as in teaching and educating would-be editors. The audience for this book thus includes editors and teachers, but also writers, researchers and students. A deep reading of this book will result in a better understanding of the difference between full technical editing and its much narrower component so well known as copyediting, and will convince any prospective editor that editing should not be undertaken if the people involved do not master the art of precision and accuracy in technical (as well as in human) communication, do not possess the technical know how and computer

  4. The Express-Lane Edit: Making Editing Useful for Young Adolescents

    Science.gov (United States)

    Anderson, Jeff

    2008-01-01

    Editing is a powerful tool for writers, but are our methods of teaching it really demonstrating that power for young adolescents? The author, frustrated with students' inability to edit, blames his own approach and, beginning with a grocery store epiphany, works to develop a more effective system. Elements of his successful approach include time…

  5. Improving Student Revising and Editing Skills through the Use of Peer Editing and Writing Conferencing.

    Science.gov (United States)

    Kolling, Ann

    This report describes instructional strategies that will improve the revising and editing skills of sixth grade students during the writing process. The literature review suggested improved instruction and evaluation through a writer's workshop approach, which would include a positive environment, mini-lessons, teacher modeling, peer editing, and…

  6. Intrusion Detection Systems

    CERN Document Server

    Pietro, Roberto Di

    2008-01-01

    In our world of ever-increasing Internet connectivity, there is an on-going threat of intrusion, denial of service attacks, or countless other abuses of computer and network resources. In particular, these threats continue to persist due to the flaws of current commercial intrusion detection systems (IDSs). Intrusion Detection Systems is an edited volume by world class leaders in this field. This edited volume sheds new light on defense alert systems against computer and network intrusions. It also covers integrating intrusion alerts within security policy framework for intrusion response, rel

  7. Triplex-mediated genome targeting and editing.

    Science.gov (United States)

    Reza, Faisal; Glazer, Peter M

    2014-01-01

    Genome targeting and editing in vitro and in vivo can be achieved through an interplay of exogenously introduced molecules and the induction of endogenous recombination machinery. The former includes a repertoire of sequence-specific binding molecules for targeted induction and appropriation of this machinery, such as by triplex-forming oligonucleotides (TFOs) or triplex-forming peptide nucleic acids (PNAs) and recombinagenic donor DNA, respectively. This versatile targeting and editing via recombination approach facilitates high-fidelity and low-off-target genome mutagenesis, repair, expression, and regulation. Herein, we describe the current state-of-the-art in triplex-mediated genome targeting and editing with a perspective towards potential translational and therapeutic applications. We detail several materials and methods for the design, delivery, and use of triplex-forming and recombinagenic molecules for mediating and introducing specific, heritable, and safe genomic modifications. Furthermore we denote some guidelines for endogenous genome targeting and editing site identification and techniques to test targeting and editing efficiency. PMID:24557900

  8. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA

    Science.gov (United States)

    Zhang, Yi; Liang, Zhen; Zong, Yuan; Wang, Yanpeng; Liu, Jinxing; Chen, Kunling; Qiu, Jin-Long; Gao, Caixia

    2016-01-01

    Editing plant genomes is technically challenging in hard-to-transform plants and usually involves transgenic intermediates, which causes regulatory concerns. Here we report two simple and efficient genome-editing methods in which plants are regenerated from callus cells transiently expressing CRISPR/Cas9 introduced as DNA or RNA. This transient expression-based genome-editing system is highly efficient and specific for producing transgene-free and homozygous wheat mutants in the T0 generation. We demonstrate our protocol to edit genes in hexaploid bread wheat and tetraploid durum wheat, and show that we are able to generate mutants with no detectable transgenes. Our methods may be applicable to other plant species, thus offering the potential to accelerate basic and applied plant genome-engineering research. PMID:27558837

  9. Introduction to nuclear science, second edition

    CERN Document Server

    Bryan, Jeff C.

    2013-01-01

    This book was written to provide students who have limited backgrounds in the physical sciences and math with an accessible textbook on nuclear science. Expanding on the foundation of the bestselling first edition, Introduction to Nuclear Science, Second Edition provides a clear and complete introduction to nuclear chemistry and physics, from basic concepts to nuclear power and medical applications. Incorporating suggestions from professors using this book for their courses, the author has created a new text that is approximately 60 percent larger and more comprehensive and flexible than the first.New to This Edition: Thorough review of nuclear forensics, radiology, gamma cameras, and decay through proton or neutron emission More detailed explanations of the necessary mathematics A chapter on dosimetry of radiation fields Expanded discussion of applications, introduced earlier in the text More in-depth coverage of nuclear reactors, including a new chapter examining more reactor types, their safety systems,...

  10. Transportation Energy Data Book, Edition 19

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    1999-09-01

    The Transportation Energy Data Book: Edition 19 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (http://www-cta.ornl.gov/data/tedb.htm).

  11. Prince2 2009 edition a pocket guide

    CERN Document Server

    Hedeman, Bert

    2010-01-01

    This Pocket Guide supplies a summary of the PRINCE2 method, to provide a quick introduction as well as a structured overview of the method;Main target Group for this pocket guide is anyone who wants to get to know the method PRINCE2 or a methodical approach for project management. The book is also very useful for members of a project management team on a project using the PRINCE2 method. Furthermore this pocket guide can be used as literature for the preparation of the PRINCE2 2009 Edition Foundation exam;This pocket guide is based on PRINCE2 2009 Edition;This pocket book deals with processes,

  12. RNA Editing and Drug Discovery for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Wei-Hsuan Huang

    2013-01-01

    Full Text Available RNA editing is vital to provide the RNA and protein complexity to regulate the gene expression. Correct RNA editing maintains the cell function and organism development. Imbalance of the RNA editing machinery may lead to diseases and cancers. Recently, RNA editing has been recognized as a target for drug discovery although few studies targeting RNA editing for disease and cancer therapy were reported in the field of natural products. Therefore, RNA editing may be a potential target for therapeutic natural products. In this review, we provide a literature overview of the biological functions of RNA editing on gene expression, diseases, cancers, and drugs. The bioinformatics resources of RNA editing were also summarized.

  13. [On two editions of Yunyu Xuanji and their source].

    Science.gov (United States)

    Deng, Yue-E

    2013-01-01

    Yunyu Xuanji is considered as one of the 400 key ancient books in the 'TCM Ancient Books Protection and Use Project' by the State Bureau of TCM. Two editions of this book are hand-written copies. The Qianyao edition was finished in the 52(nd) year of the Kangxi Period (1713). The other edition (Taoshi Xianyishukoucongshu) was probably done in the Late Qing Dynasty or the period of the Republic of China. By careful comparison, the contents of the two editions are basically the same, and only the preface of the former edition has been given some changes, which were probably made by later generations. The second manuscript was written in a more standard mode. Therefore the two editions were written according to the same literature and it is possible that the latter one is the copied edition of the Qianyao edition. PMID:23879984

  14. Experimental Stochatics (2nd edition)

    International Nuclear Information System (INIS)

    for teachers of computational stochastic methods, is the main contribution of this electronic monograph. However, both the book and software suffer from several severe problems. Firstly, I feel that the structure of the text is weak. Probably this is partly the result of the text from the CD-ROM being put into a book format, but the short paragraphs and poorly structured sentences destroy the reading experience. Secondly, although the software is functional, I believe that, like me, many users will be disappointed by the quality of the user interface and the visualizations. The opportunities to interact with the simulations are limited. Thirdly, the presentation is slightly old fashioned and lacking in pedagogical structure. For example, flow charts and Pascal programs are used to present algorithms. To conclude, I am surprised that this electronic monograph warranted a second edition in this form. Teachers may find the examples useful as a starting point, but students and researchers are advised to look elsewhere. (book review)

  15. FeynEdit - a tool for drawing Feynman diagrams

    OpenAIRE

    Hahn, T.; Lang, P.

    2007-01-01

    We describe the FeynEdit tool for drawing Feynman diagrams. Input and output is done using the LaTeX macros of FeynArts, which also implies that diagrams drawn by FeynArts can be edited with FeynEdit. The LaTeX code can be conveniently transferred using copy-and-paste.

  16. 45 CFR 73.735-705 - Writing and editing.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Writing and editing. 73.735-705 Section 73.735-705... Outside Activities § 73.735-705 Writing and editing. (a) Employees are encouraged to engage in outside writing and editing whether or not done for compensation, when such activity is not otherwise...

  17. Human Resources Administration: A School-Based Perspective. Fourth Edition

    Science.gov (United States)

    Smith, Richard

    2009-01-01

    Enhanced and updated, this Fourth Edition of Richard E. Smith's highly successful text examines the growing role of the principal in planning, hiring, staff development, supervision, and other human resource functions. The Fourth Edition includes new sections on ethics, induction, and the role of the mentor teacher. This edition also introduces…

  18. Soil Carbon Sequestration and the Greenhouse Effect (2nd Edition)

    Science.gov (United States)

    This volume is a second edition of the book “Soil Carbon Sequestration and The Greenhouse Effect”. The first edition was published in 2001 as SSSA Special Publ. #57. The present edition is an update of the concepts, processes, properties, practices and the supporting data. All chapters are new co...

  19. Spectral editing for in vivo 13C magnetic resonance spectroscopy

    Science.gov (United States)

    Xiang, Yun; Shen, Jun

    2012-01-01

    In vivo detection of carboxylic/amide carbons is a promising technique for studying cerebral metabolism and neurotransmission due to the very low RF power required for proton decoupling. In the carboxylic/amide region, however, there is severe spectral overlap between acetate C1 and glutamate C5, complicating studies that use acetate as an astroglia-specific substrate. There are no known in vivo MRS techniques that can spectrally resolve acetate C1 and glutamate C5 singlets. In this study, we propose to spectrally separate acetate C1 and glutamate C5 by a two-step J-editing technique after introducing homonuclear 13C- 13C scalar coupling between carboxylic/amide carbons and aliphatic carbons. By infusing [1,2- 13C 2]acetate instead of [1- 13C]acetate the acetate doublet can be spectrally edited because of the large separation between acetate C2 and glutamate C4 in the aliphatic region. This technique can be applied to studying acetate transport and metabolism in brain in the carboxylic/amide region without spectral interference.

  20. The staging system: Display and edit module

    Science.gov (United States)

    Edwards, E.; Bernier, L.

    1976-01-01

    The Display and Edit (D and E) Module described is one of six major modules being developed for the STAGING (STructural Analysis through Generalized INteractive Graphics) System. Several remarks are included concerning the computer environment and the architecture of the data base. The utility of this module is emphasized.

  1. Thermodynamics of Fluids Under Flow Second Edition

    CERN Document Server

    Jou, David; Criado-Sancho, Manuel

    2011-01-01

    This is the second edition of the book “Thermodynamics of Fluids under Flow,” which was published in 2000 and has now been corrected, expanded and updated. This is a companion book to our other title Extended irreversible thermodynamics (D. Jou, J. Casas-Vázquez and G. Lebon, Springer, 4th edition 2010), and of the textbook Understanding non-equilibrium thermodynamics (G. Lebon, D. Jou and J. Casas-Vázquez, Springer, 2008. The present book is more specialized than its counterpart, as it focuses its attention on the non-equilibrium thermodynamics of flowing fluids, incorporating non-trivial thermodynamic contributions of the flow, going beyond local equilibrium theories, i.e., including the effects of internal variables and of external forcing due to the flow. Whereas the book's first edition was much more focused on polymer solutions, with brief glimpses into ideal and real gases, the present edition covers a much wider variety of systems, such as: diluted and concentrated polymer solutions, polymer ble...

  2. The Landscape of Qualitative Research. Third Edition

    Science.gov (United States)

    Denzin, Norman K., Ed.; Lincoln, Yvonna, Ed.

    2007-01-01

    This book, the first volume of the paperback versions of the "The SAGE Handbook of Qualitative Research, Third Edition," takes a look at the field from a broadly theoretical perspective, and is composed of the Handbook's Parts I ("Locating the Field"), II ("Major Paradigms and Perspectives"), and VI ("The Future of Qualitative Research"). "The…

  3. Collecting and Interpreting Qualitative Materials. Third Edition

    Science.gov (United States)

    Denzin, Norman K., Ed.; Lincoln, Yvonna, Ed.

    2007-01-01

    This book is the third volume of the paperback versions of "The SAGE Handbook of Qualitative Research, Third Edition." This portion of the handbook considers the tasks of collecting, analyzing, and interpreting empirical materials, and comprises the Handbook's Parts IV ("Methods of Collecting and Analyzing Empirical Materials") and V ("The Art and…

  4. Science Editing in America: An Overview

    Institute of Scientific and Technical Information of China (English)

    Barbara Gastel

    2003-01-01

    @@ In America, science editing appears to be an increasingly recognized field. In what settings do American science editors work, and what kinds of work do they do ? What is their educational background? What style manuals and other resources do they use? What organizations serve them? What topics and issues do they find of professional interest?

  5. Handbook of Qualitative Research. Second Edition.

    Science.gov (United States)

    Denzin, Norman K., Ed.; Lincoln, Yvonna S., Ed.

    This handbook's second edition represents the state of the art for the theory and practice of qualitative inquiry. It features eight new topics, including autoethnography, critical race theory, applied ethnography, queer theory, and "testimonio"every chapter in the handbook has been thoroughly revised and updated. The book contains:"Preface" (1…

  6. Some aspects of RNA repair and editing

    Directory of Open Access Journals (Sweden)

    Kovalchuk M. V.

    2010-11-01

    Full Text Available All cellular RNA molecules are damaged at the scale of DNA molecules, or even more. In the present review the RNA damaging agents, some mechanisms of RNA repair and editing, their difference from DNA repair mechanisms have been discussed.

  7. The agents of natural genome editing

    Institute of Scientific and Technical Information of China (English)

    Guenther Witzany

    2011-01-01

    The DNA serves as a stable information storage medium and every protein which is needed by the cell is produced from this blueprint via an RNA intermediate code. More recently it was found that an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on RNA transcripts. Natural genome editing on one side is the competent agent*driven generation and integration of meaningful DNA nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing on the other side designates the integration of all RNA activities acting on RNA transcripts without altering DNA-encoded genes. If we take the genetic code seriously as a natural code, there must be agents that are competent to act on this code because no natural code codes itself as no natural language speaks itself. As code editing agents,viral and subviral agents have been suggested because there are several indicators that demonstrate viruses competent in both RNA and DNA natural genome editing.

  8. Prescott’s Microbiology, Eighth Edition

    Directory of Open Access Journals (Sweden)

    Joanne J. Dobbins

    2010-04-01

    Full Text Available Review of: Prescott’s Microbiology, Eighth Edition. Joanne M. Willey, Linda M. Sherwood, and Christopher J. Woolverton. 2011. McGraw-Hill Higher Education, NewYork, NY. 1070 pages. ISBN- 978-0-07-337526-7.

  9. A Model for Flexibly Editing CSCL Scripts

    Science.gov (United States)

    Sobreira, Pericles; Tchounikine, Pierre

    2012-01-01

    This article presents a model whose primary concern and design rationale is to offer users (teachers) with basic ICT skills an intuitive, easy, and flexible way of editing scripts. The proposal is based on relating an end-user representation as a table and a machine model as a tree. The table-tree model introduces structural expressiveness and…

  10. The NMC Horizon Report: 2014 Library Edition

    NARCIS (Netherlands)

    Johnson, L; Adams Becker, S.; Estrada, V.; Freeman, A.; van den Brekel, Guus

    2014-01-01

    The NMC Horizon Report: 2014 Library Edition, examines key trends, significant challenges, and emerging technologies for their potential impact on academic and research libraries worldwide. While there are many local factors affecting libraries, there are also issues that transcend regional boundari

  11. Critical Social Theories. 2nd Edition

    Science.gov (United States)

    Agger, Ben

    2006-01-01

    Praised for its clarity and accessibility, this fully updated edition of "Critical Social Theories" presents a comprehensive analysis of leading social and cultural theories today. Diverse perspectives are addressed from feminism and cultural studies to postmodernism and critical theory. Written accessibly for students and faculty, the second…

  12. Edit propagation using geometric relationship functions

    KAUST Repository

    Guerrero, Paul

    2014-03-01

    We propose a method for propagating edit operations in 2D vector graphics, based on geometric relationship functions. These functions quantify the geometric relationship of a point to a polygon, such as the distance to the boundary or the direction to the closest corner vertex. The level sets of the relationship functions describe points with the same relationship to a polygon. For a given query point, we first determine a set of relationships to local features, construct all level sets for these relationships, and accumulate them. The maxima of the resulting distribution are points with similar geometric relationships. We show extensions to handle mirror symmetries, and discuss the use of relationship functions as local coordinate systems. Our method can be applied, for example, to interactive floorplan editing, and it is especially useful for large layouts, where individual edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds of objects by propagating relatively few edit operations. © 2014 ACM 0730-0301/2014/03- ART15 $15.00.

  13. The NMC Horizon Report: 2013 Museum Edition

    Science.gov (United States)

    Johnson, L.; Adams Becker, S.; Freeman, A.

    2013-01-01

    The "NMC Horizon Report: 2013 Museum Edition," is a co-production with the Marcus Institute for Digital Education in the Arts (MIDEA), and examines six emerging technologies for their potential impact on and use in education and interpretation within the museum environment: BYOD (Bring Your Own Device), crowdsourcing, electronic…

  14. Genome Editing in Sugarcane: Challenges Ahead

    Science.gov (United States)

    Mohan, Chakravarthi

    2016-01-01

    Genome editing opens new and unique opportunities for researchers to enhance crop production. Until 2013, the zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) were the key tools used for genome editing applications. The advent of RNA-guided engineered nucleases - the type II clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 (CRISPR-associated) system from Streptococcus pyogenes holds great potential since it is simple, effective and more versatile than ZFNs and TALENs. CRISPR/Cas9 system has already been successfully employed in several crop plants. Use of these techniques is in its infant stage in sugarcane. Jung and Altpeter (2016) have reported TALEN mediated approach for the first time to reduce lignin content in sugarcane to make it amenable for biofuel production. This is so far the only report describing genome editing in sugarcane. Large genome size, polyploidy, low transformation efficiency, transgene silencing and lack of high throughput screening techniques are certainly great challenges for genome editing in sugarcane which would be discussed in detail in this review. PMID:27790238

  15. Does Money Matter in Education? Second Edition

    Science.gov (United States)

    Baker, Bruce D.

    2016-01-01

    This second edition policy brief revisits the long and storied literature on whether money matters in providing a quality education. It includes research released since the original brief in 2012 and covers a handful of additional topics. Increasingly, political rhetoric adheres to the unfounded certainty that money does not make a difference in…

  16. Triple-frequency TurboEdit Cycle-slip Processing Method of Weakening Ionospheric Activity

    Directory of Open Access Journals (Sweden)

    HUANG Lingyong

    2015-08-01

    Full Text Available The existing triple-frequency cycle-slip detection method usually can not detect and repair the cycle-slip correctly in the ionospheric activity phase or when the magnetic storm happening. To solve the problem, the triple-frequency TurboEdit method for weakening the ionospheric error is advanced based on the dual-frequency TurboEdit method. Both the triple-frequency geometry-free and ionospheric-free combination and second-order time-difference phase geometry-free combination in this algorithm can whittle the influence of ionospheric error effectively. And then, the triple-frequency data is used to validate this algorithm, the experiment results show that this method can weaken the ionospheric error and realize the no-difference dynamicreal-time cycle-slip detection and correction under ionospheric activity phase.

  17. Nuclear-physical data editing and analysis

    International Nuclear Information System (INIS)

    Full text: At the modern stage of high energy physics development, investigation of multiple production processes of particles and nucleus-fragments and their automatical editing becomes one of the central problems of high energy physics (elementary-particles). Enormous experimental information accumulated from various registering installation put global physical problems before physicists-experimenters. One of these problems -automatic editing and receiving of correct physical data and thereby to make scientific conclusions [1]. In the article, some questions of automatic editing of experimental data are presented. Modern automatic systems of mathematical editing of data are complex programme, consisting of various components, which are called in definite sequence [2]. The editing of experimental results on ECM is a complex process, connected with using of tens thousands of information storage devices (discs and cartridges) and other external memory equipment. For processing of experimental data the programme system complexes are prepared and created. This system is used for study of hypernuclear and multiparticle processes in different scientific research institutions of Commonwealth of Independent Countries and other countries abroad [3]. At the present in Andijan State University some of processors and methodic systems are used by students of Physics Department in preparing graduation papers. In particular, the dependence of average number of fragments from energy of particles bombarding nucleus-target was investigated. The investigations made in the framework of different models of nuclei, show slow increase of the number of nuclei-fragments, depending of the energy of bombarding particle [4]. In the further the similar systems for investigation and automation of rapid and superrapid reactions, as well as processes in solid and fluid crystals will be created [5]. (author)

  18. Cloud Properties of CERES-MODIS Edition 4 and CERES-VIIRS Edition 1

    Science.gov (United States)

    Sun-Mack, Sunny; Minnis, Patrick; Chang, Fu-Lung; Hong, Gang; Arduini, Robert; Chen, Yan; Trepte, Qing; Yost, Chris; Smith, Rita; Brown, Ricky; Chu, Churngwei; Heckert, Elizabeth; Gibson, Sharon; Heck, Patrick W.

    2015-01-01

    The Clouds and Earth's Radiant Energy System (CERES) analyzes MODerate-resolution Imaging Spectroradiometer (MODIS) data and Visible Infrared Imaging Radiometer Suite (VIIRS) to derive cloud properties that are combine with aerosol and CERES broadband flux data to create a multi-parameter data set for climate study. CERES has produced over 15 years of data from Terra and over 13 years of data from Aqua using the CERES-MODIS Edition-2 cloud retrieval algorithm. A recently revised algorithm, CERESMODIS Edition 4, has been developed and is now generating enhanced cloud data for climate research (over 10 years for Terra and 8 years for Aqua). New multispectral retrievals of properties are included along with a multilayer cloud retrieval system. Cloud microphysical properties are reported at 3 wavelengths, 0.65, 1.24, and 2.1 microns to enable better estimates of the vertical profiles of cloud water contents. Cloud properties over snow are retrieved using the 1.24-micron channel. A new CERES-VIIRS cloud retrieval package was developed for the VIIRS spectral complement and is currently producing the CERES-VIIRS Edition 1 cloud dataset. The results from CERES-MODIS Edition 4 and CERES-VIIRS Edition 1 are presented and compared with each other and other datasets, including CALIPSO, CloudSat and the CERES-MODIS Edition-2 results.

  19. Variable frequency of plastid RNA editing among ferns and repeated loss of uridine-to-cytidine editing from vascular plants.

    Science.gov (United States)

    Guo, Wenhu; Grewe, Felix; Mower, Jeffrey P

    2015-01-01

    The distinct distribution and abundance of C-to-U and U-to-C RNA editing among land plants suggest that these two processes originated and evolve independently, but the paucity of information from several key lineages limits our understanding of their evolution. To examine the evolutionary diversity of RNA editing among ferns, we sequenced the plastid transcriptomes from two early diverging species, Ophioglossum californicum and Psilotum nudum. Using a relaxed automated approach to minimize false negatives combined with manual inspection to eliminate false positives, we identified 297 C-to-U and three U-to-C edit sites in the O. californicum plastid transcriptome but only 27 C-to-U and no U-to-C edit sites in the P. nudum plastid transcriptome. A broader comparison of editing content with the leptosporangiate fern Adiantum capillus-veneris and the hornwort Anthoceros formosae uncovered large variance in the abundance of plastid editing, indicating that the frequency and type of RNA editing is highly labile in ferns. Edit sites that increase protein conservation among species are more abundant and more efficiently edited than silent and non-conservative sites, suggesting that selection maintains functionally important editing. The absence of U-to-C editing from P. nudum plastid transcripts and other vascular plants demonstrates that U-to-C editing loss is a recurrent phenomenon in vascular plant evolution.

  20. Measurement and detection of radiation

    CERN Document Server

    Tsoulfanidis, Nicholas

    2011-01-01

    This is an update of the standard textbook for the field of radiation measurement. It includes illustrative examples and new problems. The research and applications of nuclear instrumentation have grown substantially since publication of the previous editions. With the miniaturization of equipment, increased speed of electronic components, and more sophisticated software, radiation detection systems are now more productively used in many disciplines, including nuclear nonproliferation, homeland security, and nuclear medicine. Continuing in the tradition of its bestselling predecessors, "Measurement and Detection of Radiation, Third Edition" illustrates the fundamentals of nuclear interactions and radiation detection with a multitude of examples and problems. It offers a clearly written, accessible introduction to nuclear instrumentation concepts. The following are new to the third edition: a new chapter on the latest applications of radiation detection, covering nuclear medicine, dosimetry, health physics, no...

  1. Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing.

    Science.gov (United States)

    Miyaoka, Yuichiro; Berman, Jennifer R; Cooper, Samantha B; Mayerl, Steven J; Chan, Amanda H; Zhang, Bin; Karlin-Neumann, George A; Conklin, Bruce R

    2016-01-01

    Precise genome-editing relies on the repair of sequence-specific nuclease-induced DNA nicking or double-strand breaks (DSBs) by homology-directed repair (HDR). However, nonhomologous end-joining (NHEJ), an error-prone repair, acts concurrently, reducing the rate of high-fidelity edits. The identification of genome-editing conditions that favor HDR over NHEJ has been hindered by the lack of a simple method to measure HDR and NHEJ directly and simultaneously at endogenous loci. To overcome this challenge, we developed a novel, rapid, digital PCR-based assay that can simultaneously detect one HDR or NHEJ event out of 1,000 copies of the genome. Using this assay, we systematically monitored genome-editing outcomes of CRISPR-associated protein 9 (Cas9), Cas9 nickases, catalytically dead Cas9 fused to FokI, and transcription activator-like effector nuclease at three disease-associated endogenous gene loci in HEK293T cells, HeLa cells, and human induced pluripotent stem cells. Although it is widely thought that NHEJ generally occurs more often than HDR, we found that more HDR than NHEJ was induced under multiple conditions. Surprisingly, the HDR/NHEJ ratios were highly dependent on gene locus, nuclease platform, and cell type. The new assay system, and our findings based on it, will enable mechanistic studies of genome-editing and help improve genome-editing technology. PMID:27030102

  2. Cucumber, melon, pumpkin, and squash: are rules of editing in flowering plants chloroplast genes so well known indeed?

    Science.gov (United States)

    Guzowska-Nowowiejska, Magdalena; Fiedorowicz, Ewa; Plader, Wojciech

    2009-04-01

    The similarities and differences in the chloroplast genes editing patterns of four species from one family (and two genera), which is the first-ever attempt at comparison of such data in closely related species, is discussed. The effective use of the chloroplast genes editing patterns in evolutionary studies, especially in evaluating the kinship between closely related species, is thereby proved. The results indicate that differences in editing patterns between different genera (Cucumis and Cucurbita) exist, and some novel editing sites can be identified even now. However, surprising is the fact of finding editing in the codon for Arg (in flowering plants detected before only in Cuscuta reflexa chloroplast genome, Funk et al.,[Funk H.T., Berg S., Krupinska K., Maier U.G. and Krause K., 2007. Complete DNA sequences of the plastid genomes of two parasitic flowering plants species, Cuscuta reflexa and Cuscuta gronovi. BMC Plant Biol. 7:45, doi: 10.1186/1471-2229-7-45.]), which was believed to have been lost during evolution before the emergence of angiosperms. In addition, the existence of silent editing in plant chloroplasts has been confirmed, and some probable reasons for its presence are pointed out herein.

  3. Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets

    Directory of Open Access Journals (Sweden)

    Quagliariello Carla

    2008-03-01

    Full Text Available Abstract Background In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded amino acid residues. Sites undergoing RNA editing evolve at a higher rate than sites not modified by the process. As a result, editing sites strongly affect the evolution of plant mitochondrial genomes, representing an important source of sequence variability and potentially informative characters. To date no clear and convincing evidence has established whether or not editing sites really affect the topology of reconstructed phylogenetic trees. For this reason, we investigated here the effect of RNA editing on the tree building process of twenty different plant mitochondrial gene sequences and by means of computer simulations. Results Based on our simulation study we suggest that the editing ‘noise’ in tree topology inference is mainly manifested at the cDNA level. In particular, editing sites tend to confuse tree topologies when artificial genomic and cDNA sequences are generated shorter than 500 bp and with an editing percentage higher than 5.0%. Similar results have been also obtained with genuine plant mitochondrial genes. In this latter instance, indeed, the topology incongruence increases when the editing percentage goes up from about 3.0 to 14.0%. However, when the average gene length is higher than 1,000 bp (rps3, matR and atp1 no differences in the comparison between inferred genomic and cDNA topologies could be detected. Conclusions Our findings by the here reported in silico and in vivo computer simulation system seem to strongly suggest that editing sites contribute in the generation of misleading phylogenetic trees if the analyzed mitochondrial gene sequence is highly edited (higher than 3.0% and reduced in length (shorter than 500 bp. In the current lack of direct experimental evidence the results

  4. Sentence-Level Rewriting Detection

    Science.gov (United States)

    Zhang, Fan; Litman, Diane

    2014-01-01

    Writers usually need iterations of revisions and edits during their writings. To better understand the process of rewriting, we need to know what has changed be-tween the revisions. Prior work mainly focuses on detecting corrections within sentences, which is at the level of words or phrases. This paper proposes to detect revision changes at the…

  5. Building java programs (3rd edition)

    CERN Document Server

    Reges, Stuart

    2013-01-01

    Building Java Programs: A Back to Basics Approach, Third Edition, introduces novice programmers to basic constructs and common pitfalls by emphasizing the essentials of procedural programming, problem solving, and algorithmic reasoning. By using objects early to solve interesting problems and defining objects later in the course, Building Java Programs develops programming knowledge for a broad audience. NEW! This edition is available with MyProgrammingLab, an innovative online homework and assessment tool. Through the power of practice and immediate personalized feedback, MyProgrammingLab helps students fully grasp the logic, semantics, and syntax of programming. Note: If you are purchasing the standalone text or electronic version, MyProgrammingLab does not come automatically packaged with the text. To purchase MyProgrammingLab, please visit: myprogramminglab.com or you can purchase a package of the physical text + MyProgrammingLab by searching the Pearson Higher Education web site. MyProgrammi...

  6. Transportation Energy Data Book, Edition 18

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy C.

    1998-09-01

    The Transportation Energy Data Book: Edition 18 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. This edition of the Data Book has 11 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 - energy Chapter 3 - emissions; Chapter 4 - transportation and the economy; Chapter 5 - highway vehicles; Chapter 6 - Light vehicles; Chapter 7 - heavy vehicles; Chapter 8 - alternative fuel vehicles; Chapter 9 - fleet vehicles; Chapter 10 - household vehicles; and Chapter 11 - nonhighway modes. The sources used represent the latest available data.

  7. Motion Editing for Time-Varying Mesh

    Science.gov (United States)

    Xu, Jianfeng; Yamasaki, Toshihiko; Aizawa, Kiyoharu

    2008-12-01

    Recently, time-varying mesh (TVM), which is composed of a sequence of mesh models, has received considerable interest due to its new and attractive functions such as free viewpoint and interactivity. TVM captures the dynamic scene of the real world from multiple synchronized cameras. However, it is expensive and time consuming to generate a TVM sequence. In this paper, an editing system is presented to reuse the original data, which reorganizes the motions to obtain a new sequence based on the user requirements. Hierarchical motion structure is observed and parsed in TVM sequences. Then, the representative motions are chosen into a motion database, where a motion graph is constructed to connect those motions with smooth transitions. After the user selects some desired motions from the motion database, the best paths are searched by a modified Dijkstra algorithm to achieve a new sequence. Our experimental results demonstrate that the edited sequences are natural and smooth.

  8. Motion Editing for Time-Varying Mesh

    Directory of Open Access Journals (Sweden)

    Kiyoharu Aizawa

    2008-08-01

    Full Text Available Recently, time-varying mesh (TVM, which is composed of a sequence of mesh models, has received considerable interest due to its new and attractive functions such as free viewpoint and interactivity. TVM captures the dynamic scene of the real world from multiple synchronized cameras. However, it is expensive and time consuming to generate a TVM sequence. In this paper, an editing system is presented to reuse the original data, which reorganizes the motions to obtain a new sequence based on the user requirements. Hierarchical motion structure is observed and parsed in TVM sequences. Then, the representative motions are chosen into a motion database, where a motion graph is constructed to connect those motions with smooth transitions. After the user selects some desired motions from the motion database, the best paths are searched by a modified Dijkstra algorithm to achieve a new sequence. Our experimental results demonstrate that the edited sequences are natural and smooth.

  9. Engineering Delivery Vehicles for Genome Editing.

    Science.gov (United States)

    Nelson, Christopher E; Gersbach, Charles A

    2016-06-01

    The field of genome engineering has created new possibilities for gene therapy, including improved animal models of disease, engineered cell therapies, and in vivo gene repair. The most significant challenge for the clinical translation of genome engineering is the development of safe and effective delivery vehicles. A large body of work has applied genome engineering to genetic modification in vitro, and clinical trials have begun using cells modified by genome editing. Now, promising preclinical work is beginning to apply these tools in vivo. This article summarizes the development of genome engineering platforms, including meganucleases, zinc finger nucleases, TALENs, and CRISPR/Cas9, and their flexibility for precise genetic modifications. The prospects for the development of safe and effective viral and nonviral delivery vehicles for genome editing are reviewed, and promising advances in particular therapeutic applications are discussed.

  10. The Challenge of Editing Einstein's Scientific Manuscripts

    OpenAIRE

    Sauer, Tilman

    2004-01-01

    Einstein's research manuscripts provide important insights into his exceptional creativity. At the same time, they can present difficulties for a publication in the documentary edition of the Collected Papers of Albert Einstein (CPAE). The problems are illustrated by discussing how some important examples of Einstein's research manuscripts have been included in previous volumes of the CPAE series: his Scratch Notebook from the years 1910-1914, his so-called Zurich Notebook from 1912, document...

  11. Selective access and editing in a database

    Science.gov (United States)

    Maluf, David A. (Inventor); Gawdiak, Yuri O. (Inventor)

    2010-01-01

    Method and system for providing selective access to different portions of a database by different subgroups of database users. Where N users are involved, up to 2.sup.N-1 distinguishable access subgroups in a group space can be formed, where no two access subgroups have the same members. Two or more members of a given access subgroup can edit, substantially simultaneously, a document accessible to each member.

  12. Learning Good Edit Similarities with Generalization Guarantees

    OpenAIRE

    Bellet, Aurélien; Habrard, Amaury; Sebban, Marc

    2011-01-01

    Similarity and distance functions are essential to many learning algorithms, thus training them has attracted a lot of interest. When it comes to dealing with structured data (e.g., strings or trees), edit similarities are widely used, and there exists a few methods for learning them. However, these methods offer no theoretical guarantee as to the generalization performance and discriminative power of the resulting similarities. Recently, a theory of learning with good similarity functions wa...

  13. Parallel OCR for Ancient Greek Critical Editions

    OpenAIRE

    Del Grosso, Angelo; Boschetti, Federico

    2012-01-01

    This project is focused on the parallelization of OCR processes applied to Ancient Greek critical editions. Two experiments have been performed. The first experiment is related to parameters differently tuned on the nodes of the grid, in order to identify the best combination that improves the accuracy of the recognition. The second experiment concerns the application of OCR with the best parameters on sample pages by a divide et impera strategy. Results related to the performances of the par...

  14. ELECTRONIC EDITIONS OF MATHEMATICAL WORKS IN SERBIA

    OpenAIRE

    D. Blagojevic; Ž. Mijajlovic; Z. Ognjanovic

    2005-01-01

    The paper describes two ongoing projects carried out by the Mathematical Institute of Serbian Academy of Science and Arts, Belgrade and the Faculty of Mathematics, Belgrade. The projects concern building of electronic resources and presentations of electronic editions of mathematical works in Serbia. The first project is related to retro digitization of old books, articles and the other mathematical works and development of the corresponding virtual library. In the second project a database a...

  15. Edit Distance to Monotonicity in Sliding Windows

    CERN Document Server

    Chan, Ho-Leung; Lee, Lap-Kei; Pan, Jiangwei; Ting, Hing-Fung; Zhang, Qin

    2011-01-01

    Given a stream of items each associated with a numerical value, its edit distance to monotonicity is the minimum number of items to remove so that the remaining items are non-decreasing with respect to the numerical value. The space complexity of estimating the edit distance to monotonicity of a data stream is becoming well-understood over the past few years. Motivated by applications on network quality monitoring, we extend the study to estimating the edit distance to monotonicity of a sliding window covering the $w$ most recent items in the stream for any $w \\ge 1$. We give a deterministic algorithm which can return an estimate within a factor of $(4+\\eps)$ using $O(\\frac{1}{\\eps^2} \\log^2(\\eps w))$ space. We also extend the study in two directions. First, we consider a stream where each item is associated with a value from a partial ordered set. We give a randomized $(4+\\epsilon)$-approximate algorithm using $O(\\frac{1}{\\epsilon^2} \\log \\epsilon^2 w \\log w)$ space. Second, we consider an out-of-order strea...

  16. Transportation Energy Data Book. Edition 33

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Susan E. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Boundy, Robert Gary [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-07-01

    The Transportation Energy Data Book: Edition 33 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  17. Transportation Energy Data Book: Edition 34

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Susan E [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Boundy, Robert Gary [Roltek, Inc., Clinton, TN (United States)

    2015-08-01

    The Transportation Energy Data Book: Edition 34 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  18. Transportation Energy Data Book: Edition 32

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2013-08-01

    The Transportation Energy Data Book: Edition 32 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  19. Technology Roadmap: Wind Energy. 2013 edition

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-07-01

    The IEA Wind Power Technology Roadmap 2013 Edition recognises the very significant progress made since the first edition was published in 2009. The technology continues to improve rapidly, and costs of generation from land-based wind installations continue to fall. Wind power is now being deployed in countries with good resources without any dedicated financial incentives. The 2013 Edition targets an increased share (15% to 18%) of global electricity to be provided by wind power in 2050, compared to 12% in the original roadmap of 2009. However, increasing levels of low-cost wind still require predictable, supportive regulatory environments and appropriate market designs. The challenges of integrating higher levels of variable wind power into the grid need to be addressed. For offshore wind, much remains to be done to develop appropriate large-scale systems and to reduce costs. The 2013 Wind Power Roadmap also provides updated analysis on the barriers that exist for the technology and suggests ways to address them, including legal and regulatory recommendations.

  20. Transportation Energy Data Book: Edition 31

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2012-08-01

    The Transportation Energy Data Book: Edition 31 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  1. Genome Editing in Human Pluripotent Stem Cells.

    Science.gov (United States)

    Smith, Cory; Ye, Zhaohui; Cheng, Linzhao

    2016-01-01

    Pluripotent stem cells (PSCs), defined by their capacity for self-renewal and differentiation into all cell types, are an integral tool for basic biological research and disease modeling. However, full use of PSCs for research and regenerative medicine requires the ability to precisely edit their DNA to correct disease-causing mutations and for functional analysis of genetic variations. Recent advances in DNA editing of human stem cells (including PSCs) have benefited from the use of designer nucleases capable of making double-strand breaks (DSBs) at specific sequences that stimulate endogenous DNA repair. The clustered, regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has become the preferred designer nuclease for genome editing in human PSCs and other cell types. Here we describe the principles for designing a single guide RNA to uniquely target a gene of interest and describe strategies for disrupting, inserting, or replacing a specific DNA sequence in human PSCs. The improvements in efficiency and ease provided by these techniques allow individuals to precisely engineer PSCs in a way previously limited to large institutes and core facilities. PMID:27037079

  2. Transportation Energy Data Book: Edition 26

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL

    2007-07-01

    The Transportation Energy Data Book: Edition 26 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 - energy; Chapter 3 - highway vehicles; Chapter 4 - light vehicles; Chapter 5 - heavy vehicles; Chapter 6 - alternative fuel vehicles; Chapter 7 - fleet vehicles; Chapter 8 - household vehicles; and Chapter 9- nonhighway modes; Chapter 10 - transportation and the economy; Chapter 11 - greenhouse gas emissions; and Chapter 12 - criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  3. Transportation Energy Data Book: Edition 25

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL

    2006-06-01

    The Transportation Energy Data Book: Edition 25 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 - energy; Chapter 3 - highway vehicles; Chapter 4 - light vehicles; Chapter 5 - heavy vehicles; Chapter 6 - alternative fuel vehicles; Chapter 7 - fleet vehicles; Chapter 8 - household vehicles; and Chapter 9- nonhighway modes; Chapter 10 - transportation and the economy; Chapter 11 - greenhouse gas emissions; and Chapter 12 - criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  4. Transportation Energy Data Book: Edition 24

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    2005-03-08

    The ''Transportation Energy Data Book: Edition 24'' is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2--energy; Chapter 3--highway vehicles; Chapter 4--light vehicles; Chapter 5--heavy vehicles; Chapter 6--alternative fuel vehicles; Chapter 7--fleet vehicles; Chapter 8--household vehicles; and Chapter 9--nonhighway modes; Chapter 10--transportation and the economy; Chapter 11--greenhouse gas emissions; and Chapter 12--criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  5. Transportation Energy Data Book: Edition 23

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    2003-10-24

    The ''Transportation Energy Data Book: Edition 23'' is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (www-cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2--energy; Chapter 3--highway vehicles; Chapter 4--light vehicles; Chapter 5--heavy vehicles; Chapter 6--alternative fuel vehicles; Chapter 7--fleet vehicles; Chapter 8--household vehicles; and Chapter 9--nonhighway modes; Chapter 10--transportation and the economy; Chapter 11--greenhouse gas emissions; and Chapter 12--criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  6. Transportation Energy Data Book (Edition 20)

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    2000-10-09

    The ''Transportation Energy Data Book: Edition 20'' is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (www-cta.ornl.gov/data/tedb.htm). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2--energy; Chapter 3--greenhouse gas emissions; Chapter 4--criteria pollutant emissions; Chapter 5--transportation and the economy; Chapter 6--highway vehicles; Chapter 7--light vehicles; Chapter 8--heavy vehicles; Chapter 9--alternative fuel vehicles; Chapter 10--fleet vehicles; Chapter 11--household vehicles; and Chapter 12--nonhighway modes. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  7. Transportation Energy Data Book: Edition 21

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    2001-09-13

    The ''Transportation Energy Data Book: Edition 21'' is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (www-cta.ornl.gov/data/tedb.htm). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2--energy; Chapter 3--greenhouse gas emissions; Chapter 4--criteria pollutant emissions; Chapter 5--transportation and the economy; Chapter 6--highway vehicles; Chapter 7--light vehicles; Chapter 8--heavy vehicles; Chapter 9--alternative fuel vehicles; Chapter 10--fleet vehicles; Chapter 11--household vehicles; and Chapter 12--nonhighway modes. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  8. Transportation Energy Data Book: Edition 29

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2010-07-01

    The Transportation Energy Data Book: Edition 29 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  9. Transportation Energy Data Book: Edition 30

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2011-07-01

    The Transportation Energy Data Book: Edition 30 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  10. Transportation Energy Data Book: Edition 27

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2008-06-01

    The Transportation Energy Data Book: Edition 27 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; and Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  11. Transportation Energy Data Book: Edition 28

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2009-06-01

    The Transportation Energy Data Book: Edition 28 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with U.S Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program and the Hydrogen, Fuel Cells, and Infrastructure Technologies Program. Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; and Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  12. TALEN gene editing takes aim on HIV.

    Science.gov (United States)

    Benjamin, Ronald; Berges, Bradford K; Solis-Leal, Antonio; Igbinedion, Omoyemwen; Strong, Christy L; Schiller, Martin R

    2016-09-01

    Transcription activator-like effector nucleases (TALENs) are one of several types of programmable, engineered nucleases that bind and cleave specific DNA sequences. Cellular machinery repairs the cleaved DNA by introducing indels. In this review, we emphasize the potential, explore progress, and identify challenges in using TALENs as a therapeutic tool to treat HIV infection. TALENs have less off-target editing and can be more effective at tolerating HIV escape mutations than CRISPR/Cas-9. Scientists have explored TALEN-mediated editing of host genes such as viral entry receptors (CCR5 and CXCR4) and a protein involved in proviral integration (LEDGF/p75). Viral targets include the proviral DNA, particularly focused on the long terminal repeats. Major challenges with translating gene therapy from bench to bedside are improving cleavage efficiency and delivery, while minimizing off-target editing, cytotoxicity, and immunogenicity. However, rapid improvements in TALEN technology are enhancing cleavage efficiency and specificity. Therapeutic testing in animal models of HIV infection will help determine whether TALENs are a viable HIV treatment therapy. TALENs or other engineered nucleases could shift the therapeutic paradigm from life-long antiretroviral therapy toward eradication of HIV infection.

  13. A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells

    OpenAIRE

    Findlay, Scott D.; Vincent, Krista M.; Jennifer R. Berman; Postovit, Lynne-Marie

    2016-01-01

    The rapid adoption of gene editing tools such as CRISPRs and TALENs for research and eventually therapeutics necessitates assays that can rapidly detect and quantitate the desired alterations. Currently, the most commonly used assay employs “mismatch nucleases” T7E1 or “Surveyor” that recognize and cleave heteroduplexed DNA amplicons containing mismatched base-pairs. However, this assay is prone to false positives due to cancer-associated mutations and/or SNPs and requires large amounts of st...

  14. CRISPR/Cas9-Mediated Genome Editing in Soybean Hairy Roots.

    Directory of Open Access Journals (Sweden)

    Yupeng Cai

    Full Text Available As a new technology for gene editing, the CRISPR (clustered regularly interspaced short palindromic repeat/Cas (CRISPR-associated system has been rapidly and widely used for genome engineering in various organisms. In the present study, we successfully applied type II CRISPR/Cas9 system to generate and estimate genome editing in the desired target genes in soybean (Glycine max (L. Merrill.. The single-guide RNA (sgRNA and Cas9 cassettes were assembled on one vector to improve transformation efficiency, and we designed a sgRNA that targeted a transgene (bar and six sgRNAs that targeted different sites of two endogenous soybean genes (GmFEI2 and GmSHR. The targeted DNA mutations were detected in soybean hairy roots. The results demonstrated that this customized CRISPR/Cas9 system shared the same efficiency for both endogenous and exogenous genes in soybean hairy roots. We also performed experiments to detect the potential of CRISPR/Cas9 system to simultaneously edit two endogenous soybean genes using only one customized sgRNA. Overall, generating and detecting the CRISPR/Cas9-mediated genome modifications in target genes of soybean hairy roots could rapidly assess the efficiency of each target loci. The target sites with higher efficiencies can be used for regular soybean transformation. Furthermore, this method provides a powerful tool for root-specific functional genomics studies in soybean.

  15. The levels of edit. [technical writing in science

    Science.gov (United States)

    Vanburen, R.; Buehler, M. F.; Wallenbrock, D. (Editor)

    1976-01-01

    The editorial process is analyzed, and five levels of edit are identified. These levels represent cumulative combinations of nine types of edit: (1) coordination, (2) policy, (3) integrity, (4) screening, (5) copy clarification, (6) Mechanical Style, (7) Language, and (9) substantive. The levels and types of edit, although developed for specific use with external reports at the Jet Propulsion Laboratory, cover the general range of technical editing, especially as it applies to an in-house technical publications organization. Each type of edit is set forth in terms of groups of actions to be performed by the editor. The edit-level concept has enhanced understanding and communication among editors, authors, and publications managers concerning the specific editorial work to be done on each manuscript. It has also proved useful as a management tool for estimating and monitoring cost.

  16. REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla

    2011-03-01

    RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/.

  17. Tree edit distance as a baseline approach for paraphrase representation

    OpenAIRE

    Vila Rigat, Marta; Dras, Mark

    2012-01-01

    Finding an adequate paraphrase representation formalism is a challenging issue in Natural Language Processing. In this paper, we analyse the performance of Tree Edit Distance as a paraphrase representation baseline. Our experiments using Edit Distance Textual Entailment Suite show that, as Tree Edit Distance consists of a purely syntactic approach, paraphrase alternations not based on structural reorganizations do not find an adequate representation. They also show that there is much scope fo...

  18. Learning Stochastic Edit Distance: application in handwritten character recognition

    OpenAIRE

    Oncina, Jose; Sebban, Marc

    2006-01-01

    Many pattern recognition algorithms are based on the nearest neighbour search and use the well known edit distance, for which the primitive edit costs are usually fixed in advance. In this article, we aim at learning an unbiased stochastic edit distance in the form of a finite-state transducer from a corpus of (input,output) pairs of strings. Contrary to the other standard methods, which generally use the Expectation Maximisation algorithm, our algorithm learns a transducer independently on t...

  19. 5. Defining Electronic Editions: A Historical and Functional Perspective

    OpenAIRE

    Vanhoutte, Edward

    2013-01-01

    1. Introduction Since Peter Robinson published the first electronic edition in a series designed to accommodate all of Chaucer’s Canterbury Tales, he has been theorizing and writing about the nature and definition of electronic editions. Along with Jerome McGann and others, he has been at the centre of the debate on electronic textual editing since he began work on the collation and textual criticism of Icelandic manuscripts, for which he developed programs collectively called Collate. Becaus...

  20. Pentatricopeptide repeat proteins involved in plant organellar RNA editing

    OpenAIRE

    Yagi, Yusuke; Tachikawa, Makoto; Noguchi, Hisayo; Satoh, Soichirou; Obokata, Junichi; Nakamura, Takahiro

    2013-01-01

    C-to-U RNA editing has been widely observed in organellar RNAs in terrestrial plants. Recent research has revealed the significance of a large, plant-specific family of pentatricopeptide repeat (PPR) proteins for RNA editing and other RNA processing events in plant mitochondria and chloroplasts. PPR protein is a sequence-specific RNA-binding protein that identifies specific C residues for editing. Discovery of the RNA recognition code for PPR motifs, including verification and prediction of t...

  1. Fact book on aging in British Columbia, 5th Edition

    OpenAIRE

    Wister, Andrew V; Sixsmith, Andrew; Adams, Raymond G.; Sinden, Danielle

    2009-01-01

    This fifth edition of the Fact Book updates the figures with data from the 2006 census and supplemental sources. Like the first four editions of the Fact Book, this edition references all source documents and presents data primarily in numeric tabular form. Topics covered in this document are listed in the Table of Contents and include: the size and historical rate of growth of the elderly population of British Columbia; trends in life expectancy, mortality rates and causes of death; the mari...

  2. Fact book on aging in British Columbia, 4th Edition

    OpenAIRE

    Wister, Andrew V; Gutman, Gloria M.; Adams, Raymond G.; Chou, Pak Hei Benedito

    2006-01-01

    This fourth edition of the Fact Book updates the figures with data from the 2001 census and supplemental sources. Like the first three editions of the Fact Book, the fourth edition references all source documents and presents data primarily in numeric tabular form. Topics covered in this document are listed in the Table of Contents and include: the size and historical rate of growth of the elderly population of British Columbia; trends in life expectancy, mortality rates and causes of death; ...

  3. Towards a new era in medicine: therapeutic genome editing.

    Science.gov (United States)

    Porteus, Matthew H

    2015-12-22

    Genome editing is the process of precisely modifying the nucleotide sequence of the genome. It has provided a powerful approach to research questions but, with the development of a new set of tools, it is now possible to achieve frequencies of genome editing that are high enough to be useful therapeutically. Genome editing is being developed to treat not only monogenic diseases but also infectious diseases and diseases that have both a genetic and an environmental component.

  4. On the graph edit distance cost: Properties and applications

    OpenAIRE

    Solé Ribalta, Albert; Serratosa Casanelles, Francesc; Sanfeliu Cortés, Alberto

    2012-01-01

    We model the edit distance as a function in a labelling space. A labelling space is an Euclidean space where coordinates are the edit costs. Through this model, we define a class of cost. A class of cost is a region in the labelling space that all the edit costs have the same optimal labelling. Moreover, we characterise the distance value through the labelling space. This new point of view of the edit distance gives as the opportunity of defining some interesting properties that are useful fo...

  5. DNA-free genome editing methods for targeted crop improvement.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala

    2016-07-01

    Evolution of the next-generation clustered, regularly interspaced, short palindromic repeat/Cas9 (CRISPR/Cas9) genome editing tools, ribonucleoprotein (RNA)-guided endonuclease (RGEN) RNPs, is paving the way for developing DNA-free genetically edited crop plants. In this review, I discuss the various methods of RGEN RNPs tool delivery into plant cells and their limitations to adopt this technology to numerous crop plants. Furthermore, focus is given on the importance of developing DNA-free genome edited crop plants, including perennial crop plants. The possible regulation on the DNA-free, next-generation genome-edited crop plants is also highlighted. PMID:27100964

  6. Beyond Author-Centricity in Scholarly Editing

    Directory of Open Access Journals (Sweden)

    Hans Walter Gabler

    2012-03-01

    Full Text Available Authorship – authority – authorisation – the author – the author’s will – the author’s intention: these form a cluster of notions whose validity for scholarly editing I fundamentally question. Taking measure from a historical survey of the discipline’s principles and practice from their institution under the dominance of stemmatics up to their main present-day ‘author orientation’ (Shillingsburg 1996, I see the need to split the terms ‘author’ and ‘authorship’ into a pragmatic versus a conceptual aspect. What textual scholarship engages with, directly and tangibly, is not authors but texts (and equally not works but texts, materially inscribed in transmissions. In the materiality and artifice of texts, ‘authoriality’ is accessible conceptually only, in a manner analog-ous to the Foucauldian ‘author function’. Under such premises, as well, ‘authority’, ‘authorisation’ and ‘authorial intention’ become recognisable as exogenous to texts, not integral to them. Consequently, I propose to abandon ‘authority’, ‘authorisation’ and ‘authorial intention’ as overriding principles and arbiters in editorial scholarship. Scholarly editing instead should re-situate itself in relation to texts, to textual criticism, to literary criticism and to literary theory alike, and do so by re-focussing the method-ology of its own practice. It should relinquish the external props termed ‘authorised document’, ‘textual authority’, or ‘authorial intention’ hitherto deferred to. Instead, it should revitalise skills fundamental to inherited editorial scholarship, namely those of critically assessing, and of editorially realising, textual validity. To re-embed editorial scholarship in literary criticism and theory, moreover, the interpretative and hermeneutic dimensions of textual criticism and scholarly editing will need to be freshly mapped.

  7. Special Edition: Environment in Sustainable Development

    Directory of Open Access Journals (Sweden)

    Stephen Morse

    2014-11-01

    Full Text Available When we were invited by the editors of Sustainability to put together a special edition on “Environment in Sustainable Development” our first reaction was to question whether this was really needed. After all, the environment has long been regarded as a central plank in sustainability and there are countless articles and books published on an annual basis that explore the impact of our economic and social activities on our environment. Just what is it that a special edition can achieve? What new angles could we hope to provide? Our initial thinking was to link the special edition to a particular, almost unique, location in time rather than space. We are in the process of recovering, albeit stuttering, from the deepest economic crash experienced by the European and North American economies. The crash has brought some national economies to their knees and, if economic commentators are to be believed, almost destroyed the Euro. Recovery from that crash has been slow and it is arguable whether at the time of writing this has developed much momentum. There is still the skewed perception that prosperity equals economic growth and that economic growth can take place without real (sustainable development or by simply implementing austerity measures and surely without people’s participation. An analogy from National Parks worldwide is when conservation agencies try to enforce protection without local people’s support. All such attempts have either failed or resurrected only once people’s involvement was secured and guaranteed. The unidirectional austerity measures imposed mainly in the countries of southern Europe have destroyed social cohesion leaving deeply wounded societies, while at the same time have also put up for grabs important assets (including natural capital in each of these countries and therefore in jeopardy even their long term recovery.

  8. Targeted Genome Regulation and Editing in Plants

    KAUST Repository

    Piatek, Agnieszka

    2016-03-01

    The ability to precisely regulate gene expression patterns and to modify genome sequence in a site-specific manner holds much promise in determining gene function and linking genotype to phenotype. DNA-binding modules have been harnessed to generate customizable and programmable chimeric proteins capable of binding to site-specific DNA sequences and regulating the genome and epigenome. Modular DNA-binding domains from zinc fingers (ZFs) and transcriptional activator-like effectors (TALEs) are amenable to engineering to bind any DNA target sequence of interest. Deciphering the code of TALE repeat binding to DNA has helped to engineer customizable TALE proteins capable of binding to any sequence of interest. Therefore TALE repeats provide a rich resource for bioengineering applications. However, the TALE system is limited by the requirement to re-engineer one or two proteins for each new target sequence. Recently, the clustered regularly interspaced palindromic repeats (CRISPR)/ CRISPR associated 9 (Cas9) has been used as a versatile genome editing tool. This machinery has been also repurposed for targeted transcriptional regulation. Due to the facile engineering, simplicity and precision, the CRISPR/Cas9 system is poised to revolutionize the functional genomics studies across diverse eukaryotic species. In this dissertation I employed transcription activator-like effectors and CRISPR/Cas9 systems for targeted genome regulation and editing and my achievements include: 1) I deciphered and extended the DNA-binding code of Ralstonia TAL effectors providing new opportunities for bioengineering of customizable proteins; 2) I repurposed the CRISPR/Cas9 system for site-specific regulation of genes in plant genome; 3) I harnessed the power of CRISPR/Cas9 gene editing tool to study the function of the serine/arginine-rich (SR) proteins.

  9. Enhancing Student Revising and Editing Skills through Writing Conferences and Peer Editing.

    Science.gov (United States)

    Stemper, Julie

    This report describes instructional strategies to improve the revising and editing skills of sixth grade students during the writing process. The literature review suggested improved instruction and evaluation through a writing workshop approach as a possible solution to the problem of poor revision skills. Within this structure, research also…

  10. Anatomy and Physiology. Module Set II: Major Body Systems. Teacher Edition [and] Student Edition. Surgical Technology.

    Science.gov (United States)

    Hilley, Robert

    This document, which is the second part of a two-part set of modules on anatomy and physiology for future surgical technicians, contains the teacher and student editions of an introduction to anatomy and physiology that consists of modules on the following body systems: integumentary system; skeletal system; muscular system; nervous system;…

  11. Emerging technologies planning guide, 1993 edition

    Energy Technology Data Exchange (ETDEWEB)

    1992-11-01

    Information system technology enhancements during the next five years are expected to provide some of the most significant individual and organization work improvements ever made in the office environment. This guide is an aid to planning these technologies and assessing their roles in improving the effectiveness of Headquarters programs. Their implementation will cost-effectively support Departmental operations and the National Energy Strategy. At the hear of this process is an understanding of the relationship which exists between technology introduction and the planning, budgeting and acquisition process. The 1993 edition of this guide covers the 1993--1997 time frame.

  12. Country Nuclear Power Profiles - 2013 Edition

    International Nuclear Information System (INIS)

    The Country Nuclear Power Profiles compile background information on the status and development of nuclear power programmes in Member States. The CNPP summarizes organizational and industrial aspects of nuclear power programs and provides information about the relevant legislative, regulatory, and international framework in each country. Its descriptive and statistical overview of the overall economic, energy, and electricity situation in each country and its nuclear power framework is intended to serve as an integrated source of key background information about nuclear power programs in the world. This 2013 edition, issued on CD-ROM and Web pages, contains updated country information for 51 countries

  13. The KDF9 programme EDIT1

    International Nuclear Information System (INIS)

    EDIT1 is a KDF9 Fortran programme for producing a nuclear data tape, either in binary records, or on the BCD low density mode satisfying the format requirements of the UKAEA nuclear data library described by Parker (AWRE 0-70/63). The programme operates only on complete files which may be in binary or BCD mode for input though the single IBM compatible tape unit cannot be used for both input and output in the same job. Programmes using the data library on the KDF9 will operate in the binary mode but facilities for reading and writing BCD card image libraries are necessary for compatibility with other computer installations. (author)

  14. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases.

    Science.gov (United States)

    Renaud, Jean-Baptiste; Boix, Charlotte; Charpentier, Marine; De Cian, Anne; Cochennec, Julien; Duvernois-Berthet, Evelyne; Perrouault, Loïc; Tesson, Laurent; Edouard, Joanne; Thinard, Reynald; Cherifi, Yacine; Menoret, Séverine; Fontanière, Sandra; de Crozé, Noémie; Fraichard, Alexandre; Sohm, Frédéric; Anegon, Ignacio; Concordet, Jean-Paul; Giovannangeli, Carine

    2016-03-01

    Genome editing has now been reported in many systems using TALEN and CRISPR-Cas9 nucleases. Precise mutations can be introduced during homology-directed repair with donor DNA carrying the wanted sequence edit, but efficiency is usually lower than for gene knockout and optimal strategies have not been extensively investigated. Here, we show that using phosphorothioate-modified oligonucleotides strongly enhances genome editing efficiency of single-stranded oligonucleotide donors in cultured cells. In addition, it provides better design flexibility, allowing insertions more than 100 bp long. Despite previous reports of phosphorothioate-modified oligonucleotide toxicity, clones of edited cells are readily isolated and targeted sequence insertions are achieved in rats and mice with very high frequency, allowing for homozygous loxP site insertion at the mouse ROSA locus in particular. Finally, when detected, imprecise knockin events exhibit indels that are asymmetrically positioned, consistent with genome editing taking place by two steps of single-strand annealing. PMID:26923600

  15. Heritable genome editing with CRISPR/Cas9 induces anosmia in a crop pest moth.

    Science.gov (United States)

    Koutroumpa, Fotini A; Monsempes, Christelle; François, Marie-Christine; de Cian, Anne; Royer, Corinne; Concordet, Jean-Paul; Jacquin-Joly, Emmanuelle

    2016-01-01

    Lepidoptera suffer critical lack of genetic tools and heritable genome edition has been achieved only in a few model species. Here we demonstrate that the CRISPR/Cas9 system is highly efficient for genome editing in a non-model crop pest Lepidoptera, the noctuid moth Spodoptera littoralis. We knocked-out the olfactory receptor co-receptor Orco gene to investigate its function in Lepidoptera olfaction. We find that 89.6% of the injected individuals carried Orco mutations, 70% of which transmitted them to the next generation. CRISPR/Cas9-mediated Orco knockout caused defects in plant odor and sex pheromone olfactory detection in homozygous individuals. Our work genetically defines Orco as an essential OR partner for both host and mate detection in Lepidoptera, and demonstrates that CRISPR/Cas9 is a simple and highly efficient genome editing technique in noctuid pests opening new routes for gene function analysis and the development of novel pest control strategies. PMID:27403935

  16. Detection of signals in noise

    CERN Document Server

    McDonough, Robert N

    1995-01-01

    The Second Edition is an updated revision to the authors highly successful and widely used introduction to the principles and application of the statistical theory of signal detection. This book emphasizes those theories that have been found to be particularly useful in practice including principles applied to detection problems encountered in digital communications, radar, and sonar.Detection processing based upon the fast Fourier transform

  17. Country Nuclear Power Profiles - 2009 Edition

    International Nuclear Information System (INIS)

    The Country Nuclear Power Profiles compiles background information on the status and development of nuclear power programs in Member States. It consists of organizational and industrial aspects of nuclear power programs and provides information about the relevant legislative, regulatory, and international framework in each country. Its descriptive and statistical overview of the overall economic, energy, and electricity situation in each country, and its nuclear power framework is intended to serve as an integrated source of key background information about nuclear power programs in the world. The preparation of Country Nuclear Power Profiles (CNPP) was initiated in 1990s. It responded to a need for a database and a technical publication containing a description of the energy and economic situation, the energy and the electricity sector, and the primary organizations involved in nuclear power in IAEA Member States. This is the 2009 edition issued on CD-ROM and Web pages. It updates the country information for 44 countries. The CNPP is updated based on information voluntarily provided by participating IAEA Member States. Participants include the 30 countries that have operating nuclear power plants, as well as 14 countries having past or planned nuclear power programmes (Bangladesh, Egypt, Ghana, Indonesia, the Islamic Republic of Iran, Italy, Kazakhstan, Nigeria, Philippines, Poland, Thailand, Tunisia, Turkey and Vietnam). For the 2009 edition, 26 countries provided updated or new profiles. For the other countries, the IAEA updated the profile statistical tables on nuclear power, energy development, and economic indicators based on information from IAEA and World Bank databases

  18. Gene regulation by mRNA editing

    Energy Technology Data Exchange (ETDEWEB)

    Ashkenas, J. [Univ. of Washington, Seattle, WA (United States)

    1997-02-01

    The commonly cited figure of 10{sup 5} genes in the human genome represents a tremendous underestimate of our capacity to generate distinct gene products with unique functions. Our cells possess an impressive collection of tools for altering the products of a single gene to create a variety of proteins. The different gene products may have related but distinct functions, allowing cells of different types or at different developmental stages to fine-tune their patterns of gene expression. These tools may act in the cytoplasm, as when proteins undergo post-translational modifications, or in the nucleus, in the processing of pre-mRNA. Two forms of intranuclear fine-tuning are well established and widely studied: alternative splicing of pre-mRNAs and alternative polyadenylation site selection. In recent years it has become clear that cells possess yet another tool to create RNA sequence diversity, mRNA editing. The term {open_quotes}editing{close_quotes} is applied to posttranscriptional modifications of a purine or pyrimidine, which alter an mRNA sequence as it is read, for example, by ribosomes. Covalent changes to the structure of nucleotide bases are well known to occur on tRNA and rRNA molecules, but such changes in mRNA sequence are novel in that they have the capacity to change specific protein sequences. 43 refs., 1 fig.

  19. Earth's Dynamic Systems, 8th Edition

    Science.gov (United States)

    Winterer, Edward L.

    From the very first edition, Hamblin and Christiansen's elementary geology text, Earth's Dynamic Systems, has stood above its competitors in the quality of its illustrations— all of them now in color. These are exceptionally well planned to bring out essential points of the text and are models of clarity and artistic design, especially the three-dimensional cutaway diagrams of tectonic and geomorphic features. Many new drawings and photos have been incorporated in this 8th edition, including dramatic pictures of planetary surfaces. Each of the 25 chapters begins with an opening statement that puts the chapter in a larger context and closes with a list of key terms, some thought-provoking review questions, a list of suggested readings in more advanced works, and—a novel and useful feature—a list of Web sites germane to the chapter. An illustrated glossary and a useful index complete the book. Pages feature wake-up questions for the student, such as “How do we know that streams erode the valleys through which they flow?”

  20. How Online Access Changed Amateur Video Editing

    Directory of Open Access Journals (Sweden)

    Eugster Benjamin

    2014-12-01

    Full Text Available Digital technology has often been discussed in relation to how it changed either the production or the reception of audiovisual cultures. This paper will consider a combination of both as a crucial part in understanding strategies of inter- and transmedial amateur creativity. Based on an experimental ethnography of the online video subgenre/subculture “YouTubePoop,” the paper will elaborate on the connection between the individual experience and the creation of digital media. The loose collective of independent amateurs behind the YouTubePoop videos makes use of already existing audiovisual material ranging from television shows to videos of other YouTube users. The re-created remixes and mash-ups are characterized by their random selection of original material and their nonsensical humour. Hence, the rapid montage of this heterogeneous content is just as much part of the intensified aesthetic expressiveness as are the applied special effects available in the digital video editing software. Both aspects highlight the strong interdependence of the rapid accessibility of online content and digital technology and the new aesthetic expressions they are fostering. The paper will show how the experience and navigation of digital interfaces (editing software, media players, or homepages affect the design and practice of these video-remixes. This will open the discussion about intertextual strategies of media appropriation to an aesthetic and praxeological analysis of media interaction.

  1. Editing DNA Methylation in the Mammalian Genome.

    Science.gov (United States)

    Liu, X Shawn; Wu, Hao; Ji, Xiong; Stelzer, Yonatan; Wu, Xuebing; Czauderna, Szymon; Shu, Jian; Dadon, Daniel; Young, Richard A; Jaenisch, Rudolf

    2016-09-22

    Mammalian DNA methylation is a critical epigenetic mechanism orchestrating gene expression networks in many biological processes. However, investigation of the functions of specific methylation events remains challenging. Here, we demonstrate that fusion of Tet1 or Dnmt3a with a catalytically inactive Cas9 (dCas9) enables targeted DNA methylation editing. Targeting of the dCas9-Tet1 or -Dnmt3a fusion protein to methylated or unmethylated promoter sequences caused activation or silencing, respectively, of an endogenous reporter. Targeted demethylation of the BDNF promoter IV or the MyoD distal enhancer by dCas9-Tet1 induced BDNF expression in post-mitotic neurons or activated MyoD facilitating reprogramming of fibroblasts into myoblasts, respectively. Targeted de novo methylation of a CTCF loop anchor site by dCas9-Dnmt3a blocked CTCF binding and interfered with DNA looping, causing altered gene expression in the neighboring loop. Finally, we show that these tools can edit DNA methylation in mice, demonstrating their wide utility for functional studies of epigenetic regulation. PMID:27662091

  2. Safe Handling of Radioisotopes. 1973 Edition

    International Nuclear Information System (INIS)

    Under its Statute the International Atomic Energy Agency is empowered to provide for the application of standards of safety for protection against radiation to its own operations and to operations making use of assistance provided by it or with which it is otherwise directly associated. To this end authorities receiving such assistance are required to observe relevant health and safety measures prescribed by the Agency. As a first step, it was considered an urgent task to provide users of radionuclides with a manual of practice for the safe handling of these substances. The first edition of such a manual was published in 1958 and represented the first of the ''Safety Series'', a series of manuals and codes on health and safety published by the Agency. It was prepared after careful consideration of existing national and international codes of radiation safety by a group of international experts and in consultation with other international bodies. This edition presents the second revision. In response to the suggestion made by some Member States, the term 'radioisotopes' has been changed to 'radionuclides' in the title and, as appropriate, in the text because the term 'radionuclides' includes the radioactive element itself as well as the isotopes. The series of manuals and codes published in the Safety Series and the Technical Reports Series give more complete advice to the user on specialized topics.

  3. Conversion Tables. Volume 1, LC-Dewey. Second Edition.

    Science.gov (United States)

    Scott, Mona L.

    This volume contains tables that list Library of Congress classification numbers (i.e., call numbers) with corresponding Dewey Decimal classification numbers and related Library of Congress subject headings. Materials referenced in the conversion tables are the 21st edition of the "Dewey Decimal Classification," the most current edition of the…

  4. Conversion Tables. Volume 2, Dewey-LC. Second Edition.

    Science.gov (United States)

    Scott, Mona L.

    This volume contains tables that list Dewey Decimal classification numbers (i.e., call numbers) with corresponding Library of Congress classification numbers and related Library of Congress subject headings. Materials referenced in the conversion tables are the 21st edition of the "Dewey Decimal Classification", the most current edition of the…

  5. SEDiL: Software for Edit Distance Learning

    OpenAIRE

    Boyer, Laurent; Esposito, Yann; Habrard, Amaury; Oncina, Jose; Sebban, Marc

    2008-01-01

    In this paper, we present SEDiL, a Software for Edit Distance Learning. SEDiL is an innovative prototype implementation grouping together most of the state of the art methods that aim to automatically learn the parameters of string and tree edit distances.

  6. The Kamusi Project Edit Engine: A Tool for Collaborative Lexicography.

    Science.gov (United States)

    Benjamin, Martin; Biersteker, Ann

    2001-01-01

    Discusses the design and implementation of the Kamusi Project Edit Engine, a Web-based software system uniquely suited to the needs of Swahili collaborative lexicography. Describes the edit engine, including organization of the lexicon and the mechanics by which participants use the system, discusses philosophical issues confronted in the design,…

  7. Introduction to Educational Administration: Standards, Theories, and Practice. Second Edition

    Science.gov (United States)

    Fiore, Douglas J.

    2009-01-01

    Organized around the ISLLC standards, this text introduces students to the concepts and theories of educational leadership. The new edition adds coverage of such topics as data usage, ethics, innovative hiring practices, and student discipline. Appearing in the second edition are chapter-ending sections called "Point-Counterpoint" which prompt…

  8. Recollection Rejection: How Children Edit Their False Memories.

    Science.gov (United States)

    Brainerd, C. J.; Reyna, V. F.

    2002-01-01

    Presents new measure of children's use of an editing operation that suppresses false memories by accessing verbatim traces of true events. Application of the methodology showed that false-memory editing increased dramatically between early and middle childhood. Measure reacted appropriately to experimental manipulations. Developmental reductions…

  9. Students' Editing Skills and Attitudes toward Word Processing.

    Science.gov (United States)

    Joram, Elana; And Others

    1990-01-01

    Investigates the writing attitudes and text editing skills of students with considerable experience using word-processing systems toward word processing for different phases of the writing process. Finds the students are poor at text editing and typing. Finds that the students prefer paper and pencil for composing first drafts and prefer word…

  10. An Introduction to Music Therapy: Theory and Practice. Third Edition

    Science.gov (United States)

    Davis, William B.; Gfeller, Kate E.; Thaut, Michael H.

    2008-01-01

    "An Introduction to Music Therapy: Theory and Practice, Third Edition," provides a comprehensive overview of the practice of music therapy for the 21st century. It looks at where we have been, where we are today, and where we might be in the future. Combining sound pedagogy with recent research findings, this new edition has been updated and…

  11. A minimum principle in mRNA editing of Physarum ?

    CERN Document Server

    Frappat, L; Sorba, Paul

    2000-01-01

    mRNA editing in three sequences of Physarum polycephalum is analyzed. Once fixed the edited peptide chain, the nature of the inserted nucleotides and the position of the insertion sites are explained by introducing a minimum principle in the framework of the crystal basis model of the genetic code introduced by the authors.

  12. Qualitative Data Analysis: A Methods Sourcebook. Third Edition

    Science.gov (United States)

    Miles, Matthew B.; Huberman, A. Michael; Saldana, Johnny

    2014-01-01

    The Third Edition of Miles & Huberman's classic research methods text is updated and streamlined by Johnny Saldaña, author of "The Coding Manual for Qualitative Researchers." Several of the data display strategies from previous editions are now presented in re-envisioned and reorganized formats to enhance reader accessibility and…

  13. Textual Challenges: A Brief Guide to Choosing Shakespearean Editions

    Science.gov (United States)

    Cornell, Christine; Malcolmson, Patrick

    2012-01-01

    How should educators go about selecting appropriate editions of Shakespeare's plays for use in political science courses? Shakespeare is turning up on many politics syllabi, but, at times, the editions chosen seem to reflect primarily a concern for price or publisher reputation over pedagogical and scholarly considerations. This article offers an…

  14. Genome editing: intellectual property and product development in plant biotechnology.

    Science.gov (United States)

    Schinkel, Helga; Schillberg, Stefan

    2016-07-01

    Genome editing is a revolutionary technology in molecular biology. While scientists are fascinated with the unlimited possibilities provided by directed and controlled changes in DNA in eukaryotes and have eagerly adopted such tools for their own experiments, an understanding of the intellectual property (IP) implications involved in bringing genome editing-derived products to market is often lacking. Due to the ingenuity of genome editing, the time between new product conception and its actual existence can be relatively short; therefore knowledge about IP of the various genome editing methods is relevant. This point must be regarded in a national framework as patents are instituted nationally. Therefore, when designing scientific work that could lead to a product, it is worthwhile to consider the different methods used for genome editing not only for their scientific merits but also for their compatibility with a speedy and reliable launch into the desired market. PMID:27146974

  15. THE TEXT OF CAXTON'S SECOND EDITION OF THE CANTERBURY TALES

    Directory of Open Access Journals (Sweden)

    Bordalejo Bárbara

    2005-12-01

    Full Text Available This article describes recent research on the textual relationship between the first and second editions of the Canterbury Tales printed in England by William Caxton and it also explores the textual affiliations of the manuscript source for the corrections in the second edition. Using both computerised and manual methods the variant readings between the first and second editions of the Tales are isolated. Examples of the textual affiliations of the manuscript source of Caxton's second edition are analysed. This article concludes that the manuscript source for the corrections introduced in Caxton's second edition of the Tales was of the same quality as tlie best extant manuscripts and that its readings can help our understanding of the textual tradition and can clarify the text for editors of the Tales.

  16. First Season Catfish Farming. A Workbook for Beginning Pond and Cage Culture of Channel Catfish. Teacher Edition and Student Edition.

    Science.gov (United States)

    Oklahoma State Board of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

    This workbook, comprised of both the teacher and student editions, presents guidelines useful for first-year catfish farmers in Oklahoma using pond or cage cultures to raise channel catfish. The teacher edition is a set of unit guidelines only. Contents include a list of suggested readings, important addresses with types of information available…

  17. NEW APPROACHES IN TEXTUAL EDITING. A SELECTION OF ELECTRONIC EDITIONS UNDER ANALYSIS

    Directory of Open Access Journals (Sweden)

    Isabel De la Cruz

    2005-12-01

    Full Text Available In the present article, we make an approach to the world of digital editions available in electronic format. Using as a starting point Professor González Fernández-Corugedo's classification of some of the best web pages related to the topic (available at http://www.uniovi.es/HELL/Hyptxed.html we have examined the design and contents of some sites that deal with texts mainly in Old and Middle English. The readers are offered an outline of what they are expected to find in every page, highlighting their main virtues and shortcomings. As a result of the analysis of al1 these pages we are ready to propose certain steps necessary in the elaboration of a 'good' electronic edition.

  18. INES: The International Nuclear and Radiological Event Scale User's Manual. 2008 Edition (Spanish Edition)

    International Nuclear Information System (INIS)

    INES, the International Nuclear and Radiological Event Scale, was developed in 1990 by experts convened by the IAEA and the OECD Nuclear Energy Agency with the aim of communicating the safety significance of events. This edition of the INES User?s Manual is designed to facilitate the task of those who are required to rate the safety significance of events using the scale. It includes additional guidance and clarifications, and provides examples and comments on the continued use of INES. With this new edition, it is anticipated that INES will be widely used by Member States and become the worldwide scale for putting into proper perspective the safety significance of any event associated with the transport, storage and use of radioactive material and radiation sources, whether or not the event occurs at a facility.

  19. High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells

    Directory of Open Access Journals (Sweden)

    Jared Carlson-Stevermer

    2016-01-01

    Full Text Available CRISPR-Cas9 gene editing of human cells and tissues holds much promise to advance medicine and biology, but standard editing methods require weeks to months of reagent preparation and selection where much or all of the initial edited samples are destroyed during analysis. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs, separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.

  20. High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells.

    Science.gov (United States)

    Carlson-Stevermer, Jared; Goedland, Madelyn; Steyer, Benjamin; Movaghar, Arezoo; Lou, Meng; Kohlenberg, Lucille; Prestil, Ryan; Saha, Krishanu

    2016-01-12

    CRISPR-Cas9 gene editing of human cells and tissues holds much promise to advance medicine and biology, but standard editing methods require weeks to months of reagent preparation and selection where much or all of the initial edited samples are destroyed during analysis. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs, separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.

  1. Stirling engine design manual, 2nd edition

    Science.gov (United States)

    Martini, W. R.

    1983-01-01

    This manual is intended to serve as an introduction to Stirling cycle heat engines, as a key to the available literature on Stirling engines and to identify nonproprietary Stirling engine design methodologies. Two different fully described Stirling engines are discussed. Engine design methods are categorized as first order, second order, and third order with increased order number indicating increased complexity. FORTRAN programs are listed for both an isothermal second order design program and an adiabatic second order design program. Third order methods are explained and enumerated. In this second edition of the manual the references are updated. A revised personal and corporate author index is given and an expanded directory lists over 80 individuals and companies active in Stirling engines.

  2. TALEN-Mediated Mutagenesis and Genome Editing.

    Science.gov (United States)

    Ma, Alvin C H; Chen, Yi; Blackburn, Patrick R; Ekker, Stephen C

    2016-01-01

    Transcription activator-like effectors (TALEs) are important genomic tools with customizable DNA-binding motifs for locus-specific modifications. In particular, TALE nucleases or TALENs have been successfully used in the zebrafish model system to introduce targeted mutations via repair of double-stranded breaks (DSBs) either through nonhomologous end joining (NHEJ) or by homology-directed repair (HDR) and homology-independent repair in the presence of a donor template. Compared with other customizable nucleases, TALENs offer high binding specificity and fewer sequence constraints in targeting the genome, with comparable mutagenic activity. Here, we describe a detailed in silico design tool for zebrafish genome editing for TALENs and CRISPR/Cas9 custom restriction enzymes using Mojo Hand 2.0 software. PMID:27464798

  3. European Code against Cancer 4th Edition

    DEFF Research Database (Denmark)

    Friis, Søren; Kesminiene, Ausrele; Espina, Carolina;

    2015-01-01

    of treatment, and initiation according to the time of menopause. Carcinogenicity has also been established for anti-neoplastic agents used in cancer therapy, immunosuppressants, oestrogen-progestogen contraceptives, and tamoxifen. Medical use of ionising radiation, an established carcinogen, can provide major......The 4th edition of the European Code against Cancer recommends limiting - or avoiding when possible - the use of hormone replacement therapy (HRT) because of the increased risk of cancer, nevertheless acknowledging that prescription of HRT may be indicated under certain medical conditions. Current...... evidence shows that HRT, generally prescribed as menopausal hormone therapy, is associated with an increased risk of cancers of the breast, endometrium, and ovary, with the risk pattern depending on factors such as the type of therapy (oestrogen-only or combined oestrogen-progestogen), duration...

  4. Fundamentals of analytical chemistry, 5th edition

    International Nuclear Information System (INIS)

    Fundamentals of Analytical Chemistry is divided into three roughly equal parts. The first 14 chapters cover classical methods of analysis, including titrimetry and gravimetry as well as solution equilibria and statistical analysis. The next 11 chapters address electroanalytical, optical, and chromatographic methods of analysis. The remainder of the text is devoted to discussions of sample manipulation and pretreatment, good laboratory practices, and detailed directions for performing examples of 17 different types of classical and instrumental analyses. Like its predecessors, this fifth edition provides comprehensive coverage of classical analytical methods and the major instrumental ones in a literary style that is clear, straightforward, and readable. New terms are carefully defined as they are introduced, and each term is italicized for emphasis and for ease of relocation by the student who may forget its meaning. The chapters on analyses of real-world samples, on avoiding interferences, and on techniques for sample preparation should prove especially useful for the practicing chemist

  5. Effects of nuclear weapons. Third edition

    Energy Technology Data Exchange (ETDEWEB)

    Glasstone, S.; Dolan, P.J.

    1977-01-01

    Since the last edition of ''The Effects of Nuclear Weapons'' in 1962 much new information has become available concerning nuclear weapon effects. This has come in part from the series of atmospheric tests, including several at very high altitudes, conducted in the Pacific Ocean area in 1962. In addition, laboratory studies, theoretical calculations, and computer simulations have provided a better understanding of the various effects. A new chapter has been added on the electromagnetic pulse. The chapter titles are as follows: general principles of nuclear explosions; descriptions of nuclear explosions; air blast phenomena in air and surface bursts; air blast loading; structural damage from air blast; shock effects of surface and subsurface bursts; thermal radiation and its effects; initial nuclear radiation; residual nuclear radiation and fallout; radio and radar effects; the electromagnetic pulse and its effects; and biological effects. (LTN)

  6. WYLBUR reference manual. [For interactive text editing

    Energy Technology Data Exchange (ETDEWEB)

    Krupp, R.F.; Messina, P.C.; Peavler, J.M.; Schustack, S.; Starai, T.

    1977-04-01

    WYLBUR is a system for manipulating various kinds of text, such as computer programs, manuscripts, letters, forms, articles, or reports. Its on-line interactive text-editing capabilities allow the user to create, change, and correct text, and to search and display it. WYLBUR also has facilities for job submission and retrieval from remote terminals that make it possible for a user to inquire about the status of any job in the system, cancel jobs that are executing or awaiting execution, reroute output, raise job priority, or get information on the backlog of batch jobs. WYLBUR also has excellent recovery capabilities and a fast response time. This manual describes the WYLBUR version currently used at ANL. It is intended primarily as a reference manual; thus, examples of WYLBUR commands are kept to a minimum. (RWR)

  7. Flatland an edition with notes and commentary

    CERN Document Server

    Abbott, Edwin A; Banchoff, Thomas F

    2010-01-01

    Flatland, Edwin Abbott Abbott's story of a two-dimensional universe, as told by one of its inhabitants who is introduced to the mysteries of three-dimensional space, has enjoyed an enduring popularity from the time of its publication in 1884. This fully annotated edition enables the modern-day reader to understand and appreciate the many "dimensions" of this classic satire. Mathematical notes and illustrations enhance the usefulness of Flatland as an elementary introduction to higher-dimensional geometry. Historical notes show connections to late-Victorian England and to classical Greece. Citations from Abbott's other writings as well as the works of Plato and Aristotle serve to interpret the text. Commentary on language and literary style includes numerous definitions of obscure words. An appendix gives a comprehensive account of the life and work of Flatland's remarkable author.

  8. Atomic Energy Control Board vocabulary - preliminary edition

    International Nuclear Information System (INIS)

    This preliminary edition was prepared at the Board's request to help it establish a standardized terminology. It was produced by scanning the 99 French and English documents listed at the end of this Vocabulary. The documents include legislation concerning atomic energy and the transportation of radioactive materials, as well as the Board's publications, such as the Consultative Documents, Regulatory Documents and Notices. The terms included from the following areas are: radiation protection, reactor technology, nuclear fuel cycle, radioactive material packaging and transportation, radioactive waste management, uranium mines, and medical and industrial applications of radioelements. Also included are the titles of publications and the names of organizations and units. The vocabulary contains 2,589 concepts, sometimes accompanied by definitions, contexts or usage examples. Where terms have been standardized by the Canadian Committee for the Standardization of Nuclear Terminology, this has been indicated. Where possible, we have verified the terms using the TERMIUM, the Government of Canada Linguistic Data Bank. (author)

  9. National solar energy education directory. Second edition

    Energy Technology Data Exchange (ETDEWEB)

    Corcoleotes, G; Cronin, S; Kramer, K; O& #x27; Connor, K

    1980-01-01

    The information contained in this directory is derived from responses to a national survey of educational institutions and organizations involved in solar energy educational activities beyond the secondary school level. Phone calls and follow-up mail requests were used to gather additional information when necessary. Every survey instrument was read, coded, and edited before entry into the data base from which this directory was produced. The Directory is organized alphabetically by state. Institutions and organizations within each state are categorized according to type (Colleges and Universities, Junior/Community Colleges, Vocational/Technical Schools, and Other Educational Institutions and Organizations) and listed alphabetically within these categories. Within each institutional listing the amount of information provided will vary according to the completeness of the survey response received from that institution. (MHR)

  10. The Challenge of Editing Einstein's Scientific Manuscripts

    CERN Document Server

    Sauer, T

    2004-01-01

    Einstein's research manuscripts provide important insights into his exceptional creativity. At the same time, they can present difficulties for a publication in the documentary edition of the Collected Papers of Albert Einstein (CPAE). The problems are illustrated by discussing how some important examples of Einstein's research manuscripts have been included in previous volumes of the CPAE series: his Scratch Notebook from the years 1910-1914, his so-called Zurich Notebook from 1912, documenting his early search for a generally covariant theory of gravitation, and the Einstein-Besso manuscript from 1913, containing calculations of Mercury's perihelion advance on the basis of the Einstein-Grossmann equations. Another category of research notes are "back-of-an-envelope" calculations. A major challenge for future volumes of the CPAE series are Einstein's Berlin and Princeton research manuscripts on a unified field theory. This batch of some 1700 undated manuscript pages presents a formidable challenge also for h...

  11. Country Nuclear Power Profiles - 2010 Edition

    International Nuclear Information System (INIS)

    The Country Nuclear Power Profiles compiles background information on the status and development of nuclear power programs in Member States. It consists of organizational and industrial aspects of nuclear power programs and provides information about the relevant legislative, regulatory, and international framework in each country. Its descriptive and statistical overview of the overall economic, energy, and electricity situation in each country, and its nuclear power framework is intended to serve as an integrated source of key background information about nuclear power programs in the world. The preparation of Country Nuclear Power Profiles (CNPP) was initiated in 1990s. It responded to a need for a database and a technical publication containing a description of the energy and economic situation, the energy and the electricity sector, and the primary organizations involved in nuclear power in IAEA Member States. This is the 2010 edition issued on CD-ROM and Web pages. It updates the country information for 48 countries. The CNPP is updated based on information voluntarily provided by participating IAEA Member States. Participants include the 29 countries that have operating nuclear power plants, as well as 19 countries having past or planned nuclear power programmes (Bangladesh, Belarus, Chile, Egypt, Ghana, Indonesia, the Islamic Republic of Iran, Italy, Jordan, Kazakhstan, Lithuania, Morocco, Nigeria, Philippines, Poland, Thailand, Tunisia, Turkey and Vietnam). For the 2010 edition, 24 countries provided updated or new profiles. For the other countries, the IAEA updated the profile statistical tables on nuclear power, energy development, and economic indicators based on information from IAEA and World Bank databases. The CNPP reports have been prepared by each Member State in accordance with the IAEA format. The IAEA is not responsible for the content of these reports

  12. Country Nuclear Power Profiles - 2007 Edition

    International Nuclear Information System (INIS)

    The preparation of Country Nuclear Power Profiles (CNPP) was initiated within the framework of the IAEA's programme on assessment and feedback of nuclear power plant performance. It responded to a need for a database and a technical publication containing a description of the energy and economic situation, the energy and the electricity sector, and the primary organizations involved in nuclear power in IAEA Member States. It covers background information on the status and development of nuclear power programmes in countries having nuclear plants in operation and/or plants under construction. This is the 2007 edition issued on CD-ROM and Web pages. It updates the country information, in general, to the end of 2006 for 39 countries. The CNPP is updated based on information voluntarily provided by participating IAEA Member States. Participants include the 30 countries that have operating nuclear power plants, as well as nine countries having past or planned nuclear power programmes (Bangladesh, Egypt, Indonesia, the Islamic Republic of Iran, Italy, Kazakhstan, Poland, Turkey, and Vietnam). For the 2007 edition, 21 countries provided information to the IAEA to update their profiles. For the 18 other countries, the IAEA updated the profile statistical tables on nuclear power, energy development, and economic indicators based on information from IAEA and World Bank databases. These 18 countries are Argentina, Belgium, Bulgaria, Canada, China, Egypt, Finland, Indonesia, Japan, Mexico, Netherlands, Poland, Romania, Slovenia, South Africa, Spain, Switzerland, and Ukraine. Overall, the CNPP reviews the organizational and industrial aspects of nuclear power programmes in participating countries, and provides information about the relevant legislative, regulatory and international frameworks in each country. It compiles the current issues in the new environment within which the electricity and nuclear sector operates, i.e. energy policy, and privatization and deregulation in

  13. Country Nuclear Power Profiles - 2011 Edition

    International Nuclear Information System (INIS)

    The Country Nuclear Power Profiles compiles background information on the status and development of nuclear power programs in Member States. It consists of organizational and industrial aspects of nuclear power programs and provides information about the relevant legislative, regulatory, and international framework in each country. Its descriptive and statistical overview of the overall economic, energy, and electricity situation in each country, and its nuclear power framework is intended to serve as an integrated source of key background information about nuclear power programs in the world. The preparation of Country Nuclear Power Profiles (CNPP) was initiated in 1990s. It responded to a need for a database and a technical publication containing a description of the energy and economic situation, the energy and the electricity sector, and the primary organizations involved in nuclear power in IAEA Member States. This is the 2011 edition issued on CD-ROM and Web pages. It updates the country information for 50 countries. The CNPP is updated based on information voluntarily provided by participating IAEA Member States. Participants include the 29 countries that have operating nuclear power plants, as well as 21 countries having past or planned nuclear power programmes (Bangladesh, Belarus, Chile, Egypt, Ghana, Indonesia, the Islamic Republic of Iran, Italy, Jordan, Kazakhstan, Kuwait, Lithuania, Morocco, Nigeria, Philippines, Poland, Syrian Arab Republic, Thailand, Tunisia, Turkey and Vietnam). For the 2011 edition, 23 countries provided updated or new profiles. For the other countries, the IAEA updated the profile statistical tables on nuclear power, energy development, and economic indicators based on information from IAEA and World Bank databases.

  14. TALE: a tale of genome editing.

    Science.gov (United States)

    Zhang, Mingjie; Wang, Feng; Li, Shifei; Wang, Yan; Bai, Yun; Xu, Xueqing

    2014-01-01

    Transcription activator-like effectors (TALEs), first identified in Xanthomonas bacteria, are naturally occurring or artificially designed proteins that modulate gene transcription. These proteins recognize and bind DNA sequences based on a variable numbers of tandem repeats. Each repeat is comprised of a set of ∼ 34 conserved amino acids; within this conserved domain, there are usually two amino acids that distinguish one TALE from another. Interestingly, TALEs have revealed a simple cipher for the one-to-one recognition of proteins for DNA bases. Synthetic TALEs have been used to successfully target genes in a variety of species, including humans. Depending on the type of functional domain that is fused to the TALE of interest, these proteins can have diverse biological effects. For example, after binding DNA, TALEs fused to transcriptional activation domains can function as robust transcription factors (TALE-TFs), while fused to restriction endonucleases (TALENs) can cut DNA. Targeted genome editing, in theory, is capable of modifying any endogenous gene sequence of interest; this can be performed in cells or organisms, and may be applied to clinical gene-based therapies in the future. With current technologies, highly accurate, specific, and reliable gene editing cannot be achieved. Thus, recognition and binding mechanisms governing TALE biology are currently hot research areas. In this review, we summarize the major advances in TALE technology over the past several years with a focus on the interaction between TALEs and DNA, TALE design and construction, potential applications for this technology, and unique characteristics that make TALEs superior to zinc finger endonucleases.

  15. The clinical applications of genome editing in HIV.

    Science.gov (United States)

    Wang, Cathy X; Cannon, Paula M

    2016-05-26

    HIV/AIDS has long been at the forefront of the development of gene- and cell-based therapies. Although conventional gene therapy approaches typically involve the addition of anti-HIV genes to cells using semirandomly integrating viral vectors, newer genome editing technologies based on engineered nucleases are now allowing more precise genetic manipulations. The possible outcomes of genome editing include gene disruption, which has been most notably applied to the CCR5 coreceptor gene, or the introduction of small mutations or larger whole gene cassette insertions at a targeted locus. Disruption of CCR5 using zinc finger nucleases was the first-in-human application of genome editing and remains the most clinically advanced platform, with 7 completed or ongoing clinical trials in T cells and hematopoietic stem/progenitor cells (HSPCs). Here we review the laboratory and clinical findings of CCR5 editing in T cells and HSPCs for HIV therapy and summarize other promising genome editing approaches for future clinical development. In particular, recent advances in the delivery of genome editing reagents and the demonstration of highly efficient homology-directed editing in both T cells and HSPCs are expected to spur the development of even more sophisticated applications of this technology for HIV therapy. PMID:27053530

  16. Free Appearance-Editing with Improved Poisson Image Cloning

    Institute of Scientific and Technical Information of China (English)

    Xiao-Hui Bie; Hao-Da Huang; Wen-Cheng Wang

    2011-01-01

    In this paper,we present a new edit tool for the user to conveniently preserve or freely edit the object appearance during seamless image composition.We observe that though Poisson image editing is effective for seamless image composition.Its color bleeding (the color of the target image is propagated into the source image) is not always desired in applications,and it provides no way to allow the user to edit the appearance of the source image.To make it more flexible and practical,we introduce new energy terms to control the appearance change,and integrate them into the Poisson image editing framework.The new energy function could still be realized using efficient sparse linear solvers,and the user can interactively refine the constraints.With the new tool,the user can enjoy not only seamless image composition,but also the flexibility to preserve or manipulate the appearance of the source image at the same time.This provides more potential for creating new images.Experimental results demonstrate the effectiveness of our new edit tool,with similar time cost to the original Poisson image editing.

  17. User-friendly graph editing for procedural modeling of buildings.

    Science.gov (United States)

    Patow, Gustavo

    2012-01-01

    A proposed rule-based editing metaphor intuitively lets artists create buildings without changing their workflow. It's based on the realization that the rule base represents a directed acyclic graph and on a shift in the development paradigm from product-based to rule-based representations. Users can visually add or edit rules, connect them to control the workflow, and easily create commands that expand the artist's toolbox (for example, Boolean operations or local controlling operators). This approach opens new possibilities, from model verification to model editing through graph rewriting. PMID:24804948

  18. Efficient Mitochondrial Genome Editing by CRISPR/Cas9

    OpenAIRE

    Areum Jo; Sangwoo Ham; Gum Hwa Lee; Yun-Il Lee; SangSeong Kim; Yun-Song Lee; Joo-Ho Shin; Yunjong Lee

    2015-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been widely used for nuclear DNA editing to generate mutations or correct specific disease alleles. Despite its flexible application, it has not been determined if CRISPR/Cas9, originally identified as a bacterial defense system against virus, can be targeted to mitochondria for mtDNA editing. Here, we show that regular FLAG-Cas9 can localize to mitochondria to edit mitochondrial DNA with sgRNAs targeting s...

  19. Mesh Geometric Editing Approach Based on Gpu Texture

    Directory of Open Access Journals (Sweden)

    Guiping Qian

    2012-09-01

    Full Text Available This paper presents a novel interactive mesh editing approach based on GPU texture mapping. The main feature is that it copies 2D surface geometry information to GPU frame buffer. The planar mesh information is transformed into GPU texture and placed on apposite position of target mesh. 3D information is retrieved after stitching two mesh components from the primitive vertex coordinates. When running real-time mesh cloning operator, our mesh editing approach can copy arbitrary irregular geometric features from source mesh to target mesh. Experimental results indicate that our method can outperform previous related mesh editing techniques.

  20. Towards Normalizing the Edit Distance Using a Genetic Algorithms-Based Scheme

    OpenAIRE

    Muhammad Fuad, Muhammad Marwan

    2012-01-01

    The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in terms of edit operations but rather in terms of the edit path. In this paper we propose a new derivative of the edit distance that also takes into consideration the lengths of the two strings, but the new distance is related directly to the edit distance. The ...

  1. Towards social acceptance of plant breeding by genome editing.

    Science.gov (United States)

    Araki, Motoko; Ishii, Tetsuya

    2015-03-01

    Although genome-editing technologies facilitate efficient plant breeding without introducing a transgene, it is creating indistinct boundaries in the regulation of genetically modified organisms (GMOs). Rapid advances in plant breeding by genome-editing require the establishment of a new global policy for the new biotechnology, while filling the gap between process-based and product-based GMO regulations. In this Opinion article we review recent developments in producing major crops using genome-editing, and we propose a regulatory model that takes into account the various methodologies to achieve genetic modifications as well as the resulting types of mutation. Moreover, we discuss the future integration of genome-editing crops into society, specifically a possible response to the 'Right to Know' movement which demands labeling of food that contains genetically engineered ingredients.

  2. A Method for Genome Editing in Human Pluripotent Stem Cells.

    Science.gov (United States)

    Smith, Cory; Ye, Zhaohui; Cheng, Linzhao

    2016-01-01

    Human pluripotent stem cells (PSCs) hold great potential for regenerative medicine and currently are being used as a research tool for basic discovery and disease modeling. To evaluate the role of a single genetic variant, a system of genome editing is needed to precisely mutate any desired DNA sequence in isolation and measure its effect on phenotype when compared to the isogenic parental PSC from which it was derived. This protocol describes the general targeting schemes used by researchers to edit PSCs to knock out, knock-in, or precisely alter a single nucleotide, covering conditions for electroporation, clonal isolation, and screening of edited PSCs for the targeted mutation. These recent advances simplify the procedure for genome editing, allowing individual researchers to induce nearly any desired mutation to further study its function or to reverse a disease-causing variant for future applications in regenerative medicine. PMID:27037073

  3. Developing Editing Skills in the Beginning Technical Writing Class.

    Science.gov (United States)

    Forbes, Christopher J.

    1986-01-01

    Offers a plan for developing student editing skills in the beginning technical writing class. Suggests guidelines that parallel the revision-oriented heuristics of such scholars as Michael Flanigan and Linda Flower. (FL)

  4. Air Sampling Instruments for Evaluation of Atmospheric Contaminants. Fourth Edition.

    Science.gov (United States)

    American Conference of Governmental Industrial Hygienists, Cincinnati, OH.

    This text, a revision and extension of the first three editions, consists of papers discussing the basic considerations in sampling air for specific purposes, sampler calibration, systems components, sample collectors, and descriptions of air-sampling instruments. (BT)

  5. Towards social acceptance of plant breeding by genome editing.

    Science.gov (United States)

    Araki, Motoko; Ishii, Tetsuya

    2015-03-01

    Although genome-editing technologies facilitate efficient plant breeding without introducing a transgene, it is creating indistinct boundaries in the regulation of genetically modified organisms (GMOs). Rapid advances in plant breeding by genome-editing require the establishment of a new global policy for the new biotechnology, while filling the gap between process-based and product-based GMO regulations. In this Opinion article we review recent developments in producing major crops using genome-editing, and we propose a regulatory model that takes into account the various methodologies to achieve genetic modifications as well as the resulting types of mutation. Moreover, we discuss the future integration of genome-editing crops into society, specifically a possible response to the 'Right to Know' movement which demands labeling of food that contains genetically engineered ingredients. PMID:25726138

  6. A model for codon position bias in RNA editing

    CERN Document Server

    Liu, T; Liu, Tsunglin; Bundschuh, Ralf

    2005-01-01

    RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of {\\it Physarum polycephalum}, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in {\\it Physarum}. This suggests that the codon position bias in {\\it Physarum} is mainly a consequence of selection at the protein level.

  7. [The Washington summit: orange light for genome editing?].

    Science.gov (United States)

    Jordan, Bertrand

    2016-02-01

    The summit organised in early December 2015 considered in depth the various issues (technical, scientific, societal and ethical) raised by the prospect of genome editing using the extremely effective CRISPR system. Germline editing (for therapeutic or "enhancement" purposes) was stated to be irresponsible under current conditions, but the possibility that this could be considered in the future was not excluded; a mechanism for monitoring progress and possibly revising recommendations was proposed.

  8. SCOPE: A Scientific Compound Object Publishing and Editing System

    OpenAIRE

    Kwok Cheung; Jane Hunter; Anna Lashtabeg; John Drennan

    2008-01-01

    This paper presents the SCOPE (Scientific Compound Object Publishing and Editing) system which is designed to enable scientists to easily author, publish and edit scientific compound objects. Scientific compound objects encapsulate the various datasets and resources generated or utilized during a scientific experiment or discovery process, within a single compound object, for publishing and exchange. The adoption of “named graphs” to represent these compound objects enables provenance informa...

  9. The edit distance for Reeb graphs of surfaces

    OpenAIRE

    Di Fabio, Barbara; Landi, Claudia

    2014-01-01

    Reeb graphs are structural descriptors that capture shape properties of a topological space from the perspective of a chosen function. In this work we define a combinatorial metric for Reeb graphs of orientable surfaces in terms of the cost necessary to transform one graph into another by edit operations. The main contributions of this paper are the stability property and the optimality of this edit distance. More precisely, the stability result states that changes in the functions, measur...

  10. Approximate Membership for Regular Languages modulo the Edit Distance

    OpenAIRE

    Ndione, Antoine,; Lemay, Aurélien; Niehren, Joachim

    2013-01-01

    We present a probabilistic algorithm for testing approximate membership of words to regular languages modulo the edit distance. The time complexity of our algorithm, which is independent of the size of the input word, is polynomial in the size of the input automaton and the inverse error precision. All previous property testing algorithms for regular languages, whether they consider approximations modulo the Hamming distance or the edit distance with moves, run in exponential time if not fixi...

  11. Oligonucleotide-mediated gene editing of Apolipoprotein A-I.

    OpenAIRE

    Disterer, P

    2008-01-01

    Apolipoprotein A-I (ApoA-I) is the major protein constituent of high density lipoprotein (HDL) and controls reverse cholesterol transport, an important process in preventing atherosclerosis. A natural point mutation, ApoA-lMiiano (ApoA-Im) enhances the atheroprotective potential of HDL. Here, I attempt to introduce this specific modification into the genome of mammalian cells using the gene therapy strategy of oligonucleotide-mediated gene editing. I showed successful APOA-I gene editing in r...

  12. SECONDARY RECEPTOR EDITING IN THE GENERATION OF AUTOIMMUNITY

    Science.gov (United States)

    Eisenberg, Robert A.

    2012-01-01

    Receptor editing is the process that replaces the heavy chain or light chain variable region genes in a B-cell immunoglobulin receptor that is already productively rearranged. It is a major mechanism in the bone marrow for maintaining B-cell tolerance to autoantigens. We propose that a pathological autoimmune process can use receptor editing to induce the de novo creation and activation of B cells with autoreactive receptors in the peripheral immune system. PMID:22349618

  13. [The Washington summit: orange light for genome editing?].

    Science.gov (United States)

    Jordan, Bertrand

    2016-02-01

    The summit organised in early December 2015 considered in depth the various issues (technical, scientific, societal and ethical) raised by the prospect of genome editing using the extremely effective CRISPR system. Germline editing (for therapeutic or "enhancement" purposes) was stated to be irresponsible under current conditions, but the possibility that this could be considered in the future was not excluded; a mechanism for monitoring progress and possibly revising recommendations was proposed. PMID:26936181

  14. Towards a critical edition of Fibonacci’s Liber Abaci

    Directory of Open Access Journals (Sweden)

    Giuseppe Germano

    2013-11-01

    Full Text Available A group of research working at the University of Naples Federico II aim to achieve the goal to offer a modern scientific and widely accessible edition of Fibonacci’s treatise. With a linguistic-philological, an historical-mathematical and a computer approach it has pointed out the value and the need for a multidisciplinary research in order to achieve the goal of making this edition adequately available to the scientific community.

  15. Transmission Electron Microscopy and Diffractometry of Materials (Third Edition)

    OpenAIRE

    Fultz, Brent; Howe, James M.

    2007-01-01

    This book explains concepts of transmission electron microscopy (TEM) and x-ray diffractometry (XRD) that are important for the characterization of materials. The third edition has been updated to cover important technical developments, including the remarkable recent improvement in resolution of the TEM. This edition is not substantially longer than the second, but all chapters have been updated and revised for clarity. A new chapter on high resolution STEM methods has been added. The book e...

  16. Spatio-temporal regulation of ADAR editing during development in porcine neural tissues

    DEFF Research Database (Denmark)

    Venø, Morten Trillingsgaard; Bramsen, Jesper Bertram; Bendixen, Christian;

    2012-01-01

    Editing by ADAR enzymes is essential for mammalian life. Still, knowledge of the spatio-temporal editing patterns in mammals is limited. By use of 454 amplicon sequencing we examined the editing status of 12 regionally extracted mRNAs from porcine developing brain encompassing a total of 64 putat...... putative ADAR editing sites. In total 24 brain tissues, dissected from up to five regions from embryonic gestation day 23, 42, 60, 80, 100 and 115, were examined for editing....

  17. Statistical optimisation techniques in fatigue signal editing problem

    Energy Technology Data Exchange (ETDEWEB)

    Nopiah, Z. M.; Osman, M. H. [Fundamental Engineering Studies Unit Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM (Malaysia); Baharin, N.; Abdullah, S. [Department of Mechanical and Materials Engineering Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM (Malaysia)

    2015-02-03

    Success in fatigue signal editing is determined by the level of length reduction without compromising statistical constraints. A great reduction rate can be achieved by removing small amplitude cycles from the recorded signal. The long recorded signal sometimes renders the cycle-to-cycle editing process daunting. This has encouraged researchers to focus on the segment-based approach. This paper discusses joint application of the Running Damage Extraction (RDE) technique and single constrained Genetic Algorithm (GA) in fatigue signal editing optimisation.. In the first section, the RDE technique is used to restructure and summarise the fatigue strain. This technique combines the overlapping window and fatigue strain-life models. It is designed to identify and isolate the fatigue events that exist in the variable amplitude strain data into different segments whereby the retention of statistical parameters and the vibration energy are considered. In the second section, the fatigue data editing problem is formulated as a constrained single optimisation problem that can be solved using GA method. The GA produces the shortest edited fatigue signal by selecting appropriate segments from a pool of labelling segments. Challenges arise due to constraints on the segment selection by deviation level over three signal properties, namely cumulative fatigue damage, root mean square and kurtosis values. Experimental results over several case studies show that the idea of solving fatigue signal editing within a framework of optimisation is effective and automatic, and that the GA is robust for constrained segment selection.

  18. Statistical optimisation techniques in fatigue signal editing problem

    International Nuclear Information System (INIS)

    Success in fatigue signal editing is determined by the level of length reduction without compromising statistical constraints. A great reduction rate can be achieved by removing small amplitude cycles from the recorded signal. The long recorded signal sometimes renders the cycle-to-cycle editing process daunting. This has encouraged researchers to focus on the segment-based approach. This paper discusses joint application of the Running Damage Extraction (RDE) technique and single constrained Genetic Algorithm (GA) in fatigue signal editing optimisation.. In the first section, the RDE technique is used to restructure and summarise the fatigue strain. This technique combines the overlapping window and fatigue strain-life models. It is designed to identify and isolate the fatigue events that exist in the variable amplitude strain data into different segments whereby the retention of statistical parameters and the vibration energy are considered. In the second section, the fatigue data editing problem is formulated as a constrained single optimisation problem that can be solved using GA method. The GA produces the shortest edited fatigue signal by selecting appropriate segments from a pool of labelling segments. Challenges arise due to constraints on the segment selection by deviation level over three signal properties, namely cumulative fatigue damage, root mean square and kurtosis values. Experimental results over several case studies show that the idea of solving fatigue signal editing within a framework of optimisation is effective and automatic, and that the GA is robust for constrained segment selection

  19. Genome Editing: A New Approach to Human Therapeutics.

    Science.gov (United States)

    Porteus, Matthew

    2016-01-01

    The ability to manipulate the genome with precise spatial and nucleotide resolution (genome editing) has been a powerful research tool. In the past decade, the tools and expertise for using genome editing in human somatic cells and pluripotent cells have increased to such an extent that the approach is now being developed widely as a strategy to treat human disease. The fundamental process depends on creating a site-specific DNA double-strand break (DSB) in the genome and then allowing the cell's endogenous DSB repair machinery to fix the break such that precise nucleotide changes are made to the DNA sequence. With the development and discovery of several different nuclease platforms and increasing knowledge of the parameters affecting different genome editing outcomes, genome editing frequencies now reach therapeutic relevance for a wide variety of diseases. Moreover, there is a series of complementary approaches to assessing the safety and toxicity of any genome editing process, irrespective of the underlying nuclease used. Finally, the development of genome editing has raised the issue of whether it should be used to engineer the human germline. Although such an approach could clearly prevent the birth of people with devastating and destructive genetic diseases, questions remain about whether human society is morally responsible enough to use this tool.

  20. Molecular Biology of the Cell, Sixth Edition; ISBN: 9780815344643; and Molecular Biology of the Cell, Sixth Edition, The Problems Book; ISBN 9780815344537

    Directory of Open Access Journals (Sweden)

    Stephen Bustin

    2015-11-01

    Full Text Available The latest edition maintains the excellence and appeal of the previous editions. Its clear text and outstanding illustrations, together with the complementary problems book make this an essential companion for students and lecturers alike.

  1. Labview advanced programming techniques, second edition

    CERN Document Server

    Bitter, Rick; Nawrocki, Matt

    2006-01-01

    Whether seeking deeper knowledge of LabVIEW®'s capabilities or striving to build enhanced VIs, professionals know they will find everything they need in LabVIEW: Advanced Programming Techniques. Now accompanied by LabVIEW 2011, this classic second edition, focusing on LabVIEW 8.0, delves deeply into the classic features that continue to make LabVIEW one of the most popular and widely used graphical programming environments across the engineering community. The authors review the front panel controls, the Standard State Machine template, drivers, the instrument I/O assistant, error handling functions, hyperthreading, and Express VIs. It covers the introduction of the Shared Variables function in LabVIEW 8.0 and explores the LabVIEW project view. The chapter on ActiveX includes discussion of the Microsoft™ .NET® framework and new examples of programming in LabVIEW using .NET. Numerous illustrations and step-by-step explanations provide hands-on guidance. Reviewing LabVIEW 8.0 and accompanied by the latest s...

  2. Biomass Energy Data Book: Edition 4

    Energy Technology Data Exchange (ETDEWEB)

    Boundy, Robert Gary [ORNL; Diegel, Susan W [ORNL; Wright, Lynn L [ORNL; Davis, Stacy Cagle [ORNL

    2011-12-01

    The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Biomass Program in the Energy Efficiency and Renewable Energy (EERE) program of the Department of Energy (DOE). Designed for use as a convenient reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use, including discussions on sustainability. This is the fourth edition of the Biomass Energy Data Book which is only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass, is a section on biofuels which covers ethanol, biodiesel and bio-oil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is on the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also two appendices which include frequently needed conversion factors, a table of selected biomass feedstock characteristics, and discussions on sustainability. A glossary of terms and a list of acronyms are also included for the reader's convenience.

  3. Biomass Energy Data Book: Edition 3

    Energy Technology Data Exchange (ETDEWEB)

    Boundy, Robert Gary [ORNL; Davis, Stacy Cagle [ORNL

    2010-12-01

    The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Biomass Program in the Energy Efficiency and Renewable Energy (EERE) program of the Department of Energy (DOE). Designed for use as a convenient reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use, including discussions on sustainability. This is the third edition of the Biomass Energy Data Book which is only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass, is a section on biofuels which covers ethanol, biodiesel and bio-oil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is on the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also four appendices which include frequently needed conversion factors, a table of selected biomass feedstock characteristics, and discussions on sustainability. A glossary of terms and a list of acronyms are also included for the reader's convenience.

  4. Comparative biomechanics: life's physical world (second edition)

    CERN Document Server

    Vogel, Steven

    2013-01-01

    Why do you switch from walking to running at a specific speed? Why do tall trees rarely blow over in high winds? And why does a spore ejected into air at seventy miles per hour travel only a fraction of an inch? Comparative Biomechanics is the first and only textbook that takes a comprehensive look at the mechanical aspects of life--covering animals and plants, structure and movement, and solids and fluids. An ideal entry point into the ways living creatures interact with their immediate physical world, this revised and updated edition examines how the forms and activities of animals and plants reflect the materials available to nature, considers rules for fluid flow and structural design, and explores how organisms contend with environmental forces. Drawing on physics and mechanical engineering, Steven Vogel looks at how animals swim and fly, modes of terrestrial locomotion, organism responses to winds and water currents, circulatory and suspension-feeding systems, and the relationship between size and mech...

  5. The sun and space weather Second Edition

    CERN Document Server

    Hanslmeier, Arnold

    2007-01-01

    This second edition is a great enhancement of literature which will help the reader get deeper into the specific topics. There are new sections included such as space weather data sources and examples, new satellite missions, and the latest results. At the end a comprehensive index is given which will allow the reader to quickly find his topics of interest. The Sun and Space weather are two rapidly evolving topics. The importance of the Sun for the Earth, life on Earth, climate and weather processes was recognized long ago by the ancients. Now, for the first time there is a continuous surveillance of solar activity at nearly all wavelengths. These data can be used to improve our understanding of the complex Sun-Earth interaction. The first chapters of the book deal with the Sun as a star and its activity phenomena as well as its activity cycle in order to understand the complex physics of the Sun-Earth system. The reader will see that there are many phenomena but still no definite explanations and models exis...

  6. Transportation energy data book: Edition 15

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    1995-05-01

    The Transportation Energy Data Book: Edition 15 is a statistical compendium. Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. Purpose of this document is to present relevant statistical data in the form of tables and graphs. Each of the major transportation modes is treated in separate chapters or sections. Chapter I compares US transportation data with data from other countries. Aggregate energy use and energy supply data for all modes are presented in Chapter 2. The highway mode, which accounts for over three-fourths of total transportation energy consumption, is dealt with in Chapter 3. Topics in this chapter include automobiles, trucks, buses, fleet vehicles, federal standards, fuel economies, and high-occupancy vehicle lane data. Household travel behavior characteristics are displayed in Chapter 4. Chapter 5 contains information on alternative fuels and alternative fuel vehicles. Chapter 6 covers the major nonhighway modes: air, water, and rail. The last chapter, Chapter 7, presents data environmental issues relating to transportation.

  7. KEIMS utility manual (edition 1.0)

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yeun Seung; Eom, Young Sam; Choi, Jin Yeup; Nam, Ji Hwa [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1996-06-01

    Since 1987 when KAERI had started Yonggwang 3 and 4 NSSS system design project, KAERI has carried out so many NSSS system design projects such as Ulchin 3 and 4, Wolsong 2, 3 and 4 and Yonggwang 5 and 6 with fixed members that necessity of increasing productivity has been raised. To improve design work efficiency, it was considered that computerization of workflow which took so much man-power and business time. As result of investigation of design workflow to reduce man-power loss. It was suggested that DDA (Document Distribution for Agreement) workflow, design document stored in DDCD (Document Distribution and Control Center), IOC (Interoffice Correspondence) document, Letter, PM Memo should be preferentially computerized. On the basis of these computerization requirements, MEDIS (Modular Engineering Document Imaging System) was selected. Prototype had been implemented during 1995.9 -1995.12, and from 1996.1 KEIMS (KAERI Engineering Information Management System) has been operated. This MEDIS system utility manual was composed of several technical memos which has been described on customization of MEDIS fit to KEIMS, program development for system check, and information control of database. Further edition would be released as utility technical memo added. (Author) .new.

  8. Biomass Energy Data Book: Edition 2

    Energy Technology Data Exchange (ETDEWEB)

    Wright, Lynn L [ORNL; Boundy, Robert Gary [ORNL; Badger, Philip C [ORNL; Perlack, Robert D [ORNL; Davis, Stacy Cagle [ORNL

    2009-12-01

    The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Biomass Program in the Energy Efficiency and Renewable Energy (EERE) program of the Department of Energy (DOE). Designed for use as a convenient reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use, including discussions on sustainability. This is the second edition of the Biomass Energy Data Book which is only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass, is a section on biofuels which covers ethanol, biodiesel and bio-oil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is on the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also four appendices which include frequently needed conversion factors, a table of selected biomass feedstock characteristics, assumptions for selected tables and figures, and discussions on sustainability. A glossary of terms and a list of acronyms are also included for the reader's convenience.

  9. Transportation energy data book: edition 16

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C. [Lockheed Martin Energy Systems, Inc., Oak Ridge, TN (United States); McFarlin, D.N. [Tennessee Univ., Knoxville, TN (United States)

    1996-07-01

    The Transportation Energy Data Book: Edition 16 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. Each of the major transportation modes is treated in separate chapters or sections. Chapter 1 compares U.S. transportation data with data from other countries. Aggregate energy use and energy supply data for all modes are presented in Chapter 2. The highway mode, which accounts for over three-fourths of total transportation energy consumption, is dealt with in Chapter 3. Topics in this chapter include automobiles, trucks, buses, fleet vehicles, federal standards, fuel economies, and high- occupancy vehicle lane data. Household travel behavior characteristics are displayed in Chapter 4. Chapter 5 contains information on alternative fuels and alternative fuel vehicles. Chapter 6 covers the major nonhighway modes: air, water, and rail. The last chapter, Chapter 7, presents data on environmental issues relating to transportation.

  10. Biomass Energy Data Book: Edition 1

    Energy Technology Data Exchange (ETDEWEB)

    Wright, Lynn L [ORNL; Boundy, Robert Gary [ORNL; Perlack, Robert D [ORNL; Davis, Stacy Cagle [ORNL; Saulsbury, Bo [ORNL

    2006-09-01

    The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of the Biomass Program and the Office of Planning, Budget and Analysis in the Department of Energy's Energy Efficiency and Renewable Energy (EERE) program. Designed for use as a desk-top reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use. This is the first edition of the Biomass Energy Data Book and is currently only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass is a section on biofuels which covers ethanol, biodiesel and BioOil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is about the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also three appendices which include measures of conversions, biomass characteristics and assumptions for selected tables and figures. A glossary of terms and a list of acronyms are also included for the reader's convenience.

  11. Toward Modeling the Social Edition: An Approach to Understanding the Electronic Scholarly Edition in the Context of New and Emerging Social Media

    NARCIS (Netherlands)

    R. Siemens; M. Timney; C. Leitch; C. Koolen; A. Garnett

    2012-01-01

    This article explores building blocks in extant and emerging social media toward the possibilities they offer to the scholarly edition in electronic form, positing that we are witnessing the nascent stages of a new ‘social’ edition existing at the intersection of social media and digital editing. Be

  12. Practical Concerns Regarding the 7th Edition AJCC Staging Guidelines

    Directory of Open Access Journals (Sweden)

    D. Buethe

    2011-01-01

    Full Text Available The 7th edition of the AJCC Cancer Staging Manual represents a dramatic shift in the way that cutaneous squamous cell carcinoma (cSCC is staged, in that it is first attempt to incorporate evidence-based medicine into the staging guidelines for cSCC. In our opinion, the changes made to the seventh edition represent a significant improvement over previous editions and will ultimately lead to improved patient stratification, more accurate prognostic data, and a better framework to guide clinical decision making. However, there are a number of issues within the latest guidelines that require clarification or are impractical for clinical practice. The purpose of this paper is to highlight the key changes to the 6th edition staging manual as they pertain to cSCC, to point out impractical component of the 7th edition and/or aspects that require further clarification, and to make recommendations that address any current shortcomings to improve subsequent editions. Specific focus will be given to the inclusion of separate guidelines for cSCC and Merkel cell carcinoma (MCC, the incorporation of high-risk factors as modifiers of T stage, the addition of new guidelines for advanced T stage, and the changes in stratification of lymph node status. This paper is modified from a more comprehensive treatment of the staging of nonmelanoma skin cancer by Warner and Cockerell entitled “The new 7th edition American joint committee on cancer staging of cutaneous nonmelanoma skin cancer: a critical review,” in the American Journal of Clinical Dermatology (paper accepted, pending publication.

  13. Organelle RNA recognition motif-containing (ORRM) proteins are plastid and mitochondrial editing factors in Arabidopsis.

    Science.gov (United States)

    Shi, Xiaowen; Bentolila, Stephane; Hanson, Maureen R

    2016-05-01

    Post-transcriptional C-to-U RNA editing occurs at specific sites in plastid and plant mitochondrial transcripts. Members of the Arabidopsis pentatricopeptide repeat (PPR) motif-containing protein family and RNA-editing factor Interacting Protein (RIP, also known as MORF) family have been characterized as essential components of the RNA editing apparatus. Recent studies reveal that several organelle-targeted RNA recognition motif (RRM)-containing proteins are involved in either plastid or mitochondrial RNA editing. ORRM1 (Organelle RRM protein 1) is essential for plastid editing, whereas ORRM2, ORRM3 and ORRM4 are involved in mitochondrial RNA editing. The RRM domain of ORRM1, ORRM3 and ORRM4 is required for editing activity, whereas the auxiliary RIP and Glycine-Rich (GR) domains mediate the ORRM proteins' interactions with other editing factors. The identification of the ORRM proteins as RNA editing factors further expands our knowledge of the composition of the editosome. PMID:27082488

  14. RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species.

    Science.gov (United States)

    Wang, Wenqin; Zhang, Wei; Wu, Yongrui; Maliga, Pal; Messing, Joachim

    2015-01-01

    RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor. PMID:26517707

  15. A Critical study and Analysis of the New Edition of Tarikh Beihaqi

    Directory of Open Access Journals (Sweden)

    فرامرز ادینه کلات

    2012-03-01

    Full Text Available The new edition of Tarikh Beihaqi, the precious work by Abu Al-Fazl Beihaqi, was published by attempts of Dr. Mohammad Jafar Yahaqi and Mahdi Seyyedi, in the winter of 2010. Before this, famous masters such as Adib Pishavari, Saeed Nafisi, Dr. Qasem Ghani, and Dr. Ali Akbar Fayyaz had edited this prominent work. The new edition and the research, however, is of a special value, for besides the accurate contrastive study of several manuscripts and previous editions, and providing a critical edition for it, many of the defects of the previous editions are corrected. Among the significant advantages of the new edition, a comprehensive preface, abundant explanations and corrigenda, and various indexes are to be mentioned. This essay is to present some corrective suggestions by a critical study on this new edition, mentioning advantages and strong points, as well as some defects. Key Words: Tarikh Beihaqi, Abu Al-Fazl Beihaqi, Editing, Textology.

  16. Deletions in cox2 mRNA result in loss of splicing and RNA editing and gain of novel RNA editing sites.

    Directory of Open Access Journals (Sweden)

    Stefanie Grüttner

    Full Text Available As previously demonstrated, the maize cox2 RNA is fully edited in cauliflower mitochondria. Use of constructs with a deleted cox2 intron, however, led to a loss of RNA editing at almost all editing sites, with only a few sites still partially edited. Likewise, one deletion in exon 1 and three in exon 2 abolish RNA editing at all cox2 sites analyzed. Furthermore, intron splicing is abolished using these deletions. Mutation of a cytosine residue, which is normally edited and localized directly adjacent to the intron, to thymidine did not result in restoration of splicing, indicating that the loss of splicing was not due to loss of RNA editing. One deletion in exon 2 did not lead to loss of splicing. Instead, most editing sites were found to be edited, only three were not edited. Unexpectedly, we observed additional RNA editing events at new sites. Thus it appears that deletions in the cox2 RNA sequence can have a strong effect on RNA processing, leading to loss of splicing, loss of editing at all sites, or even to a gain of new editing sites. As these effects are not limited to the vicinity of the respective deletions, but appear to be widespread or even affect all editing sites, they may not be explained by the loss of PPR binding sites. Instead, it appears that several parts of the cox2 transcript are required for proper RNA processing. This indicates the roles of the RNA sequence and structural elements in the recognition of the editing sites.

  17. Detailed phenotypic and molecular analyses of genetically modified mice generated by CRISPR-Cas9-mediated editing.

    Directory of Open Access Journals (Sweden)

    Bijal A Parikh

    Full Text Available The bacterial CRISPR-Cas9 system has been adapted for use as a genome editing tool. While several recent reports have indicated that successful genome editing of mice can be achieved, detailed phenotypic and molecular analyses of the mutant animals are limited. Following pronuclear micro-injection of fertilized eggs with either wild-type Cas9 or the nickase mutant (D10A and single or paired guide RNA (sgRNA for targeting of the tyrosinase (Tyr gene, we assessed genome editing in mice using rapid phenotypic readouts (eye and coat color. Mutant mice with insertions or deletions (indels in Tyr were efficiently generated without detectable off-target cleavage events. Gene correction of a single nucleotide by homologous recombination (HR could only occur when the sgRNA recognition sites in the donor DNA were modified. Gene repair did not occur if the donor DNA was not modified because Cas9 catalytic activity was completely inhibited. Our results indicate that allelic mosaicism can occur following -Cas9-mediated editing in mice and appears to correlate with sgRNA cleavage efficiency at the single-cell stage. We also show that larger than expected deletions may be overlooked based on the screening strategy employed. An unbiased analysis of all the deleted nucleotides in our experiments revealed that the highest frequencies of nucleotide deletions were clustered around the predicted Cas9 cleavage sites, with slightly broader distributions than expected. Finally, additional analysis of founder mice and their offspring indicate that their general health, fertility, and the transmission of genetic changes were not compromised. These results provide the foundation to interpret and predict the diverse outcomes following CRISPR-Cas9-mediated genome editing experiments in mice.

  18. Next-Generation Sequencing and Genome Editing in Plant Virology

    Science.gov (United States)

    Hadidi, Ahmed; Flores, Ricardo; Candresse, Thierry; Barba, Marina

    2016-01-01

    Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21–24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.

  19. Next-Generation Sequencing and Genome Editing in Plant Virology.

    Science.gov (United States)

    Hadidi, Ahmed; Flores, Ricardo; Candresse, Thierry; Barba, Marina

    2016-01-01

    Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology. PMID:27617007

  20. Next-Generation Sequencing and Genome Editing in Plant Virology

    Directory of Open Access Journals (Sweden)

    Ahmed Hadidi

    2016-08-01

    Full Text Available Next-generation sequencing (NGS has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus; beet curly top virus and beet severe curly top virus (curtovirus; and bean yellow dwarf virus (mastrevirus. The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus and cucumber vein yellowing virus (ipomovirus, family, Potyviridae by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.Keywords: Next-generation sequencing, NGS, plant virology, plant viruses, viroids, resistance to plant viruses by CRISPR-Cas9

  1. Next-Generation Sequencing and Genome Editing in Plant Virology

    Science.gov (United States)

    Hadidi, Ahmed; Flores, Ricardo; Candresse, Thierry; Barba, Marina

    2016-01-01

    Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21–24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology. PMID:27617007

  2. Geminivirus-Mediated Genome Editing in Potato (Solanum tuberosum L.) Using Sequence-Specific Nucleases.

    Science.gov (United States)

    Butler, Nathaniel M; Baltes, Nicholas J; Voytas, Daniel F; Douches, David S

    2016-01-01

    Genome editing using sequence-specific nucleases (SSNs) is rapidly being developed for genetic engineering in crop species. The utilization of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems (CRISPR/Cas) for inducing double-strand breaks facilitates targeting of virtually any sequence for modification. Targeted mutagenesis via non-homologous end-joining (NHEJ) has been demonstrated extensively as being the preferred DNA repair pathway in plants. However, gene targeting via homologous recombination (HR) remains more elusive but could be a powerful tool for directed DNA repair. To overcome barriers associated with gene targeting, a geminivirus replicon (GVR) was used to deliver SSNs targeting the potato ACETOLACTATE SYNTHASE1 (ALS1) gene and repair templates designed to incorporate herbicide-inhibiting point mutations within the ALS1 locus. Transformed events modified with GVRs held point mutations that were capable of supporting a reduced herbicide susceptibility phenotype, while events transformed with conventional T-DNAs held no detectable mutations and were similar to wild-type. Regeneration of transformed events improved detection of point mutations that supported a stronger reduced herbicide susceptibility phenotype. These results demonstrate the use of geminiviruses for delivering genome editing reagents in plant species, and a novel approach to gene targeting in a vegetatively propagated species. PMID:27493650

  3. A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells.

    Science.gov (United States)

    Findlay, Scott D; Vincent, Krista M; Berman, Jennifer R; Postovit, Lynne-Marie

    2016-01-01

    The rapid adoption of gene editing tools such as CRISPRs and TALENs for research and eventually therapeutics necessitates assays that can rapidly detect and quantitate the desired alterations. Currently, the most commonly used assay employs "mismatch nucleases" T7E1 or "Surveyor" that recognize and cleave heteroduplexed DNA amplicons containing mismatched base-pairs. However, this assay is prone to false positives due to cancer-associated mutations and/or SNPs and requires large amounts of starting material. Here we describe a powerful alternative wherein droplet digital PCR (ddPCR) can be used to decipher homozygous from heterozygous mutations with superior levels of both precision and sensitivity. We use this assay to detect knockout inducing alterations to stem cell associated proteins, NODAL and SFRP1, generated using either TALENs or an "all-in-one" CRISPR/Cas plasmid that we have modified for one-step cloning and blue/white screening of transformants. Moreover, we highlight how ddPCR can be used to assess the efficiency of varying TALEN-based strategies. Collectively, this work highlights how ddPCR-based screening can be paired with CRISPR and TALEN technologies to enable sensitive, specific, and streamlined approaches to gene editing and validation. PMID:27089539

  4. Uncertain Training Data Edition for Automatic Object-Based Change Map Extraction

    Science.gov (United States)

    Hajahmadi, S.; Mokhtarzadeh, M.; Mohammadzadeh, A.; Valadanzouj, M. J.

    2013-09-01

    Due to the rapid transformation of the societies, and the consequent growth of the cities, it is necessary to study these changes in order to achieve better control and management of urban areas and assist the decision-makers. Change detection involves the ability to quantify temporal effects using multi-temporal data sets. The available maps of the under study area is one of the most important sources for this reason. Although old data bases and maps are a great resource, it is more than likely that the training data extracted from them might contain errors, which affects the procedure of the classification; and as a result the process of the training sample editing is an essential matter. Due to the urban nature of the area studied and the problems caused in the pixel base methods, object-based classification is applied. To reach this, the image is segmented into 4 scale levels using a multi-resolution segmentation procedure. After obtaining the segments in required levels, training samples are extracted automatically using the existing old map. Due to the old nature of the map, these samples are uncertain containing wrong data. To handle this issue, an editing process is proposed according to K-nearest neighbour and k-means algorithms. Next, the image is classified in a multi-resolution object-based manner and the effects of training sample refinement are evaluated. As a final step this classified image is compared with the existing map and the changed areas are detected.

  5. Geminivirus-Mediated Genome Editing in Potato (Solanum tuberosum L.) Using Sequence-Specific Nucleases

    Science.gov (United States)

    Butler, Nathaniel M.; Baltes, Nicholas J.; Voytas, Daniel F.; Douches, David S.

    2016-01-01

    Genome editing using sequence-specific nucleases (SSNs) is rapidly being developed for genetic engineering in crop species. The utilization of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems (CRISPR/Cas) for inducing double-strand breaks facilitates targeting of virtually any sequence for modification. Targeted mutagenesis via non-homologous end-joining (NHEJ) has been demonstrated extensively as being the preferred DNA repair pathway in plants. However, gene targeting via homologous recombination (HR) remains more elusive but could be a powerful tool for directed DNA repair. To overcome barriers associated with gene targeting, a geminivirus replicon (GVR) was used to deliver SSNs targeting the potato ACETOLACTATE SYNTHASE1 (ALS1) gene and repair templates designed to incorporate herbicide-inhibiting point mutations within the ALS1 locus. Transformed events modified with GVRs held point mutations that were capable of supporting a reduced herbicide susceptibility phenotype, while events transformed with conventional T-DNAs held no detectable mutations and were similar to wild-type. Regeneration of transformed events improved detection of point mutations that supported a stronger reduced herbicide susceptibility phenotype. These results demonstrate the use of geminiviruses for delivering genome editing reagents in plant species, and a novel approach to gene targeting in a vegetatively propagated species. PMID:27493650

  6. Image editing with Adobe Photoshop 6.0.

    Science.gov (United States)

    Caruso, Ronald D; Postel, Gregory C

    2002-01-01

    The authors introduce Photoshop 6.0 for radiologists and demonstrate basic techniques of editing gray-scale cross-sectional images intended for publication and for incorporation into computerized presentations. For basic editing of gray-scale cross-sectional images, the Tools palette and the History/Actions palette pair should be displayed. The History palette may be used to undo a step or series of steps. The Actions palette is a menu of user-defined macros that save time by automating an action or series of actions. Converting an image to 8-bit gray scale is the first editing function. Cropping is the next action. Both decrease file size. Use of the smallest file size necessary for the purpose at hand is recommended. Final file size for gray-scale cross-sectional neuroradiologic images (8-bit, single-layer TIFF [tagged image file format] at 300 pixels per inch) intended for publication varies from about 700 Kbytes to 3 Mbytes. Final file size for incorporation into computerized presentations is about 10-100 Kbytes (8-bit, single-layer, gray-scale, high-quality JPEG [Joint Photographic Experts Group]), depending on source and intended use. Editing and annotating images before they are inserted into presentation software is highly recommended, both for convenience and flexibility. Radiologists should find that image editing can be carried out very rapidly once the basic steps are learned and automated.

  7. Oligonucleotide-directed mutagenesis for precision gene editing.

    Science.gov (United States)

    Sauer, Noel J; Mozoruk, Jerry; Miller, Ryan B; Warburg, Zachary J; Walker, Keith A; Beetham, Peter R; Schöpke, Christian R; Gocal, Greg F W

    2016-02-01

    Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed. PMID:26503400

  8. Physics and engineering of radiation detection

    CERN Document Server

    Ahmed, Syed Naeem

    2015-01-01

    Physics and Engineering of Radiation Detection presents an overview of the physics of radiation detection and its applications. It covers the origins and properties of different kinds of ionizing radiation, their detection and measurement, and the procedures used to protect people and the environment from their potentially harmful effects. The second edition is fully revised and provides the latest developments in detector technology and analyses software. Also, more material related to measurements in particle physics and a complete solutions manual have been added.

  9. Space Science Reference Guide, 2nd Edition

    Science.gov (United States)

    Dotson, Renee (Editor)

    2003-01-01

    This Edition contains the following reports: GRACE: Gravity Recovery and Climate Experiment; Impact Craters in the Solar System; 1997 Apparition of Comet Hale-Bopp Historical Comet Observations; Baby Stars in Orion Solve Solar System Mystery; The Center of the Galaxy; The First Rock in the Solar System; Fun Times with Cosmic Rays; The Gamma-Ray Burst Next Door; The Genesis Mission: An Overview; The Genesis Solar Wind Sample Return Mission; How to Build a Supermassive Black Hole; Journey to the Center of a Neutron Star; Kepler's Laws of Planetary Motion; The Kuiper Belt and Oort Cloud ; Mapping the Baby Universe; More Hidden Black Hole Dangers; A Polarized Universe; Presolar Grains of Star Dust: Astronomy Studied with Microscopes; Ring Around the Black Hole; Searching Antarctic Ice for Meteorites; The Sun; Astrobiology: The Search for Life in the Universe; Europa and Titan: Oceans in the Outer Solar System?; Rules for Identifying Ancient Life; Inspire ; Remote Sensing; What is the Electromagnetic Spectrum? What is Infrared? How was the Infrared Discovered?; Brief History of Gyroscopes ; Genesis Discovery Mission: Science Canister Processing at JSC; Genesis Solar-Wind Sample Return Mission: The Materials ; ICESat: Ice, Cloud, and Land Elevation Satellite ICESat: Ice, Cloud, and Land; Elevation Satellite ICESat: Ice, Cloud, and Land Elevation Satellite ICESat: Ice, Cloud, and Land Elevation Satellite ICESat: Ice, Cloud, and Land Elevation Satellite Measuring Temperature Reading; The Optical Telescope ; Space Instruments General Considerations; Damage by Impact: The Case at Meteor Crater, Arizona; Mercury Unveiled; New Data, New Ideas, and Lively Debate about Mercury; Origin of the Earth and Moon; Space Weather: The Invisible Foe; Uranus, Neptune, and the Mountains of the Moon; Dirty Ice on Mars; For a Cup of Water on Mars; Life on Mars?; The Martian Interior; Meteorites from Mars, Rocks from Canada; Organic Compounds in Martian Meteorites May be Terrestrial

  10. Recognition of Non-Compound Handwritten Devnagari Characters using a Combination of MLP and Minimum Edit Distance

    Directory of Open Access Journals (Sweden)

    S. Arora, D. Bhattacharjee, M. Nasipuri, D. K. Basu & M. Kundu

    2010-03-01

    Full Text Available This paper deals with a new method for recognition of offline Handwritten noncompoundDevnagari Characters in two stages. It uses two well known andestablished pattern recognition techniques: one using neural networks and theother one using minimum edit distance. Each of these techniques is applied ondifferent sets of characters for recognition. In the first stage, two sets of featuresare computed and two classifiers are applied to get higher recognition accuracy.Two MLP’s are used separately to recognize the characters. For one of theMLP’s the characters are represented with their shadow features and for theother chain code histogram feature is used. The decision of both MLP’s iscombined using weighted majority scheme. Top three results produced bycombined MLP’s in the first stage are used to calculate the relative differencevalues. In the second stage, based on these relative differences character set isdivided into two. First set consists of the characters with distinct shapes andsecond set consists of confused characters, which appear very similar in shapes.Characters of distinct shapes of first set are classified using MLP. Confused characters in second set are classified using minimum edit distance method.Method of minimum edit distance makes use of corner detected in a characterimage using modified Harris corner detection technique. Experiment on thismethod is carried out on a database of 7154 samples. The overall recognition isfound to be 90.74%.

  11. HMMEditor: a visual editing tool for profile hidden Markov model

    Directory of Open Access Journals (Sweden)

    Cheng Jianlin

    2008-03-01

    Full Text Available Abstract Background Profile Hidden Markov Model (HMM is a powerful statistical model to represent a family of DNA, RNA, and protein sequences. Profile HMM has been widely used in bioinformatics research such as sequence alignment, gene structure prediction, motif identification, protein structure prediction, and biological database search. However, few comprehensive, visual editing tools for profile HMM are publicly available. Results We develop a visual editor for profile Hidden Markov Models (HMMEditor. HMMEditor can visualize the profile HMM architecture, transition probabilities, and emission probabilities. Moreover, it provides functions to edit and save HMM and parameters. Furthermore, HMMEditor allows users to align a sequence against the profile HMM and to visualize the corresponding Viterbi path. Conclusion HMMEditor provides a set of unique functions to visualize and edit a profile HMM. It is a useful tool for biological sequence analysis and modeling. Both HMMEditor software and web service are freely available.

  12. Rome m: The functional gastrointestinal disorders, third edition, 2006

    Institute of Scientific and Technical Information of China (English)

    Randa Mostafa

    2008-01-01

    Functional gastrointestinal disorders (FGIDs) represent a common and important class of disorders within gastroenterology. Rome I, the first edition was published in 1994, with symptom-based diagnostic criteria for FGIDs. These criteria began to change the diagnostic approach to FGIDs, and no longer considered "diagnoses of exclusion" but rather "diagnoses of inclusion". Rome n, the second edition published in 2000, resulted from the continual process of analyzing new scientific and clinical evidence in the study of FGIDs. Rome n, diagnostic criteria for irritable bowel syndrome (IBS), was extended with a focus on the frequency of symptoms occurring twelve weeks (not necessarily consecutive weeks) within twelve months. ROME m, the third edition, conservative one, was published in September 2006, with changes made only where there is good evidence to do so. Some of the differences between Rome n and Rome m criteria are highlighted in this issue.

  13. Advances in therapeutic CRISPR/Cas9 genome editing.

    Science.gov (United States)

    Savić, Nataša; Schwank, Gerald

    2016-02-01

    Targeted nucleases are widely used as tools for genome editing. Two years ago the clustered regularly interspaced short palindromic repeat (CRISPR)-associated Cas9 nuclease was used for the first time, and since then has largely revolutionized the field. The tremendous success of the CRISPR/Cas9 genome editing tool is powered by the ease design principle of the guide RNA that targets Cas9 to the desired DNA locus, and by the high specificity and efficiency of CRISPR/Cas9-generated DNA breaks. Several studies recently used CRISPR/Cas9 to successfully modulate disease-causing alleles in vivo in animal models and ex vivo in somatic and induced pluripotent stem cells, raising hope for therapeutic genome editing in the clinics. In this review, we will summarize and discuss such preclinical CRISPR/Cas9 gene therapy reports.

  14. Simple Genome Editing of Rodent Intact Embryos by Electroporation.

    Directory of Open Access Journals (Sweden)

    Takehito Kaneko

    Full Text Available The clustered regularly interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas system is a powerful tool for genome editing in animals. Recently, new technology has been developed to genetically modify animals without using highly skilled techniques, such as pronuclear microinjection of endonucleases. Technique for animal knockout system by electroporation (TAKE method is a simple and effective technology that produces knockout rats by introducing endonuclease mRNAs into intact embryos using electroporation. Using TAKE method and CRISPR/Cas system, the present study successfully produced knockout and knock-in mice and rats. The mice and rats derived from embryos electroporated with Cas9 mRNA, gRNA and single-stranded oligodeoxynucleotide (ssODN comprised the edited targeted gene as a knockout (67% of mice and 88% of rats or knock-in (both 33%. The TAKE method could be widely used as a powerful tool to produce genetically modified animals by genome editing.

  15. Harnessing CRISPR-Cas systems for bacterial genome editing.

    Science.gov (United States)

    Selle, Kurt; Barrangou, Rodolphe

    2015-04-01

    Manipulation of genomic sequences facilitates the identification and characterization of key genetic determinants in the investigation of biological processes. Genome editing via clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) constitutes a next-generation method for programmable and high-throughput functional genomics. CRISPR-Cas systems are readily reprogrammed to induce sequence-specific DNA breaks at target loci, resulting in fixed mutations via host-dependent DNA repair mechanisms. Although bacterial genome editing is a relatively unexplored and underrepresented application of CRISPR-Cas systems, recent studies provide valuable insights for the widespread future implementation of this technology. This review summarizes recent progress in bacterial genome editing and identifies fundamental genetic and phenotypic outcomes of CRISPR targeting in bacteria, in the context of tool development, genome homeostasis, and DNA repair.

  16. Editing Newton in Geneva and Rome: The Annotated Edition of the Principia by Calandrini, Le Seur and Jacquier.

    Science.gov (United States)

    Guicciardini, Niccolò

    2015-07-01

    This contribution examines the circumstances of composition of the annotated edition of Newton's Principia that was printed in Geneva in 1739-1742, which ran to several editions and was still in print in Britain in the mid-nineteenth century. This edition was the work of the Genevan Professor of Mathematics, Jean Louis Calandrini, and of two Minim friars based in Rome, Thomas Le Seur and François Jacquier. The study of the context in which this edition was conceived sheds light on the early reception of Newtonianism in Geneva and Rome. By taking into consideration the careers of Calandrini, Le Seur and Jacquier, as authors, lecturers and leading characters of Genevan and Roman cultural life, I will show that their involvement in the enterprise of annotating Newton's Principia answered specific needs of Genevan and Roman culture. The publication and reception of the Genevan annotated edition has also a broader European dimension. Both Calandrini and Jacquier were in touch with the French république des lettres, most notably with Clairaut and Du Châtelet, and with the Bernoulli family in Basel. Therefore, this study is also relevant for the understanding of the dissemination of Newton's ideas in Europe.

  17. Explanatory Supplement to the Astronomical Almanac (3rd Edition)

    Science.gov (United States)

    Urban, Sean E.; Seidelmann, P. K.

    2014-01-01

    Publications and software from the the Astronomical Applications Department of the US Naval Observatory (USNO) are used throughout the world, not only in the Department of Defense for safe navigation, but by many people including other navigators, astronomers, aerospace engineers, and geodesists. Products such as The Nautical Almanac, The Astronomical Almanac, and the Multiyear Interactive Computer Almanac (MICA) are regarded as international standards. To maintain credibility, it is imperative that the methodologies employed and the data used are well documented. "The Explanatory Supplement to the Astronomical Almanac" (hereafter, "The ES") is a major source of such documentation. It is a comprehensive reference book on positional astronomy, covering the theories and algorithms used to produce The Astronomical Almanac, an annual publication produced jointly by the Nautical Almanac Office of USNO and Her Majesty's Nautical Almanac Office (HMNAO). The first edition of The ES appeared in 1961, and the second followed in 1992. Several major changes have taken place in fundamental astronomy since the second edition was published. Advances in radio observations allowed the celestial reference frame to be tied to extragalactic radio sources, thus the International Celestial Reference System replaced the FK5 system. The success of ESA's Hipparcos satellite dramatically altered observational astrometry. Improvements in Earth orientation observations lead to new precession and nutation theories. Additionally, a new positional paradigm, no longer tied to the ecliptic and equinox, was accepted. Largely because of these changes, staff at USNO and HMNAO decided the time was right for the next edition of The ES. The third edition is now available; it is a complete revision of the 1992 book. Along with subjects covered in the previous two editions, the book also contains descriptions of the major advancements in positional astronomy over the last 20 years, some of which are

  18. Efficient Mitochondrial Genome Editing by CRISPR/Cas9

    Directory of Open Access Journals (Sweden)

    Areum Jo

    2015-01-01

    Full Text Available The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9 system has been widely used for nuclear DNA editing to generate mutations or correct specific disease alleles. Despite its flexible application, it has not been determined if CRISPR/Cas9, originally identified as a bacterial defense system against virus, can be targeted to mitochondria for mtDNA editing. Here, we show that regular FLAG-Cas9 can localize to mitochondria to edit mitochondrial DNA with sgRNAs targeting specific loci of the mitochondrial genome. Expression of FLAG-Cas9 together with gRNA targeting Cox1 and Cox3 leads to cleavage of the specific mtDNA loci. In addition, we observed disruption of mitochondrial protein homeostasis following mtDNA truncation or cleavage by CRISPR/Cas9. To overcome nonspecific distribution of FLAG-Cas9, we also created a mitochondria-targeted Cas9 (mitoCas9. This new version of Cas9 localizes only to mitochondria; together with expression of gRNA targeting mtDNA, there is specific cleavage of mtDNA. MitoCas9-induced reduction of mtDNA and its transcription leads to mitochondrial membrane potential disruption and cell growth inhibition. This mitoCas9 could be applied to edit mtDNA together with gRNA expression vectors without affecting genomic DNA. In this brief study, we demonstrate that mtDNA editing is possible using CRISPR/Cas9. Moreover, our development of mitoCas9 with specific localization to the mitochondria should facilitate its application for mitochondrial genome editing.

  19. Efficient and allele-specific genome editing of disease loci in human iPSCs.

    Science.gov (United States)

    Smith, Cory; Abalde-Atristain, Leire; He, Chaoxia; Brodsky, Brett R; Braunstein, Evan M; Chaudhari, Pooja; Jang, Yoon-Young; Cheng, Linzhao; Ye, Zhaohui

    2015-03-01

    Efficient and precise genome editing is crucial for realizing the full research and therapeutic potential of human induced pluripotent stem cells (iPSCs). Engineered nucleases including CRISPR/Cas9 and transcription activator like effector nucleases (TALENs) provide powerful tools for enhancing gene-targeting efficiency. In this study, we investigated the relative efficiencies of CRISPR/Cas9 and TALENs in human iPSC lines for inducing both homologous donor-based precise genome editing and nonhomologous end joining (NHEJ)-mediated gene disruption. Significantly higher frequencies of NHEJ-mediated insertions/deletions were detected at several endogenous loci using CRISPR/Cas9 than using TALENs, especially at nonexpressed targets in iPSCs. In contrast, comparable efficiencies of inducing homologous donor-based genome editing were observed at disease-associated loci in iPSCs. In addition, we investigated the specificity of guide RNAs used in the CRISPR/Cas9 system in targeting disease-associated point mutations in patient-specific iPSCs. Using myeloproliferative neoplasm patient-derived iPSCs that carry an acquired JAK2-V617F point mutation and α1-antitrypsin (AAT) deficiency patient-derived iPSCs that carry an inherited Z-AAT point mutation, we demonstrate that Cas9 can specifically target either the mutant or the wild-type allele with little disruption at the other allele differing by a single nucleotide. Overall, our results demonstrate the advantages of the CRISPR/Cas9 system in allele-specific genome targeting and in NHEJ-mediated gene disruption.

  20. Editing at the crossroad of innate and adaptive immunity.

    Science.gov (United States)

    Turelli, Priscilla; Trono, Didier

    2005-02-18

    Genetic information can be altered through the enzymatic modification of nucleotide sequences. This process, known as editing, was originally identified in the mitochondrial RNA of trypanosomes and later found to condition events as diverse as neurotransmission and lipid metabolism in mammals. Recent evidence reveals that editing enzymes may fulfill one of their most essential roles in the defense against infectious agents: first, as the mediators of antibody diversification, a step crucial for building adaptive immunity, and second, as potent intracellular poisons for the replication of viruses. Exciting questions are raised, which take us to the depth of the intimate relations between vertebrates and the microbial underworld.

  1. Recent Advances in Genome Editing Using CRISPR/Cas9

    OpenAIRE

    Ding, Yuduan; Li, Hong; Chen, Ling-Ling; Xie, Kabin

    2016-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is a versatile tool for genome engineering that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This simple RNA-guided genome-editing technology has become a revolutionary tool in biology and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing method, summarize the recent advances in CRISPR/Cas9 ...

  2. Atmel AVR Microcontroller Primer Programming and Interfacing, Second Edition

    CERN Document Server

    Barrett, Steven F

    2012-01-01

    This textbook provides practicing scientists and engineers a primer on the Atmel AVR microcontroller. In this second edition we highlight the popular ATmega164 microcontroller and other pin-for-pin controllers in the family with a complement of flash memory up to 128 kbytes. The second edition also adds a chapter on embedded system design fundamentals and provides extended examples on two different autonomous robots. Our approach is to provide the fundamental skills to quickly get up and operating with this internationally popular microcontroller. We cover the main subsystems aboard the ATmega

  3. In vivo genome editing using Staphylococcus aureus Cas9

    OpenAIRE

    Ran, F Ann; Cong, Le; Yan, Winston X.; Scott, David A.; Gootenberg, Jonathan S.; Kriz, Andrea J.; Zetsche, Bernd; Shalem, Ophir; Wu, Xuebing; Makarova, Kira S.; Koonin, Eugene; Sharp, Phillip A.; Zhang, Feng

    2015-01-01

    The RNA-guided endonuclease Cas9 has emerged as a versatile genome-editing platform. However, the size of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for basic research and therapeutic applications that employ the highly versatile adeno-associated virus (AAV) delivery vehicle. Here, we characterize six smaller Cas9 orthologs and show that Cas9 from Staphylococcus aureus (SaCas9) can edit the genome with efficiencies similar to those of SpCas9, while being >1...

  4. Inducible in vivo genome editing with CRISPR/Cas9

    OpenAIRE

    Dow, Lukas E.; Fisher, Jonathan; O'Rourke, Kevin P; Muley, Ashlesha; Kastenhuber, Edward R.; Livshits, Geulah; Tschaharganeh, Darjus F.; Socci, Nicholas D.; Lowe, Scott W.

    2015-01-01

    CRISPR/Cas9-based genome editing enables the rapid genetic manipulation of any genomic locus without the need for gene targeting by homologous recombination. Here we describe a conditional transgenic approach that allows temporal control of CRISPR/Cas9 activity for inducible genome editing in adult mice. We show that doxycycline-regulated Cas9 induction enables widespread gene disruption in multiple tissues and that limiting the duration of Cas9 expression or using a Cas9D10A (Cas9n) variant,...

  5. Approximating Edit Distance in Near-Linear Time

    OpenAIRE

    Andoni, Alexandr; Onak, Krzysztof

    2011-01-01

    We show how to compute the edit distance between two strings of length n up to a factor of 2^{\\~O(sqrt(log n))} in n^(1+o(1)) time. This is the first sub-polynomial approximation algorithm for this problem that runs in near-linear time, improving on the state-of-the-art n^(1/3+o(1)) approximation. Previously, approximation of 2^{\\~O(sqrt(log n))} was known only for embedding edit distance into l_1, and it is not known if that embedding can be computed in less than quadratic time.

  6. 78 FR 49271 - Draft Guidance for Industry on Frequently Asked Questions About Medical Foods; Second Edition...

    Science.gov (United States)

    2013-08-13

    ... HUMAN SERVICES Food and Drug Administration Draft Guidance for Industry on Frequently Asked Questions About Medical Foods; Second Edition; Availability AGENCY: Food and Drug Administration, HHS. ACTION... guidance for industry entitled ``Frequently Asked Questions About Medical Foods; Second Edition.''...

  7. Measurement and detection of radiation

    CERN Document Server

    Tsoulfanidis, Nicholas

    2015-01-01

    This fourth edition reflects recent major developments that have occurred in radiation detector materials, systems, and applications. It continues to provide the most practical and up-to-date introduction to radiation detector technology, proper measurement techniques, and analysis of results for engineers and scientists using radiation sources. New chapters emphasize the expanded use of radiation detection systems in nuclear non-proliferation, homeland security, and nuclear medicine. The book also discusses the correct ways to perform measurements following current health physics procedures.

  8. Application Progress of CRISPR/Cas9 System for Gene Editing in Tumor Research

    OpenAIRE

    Liu, Chao; Li, Zhiwei; Zhang, Yanqiao

    2015-01-01

    TCRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated nuclease 9) gene editing system is a new type of gene editing technology developed based on the immune mechanism of archaea resisting the invasion of exogenous nucleic acid. Compared with traditional gene editing system, CRISPR/Cas9 system is more efficient, easier operating, and less cytotoxic. Currently, CRISPR/Cas9 gene editing technology has been applied to many aspects of cancer research, including r...

  9. The moss Physcomitrella patens, a model plant for the study of RNA editing in plant organelles

    OpenAIRE

    Tasaki, Eiji; Sugita, Mamoru

    2010-01-01

    RNA editing is an enigmatic phenomenon in which specific cytidines (C) in the transcripts are changed to uridines (U). In flowering plants, over 500 editing sites have been identified in the mitochondria and plastids. By contrast, in a moss Physcomitrella patens, only 12 editing sites are found in both organelles. Recent extensive genetics studies have revealed involvement of the pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain (PPR-DYW) in site-specific RNA editing events...

  10. Dynamic Generation and Editing System for Wrongly Written Chinese Characters Font

    OpenAIRE

    Qingsheng Li; Xiao Li

    2015-01-01

    The uniqueness of Chinese makes Chinese language a hotspot in language learning. In view of the problem of wrongly written character teaching in Chinese language teaching, it provides a simple, convenient, and efficient input method of wrongly written characters and realizes a dynamic generation and editing system for wrongly written Chinese character font, which solves the problems of real-time edit, coding, and input of wrongly written character in editing process using dynamic editing tech...

  11. Editing efficiency of a Drosophila gene correlates with a distant splice site selection

    OpenAIRE

    AGRAWAL, RITESH; Stormo, Gary D.

    2005-01-01

    RNA editing and alternative splicing are two processes that increase protein diversity. The relationship between the two processes is not well understood. There are a few examples of correlations between editing and alternative splicing, but these are all nearby effects. A search for alternative splicing among 16 edited genes in Drosophila reveals two novel instances of alternative splicing. In one example where alternative splicing occurs downstream of editing, a strong correlation between e...

  12. Standards of specialized diabetes care. Edited by Dedov II, Shestakova MV (6th edition

    Directory of Open Access Journals (Sweden)

    Ivan Ivanovich Dedov

    2013-06-01

    Full Text Available Dear Colleagues!We are glad to present the 6th Edition of Standards of Diabetes Care. These evidence-based guidelines were designed to standardize and facilitate diabetes care in all regions of the Russian Federation. The Standards are updated on the regular basis to incorporate new data and relevant recommendations from national and international clinical societies, including World Health Organization Guidelines (WHO, 2011, International Diabetes Federation (IDF, 2011, American Diabetes Association (ADA, 2013, American Association of Clinical Endocrinologists (AACE, 2009, International Society for Pediatric and Adolescent Diabetes (ISPAD, 2009 and Russian Association of Endocrinologists (RAE, 2011, 2012. Current edition of the “Standards” also integrates results of completed randomized clinical trials (ADVANCE, ACCORD, VADT, UKPDS, etc., as well as findings from the national studies of diabetes mellitus (DM, conducted in close partnership with a number of Russian hospitals.Latest data indicates that prevalence of DM increased during the last decade more than two-fold, reaching some 371 million patients by 2013. According to the current estimation by the International Diabetes Federation, every tenth inhabitant of the planet will be suffering from DM by 2030. These observations resulted in the UN Resolution 61/225 passed on 20.12.2006 that encouraged all Member States “to develop national policies for the prevention, treatment and care of diabetes”.Like many other countries, Russian Federation experiences a sharp rise in the prevalence of DM. According to Russian State Diabetes Register, there are at least 3.799 million patients with DM in this country. However, the epidemiological survey conducted by the Federal Endocrinology Research Centre during 2002-2010 suggests that actual prevalence is 3 to 4 times greater than the officially recognized and, by this estimate, amounts to 9-10 million persons, comprising 7% of the

  13. A population-based evaluation of the seventh edition of the TNM system for lung cancer

    DEFF Research Database (Denmark)

    Strand, T-E; Rostad, H; Wentzel-Larsen, T;

    2010-01-01

    and the seventh edition of the TNM system. We compared survival differences adjusting for known prognostic factors. Furthermore, we evaluated the overall predictive ability of both editions using Harrell's concordance index. Survival curves by stage for each of the editions were similar; however, a better...

  14. Financial Accounting for Local and State School Systems: 2014 Edition. NCES 2015-347

    Science.gov (United States)

    Allison, Gregory S.

    2015-01-01

    The 2014 edition of "Financial Accounting for Local and State School Systems" updates the 2009 (see ED505993) and 2003 editions of the handbook. The 2003 edition was the work of the NCES National Forum on Education Statistics, Core Finance Data Task Force. That task force systematically rewrote nearly the entire text, incorporating new…

  15. Substantive Editing as a Form of Plagiarism among Postgraduate Students in Australia

    Science.gov (United States)

    Lines, Lisa

    2016-01-01

    In university plagiarism policies, and in the research into plagiarism, one form of collusion remains virtually unacknowledged: substantive editing performed by editors. While almost all Australian universities allow postgraduate students to have their thesis professionally edited, "substantive" editing is prohibited. This article…

  16. Genes (including RNA editing information) - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RMG Genes... (including RNA editing information) Data detail Data name Genes (including RNA editing information...ase Site Policy | Contact Us Genes (including RNA editing information) - RMG | LSDB Archive ...

  17. Targeted genome editing of sweet orange using Cas9/sgRNA.

    Directory of Open Access Journals (Sweden)

    Hongge Jia

    Full Text Available Genetic modification, including plant breeding, has been widely used to improve crop yield and quality, as well as to increase disease resistance. Targeted genome engineering is expected to contribute significantly to future varietal improvement, and genome editing technologies using zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9/single guide RNA (sgRNA have already been successfully used to genetically modify plants. However, to date, there has been no reported use of any of the current genome editing approaches in sweet orange, an important fruit crop. In this study, we first developed a novel tool, Xcc-facilitated agroinfiltration, for enhancing transient protein expression in sweet orange leaves. We then successfully employed Xcc-facilitated agroinfiltration to deliver Cas9, along with a synthetic sgRNA targeting the CsPDS gene, into sweet orange. DNA sequencing confirmed that the CsPDS gene was mutated at the target site in treated sweet orange leaves. The mutation rate using the Cas9/sgRNA system was approximately 3.2 to 3.9%. Off-target mutagenesis was not detected for CsPDS-related DNA sequences in our study. This is the first report of targeted genome modification in citrus using the Cas9/sgRNA system-a system that holds significant promise for the study of citrus gene function and for targeted genetic modification.

  18. Outdoor Biology Instructional Strategies Trial Edition. Set III.

    Science.gov (United States)

    Fairwell, Kay, Ed.; And Others

    The predominant focus of the 24 Outdoor Biology Instructional Strategies (OBIS) Trial Edition Set III activities is on animal behavior, and the adaptations and diversity of both plants and animals. Night time activities, games, investigation, experimentation, and crafts are used to study ants, birds, clams, water snails, water striders, spiders,…

  19. Towards a Model of Critical Digital Edition of Lope's Theatre

    Directory of Open Access Journals (Sweden)

    Marco Presotto

    2015-01-01

    Full Text Available The article presents a project in progress that deals with the digital edition of Lope de Vega’s La dama boba. The article describes the rationale behind the main solutions adopted so far, as well as the context of production and the goals of the project.

  20. The LSAT Exposed: Tricks from 12 LSATs. Second Edition.

    Science.gov (United States)

    White, David M.

    This book discusses tricks for answering questions on the Law School Admission Test (LSAT). The tricks are based on an analysis of 12 editions of the LSAT which have been made public pursuant to New York's Truth in Testing Law. Sample LSAT questions published by the Law School Admission Council are referenced to exemplify the tricks' applications…

  1. Therapeutic Uses of Music with Older Adults. Second Edition

    Science.gov (United States)

    Clair, Alicia Ann; Memmott, Jenny

    2008-01-01

    In this comprehensively updated second edition, written by Alicia Ann Clair and Jenny Memmott the extraordinary benefits of music therapy for older adults are detailed. "Therapeutic Uses of Music with Older Adults" not only examines these benefits but also clarifies the reasons that music is beneficial. This important book shows both informal and…

  2. Pertinent Discussions Toward Modeling the Social Edition: Annotated Bibliographies

    NARCIS (Netherlands)

    R. Siemens; M. Timney; C. Leitch; C. Koolen; A. Garnett

    2012-01-01

    The two annotated bibliographies present in this publication document and feature pertinent discussions toward the activity of modeling the social edition, first exploring reading devices, tools and social media issues and, second, social networking tools for professional readers in the Humanities.

  3. Interactive graphic editing tools in bioluminescent imaging simulation

    Science.gov (United States)

    Li, Hui; Tian, Jie; Luo, Jie; Wang, Ge; Cong, Wenxiang

    2005-04-01

    It is a challenging task to accurately describe complicated biological tissues and bioluminescent sources in bioluminescent imaging simulation. Several graphic editing tools have been developed to efficiently model each part of the bioluminescent simulation environment and to interactively correct or improve the initial models of anatomical structures or bioluminescent sources. There are two major types of graphic editing tools: non-interactive tools and interactive tools. Geometric building blocks (i.e. regular geometric graphics and superquadrics) are applied as non-interactive tools. To a certain extent, complicated anatomical structures and bioluminescent sources can be approximately modeled by combining a sufficient large number of geometric building blocks with Boolean operators. However, those models are too simple to describe the local features and fine changes in 2D/3D irregular contours. Therefore, interactive graphic editing tools have been developed to facilitate the local modifications of any initial surface model. With initial models composed of geometric building blocks, interactive spline mode is applied to conveniently perform dragging and compressing operations on 2D/3D local surface of biological tissues and bioluminescent sources inside the region/volume of interest. Several applications of the interactive graphic editing tools will be presented in this article.

  4. System description: Isabelle/jEdit in 2014

    OpenAIRE

    Wenzel, Makarius

    2014-01-01

    This is an updated system description for Isabelle/jEdit, according to the official release Isabelle2014 (August 2014). The following new PIDE concepts are explained: asynchronous print functions and document overlays, syntactic and semantic completion, editor navigation, management of auxiliary files within the document-model.

  5. A Flexible Decision Tool for Implementing Post-editing Guidelines

    OpenAIRE

    Rico Pérez, Celia

    2012-01-01

    This paper presents a flexible tool which supports the decision making process involved in defining post-editing guidelines. It is inspired by the work of O’Brien (2012) towards a translation quality assessment model, briefly reviewed here with a view to No data (2012)

  6. Fostering Teacher Candidates' Reflective Practice through Video Editing

    Science.gov (United States)

    Trent, Margaret; Gurvitch, Rachel

    2015-01-01

    Recently, interest in using video to promote the reflective practice in preservice teacher education has increased. Video recordings of teaching incidents inspire the reflective practice in preservice teachers by allowing them to analyze instruction and view teaching in an objective light. As an extension of video recording, video editing has…

  7. Optimization of genome editing through CRISPR-Cas9 engineering.

    Science.gov (United States)

    Zhang, Jian-Hua; Adikaram, Poorni; Pandey, Mritunjay; Genis, Allison; Simonds, William F

    2016-04-01

    CRISPR (Clustered Regularly-Interspaced Short Palindromic Repeats)-Cas9 (CRISPR associated protein 9) has rapidly become the most promising genome editing tool with great potential to revolutionize medicine. Through guidance of a 20 nucleotide RNA (gRNA), CRISPR-Cas9 finds and cuts target protospacer DNA precisely 3 base pairs upstream of a PAM (Protospacer Adjacent Motif). The broken DNA ends are repaired by either NHEJ (Non-Homologous End Joining) resulting in small indels, or by HDR (Homology Directed Repair) for precise gene or nucleotide replacement. Theoretically, CRISPR-Cas9 could be used to modify any genomic sequences, thereby providing a simple, easy, and cost effective means of genome wide gene editing. However, the off-target activity of CRISPR-Cas9 that cuts DNA sites with imperfect matches with gRNA have been of significant concern because clinical applications require 100% accuracy. Additionally, CRISPR-Cas9 has unpredictable efficiency among different DNA target sites and the PAM requirements greatly restrict its genome editing frequency. A large number of efforts have been made to address these impeding issues, but much more is needed to fully realize the medical potential of CRISPR-Cas9. In this article, we summarize the existing problems and current advances of the CRISPR-Cas9 technology and provide perspectives for the ultimate perfection of Cas9-mediated genome editing.

  8. Baishideng's century goal: Editing and publishing high-quality articles

    Institute of Scientific and Technical Information of China (English)

    Lian-Sheng Ma

    2009-01-01

    Baishideng's goal over the next few years is to edit and publish high-quality articles through the open-access model, to maximize the benefits to members of the editorial board, authors and readers, as well as achieving social and economic benefits.

  9. Review of traffic conflicts technique studies. Third edition.

    NARCIS (Netherlands)

    Kraay, J.H.

    1983-01-01

    A review of literature concerning traffic conflicts technique studies is presented. The 204 references arranged, alphabetically by authors' names are given with abstracts. The procedure used in comping this survey is outlined. Third revised edition, with 103 new publications since 1979.

  10. Air Pollution Manual, Part 1--Evaluation. Second Edition.

    Science.gov (United States)

    Giever, Paul M., Ed.

    Due to the great increase in technical knowledge and improvement in procedures, this second edition has been prepared to update existing information. Air pollution legislation is reviewed. Sources of air pollution are examined extensively. They are treated in terms of natural sources, man-made sources, metropolitan regional emissions, emission…

  11. Using Technology with Classroom Instruction that Works. Second Edition

    Science.gov (United States)

    Kuhn, Matt; Hubbell, Elizabeth R.; Pitler, Howard

    2012-01-01

    If you've upgraded to the second edition of the landmark book "Classroom Instruction That Works," you need this companion guide to help you use technology to support research-based instruction. The authors follow the revised Instructional Planning Guide that makes it easier for you to know when to emphasize each of the instructional strategies,…

  12. Interactive Translation Prediction versus Conventional Post-editing in Practice

    DEFF Research Database (Denmark)

    Sanchis-Trilles, German; Alabau, Vicent; Buck, Christian;

    2014-01-01

    We conducted a field trial in computer-assisted professional translation to compare Interactive Translation Prediction (ITP) against conventional post- editing (PE) of machine translation (MT) output. In contrast to the conventional PE set-up, where an MT system first produces a static translatio...

  13. Action Research: Improving Schools and Empowering Educators. Third Edition

    Science.gov (United States)

    Mertler, Craig A.

    2011-01-01

    Written for pre- and in-service educators, this "Third Edition" of Craig A. Mertler's "Action Research: Improving Schools and Empowering Educators" introduces the process of conducting one's own classroom- or school-based action research in conjunction with everyday instructional practices and activities. The text provides educators with the…

  14. What! I Have To Give a Speech? 2nd Edition.

    Science.gov (United States)

    Snyder, Kenneth; Murphy, Thomas J.

    Noting that fear of public speaking is shared by people of all types, the second edition of this book offers practical, easy-to-follow strategies for confident and effective public speaking. The book discusses the following aspects of public speaking: what to talk about; how to research a topic; how to organize a speech; how to keep an audience…

  15. Fluency Training a Writing Skill: Editing for Concision

    Science.gov (United States)

    Dermer, Marshall L.; Lopez, Shannon L.; Messling, Paul A., III

    2009-01-01

    The goal of this study was to design and evaluate fluency-based training units to help students eliminate inconcision. Participants first completed a 1.5-hr lesson on writing concisely and then a 5-min test during which they edited sentences containing inconcise text from the training units. Subsequently, participants were randomly assigned to an…

  16. Test Review: Wechsler Abbreviated Scale of Intelligence, Second Edition

    Science.gov (United States)

    Irby, Sarah M.; Floyd, Randy G.

    2013-01-01

    The Wechsler Abbreviated Scale of Intelligence, Second Edition (WASI-II; Wechsler, 2011) is a brief intelligence test designed for individuals aged 6 through 90 years. It is a revision of the Wechsler Abbreviated Scale of Intelligence (WASI; Wechsler, 1999). During revision, there were three goals: enhancing the link between the Wechsler…

  17. Mathematics in Early Years Education. 3rd Edition

    Science.gov (United States)

    Montague-Smith, Ann; Price, Alison

    2012-01-01

    This third edition of the best-selling "Mathematics in Nursery Education" provides an accessible introduction to the teaching of mathematics in the early years. Covering all areas of mathematics learning--number and counting, calculation, pattern, shape, measures and data handling--it summarises the research findings and underlying key concepts…

  18. An Introduction to Early Childhood Studies. Second Edition

    Science.gov (United States)

    Maynard, Trisha, Ed.; Thomas, Nigel, Ed.

    2009-01-01

    The second edition of this best-selling textbook provides students and practitioners with a broad introduction to, and critical analysis of, the main theories and issues within the field of early childhood studies. The book adopts a multi-disciplinary approach and pulls together all the key themes involved in the study of young children and…

  19. Introduction to Approaches in Music Therapy. Second Edition

    Science.gov (United States)

    Darrow, Alice Ann, Ed.

    2008-01-01

    The second edition of "Introduction to Approaches in Music Therapy" includes a new introductory chapter that addresses historical perspectives on the approaches, a rationale for the categorization of approaches, and discussion on professional issues related to the use of these approaches. Each of the chapters addressing approaches includes updated…

  20. Grants for Arts, Culture & the Humanities. 2012 Digital Edition

    Science.gov (United States)

    Foundation Center, 2011

    2011-01-01

    This publication is only available as a downloadable file. See who's giving and getting grants in your field. Strengthen your search for funds with the Foundation Center's digital edition of "Grants for Arts, Culture & The Humanities." This new "Grant Guide" reveals the scope of current foundation giving in the field. You'll find descriptions of…

  1. Consumer acceptance of food crops developed by genome editing.

    Science.gov (United States)

    Ishii, Tetsuya; Araki, Motoko

    2016-07-01

    One of the major problems regarding consumer acceptance of genetically modified organisms (GMOs) is the possibility that their transgenes could have adverse effects on the environment and/or human health. Genome editing, represented by the CRISPR/Cas9 system, can efficiently achieve transgene-free gene modifications and is anticipated to generate a wide spectrum of plants. However, the public attitude against GMOs suggests that people will initially be unlikely to accept these plants. We herein explored the bottlenecks of consumer acceptance of transgene-free food crops developed by genome editing and made some recommendations. People should not pursue a zero-risk bias regarding such crops. Developers are encouraged to produce cultivars with a trait that would satisfy consumer needs. Moreover, they should carefully investigate off-target mutations in resultant plants and initially refrain from agricultural use of multiplex genome editing for better risk-benefit communication. The government must consider their regulatory status and establish appropriate regulations if necessary. The government also should foster communication between the public and developers. If people are informed of the benefits of genome editing-mediated plant breeding and trust in the relevant regulations, and if careful risk-benefit communication and sincere considerations for the right to know approach are guaranteed, then such transgene-free crops could gradually be integrated into society. PMID:27038939

  2. The Literature Review: Six Steps to Success. Second Edition

    Science.gov (United States)

    Machi, Lawrence A.; McEvoy, Brenda T.

    2012-01-01

    This new edition of the best-selling book offers graduate students in education and the social sciences a road map to developing and writing an effective literature review for a research project, thesis, or dissertation. Organized around a proven six-step model and incorporating technology into all of the steps, the book provides examples,…

  3. Brief Intervention for School Problems: Outcome Informed Strategies, Second Edition

    Science.gov (United States)

    Murphy, John J.; Duncan, Barry L.

    2007-01-01

    Now in a revised and updated second edition, this highly practical guide provides innovative strategies for resolving academic and behavioral difficulties by enlisting the strengths and resources of students, parents, and teachers. Extensive new case material illustrates the authors' creative approach to building solutions and "busting problems"…

  4. Improving Science Education and Understanding through Editing Wikipedia

    Science.gov (United States)

    Moy, Cheryl L.; Locke, Jonas R.; Coppola, Brian P.; McNeil, Anne J.

    2010-01-01

    This paper describes a graduate-level class project centered on editing chemistry-related entries in Wikipedia. This project enables students to work collaboratively, explore advanced concepts in chemistry, and learn how to communicate science to a diverse audience, including the general public. The format and structure of the project is outlined…

  5. The Copyright Book: A Practical Guide. Fourth Edition.

    Science.gov (United States)

    Strong, William S.

    In response to important changes in copyright law as the United States accommodates itself to the Berne Convention and develops means to take account of new technologies, this guide puts these changes in a form and context that will make sense to persons who are concerned about their rights under the law. New material in the fourth edition of this…

  6. Journal Editing and Ethical Research Practice: Perspectives of Journal Editors

    Science.gov (United States)

    Randell-Moon, Holly; Anderson, Nicole; Bretag, Tracey; Burke, Anthony; Grieshaber, Sue; Lambert, Anthony; Saltmarsh, David; Yelland, Nicola

    2011-01-01

    This article offers perspectives from academics with recent journal editing experience on a range of ethical issues and dilemmas that regularly pose challenges for those in editorial roles. Each contributing author has provided commentary and reflection on a select topic that was identified in the research literature concerning academic publishing…

  7. Reading Comprehension: Strategies for Independent Learners. Second Edition

    Science.gov (United States)

    Blachowicz, Camille; Ogle, Donna

    2008-01-01

    The authors offer specific classroom practices that help K-9 students compare and evaluate print and online sources, develop vocabulary, build study and test-taking skills, and become motivated readers. The second edition reflects new research on informational literacy and academic and content-specific vocabulary development, and also discusses…

  8. Research in Special Education: Designs, Methods, and Applications. Second Edition

    Science.gov (United States)

    Rumrill, Phillip D., Jr.; Cook, Bryan G.; Wiley, Andrew L.

    2011-01-01

    The goal of this second edition is to provide a comprehensive overview of the philosophical, ethical, methodological, and analytical fundamentals of social science and educational research, as well as specify aspects of special education research that distinguish it from scientific inquiry in other fields of education and human services. Foremost…

  9. A Short History of the Movies. Second Edition.

    Science.gov (United States)

    Mast, Gerald

    This second edition of "A Short History of the Movies" includes expanded information and judgments about some of the "old masters" of film; an updated discussion of the "new masters"; and new sections on Japanese, Indian, and Czech cinema. In general, this history reveals significant trends in film history. American films are the primary focus,…

  10. Multicultural Education: Issues and Perspectives. 6th Edition

    Science.gov (United States)

    Banks, James A.; Banks, Cherry A. McGee

    2006-01-01

    Today's classrooms are more diverse than ever before. In order to reach these students, educators must be aware of the issues facing their various cultural, racial, ethnic, and language groups. Focusing on the pertinent issues in multicultural education, this new edition raises these critical issues and facilitates meaningful discussion. It has…

  11. [The meaning of the sixth edition of "Organon der Heilkunst"].

    Science.gov (United States)

    Schmidt, Josef M

    2002-01-01

    Like any artist, the paractitioner of the healing art should exactly know his tools, i.e. his medicines and the directions for their application. In addition, he should be able to rely on their genuineness. Regarding the tool "Organon", considerable uncertainty has been expressed by some physicians about the authenticity of Hahnemann's instructions for preparing and applying Q-potencies, as described in the sixth edition of the Organon of Medicine published by Richard Haehl in 1921. Since 1992, however, the first text-critical edition of the sixth edition of the Organonis available. Unlike Haehl's edition this one is exclusively based on Hahnemann's original manuscript and precisely transcribing all its handwriting, vouches for its authenticity. Hence there is no reason left to ignore Hahnemanns instructions concerning Q-potencies. This paper presents the history of the reception of Q-potencies as well as their prerequisites and evolution up to Hahnemann's final modifications of his earlier directions. As it turns out, these late instructions of Hahnemann do not mean complete change of all his previous opinions. Rather they are the logical completion of a course followed by him for ten years already. Q-potencies were Hahnemann's solution of the following therapeutic dilemma: on the one side physicians are inclined to repeat the dose of a high potency as often as possible in order to accelerate the process of healing; on the other side they should refrain from repeating the dose to avoid violent aggravations of the state of the patient.

  12. 75 FR 42786 - Accounting Guide for LSC Recipients (2010 Edition)

    Science.gov (United States)

    2010-07-22

    ... Accounting Guide for LSC Recipients (2010 Edition) AGENCY: Legal Services Corporation. ACTION: Notice. SUMMARY: The Legal Services Corporation (LSC) is revising the Accounting Guide for LSC Recipients to reflect changes that have occurred since the last publication of the Accounting Guide (the ``Guide'')...

  13. Grants for Libraries & Information Services. 2012 Digital Edition

    Science.gov (United States)

    Foundation Center, 2011

    2011-01-01

    This publication is only available as a downloadable file. See who's giving and getting grants in your field. Strengthen your search for funds with the Foundation Center's digital edition of "Grants for Libraries & Information Services." This new "Grant Guide" reveals the scope of current foundation giving in the field. You'll find descriptions of…

  14. Consumer acceptance of food crops developed by genome editing.

    Science.gov (United States)

    Ishii, Tetsuya; Araki, Motoko

    2016-07-01

    One of the major problems regarding consumer acceptance of genetically modified organisms (GMOs) is the possibility that their transgenes could have adverse effects on the environment and/or human health. Genome editing, represented by the CRISPR/Cas9 system, can efficiently achieve transgene-free gene modifications and is anticipated to generate a wide spectrum of plants. However, the public attitude against GMOs suggests that people will initially be unlikely to accept these plants. We herein explored the bottlenecks of consumer acceptance of transgene-free food crops developed by genome editing and made some recommendations. People should not pursue a zero-risk bias regarding such crops. Developers are encouraged to produce cultivars with a trait that would satisfy consumer needs. Moreover, they should carefully investigate off-target mutations in resultant plants and initially refrain from agricultural use of multiplex genome editing for better risk-benefit communication. The government must consider their regulatory status and establish appropriate regulations if necessary. The government also should foster communication between the public and developers. If people are informed of the benefits of genome editing-mediated plant breeding and trust in the relevant regulations, and if careful risk-benefit communication and sincere considerations for the right to know approach are guaranteed, then such transgene-free crops could gradually be integrated into society.

  15. Resources for the design of CRISPR gene editing experiments

    OpenAIRE

    Graham, Daniel B.; David E Root

    2015-01-01

    CRISPR-based approaches have quickly become a favored method to perturb genes to uncover their functions. Here, we review the key considerations in the design of genome editing experiments, and survey the tools and resources currently available to assist users of this technology.

  16. BOOK REVIEW: A First Course in General Relativity (Second Edition) A First Course in General Relativity (Second Edition)

    Science.gov (United States)

    Poisson, Eric

    2010-05-01

    A few years ago, in my review of Sean Carroll's book in Classical and Quantum Gravity [1], I wrote that while the 1970s was the decade of Weinberg [2] and Misner, Thorne and Wheeler [3], and while the eighties was the decade of Schutz [4] and Wald [5], the 2000s was clearly the decade of Hartle [6] and Carroll [7]. In my opinion, these books continue to stand out in the surprisingly dense crowd of introductory textbooks on general relativity. At the dawn of this new decade I look forward to see what fresh pedagogical insights will be produced next, and who will be revealed as the winners of the 2010s. It is, of course, much too early to tell, but Schutz is back, and he will set the standard just as he did back in 1985. This is the long-awaited second edition of his `First Course', a short, accessible, and very successful introduction to general relativity. The changes from the first edition are modest: Schutz wisely refrained from bloating the text with new topics, and limited himself to updating his discussion of gravitational-wave sources and detectors, neutron-star and black-hole astrophysics, and suggestions for further reading. Most importantly, he completely rewrote the chapter on cosmology, a topic that has evolved enormously since the first edition. The book begins in chapter 1 with a beautiful review of special relativity that emphasizes spacetime geometry and stays away from an algebraic approach based on the Lorentz transformation, which appears only later in the chapter. This is followed up in chapters 2 and 3 with an introduction to vector and tensor analysis in flat spacetime. The point of view is modern (tensors are defined as linear mapping of vectors and one-forms into real numbers) but the presentation is very accessible and avoids an overload of mathematical fine print. In chapter 4 the book introduces the spacetime description of fluids; it is here that the energy-momentum tensor makes its first appearance. The move to curved spacetime is

  17. Coming 5th Edition of the API Standard 618: major changes compared to the API 618, 4th edition

    NARCIS (Netherlands)

    Pyle, A.; Eijk, A.; Elferink, H.

    2003-01-01

    This paper will present the highlights of changes that will be found in the 5th Edition of API 618, which is expected to be published in late 2003 or early 2004. Approximately every 5 years the API Standards are revised in such a way that the latest field experiences and proven designs are included

  18. What Video Games Have to Teach Us about Learning and Literacy. Second Edition: Revised and Updated Edition

    Science.gov (United States)

    Gee, James Paul

    2007-01-01

    The author begins his classic book with "I want to talk about video games--yes, even violent video games--and say some positive things about them." With this simple but explosive statement, one of America's most well-respected educators looks seriously at the good that can come from playing video games. In this revised edition, new games like…

  19. Books authored/co-authored and edited/co-edited by members of staff of the Department of Medieval/Medieval and Renaissance Archaeology, Aarhus University, 1971-2014

    DEFF Research Database (Denmark)

    Roesdahl, Else

    2015-01-01

    Chronologically organized list of books authored/co-authored and edited/co-edited by members of staff of the Department of Medieval and Renaissance Archaeology, Aarhus University, 1971-2014......Chronologically organized list of books authored/co-authored and edited/co-edited by members of staff of the Department of Medieval and Renaissance Archaeology, Aarhus University, 1971-2014...

  20. Changes in the APA "Publication Manual": How the New Fifth Edition Will Affect Research Reporting in the Social Sciences.

    Science.gov (United States)

    Daniel, Larry G.

    The American Psychological Association (APA) has recently published the fifth edition of its "Publication Manual." This paper provides a brief overview of how this edition differs from previous editions and summarizes features of the new edition that will be likely to have an impact on social science research over the next several years. Both…

  1. A Guide to the Elements, Rev. Edition (by Albert Stwertka)

    Science.gov (United States)

    Berger, Reviewed By Daniel

    1999-12-01

    This edition is identical in format and content to the 1996 edition, now sold as the "library edition", except that the names and information for elements 104-109 have been updated. My earlier review still applies; a page-by-page comparison found this edition identical to the first except as noted in the previous sentence. The major revision has been in size and price. The 50% price reduction is welcome, but the format was not changed when the size was reduced, and the resulting 9-point font puts readers at risk of eyestrain. I would like to correct one of the criticisms in my earlier review There is excellent discussion of the industrial uses of each element, as well as its most common source minerals. The more economically important elements are given extensive discussions, detailing industrial uses of the element and its compounds. However, biological activity is given spotty coverage. There is no mention - under "iron" or elsewhere - of the central biological role of iron in oxygen transport or of magnesium in photosynthesis. When coverage appears it is not bad: the roles of calcium in vertebrate and invertebrate skeletons, of fluorine in reducing tooth decay by changing hydroxyapatite to fluorapatite, and of cobalt in vitamin B12 are discussed. While information on transuranium elements has been updated, there has been no attempt to correct several minor errors in spelling, placement, or even information. On page 14 the 1s subshell appears as part of the L (n = 2) shell, and upon the electrolysis of molten sodium chloride on page 54, "sodium collects atthe cathode, and chloride [sic] at...the anode." On page 73 the etymology of "potash" is still given as "potassium-rich ash" rather than "ash burned down in pots", though it is obvious that the latter is intended. On page 74, a picture caption claims that black powder ("potassium nitrate, wood charcoal, and sulfur") is used in modern, high-powered rifle cartridges. In spite of the mistakes, which are relatively

  2. Post-Editing Error Correction Algorithm for Speech Recognition using Bing Spelling Suggestion

    CERN Document Server

    Bassil, Youssef

    2012-01-01

    ASR short for Automatic Speech Recognition is the process of converting a spoken speech into text that can be manipulated by a computer. Although ASR has several applications, it is still erroneous and imprecise especially if used in a harsh surrounding wherein the input speech is of low quality. This paper proposes a post-editing ASR error correction method and algorithm based on Bing's online spelling suggestion. In this approach, the ASR recognized output text is spell-checked using Bing's spelling suggestion technology to detect and correct misrecognized words. More specifically, the proposed algorithm breaks down the ASR output text into several word-tokens that are submitted as search queries to Bing search engine. A returned spelling suggestion implies that a query is misspelled; and thus it is replaced by the suggested correction; otherwise, no correction is performed and the algorithm continues with the next token until all tokens get validated. Experiments carried out on various speeches in differen...

  3. 200 years Organon of Medicine - A comparative review of its six editions (1810-1842).

    Science.gov (United States)

    Schmidt, Josef M

    2010-10-01

    In 2010 the 200th anniversary of the Organon is celebrated by the homeopathic community. Samuel Hahnemann's Organon of Rational Therapeutics, published in 1810, however, marks neither the beginning of homeopathy nor the endpoint of its development. On the one hand, its contents are based on terms and concepts developed and published by Hahnemann during the preceding two decades. On the other hand, the five revised editions of the Organon that followed in the next three decades contain major changes of theory and conceptions. Hahnemann's basic idea, running through all the stages of the foundation, elaboration, and defence of his doctrine, may be detected by a comparative review of his works from a historical and philosophical perspective.

  4. Mitochondrial tRNA 5'-editing in Dictyostelium discoideum and Polysphondylium pallidum.

    Science.gov (United States)

    Abad, Maria G; Long, Yicheng; Kinchen, R Dimitri; Schindel, Elinor T; Gray, Michael W; Jackman, Jane E

    2014-05-30

    Mitochondrial tRNA (mt-tRNA) 5'-editing was first described more than 20 years ago; however, the first candidates for 5'-editing enzymes were only recently identified in a eukaryotic microbe (protist), the slime mold Dictyostelium discoideum. In this organism, eight of 18 mt-tRNAs are predicted to be edited based on the presence of genomically encoded mismatched nucleotides in their aminoacyl-acceptor stem sequences. Here, we demonstrate that mt-tRNA 5'-editing occurs at all predicted sites in D. discoideum as evidenced by changes in the sequences of isolated mt-tRNAs compared with the expected sequences encoded by the mitochondrial genome. We also identify two previously unpredicted editing events in which G-U base pairs are edited in the absence of any other genomically encoded mismatches. A comparison of 5'-editing in D. discoideum with 5'-editing in another slime mold, Polysphondylium pallidum, suggests organism-specific idiosyncrasies in the treatment of U-G/G-U pairs. In vitro activities of putative D. discoideum editing enzymes are consistent with the observed editing reactions and suggest an overall lack of tRNA substrate specificity exhibited by the repair component of the editing enzyme. Although the presence of terminal mismatches in mt-tRNA sequences is highly predictive of the occurrence of mt-tRNA 5'-editing, the variability in treatment of U-G/G-U base pairs observed here indicates that direct experimental evidence of 5'-editing must be obtained to understand the complete spectrum of mt-tRNA editing events in any species. PMID:24737330

  5. Tracking Amendments to Legislation and Other Political Texts with a Novel Minimum-Edit-Distance Algorithm: DocuToads

    DEFF Research Database (Denmark)

    Hermansson, Henrik Alf Jonas; Cross, James

    2015-01-01

    Political scientists often nd themselves tracking amendments to political texts. As different actors weigh in, texts change as they are drafted and redrafted, reflecting political preferences and power. This study provides a novel solution to the problem of detecting amendments to political text......) and substantive amount of amendments made between version of texts. To illustrate the usefulness and eciency of the approach we replicate two existing studies from the field of legislative studies. Our results demonstrate that minimum edit distance methods can produce superior measures of text amendments to hand...

  6. The EDIT school trains future experts in detector technologies

    CERN Multimedia

    CERN Bulletin

    2011-01-01

    The Excellence in Detectors and Instrumentation Technologies (EDIT) School has just taken place for the first time. The enthusiastic feedback from the organizers and the participants shows how the School’s format is just the right formula for today’s young researchers specializing in experimental physics. To mark the importance of the event, Rolf Heuer dedicated the School to Georges Charpak.   Rolf Heuer and Pier Oddone visit Building 154, which hosted some of the EDIT School laboratory activities. Like many other branches of science, today’s particle physics relies on very complex instruments to provide the performance that unresolved questions require. When we say ‘particle physics’ we actually mean a whole lot of different specializations that young researchers choose to pursue when they are at university. “In the present situation, it might very well happen that an experimental particle physicist at the end of his/her studies has ne...

  7. Review of particle properties. 25th anniversary edition

    International Nuclear Information System (INIS)

    This review is a reprint of Physics Letters, Vol. IIIB, April 22, 1982, and is an updating through December 1981 of our previous review of particle properties [Particle Data Group (1980)]. As in previous editions we have attempted to make the text as complete and self-contained as possible. The results of our compilation are presented in two sections, the Tables of Particle Properties and the Data Card Listings. The Tables summarize the properties of only those particles whose existence is in our judgment experimentally well founded and which have a high probability of standing the test of time. The Data Card Listings give up-to-date information, with references, on all reported particles, whether considered well established or not. The Listings also contain mini-reviews on questions of interest. As in previous editions, we include a section of miscellaneous tables, figures, and formulae. These are aimed at the practicing high energy physics experimentalist

  8. DNA Editing by APOBECs: A Genomic Preserver and Transformer.

    Science.gov (United States)

    Knisbacher, Binyamin A; Gerber, Doron; Levanon, Erez Y

    2016-01-01

    Information warfare is not limited to the cyber world because it is waged within our cells as well. The unique AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family comprises proteins that alter DNA sequences by converting deoxycytidines to deoxyuridines through deamination. This C-to-U DNA editing enables them to inhibit parasitic viruses and retrotransposons by disrupting their genomic content. In addition to attacking genomic invaders, APOBECs can target their host genome, which can be beneficial by initiating processes that create antibody diversity needed for the immune system or by accelerating the rate of evolution. AID can also alter gene regulation by removing epigenetic modifications from genomic DNA. However, when uncontrolled, these powerful agents of change can threaten genome stability and eventually lead to cancer. PMID:26608778

  9. [One hundred years of Freud editions in The Netherlands].

    Science.gov (United States)

    Greven, Elsbeth

    2009-01-01

    The history of Dutch editions of Freud is discussed from a publisher's point of view. The author focuses on the main publishers involved in presenting Freud's work to the Dutch public: S. C. van Doesburgh, De Wereldbibliotheek, De Bezige Bij and Uitgeverij Boom. She describes their role, together with their networks of translators, editors and psychoanalysts, in the production, perception and reception of Freud's work--and hence in the development of psychoanalysis in The Netherlands--as well as their approaches to translation, publishing strategies and use of paratextual resources. Three main stages can be identified: 1. 1912 to World War I (Freud was introduced), 2. World War I to 1950 (Freud was popularised), and 3. 1960 to 1990 (Freud was canonised, but also criticised). A fourth stage, the historicisation of Freud, began in 2006 with a new, scholarly edition of his Werken, arranged in chronological order.

  10. Exploring the Secrets of the Aurora Second Edition

    CERN Document Server

    Akasofu, Syun-Ichi

    2007-01-01

    This new edition of Exploring the Secrets of the Aurora is based on the author's own experiences as a scientist. It describes the history of progress made in auroral science and magnetospheric physics by providing examples of ideas, controversies, struggles, acceptance, and success. Although no general methodologies are mentioned, the hope is that the reader will learn about the history of progress in auroral science and examples of dealing with the many controversies. This book aims to help young scientific researchers learn how to persevere during periods of controversy and struggles for acceptance. In this second edition, by utilizing multiple examples, Akasofu is successful in demonstrating the importance and usefulness of Synthesis. "Probably the book's most valuable contribution to the history of space physics is precisely the narration of the discovery of substorms.---The book has special features.---Akasofu's coverage of the history of pre-space age solar-terrestrial relations is the most comprehensiv...

  11. From hacking the human genome to editing organs.

    Science.gov (United States)

    Tobita, Takamasa; Guzman-Lepe, Jorge; Collin de l'Hortet, Alexandra

    2015-01-01

    In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies.

  12. Genome Editing and Its Applications in Model Organisms

    Directory of Open Access Journals (Sweden)

    Dongyuan Ma

    2015-12-01

    Full Text Available Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and the clustered regularly-interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas, has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine.

  13. From hacking the human genome to editing organs.

    Science.gov (United States)

    Tobita, Takamasa; Guzman-Lepe, Jorge; Collin de l'Hortet, Alexandra

    2015-01-01

    In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies. PMID:26588350

  14. A TALE nuclease architecture for efficient genome editing.

    Science.gov (United States)

    Miller, Jeffrey C; Tan, Siyuan; Qiao, Guijuan; Barlow, Kyle A; Wang, Jianbin; Xia, Danny F; Meng, Xiangdong; Paschon, David E; Leung, Elo; Hinkley, Sarah J; Dulay, Gladys P; Hua, Kevin L; Ankoudinova, Irina; Cost, Gregory J; Urnov, Fyodor D; Zhang, H Steve; Holmes, Michael C; Zhang, Lei; Gregory, Philip D; Rebar, Edward J

    2011-02-01

    Nucleases that cleave unique genomic sequences in living cells can be used for targeted gene editing and mutagenesis. Here we develop a strategy for generating such reagents based on transcription activator-like effector (TALE) proteins from Xanthomonas. We identify TALE truncation variants that efficiently cleave DNA when linked to the catalytic domain of FokI and use these nucleases to generate discrete edits or small deletions within endogenous human NTF3 and CCR5 genes at efficiencies of up to 25%. We further show that designed TALEs can regulate endogenous mammalian genes. These studies demonstrate the effective application of designed TALE transcription factors and nucleases for the targeted regulation and modification of endogenous genes.

  15. FLASH Assembly of TALENs Enables High-Throughput Genome Editing

    OpenAIRE

    Reyon, Deepak; Tsai, Shengdar Q.; Khayter, Cyd; Foden, Jennifer A.; Sander, Jeffry D.; Joung, J. Keith

    2012-01-01

    Engineered transcription activator-like effector nucleases (TALENs) have shown promise as facile and broadly applicable genome editing tools. However, no publicly available high-throughput method for constructing TALENs has been published and large-scale assessments of the success rate and targeting range of the technology remain lacking. Here we describe the Fast Ligation-based Automatable Solid-phase High-throughput (FLASH) platform, a rapid and cost-effective method we developed to enable ...

  16. CRISPR-mediated genome editing of Plasmodium falciparum malaria parasites.

    Science.gov (United States)

    Lee, Marcus Cs; Fidock, David A

    2014-01-01

    The development of the CRISPR-Cas system is revolutionizing genome editing in a variety of organisms. The system has now been used to manipulate the genome of Plasmodium falciparum, the most lethal malaria-causing species. The ability to generate gene deletions or nucleotide substitutions rapidly and economically promises to accelerate the analysis of novel drug targets and to help elucidate the function of specific genes or gene families, while complementing genome-wide association studies.

  17. CRISPR-mediated genome editing of Plasmodium falciparum malaria parasites

    OpenAIRE

    Lee, Marcus CS; David A Fidock

    2014-01-01

    The development of the CRISPR-Cas system is revolutionizing genome editing in a variety of organisms. The system has now been used to manipulate the genome of Plasmodium falciparum, the most lethal malaria-causing species. The ability to generate gene deletions or nucleotide substitutions rapidly and economically promises to accelerate the analysis of novel drug targets and to help elucidate the function of specific genes or gene families, while complementing genome-wide association studies.

  18. Identification of RNA editing sites in the SNP database

    OpenAIRE

    Eisenberg, Eli; Adamsky, Konstantin; Cohen, Lital; Amariglio, Ninette; Hirshberg, Abraham; Rechavi, Gideon; Levanon, Erez Y.

    2005-01-01

    The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing c...

  19. Modeling editing behavior for editors of graphical languages

    OpenAIRE

    2010-01-01

    This thesis presents a framework that expands upon the idea of a fully model-driven approach to editor development for Graphical Domain Specific Languages (DSL), originally put forth by the Graphical Modeling Framework (GMF). The framework's main component consists of a language for the declarative definition of editing behavior for said editors. We define the Behavioral Definition Language (BDL), and the execution semantics of a BDL-instance, Behavioral Definitions (BD). Inconsi...

  20. The application of genome editing in studying hearing loss.

    Science.gov (United States)

    Zou, Bing; Mittal, Rahul; Grati, M'hamed; Lu, Zhongmin; Shu, Yilai; Tao, Yong; Feng, Youg; Xie, Dinghua; Kong, Weijia; Yang, Shiming; Chen, Zheng-Yi; Liu, Xuezhong

    2015-09-01

    Targeted genome editing mediated by clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) technology has emerged as one of the most powerful tools to study gene functions, and with potential to treat genetic disorders. Hearing loss is one of the most common sensory disorders, affecting approximately 1 in 500 newborns with no treatment. Mutations of inner ear genes contribute to the largest portion of genetic deafness. The simplicity and robustness of CRISPR/Cas9-directed genome editing in human cells and model organisms such as zebrafish, mice and primates make it a promising technology in hearing research. With CRISPR/Cas9 technology, functions of inner ear genes can be studied efficiently by the disruption of normal gene alleles through non-homologous-end-joining (NHEJ) mechanism. For genetic hearing loss, CRISPR/Cas9 has potential to repair gene mutations by homology-directed-repair (HDR) or to disrupt dominant mutations by NHEJ, which could restore hearing. Our recent work has shown CRISPR/Cas9-mediated genome editing can be efficiently performed in the mammalian inner ear in vivo. Thus, application of CRISPR/Cas9 in hearing research will open up new avenues for understanding the pathology of genetic hearing loss and provide new routes in the development of treatment to restore hearing. In this review, we describe major methodologies currently used for genome editing. We will highlight applications of these technologies in studies of genetic disorders and discuss issues pertaining to applications of CRISPR/Cas9 in auditory systems implicated in genetic hearing loss.

  1. The Book of Touch edited by Constance Classen

    OpenAIRE

    Redhead, Professor Steve

    2006-01-01

    Acclaimed author Constance Classen’s edited collection of sensual studies, The Book of Touch, is an intriguing contribution to the already excellent Sensory Formations series published by Berg. Other books in the series which I have seen include The Auditory Culture Reader (superb for anyone teaching the regulation, production and consumption of popular music culture) and The Visual Culture Reader (perfect for film and television studies). Other titles which I have yet to investigate from the...

  2. Editing of EIA coded, numerically controlled, machine tool tapes

    Science.gov (United States)

    Weiner, J. M.

    1975-01-01

    Editing of numerically controlled (N/C) machine tool tapes (8-level paper tape) using an interactive graphic display processor is described. A rapid technique required for correcting production errors in N/C tapes was developed using the interactive text editor on the IMLAC PDS-ID graphic display system and two special programs resident on disk. The correction technique and special programs for processing N/C tapes coded to EIA specifications are discussed.

  3. Standard and reference materials for marine science, revised edition, 1993

    OpenAIRE

    IOC for UNESCO

    1993-01-01

    This is the third edition of the catalog of reference materials suited for use in marine science, originally compiled in 1986 for NOAA, IOC and UNEP. The catalog lists close to 2,000 reference materials from sixteen producers and contains information about their proper use, sources, availability, and analyte concentrations. Indices are included for elements, isotopes, and organic compounds, as are cross references to CAS registry numbers, alternate names, and chemical structures of selected o...

  4. Poster Paper: Editable Artefact: Stonehenge Megalithic Puzzle Project

    OpenAIRE

    Unver, Ertu; Taylor, Andrew; Hughes, Daniel

    2010-01-01

    This Poster paper is presented during University of Huddersfield Research Festival 8 - 18 March 2010. The main objective of this project is to produce physical models using 3D Stereolithography machines. Paper also cover the process of editing data preperation, 3D Scan Data surface generation and processing. 3D modelling and Virtual Reality in the context of heritage sites and archaeology is a very active field. Photogrammetric and Geomatic data gathering mean that 3D modelling can p...

  5. Syntax Editing for Mark 4-A System Performance Test Software

    Science.gov (United States)

    Jacobson, G. N.

    1983-01-01

    This article describes the syntax editing concepts used by the Operations Sustaining Engineering Section in implementing System Performance Test software for the Mark 4-A era. The processing functions are discussed, as well as the necessary data structures and table generation macros used in implementing those functions. In addition, the procedural and software interfaces which have been developed for users of the syntax editor are described, including the forms required for establishing directive and parameter characteristics.

  6. Gesture and Speech in Interaction - 4th edition (GESPIN 4)

    OpenAIRE

    Ferré, Gaëlle; Mark, Tutton

    2015-01-01

    International audience The fourth edition of Gesture and Speech in Interaction (GESPIN) was held in Nantes, France. With more than 40 papers, these proceedings show just what a flourishing field of enquiry gesture studies continues to be. The keynote speeches of the conference addressed three different aspects of multimodal interaction:gesture and grammar, gesture acquisition, and gesture and social interaction. In a talk entitled Qualitiesof event construal in speech and gesture: Aspect a...

  7. Creation of Learning Web Pages for Digital Photo Editing

    OpenAIRE

    Tymeš, Radek

    2013-01-01

    Main plot of this thesis is to take a look on issues with editing photos in graphic editor GIMP. First part is focused on terms from fields such as digital photography, raster graphics and GIMP environment including GIMP's basic functions and attributes. Second part of thesis is creation of e-learning website and related lectures, that contains selected graphic operations shown on photo examples including complete procedure.

  8. Authoring, Editing and Visualizing Compound Objects for Literary Scholarship

    OpenAIRE

    Gerber, Anna; Hunter, Jane

    2010-01-01

    This paper presents LORE (Literature Object Re-use and Exchange), a light-weight tool designed to enable scholars and teachers of literature to author, edit and publish OAI-ORE-compliant compound information objects that encapsulate related digital resources and bibliographic re-cords. LORE provides a graphical user interface for creating, labelling and visualizing typed rela-tionships between individual objects using terms from a bibliographic ontology based on the IFLA FRBR. After creating ...

  9. Macromodels of the Romanian transition economy, Second edition

    OpenAIRE

    Dobrescu, Emilian

    1998-01-01

    The book develops the main lines of thought contained in “Macromodels of the Romanian transition economy”, edited in 1996 by the “Expert Publishing House”. The 1997 version of the macromodel (Dobrescu 1997 b) has included some changes, the following being the most important: - the introduction of the special block for demographic variables (population, labour force, retired people); - the connection of the annual indicators with a monthly block dedicated to the evolution of export a...

  10. Improvement of Synthetic Biology Tools for DNA Editing

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda

    with the development and improvement of DNA editing strategies,compatible with other DNA assembly methodologies, genome engineering and,eventually, automation processes. Expanding and optimizing the synbio toolkit has important applications in pathway optimization for metabolic engineering, design and characterization...... of gene circuits, synthesis of whole genomes and natural product discovery. In line with this, it is also described in this thesis how discovery of new cytochromes P450 (CYPs) from marine bacteria could benefit industrial processes....

  11. Mission Data System Java Edition Version 7

    Science.gov (United States)

    Reinholtz, William K.; Wagner, David A.

    2013-01-01

    The Mission Data System framework defines closed-loop control system abstractions from State Analysis including interfaces for state variables, goals, estimators, and controllers that can be adapted to implement a goal-oriented control system. The framework further provides an execution environment that includes a goal scheduler, execution engine, and fault monitor that support the expression of goal network activity plans. Using these frameworks, adapters can build a goal-oriented control system where activity coordination is verified before execution begins (plan time), and continually during execution. Plan failures including violations of safety constraints expressed in the plan can be handled through automatic re-planning. This version optimizes a number of key interfaces and features to minimize dependencies, performance overhead, and improve reliability. Fault diagnosis and real-time projection capabilities are incorporated. This version enhances earlier versions primarily through optimizations and quality improvements that raise the technology readiness level. Goals explicitly constrain system states over explicit time intervals to eliminate ambiguity about intent, as compared to command-oriented control that only implies persistent intent until another command is sent. A goal network scheduling and verification process ensures that all goals in the plan are achievable before starting execution. Goal failures at runtime can be detected (including predicted failures) and handled by adapted response logic. Responses can include plan repairs (try an alternate tactic to achieve the same goal), goal shedding, ignoring the fault, cancelling the plan, or safing the system.

  12. Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology.

    Science.gov (United States)

    Alagoz, Yagiz; Gurkok, Tugba; Zhang, Baohong; Unver, Turgay

    2016-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease system is a powerful RNA-guided genome editing tool. CRISPR/Cas9 has been well studied in model plant species for targeted genome editing. However, few studies have been reported on plant species without whole genome sequence information. Currently, no study has been performed to manipulate metabolic pathways using CRISPR/Cas9. In this study, the type II CRISPR/SpCas9 system was used to knock out, via nonhomologous end-joining genome repair, the 4'OMT2 in opium poppy (Papaver somniferum L.), a gene which regulates the biosythesis of benzylisoquinoline alkaloids (BIAs). For sgRNA transcription, viral-based TRV and synthetic binary plasmids were designed and delivered into plant cells with a Cas9 encoding-synthetic vector by Agrobacterium-mediated transformation. InDels formed by CRISPR/Cas9 were detected by sequence analysis. Our results showed that the biosynthesis of BIAs (e.g. morphine, thebaine) was significantly reduced in the transgenic plants suggesting that 4'OMT2 was efficiently knocked-out by our CRISPR-Cas9 genome editing approach. In addition, a novel uncharacterized alkaloid was observed only in CRISPR/Cas9 edited plants. Thus, the applicabilitiy of the CRISPR/Cas9 system was demonstrated for the first time for medicinal aromatic plants by sgRNAs transcribed from both synthetic and viral vectors to regulate BIA metabolism and biosynthesis. PMID:27483984

  13. Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology.

    Science.gov (United States)

    Alagoz, Yagiz; Gurkok, Tugba; Zhang, Baohong; Unver, Turgay

    2016-08-03

    Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease system is a powerful RNA-guided genome editing tool. CRISPR/Cas9 has been well studied in model plant species for targeted genome editing. However, few studies have been reported on plant species without whole genome sequence information. Currently, no study has been performed to manipulate metabolic pathways using CRISPR/Cas9. In this study, the type II CRISPR/SpCas9 system was used to knock out, via nonhomologous end-joining genome repair, the 4'OMT2 in opium poppy (Papaver somniferum L.), a gene which regulates the biosythesis of benzylisoquinoline alkaloids (BIAs). For sgRNA transcription, viral-based TRV and synthetic binary plasmids were designed and delivered into plant cells with a Cas9 encoding-synthetic vector by Agrobacterium-mediated transformation. InDels formed by CRISPR/Cas9 were detected by sequence analysis. Our results showed that the biosynthesis of BIAs (e.g. morphine, thebaine) was significantly reduced in the transgenic plants suggesting that 4'OMT2 was efficiently knocked-out by our CRISPR-Cas9 genome editing approach. In addition, a novel uncharacterized alkaloid was observed only in CRISPR/Cas9 edited plants. Thus, the applicabilitiy of the CRISPR/Cas9 system was demonstrated for the first time for medicinal aromatic plants by sgRNAs transcribed from both synthetic and viral vectors to regulate BIA metabolism and biosynthesis.

  14. Joint Confirmatory Factor Analysis of the Woodcock-Johnson Tests of Cognitive Abilities, Third Edition, and the Stanford-Binet Intelligence Scales, Fifth Edition, with a Preschool Population

    Science.gov (United States)

    Chang, Mei; Paulson, Sharon E.; Finch, W. Holmes; Mcintosh, David E.; Rothlisberg, Barbara A.

    2014-01-01

    This study examined the underlying constructs measured by the Woodcock-Johnson Tests of Cognitive Abilities, Third Edition (WJ-III COG) and the Stanford-Binet Intelligence Scales, Fifth Edition (SB5), based on the Cattell-Horn-Carrol (CHC) theory of cognitive abilities. This study reports the results of the first joint confirmatory factor analysis…

  15. The expression of apoB mRNA editing factors is not the sole determinant for the induction of editing in differentiating Caco-2 cells

    Energy Technology Data Exchange (ETDEWEB)

    Galloway, Chad A. [Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Ave., Rochester, NY 14642 (United States); Smith, Harold C., E-mail: harold.smith@rochester.edu [Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Ave., Rochester, NY 14642 (United States)

    2010-01-01

    Apolipoprotein B mRNA is edited at cytidine 6666 in the enterocytes lining the small intestine of all mammals; converting a CAA codon to a UAA stop codon. The conversion is {approx}80% efficient in this tissue and leads to the expression of the truncated protein, ApoB48, essential for secretion of dietary lipid as chylomicrons. Caco-2 cell raft cultures have been used as an in vitro model for the induction of editing activity during human small intestinal cell differentiation. This induction of apoB mRNA editing has been ascribed to the expression of APOBEC-1. In agreement our data demonstrated differentiation-dependent induction of expression of the editing enzyme APOBEC-1 and in addition we show alternative splicing of the essential auxiliary factor ACF. However, transfection of these editing factors in undifferentiated proliferating Caco-2 cells was not sufficient to induce robust apoB mRNA editing activity. Only differentiation of Caco-2 cells could induce more physiological like levels of apoB mRNA editing. The data suggested that additional regulatory mechanism(s) were induced by differentiation that controlled the functional activity of editing factors.

  16. The expression of apoB mRNA editing factors is not the sole determinant for the induction of editing in differentiating Caco-2 cells

    International Nuclear Information System (INIS)

    Apolipoprotein B mRNA is edited at cytidine 6666 in the enterocytes lining the small intestine of all mammals; converting a CAA codon to a UAA stop codon. The conversion is ∼80% efficient in this tissue and leads to the expression of the truncated protein, ApoB48, essential for secretion of dietary lipid as chylomicrons. Caco-2 cell raft cultures have been used as an in vitro model for the induction of editing activity during human small intestinal cell differentiation. This induction of apoB mRNA editing has been ascribed to the expression of APOBEC-1. In agreement our data demonstrated differentiation-dependent induction of expression of the editing enzyme APOBEC-1 and in addition we show alternative splicing of the essential auxiliary factor ACF. However, transfection of these editing factors in undifferentiated proliferating Caco-2 cells was not sufficient to induce robust apoB mRNA editing activity. Only differentiation of Caco-2 cells could induce more physiological like levels of apoB mRNA editing. The data suggested that additional regulatory mechanism(s) were induced by differentiation that controlled the functional activity of editing factors.

  17. Mojo Hand, a TALEN design tool for genome editing applications

    Directory of Open Access Journals (Sweden)

    Neff Kevin L

    2013-01-01

    Full Text Available Abstract Background Recent studies of transcription activator-like (TAL effector domains fused to nucleases (TALENs demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications. Results We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org. We describe the algorithm and its implementation. The features of Mojo Hand include (1 automatic download of genomic data from the National Center for Biotechnology Information, (2 analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3 selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4 output files designed for subsequent TALEN construction using the Golden Gate assembly method. Conclusions Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.

  18. Newer Gene Editing Technologies toward HIV Gene Therapy

    Directory of Open Access Journals (Sweden)

    Premlata Shankar

    2013-11-01

    Full Text Available Despite the great success of highly active antiretroviral therapy (HAART in ameliorating the course of HIV infection, alternative therapeutic approaches are being pursued because of practical problems associated with life-long therapy. The eradication of HIV in the so-called “Berlin patient” who received a bone marrow transplant from a CCR5-negative donor has rekindled interest in genome engineering strategies to achieve the same effect. Precise gene editing within the cells is now a realistic possibility with recent advances in understanding the DNA repair mechanisms, DNA interaction with transcription factors and bacterial defense mechanisms. Within the past few years, four novel technologies have emerged that can be engineered for recognition of specific DNA target sequences to enable site-specific gene editing: Homing Endonuclease, ZFN, TALEN, and CRISPR/Cas9 system. The most recent CRISPR/Cas9 system uses a short stretch of complementary RNA bound to Cas9 nuclease to recognize and cleave target DNA, as opposed to the previous technologies that use DNA binding motifs of either zinc finger proteins or transcription activator-like effector molecules fused to an endonuclease to mediate sequence-specific DNA cleavage. Unlike RNA interference, which requires the continued presence of effector moieties to maintain gene silencing, the newer technologies allow permanent disruption of the targeted gene after a single treatment. Here, we review the applications, limitations and future prospects of novel gene-editing strategies for use as HIV therapy.

  19. Ancient sedimentary environments and their subsurface diagnosis, third edition

    Energy Technology Data Exchange (ETDEWEB)

    Selley, R.C.

    1985-01-01

    All the worlds coal, most of its petroleum, and many ore deposits occur within sedimentary rocks (sandstones, limestones and shales). The distribution of these minerals is closely related to the sedimentary environment of the host rock. For example, an oil field trapped in an old beach sand will be elongated parallel to the basin margin, while a bed of coal within an abandoned river channel will trend into the basin. This book shows how to diagnose the depositional environments of sedimentary rocks and indicates how this knowledge may be applied to the search for petroleum, coal and sedimentary ore deposits. The first edition of this book appeared in 1970. It was primarily concerned with the interpretation of sedimentary environments from outcrop, from an aesthetic stance, with no thought of vulgar commercial application. The second edition (1977) reflected the author's experience in the oil industry and included sections on the use of geophysical well logs in subsurface facies analysis. In recent years the field that is loosely termed seismic stratigraphy developed, where sedimentary concepts are applied to the interpretation of seismic data. Today seismic surveys may delineate channels, deltas, reefs, submarine fans, and other deposits. The thrid edition contains sections on the seismic characteristics of the various sedimentary facies, and the sections on metalliferous sedimentary deposits and recent environments have been expanded.

  20. Advancing Crop Transformation in the Era of Genome Editing.

    Science.gov (United States)

    Altpeter, Fredy; Springer, Nathan M; Bartley, Laura E; Blechl, Ann E; Brutnell, Thomas P; Citovsky, Vitaly; Conrad, Liza J; Gelvin, Stanton B; Jackson, David P; Kausch, Albert P; Lemaux, Peggy G; Medford, June I; Orozco-Cárdenas, Martha L; Tricoli, David M; Van Eck, Joyce; Voytas, Daniel F; Walbot, Virginia; Wang, Kan; Zhang, Zhanyuan J; Stewart, C Neal

    2016-07-01

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.

  1. The Regulatory Status of Genome-edited Crops.

    Science.gov (United States)

    Wolt, Jeffrey D; Wang, Kan; Yang, Bing

    2016-02-01

    Genome editing with engineered nucleases (GEEN) represents a highly specific and efficient tool for crop improvement with the potential to rapidly generate useful novel phenotypes/traits. Genome editing techniques initiate specifically targeted double strand breaks facilitating DNA-repair pathways that lead to base additions or deletions by non-homologous end joining as well as targeted gene replacements or transgene insertions involving homology-directed repair mechanisms. Many of these techniques and the ancillary processes they employ generate phenotypic variation that is indistinguishable from that obtained through natural means or conventional mutagenesis; and therefore, they do not readily fit current definitions of genetically engineered or genetically modified used within most regulatory regimes. Addressing ambiguities regarding the regulatory status of genome editing techniques is critical to their application for development of economically useful crop traits. Continued regulatory focus on the process used, rather than the nature of the novel phenotype developed, results in confusion on the part of regulators, product developers, and the public alike and creates uncertainty as of the use of genome engineering tools for crop improvement. PMID:26251102

  2. In Vivo Delivery Systems for Therapeutic Genome Editing

    Directory of Open Access Journals (Sweden)

    Luyao Wang

    2016-04-01

    Full Text Available Therapeutic genome editing technology has been widely used as a powerful tool for directly correcting genetic mutations in target pathological tissues and cells to cure of diseases. The modification of specific genomic sequences can be achieved by utilizing programmable nucleases, such as Meganucleases, zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and the clustered regularly-interspaced short palindromic repeat-associated nuclease Cas9 (CRISPR/Cas9. However, given the properties, such as large size, negative charge, low membrane penetrating ability, as well as weak tolerance for serum, and low endosomal escape, of these nucleases genome editing cannot be successfully applied unless in vivo delivery of related programmable nucleases into target organisms or cells is achieved. Here, we look back at delivery strategies having been used in the in vivo delivery of three main genome editing nucleases, followed by methodologies currently undergoing testing in clinical trials, and potential delivery strategies provided by analyzing characteristics of nucleases and commonly used vectors.

  3. RNA Editing Sites Exist in Protein-coding Genes in the Chloroplast Genome of Cycas taitungensis

    Institute of Scientific and Technical Information of China (English)

    Haiyan Chen; Likun Deng; Yuan Jiang; Ping Lu; Jianing Yu

    2011-01-01

    RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations.In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes,especially in seed plants.Using prediction and experimental determination,we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis.A total of 85 editing sites were identified in 25 transcripts.Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution.The editing in the first and third codon position disappeared quicker than that in the second codon position,ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids.These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction.Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas,most likely due to slower evolution speed.

  4. The impact of continuity editing in narrative film on event segmentation.

    Science.gov (United States)

    Magliano, Joseph P; Zacks, Jeffrey M

    2011-01-01

    Filmmakers use continuity editing to engender a sense of situational continuity or discontinuity at editing boundaries. The goal of this study was to assess the impact of continuity editing on how people perceive the structure of events in a narrative film and to identify brain networks that are associated with the processing of different types of continuity editing boundaries. Participants viewed a commercially produced film and segmented it into meaningful events, while brain activity was recorded with functional magnetic resonance imaging (MRI). We identified three degrees of continuity that can occur at editing locations: edits that are continuous in space, time, and action; edits that are discontinuous in space or time but continuous in action; and edits that are discontinuous in action as well as space or time. Discontinuities in action had the biggest impact on behavioral event segmentation, and discontinuities in space and time had minor effects. Edits were associated with large transient increases in early visual areas. Spatial-temporal changes and action changes produced strikingly different patterns of transient change, and they provided evidence that specialized mechanisms in higher order perceptual processing regions are engaged to maintain continuity of action in the face of spatiotemporal discontinuities. These results suggest that commercial film editing is shaped to support the comprehension of meaningful events that bridge breaks in low-level visual continuity, and even breaks in continuity of spatial and temporal location. PMID:21972849

  5. An introduction to programming using visual basic 2012(wvisual studio 2012 express edition dvd) (9th edition)

    CERN Document Server

    Schneider, David I.

    2013-01-01

    An Introduction to Programming Using Visual Basic 2012, Ninth Edition —consistently praised by both students and instructors — is designed for readers with no prior computer programming experience. Now updated for Visual Basic 2012, Schneider focuses on teaching problem-solving skills and sustainable programming skills. A broad range of real-world examples, section-ending exercises, case studies, and programming projects gives readers more hands-on experience than any other Visual Basic book on the market. NEW! This edition is available with MyProgrammingLab, an innovative online homework and assessment tool. Through the power of practice and immediate personalized feedback, MyProgrammingLab helps students fully grasp the logic, semantics, and syntax of programming. Note: If you are purchasing the standalone text or electronic version, MyProgrammingLab does not come automatically packaged with the text. To purchase MyProgrammingLab, please visit: myprogramminglab.com or you can purchase a...

  6. CTBTO Annual Report 2010 (French Edition)

    International Nuclear Information System (INIS)

    monitoring, which is an important verification technology for detecting and locating an atmospheric nuclear explosion, was introduced into operations at the International Data Centre (IDC) in February 2010. During 2010, additional noble gas systems were transferred into IDC operations. At the end of the year, a total of 27 noble gas systems were in provisional operation at IMS radionuclide stations. Efforts were also made to further enhance the capabilities to perform atmospheric transport modelling and to deliver high quality products to States Signatories. Now, atmospheric backtracking calculations are performed daily for each of the IMS radionuclide stations with near real time meteorological data obtained from the European Centre for Medium-Range Weather Forecasts. The state of health system was deployed in the IDC Operations Centre. The system software facilitates the tasks of monitoring and detecting incidents and problems in the IMS network (stations, links in the Global Communications Infrastructure, servers, databases, hardware, software, etc.). Also, IDC application software was converted and updated to run on open source systems. In 2009, an on-site inspection (OSI) action plan, resulting from the review and follow-up of the lessons learned from the 2008 Integrated Field Exercise (IFE), was prepared. This was further developed to provide a framework for furthering the OSI regime in a project oriented manner. The action plan outlines various projects in five main areas of development, namely policy planning and operations, operations support and logistics, techniques and equipment, training, and procedures and documentation. The projects are intended to steer the build-up of OSI operational capability and assist in the preparation and conduct of the next IFE. OSI policies and operational procedures were developed further and advances were made in, inter alia, the implementation of an Integrated Inspection Support System. Training focused on the preparations for the

  7. CTBTO Annual Report 2011 (Spanish Edition)

    International Nuclear Information System (INIS)

    monitoring, which is an important verification technology for detecting and locating an atmospheric nuclear explosion, was introduced into operations at the International Data Centre (IDC) in February 2010. During 2010, additional noble gas systems were transferred into IDC operations. At the end of the year, a total of 27 noble gas systems were in provisional operation at IMS radionuclide stations. Efforts were also made to further enhance the capabilities to perform atmospheric transport modelling and to deliver high quality products to States Signatories. Now, atmospheric backtracking calculations are performed daily for each of the IMS radionuclide stations with near real time meteorological data obtained from the European Centre for Medium-Range Weather Forecasts. The state of health system was deployed in the IDC Operations Centre. The system software facilitates the tasks of monitoring and detecting incidents and problems in the IMS network (stations, links in the Global Communications Infrastructure, servers, databases, hardware, software, etc.). Also, IDC application software was converted and updated to run on open source systems. In 2009, an on-site inspection (OSI) action plan, resulting from the review and follow-up of the lessons learned from the 2008 Integrated Field Exercise (IFE), was prepared. This was further developed to provide a framework for furthering the OSI regime in a project oriented manner. The action plan outlines various projects in five main areas of development, namely policy planning and operations, operations support and logistics, techniques and equipment, training, and procedures and documentation. The projects are intended to steer the build-up of OSI operational capability and assist in the preparation and conduct of the next IFE. OSI policies and operational procedures were developed further and advances were made in, inter alia, the implementation of an Integrated Inspection Support System. Training focused on the preparations for the

  8. Estimation and detection information trade-off for x-ray system optimization

    Science.gov (United States)

    Cushing, Johnathan B.; Clarkson, Eric W.; Mandava, Sagar; Bilgin, Ali

    2016-05-01

    X-ray Computed Tomography (CT) systems perform complex imaging tasks to detect and estimate system parameters, such as a baggage imaging system performing threat detection and generating reconstructions. This leads to a desire to optimize both the detection and estimation performance of a system, but most metrics only focus on one of these aspects. When making design choices there is a need for a concise metric which considers both detection and estimation information parameters, and then provides the user with the collection of possible optimal outcomes. In this paper a graphical analysis of Estimation and Detection Information Trade-off (EDIT) will be explored. EDIT produces curves which allow for a decision to be made for system optimization based on design constraints and costs associated with estimation and detection. EDIT analyzes the system in the estimation information and detection information space where the user is free to pick their own method of calculating these measures. The user of EDIT can choose any desired figure of merit for detection information and estimation information then the EDIT curves will provide the collection of optimal outcomes. The paper will first look at two methods of creating EDIT curves. These curves can be calculated using a wide variety of systems and finding the optimal system by maximizing a figure of merit. EDIT could also be found as an upper bound of the information from a collection of system. These two methods allow for the user to choose a method of calculation which best fits the constraints of their actual system.

  9. Estimation and detection information trade-off for x-ray system optimization

    Science.gov (United States)

    Cushing, Johnathan B.; Clarkson, Eric W.; Mandava, Sagar; Bilgin, Ali

    2016-05-01

    X-ray Computed Tomography (CT) systems perform complex imaging tasks to detect and estimate system parameters, such as a baggage imaging system performing threat detection and generating reconstructions. This leads to a desire to optimize both the detection and estimation performance of a system, but most metrics only focus on one of these aspects. When making design choices there is a need for a concise metric which considers both detection and estimation information parameters, and then provides the user with the collection of possible optimal outcomes. In this paper a graphical analysis of Estimation and Detection Information Trade-off (EDIT) will be explored. EDIT produces curves which allow for a decision to be made for system optimization based on design constraints and costs associated with estimation and detection. EDIT analyzes the system in the estimation information and detection information space where the user is free to pick their own method of calculating these measures. The user of EDIT can choose any desired figure of merit for detection information and estimation information then the EDIT curves will provide the collection of optimal outcomes. The paper will first look at two methods of creating EDIT curves. These curves can be calculated using a wide variety of systems and finding the optimal system by maximizing a figure of merit. EDIT could also be found as an upper bound of the information from a collection of system. These two methods allow for the user to choose a method of calculation which best fits the constraints of their actual system.

  10. Dynamic Generation and Editing System for Wrongly Written Chinese Characters Font

    Directory of Open Access Journals (Sweden)

    Qingsheng Li

    2015-01-01

    Full Text Available The uniqueness of Chinese makes Chinese language a hotspot in language learning. In view of the problem of wrongly written character teaching in Chinese language teaching, it provides a simple, convenient, and efficient input method of wrongly written characters and realizes a dynamic generation and editing system for wrongly written Chinese character font, which solves the problems of real-time edit, coding, and input of wrongly written character in editing process using dynamic editing technology, and provides a convenient input method of wrongly written character in editing, printing, typesetting, and the research of digital Chinese language teaching. This method can also be used in dynamic editing, generation and processing of ancient variants, Oracle bone inscriptions, Bronze inscription, folk combined characters, and other fonts.

  11. Efficient Editing of Malaria Parasite Genome Using the CRISPR/Cas9 System

    OpenAIRE

    Zhang, Cui; Xiao, Bo; Jiang, Yuanyuan; Zhao, Yihua; Li, Zhenkui; Gao, Han; Ling, Yuan; Wei, Jun; Li, Shaoneng; Lu, Mingke; Su, Xin-zhuan; Cui, Huiting; Yuan, Jing

    2014-01-01

    ABSTRACT Malaria parasites are unicellular organisms residing inside the red blood cells, and current methods for editing the parasite genes have been inefficient. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and Cas9 endonuclease-mediated genome editing) system is a new powerful technique for genome editing and has been widely employed to study gene function in various organisms. However, whether this technique can be applied to modify the genomes of malaria par...

  12. Building an online magazine: a proposal for redesigning Western Living’s online edition

    OpenAIRE

    Chen, Annie Pei-Hsuan

    2010-01-01

    This report examines the trends in online publishing and online advertising, and how they impact the consumer magazine industry. It analyzes the web model of Vancouver magazine and the successful revamp of its online edition, and proposes changes that its sister magazine, Western Living, could make to respond to the changing environment and integrate the online and print editions. The paper also discusses how a magazine can optimize its online edition to make it successful and financially via...

  13. Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion

    OpenAIRE

    Shao Mingfu; Lin Yu

    2012-01-01

    Abstract Computing the edit distance between two genomes under certain operations is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under the DCJ model can be easily computed for genomes without duplicate genes. In this paper, we study the edit distance for genomes with duplicate genes under a model that includes DCJ operations, insertions and ...

  14. Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium

    OpenAIRE

    Pyne, Michael E.; Mark R. Bruder; Murray Moo-Young; Chung, Duane A; C. Perry Chou

    2016-01-01

    Application of CRISPR-Cas9 systems has revolutionized genome editing across all domains of life. Here we report implementation of the heterologous Type II CRISPR-Cas9 system in Clostridium pasteurianum for markerless genome editing. Since 74% of species harbor CRISPR-Cas loci in Clostridium, we also explored the prospect of co-opting host-encoded CRISPR-Cas machinery for genome editing. Motivation for this work was bolstered from the observation that plasmids expressing heterologous cas9 resu...

  15. Editing the UMLS Metathesaurus: Review and Enhancement of a Computed Knowledge Source

    OpenAIRE

    Sperzel, David; Erlbaum, Mark; Fuller, Lloyd; Sherertz, David; Olson, Nels; Schuyler, Peri; Hole, William; Savage, Allan; Passarelli, Philip; Tuttle, Mark

    1990-01-01

    This paper describes the editing of Meta-1, the first official version of the National Library of Medicine's (NLM) Unified Medical Language System (UMLS) Metathesaurus. After a preliminary version of Meta-1 was generated by automated techniques, it was edited by domain experts. The goal of editing was to enhance approximately 30,000 Metathesaurus entries and to correct “errors of commission” introduced by the automated techniques. Enhancements were made by assigning semantic types (such as “D...

  16. Editorial of the twenty first edition of Ambiente & Agua - An Interdisciplinary Journal of Applied Science

    Directory of Open Access Journals (Sweden)

    Getulio Teixeira Batista

    2013-04-01

    Full Text Available This issue marks the 21st edition of Ambiente & Agua. This edition has included 20 peer evaluated and reviewed articles, and all editions were published on time. We continue to employ a policy of complete open access, and to foster the visibility of articles. We continue to register the doi of all articles and to publish each issue as a single document in addition to the individual articles. This editorial emphasizes new important recognition received by the Ambiente & Agua journal.

  17. TbRGG2 facilitates kinetoplastid RNA editing initiation and progression past intrinsic pause sites.

    Science.gov (United States)

    Ammerman, Michelle L; Presnyak, Vladimir; Fisk, John C; Foda, Bardees M; Read, Laurie K

    2010-11-01

    TbRGG2 is an essential kinetoplastid RNA editing accessory factor that acts specifically on pan-edited RNAs. To understand the mechanism of TbRGG2 action, we undertook an in-depth analysis of edited RNA populations in TbRGG2 knockdown cells and an in vitro examination of the biochemical activities of the protein. We demonstrate that TbRGG2 down-regulation more severely impacts editing at the 5' ends of pan-edited RNAs than at their 3' ends. The initiation of editing is reduced to some extent in TbRGG2 knockdown cells. In addition, TbRGG2 plays a post-initiation role as editing becomes stalled in TbRGG2-depleted cells, resulting in an overall decrease in the 3' to 5' progression of editing. Detailed analyses of edited RNAs from wild-type and TbRGG2-depleted cells reveal that TbRGG2 facilitates progression of editing past intrinsic pause sites that often correspond to the 3' ends of cognate guide RNAs (gRNAs). In addition, noncanonically edited junction regions are either absent or significantly shortened in TbRGG2-depleted cells, consistent with impaired gRNA transitions. Sequence analysis further suggests that TbRGG2 facilitates complete utilization of certain gRNAs. In vitro RNA annealing and in vivo RNA unwinding assays demonstrate that TbRGG2 can modulate RNA-RNA interactions. Collectively, these data are consistent with a model in which TbRGG2 facilitates initiation and 3' to 5' progression of editing through its ability to affect gRNA utilization, both during the transition between specific gRNAs and during usage of certain gRNAs. PMID:20855539

  18. Revolution or Remediation? A Study of Electronic Scholarly Editions on the Web

    Directory of Open Access Journals (Sweden)

    Lina Karlsson

    2004-04-01

    Full Text Available The study examines in what form and to what extent media specific value-adding features are present in a selection of scholarly editions of literary works on the Web, concentrating on hypertextuality, interactivity and hypermediality. Besides form and extent, the study investigates whether or not the construction of the editions corresponds to theories and guidelines about how electronic scholarly editions should be designed to generate an added value from a scholarly point of view. The empirical approach is mainly qualitative and the selection consists of 31 editions. The results show that a majority of the editions does not incorporate all of the value-adding aspects. Mainly, the ability to use hyperlinks to bring larger amount of material together, and the use of links to show inter- and intratextual relations, have been realized. Only a minority of the editions exploit the possibilities of interactivity, especially the ability to read and submit user comments. Few editions integrate forms of media that a printed edition can not handle, i.e. sound and moving pictures. The conclusion of the study is that web editions seem to reproduce features of the printed media and do not fulfil the potential of the Web to any larger extent.

  19. Post-editing machine translated text in a commercial setting: Observation and statistical analysis

    OpenAIRE

    Tatsumi, Midori

    2010-01-01

    Machine translation systems, when they are used in a commercial context for publishing purposes, are usually used in combination with human post-editing. Thus understanding human post-editing behaviour is crucial in order to maximise the benefit of machine translation systems. Though there have been a number of studies carried out on human post-editing to date, there is a lack of large-scale studies on post-editing in industrial contexts which focus on the activity in real-life settings. This...

  20. CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Ronda, Carlotta; Maury, Jerome; Jakociunas, Tadas;

    2015-01-01

    episomal vectors. Existing approaches for achieving stable simultaneous genome integrations of multiple DNA fragments often result in relatively low integration efficiencies and furthermore rely on the use of selection markers. Results: Here, we have developed a novel method, CrEdit (CRISPR/Cas9 mediated...... genome Editing), which utilizes targeted double strand breaks caused by CRISPR/Cas9 to significantly increase the efficiency of homologous integration in order to edit and manipulate genomic DNA. Using CrEdit, the efficiency and locus specificity of targeted genome integrations reach close to 100...

  1. [The application of CRISPR/Cas9 genome editing technology in cancer research].

    Science.gov (United States)

    Wang, Dayong; Ma, Ning; Hui, Yang; Gao, Xu

    2016-01-01

    The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease) genome editing technology has become more and more popular in gene editing because of its simple design and easy operation. Using the CRISPR/Cas9 system, researchers can perform site-directed genome modification at the base level. Moreover, it has been widely used in genome editing in multiple species and related cancer research. In this review, we summarize the application of the CRISPR/Cas9 system in cancer research based on the latest research progresses as well as our understanding of cancer research and genome editing techniques.

  2. [Textual research of existing block-printed edition of Source of Acupuncture and Moxibustion (Zhenjiu Fengyuan)].

    Science.gov (United States)

    Soldan, Jan; Ren, Yu-Lan; Zou, Peng; Liang, Fan-Rong

    2013-08-01

    Based on comprehensive arrangement and analysis of edition origin and development, system, characteristic, archive holding situation of Zhenjiu Fengyuan (Source of Acupuncture and Moxibustion writlen) by LI Xue-chuan in Qing dynasty, the error and mistakes in Summary of TCM Ancient books in China, Union Catalog of TCM Books and Grand Chinese Dictionary of Medical Books are pointed out. On the other hand, under full evaluation and comparison among three types of block-printed editions, Dihua Caotang edition in 2 years of Daoguang emperor, Qing Dynasty (about 1822) that is collected in the library of Beijing University of CM is considered as good edition. PMID:24195227

  3. Distinct role of Arabidopsis mitochondrial P-type pentatricopeptide repeat protein-modulating editing protein, PPME, in nad1 RNA editing.

    Science.gov (United States)

    Leu, Kuan-Chieh; Hsieh, Ming-Hsiun; Wang, Huei-Jing; Hsieh, Hsu-Liang; Jauh, Guang-Yuh

    2016-06-01

    The mitochondrion is an important power generator in most eukaryotic cells. To preserve its function, many essential nuclear-encoded factors play specific roles in mitochondrial RNA metabolic processes, including RNA editing. RNA editing consists of post-transcriptional deamination, which alters specific nucleotides in transcripts to mediate gene expression. In plant cells, many pentatricopeptide repeat proteins (PPRs) participate in diverse organellar RNA metabolic processes, but only PLS-type PPRs are involved in RNA editing. Here, we report a P-type PPR protein from Arabidopsis thaliana, P-type PPR-Modulating Editing (PPME), which has a distinct role in mitochondrial nad1 RNA editing via RNA binding activity. In the homozygous ppme mutant, cytosine (C)-to-uracil (U) conversions at both the nad1-898 and 937 sites were abolished, disrupting Arg(300)-to-Trp(300) and Pro(313)-to-Ser(313) amino acid changes in the mitochondrial NAD1 protein. NAD1 is a critical component of mitochondrial respiration complex I; its activity is severely reduced in the homozygous ppme mutant, resulting in significantly altered growth and development. Both abolished RNA editing and defective complex I activity were completely rescued by CaMV 35S promoter- and PPME native promoter-driven PPME genomic fragments tagged with GFP in a homozygous ppme background. Our experimental results demonstrate a distinct role of a P-type PPR protein, PPME, in RNA editing in plant organelles. PMID:27149614

  4. Fast and sensitive detection of indels induced by precise gene targeting

    DEFF Research Database (Denmark)

    Yang, Zhang; Steentoft, Catharina; Hauge, Camilla;

    2015-01-01

    The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect...... and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect...... by traditional methods. Here we present a method for fast, sensitive and simple indel detection that accurately defines indel sizes down to ±1 bp. The method coined IDAA for Indel Detection by Amplicon Analysis is based on tri-primer amplicon labelling and DNA capillary electrophoresis detection, and IDAA...

  5. Editing CCR5: a novel approach to HIV gene therapy.

    Science.gov (United States)

    Cornu, Tatjana I; Mussolino, Claudio; Bloom, Kristie; Cathomen, Toni

    2015-01-01

    Acquired immunodeficiency syndrome (AIDS) is a life-threatening disorder caused by infection of individuals with the human immunodeficiency virus (HIV). Entry of HIV-1 into target cells depends on the presence of two surface proteins on the cell membrane: CD4, which serves as the main receptor, and either CCR5 or CXCR4 as a co-receptor. A limited number of people harbor a genomic 32-bp deletion in the CCR5 gene (CCR5∆32), leading to expression of a truncated gene product that provides resistance to HIV-1 infection in individuals homozygous for this mutation. Moreover, allogeneic hematopoietic stem cell (HSC) transplantation with CCR5∆32 donor cells seems to confer HIV-1 resistance to the recipient as well. However, since Δ32 donors are scarce and allogeneic HSC transplantation is not exempt from risks, the development of gene editing tools to knockout CCR5 in the genome of autologous cells is highly warranted. Targeted gene editing can be accomplished with designer nucleases, which essentially are engineered restriction enzymes that can be designed to cleave DNA at specific sites. During repair of these breaks, the cellular repair pathway often introduces small mutations at the break site, which makes it possible to disrupt the ability of the targeted locus to express a functional protein, in this case CCR5. Here, we review the current promise and limitations of CCR5 gene editing with engineered nucleases, including factors affecting the efficiency of gene disruption and potential off-target effects. PMID:25757618

  6. Potential pitfalls of CRISPR/Cas9-mediated genome editing.

    Science.gov (United States)

    Peng, Rongxue; Lin, Guigao; Li, Jinming

    2016-04-01

    Recently, a novel technique named the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas)9 system has been rapidly developed. This genome editing tool has improved our ability tremendously with respect to exploring the pathogenesis of diseases and correcting disease mutations, as well as phenotypes. With a short guide RNA, Cas9 can be precisely directed to target sites, and functions as an endonuclease to efficiently produce breaks in DNA double strands. Over the past 30 years, CRISPR has evolved from the 'curious sequences of unknown biological function' into a promising genome editing tool. As a result of the incessant development in the CRISPR/Cas9 system, Cas9 co-expressed with custom guide RNAs has been successfully used in a variety of cells and organisms. This genome editing technology can also be applied to synthetic biology, functional genomic screening, transcriptional modulation and gene therapy. However, although CRISPR/Cas9 has a broad range of action in science, there are several aspects that affect its efficiency and specificity, including Cas9 activity, target site selection and short guide RNA design, delivery methods, off-target effects and the incidence of homology-directed repair. In the present review, we highlight the factors that affect the utilization of CRISPR/Cas9, as well as possible strategies for handling any problems. Addressing these issues will allow us to take better advantage of this technique. In addition, we also review the history and rapid development of the CRISPR/Cas system from the time of its initial discovery in 2012. PMID:26535798

  7. Editing a Normal Science Journal in Social Science

    OpenAIRE

    Linton C. Freeman

    2009-01-01

    Editer un journal de science normale dans les sciences sociales : Cet papier mets en évidence quelqu'unes des différences entre les journaux de "science normale" dans des disciplines telles que la physique et la chimie, et des "sciences non-normales" dans des disciplines de sciences sociales. L'article montre qu'un journal, Social Networks, ressemble plus à un journal de science normale qu'un journal typique des sciences sociales. L'auteur montre que les propriétés de sciences normales de la ...

  8. Java2 Enterprise Edition 14 (J2EE 14) Bible

    CERN Document Server

    McGovern, James; Fain, Yakov; Gordon, Jason; Henry, Ethan; Hurst, Walter; Jain, Ashish; Little, Mark; Nagarajan, Vaidyanathan; Oak, Harshad; Phillips, Lee Anne

    2011-01-01

    Java 2 Enterprise Edition (J2EE) is the specification that all enterprise Java developers need to build multi-tier applications, and also the basis for BEA's WebLogic Application Server and IBM's WebSphereRevised to be current with the significant J2EE 1.4 update that will drive substantial developer interestWritten by a top-selling team of eleven experts who provide unique and substantial business examples in a vendor-neutral format, making the information applicable to various application serversCovers patterns, J2EE application servers, frameworks, Ant, and continuous availabilityIncludes e

  9. Enhancing Learner Autonomy in an On-line Editing Programme

    Directory of Open Access Journals (Sweden)

    Hebe Wong

    2011-09-01

    Full Text Available Little (1999 argues that in formal educational contexts, “the basis of learner autonomy is acceptance of responsibility for one’s own learning” (p.11. An autonomous learner takes responsibility for various aspects of learning (Benson & Voller, 1997; Holec, 1981. This study examines how learner autonomy opportunities were provided at various stages of writing in an on-line editing programme for a group of electronic engineering students and how the students took charge of their language learning when receiving feedback on their technical writing. The impact on their own learning effectiveness of the decisions students made is also discussed.

  10. Current Progress in Therapeutic Gene Editing for Monogenic Diseases.

    Science.gov (United States)

    Prakash, Versha; Moore, Marc; Yáñez-Muñoz, Rafael J

    2016-03-01

    Programmable nucleases allow defined alterations in the genome with ease-of-use, efficiency, and specificity. Their availability has led to accurate and widespread genome engineering, with multiple applications in basic research, biotechnology, and therapy. With regard to human gene therapy, nuclease-based gene editing has facilitated development of a broad range of therapeutic strategies based on both nonhomologous end joining and homology-dependent repair. This review discusses current progress in nuclease-based therapeutic applications for a subset of inherited monogenic diseases including cystic fibrosis, Duchenne muscular dystrophy, diseases of the bone marrow, and hemophilia and highlights associated challenges and future prospects. PMID:26765770

  11. Genome Editing of Structural Variations: Modeling and Gene Correction.

    Science.gov (United States)

    Park, Chul-Yong; Sung, Jin Jea; Kim, Dong-Wook

    2016-07-01

    The analysis of chromosomal structural variations (SVs), such as inversions and translocations, was made possible by the completion of the human genome project and the development of genome-wide sequencing technologies. SVs contribute to genetic diversity and evolution, although some SVs can cause diseases such as hemophilia A in humans. Genome engineering technology using programmable nucleases (e.g., ZFNs, TALENs, and CRISPR/Cas9) has been rapidly developed, enabling precise and efficient genome editing for SV research. Here, we review advances in modeling and gene correction of SVs, focusing on inversion, translocation, and nucleotide repeat expansion. PMID:27016031

  12. Hackers Heroes of the Computer Revolution - 25th Anniversary Edition

    CERN Document Server

    Levy, Steven

    2010-01-01

    This 25th anniversary edition of Steven Levy's classic book traces the exploits of the computer revolution's original hackers -- those brilliant and eccentric nerds from the late 1950s through the early '80s who took risks, bent the rules, and pushed the world in a radical new direction. With updated material from noteworthy hackers such as Bill Gates, Mark Zuckerberg, Richard Stallman, and Steve Wozniak, Hackers is a fascinating story that begins in early computer research labs and leads to the first home computers. Levy profiles the imaginative brainiacs who found clever and unorthodox sol

  13. Measuring Editing Skills: Passage Correction and Peer Feedback

    OpenAIRE

    Barrow, Jack; Kanel, Kim; Swenson, Tamara

    1992-01-01

    This paper reports on research currently in progress on the use of Passage Correction (PC) tests as a measure of editing ability. This is one aspect of an overall study on the value of peer versus teacher feedback for improving overall scores on a standard composition profile. Subjects are 138 first-year students at two junior colleges in Osaka. Subjects were administered pre- and post-test PCs and pre- and post-test compositions. No significant differences were found between the peer and tea...

  14. CRISPR-Cas9-Mediated Genome Editing in Leishmania donovani

    OpenAIRE

    Zhang, Wen-Wei; Matlashewski, Greg

    2015-01-01

    ABSTRACT The prokaryotic CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9, an RNA-guided endonuclease, has been shown to mediate efficient genome editing in a wide variety of organisms. In the present study, the CRISPR-Cas9 system has been adapted to Leishmania donovani, a protozoan parasite that causes fatal human visceral leishmaniasis. We introduced the Cas9 nuclease into L. donovani and generated guide RNA (gRNA) expression vectors by using the L. donovani rRNA promo...

  15. Probability and Statistics The Science of Uncertainty (Revised Edition)

    CERN Document Server

    Tabak, John

    2011-01-01

    Probability and Statistics, Revised Edition deals with the history of probability, describing the modern concept of randomness and examining "pre-probabilistic" ideas of what most people today would characterize as randomness. This revised book documents some historically important early uses of probability to illustrate some very important probabilistic questions. It goes on to explore statistics and the generations of mathematicians and non-mathematicians who began to address problems in statistical analysis, including the statistical structure of data sets as well as the theory of

  16. Pro Tools 9 music production, recording, editing and mixing

    CERN Document Server

    Collins, Mike

    2012-01-01

    Prepare yourself to be a great producer when using Pro Tools in your studio. Pro Tools 9: Music Production, Recording, Editing & Mixing is the definitive guide to the software for new and professional users, providing you with all the vital techniques that you need to know. Covering both Pro Tools HD 9 and Pro Tools 9 software, this book is extensively illustrated in color and packed with time saving hints and tips - making it a great reference to keep on hand.* Become an expert Pro Tools user and fully unlock the potential of your system! * Discover how to achieve complete co

  17. CRISPR/Cas9 technology for targeted genome editing

    Directory of Open Access Journals (Sweden)

    Lomov N. A.

    2015-08-01

    Full Text Available CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats are the segments of prokaryotic DNA containing short repeats in its nucleotide sequence. Today we know that this is a bacterial protection system against viral DNA. The molecular components of CRISPR/Cas9 system have been used for a gene editing in eukaryotes since 2013. But as any other method it also has the limitations and drawbacks. Here we are going to review the history of CRISPR biology and to discuss the possibilities that this new technology provides to researchers as well as the prospects for its use in the medical research and treatment.

  18. Algebra Sets, Symbols, and the Language of Thought (Revised Edition)

    CERN Document Server

    Tabak, John

    2011-01-01

    Algebra, Revised Edition describes the history of both strands of algebraic thought. This updated resource describes some of the earliest progress in algebra as well as some of the mathematicians in Mesopotamia, Egypt, China, and Greece who contributed to this early period. It goes on to explore the many breakthroughs in algebraic techniques as well as how letters were used to represent numbers. New material has been added to the chapter on "modern" algebra, a type of mathematical research that continues to occupy the attention of many mathematicians today.

  19. Dictionary of modern English usage the classic first edition

    CERN Document Server

    Fowler, H W

    2009-01-01

    No book had more influence on twentieth-century attitudes to the English language in Britain than Henry Fowler's Dictionary of Modern English Usage. It rapidly became the standard work of reference for the correct use of English in terms of choice of words, grammar, and style. Much loved for his firm opinions, passion, and dry humour, Fowler has stood the test of time and is still considered the best arbiter of good practice. Now one of today's leading experts on thelanguage, David Crystal, has reassessed Fowler's contribution in this fascinating new edition. Crystal goes beyond the popular my

  20. [Regimento proueytoso and Modus curandi: edition of the texts].

    Science.gov (United States)

    Rosa, Maria Carlota; de Carvalho, Diana Maul; Teixeira, Dante Martins

    2005-01-01

    This issue features facsimiles of Regimento proueytoso contra ha pestenença and Modus curandi cum balsamo, based on the original texts housed in the Biblioteca Pública de Evora and the Biblioteca Nacional de Portugal, respectively. Semi-diplomatic editions of both facsimiles--with transliterations into modern characters--have also been provided. These are followed by translations, in the case of Regimento from old to modern Portuguese and in the case of Modus curandi from Latin to modern-day Portuguese. This text explains the criteria used in preparing the semi-diplomatic versions and in modernizing the text of Regimento.