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Sample records for comprehensive transcript index

  1. 21 CFR 1316.63 - Official transcript; index; corrections.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Official transcript; index; corrections. 1316.63 Section 1316.63 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE ADMINISTRATIVE FUNCTIONS, PRACTICES, AND PROCEDURES Administrative Hearings § 1316.63 Official transcript; index...

  2. Comprehensive Behavioral Analysis of Activating Transcription Factor 5-Deficient Mice

    Directory of Open Access Journals (Sweden)

    Mariko Umemura

    2017-07-01

    Full Text Available Activating transcription factor 5 (ATF5 is a member of the CREB/ATF family of basic leucine zipper transcription factors. We previously reported that ATF5-deficient (ATF5-/- mice demonstrated abnormal olfactory bulb development due to impaired interneuron supply. Furthermore, ATF5-/- mice were less aggressive than ATF5+/+ mice. Although ATF5 is widely expressed in the brain, and involved in the regulation of proliferation and development of neurons, the physiological role of ATF5 in the higher brain remains unknown. Our objective was to investigate the physiological role of ATF5 in the higher brain. We performed a comprehensive behavioral analysis using ATF5-/- mice and wild type littermates. ATF5-/- mice exhibited abnormal locomotor activity in the open field test. They also exhibited abnormal anxiety-like behavior in the light/dark transition test and open field test. Furthermore, ATF5-/- mice displayed reduced social interaction in the Crawley’s social interaction test and increased pain sensitivity in the hot plate test compared with wild type. Finally, behavioral flexibility was reduced in the T-maze test in ATF5-/- mice compared with wild type. In addition, we demonstrated that ATF5-/- mice display disturbances of monoamine neurotransmitter levels in several brain regions. These results indicate that ATF5 deficiency elicits abnormal behaviors and the disturbance of monoamine neurotransmitter levels in the brain. The behavioral abnormalities of ATF5-/- mice may be due to the disturbance of monoamine levels. Taken together, these findings suggest that ATF5-/- mice may be a unique animal model of some psychiatric disorders.

  3. A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms.

    Science.gov (United States)

    Lai, Fu-Jou; Chang, Hong-Tsun; Huang, Yueh-Min; Wu, Wei-Sheng

    2014-01-01

    Eukaryotic transcriptional regulation is known to be highly connected through the networks of cooperative transcription factors (TFs). Measuring the cooperativity of TFs is helpful for understanding the biological relevance of these TFs in regulating genes. The recent advances in computational techniques led to various predictions of cooperative TF pairs in yeast. As each algorithm integrated different data resources and was developed based on different rationales, it possessed its own merit and claimed outperforming others. However, the claim was prone to subjectivity because each algorithm compared with only a few other algorithms and only used a small set of performance indices for comparison. This motivated us to propose a series of indices to objectively evaluate the prediction performance of existing algorithms. And based on the proposed performance indices, we conducted a comprehensive performance evaluation. We collected 14 sets of predicted cooperative TF pairs (PCTFPs) in yeast from 14 existing algorithms in the literature. Using the eight performance indices we adopted/proposed, the cooperativity of each PCTFP was measured and a ranking score according to the mean cooperativity of the set was given to each set of PCTFPs under evaluation for each performance index. It was seen that the ranking scores of a set of PCTFPs vary with different performance indices, implying that an algorithm used in predicting cooperative TF pairs is of strength somewhere but may be of weakness elsewhere. We finally made a comprehensive ranking for these 14 sets. The results showed that Wang J's study obtained the best performance evaluation on the prediction of cooperative TF pairs in yeast. In this study, we adopted/proposed eight performance indices to make a comprehensive performance evaluation on the prediction results of 14 existing cooperative TFs identification algorithms. Most importantly, these proposed indices can be easily applied to measure the performance of new

  4. Comprehensive evaluation of global energy interconnection development index

    Science.gov (United States)

    Liu, Lin; Zhang, Yi

    2018-04-01

    Under the background of building global energy interconnection and realizing green and low-carbon development, this article constructed the global energy interconnection development index system which based on the current situation of global energy interconnection development. Through using the entropy method for the weight analysis of global energy interconnection development index, and then using gray correlation method to analyze the selected countries, this article got the global energy interconnection development index ranking and level classification.

  5. Comprehensive evaluation index system of total supply capability in distribution network

    Science.gov (United States)

    Zhang, Linyao; Wu, Guilian; Yang, Jingyuan; Jia, Shuangrui; Zhang, Wei; Sun, Weiqing

    2018-01-01

    Aiming at the lack of a comprehensive evaluation of the distribution network, based on the existing distribution network evaluation index system, combined with the basic principles of constructing the evaluation index, put forward a new evaluation index system of distribution network capacity. This paper is mainly based on the total supply capability of the distribution network, combining single index and various factors, into a multi-evaluation index of the distribution network, thus forming a reasonable index system, and various indicators of rational quantification make the evaluation results more intuitive. In order to have a comprehensive judgment of distribution network, this paper uses weights to analyse the importance of each index, verify the rationality of the index system through the example, it is proved that the rationality of the index system, so as to guide the direction of distribution network planning.

  6. Comprehensive analysis of the transcriptional profile of the Mediator complex across human cancer types.

    Science.gov (United States)

    Syring, Isabella; Klümper, Niklas; Offermann, Anne; Braun, Martin; Deng, Mario; Boehm, Diana; Queisser, Angela; von Mässenhausen, Anne; Brägelmann, Johannes; Vogel, Wenzel; Schmidt, Doris; Majores, Michael; Schindler, Anne; Kristiansen, Glen; Müller, Stefan C; Ellinger, Jörg; Shaikhibrahim, Zaki; Perner, Sven

    2016-04-26

    The Mediator complex is a key regulator of gene transcription and several studies demonstrated altered expressions of particular subunits in diverse human diseases, especially cancer. However a systematic study deciphering the transcriptional expression of the Mediator across different cancer entities is still lacking.We therefore performed a comprehensive in silico cancer vs. benign analysis of the Mediator complex subunits (MEDs) for 20 tumor entities using Oncomine datasets. The transcriptional expression profiles across almost all cancer entities showed differentially expressed MEDs as compared to benign tissue. Differential expression of MED8 in renal cell carcinoma (RCC) and MED12 in lung cancer (LCa) were validated and further investigated by immunohistochemical staining on tissue microarrays containing large numbers of specimen. MED8 in clear cell RCC (ccRCC) associated with shorter survival and advanced TNM stage and showed higher expression in metastatic than primary tumors. In vitro, siRNA mediated MED8 knockdown significantly impaired proliferation and motility in ccRCC cell lines, hinting at a role for MED8 to serve as a novel therapeutic target in ccRCC. Taken together, our Mediator complex transcriptome proved to be a valid tool for identifying cancer-related shifts in Mediator complex composition, revealing that MEDs do exhibit cancer specific transcriptional expression profiles.

  7. A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

    Directory of Open Access Journals (Sweden)

    YA-FEN eLIN

    2014-06-01

    Full Text Available Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of heavy metal exposure adaptation, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23830 transcript sequences (isotigs with an average length of 1025 bps were determined for roots, shoots and inflorescences of N. caerulescens accession ‘Ganges’ by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When compared to a Brassicaceae proteome set, 22,232 (93.2% of the N. caerulescens isotigs (corresponding to 19191 isogroups had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3, clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposure.

  8. Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes

    Directory of Open Access Journals (Sweden)

    Deyholos Michael K

    2006-10-01

    Full Text Available Abstract Background Roots are an attractive system for genomic and post-genomic studies of NaCl responses, due to their primary importance to agriculture, and because of their relative structural and biochemical simplicity. Excellent genomic resources have been established for the study of Arabidopsis roots, however, a comprehensive microarray analysis of the root transcriptome following NaCl exposure is required to further understand plant responses to abiotic stress and facilitate future, systems-based analyses of the underlying regulatory networks. Results We used microarrays of 70-mer oligonucleotide probes representing 23,686 Arabidopsis genes to identify root transcripts that changed in relative abundance following 6 h, 24 h, or 48 h of hydroponic exposure to 150 mM NaCl. Enrichment analysis identified groups of structurally or functionally related genes whose members were statistically over-represented among up- or down-regulated transcripts. Our results are consistent with generally observed stress response themes, and highlight potentially important roles for underappreciated gene families, including: several groups of transporters (e.g. MATE, LeOPT1-like; signalling molecules (e.g. PERK kinases, MLO-like receptors, carbohydrate active enzymes (e.g. XTH18, transcription factors (e.g. members of ZIM, WRKY, NAC, and other proteins (e.g. 4CL-like, COMT-like, LOB-Class 1. We verified the NaCl-inducible expression of selected transcription factors and other genes by qRT-PCR. Conclusion Micorarray profiling of NaCl-treated Arabidopsis roots revealed dynamic changes in transcript abundance for at least 20% of the genome, including hundreds of transcription factors, kinases/phosphatases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this stress response. Our identification of these transcriptional responses, and groups of evolutionarily related genes with either similar or divergent

  9. Global Transcription Profiling Reveals Comprehensive Insights into Hypoxic Response in Arabidopsis1[w

    Science.gov (United States)

    Liu, Fenglong; VanToai, Tara; Moy, Linda P.; Bock, Geoffrey; Linford, Lara D.; Quackenbush, John

    2005-01-01

    Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic PSAG12:ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants. PMID:15734912

  10. Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis.

    Science.gov (United States)

    Liu, Fenglong; Vantoai, Tara; Moy, Linda P; Bock, Geoffrey; Linford, Lara D; Quackenbush, John

    2005-03-01

    Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic P(SAG12):ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants.

  11. Comprehensive bibliographic coverage of the social sciences and humanities in a citation index

    DEFF Research Database (Denmark)

    Sivertsen, Gunnar; Larsen, Birger

    2012-01-01

    A well-designed and comprehensive citation index for the social sciences and humanities has many potential uses, but has yet to be realised. Significant parts of the scholarly production in these areas are not published in international journals, but in national scholarly journals, in book chapters...... or in monographs. The potential for covering these literatures more comprehensively can now be investigated empirically using a complete publication output data set from the higher education sector of an entire country (Norway). We find that while the international journals in the social sciences and humanities...... are promising for a more comprehensive coverage of the social sciences and humanities....

  12. Comprehensive analysis of the specificity of transcription activator-like effector nucleases

    DEFF Research Database (Denmark)

    Juillerat, Alexandre; Dubois, Gwendoline; Valton, Julien

    2014-01-01

    A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within...... their target site. The ability to predict the specificity of targeting is thus highly desirable. Here, we describe the first comprehensive experimental study focused on the specificity of the four commonly used repeat variable diresidues (RVDs; NI:A, HD:C, NN:G and NG:T) incorporated in transcription activator......-like effector nucleases (TALEN). The analysis of >15 500 unique TALEN/DNA cleavage profiles allowed us to monitor the specificity gradient of the RVDs along a TALEN/DNA binding array and to present a specificity scoring matrix for RVD/nucleotide association. Furthermore, we report that TALEN can only...

  13. PRISM offers a comprehensive genomic approach to transcription factor function prediction

    KAUST Repository

    Wenger, A. M.; Clarke, S. L.; Guturu, H.; Chen, J.; Schaar, B. T.; McLean, C. Y.; Bejerano, G.

    2013-01-01

    The human genome encodes 1500-2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells.

  14. Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets.

    Science.gov (United States)

    Reimand, Jüri; Vaquerizas, Juan M; Todd, Annabel E; Vilo, Jaak; Luscombe, Nicholas M

    2010-08-01

    Transcription factor (TF) perturbation experiments give valuable insights into gene regulation. Genome-scale evidence from microarray measurements may be used to identify regulatory interactions between TFs and targets. Recently, Hu and colleagues published a comprehensive study covering 269 TF knockout mutants for the yeast Saccharomyces cerevisiae. However, the information that can be extracted from this valuable dataset is limited by the method employed to process the microarray data. Here, we present a reanalysis of the original data using improved statistical techniques freely available from the BioConductor project. We identify over 100,000 differentially expressed genes-nine times the total reported by Hu et al. We validate the biological significance of these genes by assessing their functions, the occurrence of upstream TF-binding sites, and the prevalence of protein-protein interactions. The reanalysed dataset outperforms the original across all measures, indicating that we have uncovered a vastly expanded list of relevant targets. In summary, this work presents a high-quality reanalysis that maximizes the information contained in the Hu et al. compendium. The dataset is available from ArrayExpress (accession: E-MTAB-109) and it will be invaluable to any scientist interested in the yeast transcriptional regulatory system.

  15. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

    Science.gov (United States)

    Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J.

    2013-01-01

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. PMID:23175603

  16. PRISM offers a comprehensive genomic approach to transcription factor function prediction

    KAUST Repository

    Wenger, A. M.

    2013-02-04

    The human genome encodes 1500-2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells.

  17. HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.; Medvedeva, Yulia A.; Schaefer, Ulf; Kasianov, Artem S.; Vorontsov, Ilya E.; Bajic, Vladimir B.; Makeev, Vsevolod J.

    2012-01-01

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.

  18. HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

    KAUST Repository

    Kulakovskiy, Ivan V.

    2012-11-21

    Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.

  19. PlantNATsDB: a comprehensive database of plant natural antisense transcripts.

    Science.gov (United States)

    Chen, Dijun; Yuan, Chunhui; Zhang, Jian; Zhang, Zhao; Bai, Lin; Meng, Yijun; Chen, Ling-Ling; Chen, Ming

    2012-01-01

    Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a 'Gene Set Analysis' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/.

  20. [Frail-VIG index: Design and evaluation of a new frailty index based on the Comprehensive Geriatric Assessment].

    Science.gov (United States)

    Amblàs-Novellas, Jordi; Martori, Joan Carles; Molist Brunet, Núria; Oller, Ramon; Gómez-Batiste, Xavier; Espaulella Panicot, Joan

    Frailty is closely linked to health results. Frailty indexes (FI) and the Comprehensive Geriatric Assessment (CGA) are multidimensional tools. FI serve to quantitatively measure frailty levels. They have shown to have an excellent correlation with mortality. However, they are infrequently used in clinical practice. Given the need for new, more concise, and pragmatic FI, a new FI is proposed based on a CGA (Frail-VIG Index). A prospective, observational, longitudinal study was conducted, with cohort follow up at 12 months or death. Participants were patients admitted in the Geriatric Unit of the University Hospital of Vic (Barcelona, Spain) during 2014. Contrast of hypothesis log-rank for survival curves according to Frail-VIG index, and analysis of ROC curves were performed to assess prognostic capacity. A total of 590 patients were included (mean age=86.39). Mortality rate at 12 months was 46.4%. The comparative analysis showed statistically significant differences (P<.05) for almost all variables included in the Frail-VIG index. Survival curves also show significant differences (X 2 =445, P<.001) for the different Frail-VIG index scores. The area under the ROC curve at 12 months was 0.9 (0.88-0.92). An administration time of the Index is estimated at less than 10minutes. Results endorse the Frail-VIG index as a simple (as for contents), rapid (for administration time) tool, with discriminative (for situational diagnosis) and predictive capacity (high correlation with mortality). Copyright © 2016 SEGG. Publicado por Elsevier España, S.L.U. All rights reserved.

  1. Automatic generation of the index of productive syntax for child language transcripts.

    Science.gov (United States)

    Hassanali, Khairun-nisa; Liu, Yang; Iglesias, Aquiles; Solorio, Thamar; Dollaghan, Christine

    2014-03-01

    The index of productive syntax (IPSyn; Scarborough (Applied Psycholinguistics 11:1-22, 1990) is a measure of syntactic development in child language that has been used in research and clinical settings to investigate the grammatical development of various groups of children. However, IPSyn is mostly calculated manually, which is an extremely laborious process. In this article, we describe the AC-IPSyn system, which automatically calculates the IPSyn score for child language transcripts using natural language processing techniques. Our results show that the AC-IPSyn system performs at levels comparable to scores computed manually. The AC-IPSyn system can be downloaded from www.hlt.utdallas.edu/~nisa/ipsyn.html .

  2. Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

    Directory of Open Access Journals (Sweden)

    Arnoldo J Müller-Molina

    Full Text Available To know the map between transcription factors (TFs and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters.

  3. A comprehensive analysis of microProteins reveals their potentially widespread mechanism of transcriptional regulation

    NARCIS (Netherlands)

    Magnani, Enrico; de Klein, Niek; Nam, Hye-In; Kim, Jung-Gun; Pham, Kimberly; Fiume, Elisa; Mudgett, Mary Beth; Rhee, Seung Yon

    2014-01-01

    Truncated transcription factor-like proteins called microProteins (miPs) can modulate transcription factor activities, thereby increasing transcriptional regulatory complexity. To understand their prevalence, evolution, and function, we predicted over 400 genes that encode putative miPs from

  4. Comprehensive analysis of the renal transcriptional response to acute uranyl nitrate exposure

    Directory of Open Access Journals (Sweden)

    Argiles Angel

    2006-01-01

    Full Text Available Abstract Background Chemical and radiological toxicities related to uranium acute exposure have been widely studied in nuclear fuel workers and military personnel. It is well known that uranyl nitrate induces acute renal failure (ARF. However, the mechanisms of this metal-induced injury are not well defined at the molecular level. Results Renal function and histology were assessed in mice receiving uranyl nitrate (UN(+ and controls (UN(-. To identify the genomic response to uranium exposure, serial analysis gene expression (SAGE of the kidney was performed in both groups. Over 43,000 mRNA SAGE tags were sequenced. A selection of the differentially expressed transcripts was confirmed by real-time quantitative PCR and Western blotting. UN(+ animals developed renal failure and displayed the characteristic histological lesions of UN nephropathy. Of the >14,500 unique tags identified in both libraries, 224 had a modified expression level; they are known to participate in inflammation, ion transport, signal transduction, oxidative stress, apoptosis, metabolism, and catabolism. Several genes that were identified had not previously been evaluated within the context of toxic ARF such as translationally controlled tumor protein, insulin like growth factor binding protein 7 and ribosomal protein S29, all apoptosis related genes. Conclusion We report a comprehensive description of the UN induced modifications in gene expression levels, including the identification of genes previously unrelated to ARF. The study of these genes and the metabolisms they control should improve our understanding of toxic ARF and enlighten on the molecular targets for potential therapeutic interventions.

  5. A new comprehensive index for discriminating adulteration in bovine raw milk.

    Science.gov (United States)

    Liu, Jing; Ren, Jing; Liu, Zhen-Min; Guo, Ben-Heng

    2015-04-01

    This paper proposes a new comprehensive index, called Q, which can effectively discriminate artificial adulterated milk from unadulterated milk. Both normal and adulterated samples of bovine raw milk were analysed by Fourier transform infrared spectroscopic instrument to measure the traditional indices of quality, including fat (FAT), protein (PRO), lactose (LAC), total solids (TS), non-fat solid (NFS), freezing point (FP) and somatic cell counts (SCC). From these traditional indices, this paper elaborates a method to build the index Q. First, correlated analysis and principle component analysis were used to select parameter pairs TS-FAT and FP-LAC as predominant variables. Second, linear-regression analysis and residual analysis are applied to determine the index Q and its discriminating ranges. The verification and two-blind trial results suggested that index Q could accurately detect milk adulteration with maltodextrin and water (as low as 1.0% of adulteration proportions), and with other nine kinds of synthetic adulterants (as low as 0.5% of adulteration proportions). Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Comprehensive Interrogation of Natural TALE DNA Binding Modules and Transcriptional Repressor Domains

    Science.gov (United States)

    Cong, Le; Zhou, Ruhong; Kuo, Yu-chi; Cunniff, Margaret; Zhang, Feng

    2012-01-01

    Transcription activator-like effectors (TALE) are sequence-specific DNA binding proteins that harbor modular, repetitive DNA binding domains. TALEs have enabled the creation of customizable designer transcriptional factors and sequence-specific nucleases for genome engineering. Here we report two improvements of the TALE toolbox for achieving efficient activation and repression of endogenous gene expression in mammalian cells. We show that the naturally occurring repeat variable diresidue (RVD) Asn-His (NH) has high biological activity and specificity for guanine, a highly prevalent base in mammalian genomes. We also report an effective TALE transcriptional repressor architecture for targeted inhibition of transcription in mammalian cells. These findings will improve the precision and effectiveness of genome engineering that can be achieved using TALEs. PMID:22828628

  7. Systematic comparison of ORC configurations by means of comprehensive performance indexes

    International Nuclear Information System (INIS)

    Branchini, Lisa; De Pascale, Andrea; Peretto, Antonio

    2013-01-01

    The Organic Rankine Cycle (ORC) is considered as an emerging technology for power generation through heat recovering from different thermal sources, based on the use of organic fluids as working medium. This paper presents a numerical study to assess the relevance: i) of the thermodynamic cycle, ii) of the main design parameters and iii) of the working fluid, on the achievable performance. The ORC performance is here calculated in terms of six different thermodynamic indexes, offering comprehensive information, namely: cycle efficiency, specific work, recovery efficiency, turbine volumetric expansion ratio, ORC fluid-to-hot source mass flow ratio and heat exchangers size parameter. In the framework of a systematic investigation approach, various possible modifications to the simple ORC plant layout are here analyzed and compared, in order to improve the ORC recovery performance; arrangements such as recuperation, superheated cycle, supercritical conditions, regenerative cycle and their combinations are taken into account. The investigation is carried out by means of an in-house developed calculation tool, based on a thermodynamic property database of the considered fluids, including aromatics, siloxanes, refrigerants and hydrocarbons. A comprehensive parametric analysis of these cycles at different hot source temperature and different evaporation pressure values is carried out. The objectives of this investigation are to provide useful guidelines to select the ORC configuration, the most appropriate fluid and to define the operating parameters, depending on the specific application. Thermodynamic results are also related with sizing of ORC components and thus can be used for economic assessment of the different ORC design alternatives. -- Highlights: • Systematic comparison of ORC thermodynamic arrangements is performed. • Performance is calculated introducing six comprehensive energy and size/economic indexes. • An in-house-developed calculation tool is used

  8. Comprehensive drought characteristics analysis based on a nonlinear multivariate drought index

    Science.gov (United States)

    Yang, Jie; Chang, Jianxia; Wang, Yimin; Li, Yunyun; Hu, Hui; Chen, Yutong; Huang, Qiang; Yao, Jun

    2018-02-01

    It is vital to identify drought events and to evaluate multivariate drought characteristics based on a composite drought index for better drought risk assessment and sustainable development of water resources. However, most composite drought indices are constructed by the linear combination, principal component analysis and entropy weight method assuming a linear relationship among different drought indices. In this study, the multidimensional copulas function was applied to construct a nonlinear multivariate drought index (NMDI) to solve the complicated and nonlinear relationship due to its dependence structure and flexibility. The NMDI was constructed by combining meteorological, hydrological, and agricultural variables (precipitation, runoff, and soil moisture) to better reflect the multivariate variables simultaneously. Based on the constructed NMDI and runs theory, drought events for a particular area regarding three drought characteristics: duration, peak, and severity were identified. Finally, multivariate drought risk was analyzed as a tool for providing reliable support in drought decision-making. The results indicate that: (1) multidimensional copulas can effectively solve the complicated and nonlinear relationship among multivariate variables; (2) compared with single and other composite drought indices, the NMDI is slightly more sensitive in capturing recorded drought events; and (3) drought risk shows a spatial variation; out of the five partitions studied, the Jing River Basin as well as the upstream and midstream of the Wei River Basin are characterized by a higher multivariate drought risk. In general, multidimensional copulas provides a reliable way to solve the nonlinear relationship when constructing a comprehensive drought index and evaluating multivariate drought characteristics.

  9. A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance

    Directory of Open Access Journals (Sweden)

    Wang Xiaowei

    2008-12-01

    Full Text Available Abstract Background Quantitative polymerase chain reaction (QPCR is a widely applied analytical method for the accurate determination of transcript abundance. Primers for QPCR have been designed on a genomic scale but non-specific amplification of non-target genes has frequently been a problem. Although several online databases have been created for the storage and retrieval of experimentally validated primers, only a few thousand primer pairs are currently present in existing databases and the primers are not designed for use under a common PCR thermal profile. Results We previously reported the implementation of an algorithm to predict PCR primers for most known human and mouse genes. We now report the use of that resource to identify 17483 pairs of primers that have been experimentally verified to amplify unique sequences corresponding to distinct murine transcripts. The primer pairs have been validated by gel electrophoresis, DNA sequence analysis and thermal denaturation profile. In addition to the validation studies, we have determined the uniformity of amplification using the primers and the technical reproducibility of the QPCR reaction using the popular and inexpensive SYBR Green I detection method. Conclusion We have identified an experimentally validated collection of murine primer pairs for PCR and QPCR which can be used under a common PCR thermal profile, allowing the evaluation of transcript abundance of a large number of genes in parallel. This feature is increasingly attractive for confirming and/or making more precise data trends observed from experiments performed with DNA microarrays.

  10. Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

    Science.gov (United States)

    Jankowski, Aleksander; Szczurek, Ewa; Jauch, Ralf; Tiuryn, Jerzy; Prabhakar, Shyam

    2013-01-01

    The binding of transcription factors (TFs) to their specific motifs in genomic regulatory regions is commonly studied in isolation. However, in order to elucidate the mechanisms of transcriptional regulation, it is essential to determine which TFs bind DNA cooperatively as dimers and to infer the precise nature of these interactions. So far, only a small number of such dimeric complexes are known. Here, we present an algorithm for predicting cell-type–specific TF–TF dimerization on DNA on a large scale, using DNase I hypersensitivity data from 78 human cell lines. We represented the universe of possible TF complexes by their corresponding motif complexes, and analyzed their occurrence at cell-type–specific DNase I hypersensitive sites. Based on ∼1.4 billion tests for motif complex enrichment, we predicted 603 highly significant cell-type–specific TF dimers, the vast majority of which are novel. Our predictions included 76% (19/25) of the known dimeric complexes and showed significant overlap with an experimental database of protein–protein interactions. They were also independently supported by evolutionary conservation, as well as quantitative variation in DNase I digestion patterns. Notably, the known and predicted TF dimers were almost always highly compact and rigidly spaced, suggesting that TFs dimerize in close proximity to their partners, which results in strict constraints on the structure of the DNA-bound complex. Overall, our results indicate that chromatin openness profiles are highly predictive of cell-type–specific TF–TF interactions. Moreover, cooperative TF dimerization seems to be a widespread phenomenon, with multiple TF complexes predicted in most cell types. PMID:23554463

  11. [Development of an index system for the comprehensive evaluation on public health emergency events surveillance system in China].

    Science.gov (United States)

    Hong, Zhiheng; Ni, Daxin; Cao, Yang; Meng, Ling; Tu, Wenxiao; Li, Leilei; Li, Qun; Jin, Lianmei

    2015-06-01

    To establish a comprehensive evaluation index system for the China Public Health Emergency Events Surveillance System (CPHEESS). A draft index system was built through literature review and under the consideration of the characteristics on CPHEESS. Delphi method was adapted to determine the final index system. The index system was divided into primary, secondary and tertiary levels. There were 4 primary indicators: System structure, Network platform, Surveillance implementation reports with Data analysis and utilization. There were 16 secondary and 70 tertiary indicators being set, with System structure including 14 tertiary indicators (accounted for 20.00%), 21 Network platforms (accounted for 30.00%). Twenty-four Surveillance implementation reports (accounted for 34.29%), 11 Data analysis and utilization (accounted for 15.71%). The average score of importance of each indicators was 4.29 (3.77-4.94), with an average coefficient variation as 0.14 (0.12-0.16). The mean Chronbach's α index was 0.84 (0.81-0.89). The adaptability of each related facilities indicator was specified. The primary indicators were set in accordance with the characteristics and goals of the surveillance systems. Secondary indicators provided key elements in the management and control of the system while the tertiary indicators were available and operative. The agreement rate of experts was high with good validity and reliability. This index system could be used for CPHEESS in future.

  12. A Fuzzy Expression Way for Air Quality Index with More Comprehensive Information

    OpenAIRE

    Yujie Wang; Mingxuan Zhao; Yulin Han; Jian Zhou

    2017-01-01

    The Air Quality Index (AQI) is an evaluating indicator for the atmospheric environment released by various environmental monitoring centers to communicate the present air quality status to the public, which is calculated by the aid of the monitored concentrations of six common air pollutants and relevant computational formulae. Considering that the historical data of daily overall AQI illustrated by the traditional expression way merely contain limited information about the original data, thi...

  13. A Fuzzy Expression Way for Air Quality Index with More Comprehensive Information

    Directory of Open Access Journals (Sweden)

    Yujie Wang

    2017-01-01

    Full Text Available The Air Quality Index (AQI is an evaluating indicator for the atmospheric environment released by various environmental monitoring centers to communicate the present air quality status to the public, which is calculated by the aid of the monitored concentrations of six common air pollutants and relevant computational formulae. Considering that the historical data of daily overall AQI illustrated by the traditional expression way merely contain limited information about the original data, this paper puts forward a more concrete and intuitive way to express the air quality in the past day. By analyzing the data concerning individual air quality indices of pollutants gathered from five cities of China for six consecutive months and conducting the curve fitting, each sub-index is recommended to be set as a Gaussian fuzzy number. Accordingly, taking advantage of the novel operational law for fuzzy numbers, the fuzzy distribution and membership function of the daily overall AQI can be deduced immediately, which as a reference contributes to the users acquiring the information more intuitively and facilitates making plans or decisions. Subsequently, a case study taking Shanghai as a background is conducted to elaborate the application of the proposed approach. Furthermore, the line chart reflecting the overall air quality status in a past period is depicted, based on which an example of selecting a tourist destination is given to demonstrate its utilization.

  14. The assessment of eco-design with a comprehensive index incorporating environmental impact and economic profit

    Science.gov (United States)

    Yang, Shuo; Fu, Yun; Wang, Xiuteng; Xu, Bingsheng; Li, Zheng

    2017-11-01

    Eco-design is an advanced design approach which plays an important part in the national innovation project and serves as a key point for the successful transformation of the supply structure. However, the practical implementation of the pro-environmental designs and technologies always faces a dilemma situation, where some processes can effectively control their emissions to protect the environment at relatively high costs, while others pursue the individual interest in making profit by ignoring the possible adverse environmental impacts. Thus, the assessment on the eco-design process must be carried out based on the comprehensive consideration of the economic and environmental aspects. Presently, the assessment systems in China are unable to fully reflect the new environmental technologies regarding their innovative features or performance. Most of the assessment systems adopt scoring method based on the judgments of the experts, which are easy to use but somewhat subjective. The assessment method presented in this paper includes the environmental impact (EI) assessment based on LCA principal and willingness-to-pay theory, and economic profit (EP) assessment mainly based on market price. The results from the assessment are in the form of EI/EP, which evaluate the targeted process from a combined perspective of environmental and economic performance. A case study was carried out upon the utilization process of coal fly ash, which indicates the proposed method can compare different technical processes in an effective and objective manner, and provide explicit and insightful suggestions for decision making.

  15. INDEX

    OpenAIRE

    Pette, Dirk; Gondin, Julien; Bizzarini, Emiliana; Kern, Helmut; Hofer, Christian; L?fler, Stefan; Mayr, Winfried; M?dlin, Michaela; Urban, Samantha; Kern, Helmut; Biowski, Peter; Marcante, Andrea; Baba, Alfonc; Ghezzo, Luca; Weis, Luca

    2017-01-01

    It is well known that repeated bouts of exercise (i.e. exercise training) lead to an elevated content of mitochondria within muscle. This adaptation confers metabolic advantages during exercise, such as an increase in the aerobic metabolism of lipids, reduced glycogen usage, and diminished lactate production. The molecular basis for this increase in organelle content involves the activation of PGC-1? along with numerous transcription factors which increase the expression of nuclear genes enco...

  16. Water Quality Assessment for Deep-water Channel area of Guangzhou Port based on the Comprehensive Water Quality Identification Index Method

    Science.gov (United States)

    Chen, Yi

    2018-03-01

    The comprehensive water quality identification index method is able to assess the general water quality situation comprehensively and represent the water quality classification; water environment functional zone achieves pollution level and standard objectively and systematically. This paper selects 3 representative zones along deep-water channel of Guangzhou port and applies comprehensive water quality identification index method to calculate sea water quality monitoring data for different selected zones from year 2006 to 2014, in order to investigate the temporal variation of water quality along deep-water channel of Guangzhou port. The comprehensive water quality level from north to south presents an increased trend, and the water quality of the three zones in 2014 is much better than in 2006. This paper puts forward environmental protection measurements and suggestions for Pearl River Estuary, provides data support and theoretical basis for studied sea area pollution prevention and control.

  17. Indexed

    CERN Document Server

    Hagy, Jessica

    2008-01-01

    Jessica Hagy is a different kind of thinker. She has an astonishing talent for visualizing relationships, capturing in pictures what is difficult for most of us to express in words. At indexed.blogspot.com, she posts charts, graphs, and Venn diagrams drawn on index cards that reveal in a simple and intuitive way the large and small truths of modern life. Praised throughout the blogosphere as “brilliant,” “incredibly creative,” and “comic genius,” Jessica turns her incisive, deadpan sense of humor on everything from office politics to relationships to religion. With new material along with some of Jessica’s greatest hits, this utterly unique book will thrill readers who demand humor that makes them both laugh and think.

  18. Assessment of Comprehensive Environmental Pollution Index of Kurichi Industrial Cluster, Coimbatore District, Tamil Nadu, India - a Case Study

    Directory of Open Access Journals (Sweden)

    Ramasamy Rajamanickam

    2018-01-01

    Full Text Available Comprehensive Environmental Pollution Index (CEPI is a rational number to characterize the quality of the environment at a given location following the algorithm of source, pathway, and receptor. As CEPI increases, there will be adverse effectson the receiving environment. Central Pollution Control Board (CPCB has brought out revised criteria for evaluation of CEPI by replacing the criteria issued in 2010. The revised criteria are issued to overcome the subjectivity factors of health impact studies on humans, floraand fauna. Kurichi Industrial Cluster in Coimbatore District is an engineering industrial estate housing foundries, forging units, metal finishingand fabrication units. In January 2010, the Ministry of Environment and Forests, Government of India declared Kurichi as critically polluted area and imposed moratorium on new projects and for expansion of the existing units. This declaration was made based on the CEPI score which was calculated as more than 70. Thereafter, the industries and the local stake holders have implemented various pollution control measures and hence the CEPI score has come down less than 70 and so the moratorium was lifted in October 2010. In this paper, the CEPI score is calculated based on the revised criteria and using the environmental quality monitoring data collected in April 2017. It is found that the CEPI score is below 70 which imply that the industrial units are operating and maintaining the pollution control measures consistently. However, taking a policy decision based on the CEPI score, one should be cautious on the adequacy of data and the parameters selected.

  19. A Comprehensive Review of School-Based Body Mass Index Screening Programs and Their Implications for School Health: Do the Controversies Accurately Reflect the Research?

    Science.gov (United States)

    Ruggieri, Dominique G.; Bass, Sarah B.

    2015-01-01

    Background: Whereas legislation for body mass index (BMI) surveillance and screening programs has passed in 25 states, the programs are often subject to ethical debates about confidentiality and privacy, school-to-parent communication, and safety and self-esteem issues for students. Despite this debate, no comprehensive analysis has been completed…

  20. Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses.

    Directory of Open Access Journals (Sweden)

    Jared D Sharp

    Full Text Available Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.

  1. Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses.

    Science.gov (United States)

    Sharp, Jared D; Singh, Atul K; Park, Sang Tae; Lyubetskaya, Anna; Peterson, Matthew W; Gomes, Antonio L C; Potluri, Lakshmi-Prasad; Raman, Sahadevan; Galagan, James E; Husson, Robert N

    2016-01-01

    Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.

  2. Validity of the American Board of Orthodontics Discrepancy Index and the Peer Assessment Rating Index for comprehensive evaluation of malocclusion severity.

    Science.gov (United States)

    Liu, S; Oh, H; Chambers, D W; Baumrind, S; Xu, T

    2017-08-01

    To assess the validity of the American Board of Orthodontics Discrepancy Index (ABO-DI) and Peer Assessment Rating (PAR) Index in evaluating malocclusion severity in Chinese orthodontic patients. A stratified random sample of 120 orthodontic patients based on Angle classification was collected from six university orthodontic centres. Sixty-nine orthodontists rated malocclusion severity on a five-point scale by assessing a full set of pre-treatment records for each case and listed reasons for their decision. Their judgement was then compared with ABO-DI and PAR scores determined by three calibrated examiners. Excellent interexaminer reliability of clinician judgement, ABO-DI and PAR index was demonstrated by the Intraclass Correlation Coefficient (rho= 0.995, 0.990 and 0.964, respectively). Both the ABO-DI and US-PAR index showed good correlation with clinician judgement (r=.700 and r=.707, respectively). There was variability among the different Angle classifications: the ABO-DI showed the highest correlation with clinician judgement in Class II patients (r=.780), whereas the US-PAR index showed the highest correlation with clinician judgement in Class III patients (r=.710). Both indices demonstrated the lowest correlations with clinician judgement in Class I patients. With strong interexaminer agreement, the panel consensus was used for validating the ABO-DI and US-PAR index for malocclusion severity. Overall, the ABO-DI and US-PAR index were reliable for measuring malocclusion severity with significantly variable weightings for different Angle classifications. Further modification of the indices for different Angle classification may be indicated. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. [Comparative study on promoting blood effects of Danshen-Honghua herb pair with different preparations based on chemometrics and multi-attribute comprehensive index methods].

    Science.gov (United States)

    Qu, Cheng; Tang, Yu-Ping; Shi, Xu-Qin; Zhou, Gui-Sheng; Shang, Er-Xin; Shang, Li-Li; Guo, Jian-Ming; Liu, Pei; Zhao, Jing; Zhao, Bu-Chang; Duan, Jin-Ao

    2017-08-01

    To evaluate the promoting blood circulation and removing blood stasis effects of Danshen-Honghua(DH) herb pair with different preparations (alcohol, 50% alcohol and water) on blood rheology and coagulation functions in acute blood stasis rats, and optimize the best preparation method of DH based on principal component analysis(PCA), hierarchical cluster heatmap analysis and multi-attribute comprehensive index methods. Ice water bath and subcutaneous injection of adrenaline were both used to establish the acute blood stasis rat model. Then the blood stasis rats were administrated intragastrically with DH (alcohol, 50% alcohol and water) extracts. The whole blood viscosity(WBV), plasma viscosity(PV), erythrocyte sedimentation rate(ESR) and haematocrit(HCT) were tested to observe the effects of DH herb pair with different preparations and doses on hemorheology of blood stasis rats; the activated partial thromboplastin time(APTT), thrombin time(TT), prothrombin time(PT), and plasma fibrinogen(FIB) were tested to observe the effects of DH herb pair with different preparations on blood coagulation function and platelet aggregation of blood stasis rats. Then PCA, hierarchical cluster heatmap analysis and multi-attribute comprehensive index methods were all used to comprehensively evaluate the total promoting blood circulation and removing blood stasis effects of DH herb pair with different preparations. The hemorheological indexes and coagulation parameters of model group had significant differences with normal blank group. As compared with the model group, the DH herb pair with different preparations at low, middle and high doses could improve the blood hemorheology indexes and coagulation parameters in acute blood stasis rats with dose-effect relation. Based on the PCA, hierarchical cluster heatmap analysis and multi-attribute comprehensive index methods, the high dose group of 50% alcohol extract had the best effect of promoting blood circulation and removing blood

  4. Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L..

    Directory of Open Access Journals (Sweden)

    Swati Puranik

    Full Text Available The NAC proteins represent a major plant-specific transcription factor family that has established enormously diverse roles in various plant processes. Aided by the availability of complete genomes, several members of this family have been identified in Arabidopsis, rice, soybean and poplar. However, no comprehensive investigation has been presented for the recently sequenced, naturally stress tolerant crop, Setaria italica (foxtail millet that is famed as a model crop for bioenergy research. In this study, we identified 147 putative NAC domain-encoding genes from foxtail millet by systematic sequence analysis and physically mapped them onto nine chromosomes. Genomic organization suggested that inter-chromosomal duplications may have been responsible for expansion of this gene family in foxtail millet. Phylogenetically, they were arranged into 11 distinct sub-families (I-XI, with duplicated genes fitting into one cluster and possessing conserved motif compositions. Comparative mapping with other grass species revealed some orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of genes. The evolutionary significance as duplication and divergence of NAC genes based on their amino acid substitution rates was understood. Expression profiling against various stresses and phytohormones provides novel insights into specific and/or overlapping expression patterns of SiNAC genes, which may be responsible for functional divergence among individual members in this crop. Further, we performed structure modeling and molecular simulation of a stress-responsive protein, SiNAC128, proffering an initial framework for understanding its molecular function. Taken together, this genome-wide identification and expression profiling unlocks new avenues for systematic functional analysis of novel NAC gene family candidates which may be applied for improvising stress adaption in plants.

  5. Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.).

    Science.gov (United States)

    Puranik, Swati; Sahu, Pranav Pankaj; Mandal, Sambhu Nath; B, Venkata Suresh; Parida, Swarup Kumar; Prasad, Manoj

    2013-01-01

    The NAC proteins represent a major plant-specific transcription factor family that has established enormously diverse roles in various plant processes. Aided by the availability of complete genomes, several members of this family have been identified in Arabidopsis, rice, soybean and poplar. However, no comprehensive investigation has been presented for the recently sequenced, naturally stress tolerant crop, Setaria italica (foxtail millet) that is famed as a model crop for bioenergy research. In this study, we identified 147 putative NAC domain-encoding genes from foxtail millet by systematic sequence analysis and physically mapped them onto nine chromosomes. Genomic organization suggested that inter-chromosomal duplications may have been responsible for expansion of this gene family in foxtail millet. Phylogenetically, they were arranged into 11 distinct sub-families (I-XI), with duplicated genes fitting into one cluster and possessing conserved motif compositions. Comparative mapping with other grass species revealed some orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of genes. The evolutionary significance as duplication and divergence of NAC genes based on their amino acid substitution rates was understood. Expression profiling against various stresses and phytohormones provides novel insights into specific and/or overlapping expression patterns of SiNAC genes, which may be responsible for functional divergence among individual members in this crop. Further, we performed structure modeling and molecular simulation of a stress-responsive protein, SiNAC128, proffering an initial framework for understanding its molecular function. Taken together, this genome-wide identification and expression profiling unlocks new avenues for systematic functional analysis of novel NAC gene family candidates which may be applied for improvising stress adaption in plants.

  6. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

    Science.gov (United States)

    The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are well characterized in Arabidopsis (Arabidopsis thaliana), ...

  7. Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT genomic binding patterns discerns cell-specific cis-regulatory modules

    Directory of Open Access Journals (Sweden)

    Kang Keunsoo

    2013-01-01

    Full Text Available Abstract Background Cytokine-activated transcription factors from the STAT (Signal Transducers and Activators of Transcription family control common and context-specific genetic programs. It is not clear to what extent cell-specific features determine the binding capacity of seven STAT members and to what degree they share genetic targets. Molecular insight into the biology of STATs was gained from a meta-analysis of 29 available ChIP-seq data sets covering genome-wide occupancy of STATs 1, 3, 4, 5A, 5B and 6 in several cell types. Results We determined that the genomic binding capacity of STATs is primarily defined by the cell type and to a lesser extent by individual family members. For example, the overlap of shared binding sites between STATs 3 and 5 in T cells is greater than that between STAT5 in T cells and non-T cells. Even for the top 1,000 highly enriched STAT binding sites, ~15% of STAT5 binding sites in mouse female liver are shared by other STATs in different cell types while in T cells ~90% of STAT5 binding sites are co-occupied by STAT3, STAT4 and STAT6. In addition, we identified 116 cis-regulatory modules (CRM, which are recognized by all STAT members across cell types defining a common JAK-STAT signature. Lastly, in liver STAT5 binding significantly coincides with binding of the cell-specific transcription factors HNF4A, FOXA1 and FOXA2 and is associated with cell-type specific gene transcription. Conclusions Our results suggest that genomic binding of STATs is primarily determined by the cell type and further specificity is achieved in part by juxtaposed binding of cell-specific transcription factors.

  8. Spatial Heterogeneity of Leaf Area Index (LAI) and Its Temporal Course on Arable Land: Combining Field Measurements, Remote Sensing and Simulation in a Comprehensive Data Analysis Approach (CDAA)

    Science.gov (United States)

    Korres, Wolfgang; Montzka, Carsten; Fiener, Peter; Wilken, Florian; Stadler, Anja; Waldhoff, Guido; Schneider, Karl

    2016-01-01

    The ratio of leaf area to ground area (leaf area index, LAI) is an important state variable in ecosystem studies since it influences fluxes of matter and energy between the land surface and the atmosphere. As a basis for generating temporally continuous and spatially distributed datasets of LAI, the current study contributes an analysis of its spatial variability and spatial structure. Soil-vegetation-atmosphere fluxes of water, carbon and energy are nonlinearly related to LAI. Therefore, its spatial heterogeneity, i.e., the combination of spatial variability and structure, has an effect on simulations of these fluxes. To assess LAI spatial heterogeneity, we apply a Comprehensive Data Analysis Approach that combines data from remote sensing (5 m resolution) and simulation (150 m resolution) with field measurements and a detailed land use map. Test area is the arable land in the fertile loess plain of the Rur catchment on the Germany-Belgium-Netherlands border. LAI from remote sensing and simulation compares well with field measurements. Based on the simulation results, we describe characteristic crop-specific temporal patterns of LAI spatial variability. By means of these patterns, we explain the complex multimodal frequency distributions of LAI in the remote sensing data. In the test area, variability between agricultural fields is higher than within fields. Therefore, spatial resolutions less than the 5 m of the remote sensing scenes are sufficient to infer LAI spatial variability. Frequency distributions from the simulation agree better with the multimodal distributions from remote sensing than normal distributions do. The spatial structure of LAI in the test area is dominated by a short distance referring to field sizes. Longer distances that refer to soil and weather can only be derived from remote sensing data. Therefore, simulations alone are not sufficient to characterize LAI spatial structure. It can be concluded that a comprehensive picture of LAI spatial

  9. Neuronal activity-regulated gene transcription: how are distant synaptic signals conveyed to the nucleus? [v1; ref status: indexed, http://f1000r.es/TYJStu

    Directory of Open Access Journals (Sweden)

    Miriam Matamales

    2012-12-01

    Full Text Available Synaptic activity can trigger gene expression programs that are required for the stable change of neuronal properties, a process that is essential for learning and memory. Currently, it is still unclear how the stimulation of dendritic synapses can be coupled to transcription in the nucleus in a timely way given that large distances can separate these two cellular compartments. Although several mechanisms have been proposed to explain long distance communication between synapses and the nucleus, the possible co-existence of these models and their relevance in physiological conditions remain elusive. One model suggests that synaptic activation triggers the translocation to the nucleus of certain transcription regulators localised at postsynaptic sites that function as synapto-nuclear messengers. Alternatively, it has been hypothesised that synaptic activity initiates propagating regenerative intracellular calcium waves that spread through dendrites into the nucleus where nuclear transcription machinery is thereby regulated. It has also been postulated that membrane depolarisation of voltage-gated calcium channels on the somatic membrane is sufficient to increase intracellular calcium concentration and activate transcription without the need for transported signals from distant synapses. Here I provide a critical overview of the suggested mechanisms for coupling synaptic stimulation to transcription, the underlying assumptions behind them and their plausible physiological significance.

  10. A methodology for comprehensive breast cancer Ki67 labeling index with intra-tumor heterogeneity appraisal based on hexagonal tiling of digital image analysis data.

    Science.gov (United States)

    Plancoulaine, Benoit; Laurinaviciene, Aida; Herlin, Paulette; Besusparis, Justinas; Meskauskas, Raimundas; Baltrusaityte, Indra; Iqbal, Yasir; Laurinavicius, Arvydas

    2015-10-19

    Digital image analysis (DIA) enables higher accuracy, reproducibility, and capacity to enumerate cell populations by immunohistochemistry; however, the most unique benefits may be obtained by evaluating the spatial distribution and intra-tissue variance of markers. The proliferative activity of breast cancer tissue, estimated by the Ki67 labeling index (Ki67 LI), is a prognostic and predictive biomarker requiring robust measurement methodologies. We performed DIA on whole-slide images (WSI) of 302 surgically removed Ki67-stained breast cancer specimens; the tumour classifier algorithm was used to automatically detect tumour tissue but was not trained to distinguish between invasive and non-invasive carcinoma cells. The WSI DIA-generated data were subsampled by hexagonal tiling (HexT). Distribution and texture parameters were compared to conventional WSI DIA and pathology report data. Factor analysis of the data set, including total numbers of tumor cells, the Ki67 LI and Ki67 distribution, and texture indicators, extracted 4 factors, identified as entropy, proliferation, bimodality, and cellularity. The factor scores were further utilized in cluster analysis, outlining subcategories of heterogeneous tumors with predominant entropy, bimodality, or both at different levels of proliferative activity. The methodology also allowed the visualization of Ki67 LI heterogeneity in tumors and the automated detection and quantitative evaluation of Ki67 hotspots, based on the upper quintile of the HexT data, conceptualized as the "Pareto hotspot". We conclude that systematic subsampling of DIA-generated data into HexT enables comprehensive Ki67 LI analysis that reflects aspects of intra-tumor heterogeneity and may serve as a methodology to improve digital immunohistochemistry in general.

  11. Comprehensive analysis of differential co-expression patterns reveal transcriptional dysregulation mechanism and identify novel prognostic lncRNAs in esophageal squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Li Z

    2017-06-01

    Full Text Available Zhen Li,1 Qianlan Yao,1 Songjian Zhao,1 Yin Wang,2,3 Yixue Li,1,4 Zhen Wang4 1School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 2Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 3Collaborative Innovation Center for Genetics and Development, Fudan University, 4Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China Abstract: Esophageal squamous cell carcinoma (ESCC is one of the most common malignancies worldwide and occurs at a relatively high frequency in People’s Republic of China. However, the molecular mechanism underlying ESCC is still unclear. In this study, the mRNA and long non-coding RNA (lncRNA expression profiles of ESCC were downloaded from the Gene Expression Omnibus database, and then differential co-expression analysis was used to reveal the altered co-expression relationship of gene pairs in ESCC tumors. A total of 3,709 mRNAs and 923 lncRNAs were differentially co-expressed between normal and tumor tissues, and we found that most of the gene pairs lost associations in the tumor tissues. The differential regulatory networking approach deciphered that transcriptional dysregulation was ubiquitous in ESCC, and most of the differentially regulated links were modulated by 37 TFs. Our study also found that two novel lncRNAs (ADAMTS9-AS1 and AP000696.2 might be essential in the development of ectoderm and epithelial cells, which could significantly stratify ESCC patients into high-risk and low-risk groups, and were much better than traditional clinical tumor markers. Further inspection of two risk groups showed that the changes in TF-target regulation in the high-risk patients were significantly higher than those in the low-risk patients. In addition, four signal transduction-related DCmRNAs (ERBB3, ENSA, KCNK7, MFSD5

  12. Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features

    KAUST Repository

    Ramaprasad, Abhinay

    2015-04-13

    Toxoplasma gondii is an important protozoan parasite that infects all warm-blooded animals and causes opportunistic infections in immuno-compromised humans. Its closest relative, Neospora caninum, is an important veterinary pathogen that causes spontaneous abortion in livestock. Comparative genomics of these two closely related coccidians has been of particular interest to identify genes that contribute to varied host cell specificity and disease. Here, we describe a manual evaluation of these genomes based on strand-specific RNA sequencing and shotgun proteomics from the invasive tachyzoite stages of these two parasites. We have corrected predicted structures of over one third of the previously annotated gene models and have annotated untranslated regions (UTRs) in over half of the predicted protein-coding genes. We observe distinctly long UTRs in both the organisms, almost four times longer than other model eukaryotes. We have also identified a putative set of cis-natural antisense transcripts (cis-NATs) and long intergenic non-coding RNAs (lincRNAs). We have significantly improved the annotation quality in these genomes that would serve as a manually curated dataset for Toxoplasma and Neospora research communities.

  13. Neuronal activity-regulated gene transcription: how are distant synaptic signals conveyed to the nucleus? [v1; ref status: indexed, http://f1000r.es/TYJStu

    OpenAIRE

    Miriam Matamales

    2012-01-01

    Synaptic activity can trigger gene expression programs that are required for the stable change of neuronal properties, a process that is essential for learning and memory. Currently, it is still unclear how the stimulation of dendritic synapses can be coupled to transcription in the nucleus in a timely way given that large distances can separate these two cellular compartments. Although several mechanisms have been proposed to explain long distance communication between synapses and the nucle...

  14. Transcriptional profiles of cytokine/chemokine factors of immune cell-homing to the parasitic lesions: a comprehensive one-year course study in the liver of E. multilocularis-infected mice.

    Directory of Open Access Journals (Sweden)

    Junhua Wang

    Full Text Available Pathogenesis of chronically developing alveolar echinococcosis (AE is characterized by a continuous, granulomatous, periparasitic infiltration of immune cells surrounding the metacestode of Echinococcus multilocularis (E.multilocularis in the affected liver. A detailed cytokine and chemokine profile analysis of the periparasitic infiltrate in the liver has, however, not yet been carried out in a comprehensive way all along the whole course of infection in E. multilocularis intermediate hosts. We thus assessed the hepatic gene expression profiles of 18 selected cytokine and chemokine genes using qRT-PCR in the periparasitic immune reaction and the subsequent adjacent, not directly affected, liver tissue of mice from day 2 to day 360 post intra-hepatic injection of metacestode. DNA microarray analysis was also used to get a more complete picture of the transcriptional changes occurring in the liver surrounding the parasitic lesions. Profiles of mRNA expression levels in the hepatic parasitic lesions showed that a mixed Th1/Th2 immune response, characterized by the concomitant presence of IL-12α, IFN-γ and IL-4, was established very early in the development of E. multilocularis. Subsequently, the profile extended to a combined tolerogenic profile associating IL-5, IL-10 and TGF-β. IL-17 was permanently expressed in the liver, mostly in the periparasitic infiltrate; this was confirmed by the increased mRNA expression of both IL-17A and IL-17F from a very early stage, with a subsequent decrease of IL-17A after this first initial rise. All measured chemokines were significantly expressed at a given stage of infection; their expression paralleled that of the corresponding Th1, Th2 or Th17 cytokines. In addition to giving a comprehensive insight in the time course of cytokines and chemokines in E. multilocularis lesion, this study contributes to identify new targets for possible immune therapy to minimize E. multilocularis-related pathology and to

  15. Comprehensive Care

    Science.gov (United States)

    ... Comprehensive Care Share this page Facebook Twitter Email Comprehensive Care Understand the importance of comprehensive MS care ... In this article A complex disease requires a comprehensive approach Today multiple sclerosis (MS) is not a ...

  16. [Index screening and comprehensive evaluation of phenotypic traits of low nitrogen tolerance using BILs population derived from Dongxiang wild rice (Oryza rufipogon Griff)].

    Science.gov (United States)

    Hu, Biao-lin; Li, Xia; Wan, Yong; Qiu, Zai-hui; Nie, Yuan-yuan; Xie, Jian-kun

    2015-08-01

    To identify the low nitrogen tolerance of Dongxiang wild rice (DXWR) and its progenies, ten phenotypic traits including plant height (PH), heading day (HD), panicle length (PL), number of effective tillers per plant (NETP), number of filled grains per panicle (NFGP), number of grains per panicle (NGP), grain density (GD), spikelet fertility (SF), 1000-grain mass (TGM) and grain yield per plant (GYP) were studied under normal and low nitrogen treatments, using backcross inbred lines (BILs) of Xieqingzao B//DXWR/Xieqingzao B in BC1 F12. Comprehensive evaluation on the low nitrogen tolerance of the BILs population was conducted using principal component analysis and the subordinate function. The evaluation results indicated that the low nitrogen tolerance of the line 116, 143 and 157 was the strongest, which could be served as the intermediate materials for genetic studies on the low nitrogen tolerance of DXWR and breeding for the low nitrogen tolerance in rice. The optimal regression equation of the low nitrogen tolerance in rice was established using stepwise regression analysis. The relative values of five traits including PH, NGP, SF, TGM and GYP were screened out and could be used as comprehensive evaluation indices for the low nitrogen tolerance in the whole growth stage. Therefore, more attention should be paid to the relative values of these five traits, especially for NGP and GYP, in the genetic improvement of the low nitrogen tolerance in rice.

  17. Comprehensive Analysis of the Association of Clinically Relevant Values of Ki-67 Labeling Index with Clinicopathologic and Immunohistochemical Criteria in Female Invasive Breast Carcinoma

    Directory of Open Access Journals (Sweden)

    Saba El-Gendi

    2018-03-01

    Full Text Available Objective: Breast cancer aggressiveness is related to tumor cell proliferation. Despite this, the Ki-67 index is not recommended for routine use in newly diagnosed breast carcinomas. Material and Methods: A total of 164 invasive breast carcinomas were stratified into the intrinsic molecular subtypes based on estrogen receptor, progesterone receptor (PR, HER2, and Ki-67 immunostaining. We studied the distribution of Ki-67 among the molecular subtypes and correlated it with clinicopathologic parameters. Furthermore, the change in the Ki-67 index with tumor size, grade and lymph node (LN status among the molecular subtypes was examined. Results: As a continuous variable, the median Ki-67 did not show significant differences with the clinicopathological variables. At a cutoff ≥14%, it correlated significantly with the mitotic index. At a cutoff ≥20%, it additionally correlated with the PR status. The median Ki-67 level varied significantly between luminal A and all other molecular subtypes. The median Ki-67 level in T1/T2 tumors compared to T3/T4 tumors was slightly higher in luminal B HER2+, slightly lower in HER2 enriched, and nearly similar among luminal A, triple negative and luminal B HER2-subtypes, yet without statistical significance. The median Ki-67 was lower in G1/G2 compared to G3 tumors in all-except luminal B HER2-positive subtype but without statistical significance. The Ki-67 distribution change between N0/N1 and N2/N3 cases among the molecular subtypes was significant. Conclusions: The impact of Ki-67 as a proliferation marker on the biological behavior of breast carcinomas is context dependent, and its clinical utility increases when interpreted in combination with other prognostic markers in the context of the molecular subtypes. Further studies, on larger sample sizes are recommended to unravel how the molecular types can affect the relation between Ki-67 and clinicopathological characteristics, particularly the LN status. [J

  18. Check and evaluation system on heat metering and energy efficiency retrofit of existing residential buildings in northern heating areas of china based on multi-index comprehensive evaluation method

    International Nuclear Information System (INIS)

    Zhao Jing; Wu Yong; Zhu Neng

    2009-01-01

    Heat metering and energy efficiency retrofit of existing residential buildings in northern heating areas of China is organized and implemented in a large scale by local government in 15 provinces of North China with the unified guidance and control of central government. Firstly, this paper introduced the target of energy-saving reformation of existing residential buildings in North China and the importance of check and evaluation on this target, then pointed out the necessity of building up an evaluation system for energy-saving retrofit. According to the analytical hierarchy process (AHP), three-grade evaluation system was built up for heat metering and energy efficiency retrofit of existing residential buildings in northern heating areas of China. Also, based on multi-index comprehensive evaluation method combined with life cycle assessment (LCA) theory, post-evaluation thought and successful degree evaluation method, a mathematical model was established. Finally, a set of scientific method for evaluating heat metering and energy efficiency retrofit of existing residential buildings in northern heating areas of China systematically, scientifically, comprehensively and objectively was created.

  19. INDEXING AND INDEX FUNDS

    Directory of Open Access Journals (Sweden)

    HAKAN SARITAŞ

    2013-06-01

    Full Text Available Proponents of the efficient market hypothesis believe that active portfolio management is largely wasted effort and unlikely to justify the expenses incurred. Therefore, they advocate a passive investment strategy that makes no attempt to outsmart the market. One common strategy for passive management is indexing where a fund is designed to replicate the performance of a broad-based index of stocks and bonds. Traditionally, indexing was used by institutional investors, but today, the use of index funds proliferated among individual investors. Over the years, both international and domestic index funds have disproportionately outperformed the market more than the actively managed funds have.

  20. Unavailability of thymidine kinase does not preclude the use of German comprehensive prognostic index: results of an external validation analysis in early chronic lymphocytic leukemia and comparison with MD Anderson Cancer Center model.

    Science.gov (United States)

    Molica, Stefano; Giannarelli, Diana; Mirabelli, Rosanna; Levato, Luciano; Russo, Antonio; Linardi, Maria; Gentile, Massimo; Morabito, Fortunato

    2016-01-01

    A comprehensive prognostic index that includes clinical (i.e., age, sex, ECOG performance status), serum (i.e., ß2-microglobulin, thymidine kinase [TK]), and molecular (i.e., IGVH mutational status, del 17p, del 11q) markers developed by the German CLL Study Group (GCLLSG) was externally validated in a prospective, community-based cohort consisting of 338 patients with early chronic lymphocytic leukemia (CLL) using as endpoint the time to first treatment (TTFT). Because serum TK was not available, a slightly modified version of the model based on seven instead of eight prognostic variables was used. By German index, 62.9% of patients were scored as having low-risk CLL (score 0-2), whereas 37.1% had intermediate-risk CLL (score 3-5). This stratification translated into a significant difference in the TTFT [HR = 4.21; 95% C.I. (2.71-6.53); P reliability [HR = 2.73; 95% C.I. (1.79-4.17); P German score. The c-statistic of the MDACC model was 0.65 (range, 0.53-0.78) a level below that of the German index [0.71 (range, 0.60-0.82)] and below the accepted 0.7 threshold necessary to have value at the individual patient level. Results of this external comparative validation analysis strongly support the German score as the benchmark for comparison of any novel prognostic scheme aimed at evaluating the TTFT in patients with early CLL even when a modified version which does not include TK is utilized. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. Alternative staffing services. Contract transcription.

    Science.gov (United States)

    Tessier, C

    1992-03-01

    Contract medical transcription services can be of great assistance in meeting the demands for transcription, without jeopardizing patient, physician, or institutional confidentiality. You simply must require the contract service to provide at least the same degree of protection and preservation of confidentiality that you should require inhouse. To achieve this you must make these requirements explicit, comprehensive, comprehensible, believable, and enforceable. Discuss the requirements with prospective contractors. Review them at least annually with existing contractors and when contracts are due for renewal. Be sure to specify the consequence of breaching confidentiality, and if there are breaches, enforce the terms of the contract. Consult your institution's legal counsel both in developing the contract and in enforcing its provisions. Take into consideration your department's and institution's policies, AHIMA's statement on confidentiality, as well as local, state, and federal laws. Above all, never lose sight of the patient. Ultimately, it is not patient information that you are obligated to protect. It is the patient.

  2. Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data

    Directory of Open Access Journals (Sweden)

    Tu Kang

    2007-06-01

    Full Text Available Abstract Background The wide use of Affymetrix microarray in broadened fields of biological research has made the probeset annotation an important issue. Standard Affymetrix probeset annotation is at gene level, i.e. a probeset is precisely linked to a gene, and probeset intensity is interpreted as gene expression. The increased knowledge that one gene may have multiple transcript variants clearly brings up the necessity of updating this gene-level annotation to a refined transcript-level. Results Through performing rigorous alignments of the Affymetrix probe sequences against a comprehensive pool of currently available transcript sequences, and further linking the probesets to the International Protein Index, we generated transcript-level or protein-level annotation tables for two popular Affymetrix expression arrays, Mouse Genome 430A 2.0 Array and Human Genome U133A Array. Application of our new annotations in re-examining existing expression data sets shows increased expression consistency among synonymous probesets and strengthened expression correlation between interacting proteins. Conclusion By refining the standard Affymetrix annotation of microarray probesets from the gene level to the transcript level and protein level, one can achieve a more reliable interpretation of their experimental data, which may lead to discovery of more profound regulatory mechanism.

  3. Indexing from thesauri to the semantic web

    CERN Document Server

    de Keyser, Piet

    2012-01-01

    Indexing consists of both novel and more traditional techniques. Cutting-edge indexing techniques, such as automatic indexing, ontologies, and topic maps, were developed independently of older techniques such as thesauri, but it is now recognized that these older methods also hold expertise. Indexing describes various traditional and novel indexing techniques, giving information professionals and students of library and information sciences a broad and comprehensible introduction to indexing. This title consists of twelve chapters: an Introduction to subject readings and theasauri; Automatic i

  4. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein coding...... regions, the map of transcripts is very complex due to small transcripts from the flanking ends of the transcription unit, the use of multiple start and stop sites for the main transcript, production of multiple functional RNA molecules from the same primary transcript, and RNA molecules made...... by independent transcription from within the unit. In genomic regions separating those that encode proteins or highly abundant RNA molecules with known function, transcripts are generally of low abundance and short-lived. In most of these cases, it is unclear to what extent a function is related to transcription...

  5. A p53-like transcription factor similar to Ndt80 controls the response to nutrient stress in the filamentous fungus, Aspergillus nidulans [v1; ref status: indexed, http://f1000r.es/y2

    Directory of Open Access Journals (Sweden)

    Margaret E Katz

    2013-03-01

    Full Text Available The Aspergillus nidulans xprG gene encodes a putative transcriptional activator that is a member of the Ndt80 family in the p53-like superfamily of proteins. Previous studies have shown that XprG controls the production of extracellular proteases in response to starvation. We undertook transcriptional profiling to investigate whether XprG has a wider role as a global regulator of the carbon nutrient stress response. Our microarray data showed that the expression of a large number of genes, including genes involved in secondary metabolism, development, high-affinity glucose uptake and autolysis, were altered in an xprGΔ null mutant. Many of these genes are known to be regulated in response to carbon starvation. We confirmed that sterigmatocystin and penicillin production is reduced in xprG- mutants. The loss of fungal mass and secretion of pigments that accompanies fungal autolysis in response to nutrient depletion was accelerated in an xprG1 gain-of-function mutant and decreased or absent in an xprG- mutant. The results support the hypothesis that XprG plays a major role in the response to carbon limitation and that nutrient sensing may represent one of the ancestral roles for the p53-like superfamily. Disruption of the AN6015 gene, which encodes a second Ndt80-like protein, showed that it is required for sexual reproduction in A. nidulans.

  6. Walkability Index

    Science.gov (United States)

    The Walkability Index dataset characterizes every Census 2010 block group in the U.S. based on its relative walkability. Walkability depends upon characteristics of the built environment that influence the likelihood of walking being used as a mode of travel. The Walkability Index is based on the EPA's previous data product, the Smart Location Database (SLD). Block group data from the SLD was the only input into the Walkability Index, and consisted of four variables from the SLD weighted in a formula to create the new Walkability Index. This dataset shares the SLD's block group boundary definitions from Census 2010. The methodology describing the process of creating the Walkability Index can be found in the documents located at ftp://newftp.epa.gov/EPADataCommons/OP/WalkabilityIndex.zip. You can also learn more about the Smart Location Database at https://edg.epa.gov/data/Public/OP/Smart_Location_DB_v02b.zip.

  7. AP Index

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Planetary Amplitude index - Bartels 1951. The a-index ranges from 0 to 400 and represents a K-value converted to a linear scale in gammas (nanoTeslas)--a scale that...

  8. Index to the AEC/ERDA/DOE Air Cleaning Conferences

    International Nuclear Information System (INIS)

    Burchsted, C.A.

    1980-01-01

    A comprehensive index to the papers in the second through sixteenth AEC/ERDA/DOE Nuclear Air Cleaning Conference is discussed. The index will be published in early 1981 and will be designated as Volume 3 of the proceeding of the sixteenth conference. The index has three parts, a straight numeric tabulation, an author index, and a key word in context (KWIC) index

  9. Transcriptional regulation by competing transcription factor modules.

    Directory of Open Access Journals (Sweden)

    Rutger Hermsen

    2006-12-01

    Full Text Available Gene regulatory networks lie at the heart of cellular computation. In these networks, intracellular and extracellular signals are integrated by transcription factors, which control the expression of transcription units by binding to cis-regulatory regions on the DNA. The designs of both eukaryotic and prokaryotic cis-regulatory regions are usually highly complex. They frequently consist of both repetitive and overlapping transcription factor binding sites. To unravel the design principles of these promoter architectures, we have designed in silico prokaryotic transcriptional logic gates with predefined input-output relations using an evolutionary algorithm. The resulting cis-regulatory designs are often composed of modules that consist of tandem arrays of binding sites to which the transcription factors bind cooperatively. Moreover, these modules often overlap with each other, leading to competition between them. Our analysis thus identifies a new signal integration motif that is based upon the interplay between intramodular cooperativity and intermodular competition. We show that this signal integration mechanism drastically enhances the capacity of cis-regulatory domains to integrate signals. Our results provide a possible explanation for the complexity of promoter architectures and could be used for the rational design of synthetic gene circuits.

  10. AA Index

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The geomagnetic aa index provides a long climatology of global geomagnetic activity using 2 antipodal observatories at Greenwich and Melbourne- IAGA Bulletin 37,...

  11. Walkability Index

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Walkability Index dataset characterizes every Census 2010 block group in the U.S. based on its relative walkability. Walkability depends upon characteristics of...

  12. Diversity Index

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — This map service summarizes racial and ethnic diversity in the United States in 2012.The Diversity Index shows the likelihood that two persons chosen at random from...

  13. AUTHOR INDEX

    Indian Academy of Sciences (India)

    a granitic terrain of southern India using factor analysis and GIS. 1059. Radhakrishna M see Dev Sheena V .... Landslide susceptibility analysis using Probabilistic. Certainty Factor ... index via entropy-difference analysis. 687. Yidana Sandow ...

  14. Intelligent indexing

    International Nuclear Information System (INIS)

    Farkas, J.

    1992-01-01

    In this paper we discuss the relevance of artificial intelligence to the automatic indexing of natural language text. We describe the use of domain-specific semantically-based thesauruses and address the problem of creating adequate knowledge bases for intelligent indexing systems. We also discuss the relevance of the Hilbert space ι 2 to the compact representation of documents and to the definition of the similarity of natural language texts. (author). 17 refs., 2 figs

  15. Intelligent indexing

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, J

    1993-12-31

    In this paper we discuss the relevance of artificial intelligence to the automatic indexing of natural language text. We describe the use of domain-specific semantically-based thesauruses and address the problem of creating adequate knowledge bases for intelligent indexing systems. We also discuss the relevance of the Hilbert space {iota}{sup 2} to the compact representation of documents and to the definition of the similarity of natural language texts. (author). 17 refs., 2 figs.

  16. WRKY transcription factors

    Science.gov (United States)

    Bakshi, Madhunita; Oelmüller, Ralf

    2014-01-01

    WRKY transcription factors are one of the largest families of transcriptional regulators found exclusively in plants. They have diverse biological functions in plant disease resistance, abiotic stress responses, nutrient deprivation, senescence, seed and trichome development, embryogenesis, as well as additional developmental and hormone-controlled processes. WRKYs can act as transcriptional activators or repressors, in various homo- and heterodimer combinations. Here we review recent progress on the function of WRKY transcription factors in Arabidopsis and other plant species such as rice, potato, and parsley, with a special focus on abiotic, developmental, and hormone-regulated processes. PMID:24492469

  17. Linking Core Promoter Classes to Circadian Transcription.

    Directory of Open Access Journals (Sweden)

    Pål O Westermark

    2016-08-01

    Full Text Available Circadian rhythms in transcription are generated by rhythmic abundances and DNA binding activities of transcription factors. Propagation of rhythms to transcriptional initiation involves the core promoter, its chromatin state, and the basal transcription machinery. Here, I characterize core promoters and chromatin states of genes transcribed in a circadian manner in mouse liver and in Drosophila. It is shown that the core promoter is a critical determinant of circadian mRNA expression in both species. A distinct core promoter class, strong circadian promoters (SCPs, is identified in mouse liver but not Drosophila. SCPs are defined by specific core promoter features, and are shown to drive circadian transcriptional activities with both high averages and high amplitudes. Data analysis and mathematical modeling further provided evidence for rhythmic regulation of both polymerase II recruitment and pause release at SCPs. The analysis provides a comprehensive and systematic view of core promoters and their link to circadian mRNA expression in mouse and Drosophila, and thus reveals a crucial role for the core promoter in regulated, dynamic transcription.

  18. Virginia ESI: INDEX (Index Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains vector polygons representing the boundaries of all hardcopy cartographic products produced as part of the Environmental Sensitivity Index...

  19. Comprehensive Psychiatric Evaluation

    Science.gov (United States)

    ... Facts for Families Guide Facts for Families - Vietnamese Comprehensive Psychiatric Evaluation No. 52; Updated October 2017 Evaluation ... with serious emotional and behavioral problems need a comprehensive psychiatric evaluation. Comprehensive psychiatric evaluations usually require a ...

  20. Children's hypertext comprehension

    NARCIS (Netherlands)

    Segers, P.C.J.; Segers, E.; Broek, P. van den

    2017-01-01

    The present chapter gives an overview of the literature on hypertext comprehension, children's hypertext comprehension and individual variation therein, ending with a perspective for future research. Hypertext comprehension requires the reader to make bridging inferences between the different parts

  1. Indexing mechanisms

    International Nuclear Information System (INIS)

    Wood, A.G.; Parker, G.E.; Berry, R.

    1976-01-01

    It is stated that the indexing mechanism described can be used in a nuclear reactor fuel element inspection rig. It comprises a tubular body adapted to house a canister containing a number of fuel elements located longtitudinally, and has two chucks spaced apart for displacing the fuel elements longitudinally in a stepwise manner, together with a plunger mechanism for displacing them successively into the chucks. A measuring unit is located between the chucks for measuring the diameter of the fuel elements at intervals about their circumferences, and a secondary indexing mechanism is provided for rotating the measuring unit in a stepwise manner. (U.K.)

  2. Author Index

    Indian Academy of Sciences (India)

    user1

    Astr. (2012) 33, 419–420. Author Index. 419. AGGARWAL SUNNY. Photoionization Cross-Section of Chlorine-like Iron, 291. AMBASTHA ASHOK see Das, A. C., 1. ARAKIDA HIDEYOSHI. Effect of Inhomogeneity of the Universe on a Gravitationally. Bound Local System: A No-Go Result for Explaining the Secular Increase in.

  3. AUTHOR INDEX

    Indian Academy of Sciences (India)

    automorphic solutions to fractional order abstract integro-differential equations. 323. Afrouzi G A see Ala Samira ... 521. Agarwal Praveen. Certain fractional integral operators and the generalized multi-index Mittag- ... of positive solutions for sys- tems of second order multi-point bound- ary value problems on time scales 353.

  4. Afghanistan Index

    DEFF Research Database (Denmark)

    Linnet, Poul Martin

    2007-01-01

    basis. The data are divided into different indicators such as security, polls, drug, social, economic, refugees etc. This represents a practical division and does not indicate that a picture as to for instance security can be obtained by solely looking at the data under security. In order to obtain...... a more valid picture on security this must incorporate an integrated look on all data meaning that for instance the economic data provides an element as to the whole picture of security.......The Afghanistan index is a compilation of quantitative and qualitative data on the reconstruction and security effort in Afghanistan. The index aims at providing data for benchmarking of the international performance and thus provides the reader with a quick possibility to retrieve valid...

  5. Comprehensive metabolic panel

    Science.gov (United States)

    Metabolic panel - comprehensive; Chem-20; SMA20; Sequential multi-channel analysis with computer-20; SMAC20; Metabolic panel 20 ... Chernecky CC, Berger BJ. Comprehensive metabolic panel (CMP) - blood. In: ... Tests and Diagnostic Procedures . 6th ed. St Louis, MO: ...

  6. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

    Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I

    2012-01-01

    mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written......ABSTRACT: Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130...

  7. SoyDB: a knowledge database of soybean transcription factors

    Directory of Open Access Journals (Sweden)

    Valliyodan Babu

    2010-01-01

    Full Text Available Abstract Background Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors. Description The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database for all the transcription factors in the soybean genome. The database contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous templates in the Protein Data Bank (PDB, protein family classifications, multiple sequence alignments, consensus protein sequence motifs, web logo of each family, and web links to the soybean transcription factor database PlantTFDB, known EST sequences, and other general protein databases including Swiss-Prot, Gene Ontology, KEGG, EMBL, TAIR, InterPro, SMART, PROSITE, NCBI, and Pfam. The database can be accessed via an interactive and convenient web server, which supports full-text search, PSI-BLAST sequence search, database browsing by protein family, and automatic classification of a new protein sequence into one of 64 annotated transcription factor families by hidden Markov models. Conclusions A comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.

  8. Computational Investigations of Post-Transcriptional Regulation

    DEFF Research Database (Denmark)

    Rasmussen, Simon Horskjær

    and miRNA regulation was studied by cross-linking immunoprecipitation (CLIP) and RBP double knockdown experiments. A comprehensive analysis of 107 CLIP datasets of 49 RBPs demonstrated that RBPs modulate miRNA regulation. Results suggest it is mediated by RBP-binding hotspots that likely...... investigated using high-throughput data. Analysis of IMP RIP-seq, iCLIP and RNA-seq datasets identified transcripts associated with cytoplasmic IMP ribonucleoproteins. Many of these transcripts were functionally involved in actin cytoskeletal remodeling. Further analyses of this data permitted estimation...... of a bipartite motif, composed of an AU-rich and a CA-rich domain. In addition, a regulatory motif discovery method was developed and applied to identify motifs using differential expression data and CLIP-data in the above investigations. This thesis increased the understanding of the role of RBPs in mi...

  9. Basal transcription machinery

    Indian Academy of Sciences (India)

    2007-03-29

    Mar 29, 2007 ... The holoenzyme of prokaryotic RNA polymerase consists of the core enzyme, made of two , , ' and subunits, which lacks promoter selectivity and a sigma () subunit which enables the core enzyme to initiate transcription in a promoter dependent fashion. A stress sigma factor s, in prokaryotes ...

  10. Machine Dictation and Transcription.

    Science.gov (United States)

    Harvey, Evelyn; And Others

    This instructional package contains both an instructor's manual and a student's manual for a course in machine dictation and transcription. The instructor's manual contains an overview with tips on teaching the course, letters for dictation, and a key to the letters. The student's manual contains an overview of the course and of the skills needed…

  11. Transcriptional Regulation in Haematopoiesis:

    DEFF Research Database (Denmark)

    Lauridsen, Felicia K B

    with the capacity to both self-renew and differentiate. This thesis is built upon two studies, which investigate two different aspects of the haematopoietic system; heterogeneity within the HSC compartment (presented in manuscript I), and the interplay between transcription factors controlling granulocyte/ monocyte...

  12. An index of financial safety of China

    Directory of Open Access Journals (Sweden)

    Xiaojun Jia

    2015-04-01

    Full Text Available Purpose: This paper combines a synthetic index system by the variables and evaluates China’s financial safety through the change of indexes in a comprehensive way. First of all, it builds the financial industry evaluation index system composed of 25indicators in terms of the operation of the financial industry and external economic environment and particularly takes into consideration factors which might trigger liquidity risks such as off-balance-sheet business, interbank business and shadow banking; then it selects 10 indicators to conduct empirical analysis and identifies the indicator weight through principal component analysis; finally it combines the financial safety indexes through the linear weighted comprehensive evaluation model.Design/methodology/approach: Synthesis of indexes is made by constructing a proper comprehensive evaluation mathematical model, integrating a number of evaluation indexes into one comprehensive evaluation index and then obtaining corresponding comprehensive evaluation results. In this paper, it selects 10 indexes to conduct empirical analysis and identifies the index weight through principal component analysis; finally it combines the financial safety indexes through the linear weighted comprehensive evaluation model. Principal component analysis (PCA is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. PCA was invented in 1901 and was later independently developed (and named by Harold Hotelling in the 1930s.Findings: From 2003 to 2013 China’s financial safety indexes fluctuated. From 2003 to 2007 indexes rose, which indicates China’s financial safety status gradually improved; from 2007 to 2009 indexes declined, which indicates due to the impact of subprime crisis, China’s financial safety status took a turn for the worse; from 2009 to 2012

  13. Study on comprehensive evaluation model for nuclear power plant control room layout

    International Nuclear Information System (INIS)

    Zhu Yiming; Liu Yuan; Fan Huixian

    2010-01-01

    A comprehensive evaluation model for layout of the main control room of nuclear power plants was proposed. Firstly the design scope and principle for the layout of the main control room were defined based on the standards, and then the index system for the comprehensive evaluation was established. Finally, comprehensive evaluation was carried out for the layout design by applying the fuzzy comprehensive evaluation method in the index system. (authors)

  14. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli

    DEFF Research Database (Denmark)

    Seo, Sang Woo; Kim, Donghyuk; Latif, Haythem

    2014-01-01

    The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism. However, the full regulatory potential of Fur remains undefined. Here we comprehensively reconstruct the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response...

  15. Comparing the Palmer Drought Index and the Standardized Precipitation Index for Zagreb Gric Observatory

    Science.gov (United States)

    Pandzic, K.; Likso, T.

    2012-04-01

    Conventional Palmer Drought Index (PDI) and recent Standardized Precipitation Index (SPI) for Zagreb Gric Observatory are compared by spectral analysis technique. Data for a period 1862-2010 are used. The results indicate that SPI is simpler for interpretation but PDI more comprehensive index. On the other side, lack of temperature within SPI, make impossible application of it on climate change interpretation. Possible applications of them in irrigation scheduling system is considered as well for drought risk assessment.

  16. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager

    2015-01-01

    This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most of the ex......This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most...... topoisomerase-DNA cleavage complex. The second study is an investigation of how topoisomerases influence gene regulation by keeping the genome in an optimal topological state....

  17. Deciphering Transcriptional Regulation

    DEFF Research Database (Denmark)

    Valen, Eivind

    The myriad of cells in the human body are all made from the same blueprint: the human genome. At the heart of this diversity lies the concept of gene regulation, the process in which it is decided which genes are used where and when. Genes do not function as on/off buttons, but more like a volume...... mostly near the start of the gene known as the promoter. This region contains patterns scattered in the DNA that the TFs can recognize and bind to. Such binding can prompt the assembly of the pre-initiation complex which ultimately leads to transcription of the gene. In order to achieve the regulation...... on what characterizes a hippocampus promoter. Pairing CAGE with TF binding site prediction we identi¿ed a likely key regulator of hippocampus. Finally, we developed a method for CAGE exploration. While the DeepCAGE library characterized a full 1.4 million transcription initiation events it did not capture...

  18. TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.

    Science.gov (United States)

    Jorjani, Hadi; Zavolan, Mihaela

    2014-04-01

    Accurate identification of transcription start sites (TSSs) is an essential step in the analysis of transcription regulatory networks. In higher eukaryotes, the capped analysis of gene expression technology enabled comprehensive annotation of TSSs in genomes such as those of mice and humans. In bacteria, an equivalent approach, termed differential RNA sequencing (dRNA-seq), has recently been proposed, but the application of this approach to a large number of genomes is hindered by the paucity of computational analysis methods. With few exceptions, when the method has been used, annotation of TSSs has been largely done manually. In this work, we present a computational method called 'TSSer' that enables the automatic inference of TSSs from dRNA-seq data. The method rests on a probabilistic framework for identifying both genomic positions that are preferentially enriched in the dRNA-seq data as well as preferentially captured relative to neighboring genomic regions. Evaluating our approach for TSS calling on several publicly available datasets, we find that TSSer achieves high consistency with the curated lists of annotated TSSs, but identifies many additional TSSs. Therefore, TSSer can accelerate genome-wide identification of TSSs in bacterial genomes and can aid in further characterization of bacterial transcription regulatory networks. TSSer is freely available under GPL license at http://www.clipz.unibas.ch/TSSer/index.php

  19. Transcriptional networks controlling adipocyte differentiation

    DEFF Research Database (Denmark)

    Siersbæk, R; Mandrup, Susanne

    2011-01-01

    " of the transcription factor networks operating at specific time points during adipogenesis. Using such global "snapshots," we have demonstrated that dramatic remodeling of the chromatin template occurs within the first few hours following adipogenic stimulation and that many of the early transcription factors bind...... in a cooperative fashion to transcription factor hotspots. Such hotspots are likely to represent key chromatin nodes, where many adipogenic signaling pathways converge to drive the adipogenic transcriptional reprogramming....

  20. Case in Language Comprehension

    NARCIS (Netherlands)

    Bader, Markus; Lamers, Monique

    2012-01-01

    Research on human language comprehension has been heavily influenced by properties of the English language. Since case plays only a minor role in English, its role for language comprehension has only recently become a topic for extensive research on psycholinguistics. In the psycholinguistic

  1. Spectrum of Physics Comprehension

    Science.gov (United States)

    Blasiak, W.; Godlewska, M.; Rosiek, R.; Wcislo, D.

    2012-01-01

    The paper presents the results of research on the relationship between self-assessed comprehension of physics lectures and final grades of junior high school students (aged 13-15), high school students (aged 16-18) and physics students at the Pedagogical University of Cracow, Poland (aged 21). Students' declared level of comprehension was measured…

  2. Informed consent comprehension in African research settings.

    Science.gov (United States)

    Afolabi, Muhammed O; Okebe, Joseph U; McGrath, Nuala; Larson, Heidi J; Bojang, Kalifa; Chandramohan, Daniel

    2014-06-01

    Previous reviews on participants' comprehension of informed consent information have focused on developed countries. Experience has shown that ethical standards developed on Western values may not be appropriate for African settings where research concepts are unfamiliar. We undertook this review to describe how informed consent comprehension is defined and measured in African research settings. We conducted a comprehensive search involving five electronic databases: Medline, Embase, Global Health, EthxWeb and Bioethics Literature Database (BELIT). We also examined African Index Medicus and Google Scholar for relevant publications on informed consent comprehension in clinical studies conducted in sub-Saharan Africa. 29 studies satisfied the inclusion criteria; meta-analysis was possible in 21 studies. We further conducted a direct comparison of participants' comprehension on domains of informed consent in all eligible studies. Comprehension of key concepts of informed consent varies considerably from country to country and depends on the nature and complexity of the study. Meta-analysis showed that 47% of a total of 1633 participants across four studies demonstrated comprehension about randomisation (95% CI 13.9-80.9%). Similarly, 48% of 3946 participants in six studies had understanding about placebo (95% CI 19.0-77.5%), while only 30% of 753 participants in five studies understood the concept of therapeutic misconception (95% CI 4.6-66.7%). Measurement tools for informed consent comprehension were developed with little or no validation. Assessment of comprehension was carried out at variable times after disclosure of study information. No uniform definition of informed consent comprehension exists to form the basis for development of an appropriate tool to measure comprehension in African participants. Comprehension of key concepts of informed consent is poor among study participants across Africa. There is a vital need to develop a uniform definition for

  3. In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Bischoff Emmanuel

    2010-01-01

    Full Text Available Abstract Background Malaria is the most important parasitic disease in the world with approximately two million people dying every year, mostly due to Plasmodium falciparum infection. During its complex life cycle in the Anopheles vector and human host, the parasite requires the coordinated and modulated expression of diverse sets of genes involved in epigenetic, transcriptional and post-transcriptional regulation. However, despite the availability of the complete sequence of the Plasmodium falciparum genome, we are still quite ignorant about Plasmodium mechanisms of transcriptional gene regulation. This is due to the poor prediction of nuclear proteins, cognate DNA motifs and structures involved in transcription. Results A comprehensive directory of proteins reported to be potentially involved in Plasmodium transcriptional machinery was built from all in silico reports and databanks. The transcription-associated proteins were clustered in three main sets of factors: general transcription factors, chromatin-related proteins (structuring, remodelling and histone modifying enzymes, and specific transcription factors. Only a few of these factors have been molecularly analysed. Furthermore, from transcriptome and proteome data we modelled expression patterns of transcripts and corresponding proteins during the intra-erythrocytic cycle. Finally, an interactome of these proteins based either on in silico or on 2-yeast-hybrid experimental approaches is discussed. Conclusion This is the first attempt to build a comprehensive directory of potential transcription-associated proteins in Plasmodium. In addition, all complete transcriptome, proteome and interactome raw data were re-analysed, compared and discussed for a better comprehension of the complex biological processes of Plasmodium falciparum transcriptional regulation during the erythrocytic development.

  4. Comprehensive benefit analysis of regional water resources based on multi-objective evaluation

    Science.gov (United States)

    Chi, Yixia; Xue, Lianqing; Zhang, Hui

    2018-01-01

    The purpose of the water resources comprehensive benefits analysis is to maximize the comprehensive benefits on the aspects of social, economic and ecological environment. Aiming at the defects of the traditional analytic hierarchy process in the evaluation of water resources, it proposed a comprehensive benefit evaluation of social, economic and environmental benefits index from the perspective of water resources comprehensive benefit in the social system, economic system and environmental system; determined the index weight by the improved fuzzy analytic hierarchy process (AHP), calculated the relative index of water resources comprehensive benefit and analyzed the comprehensive benefit of water resources in Xiangshui County by the multi-objective evaluation model. Based on the water resources data in Xiangshui County, 20 main comprehensive benefit assessment factors of 5 districts belonged to Xiangshui County were evaluated. The results showed that the comprehensive benefit of Xiangshui County was 0.7317, meanwhile the social economy has a further development space in the current situation of water resources.

  5. Quotient-Comprehension Chains

    Directory of Open Access Journals (Sweden)

    Kenta Cho

    2015-11-01

    Full Text Available Quotients and comprehension are fundamental mathematical constructions that can be described via adjunctions in categorical logic. This paper reveals that quotients and comprehension are related to measurement, not only in quantum logic, but also in probabilistic and classical logic. This relation is presented by a long series of examples, some of them easy, and some also highly non-trivial (esp. for von Neumann algebras. We have not yet identified a unifying theory. Nevertheless, the paper contributes towards such a theory by introducing the new quotient-and-comprehension perspective on measurement instruments, and by describing the examples on which such a theory should be built.

  6. Comprehensive cardiac rehabilitation

    DEFF Research Database (Denmark)

    Kruse, Marie; Hochstrasser, Stefan; Zwisler, Ann-Dorthe O

    2006-01-01

    OBJECTIVES: The costs of comprehensive cardiac rehabilitation are established and compared to the corresponding costs of usual care. The effect on health-related quality of life is analyzed. METHODS: An unprecedented and very detailed cost assessment was carried out, as no guidelines existed...... and may be as high as euro 1.877. CONCLUSIONS: Comprehensive cardiac rehabilitation is more costly than usual care, and the higher costs are not outweighed by a quality of life gain. Comprehensive cardiac rehabilitation is, therefore, not cost-effective....

  7. Transcript structure and domain display: a customizable transcript visualization tool.

    Science.gov (United States)

    Watanabe, Kenneth A; Ma, Kaiwang; Homayouni, Arielle; Rushton, Paul J; Shen, Qingxi J

    2016-07-01

    Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. TSDD is freely available for non-commercial users at http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html : jeffery.shen@unlv.nevada.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. NRC comprehensive records disposition schedule

    International Nuclear Information System (INIS)

    1992-03-01

    Title 44 United States Code, ''Public Printing and Documents,'' regulations cited in the General Services Administration's (GSA) ''Federal Information Resources Management Regulations'' (FIRMR), Part 201-9, ''Creation, Maintenance, and Use of Records,'' and regulation issued by the National Archives and Records Administration (NARA) in 36 CFR Chapter XII, Subchapter B, ''Records Management,'' require each agency to prepare and issue a comprehensive records disposition schedule that contains the NARA approved records disposition schedules for records unique to the agency and contains the NARA's General Records Schedules for records common to several or all agencies. The approved records disposition schedules specify the appropriate duration of retention and the final disposition for records created or maintained by the NRC. NUREG-0910, Rev. 2, contains ''NRC's Comprehensive Records Disposition Schedule,'' and the original authorized approved citation numbers issued by NARA. Rev. 2 totally reorganizes the records schedules from a functional arrangement to an arrangement by the host office. A subject index and a conversion table have also been developed for the NRC schedules to allow staff to identify the new schedule numbers easily and to improve their ability to locate applicable schedules

  9. Comprehensive geriatric assessment

    African Journals Online (AJOL)

    2007-09-14

    Sep 14, 2007 ... i.e. difficulty performing simple physical and mental tasks necessary for daily life. ... Definition. Comprehensive geriatric assessment (CGA) is a multidimensional .... The formation of a programme of therapy is decided on.

  10. Spectrum of physics comprehension

    International Nuclear Information System (INIS)

    Blasiak, W; Godlewska, M; Rosiek, R; Wcislo, D

    2012-01-01

    The paper presents the results of research on the relationship between self-assessed comprehension of physics lectures and final grades of junior high school students (aged 13-15), high school students (aged 16-18) and physics students at the Pedagogical University of Cracow, Poland (aged 21). Students' declared level of comprehension was measured during a physics lecture on a prearranged scale of 1-10 with the use of a personal response system designed for the purpose of this experiment. Through the use of this tool, we obtained about 2000 computer records of students' declared comprehension of a 45 min lecture, which we named ‘the spectrum of comprehension’. In this paper, we present and analyse the correlation between students' declared comprehension of the content presented in the lecture and their final learning results. (paper)

  11. PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast.

    Science.gov (United States)

    Lai, Fu-Jou; Chang, Hong-Tsun; Wu, Wei-Sheng

    2015-01-01

    Computational identification of cooperative transcription factor (TF) pairs helps understand the combinatorial regulation of gene expression in eukaryotic cells. Many advanced algorithms have been proposed to predict cooperative TF pairs in yeast. However, it is still difficult to conduct a comprehensive and objective performance comparison of different algorithms because of lacking sufficient performance indices and adequate overall performance scores. To solve this problem, in our previous study (published in BMC Systems Biology 2014), we adopted/proposed eight performance indices and designed two overall performance scores to compare the performance of 14 existing algorithms for predicting cooperative TF pairs in yeast. Most importantly, our performance comparison framework can be applied to comprehensively and objectively evaluate the performance of a newly developed algorithm. However, to use our framework, researchers have to put a lot of effort to construct it first. To save researchers time and effort, here we develop a web tool to implement our performance comparison framework, featuring fast data processing, a comprehensive performance comparison and an easy-to-use web interface. The developed tool is called PCTFPeval (Predicted Cooperative TF Pair evaluator), written in PHP and Python programming languages. The friendly web interface allows users to input a list of predicted cooperative TF pairs from their algorithm and select (i) the compared algorithms among the 15 existing algorithms, (ii) the performance indices among the eight existing indices, and (iii) the overall performance scores from two possible choices. The comprehensive performance comparison results are then generated in tens of seconds and shown as both bar charts and tables. The original comparison results of each compared algorithm and each selected performance index can be downloaded as text files for further analyses. Allowing users to select eight existing performance indices and 15

  12. EJSCREEN Indexes 2015 Public

    Data.gov (United States)

    U.S. Environmental Protection Agency — There is an EJ Index for each environmental indicator. There are eight EJ Indexes in EJSCREEN reflecting the 8 environmental indicators. The EJ Index names are:...

  13. EJSCREEN Indexes 2016 Public

    Data.gov (United States)

    U.S. Environmental Protection Agency — There is an EJ Index for each environmental indicator. There are eleven EJ Indexes in EJSCREEN reflecting the 11 environmental indicators. The EJ Index names are:...

  14. Nucleocytoplasmic shuttling of transcription factors

    DEFF Research Database (Denmark)

    Cartwright, P; Helin, K

    2000-01-01

    To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation...... of the transcriptional response is essential for cells to progress through the cell cycle in a normal manner. The involvement of cytoplasmic and nuclear accessory molecules, and the general nuclear membrane transport components, are essential for this process. Although nuclear import and export for different...... transcription factor families are regulated by similar mechanisms, there are several differences that allow for the specific activation of each transcription factor. This review discusses the general import and export pathways found to be common amongst many different transcription factors, and highlights...

  15. Transcriptional Silencing of Retroviral Vectors

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M.; Pedersen, F.S.

    1996-01-01

    . Extinction of long-term vector expression has been observed after implantation of transduced hematopoietic cells as well as fibroblasts, myoblasts and hepatocytes. Here we review the influence of vector structure, integration site and cell type on transcriptional silencing. While down-regulation of proviral...... transcription is known from a number of cellular and animal models, major insight has been gained from studies in the germ line and embryonal cells of the mouse. Key elements for the transfer and expression of retroviral vectors, such as the viral transcriptional enhancer and the binding site for the t......RNA primer for reverse transcription may have a major influence on transcriptional silencing. Alterations of these elements of the vector backbone as well as the use of internal promoter elements from housekeeping genes may contribute to reduce transcriptional silencing. The use of cell culture and animal...

  16. DNA topology and transcription

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

  17. Eukaryotic transcription factors

    DEFF Research Database (Denmark)

    Staby, Lasse; O'Shea, Charlotte; Willemoës, Martin

    2017-01-01

    Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains...... regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables....... It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms...

  18. Validation of the prosthetic esthetic index

    DEFF Research Database (Denmark)

    Özhayat, Esben B; Dannemand, Katrine

    2014-01-01

    OBJECTIVES: In order to diagnose impaired esthetics and evaluate treatments for these, it is crucial to evaluate all aspects of oral and prosthetic esthetics. No professionally administered index currently exists that sufficiently encompasses comprehensive prosthetic esthetics. This study aimed...... to validate a new comprehensive index, the Prosthetic Esthetic Index (PEI), for professional evaluation of esthetics in prosthodontic patients. MATERIAL AND METHODS: The content, criterion, and construct validity; the test-retest, inter-rater, and internal consistency reliability; and the sensitivity...... furthermore distinguish between participants and controls, indicating sufficient sensitivity. CONCLUSION: The PEI is considered a valid and reliable instrument involving sufficient aspects for assessment of the professionally evaluated esthetics in prosthodontic patients. CLINICAL RELEVANCE...

  19. THE NATURE OF COMPREHENSION.

    Science.gov (United States)

    CLELAND, DONALD L.

    THE NATURE OF COMPREHENSION IS DEFINED AND CLARIFIED. THE LITERATURE IS SURVEYED TO SHOW THAT THE DEVELOPMENT OF CONCEPTS IS IMPORTANT IN INTELLECTUAL ACTIVITIES. IT IS POINTED OUT THAT CONCEPTS ARE BUILT FROM PERCEPTS, IMAGES, SENSATION, AND MEMORIES, AND THAT THE STEPS WHICH ARE EMPLOYED AS CONCEPTS ARE BUILT AND REFINED AND INCLUDE PERCEIVING,…

  20. Comprehension Strategy Gloves.

    Science.gov (United States)

    Newman, Gayle

    2002-01-01

    Describes the idea of creating a glove for each of the comprehension strategies for use with different text structures. Notes that the gloves serve as a multisensory approach by providing visual clues through icons on each finger and the palm. Discusses three different gloves: the prereading glove, the narrative text structure glove, and the…

  1. Painless reading comprehension

    CERN Document Server

    Jones, EdD, Darolyn "Lyn"

    2016-01-01

    Reading comprehension gets easier as students learn what kind of reader they are, discover how to keep facts in their head, and much more. Bonus Online Component: includes additional games, including Beat the Clock, a line match game, and a word scramble.

  2. Comprehensive Environmental Management Process

    International Nuclear Information System (INIS)

    Hjeresen, D.L.; Roybal, S.L.

    1994-01-01

    This report contains information about Los Alamos National Laboratory's Comprehensive Environmental Management Plan. The topics covered include: waste minimization, waste generation, environmental concerns, public relations of the laboratory, and how this plan will help to answer to the demands of the laboratory as their mission changes

  3. A comprehensive psychiatric service

    DEFF Research Database (Denmark)

    Wang, A G

    1984-01-01

    A comprehensive psychiatric service was established in 1969 in the Faroe Islands. This service was created as a department of a general hospital. The spheres covered by this department, operating in the midst of the community were: acute and chronic patients, a liaison-psychiatric service...

  4. Cognitive Correlates of Listening Comprehension

    Science.gov (United States)

    Kim, Young-Suk; Phillips, Beth

    2014-01-01

    In an effort to understand cognitive foundations of oral language comprehension (i.e., listening comprehension), we examined how inhibitory control, theory of mind, and comprehension monitoring are uniquely related to listening comprehension over and above vocabulary and age. A total of 156 children in kindergarten and first grade from…

  5. Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

    OpenAIRE

    Lang, Daniel; Weiche, Benjamin; Timmerhaus, Gerrit; Richardt, Sandra; Ria?o-Pach?n, Diego M.; Corr?a, Luiz G. G.; Reski, Ralf; Mueller-Roeber, Bernd; Rensing, Stefan A.

    2010-01-01

    Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom. Here, we present the most comprehensive set of classification rules for TAPs and its application for genome-wide analyses of plants and algae. Using a dated species tree and phy...

  6. Assessing reference genes for accurate transcript normalization using quantitative real-time PCR in pearl millet [Pennisetum glaucum (L. R. Br].

    Directory of Open Access Journals (Sweden)

    Prasenjit Saha

    Full Text Available Pearl millet [Pennisetum glaucum (L. R.Br.], a close relative of Panicoideae food crops and bioenergy grasses, offers an ideal system to perform functional genomics studies related to C4 photosynthesis and abiotic stress tolerance. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR provides a sensitive platform to conduct such gene expression analyses. However, the lack of suitable internal control reference genes for accurate transcript normalization during qRT-PCR analysis in pearl millet is the major limitation. Here, we conducted a comprehensive assessment of 18 reference genes on 234 samples which included an array of different developmental tissues, hormone treatments and abiotic stress conditions from three genotypes to determine appropriate reference genes for accurate normalization of qRT-PCR data. Analyses of Ct values using Stability Index, BestKeeper, ΔCt, Normfinder, geNorm and RefFinder programs ranked PP2A, TIP41, UBC2, UBQ5 and ACT as the most reliable reference genes for accurate transcript normalization under different experimental conditions. Furthermore, we validated the specificity of these genes for precise quantification of relative gene expression and provided evidence that a combination of the best reference genes are required to obtain optimal expression patterns for both endogeneous genes as well as transgenes in pearl millet.

  7. How indexes have changed

    International Nuclear Information System (INIS)

    Farrar, G.L.

    1993-01-01

    The accompanying table compares refinery construction and operating wages monthly for the years 1990 and 1991. The Nelson-Farrar refinery construction cost indexes are inflation indexes, while the operating indexes incorporate a productivity which shows improvement with experience and the increasing size of operations. The refinery construction wage indexes in the table show a steady advance over the 2-year period. Common labor indexes moved up faster than skilled indexes. Refinery operating wages showed a steady increase, while productivities averaged higher near the end of the period. Net result is that labor costs remained steady for the period

  8. Comprehensive geophysical and geochemical method and prognosis criteria for the exploration of unconformity type uranium deposit in Russia

    International Nuclear Information System (INIS)

    Li Mao; Chen Zuyi

    2007-01-01

    According to the transcripts of the lectures by Russian experts during the investigation and training in Russia, the comprehensive geophysical and geochemical method and the prognosis criteria of Russia's unconformity type uranium deposit exploration are introduced in the paper. (authors)

  9. Comprehensive hard materials

    CERN Document Server

    2014-01-01

    Comprehensive Hard Materials deals with the production, uses and properties of the carbides, nitrides and borides of these metals and those of titanium, as well as tools of ceramics, the superhard boron nitrides and diamond and related compounds. Articles include the technologies of powder production (including their precursor materials), milling, granulation, cold and hot compaction, sintering, hot isostatic pressing, hot-pressing, injection moulding, as well as on the coating technologies for refractory metals, hard metals and hard materials. The characterization, testing, quality assurance and applications are also covered. Comprehensive Hard Materials provides meaningful insights on materials at the leading edge of technology. It aids continued research and development of these materials and as such it is a critical information resource to academics and industry professionals facing the technological challenges of the future. Hard materials operate at the leading edge of technology, and continued res...

  10. 501 reading comprehension questions

    CERN Document Server

    2014-01-01

    This updated edition offers the most extensive and varied practice for all types of questions students might face on standardized and in-class tests. With this guide, students will learn to develop expert reading strategies, understand how to read faster and with greater comprehension, overcome reading anxiety, and increase appreciation of reading for pleasure. This book's step-by-step approach provides graduated coverage that moves from the basics to more advanced reading.

  11. Western Alaska ESI: INDEX (Index Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains vector polygons representing the boundaries of all the hardcopy cartographic products produced as part of the Environmental Sensitivity Index...

  12. Frequency shifting approach towards textual transcription of heartbeat sounds.

    Science.gov (United States)

    Arvin, Farshad; Doraisamy, Shyamala; Safar Khorasani, Ehsan

    2011-10-04

    Auscultation is an approach for diagnosing many cardiovascular problems. Automatic analysis of heartbeat sounds and extraction of its audio features can assist physicians towards diagnosing diseases. Textual transcription allows recording a continuous heart sound stream using a text format which can be stored in very small memory in comparison with other audio formats. In addition, a text-based data allows applying indexing and searching techniques to access to the critical events. Hence, the transcribed heartbeat sounds provides useful information to monitor the behavior of a patient for the long duration of time. This paper proposes a frequency shifting method in order to improve the performance of the transcription. The main objective of this study is to transfer the heartbeat sounds to the music domain. The proposed technique is tested with 100 samples which were recorded from different heart diseases categories. The observed results show that, the proposed shifting method significantly improves the performance of the transcription.

  13. Frequency shifting approach towards textual transcription of heartbeat sounds

    Directory of Open Access Journals (Sweden)

    Safar Khorasani Ehsan

    2011-10-01

    Full Text Available Abstract Auscultation is an approach for diagnosing many cardiovascular problems. Automatic analysis of heartbeat sounds and extraction of its audio features can assist physicians towards diagnosing diseases. Textual transcription allows recording a continuous heart sound stream using a text format which can be stored in very small memory in comparison with other audio formats. In addition, a text-based data allows applying indexing and searching techniques to access to the critical events. Hence, the transcribed heartbeat sounds provides useful information to monitor the behavior of a patient for the long duration of time. This paper proposes a frequency shifting method in order to improve the performance of the transcription. The main objective of this study is to transfer the heartbeat sounds to the music domain. The proposed technique is tested with 100 samples which were recorded from different heart diseases categories. The observed results show that, the proposed shifting method significantly improves the performance of the transcription.

  14. Master Veteran Index (MVI)

    Data.gov (United States)

    Department of Veterans Affairs — As of June 28, 2010, the Master Veteran Index (MVI) database based on the enhanced Master Patient Index (MPI) is the authoritative identity service within the VA,...

  15. Human Use Index (Future)

    Data.gov (United States)

    U.S. Environmental Protection Agency — Human land uses may have major impacts on ecosystems, affecting biodiversity, habitat, air and water quality. The human use index (also known as U-index) is the...

  16. Human Use Index

    Data.gov (United States)

    U.S. Environmental Protection Agency — Human land uses may have major impacts on ecosystems, affecting biodiversity, habitat, air and water quality. The human use index (also known as U-index) is the...

  17. IndexCat

    Data.gov (United States)

    U.S. Department of Health & Human Services — IndexCat provides access to the digitized version of the printed Index-Catalogue of the Library of the Surgeon General's Office; eTK for medieval Latin texts; and...

  18. Body Mass Index Table

    Science.gov (United States)

    ... Families ( We Can! ) Health Professional Resources Body Mass Index Table 1 for BMI greater than 35, go ... Health Information Email Alerts Jobs and Careers Site Index About NHLBI National Institute of Health Department of ...

  19. RNA-guided transcriptional regulation

    Science.gov (United States)

    Church, George M.; Mali, Prashant G.; Esvelt, Kevin M.

    2016-02-23

    Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.

  20. Transcriptional control of megakaryocyte development.

    Science.gov (United States)

    Goldfarb, A N

    2007-10-15

    Megakaryocytes are highly specialized cells that arise from a bipotent megakaryocytic-erythroid progenitor (MEP). This developmental leap requires coordinated activation of megakaryocyte-specific genes, radical changes in cell cycle properties, and active prevention of erythroid differentiation. These programs result from upregulation of megakaryocyte-selective transcription factors, downregulation of erythroid-selective transcription factors and ongoing mediation of common erythro-megakaryocytic transcription factors. Unlike most developmental programs, no single lineage-unique family of master regulators exerts executive control over the megakaryocytic plan. Rather, an assemblage of non-unique factors and signals converge to determine lineage and differentiation. In human megakaryopoiesis, hereditary disorders of platelet production have confirmed contributions from three distinct transcription factor families. Murine models have extended this repertoire to include multiple additional factors. At a mechanistic level, the means by which these non-unique factors collaborate in the establishment of a perfectly unique cell type remains a central question.

  1. Navigating the transcriptional roadmap regulating plant secondary cell wall deposition

    Directory of Open Access Journals (Sweden)

    Steven Grant Hussey

    2013-08-01

    Full Text Available The current status of lignocellulosic biomass as an invaluable resource in industry, agriculture and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW biosynthesis. The last decade of research has revealed an extensive network of NAC, MYB and other families of transcription factors regulating Arabidopsis SCW biosynthesis, and numerous studies have explored SCW-related transcription factors in other dicots and monocots. Whilst the general structure of the Arabidopsis network has been a topic of several reviews, they have not comprehensively represented the detailed protein-DNA and protein-protein interactions described in the literature, and an understanding of network dynamics and functionality has not yet been achieved for SCW formation. Furthermore the methodologies employed in studies of SCW transcriptional regulation have not received much attention, especially in the case of non-model organisms. In this review, we have reconstructed the most exhaustive literature-based network representations to date of SCW transcriptional regulation in Arabidopsis. We include a manipulable Cytoscape representation of the Arabidopsis SCW transcriptional network to aid in future studies, along with a list of supporting literature for each documented interaction. Amongst other topics, we discuss the various components of the network, its evolutionary conservation in plants, putative modules and dynamic mechanisms that may influence network function, and the approaches that have been employed in network inference. Future research should aim to better understand network function and its response to dynamic perturbations, whilst the development and application of genome-wide approaches such as ChIP-seq and systems genetics are in progress for the study of SCW transcriptional regulation in non-model organisms.

  2. Comprehensive evaluation method in application of nuclear DCS product design

    International Nuclear Information System (INIS)

    Wang Weixin; Zhao Zhemin; Shi Yingbin

    2014-01-01

    In order to select the best design proposal in short time, the TOPSIS comprehensive evaluation method in the nuclear power plant DCS product design was introduced. It can intuitively show the different design proposals good or not good by data and shorten the time of the design proposal optimization. The design proposal selected by this method will be more reasonable and has good comprehensive performance indexes. The TOPSIS comprehensive evaluation method achieves good result in one of the nuclear power plant DCS cabinet design proposal optimization. (authors)

  3. Research on Comprehensive Evaluation Method for Heating Project Based on Analytic Hierarchy Processing

    Science.gov (United States)

    Han, Shenchao; Yang, Yanchun; Liu, Yude; Zhang, Peng; Li, Siwei

    2018-01-01

    It is effective to reduce haze in winter by changing the distributed heat supply system. Thus, the studies on comprehensive index system and scientific evaluation method of distributed heat supply project are essential. Firstly, research the influence factors of heating modes, and an index system with multiple dimension including economic, environmental, risk and flexibility was built and all indexes were quantified. Secondly, a comprehensive evaluation method based on AHP was put forward to analyze the proposed multiple and comprehensive index system. Lastly, the case study suggested that supplying heat with electricity has great advantage and promotional value. The comprehensive index system of distributed heating supply project and evaluation method in this paper can evaluate distributed heat supply project effectively and provide scientific support for choosing the distributed heating project.

  4. National Capital Planning Commission Meeting Transcripts

    Data.gov (United States)

    National Capital Planning Commission — Transcripts of the monthly (with the exception of August) National Capital Planning Commission meeting transcripts are provided for research to confirm actions taken...

  5. A comprehensive French grammar

    CERN Document Server

    Price, Glanville

    2013-01-01

    Characterized by clear and accessible explanations, numerous examples and sample sentences, a new section on register and tone, and useful appendices covering topics including age and time, A Comprehensive French Grammar, Sixth Edition is an indispensable tool for advanced students of French language and literature.A revised edition of this established, bestselling French grammarIncludes a new section on register and medium and offers expanded treatment of French punctuationFeatures numerous examples and sample sentences, and useful appendices covering topics including age, time, and dimension

  6. Comprehensive multiplatform collaboration

    Science.gov (United States)

    Singh, Kundan; Wu, Xiaotao; Lennox, Jonathan; Schulzrinne, Henning G.

    2003-12-01

    We describe the architecture and implementation of our comprehensive multi-platform collaboration framework known as Columbia InterNet Extensible Multimedia Architecture (CINEMA). It provides a distributed architecture for collaboration using synchronous communications like multimedia conferencing, instant messaging, shared web-browsing, and asynchronous communications like discussion forums, shared files, voice and video mails. It allows seamless integration with various communication means like telephones, IP phones, web and electronic mail. In addition, it provides value-added services such as call handling based on location information and presence status. The paper discusses the media services needed for collaborative environment, the components provided by CINEMA and the interaction among those components.

  7. Environmental enrichment increases transcriptional and epigenetic differentiation between mouse dorsal and ventral dentate gyrus.

    Science.gov (United States)

    Zhang, Tie-Yuan; Keown, Christopher L; Wen, Xianglan; Li, Junhao; Vousden, Dulcie A; Anacker, Christoph; Bhattacharyya, Urvashi; Ryan, Richard; Diorio, Josie; O'Toole, Nicholas; Lerch, Jason P; Mukamel, Eran A; Meaney, Michael J

    2018-01-19

    Early life experience influences stress reactivity and mental health through effects on cognitive-emotional functions that are, in part, linked to gene expression in the dorsal and ventral hippocampus. The hippocampal dentate gyrus (DG) is a major site for experience-dependent plasticity associated with sustained transcriptional alterations, potentially mediated by epigenetic modifications. Here, we report comprehensive DNA methylome, hydroxymethylome and transcriptome data sets from mouse dorsal and ventral DG. We find genome-wide transcriptional and methylation differences between dorsal and ventral DG, including at key developmental transcriptional factors. Peripubertal environmental enrichment increases hippocampal volume and enhances dorsal DG-specific differences in gene expression. Enrichment also enhances dorsal-ventral differences in DNA methylation, including at binding sites of the transcription factor NeuroD1, a regulator of adult neurogenesis. These results indicate a dorsal-ventral asymmetry in transcription and methylation that parallels well-known functional and anatomical differences, and that may be enhanced by environmental enrichment.

  8. A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

    Directory of Open Access Journals (Sweden)

    Jose L. Pruneda-Paz

    2014-07-01

    Full Text Available Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1 that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.

  9. Comprehensive overview of prostatitis.

    Science.gov (United States)

    Khan, Farhan Ullah; Ihsan, Awais Ullah; Khan, Hidayat Ullah; Jana, Ruby; Wazir, Junaid; Khongorzul, Puregmaa; Waqar, Muhammad; Zhou, Xiaohui

    2017-10-01

    Prostatitis is a common urinary tract syndrome that many doctors find problematic to treat effectively. It is the third most commonly found urinary tract disease in men after prostate cancer and Benign Prostate Hyperplasia (BPH). Prostatitis may account for 25% of all office visits made to the urological clinics complaining about the genital and urinary systems all over the world. In the present study, we classified prostatitis and comprehensively elaborated the etiology, pathogenesis, diagnosis, and treatment of acute bacterial prostatitis (category I), chronic bacterial prostatitis (category II), chronic pelvic pain syndrome (CPPS) (category III), and asymptomatic prostatitis (category IV). In addition, we also tried to get some insights about other types of prostatitis-like fungal, viral and gonococcal prostatitis. The aim of this review is to present the detail current perspective of prostatitis in a single review. To the best of our knowledge currently, there is not a single comprehensive review, which can completely elaborate this important topic in an effective way. Furthermore, this review will provide a solid platform to conduct future studies on different aspects such as risk factors, mechanism of pathogenesis, proper diagnosis, and rational treatment plans for fungal, viral, and gonococcal prostatitis. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  10. Comprehensive national energy strategy

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-04-01

    This Comprehensive National Energy Strategy sets forth a set of five common sense goals for national energy policy: (1) improve the efficiency of the energy system, (2) ensure against energy disruptions, (3) promote energy production and use in ways that respect health and environmental values, (4) expand future energy choices, and (5) cooperate internationally on global issues. These goals are further elaborated by a series of objectives and strategies to illustrate how the goals will be achieved. Taken together, the goals, objectives, and strategies form a blueprint for the specific programs, projects, initiatives, investments, and other actions that will be developed and undertaken by the Federal Government, with significant emphasis on the importance of the scientific and technological advancements that will allow implementation of this Comprehensive National Energy Strategy. Moreover, the statutory requirement of regular submissions of national energy policy plans ensures that this framework can be modified to reflect evolving conditions, such as better knowledge of our surroundings, changes in energy markets, and advances in technology. This Strategy, then, should be thought of as a living document. Finally, this plan benefited from the comments and suggestions of numerous individuals and organizations, both inside and outside of government. The Summary of Public Comments, located at the end of this document, describes the public participation process and summarizes the comments that were received. 8 figs.

  11. readability of comprehension passages in junior high school (jhs)

    African Journals Online (AJOL)

    CHARLES

    ... to enhance readability. Key Words: readability formulas, comprehension passages, Junior High School, .... Index has a manual version but in this study the electronic version was used. The ..... probably the majority of the people heard the news by word of mouth. A critical look ..... The Journal of Tourism Studies 9.2: 49-60.

  12. Psychodermatology: A comprehensive review

    Directory of Open Access Journals (Sweden)

    Savita Yadav

    2013-01-01

    Full Text Available Psychodermatology is an interesting domain of dermatology that overlaps with psychiatry. This arena in dermatology has received limited diligence, partly due to lack of training in this realm. We present here a comprehensive review of salient features and treatment updates in primary psychiatric dermatoses and have also discussed the role of psyche in psychophysiological cutaneous disorders. Secondary psychiatric morbidity is relatively common among patients visiting the dermatologists but often overlooked and uncared for. Dermatologist should be able to initiate basic pharmacotherapy, should be knowledgeable about various non-pharmacological treatments and know the right time to refer the patient to the psychiatrist. Awareness and pertinent treatment of psychodermatological disorders among dermatologists will lead to a more holistic treatment approach and better prognosis in this unique group of patients.

  13. Comprehensive Environmental Management Plan

    International Nuclear Information System (INIS)

    Hjeresen, D.L.

    1994-01-01

    The Environmental Management Program at Los Alamos National Laboratory is in the process of initiating and then implementing a Comprehensive Environmental Management Plan (CEMP). There are several environmental impact and compliance drivers for this initiative. The Los Alamos CEMP is intended to be a flexible, long-range process that predicts, minimizes, treats, and disposes of any waste generated in execution of the Los Alamos mission - even if that mission changes. The CEMP is also intended to improve stakeholder and private sector involvement and access to environmental information. The total quality environmental management (TQEM) process will benchmark Los Alamos to private sector and DOE operations, identify opportunities for improvement, prioritize among opportunities, implement projects, measure progress, and spur continuous improvement in Environmental Management operations

  14. Comprehensive nuclear materials

    CERN Document Server

    Allen, Todd; Stoller, Roger; Yamanaka, Shinsuke

    2012-01-01

    Comprehensive Nuclear Materials encapsulates a panorama of fundamental information on the vast variety of materials employed in the broad field of nuclear technology. The work addresses, in five volumes, 3,400 pages and over 120 chapter-length articles, the full panorama of historical and contemporary international research in nuclear materials, from Actinides to Zirconium alloys, from the worlds' leading scientists and engineers. It synthesizes the most pertinent research to support the selection, assessment, validation and engineering of materials in extreme nuclear environments. The work discusses the major classes of materials suitable for usage in nuclear fission, fusion reactors and high power accelerators, and for diverse functions in fuels, cladding, moderator and control materials, structural, functional, and waste materials.

  15. Supplement: Commodity Index Report

    Data.gov (United States)

    Commodity Futures Trading Commission — Shows index traders in selected agricultural markets. These traders are drawn from the noncommercial and commercial categories. The noncommercial category includes...

  16. Indexing mergers and acquisitions

    OpenAIRE

    Gang, Jianhua; Guo, Jie (Michael); Hu, Nan; Li, Xi

    2017-01-01

    We measure the efficiency of mergers and acquisitions by putting forward an index (the ‘M&A Index’) based on stochastic frontier analysis. The M&A Index is calculated for each takeover deal and is standardized between 0 and 1. An acquisition with a higher index encompasses higher efficiency. We find that takeover bids with higher M&A Indices are more likely to succeed. Moreover, the M&A Index shows a strong and positive relation with the acquirers’ post-acquisition stock perfo...

  17. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities

    Science.gov (United States)

    Fang, Xin; Sastry, Anand; Mih, Nathan; Kim, Donghyuk; Tan, Justin; Lloyd, Colton J.; Gao, Ye; Yang, Laurence; Palsson, Bernhard O.

    2017-01-01

    Transcriptional regulatory networks (TRNs) have been studied intensely for >25 y. Yet, even for the Escherichia coli TRN—probably the best characterized TRN—several questions remain. Here, we address three questions: (i) How complete is our knowledge of the E. coli TRN; (ii) how well can we predict gene expression using this TRN; and (iii) how robust is our understanding of the TRN? First, we reconstructed a high-confidence TRN (hiTRN) consisting of 147 transcription factors (TFs) regulating 1,538 transcription units (TUs) encoding 1,764 genes. The 3,797 high-confidence regulatory interactions were collected from published, validated chromatin immunoprecipitation (ChIP) data and RegulonDB. For 21 different TF knockouts, up to 63% of the differentially expressed genes in the hiTRN were traced to the knocked-out TF through regulatory cascades. Second, we trained supervised machine learning algorithms to predict the expression of 1,364 TUs given TF activities using 441 samples. The algorithms accurately predicted condition-specific expression for 86% (1,174 of 1,364) of the TUs, while 193 TUs (14%) were predicted better than random TRNs. Third, we identified 10 regulatory modules whose definitions were robust against changes to the TRN or expression compendium. Using surrogate variable analysis, we also identified three unmodeled factors that systematically influenced gene expression. Our computational workflow comprehensively characterizes the predictive capabilities and systems-level functions of an organism’s TRN from disparate data types. PMID:28874552

  18. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 432 ... Vol 13, No 2 (2008), Evidence-based nursing interventions and guidelines ... Vol 9, No 4 (2004), Exercise and depression: A treatment manual, Abstract ... informed health education during comprehensive nursing care ...

  19. Browse Title Index

    African Journals Online (AJOL)

    Items 301 - 350 of 664 ... ... of Oral Health on The Quality of Life of Elementary School Teachers, Abstract PDF ... among Jimma comprehensive high school students: Knowledge, .... Voluntary Confidential Counselling and Testing in Gurage Zone, ...

  20. Browse Title Index

    African Journals Online (AJOL)

    Items 151 - 200 of 278 ... Vol 45, No 2 (2011), Linking reading literacy assessment and teaching: ... 12 English First Additional Language Reading, Comprehension, ... and the minimising of reading problems: a South African perspective, Abstract.

  1. Transcriptional regulation of hepatic lipogenesis.

    Science.gov (United States)

    Wang, Yuhui; Viscarra, Jose; Kim, Sun-Joong; Sul, Hei Sook

    2015-11-01

    Fatty acid and fat synthesis in the liver is a highly regulated metabolic pathway that is important for very low-density lipoprotein (VLDL) production and thus energy distribution to other tissues. Having common features at their promoter regions, lipogenic genes are coordinately regulated at the transcriptional level. Transcription factors, such as upstream stimulatory factors (USFs), sterol regulatory element-binding protein 1C (SREBP1C), liver X receptors (LXRs) and carbohydrate-responsive element-binding protein (ChREBP) have crucial roles in this process. Recently, insights have been gained into the signalling pathways that regulate these transcription factors. After feeding, high blood glucose and insulin levels activate lipogenic genes through several pathways, including the DNA-dependent protein kinase (DNA-PK), atypical protein kinase C (aPKC) and AKT-mTOR pathways. These pathways control the post-translational modifications of transcription factors and co-regulators, such as phosphorylation, acetylation or ubiquitylation, that affect their function, stability and/or localization. Dysregulation of lipogenesis can contribute to hepatosteatosis, which is associated with obesity and insulin resistance.

  2. Structural insights into transcription complexes

    NARCIS (Netherlands)

    Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

    2011-01-01

    Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

  3. Transcription factor-based biosensor

    Science.gov (United States)

    Dietrich, Jeffrey A; Keasling, Jay D

    2013-10-08

    The present invention provides for a system comprising a BmoR transcription factor, a .sigma..sup.54-RNA polymerase, and a pBMO promoter operatively linked to a reporter gene, wherein the pBMO promoter is capable of expression of the reporter gene with an activated form of the BmoR and the .sigma..sup.54-RNA polymerase.

  4. Analysis in indexing

    DEFF Research Database (Denmark)

    Mai, Jens Erik

    2005-01-01

    is presented as an alternative and the paper discusses how this approach includes a broader range of analyses and how it requires a new set of actions from using this approach; analysis of the domain, users and indexers. The paper concludes that the two-step procedure to indexing is insufficient to explain...

  5. Rethinking image indexing?

    DEFF Research Database (Denmark)

    Christensen, Hans Dam

    2017-01-01

    Hans Dam Christensen, ”Rethinking image indexing?”, in: Journal of the Association for Information Science and Technology, vol. 68, no. 7, 2017, 1782-1785......Hans Dam Christensen, ”Rethinking image indexing?”, in: Journal of the Association for Information Science and Technology, vol. 68, no. 7, 2017, 1782-1785...

  6. GRI Index 2017

    OpenAIRE

    World Bank

    2017-01-01

    This World Bank GRI Index 2017 provides an overview of sustainability considerations within the World Bank’s lending and analytical services as well as its corporate activities. This index of sustainability indicators has been prepared in accordance with the internationally recognized standard for sustainability reporting, the GRI Standards: Core option (https://www.globalreporting.org). T...

  7. 2016 GRI Index

    OpenAIRE

    World Bank

    2016-01-01

    This 2016 World Bank Global Reporting Initiative (GRI) Index provides an overview of sustainability considerations within the World Bank’s lending and analytical services as well as its corporate activities. This index of sustainability indicators has been prepared in accordance with the internationally recognized standard for sustainability reporting GRI guidelines (https://www.globalrepo...

  8. Global Ecosystem Restoration Index

    DEFF Research Database (Denmark)

    Fernandez, Miguel; Garcia, Monica; Fernandez, Nestor

    2015-01-01

    The Global ecosystem restoration index (GERI) is a composite index that integrates structural and functional aspects of the ecosystem restoration process. These elements are evaluated through a window that looks into a baseline for degraded ecosystems with the objective to assess restoration...

  9. EJSCREEN Supplementary Indexes 2015 Public

    Data.gov (United States)

    U.S. Environmental Protection Agency — There are 40 supplementary EJSCREEN indexes that are divided into 5 categories: EJ Index with supplementary demographic index, Supplementary EJ Index 1 with...

  10. Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems.

    Science.gov (United States)

    Díaz-Triviño, Sara; Long, Yuchen; Scheres, Ben; Blilou, Ikram

    2017-01-01

    In plant biology, transient expression systems have become valuable approaches used routinely to rapidly study protein expression, subcellular localization, protein-protein interactions, and transcriptional activity prior to in vivo studies. When studying transcriptional regulation, luciferase reporter assays offer a sensitive readout for assaying promoter behavior in response to different regulators or environmental contexts and to confirm and assess the functional relevance of predicted binding sites in target promoters. This chapter aims to provide detailed methods for using luciferase reporter system as a rapid, efficient, and versatile assay to analyze transcriptional regulation of target genes by transcriptional regulators. We describe a series of optimized transient expression systems consisting of Arabidopsis thaliana protoplasts, infiltrated Nicotiana benthamiana leaves, and human HeLa cells to study the transcriptional regulations of two well-characterized transcriptional regulators SCARECROW (SCR) and SHORT-ROOT (SHR) on one of their targets, CYCLIN D6 (CYCD6).Here, we illustrate similarities and differences in outcomes when using different systems. The plant-based systems revealed that the SCR-SHR complex enhances CYCD6 transcription, while analysis in HeLa cells showed that the complex is not sufficient to strongly induce CYCD6 transcription, suggesting that additional, plant-specific regulators are required for full activation. These results highlight the importance of the system and suggest that including heterologous systems, such as HeLa cells, can provide a more comprehensive analysis of a complex gene regulatory network.

  11. The 2001 Comprehensive Review

    CERN Multimedia

    Åkesson, T

    A new approach for CERN to monitor the LHC-experiments' technical and scientific progress was introduced last year: The Comprehensive Reviews. A significant fraction of the full LHCC committee is mobilized during two days to review the complete project status. This event took place for ATLAS during 2-3 of July this year. With a rather exhaustive program we presented our status in 39 talks. It was a demanding and close to impossible task for the referees to comprehend the ATLAS status by listening to this massive amount of information, but from the ATLAS point-of-view we judged it important that the referees were exposed to both the progress and the remaining problem areas. The referees were satisfied with our status; probably more so this year than last year. They judged the main critical issues to be: The schedules of the barrel toroid, the end-cap TRT, the LAr barrel and end-cap A, and the MDTs. The procurement of radiation hard electronics was also thought to be a critical issue. They were informed of ...

  12. Comprehensive facilities plan

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    The Ernest Orlando Lawrence Berkeley National Laboratory`s Comprehensive Facilities Plan (CFP) document provides analysis and policy guidance for the effective use and orderly future development of land and capital assets at the Berkeley Lab site. The CFP directly supports Berkeley Lab`s role as a multiprogram national laboratory operated by the University of California (UC) for the Department of Energy (DOE). The CFP is revised annually on Berkeley Lab`s Facilities Planning Website. Major revisions are consistent with DOE policy and review guidance. Facilities planing is motivated by the need to develop facilities for DOE programmatic needs; to maintain, replace and rehabilitate existing obsolete facilities; to identify sites for anticipated programmatic growth; and to establish a planning framework in recognition of site amenities and the surrounding community. The CFP presents a concise expression of the policy for the future physical development of the Laboratory, based upon anticipated operational needs of research programs and the environmental setting. It is a product of the ongoing planning processes and is a dynamic information source.

  13. Comprehensive eye evaluation algorithm

    Science.gov (United States)

    Agurto, C.; Nemeth, S.; Zamora, G.; Vahtel, M.; Soliz, P.; Barriga, S.

    2016-03-01

    In recent years, several research groups have developed automatic algorithms to detect diabetic retinopathy (DR) in individuals with diabetes (DM), using digital retinal images. Studies have indicated that diabetics have 1.5 times the annual risk of developing primary open angle glaucoma (POAG) as do people without DM. Moreover, DM patients have 1.8 times the risk for age-related macular degeneration (AMD). Although numerous investigators are developing automatic DR detection algorithms, there have been few successful efforts to create an automatic algorithm that can detect other ocular diseases, such as POAG and AMD. Consequently, our aim in the current study was to develop a comprehensive eye evaluation algorithm that not only detects DR in retinal images, but also automatically identifies glaucoma suspects and AMD by integrating other personal medical information with the retinal features. The proposed system is fully automatic and provides the likelihood of each of the three eye disease. The system was evaluated in two datasets of 104 and 88 diabetic cases. For each eye, we used two non-mydriatic digital color fundus photographs (macula and optic disc centered) and, when available, information about age, duration of diabetes, cataracts, hypertension, gender, and laboratory data. Our results show that the combination of multimodal features can increase the AUC by up to 5%, 7%, and 8% in the detection of AMD, DR, and glaucoma respectively. Marked improvement was achieved when laboratory results were combined with retinal image features.

  14. Cultural Knowledge in News Comprehension

    DEFF Research Database (Denmark)

    Mathieu, David

    2009-01-01

    This paper presents the main lines of the design and the findings of a reception study on news comprehension. This empirical study is a comparison of the comprehension processes of Danes and French Canadians over a set of news texts from both countries. Comprehension is explored from a cultural...... perspective, through the lens of cognition and pragmatics, revealing the role played by cultural knowledge in comprehension and the underlying relationship between a text and its intended audience. It is argued that recipients ‘problematise’ the news texts, a process by which the texts answer questions...

  15. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database contains a selected set of...

  16. Burkholderia pseudomallei transcriptional adaptation in macrophages

    Directory of Open Access Journals (Sweden)

    Chieng Sylvia

    2012-07-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a facultative intracellular pathogen of phagocytic and non-phagocytic cells. How the bacterium interacts with host macrophage cells is still not well understood and is critical to appreciate the strategies used by this bacterium to survive and how intracellular survival leads to disease manifestation. Results Here we report the expression profile of intracellular B. pseudomallei following infection of human macrophage-like U937 cells. During intracellular growth over the 6 h infection period, approximately 22 % of the B. pseudomallei genome showed significant transcriptional adaptation. B. pseudomallei adapted rapidly to the intracellular environment by down-regulating numerous genes involved in metabolism, cell envelope, motility, replication, amino acid and ion transport system and regulatory function pathways. Reduced expression in catabolic and housekeeping genes suggested lower energy requirement and growth arrest during macrophage infection, while expression of genes encoding anaerobic metabolism functions were up regulated. However, whilst the type VI secretion system was up regulated, expression of many known virulence factors was not significantly modulated over the 6hours of infection. Conclusions The transcriptome profile described here provides the first comprehensive view of how B. pseudomallei survives within host cells and will help identify potential virulence factors and proteins that are important for the survival and growth of B. pseudomallei within human cells.

  17. RNA Pol II promotes transcription of centromeric satellite DNA in beetles.

    Directory of Open Access Journals (Sweden)

    Zeljka Pezer

    Full Text Available Transcripts of centromeric satellite DNAs are known to play a role in heterochromatin formation as well as in establishment of the kinetochore. However, little is known about basic mechanisms of satellite DNA expression within constitutive heterochromatin and its regulation. Here we present comprehensive analysis of transcription of abundant centromeric satellite DNA, PRAT from beetle Palorus ratzeburgii (Coleoptera. This satellite is characterized by preservation and extreme sequence conservation among evolutionarily distant insect species. PRAT is expressed in all three developmental stages: larvae, pupae and adults at similar level. Transcripts are abundant comprising 0.033% of total RNA and are heterogeneous in size ranging from 0.5 kb up to more than 5 kb. Transcription proceeds from both strands but with 10 fold different expression intensity and transcripts are not processed into siRNAs. Most of the transcripts (80% are not polyadenylated and remain in the nucleus while a small portion is exported to the cytoplasm. Multiple, irregularly distributed transcription initiation sites as well as termination sites have been mapped within the PRAT sequence using primer extension and RLM-RACE. The presence of cap structure as well as poly(A tails in a portion of the transcripts indicate RNA polymerase II-dependent transcription and a putative polymerase II promoter site overlaps the most conserved part of the PRAT sequence. The treatment of larvae with alpha-amanitin decreases the level of PRAT transcripts at concentrations that selectively inhibit pol II activity. In conclusion, stable, RNA polymerase II dependant transcripts of abundant centromeric satellite DNA, not regulated by RNAi, have been identified and characterized. This study offers a basic understanding of expression of highly abundant heterochromatic DNA which in beetle species constitutes up to 50% of the genome.

  18. A new supersymmetric index

    International Nuclear Information System (INIS)

    Cecotti, S.; Fendley, P.; Intriligator, K.; Vafa, C.

    1992-01-01

    We show that Tr(-1) F F e -βH is an index for N = 2 supersymmetric theories in two dimensions, in the sense that it is independent of almost all deformations of the theory. This index is related to the geometry of the vacua (Berry's curvature) and satisfies an exact differential equation as a function of β. For integrable theories we can also compute the index thermodynamically, using the exact S-matrix. The equivalence of these two results implies a highly non-trivial equivalence of a set of coupled integral equations with these differential equations, among them Painleve III and the affine Toda equations. (orig.)

  19. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

    International Nuclear Information System (INIS)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal; Thomsen, Bo; Larsen, Knud; Hedegaard, Jakob; Bendixen, Christian; Madsen, Lone Bruhn

    2013-01-01

    Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i

  20. Commentary on: "Comprehensive transcriptional analysis of early-stage urothelial carcinoma." Hedegaard J, Lamy P, Nordentoft I, Algaba F, Høyer S, Ulhøi BP, Vang S, Reinert T, Hermann GG, Mogensen K, Thomsen MB, Nielsen MM, Marquez M, Segersten U, Aine M, Höglund M, Birkenkamp-Demtröder K, Fristrup N, Borre M, Hartmann A, Stöhr R, Wach S, Keck B, Seitz AK, Nawroth R, Maurer T, Tulic C, Simic T, Junker K, Horstmann M, Harving N, Petersen AC, Calle ML, Steyerberg EW, Beukers W, van Kessel KE, Jensen JB, Pedersen JS, Malmström PU, Malats N, Real FX, Zwarthoff EC, Ørntoft TF, Dyrskjøt L. Cancer Cell. 2016 Jul 11;30(1):27-42.

    Science.gov (United States)

    Lee, Byron H

    2017-09-01

    Non-muscle-invasive bladder cancer (NMIBC) is a heterogeneous disease with widely different outcomes. We performed a comprehensive transcriptional analysis of 460 early-stage urothelial carcinomas and showed that NMIBC can be subgrouped into 3 major classes with basal- and luminal-like characteristics and different clinical outcomes. Large differences in biological processes such as the cell cycle, epithelial-mesenchymal transition, and differentiation were observed. Analysis of transcript variants revealed frequent mutations in genes encoding proteins involved in chromatin organization and cytoskeletal functions. Furthermore, mutations in well-known cancer driver genes (e.g., TP53 and ERBB2) were primarily found in high-risk tumors, together with APOBEC-related mutational signatures. The identification of subclasses in NMIBC may offer better prognostication and treatment selection based on subclass assignment. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Indexes to Volume 75

    Indian Academy of Sciences (India)

    SUBJECT INDEX. Mathematical .... A 10-Hz terawatt class Ti:sapphire laser system: Development and ... Indigenous development of a 2 kW RF-excited fast axial flow CO2 .... Polarized spectral features of human breast tissues through wavelet.

  2. Glycemic index and diabetes

    Science.gov (United States)

    ... Most snack foods Potatoes White rice Watermelon Meal Planning with the Glycemic Index When planning your meals: ... urac.org). URAC's accreditation program is an independent audit to verify that A.D.A.M. follows ...

  3. TOMS Absorbing Aerosol Index

    Data.gov (United States)

    Washington University St Louis — TOMS_AI_G is an aerosol related dataset derived from the Total Ozone Monitoring Satellite (TOMS) Sensor. The TOMS aerosol index arises from absorbing aerosols such...

  4. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 100 of 1034 ... Vol 49, No 2 (2007), African Index Medicus: Improving access to African ... insulin therapy initiation among patients with type 2 diabetes attending a ... Risk Factors Implicated in Diabetic Ketoacidosis (DKA), Abstract PDF.

  5. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 194 ... Journal Home > Advanced Search > Browse Title Index ... Vol 14, No 1 (2000), A functional categoriality of adjectives in ... Vol 1, No 1 (1987), Alienation and affirmation: The humanistic vision of Bessie Head, Abstract PDF.

  6. Browse Title Index

    African Journals Online (AJOL)

    Items 151 - 200 of 879 ... South African Journal of Higher Education. ... Browse Title Index ... in a USA school setting: Merging transition theory with a narrative approach, Abstract ... Citation analysis of theses and dissertations submitted at the ...

  7. Browse Title Index

    African Journals Online (AJOL)

    Items 601 - 650 of 879 ... South African Journal of Higher Education. ... Browse Title Index .... The challenge of thesis supervision in an art university, Abstract ... No 2 (2004), Robert Sternberg's mental self-government theory and its contribution to ...

  8. Palmer Drought Severity Index

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — PDSI from the Dai dataset. The Palmer Drought Severity Index (PDSI) is devised by Palmer (1965) to represent the severity of dry and wet spells over the U.S. based...

  9. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 100 of 346 ... Journal Home > Advanced Search > Browse Title Index ... and hygiene promotion services in Rungwe district, Tanzania, Abstract .... as seen in NIgerian teaching hospital: pattern and a simple classification, Abstract.

  10. Browse Title Index

    African Journals Online (AJOL)

    Items 151 - 200 of 437 ... Journal Home > Advanced Search > Browse Title Index ... prospects and realistic strategies to its implementation in Nigeria\\'s Institute of ... and Communication Technology (ICT) in information dissemination, Abstract.

  11. Browse Title Index

    African Journals Online (AJOL)

    Items 901 - 950 of 1355 ... Journal of Applied Sciences and Environmental Management. ... Journal Home > Advanced Search > Browse Title Index .... Vol 22, No 2 (2018), Performance evaluation of a locally fabricated sawdust fired oven for ...

  12. Browse Title Index

    African Journals Online (AJOL)

    Items 301 - 350 of 788 ... Journal Home > Advanced Search > Browse Title Index ... Vol 26, No 1 (2018), Gender differentials in the perception of .... Vol 25, No 1 (2017), Impact of total quality management on students' academic performance in ...

  13. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 465 ... Journal Home > Advanced Search > Browse Title Index ... and twinning data of an igbo kindred during the Nigerian Civil War, Abstract ... on laboratory estimations with special reference to clinical chemistry, Abstract.

  14. National Death Index

    Data.gov (United States)

    U.S. Department of Health & Human Services — The National Death Index (NDI) is a centralized database of death record information on file in state vital statistics offices. Working with these state offices, the...

  15. Browse Title Index

    African Journals Online (AJOL)

    Items 251 - 300 of 1260 ... Journal Home > Advanced Search > Browse Title Index ... Consumption of ammonia-nitrogen by aob in immobilized batch culture, Abstract PDF .... Vol 9, No 3S (2017): Special Issue, Design an automatic temperature ...

  16. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 294 ... Journal Home > Advanced Search > Browse Title Index. Log in or .... S Edwards, M Hlongwane, J Thwala, N Robinson ... Vol 16, No 1 (2017), Infancy of internet cafe: The substitute of ubuntu-padare pedagogy, Abstract.

  17. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 130 ... Journal Home > Advanced Search > Browse Title Index. Log in or ... using the technological pedagogical content knowledge(TPACK) framework, Abstract PDF ... Tamara N. Hrin, Dušica D. Milenković, Mirjana D. Segedinac.

  18. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 278 ... Journal Home > Advanced Search > Browse Title Index ... drie paradigmas beskou: 'n eenheid, of 'n veelheid van perspektiewe? ... Vol 45, No 1 (2011), Genre pedagogy in the mediation of socially-situated literacies ...

  19. Browse Title Index

    African Journals Online (AJOL)

    Items 551 - 600 of 879 ... Journal Home > Advanced Search > Browse Title Index ... A James, E Ralfe, L van Laren, N Ngcobo ... 1 (2011), Recognition of prior learning in promoting lifelong learning: A pedagogy of hope or a shattering of dreams?

  20. Browse Title Index

    African Journals Online (AJOL)

    Items 451 - 500 of 533 ... Journal Home > Advanced Search > Browse Title Index .... for past tense forms in Northern Sotho: verb stems with final 'm' and 'n', Abstract ... in an academic writing class: Implications for a dialogic pedagogy, Abstract.

  1. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 183 ... Journal Home > Advanced Search > Browse Title Index ... Vol 61 (2017), New interventions and sustainable solutions: .... Vol 35 (2011), Resurgence of tribal levies: Double taxation for the rural poor, Abstract PDF.

  2. Regional Snowfall Index (RSI)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA's National Climatic Data Center is now producing the Regional Snowfall Index (RSI) for significant snowstorms that impact the eastern two thirds of the U.S. The...

  3. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 736 ... Journal Home > Advanced Search > Browse Title Index ... Vol 5 (2008), A Contagious Malady: The Human Quest for Truth through Religion, Abstract ... A Study of Politeness Strategies Used by the National University of ...

  4. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 414 ... Journal Home > Advanced Search > Browse Title Index. Log in or ... of an algebraic function for the permutation of truth table columns, Abstract ... appraisal and productivity levels in selected Nigerian universities, Abstract.

  5. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 879 ... Journal Home > Advanced Search > Browse Title Index ... Vol 20, No 4 (2006), Assessing academic potential for university admission: ... Vol 16, No 2 (2002), Book Review: Rethinking truth by Higgs, P & Smith, J, Details.

  6. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 165 ... Journal Home > Advanced Search > Browse Title Index ... Vol 43 (2011), Assessment of the Learning Commons takeoff at the University of ... the archive of South Africa's Truth and Reconciliation Commission, Abstract.

  7. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 644 ... Journal Home > Advanced Search > Browse Title Index. Log in or ... Ethics review n international health research: quality assurance or bureaucratic nightmare? Details ... Audit of Management of Open Fractures, Details PDF.

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    African Journals Online (AJOL)

    Items 1 - 50 of 449 ... Vol 1, No 3 (2012), Adult Functional Literacy Curriculum: Effective Strategy for Human ... and Exchange Rate Influence on the Nigerian Stock Market Index ... for the Stimulation and Attraction of Foreign Direct Investments ...

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    African Journals Online (AJOL)

    Items 1 - 50 of 98 ... Journal Home > Advanced Search > Browse Title Index ... model for the continued professionalisation of student affairs in Africa, Abstract PDF ... Vol 2, No 2 (2014), Book Review: How College Affects Students, A Third decade ...

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    African Journals Online (AJOL)

    Items 1 - 50 of 76 ... Journal Home > Advanced Search > Browse Title Index ... Vol 4, No 1 (2011), Automation of AutoCAD for Detailing of Reinforced .... Vol 10, No 1 (2017), Housing data base for sustainable housing provision, Abstract PDF.

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    African Journals Online (AJOL)

    Items 1 - 50 of 147 ... Journal Home > Advanced Search > Browse Title Index .... Library (TEEAL) Database among faculty members in Federal University, ... Vol 5, No 2 (2014), Effects of corporate culture on the implementation of automation in ...

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    African Journals Online (AJOL)

    Items 851 - 900 of 1255 ... Vol 16, No 4 (2010), Origin and generation mechanisms of ... Vol 13, No 4 (2007), Osmotic fragility index of HBAA red blood cells in the presence of ... (2004), Photovoltaic cells, efficiency and optimization, Abstract PDF.

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    African Journals Online (AJOL)

    Items 401 - 450 of 985 ... Vol 17 (2010), Flood Frequency Analysis of Ikpoba River ... and the corresponding Refractive Index in Uniaxial Crystals, Abstract ... Vol 8 (2004), Further on stokes expansions for the finite amplitude water waves, Abstract.

  14. Transportation Services Index

    Data.gov (United States)

    Department of Transportation — The TSI is a monthly measure of the volume of services performed by the for-hire transportation sector. The index covers the activities of for-hire freight carriers,...

  15. Browse Title Index

    African Journals Online (AJOL)

    Items 201 - 250 of 531 ... Journal Home > Advanced Search > Browse Title Index ... thermal conductivity and viscosity in a flat plate solar collector, Abstract PDF .... similarity method in unsteady two-dimensional MHD boundary layer on the body ...

  16. The post-transcriptional operon

    DEFF Research Database (Denmark)

    Tenenbaum, Scott A.; Christiansen, Jan; Nielsen, Henrik

    2011-01-01

    model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness...... of the model in identifying new participants in cellular pathways as well as in deepening our understanding of cellular responses....

  17. Lattice Index Coding

    OpenAIRE

    Natarajan, Lakshmi; Hong, Yi; Viterbo, Emanuele

    2014-01-01

    The index coding problem involves a sender with K messages to be transmitted across a broadcast channel, and a set of receivers each of which demands a subset of the K messages while having prior knowledge of a different subset as side information. We consider the specific case of noisy index coding where the broadcast channel is Gaussian and every receiver demands all the messages from the source. Instances of this communication problem arise in wireless relay networks, sensor networks, and ...

  18. Pragmatic Comprehension Development through Telecollaboration

    Science.gov (United States)

    Rafieyan, Vahid; Sharafi-Nejad, Maryam; Khavari, Zahra; Eng, Lin Siew; Mohamed, Abdul Rashid

    2014-01-01

    Pragmatic comprehension can be ideally developed through contact with target language speakers. This contact can be provided in English as Foreign Language contexts through telecollaboration. To test the actual effect of telecollaboration on the development of pragmatic comprehension, 30 Iranian undergraduates of English as a Foreign Language…

  19. Reading comprehension in Parkinson's disease.

    Science.gov (United States)

    Murray, Laura L; Rutledge, Stefanie

    2014-05-01

    Although individuals with Parkinson's disease (PD) self-report reading problems and experience difficulties in cognitive-linguistic functions that support discourse-level reading, prior research has primarily focused on sentence-level processing and auditory comprehension. Accordingly, the authors investigated the presence and nature of reading comprehension in PD, hypothesizing that (a) individuals with PD would display impaired accuracy and/or speed on reading comprehension tests and (b) reading performances would be correlated with cognitive test results. Eleven adults with PD and 9 age- and education-matched control participants completed tests that evaluated reading comprehension; general language and cognitive abilities; and aspects of attention, memory, and executive functioning. The PD group obtained significantly lower scores on several, but not all, reading comprehension, language, and cognitive measures. Memory, language, and disease severity were significantly correlated with reading comprehension for the PD group. Individuals in the early stages of PD without dementia or broad cognitive deficits can display reading comprehension difficulties, particularly for high- versus basic-level reading tasks. These reading difficulties are most closely related to memory, high-level language, and PD symptom severity status. The findings warrant additional research to delineate further the types and nature of reading comprehension impairments experienced by individuals with PD.

  20. Production of the 2400 kb Duchenne muscular dystrophy (DMD) gene transcript; transcription time and cotranscriptional splicing

    Energy Technology Data Exchange (ETDEWEB)

    Tennyson, C.N.; Worton, R.G. [Univ. of Toronto and the Hospital for Sick Children, Ontario (Canada)

    1994-09-01

    The largest known gene in any organism is the human DMD gene which has 79 exons that span 2400 kb. The extreme nature of the DMD gene raises questions concerning the time required for transcription and whether splicing begins before transcription is complete. DMD gene transcription is induced as cultured human myoblasts differentiate to form multinucleated myotubes, providing a system for studying the kinetics of transcription and splicing. Using quantitative RT-PCR, transcript accumulation was monitored from four different regions within the gene following induction of expression. By comparing the accumulation of transcripts from the 5{prime} and 3{prime} ends of the gene we have shown that approximately 12 hours are required to transcribe 1770 kb of the gene, extrapolating to a time of 16 hours for the transcription unit expressed in muscle. Comparison of accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5{prime} end before transcription is complete, providing strong evidence for cotranscriptional splicing of DMD gene transcripts. Finally, the rate of transcript accumulation was reduced at the 3{prime} end of the gene relative to the 5{prime} end, perhaps due to premature termination of transcription complexes as they traverse this enormous transcription unit. The lag between transcription initiation and the appearance of complete transcripts could be important in limiting transcript production in dividing cells and to the timing of mRNA appearance in differentiating muscle.

  1. Mutual interdependence of splicing and transcription elongation.

    Science.gov (United States)

    Brzyżek, Grzegorz; Świeżewski, Szymon

    2015-01-01

    Transcription and splicing are intrinsically linked, as splicing needs a pre-mRNA substrate to commence. The more nuanced view is that the rate of transcription contributes to splicing regulation. On the other hand there is accumulating evidence that splicing has an active role in controlling transcription elongation by DNA-dependent RNA polymerase II (RNAP II). We briefly review those mechanisms and propose a unifying model where splicing controls transcription elongation to provide an optimal timing for successive rounds of splicing.

  2. Development and implementation of a business continuity management risk index.

    Science.gov (United States)

    Kadar, Michael

    This paper will present the building blocks for developing and implementing the BCM risk index; whether it is used as a comprehensive metric for risk or preparedness. This paper introduces the concept of a business continuity management (BCM) risk index--a comprehensive metric that measures and reports the status of the primary 'intended outcome' of the BCM programme to top management. In addition to measuring the primary programme output,;the BCM risk index can be used to demonstrate the overall value of the BCM programme to executive management. This is accomplished because the BCM risk index allows quantitative measurement of current risk levels and their comparison with established risk tolerances. The BCM Risk Index can provide executive management with reports on the risk level of individual business units, departments, subsidiaries or the enterprise in a way that drives both risk management and BCM initiatives. The name 'risk index' can be misleading, however. The BCM risk index concept can also be used to measure preparedness levels. In fact, implementation at DTE Energy has resulted in calling it the 'preparedness index', which is used to measure and report preparedness levels rather than risk levels.

  3. Interplay between DNA supercoiling and transcription elongation.

    Science.gov (United States)

    Ma, Jie; Wang, Michelle

    2014-01-01

    Transcription-coupled DNA supercoiling has been shown to be an important regulator of transcription that is broadly present in the cell. Here we review experimental work which shows that RNA polymerase is a powerful torsional motor that can alter DNA topology and structure, and DNA supercoiling in turn directly affects transcription elongation.

  4. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 100 of 110 ... Vol 1, No 1 (2009), Influence of Principals' Administrative Style on the Job Performance of Secondary School Teachers in Cross River State, Nigeria, Abstract. JE Bassey ... Vol 4, No 1 (2012), Lexical inference as an obstacle to reading comprehension at senior secondary schools in Botswana, Abstract.

  5. Browse Title Index

    African Journals Online (AJOL)

    Items 201 - 250 of 278 ... Vol 44, No 2 (2010), Students' Comprehension of the representation of African American Vernacular in Alice Walker's The Color Purple, Abstract. M Pretorius. Vol 50, No 1 ... Vol 46, No 2 (2012), Successful first-year learning: A social cognitive view of academic literacy, Abstract. V McGhie, C van der ...

  6. Browse Title Index

    African Journals Online (AJOL)

    Items 201 - 250 of 674 ... Gender and Behaviour. ... Vol 4, No 2 (2006), Farming in the northern mountains of Pakistan: Role of women ... Vol 15, No 2 (2017), Fostering critical thinking in initial teacher education curriculums: a comprehensive literature review ... differences in work-family, family-work conflicts and stress among ...

  7. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 184 ... Vol 1 (1978), Protecting general-linguistic hypotheses from refutation, Abstract PDF. RP Botha. Vol 10 (1983), Quantity, resolution and syllable geometry, Abstract PDF. R Lass. Vol 28 (1994), Reading comprehension research and linguistic pragmatics: Mapping out some unrecognized interdisciplinary ...

  8. Browse Title Index

    African Journals Online (AJOL)

    Vol 93, No 2 (2016), Quality of comprehensive emergency obstetric care through the lens of clinical documentation on admission to labour ward, Abstract. RJ Kosgei, D Gathara, RK Kamau, S Babu, S Mueke, EJ Cheserem, E Kihuba, J Karumbi, M Mulaku, J Aluvaala, M English, AB Kihara. Vol 80, No 8 (2003):, Quality of ...

  9. A critique of the Active Ageing Index.

    Science.gov (United States)

    São José, José Manuel de; Timonen, Virpi; Amado, Carla Alexandra Filipe; Santos, Sérgio Pereira

    2017-01-01

    Active ageing and successful ageing are ubiquitous concepts in contemporary societies. In the European Union, active ageing is monitored and promoted chiefly by the Active Ageing Index, a policy tool in use since 2012. We acknowledge that the AAI may contribute to sensitizing people, including policymakers, to the multidimensionality and complexity of the process of "ageing well". However, we note that despite being widely used and promoted, the Active Ageing Index remains under-scrutinized. In this article, we undertake a comprehensive critical analysis of the Active Ageing Index. This critical analysis is supported by the Theory of Model Ageing, the Capability Approach and, to a lesser extent, by relevant literature on composite indices. We conclude that the Active Ageing Index was developed with the paradoxical aim of deriving "the solution" from "the problem". It is an under-theorized and narrowly conceptualized index that contributes to the process of Model Ageing, as its conceptual foundation, and its domains and indicators, convey a certain model of active ageing. This model is expert-based and ingrained with a priori assumptions about the potential of older people, the domains of life and activities they value and how strongly they value them. Finally, the Active Ageing Index measures current achievements, not capabilities (i.e. the opportunity set of achievable "doings" and "beings"), resulting in a valuable but incomplete tool for policymaking purposes. We hope that this critical analysis will initiate a debate on the Active Ageing Index that, in our view, is overdue. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Teacher Talk: One Teacher's Reflections during Comprehension Strategies Instruction

    Science.gov (United States)

    Robertson, Dana A.

    2013-01-01

    This study examined one tutor's evolving use of particular talk moves during comprehension strategies instruction in a university-based clinical setting. Through engaging in audiotape reflection and transcript analysis with a coach, the tutor made shifts toward more explicit and purposeful strategies instruction, yet did not consistently…

  11. Directing traffic on DNA-How transcription factors relieve or induce transcriptional interference.

    Science.gov (United States)

    Hao, Nan; Palmer, Adam C; Dodd, Ian B; Shearwin, Keith E

    2017-03-15

    Transcriptional interference (TI) is increasingly recognized as a widespread mechanism of gene control, particularly given the pervasive nature of transcription, both sense and antisense, across all kingdoms of life. Here, we discuss how transcription factor binding kinetics strongly influence the ability of a transcription factor to relieve or induce TI.

  12. Transcriptional changes common to human cocaine, cannabis and phencyclidine abuse.

    Directory of Open Access Journals (Sweden)

    Elin Lehrmann

    2006-12-01

    Full Text Available A major goal of drug abuse research is to identify and understand drug-induced changes in brain function that are common to many or all drugs of abuse. As these may underlie drug dependence and addiction, the purpose of the present study was to examine if different drugs of abuse effect changes in gene expression that converge in common molecular pathways. Microarray analysis was employed to assay brain gene expression in postmortem anterior prefrontal cortex (aPFC from 42 human cocaine, cannabis and/or phencyclidine abuse cases and 30 control cases, which were characterized by toxicology and drug abuse history. Common transcriptional changes were demonstrated for a majority of drug abuse cases (N = 34, representing a number of consistently changed functional classes: Calmodulin-related transcripts (CALM1, CALM2, CAMK2B were decreased, while transcripts related to cholesterol biosynthesis and trafficking (FDFT1, APOL2, SCARB1, and Golgi/endoplasmic reticulum (ER functions (SEMA3B, GCC1 were all increased. Quantitative PCR validated decreases in calmodulin 2 (CALM2 mRNA and increases in apolipoprotein L, 2 (APOL2 and semaphorin 3B (SEMA3B mRNA for individual cases. A comparison between control cases with and without cardiovascular disease and elevated body mass index indicated that these changes were not due to general cellular and metabolic stress, but appeared specific to the use of drugs. Therefore, humans who abused cocaine, cannabis and/or phencyclidine share a decrease in transcription of calmodulin-related genes and increased transcription related to lipid/cholesterol and Golgi/ER function. These changes represent common molecular features of drug abuse, which may underlie changes in synaptic function and plasticity that could have important ramifications for decision-making capabilities in drug abusers.

  13. FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

    KAUST Repository

    Alam, Tanvir

    2016-10-12

    Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna

  14. FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

    KAUST Repository

    Alam, Tanvir; Uludag, Mahmut; Essack, Magbubah; Salhi, Adil; Ashoor, Haitham; Hanks, John B.; Kapfer, Craig Eric; Mineta, Katsuhiko; Gojobori, Takashi; Bajic, Vladimir B.

    2016-01-01

    Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna

  15. Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

    KAUST Repository

    Roy, Sugata

    2018-04-24

    Mycobacterium tuberculosis (Mtb) infection reveals complex and dynamic host-pathogen interactions, leading to host protection or pathogenesis. Using a unique transcriptome technology (CAGE), we investigated the promoter-based transcriptional landscape of IFNγ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene Ontology enrichment analysis for Mtb-induced differentially expressed genes revealed various terms, related to host-protection and inflammation, enriched in up-regulated genes. On the other hand, terms related to dis-regulation of cellular functions were enriched in down-regulated genes. Differential expression analysis revealed known as well as novel transcription factor genes in Mtb infection, many of them significantly down-regulated. IFNγ or IL-4/IL-13 pre-stimulation induce additional differentially expressed genes in Mtb-infected macrophages. Cluster analysis uncovered significant numbers, prolonging their expressional changes. Furthermore, Mtb infection augmented cytokine-mediated M1 and M2 pre-activations. In addition, we identified unique transcriptional features of Mtb-mediated differentially expressed lncRNAs. In summary we provide a comprehensive in depth gene expression/regulation profile in Mtb-infected macrophages, an important step forward for a better understanding of host-pathogen interaction dynamics in Mtb infection.

  16. Sustainability index for Taipei

    International Nuclear Information System (INIS)

    Lee, Y.-J.; Huang Chingming

    2007-01-01

    Sustainability indicators are an effective means of determining whether a city is moving towards sustainable development (SD). After considering the characteristics of Taipei, Taiwan, discussions with experts, scholars and government departments and an exhaustive literature review, this study selected 51 sustainability indicators corresponding to the socio-economic characteristic of Taipei City. Such indicators should be regarded as a basis for assessing SD in Taipei City. The 51 indicators are classified into economic, social, environmental and institutional dimensions. Furthermore, statistical data is adopted to identify the trend of SD from 1994 to 2004. Moreover, the sustainability index is calculated for the four dimensions and for Taipei as a whole. Analysis results demonstrate that social and environmental indicators are moving towards SD, while economic and institutional dimensions are performing relatively poorly. However, since 2002, the economic sustainability index has gradually moved towards SD. Overall, the Taipei sustainability index indicates a gradual trend towards sustainable development during the past 11 years

  17. Calculate Your Body Mass Index

    Science.gov (United States)

    ... Can! ) Health Professional Resources Calculate Your Body Mass Index Body mass index (BMI) is a measure of body fat based ... Health Information Email Alerts Jobs and Careers Site Index About NHLBI National Institute of Health Department of ...

  18. The Journey of a Transcription Factor

    DEFF Research Database (Denmark)

    Pireyre, Marie

    Plants have developed astonishing networks regulating their metabolism to adapt to their environment. The complexity of these networks is illustrated by the expansion of families of regulators such as transcription factors in the plant kingdom. Transcription factors specifically impact...... transcriptional networks by integrating exogenous and endogenous stimuli and regulating gene expression accordingly. Regulation of transcription factors and their activation is thus highly important to modulate the transcriptional programs and increase fitness of the plant in a given environment. Plant metabolism....... The biosynthetic machinery of GLS is governed by interplay of six MYB and three bHLH transcription factors. MYB28, MYB29 and MYB76 regulate methionine-derived GLS, and MYB51, MYB34 and MYB122 regulate tryptophan-derived GLS. The three bHLH transcription factors MYC2, MYC3 and MYC4 physically interact with all six...

  19. Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships.

    Science.gov (United States)

    Seok, Junhee; Kaushal, Amit; Davis, Ronald W; Xiao, Wenzhong

    2010-01-18

    The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcriptional regulation relationships from microarray data often focused on the high-throughput experimental data alone, more recent approaches have explored the integration of external knowledge bases of gene interactions. In this work, we develop an algorithm that provides improved performance in the prediction of transcriptional regulatory relationships by supplementing the analysis of microarray data with a new method of integrating information from an existing knowledge base. Using a well-known dataset of yeast microarrays and the Yeast Proteome Database, a comprehensive collection of known information of yeast genes, we show that knowledge-based predictions demonstrate better sensitivity and specificity in inferring new transcriptional interactions than predictions from microarray data alone. We also show that comprehensive, direct and high-quality knowledge bases provide better prediction performance. Comparison of our results with ChIP-chip data and growth fitness data suggests that our predicted genome-wide regulatory pairs in yeast are reasonable candidates for follow-up biological verification. High quality, comprehensive, and direct knowledge bases, when combined with appropriate bioinformatic algorithms, can significantly improve the discovery of gene regulatory relationships from high throughput gene expression data.

  20. Gradient-index optics fundamentals and applications

    CERN Document Server

    Gomez-Reino, Carlos; Bao, Carmen

    2010-01-01

    Gradient-Index (GRIN) optics provides a comprehensive and thorough treatment on fundamentals and applications of light propagation through inhomogeneous media. The book can be used both as a classroom text for students in physics and engineering and as a reference for specialists. A description of the phenomena, components and technology used in GRIN Optics are presented. The relationship to lenses, waveguides, optical connections, spatial solitons and vision is demonstrated. Applications of GRIN components and hybrid structures for optical connections, optical sensing and Talbot effect are analyzed.

  1. Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

    OpenAIRE

    Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription ...

  2. The Cognitive Mobilization Index

    Directory of Open Access Journals (Sweden)

    Antonio Alaminos

    2012-01-01

    Full Text Available This article shows how the cognitive mobilization index, designed for use in observing potential political participation, can be used as an indicator of the political climate that a particular society is going through. Following a discussion of the theoretical elaborations (and their working definitions of the concept of cognitive mobilization, a longitudinal study of various European countries is used to consider the question of how political crises influence cognitive mobilization indexes and what effects they have on the political socialization process among the youngest cohorts.

  3. ParkIndex

    DEFF Research Database (Denmark)

    Kaczynski, Andrew T; Schipperijn, Jasper; Hipp, J Aaron

    2016-01-01

    using ArcGIS 9.3 and the Community Park Audit Tool. Four park summary variables - distance to nearest park, and the number of parks, amount of park space, and average park quality index within 1 mile were analyzed in relation to park use using logistic regression. Coefficients for significant park......, planners, and citizens to evaluate the potential for park use for a given area. Data used for developing ParkIndex were collected in 2010 in Kansas City, Missouri (KCMO). Adult study participants (n=891) reported whether they used a park within the past month, and all parks in KCMO were mapped and audited...

  4. Comprehensive Error Rate Testing (CERT)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Centers for Medicare and Medicaid Services (CMS) implemented the Comprehensive Error Rate Testing (CERT) program to measure improper payments in the Medicare...

  5. The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria

    Science.gov (United States)

    Rangel, Luiz Thibério; Novaes, Jeniffer; Durham, Alan M.; Madeira, Alda Maria B. N.; Gruber, Arthur

    2013-01-01

    Parasites of the genus Eimeria infect a wide range of vertebrate hosts, including chickens. We have recently reported a comparative analysis of the transcriptomes of Eimeria acervulina, Eimeria maxima and Eimeria tenella, integrating ORESTES data produced by our group and publicly available Expressed Sequence Tags (ESTs). All cDNA reads have been assembled, and the reconstructed transcripts have been submitted to a comprehensive functional annotation pipeline. Additional studies included orthology assignment across apicomplexan parasites and clustering analyses of gene expression profiles among different developmental stages of the parasites. To make all this body of information publicly available, we constructed the Eimeria Transcript Database (EimeriaTDB), a web repository that provides access to sequence data, annotation and comparative analyses. Here, we describe the web interface, available sequence data sets and query tools implemented on the site. The main goal of this work is to offer a public repository of sequence and functional annotation data of reconstructed transcripts of parasites of the genus Eimeria. We believe that EimeriaTDB will represent a valuable and complementary resource for the Eimeria scientific community and for those researchers interested in comparative genomics of apicomplexan parasites. Database URL: http://www.coccidia.icb.usp.br/eimeriatdb/ PMID:23411718

  6. 2005 Environmental Sustainability Index (ESI)

    Data.gov (United States)

    National Aeronautics and Space Administration — The 2005 Environmental Sustainability Index (ESI) is a measure of overall progress towards environmental sustainability, developed for 146 countries. The index...

  7. Comprehensive analysis of NAC transcription factors and their expression during cucumber fruit spine development

    Science.gov (United States)

    Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide, and fruit trichomes ir spines are an important trait for external fruit quality. The mechanisms underlying spine formation are not well understood, but there is evidence of the involvement of the plant-specific NAC family of tra...

  8. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

    KAUST Repository

    Zhang, Runxuan

    2017-04-05

    Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

  9. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

    KAUST Repository

    Zhang, Runxuan; Calixto, Cristiane  P.  G.; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A.; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; ten  Have, Sara; Frei  dit  Frey, Nicolas; Hirt, Heribert; James, Allan B.; Nimmo, Hugh G.; Barta, Andrea; Kalyna, Maria; Brown, John  W.  S.

    2017-01-01

    Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

  10. Transcriptional ontogeny of the developing liver

    Directory of Open Access Journals (Sweden)

    Lee Janice S

    2012-01-01

    Full Text Available Abstract Background During embryogenesis the liver is derived from endodermal cells lining the digestive tract. These endodermal progenitor cells contribute to forming the parenchyma of a number of organs including the liver and pancreas. Early in organogenesis the fetal liver is populated by hematopoietic stem cells, the source for a number of blood cells including nucleated erythrocytes. A comprehensive analysis of the transcriptional changes that occur during the early stages of development to adulthood in the liver was carried out. Results We characterized gene expression changes in the developing mouse liver at gestational days (GD 11.5, 12.5, 13.5, 14.5, 16.5, and 19 and in the neonate (postnatal day (PND 7 and 32 compared to that in the adult liver (PND67 using full-genome microarrays. The fetal liver, and to a lesser extent the neonatal liver, exhibited dramatic differences in gene expression compared to adults. Canonical pathway analysis of the fetal liver signature demonstrated increases in functions important in cell replication and DNA fidelity whereas most metabolic pathways of intermediary metabolism were under expressed. Comparison of the dataset to a number of previously published microarray datasets revealed 1 a striking similarity between the fetal liver and that of the pancreas in both mice and humans, 2 a nucleated erythrocyte signature in the fetus and 3 under expression of most xenobiotic metabolism genes throughout development, with the exception of a number of transporters associated with either hematopoietic cells or cell proliferation in hepatocytes. Conclusions Overall, these findings reveal the complexity of gene expression changes during liver development and maturation, and provide a foundation to predict responses to chemical and drug exposure as a function of early life-stages.

  11. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 100 of 391 ... Journal Home > Advanced Search > Browse Title Index ... Efficacy of four Rodenticides on the Ghanaian Market, Abstract ... Vol 2, No 1 (2000):, Determination of some wear elements in used car engine oil and oil filter ...

  12. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 46 of 46 ... Vol 4, No 1 (2015), Fiscal Federalism and Development In Nigeria, Abstract. Dorcas Akhere Odigwe, Stanley Aibieyi. Vol 1, No 1 (2011), Good Governance Analysing Performance of Economic Community of West African States and Southern African Development Community Members on Mo Ibrahim Index ...

  13. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 73 of 73 ... Journal Home > Advanced Search > Browse Title Index ... Vol 13 (2006), The ageing eye” functional changes from cradle to gray: A ... Vol 12 (2005), The evaluation of vision in children using monocular vision acuity and ...

  14. Browse Title Index

    African Journals Online (AJOL)

    Items 201 - 224 of 224 ... Vol 13, No 2 (2010), Spatial Analysis of Particle Size Distribution of Soils Formed on ... swelling index and moisture content of white and yellow garri in ... and Composition of Milk of West African Dwarf (Wad) Sheep Fed ...

  15. Browse Title Index

    African Journals Online (AJOL)

    Items 151 - 200 of 229 ... Browse Title Index ... Issue, Title. Vol 14, No 2 ... Vol 15, No 1 (2017), Qualitative and quantitative methods of suicide research in old age, Abstract PDF ... Vol 11, No 2 (2013), Simple Algorithm in the Management of Fetal ...

  16. Nitrate leaching index

    Science.gov (United States)

    The Nitrate Leaching Index is a rapid assessment tool that evaluates nitrate (NO3) leaching potential based on basic soil and climate information. It is the basis for many nutrient management planning efforts, but it has considerable limitations because of : 1) an oversimplification of the processes...

  17. Data Citation Index

    Directory of Open Access Journals (Sweden)

    Laura L. Pavlech

    2016-01-01

    Full Text Available Introduced by Thomson Reuters in 2012 as a, ‘‘Single point of access to quality research data from repositories across disciplines and around the world’’ [1], the Data Citation Index (DCI is a searchable collection of data sets and data studies from a select list of repositories.

  18. Indexing Moving Points

    DEFF Research Database (Denmark)

    Agarwal, Pankaj K.; Arge, Lars Allan; Erickson, Jeff

    2003-01-01

    We propose three indexing schemes for storing a set S of N points in the plane, each moving along a linear trajectory, so that any query of the following form can be answered quickly: Given a rectangle R and a real value t, report all K points of S that lie inside R at time t. We first present an...

  19. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 1215 ... Journal Home > Advanced Search > Browse Title Index. Log in or ... Vol 12, No 1 (2018), Analysis of the effects of frequent strikes on academic performance of students in universities in Nigeria: Edo State as a focal point, Abstract PDF ... Vol 6, No 1 (2012), Appraisal as a Determinant for Adequate ...

  20. Browse Title Index

    African Journals Online (AJOL)

    weighted Index of Biotic Integrity (SIBI) for use in the assessment of biotic integrity in the Klip River, Gauteng, South Africa, Abstract. P J Kotze, G J Steyn, H H du Preez, C J Kleynhans. Vol 40, No 4 (2015), Diatoms as water ...

  1. Indexes to Volume 77

    Indian Academy of Sciences (India)

    2015-11-27

    Proceedings of the International Workshop/Conference on Computational Condensed Matter Physics and Materials Science (IWCCMP-2015). Posted on November 27, 2015. Guest Editors: Anurag Srivastava, C. S. Praveen, H. S. Tewari. © 2015 Indian Academy of Sciences, Bengaluru. Contact | Site index.

  2. A Tourism Conditions Index

    NARCIS (Netherlands)

    C-L. Chang (Chia-Lin); H-K. Hsu (Hui-Kuang); M.J. McAleer (Michael)

    2014-01-01

    markdownabstract__Abstract__ This paper uses monthly data from April 2005 to August 2013 for Taiwan to propose a novel tourism indicator, namely the Tourism Conditions Index (TCI). TCI accounts for the spillover weights based on the Granger causality test and estimates of the multivariate BEKK

  3. Browse Title Index

    African Journals Online (AJOL)

    Items 251 - 300 of 652 ... Journal Home > Advanced Search > Browse Title Index ... Vol 18, No 7 (2015), Introduction to virtual property: Lex virtualis ipsa ... Vol 17, No 1 (2014), Legal challenges relating to the commercial use of outer space, with ...

  4. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 100 ... Vol 5, No 1 (2010), A simple note on some empirical stochastic process ... poverty index with when the parameter is strictly between 0 and 1, Abstract PDF ... Vol 10, No 2 (2015), Bilinear regression model with Kronecker and ...

  5. Browse Title Index

    African Journals Online (AJOL)

    Items 501 - 550 of 913 ... Vol 10, No 1 (2018), Modeling and comparison of IP and fuzzy-pi ... Modeling the potential impacts of global climate change in Bangladesh: An optimal ... Vol 9, No 4S (2017): Special Issue, New flood risk index in tropical ...

  6. Browse Title Index

    African Journals Online (AJOL)

    Items 751 - 800 of 846 ... Journal Home > Advanced Search > Browse Title Index ... Vol 9, No 3S (2017): Special Issue, The effect of torrefaction on oil palm ... core competency skills of IRBM tax auditors towards their performance, Abstract PDF ... of exchange rates behavior in Malaysia by using NATREX model, Abstract PDF.

  7. Browse Title Index

    African Journals Online (AJOL)

    Items 251 - 286 of 286 ... AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced ... the Hire Purchase and credit sale Act - An unnecessary duplication ? ... Vol 21 (2015), The Influence of Peer Pressure on Adolescents' Social Behaviour, Abstract PDF ... quality indexing for predicting variation of water quality over time ...

  8. Browse Title Index

    African Journals Online (AJOL)

    Items 151 - 200 of 1463 ... Vol 14, No 4 (2014), Association between mean platelet volume levels and inflammation in SLE patients presented with arthritis, Abstract PDF ... Vol 10, No 3 (2010), Atherogenic index of plasma as useful predictor of cardiovascular risk among postmenopausal women in Enugu, Nigeria, Abstract ...

  9. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 1117 ... Journal Home > Advanced Search > Browse Title Index ... Vol 13, No 3 (2007):, an edu-ethical perspecitve on the nature of truth: case studies in elite ... 2009: September: Supplement, An empirical study of university ...

  10. Browse Title Index

    African Journals Online (AJOL)

    Items 601 - 650 of 788 ... Browse Title Index ... Issue, Title ... Vol 14, No 1 (2006), Social science research: a critique of quantitative and qualitative methods ... Vol 18, No 1 (2010), Stress among part-time business students: a study in a Ghanaian ...

  11. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 1732 ... Journal Home > Advanced Search > Browse Title Index ... Vol 10, No 3 (2007), An Audit Of Perioperative Cardiac Arrest At ... Vol 11, No 4 (2008), An Audit Of Rejected Repeated X-ray Films As A Quality Assurance ...

  12. The Index House

    International Nuclear Information System (INIS)

    Reilly, M.A.

    1990-01-01

    This paper reports on the Pennsylvania Radon Research and Demonstration Project. The project involved the monitoring of the Index House for indoor radon, and was one of the earliest programs involving indoor radon contamination. The history of the house, the investigation, and testing and remediation procedures are discussed

  13. Browse Title Index

    African Journals Online (AJOL)

    Items 351 - 400 of 823 ... Vol 9, No 2 (2016), Evaluation of antiulcer activity of aqueous ... and Practices About Tsetse Fly in Muri District, Taraba State, Nigeria ... Vol 10, No 1 (2017): Special Conference Edition, Evaluation of heavy metals' health risk index in ... of phytoplankton as bioindicators of water quality in Jakara dam, ...

  14. Browse Title Index

    African Journals Online (AJOL)

    Items 251 - 300 of 2005 ... Issue, Title. Vol 92, No 4 (2015), Blood Pressure and Obesity Index Assessment in a Typical Urban Slum in Enugu, Nigeria, Abstract. GI Ahaneku, CU Osuji, OC Oguejiofor, BC Anisiuba, VO Ikeh, JE Ahaneku. Vol 80, No 10 (2003):, Blood pressure control in a population where antihypertensives are ...

  15. Browse Title Index

    African Journals Online (AJOL)

    Items 201 - 250 of 661 ... Journal Home > Advanced Search > Browse Title Index. Log in or Register to get access to full text downloads. .... A El-Mahdy, B Bolduc, J Upadhyay, R Shoukr, A Khoury. Vol 19, No 1 (2013), Factors affecting lower calyceal stone clearance after Extracorporeal shock wave lithotripsy, Abstract PDF.

  16. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 985 ... Journal Home > Advanced Search > Browse Title Index ... Vol 17 (2010), Alternating Direction Implicit Finite Difference Time Domain Acoustic Wave Algorithm, Abstract. E Ikata .... Vol 17 (2010), Analytic derivation of the wave profile and phase speed of sixth order Stokes waves in deep water, Abstract.

  17. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 217 ... Browse Title Index. Journal Home > Advanced ... Vol 13, No 1 (2016), Access to specialized surgical care, Abstract PDF. H Saidi ... Vol 9, No 2 (2012), Clinical Assessment of the Palmaris Longus – Accuracy of common tests, Abstract PDF ... Vol 11, No 2 (2014), Clinical trials in Surgery, Abstract PDF.

  18. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 97 of 97 ... Journal Home > Advanced Search > Browse Title Index ... Vol 20, No 2 (2008), Research Note: Anthropometric data of the foot of ... Vol 26, No 1 (2014), Validation of the Automation Attitude Questionnaire for Airline Pilots ...

  19. Browse Title Index

    African Journals Online (AJOL)

    Items 351 - 400 of 400 ... Vol 2, No 1 (2007), The effects of Aloe vera [gel] on clotting time, prothrombin time and plasma fibrinogen concentration in albino Wistar rats, Abstract. D V Dapper, P N Achinike, M D Gwotmut. Vol 8, No 3 (2014), The effects of body mass index on some electrocardiographic parameters in young adults: ...

  20. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 100 of 719 ... African Journal of Aquatic Science. ... Vol 32, No 2 (2007), Algal communities associated with aquatic macrophytes ... index to Clarias gariepinus (Teleostei: Clariidae) in the Vaal River system, South Africa, Abstract ... Vol 40, No 2 (2015), Benthic macroinvertebrate assemblages in mangroves and open ...

  1. Refractive index based measurements

    DEFF Research Database (Denmark)

    2014-01-01

    In a method for performing a refractive index based measurement of a property of a fluid such as chemical composition or temperature, a chirp in the local spatial frequency of interference fringes of an interference pattern is reduced by mathematical manipulation of the recorded light intensity...

  2. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 148 ... Vol 12, No 1S (2018), Addition of anti-Toxoplasma gondii membrane immunoglobulin Y to reduce necrotic index in mice's liver, Abstract PDF. Heni Puspitasari, Lucia T. Suwanti, Mufasirin Mufasirin. Vol 6, No 2 (2012), Advances in the Diagnosis, Treatment and Control of HIV Associated Tuberculosis ...

  3. Drug Impact Index.

    Science.gov (United States)

    Western Center for Drug-Free Schools and Communities.

    The Drug Impact Index provides a set of indicators designed to determine the extent of the local drug problem in a community. Each indicator includes a technical note on the data sources, a graph showing comparative statistics on that indicator for the Portland area and for the State of Oregon, and brief remarks on the implications of the data.…

  4. Likelihood for transcriptions in a genetic regulatory system under asymmetric stable Lévy noise.

    Science.gov (United States)

    Wang, Hui; Cheng, Xiujun; Duan, Jinqiao; Kurths, Jürgen; Li, Xiaofan

    2018-01-01

    This work is devoted to investigating the evolution of concentration in a genetic regulation system, when the synthesis reaction rate is under additive and multiplicative asymmetric stable Lévy fluctuations. By focusing on the impact of skewness (i.e., non-symmetry) in the probability distributions of noise, we find that via examining the mean first exit time (MFET) and the first escape probability (FEP), the asymmetric fluctuations, interacting with nonlinearity in the system, lead to peculiar likelihood for transcription. This includes, in the additive noise case, realizing higher likelihood of transcription for larger positive skewness (i.e., asymmetry) index β, causing a stochastic bifurcation at the non-Gaussianity index value α = 1 (i.e., it is a separating point or line for the likelihood for transcription), and achieving a turning point at the threshold value β≈-0.5 (i.e., beyond which the likelihood for transcription suddenly reversed for α values). The stochastic bifurcation and turning point phenomena do not occur in the symmetric noise case (β = 0). While in the multiplicative noise case, non-Gaussianity index value α = 1 is a separating point or line for both the MFET and the FEP. We also investigate the noise enhanced stability phenomenon. Additionally, we are able to specify the regions in the whole parameter space for the asymmetric noise, in which we attain desired likelihood for transcription. We have conducted a series of numerical experiments in "regulating" the likelihood of gene transcription by tuning asymmetric stable Lévy noise indexes. This work offers insights for possible ways of achieving gene regulation in experimental research.

  5. The Springer index of viruses

    National Research Council Canada - National Science Library

    Buchen-Osmond, Cornelia; Darai, Gholamreza; Tidona, Christian A

    2002-01-01

    ... of individual transcripts and proteins, sequence accession numbers, biological properties, diseases, recombinant vector constructs, vaccine strains, key references, as well as a high-resolution particle...

  6. Conservation Priority Index for Estuarine Fish (COPIEF)

    Science.gov (United States)

    Branco, Paulo; Costa, José Lino; Raposo de Almeida, Pedro

    2008-12-01

    Public awareness regarding environmental issues has increased in recent decades. The increasing number of impact assessment studies, management and conservation plans, as well as ecological monitoring studies, demand new and more efficient techniques. Indices are an important tool to aid biologists in these studies and should allow an easier comprehension of the data by managers, decision-makers and the general public. This study presents the first multi-metrical index able to establish a hierarchical ordination of the conservation priority of the estuarine fish species using 72 species from 16 estuarine systems (W and S coasts of Portugal). The index is composed of 10 metrics, comprising species life traits, distribution and population trends. The information needed to score each metric was gathered from the published literature and the index validation was done by external means. This methodology allowed the definition of those fish species most in need of conservation planning, and those less prone to extinction in Portuguese estuarine systems. The proposed index fills a gap in our knowledge and provides a useful tool to the scientific community and to the decision-makers, being a breakthrough in the field of conservation planning of estuarine fish species.

  7. Comprehensive evaluation system of intelligent urban growth

    Science.gov (United States)

    Li, Lian-Yan; Ren, Xiao-Bin

    2017-06-01

    With the rapid urbanization of the world, urban planning has become increasingly important and necessary to ensure people have access to equitable and sustainable homes, resources and jobs.This article is to talk about building an intelligent city evaluation system.First,using System Analysis Model(SAM) which concludes literature data analysis and stepwise regression analysis to describe intelligent growth scientifically and obtain the evaluation index. Then,using the improved entropy method to obtain the weight of the evaluation index.Afterwards, establishing a complete Smart Growth Comprehensive Evaluation Model(SGCEM).Finally,testing the correctness of the model.Choosing Otago(New Zealand )and Yumen(China) as research object by data mining and SGCEM model,then we get Yumen and Otago’s rational degree’s values are 0.3485 and 0.5376 respectively. It’s believed that the Otago’s smart level is higher,and it is found that the estimated value of rationality is consistent with the reality.

  8. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis.

    Science.gov (United States)

    Liang, Kaiwei; Woodfin, Ashley R; Slaughter, Brian D; Unruh, Jay R; Box, Andrew C; Rickels, Ryan A; Gao, Xin; Haug, Jeffrey S; Jaspersen, Sue L; Shilatifard, Ali

    2015-11-05

    Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data.

    Science.gov (United States)

    Wang, Yejun; MacKenzie, Keith D; White, Aaron P

    2015-05-07

    As sequencing costs are being lowered continuously, RNA-seq has gradually been adopted as the first choice for comparative transcriptome studies with bacteria. Unlike microarrays, RNA-seq can directly detect cDNA derived from mRNA transcripts at a single nucleotide resolution. Not only does this allow researchers to determine the absolute expression level of genes, but it also conveys information about transcript structure. Few automatic software tools have yet been established to investigate large-scale RNA-seq data for bacterial transcript structure analysis. In this study, 54 directional RNA-seq libraries from Salmonella serovar Typhimurium (S. Typhimurium) 14028s were examined for potential relationships between read mapping patterns and transcript structure. We developed an empirical method, combined with statistical tests, to automatically detect key transcript features, including transcriptional start sites (TSSs), transcriptional termination sites (TTSs) and operon organization. Using our method, we obtained 2,764 TSSs and 1,467 TTSs for 1331 and 844 different genes, respectively. Identification of TSSs facilitated further discrimination of 215 putative sigma 38 regulons and 863 potential sigma 70 regulons. Combining the TSSs and TTSs with intergenic distance and co-expression information, we comprehensively annotated the operon organization in S. Typhimurium 14028s. Our results show that directional RNA-seq can be used to detect transcriptional borders at an acceptable resolution of ±10-20 nucleotides. Technical limitations of the RNA-seq procedure may prevent single nucleotide resolution. The automatic transcript border detection methods, statistical models and operon organization pipeline that we have described could be widely applied to RNA-seq studies in other bacteria. Furthermore, the TSSs, TTSs, operons, promoters and unstranslated regions that we have defined for S. Typhimurium 14028s may constitute valuable resources that can be used for

  10. Scientific Journal Indexing

    Directory of Open Access Journals (Sweden)

    Getulio Teixeira Batista

    2007-08-01

    Full Text Available It is quite impressive the visibility of online publishing compared to offline. Lawrence (2001 computed the percentage increase across 1,494 venues containing at least five offline and five online articles. Results shown an average of 336% more citations to online articles compared to offline articles published in the same venue. If articles published in the same venue are of similar quality, then they concluded that online articles are more highly cited because of their easier access. Thomson Scientific, traditionally concerned with printed journals, announced on November 28, 2005, the launch of Web Citation Index™, the multidisciplinary citation index of scholarly content from institutional and subject-based repositories (http://scientific.thomson. com/press/2005/8298416/. The Web Citation Index from the abstracting and indexing (A&I connects together pre-print articles, institutional repositories and open access (OA journals (Chillingworth, 2005. Basically all research funds are government granted funds, tax payer’s supported and therefore, results should be made freely available to the community. Free online availability facilitates access to research findings, maximizes interaction among research groups, and optimizes efforts and research funds efficiency. Therefore, Ambi-Água is committed to provide free access to its articles. An important aspect of Ambi-Água is the publication and management system of this journal. It uses the Electronic System for Journal Publishing (SEER - http://www.ibict.br/secao.php?cat=SEER. This system was translated and customized by the Brazilian Institute for Science and Technology Information (IBICT based on the software developed by the Public Knowledge Project (Open Journal Systems of the British Columbia University (http://pkp.sfu.ca/ojs/. The big advantage of using this system is that it is compatible with the OAI-PMH protocol for metadata harvesting what greatly promotes published articles

  11. Are There Gender Differences in Emotion Comprehension? Analysis of the Test of Emotion Comprehension.

    Science.gov (United States)

    Fidalgo, Angel M; Tenenbaum, Harriet R; Aznar, Ana

    2018-01-01

    This article examines whether there are gender differences in understanding the emotions evaluated by the Test of Emotion Comprehension (TEC). The TEC provides a global index of emotion comprehension in children 3-11 years of age, which is the sum of the nine components that constitute emotion comprehension: (1) recognition of facial expressions, (2) understanding of external causes of emotions, (3) understanding of desire-based emotions, (4) understanding of belief-based emotions, (5) understanding of the influence of a reminder on present emotional states, (6) understanding of the possibility to regulate emotional states, (7) understanding of the possibility of hiding emotional states, (8) understanding of mixed emotions, and (9) understanding of moral emotions. We used the answers to the TEC given by 172 English girls and 181 boys from 3 to 8 years of age. First, the nine components into which the TEC is subdivided were analysed for differential item functioning (DIF), taking gender as the grouping variable. To evaluate DIF, the Mantel-Haenszel method and logistic regression analysis were used applying the Educational Testing Service DIF classification criteria. The results show that the TEC did not display gender DIF. Second, when absence of DIF had been corroborated, it was analysed for differences between boys and girls in the total TEC score and its components controlling for age. Our data are compatible with the hypothesis of independence between gender and level of comprehension in 8 of the 9 components of the TEC. Several hypotheses are discussed that could explain the differences found between boys and girls in the belief component. Given that the Belief component is basically a false belief task, the differences found seem to support findings in the literature indicating that girls perform better on this task.

  12. Promoter proximal polyadenylation sites reduce transcription activity

    DEFF Research Database (Denmark)

    Andersen, Pia Kjølhede; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site......, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites...... on transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500...

  13. Transcription and recombination: when RNA meets DNA.

    Science.gov (United States)

    Aguilera, Andrés; Gaillard, Hélène

    2014-08-01

    A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription-replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  14. Specificity and robustness in transcription control networks.

    Science.gov (United States)

    Sengupta, Anirvan M; Djordjevic, Marko; Shraiman, Boris I

    2002-02-19

    Recognition by transcription factors of the regulatory DNA elements upstream of genes is the fundamental step in controlling gene expression. How does the necessity to provide stability with respect to mutation constrain the organization of transcription control networks? We examine the mutation load of a transcription factor interacting with a set of n regulatory response elements as a function of the factor/DNA binding specificity and conclude on theoretical grounds that the optimal specificity decreases with n. The predicted correlation between variability of binding sites (for a given transcription factor) and their number is supported by the genomic data for Escherichia coli. The analysis of E. coli genomic data was carried out using an algorithm suggested by the biophysical model of transcription factor/DNA binding. Complete results of the search for candidate transcription factor binding sites are available at http://www.physics.rockefeller.edu/~boris/public/search_ecoli.

  15. Memory mechanisms supporting syntactic comprehension.

    Science.gov (United States)

    Caplan, David; Waters, Gloria

    2013-04-01

    Efforts to characterize the memory system that supports sentence comprehension have historically drawn extensively on short-term memory as a source of mechanisms that might apply to sentences. The focus of these efforts has changed significantly in the past decade. As a result of changes in models of short-term working memory (ST-WM) and developments in models of sentence comprehension, the effort to relate entire components of an ST-WM system, such as those in the model developed by Baddeley (Nature Reviews Neuroscience 4: 829-839, 2003) to sentence comprehension has largely been replaced by an effort to relate more specific mechanisms found in modern models of ST-WM to memory processes that support one aspect of sentence comprehension--the assignment of syntactic structure (parsing) and its use in determining sentence meaning (interpretation) during sentence comprehension. In this article, we present the historical background to recent studies of the memory mechanisms that support parsing and interpretation and review recent research into this relation. We argue that the results of this research do not converge on a set of mechanisms derived from ST-WM that apply to parsing and interpretation. We argue that the memory mechanisms supporting parsing and interpretation have features that characterize another memory system that has been postulated to account for skilled performance-long-term working memory. We propose a model of the relation of different aspects of parsing and interpretation to ST-WM and long-term working memory.

  16. Indexing for summary queries

    DEFF Research Database (Denmark)

    Yi, Ke; Wang, Lu; Wei, Zhewei

    2014-01-01

    ), of a particular attribute of these records. Aggregation queries are especially useful in business intelligence and data analysis applications where users are interested not in the actual records, but some statistics of them. They can also be executed much more efficiently than reporting queries, by embedding...... returned by reporting queries. In this article, we design indexing techniques that allow for extracting a statistical summary of all the records in the query. The summaries we support include frequent items, quantiles, and various sketches, all of which are of central importance in massive data analysis....... Our indexes require linear space and extract a summary with the optimal or near-optimal query cost. We illustrate the efficiency and usefulness of our designs through extensive experiments and a system demonstration....

  17. Conformity index: A review

    International Nuclear Information System (INIS)

    Feuvret, Loic; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

    2006-01-01

    We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear

  18. A study on regional comprehensive performance evaluation indicator system of rational use of drugs

    Directory of Open Access Journals (Sweden)

    Sun Tongda

    2017-01-01

    Full Text Available The current research presents the design of a 4-degree-3-level performance evaluation indicator system of rational use of drugs for health care institutions accord with the Balanced Score Card (BSC method. Financial index, patient index, professional process index, and development and blazing new trials index are adopted in the light of scientific, guiding, operable and generalizable principles. The index weight is based on the analytic hierarchy process, and comprehensive performance evaluation indicators are calculated by a linear integrated weighting method. Its practical application in 21 state-run health care institutions in Ningbo, from 2008 to 2012, has arrived at the finding that the comprehensive performance evaluation indicator system offers a scientific, practical and effective performance management quantification and is thus worth popularizing.

  19. Browse Title Index

    African Journals Online (AJOL)

    Vol 9, No 2S (2017): Special Issue, Water quality assessment of the rivers in bauxite mining area at Kuantan Pahang, Abstract PDF. N Yaakub, M.N.A. Raoff, M.N. Haris, A.A.A. Halim, M.K.A. Kamarudin. Vol 9, No 2S (2017): Special Issue, Water quality index assesment around industrial area in Kuantan, Pahang, Abstract ...

  20. Gradient-Index Optics

    Science.gov (United States)

    2010-03-31

    nonimaging design capabilities to incorporate 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 12-04-2011 13. SUPPLEMENTARY NOTES The views, opinions...Box 12211 Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS Imaging Optics, Nonimaging Optics, Gradient Index Optics, Camera, Concentrator...imaging and nonimaging design capabilities to incorporate manufacturable GRIN lenses can provide imaging lens systems that are compact and

  1. Measurment and Reporting of Comprehensive Income: Search ...

    African Journals Online (AJOL)

    Measurment and Reporting of Comprehensive Income: Search, Challenges, ... of periods of stable and unstable economic situation and satisfies varied users' ... Keywords: Historical accounting; comprehensive income; asset valuation model.

  2. Index of cyber integrity

    Science.gov (United States)

    Anderson, Gustave

    2014-05-01

    Unfortunately, there is no metric, nor set of metrics, that are both general enough to encompass all possible types of applications yet specific enough to capture the application and attack specific details. As a result we are left with ad-hoc methods for generating evaluations of the security of our systems. Current state of the art methods for evaluating the security of systems include penetration testing and cyber evaluation tests. For these evaluations, security professionals simulate an attack from malicious outsiders and malicious insiders. These evaluations are very productive and are able to discover potential vulnerabilities resulting from improper system configuration, hardware and software flaws, or operational weaknesses. We therefore propose the index of cyber integrity (ICI), which is modeled after the index of biological integrity (IBI) to provide a holistic measure of the health of a system under test in a cyber-environment. The ICI provides a broad base measure through a collection of application and system specific metrics. In this paper, following the example of the IBI, we demonstrate how a multi-metric index may be used as a holistic measure of the health of a system under test in a cyber-environment.

  3. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    Adipocyte differentiation is tightly controlled by a transcriptional cascade, which directs the extensive reprogramming of gene expression required to convert fibroblast-like precursor cells into mature lipid-laden adipocytes. Recent global analyses of transcription factor binding and chromatin...... remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications....... Such transcription factor hotspots are likely to represent key signaling nodes which integrate multiple adipogenic signals at specific chromatin sites, thereby facilitating coordinated action on gene expression....

  4. Nursing supervision for care comprehensiveness

    Directory of Open Access Journals (Sweden)

    Lucieli Dias Pedreschi Chaves

    Full Text Available ABSTRACT Objective: To reflect on nursing supervision as a management tool for care comprehensiveness by nurses, considering its potential and limits in the current scenario. Method: A reflective study based on discourse about nursing supervision, presenting theoretical and practical concepts and approaches. Results: Limits on the exercise of supervision are related to the organization of healthcare services based on the functional and clinical model of care, in addition to possible gaps in the nurse training process and work overload. Regarding the potential, researchers emphasize that supervision is a tool for coordinating care and management actions, which may favor care comprehensiveness, and stimulate positive attitudes toward cooperation and contribution within teams, co-responsibility, and educational development at work. Final considerations: Nursing supervision may help enhance care comprehensiveness by implying continuous reflection on including the dynamics of the healthcare work process and user needs in care networks.

  5. Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize.

    Science.gov (United States)

    Wei, Kai-Fa; Chen, Juan; Chen, Yan-Feng; Wu, Ling-Juan; Xie, Dao-Xin

    2012-04-01

    The WRKY transcription factors function in plant growth and development, and response to the biotic and abiotic stresses. Although many studies have focused on the functional identification of the WRKY transcription factors, much less is known about molecular phylogenetic and global expression analysis of the complete WRKY family in maize. In this study, we identified 136 WRKY proteins coded by 119 genes in the B73 inbred line from the complete genome and named them in an orderly manner. Then, a comprehensive phylogenetic analysis of five species was performed to explore the origin and evolutionary patterns of these WRKY genes, and the result showed that gene duplication is the major driving force for the origin of new groups and subgroups and functional divergence during evolution. Chromosomal location analysis of maize WRKY genes indicated that 20 gene clusters are distributed unevenly in the genome. Microarray-based expression analysis has revealed that 131 WRKY transcripts encoded by 116 genes may participate in the regulation of maize growth and development. Among them, 102 transcripts are stably expressed with a coefficient of variation (CV) value of WRKY genes with the CV value of >15% are further analysed to discover new organ- or tissue-specific genes. In addition, microarray analyses of transcriptional responses to drought stress and fungal infection showed that maize WRKY proteins are involved in stress responses. All these results contribute to a deep probing into the roles of WRKY transcription factors in maize growth and development and stress tolerance.

  6. Pan-Cancer Mutational and Transcriptional Analysis of the Integrator Complex

    Directory of Open Access Journals (Sweden)

    Antonio Federico

    2017-04-01

    Full Text Available The integrator complex has been recently identified as a key regulator of RNA Polymerase II-mediated transcription, with many functions including the processing of small nuclear RNAs, the pause-release and elongation of polymerase during the transcription of protein coding genes, and the biogenesis of enhancer derived transcripts. Moreover, some of its components also play a role in genome maintenance. Thus, it is reasonable to hypothesize that their functional impairment or altered expression can contribute to malignancies. Indeed, several studies have described the mutations or transcriptional alteration of some Integrator genes in different cancers. Here, to draw a comprehensive pan-cancer picture of the genomic and transcriptomic alterations for the members of the complex, we reanalyzed public data from The Cancer Genome Atlas. Somatic mutations affecting Integrator subunit genes and their transcriptional profiles have been investigated in about 11,000 patients and 31 tumor types. A general heterogeneity in the mutation frequencies was observed, mostly depending on tumor type. Despite the fact that we could not establish them as cancer drivers, INTS7 and INTS8 genes were highly mutated in specific cancers. A transcriptome analysis of paired (normal and tumor samples revealed that the transcription of INTS7, INTS8, and INTS13 is significantly altered in several cancers. Experimental validation performed on primary tumors confirmed these findings.

  7. Conceptual Combination During Sentence Comprehension

    Science.gov (United States)

    Swinney, David; Love, Tracy; Walenski, Matthew; Smith, Edward E.

    2008-01-01

    This experiment examined the time course of integration of modifier-noun (conceptual) combinations during auditory sentence comprehension using cross-modal lexical priming. The study revealed that during ongoing comprehension, there is initial activation of features of the noun prior to activation of (emergent) features of the entire conceptual combination. These results support compositionality in conceptual combination; that is, they indicate that features of the individual words constituting a conceptual combination are activated prior to combination of the words into a new concept. PMID:17576278

  8. Transcriptional repression of BODENLOS by HD-ZIP transcription factor HB5 in Arabidopsis thaliana.

    NARCIS (Netherlands)

    Smet, De I.; Lau, S.; Ehrismann, J.S.; Axiotis, I.; Kolb, M.; Kientz, M.; Weijers, D.; Jürgens, G.

    2013-01-01

    In Arabidopsis thaliana, the phytohormone auxin is an important patterning agent during embryogenesis and post-embryonic development, exerting effects through transcriptional regulation. The main determinants of the transcriptional auxin response machinery are AUXIN RESPONSE FACTOR (ARF)

  9. Improving participant comprehension in the informed consent process.

    Science.gov (United States)

    Cohn, Elizabeth; Larson, Elaine

    2007-01-01

    To critically analyze studies published within the past decade about participants' comprehension of informed consent in clinical research and to identify promising intervention strategies. Integrative review of literature. The Cumulative Index of Nursing and Allied Health Literature (CINAHL), PubMed, and the Cochrane Database of Systematic Reviews and Cochrane Central Register of Controlled Trials were searched. Inclusion criteria included studies (a) published between January 1, 1996 and January 1, 2007, (b) designed as descriptive or interventional studies of comprehension of informed consent for clinical research, (c) conducted in nonpsychiatric adult populations who were either patients or volunteer participants, (d) written in English, and (e) published in peer-reviewed journals. Of the 980 studies identified, 319 abstracts were screened, 154 studies were reviewed, and 23 met the inclusion criteria. Thirteen studies (57%) were descriptive, and 10 (43%) were interventional. Interventions tested included simplified written consent documents, multimedia approaches, and the use of a trained professional (consent educator) to assist in the consent process. Collectively, no single intervention strategy was consistently associated with improved comprehension. Studies also varied in regard to the definition of comprehension and the tools used to measure it. Despite increasing regulatory scrutiny, deficiencies still exist in participant comprehension of the research in which they participate, as well as differences in how comprehension is measured and assessed. No single intervention was identified as consistently successful for improving participant comprehension, and results indicated that any successful consent process should at a minimum include various communication modes and is likely to require one-to-one interaction with someone knowledgeable about the study.

  10. Comprehensive dictionary of electrical engineering

    CERN Document Server

    Laplante, Philip A

    1998-01-01

    The Comprehensive Dictionary of Electrical Engineering is a complete lexicon covering all the fields of electrical engineering.Areas examined include:applied electrical engineeringmicrowave engineeringcontrol engineeringpower engineeringdigital systems engineeringdevice electronicsand much more! The book provides workable definitions for practicing engineers, serves as a reference and research tool for students, and offers practical information for scientists and engineers in other disciplines.

  11. Children's Comprehension of Live Theatre.

    Science.gov (United States)

    Klein, Jeanne; Fitch, Marguerite

    Two studies investigate the way in which children make sense of a play and the visual, aural, and psychological components of theatre which contribute to this comprehension. In the first study, 32 fifth graders saw "Don Quixote of La Mancha." In the second study, 45 third graders saw "Monkey, Monkey" (about the Chinese Monkey King). The day after…

  12. Listening Comprehension: Approach, Design, Procedure.

    Science.gov (United States)

    Richards, Jack C.

    1983-01-01

    Three dimensions in the teaching of listening comprehension are outlined: (1) a theory is presented that takes account of the cognitive processes used (approach); (2) listeners' needs are analyzed and a taxonomy of microskills and objectives for teaching them are proposed (design); and (3) classroom exercises and activities are suggested…

  13. Comprehensive School Alienation Program, Guidelines.

    Science.gov (United States)

    Hawaii State Dept. of Education, Honolulu. Office of Instructional Services.

    This document presents guidelines developed by the Hawaii State Department of Education's Comprehensive School Alienation Program to consolidate and strengthen the delivery of services to alienated students. It is intended to assist district staff, school administrators, and project personnel in planning and implementing program activities and…

  14. A Comprehensive General Chemistry Demonstration

    Science.gov (United States)

    Sweeder, Ryan D.; Jeffery, Kathleen A.

    2013-01-01

    This article describes the use of a comprehensive demonstration suitable for a high school or first-year undergraduate introductory chemistry class. The demonstration involves placing a burning candle in a container adjacent to a beaker containing a basic solution with indicator. After adding a lid, the candle will extinguish and the produced…

  15. Electroconvulsive Therapy: A Comprehensive Assessment

    Directory of Open Access Journals (Sweden)

    Tayfun Zeren

    2003-08-01

    Full Text Available Electroconvulsive therapy (ECT is one of the most important discoveries of psychiatric treatments. This article comprehensively assesses historical progress, mechanism of actions, practical methods, indications, side effects, complications, drug interactions of ECT and attitudes towards ECT. [Archives Medical Review Journal 2003; 12(4.000: 340-377

  16. Innovation Learning in Comprehensive Education?

    Science.gov (United States)

    Lindfors, Eila; Hilmola, Antti

    2016-01-01

    The goal of this article is to clarify the concept of innovation and by presenting a research on the basic education outcome assessment data from an innovation learning perspective, answer to a question: Do students learn innovation in comprehensive education? The empirical information in this research is based on data collected in the national…

  17. Prediction during natural language comprehension

    NARCIS (Netherlands)

    Willems, R.M.; Frank, S.L.; Nijhof, A.D.; Hagoort, P.; Bosch, A.P.J. van den

    2016-01-01

    The notion of prediction is studied in cognitive neuroscience with increasing intensity. We investigated the neural basis of 2 distinct aspects of word prediction, derived from information theory, during story comprehension. We assessed the effect of entropy of next-word probability distributions as

  18. Comprehensive School Safety Initiative Report

    Science.gov (United States)

    National Institute of Justice, 2014

    2014-01-01

    The National Institute of Justice (NIJ) developed the Comprehensive School Safety Initiative in consultation with federal partners and Congress. It is a research-focused initiative designed to increase the safety of schools nationwide through the development of knowledge regarding the most effective and sustainable school safety interventions and…

  19. Glosses, Comprehension, and Strategy Use

    Science.gov (United States)

    Ko, Myong Hee

    2005-01-01

    This study, using both qualitative and quantitative measures, investigates how different types of gloss conditions affect Korean college students' reading comprehension. One hundred and six undergraduates at a university in Korea participated in the study. Twelve were assigned to think aloud, and the rest (ninety-four) took part in the main study…

  20. Constraint Programming for Context Comprehension

    DEFF Research Database (Denmark)

    Christiansen, Henning

    2014-01-01

    A close similarity is demonstrated between context comprehension, such as discourse analysis, and constraint programming. The constraint store takes the role of a growing knowledge base learned throughout the discourse, and a suitable con- straint solver does the job of incorporating new pieces...

  1. Neuroimaging Evidence of Comprehension Monitoring

    Directory of Open Access Journals (Sweden)

    Linda Baker

    2014-04-01

    Full Text Available The purpose of this article is to synthesize the emerging neuroimaging literature that reveals how the brain responds when readers and listeners encounter texts that demand monitoring of their ongoing comprehension processes. Much of this research has been undertaken by cognitive scientists who do not frame their work in metacognitive terms, and therefore it is less likely to be familiar to psychologists who study metacognition in educational contexts. The important role of metacognition in the development and use of academic skills is widely recognized. Metacognition is typically defined as the awareness and control of one's own cognitive processes. In the domain of reading, the most important metacognitive skill is comprehension monitoring, the evaluation and regulation of comprehension. Readers who monitor their understanding realize when they have encountered difficulty making sense of the text, and they apply error correction procedures to attempt to resolve the difficulty. Metacognition depends on executive control skills that continue to develop into early adulthood, in parallel with the maturation of the executive control regions of the prefrontal cortex. Functional magnetic resonance imaging (fMRI and event-related potentials (ERP have been used for some time to study neural correlates of basic reading processes such as word identification, but it is only within recent years that researchers have turned to the higher-level processes of text comprehension. The article describes illustrative studies that reveal changes in neural activity when adults apply lexical, syntactic, or semantic standards to evaluate their understanding.

  2. Indexical Hybrid Tense Logic

    DEFF Research Database (Denmark)

    Blackburn, Patrick Rowan; Jørgensen, Klaus Frovin

    2012-01-01

    In this paper we explore the logic of now, yesterday, today and tomorrow by combining the semantic approach to indexicality pioneered by Hans Kamp [9] and refined by David Kaplan [10] with hybrid tense logic. We first introduce a special now nominal (our @now corresponds to Kamp’s original now...... operator N) and prove completeness results for both logical and contextual validity. We then add propositional constants to handle yesterday, today and tomorrow; our system correctly treats sentences like “Niels will die yesterday” as contextually unsatisfiable. Building on our completeness results for now......, we prove completeness for the richer language, again for both logical and contextual validity....

  3. Heart rate index

    DEFF Research Database (Denmark)

    Haedersdal, C; Pedersen, F H; Svendsen, J H

    1992-01-01

    after the myocardial infarction. A significant correlation (Spearman's correlation coefficient rs, p less than 0.05) was found between LVEF at rest and the following variables assessed at exercise test: 1) the heart rate at rest, 2) rise in heart rate, 3) ratio between maximal heart rate and heart rate...... at rest, 4) rise in systolic blood pressure, 5) rate pressure product at rest, 6) rise in rate pressure product, 7) ratio (rHR) between maximal rate pressure product and rate pressure product at rest, 8) total exercise time. The heart rate was corrected for effects caused by age (heart index (HR...

  4. Refractive index based measurements

    DEFF Research Database (Denmark)

    2014-01-01

    In a method for performing a refractive index based measurement of a property of a fluid such as chemical composition or temperature by observing an apparent angular shift in an interference fringe pattern produced by back or forward scattering interferometry, ambiguities in the measurement caused...... by the apparent shift being consistent with one of a number of numerical possibilities for the real shift which differ by 2n are resolved by combining measurements performed on the same sample using light paths therethrough of differing lengths....

  5. Overlapping transcription structure of human cytomegalovirus

    Indian Academy of Sciences (India)

    Transcription of human cytomegalovirus UL/b′ region has been studied extensively for some genes. In this study, transcripts of the UL140 and UL141, two of the UL/b′ genes, were identified in late RNAs of three HCMV isolates using Northern blot hybridization, cDNA library screening and RACE-PCR. At least three ...

  6. Overlapping transcription structure of human cytomegalovirus ...

    Indian Academy of Sciences (India)

    2013-01-21

    Jan 21, 2013 ... Transcription of human cytomegalovirus UL/b′ region has been studied extensively for some genes. In this study, transcripts of the UL140 and UL141, two of the UL/b′ genes, were identified in late RNAs of three HCMV isolates using Northern blot hybridization, cDNA library screening and RACE-PCR.

  7. Transcription of Byzantine Chant - Problems, Possibilities, Formats

    DEFF Research Database (Denmark)

    Troelsgård, Christian

    2007-01-01

    Discusses the problems and possibilities for transsription of Byzantine chant on the basis of medieval musical manuscripts. A relatively 'neutral' style of transcription is suggested for musicological purposes.......Discusses the problems and possibilities for transsription of Byzantine chant on the basis of medieval musical manuscripts. A relatively 'neutral' style of transcription is suggested for musicological purposes....

  8. Regulation of transcription in hyperthermophilic archaea

    NARCIS (Netherlands)

    Brinkman, A.B.

    2002-01-01

    The aim of the research presented here was to insight in the mechanisms by which transcription in hyperthermophilic archaea is regulated. To accomplish this, we have aimed (I) to identify transcriptional regulatory proteins from hyperthermophilic archaea, (II) to characterize these

  9. 45 CFR 99.27 - Official transcript.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Official transcript. 99.27 Section 99.27 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION PROCEDURE FOR HEARINGS FOR THE CHILD CARE AND DEVELOPMENT FUND Hearing Procedures § 99.27 Official transcript. The Department will...

  10. RNA polymerase II collision interrupts convergent transcription

    DEFF Research Database (Denmark)

    Hobson, David J; Wei, Wu; Steinmetz, Lars M

    2012-01-01

    Antisense noncoding transcripts, genes-within-genes, and convergent gene pairs are prevalent among eukaryotes. The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head. Here we use a combination of biochemical...

  11. Transcription regulation by the Mediator complex.

    Science.gov (United States)

    Soutourina, Julie

    2018-04-01

    Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.

  12. β-adrenergic receptor-dependent alterations in murine cardiac transcript expression are differentially regulated by gefitinib in vivo.

    Directory of Open Access Journals (Sweden)

    Jennifer A Talarico

    Full Text Available β-adrenergic receptor (βAR-mediated transactivation of epidermal growth factor receptor (EGFR has been shown to promote cardioprotection in a mouse model of heart failure and we recently showed that this mechanism leads to enhanced cell survival in part via regulation of apoptotic transcript expression in isolated primary rat neonatal cardiomyocytes. Thus, we hypothesized that this process could regulate cardiac transcript expression in vivo. To comprehensively assess cardiac transcript alterations in response to acute βAR-dependent EGFR transactivation, we performed whole transcriptome analysis of hearts from C57BL/6 mice given i.p. injections of the βAR agonist isoproterenol in the presence or absence of the EGFR antagonist gefitinib for 1 hour. Total cardiac RNA from each treatment group underwent transcriptome analysis, revealing a substantial number of transcripts regulated by each treatment. Gefitinib alone significantly altered the expression of 405 transcripts, while isoproterenol either alone or in conjunction with gefitinib significantly altered 493 and 698 distinct transcripts, respectively. Further statistical analysis was performed, confirming 473 transcripts whose regulation by isoproterenol were significantly altered by gefitinib (isoproterenol-induced up/downregulation antagonized/promoted by gefinitib, including several known to be involved in the regulation of numerous processes including cell death and survival. Thus, βAR-dependent regulation of cardiac transcript expression in vivo can be modulated by the EGFR antagonist gefitinib.

  13. Subunit architecture and functional modular rearrangements of the transcriptional mediator complex.

    Science.gov (United States)

    Tsai, Kuang-Lei; Tomomori-Sato, Chieri; Sato, Shigeo; Conaway, Ronald C; Conaway, Joan W; Asturias, Francisco J

    2014-06-05

    The multisubunit Mediator, comprising ∼30 distinct proteins, plays an essential role in gene expression regulation by acting as a bridge between DNA-binding transcription factors and the RNA polymerase II (RNAPII) transcription machinery. Efforts to uncover the Mediator mechanism have been hindered by a poor understanding of its structure, subunit organization, and conformational rearrangements. By overcoming biochemical and image analysis hurdles, we obtained accurate EM structures of yeast and human Mediators. Subunit localization experiments, docking of partial X-ray structures, and biochemical analyses resulted in comprehensive mapping of yeast Mediator subunits and a complete reinterpretation of our previous Mediator organization model. Large-scale Mediator rearrangements depend on changes at the interfaces between previously described Mediator modules, which appear to be facilitated by factors conducive to transcription initiation. Conservation across eukaryotes of Mediator structure, subunit organization, and RNA polymerase II interaction suggest conservation of fundamental aspects of the Mediator mechanism. Copyright © 2014 Elsevier Inc. All rights reserved.

  14. Discovery of a Regulatory Motif for Human Satellite DNA Transcription in Response to BATF2 Overexpression.

    Science.gov (United States)

    Bai, Xuejia; Huang, Wenqiu; Zhang, Chenguang; Niu, Jing; Ding, Wei

    2016-03-01

    One of the basic leucine zipper transcription factors, BATF2, has been found to suppress cancer growth and migration. However, little is known about the genes downstream of BATF2. HeLa cells were stably transfected with BATF2, then chromatin immunoprecipitation-sequencing was employed to identify the DNA motifs responsive to BATF2. Comprehensive bioinformatics analyses indicated that the most significant motif discovered as TTCCATT[CT]GATTCCATTC[AG]AT was primarily distributed among the chromosome centromere regions and mostly within human type II satellite DNA. Such motifs were able to prime the transcription of type II satellite DNA in a directional and asymmetrical manner. Consistently, satellite II transcription was up-regulated in BATF2-overexpressing cells. The present study provides insight into understanding the role of BATF2 in tumours and the importance of satellite DNA in the maintenance of genomic stability. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  15. A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray

    DEFF Research Database (Denmark)

    Stolc, Viktor; Li, Lei; Wang, Xiangfeng

    2005-01-01

    As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map...... transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference...... gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models...

  16. Transcriptional profiling of putative human epithelial stem cells

    Directory of Open Access Journals (Sweden)

    Koçer Salih S

    2008-07-01

    Full Text Available Abstract Background Human interfollicular epidermis is sustained by the proliferation of stem cells and their progeny, transient amplifying cells. Molecular characterization of these two cell populations is essential for better understanding of self renewal, differentiation and mechanisms of skin pathogenesis. The purpose of this study was to obtain gene expression profiles of alpha 6+/MHCI+, transient amplifying cells and alpha 6+/MHCI-, putative stem cells, and to compare them with existing data bases of gene expression profiles of hair follicle stem cells. The expression of Major Histocompatibility Complex (MHC class I, previously shown to be absent in stem cells in several tissues, and alpha 6 integrin were used to isolate MHCI positive basal cells, and MHCI low/negative basal cells. Results Transcriptional profiles of the two cell populations were determined and comparisons made with published data for hair follicle stem cell gene expression profiles. We demonstrate that presumptive interfollicular stem cells, alpha 6+/MHCI- cells, are enriched in messenger RNAs encoding surface receptors, cell adhesion molecules, extracellular matrix proteins, transcripts encoding members of IFN-alpha family proteins and components of IFN signaling, but contain lower levels of transcripts encoding proteins which take part in energy metabolism, cell cycle, ribosome biosynthesis, splicing, protein translation, degradation, DNA replication, repair, and chromosome remodeling. Furthermore, our data indicate that the cell signaling pathways Notch1 and NF-κB are downregulated/inhibited in MHC negative basal cells. Conclusion This study demonstrates that alpha 6+/MHCI- cells have additional characteristics attributed to stem cells. Moreover, the transcription profile of alpha 6+/MHCI- cells shows similarities to transcription profiles of mouse hair follicle bulge cells known to be enriched for stem cells. Collectively, our data suggests that alpha 6+/MHCI- cells

  17. A data discovery index for the social sciences.

    Science.gov (United States)

    Krämer, Thomas; Klas, Claus-Peter; Hausstein, Brigitte

    2018-04-10

    This paper describes a novel search index for social and economic research data, one that enables users to search up-to-date references for data holdings in these disciplines. The index can be used for comparative analysis of publication of datasets in different areas of social science. The core of the index is the da|ra registration agency's database for social and economic data, which contains high-quality searchable metadata from registered data publishers. Research data's metadata records are harvested from data providers around the world and included in the index. In this paper, we describe the currently available indices on social science datasets and their shortcomings. Next, we describe the motivation behind and the purpose for the data discovery index as a dedicated and curated platform for finding social science research data and gesisDataSearch, its user interface. Further, we explain the harvesting, filtering and indexing procedure and give usage instructions for the dataset index. Lastly, we show that the index is currently the most comprehensive and most accessible collection of social science data descriptions available.

  18. Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation

    DEFF Research Database (Denmark)

    Hakim-Weber, Robab; Krogsdam, Anne-M; Jørgensen, Claus

    2011-01-01

    Although many molecular regulators of adipogenesis have been identified a comprehensive catalogue of components is still missing. Recent studies showed that the retinoblastoma protein (pRb) was expressed in the cell cycle and late cellular differentiation phase during adipogenesis. To investigate...... this dual role of pRb in the early and late stages of adipogenesis we used microarrays to perform a comprehensive systems-level analysis of the common transcriptional program of the classic 3T3-L1 preadipocyte cell line, wild-type mouse embryonic fibroblasts (MEFs), and retinoblastoma gene-deficient MEFs...... of experimental data and computational analyses pinpointed a feedback-loop between Pparg and Foxo1.To analyze the effects of the retinoblastoma protein at the transcriptional level we chose a perturbated system (Rb-/- MEFs) for comparison to the transcriptional program of wild-type MEFs. Gene ontology analysis...

  19. Study on Evaluation Index System of Green mine construction

    Science.gov (United States)

    Li, xin; Yang, JunJie; Yan, Hongcai; Cao, Hongjun

    2017-11-01

    Green mine is a new and science comprehensive construction mode of mine, which runs the concept of green development through the whole process of mineral resources development and utilization, promotes the transformation and upgrading of mineral enterprises and achieves the healthy and sustainable development of mining industry. This paper is based on “the basic conditions of national green mine”, combined with the current situation of green mine construction, constructing green mine construction evaluation index system which is divided into five areas, including management, comprehensive utilization of mineral resources. technological innovation. ecological environment and cultural construction.

  20. Sperm mRNA transcripts are indicators of sub-chronic low dose testicular injury in the Fischer 344 rat.

    Directory of Open Access Journals (Sweden)

    Sara E Pacheco

    Full Text Available Current human reproductive risk assessment methods rely on semen and serum hormone analyses, which are not easily comparable to the histopathological endpoints and mating studies used in animal testing. Because of these limitations, there is a need to develop universal evaluations that reliably reflect male reproductive function. We hypothesized that toxicant-induced testicular injury can be detected in sperm using mRNA transcripts as indicators of insult. To test this, we exposed adult male Fischer 344 rats to low doses of model testicular toxicants and classically characterized the testicular injury while simultaneously evaluating sperm mRNA transcripts from the same animals. Overall, this study aimed to: 1 identify sperm transcripts altered after exposure to the model testicular toxicant, 2,5-hexanedione (HD using microarrays; 2 expand on the HD-induced transcript changes in a comprehensive time course experiment using qRT-PCR arrays; and 3 test these injury indicators after exposure to another model testicular toxicant, carbendazim (CBZ. Microarray analysis of HD-treated adult Fischer 344 rats identified 128 altered sperm mRNA transcripts when compared to control using linear models of microarray analysis (q<0.05. All transcript alterations disappeared after 3 months of post-exposure recovery. In the time course experiment, time-dependent alterations were observed for 12 candidate transcripts selected from the microarray data based upon fold change and biological relevance, and 8 of these transcripts remained significantly altered after the 3-month recovery period (p<0.05. In the last experiment, 8 candidate transcripts changed after exposure to CBZ (p<0.05. The two testicular toxicants produced distinct molecular signatures with only 4 overlapping transcripts between them, each occurring in opposite directions. Overall, these results suggest that sperm mRNA transcripts are indicators of low dose toxicant-induced testicular injury in the rat.

  1. Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice

    Directory of Open Access Journals (Sweden)

    Shuchi eSmita

    2015-12-01

    Full Text Available MYB transcription factor (TF is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental and environmental cues is a major challenge due to the complex interactions between the genetic elements. Correlation analyses are useful to unravel co-regulated gene pairs governing biological process as well as identification of new candidate hub genes in response to these complex processes. High throughput expression profiling data are highly useful for construction of co-expression networks. In the present study, we utilized transcriptome data for comprehensive regulatory network studies of MYB TFs by top down and guide gene approaches. More than 50% of OsMYBs were strongly correlated under fifty experimental conditions with 51 hub genes via top down approach. Further, clusters were identified using Markov Clustering (MCL. To maximize the clustering performance, parameter evaluation of the MCL inflation score (I was performed in terms of enriched GO categories by measuring F-score. Comparison of co-expressed cluster and clads analyzed from phylogenetic analysis signifies their evolutionarily conserved co-regulatory role. We utilized compendium of known interaction and biological role with Gene Ontology enrichment analysis to hypothesize function of coexpressed OsMYBs. In the other part, the transcriptional regulatory network analysis by guide gene approach revealed 40 putative targets of 26 OsMYB TF hubs with high correlation value utilizing 815 microarray data. The putative targets with MYB-binding cis-elements enrichment in their promoter region, functional co-occurrence as well as nuclear localization supports our finding. Specially, enrichment of MYB binding regions involved in drought-inducibility implying their regulatory role in drought

  2. 2016 Traffic Safety Culture Index

    Science.gov (United States)

    ... Newsroom SEARCH Driver Behavior & Performance 2016 Traffic Safety Culture Index This report presents the results of our annual Traffic Safety Culture Index survey, providing data on the attitudes and ...

  3. 2001 Environmental Sustainability Index (ESI)

    Data.gov (United States)

    National Aeronautics and Space Administration — The 2001 Environmental Sustainability Index (ESI) utilizes a refined methodology based on the 2000 Pilot ESI effort, to construct an index covering 122 countries...

  4. Research on fuzzy comprehensive assessment method of nuclear power plant safety culture

    International Nuclear Information System (INIS)

    Xiang Yuanyuan; Chen Xukun; Xu Rongbin

    2012-01-01

    Considering the traits of safety culture in nuclear plant, 38 safety culture assessment indexes are established from 4 aspects such as safety values, safety institution, safety behavior and safety sub- stances. Based on it, a comprehensive assessment method for nuclear power plant safety culture is constructed by using AHP (Analytic Hierarchy Process) approach and fuzzy mathematics. The comprehensive assessment method has the quality of high precision and high operability, which can support the decision making of safety culture development. (authors)

  5. Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima

    Directory of Open Access Journals (Sweden)

    Dmitry A Rodionov

    2013-08-01

    Full Text Available Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales.

  6. RNA binding specificity of Ebola virus transcription factor VP30.

    Science.gov (United States)

    Schlereth, Julia; Grünweller, Arnold; Biedenkopf, Nadine; Becker, Stephan; Hartmann, Roland K

    2016-09-01

    The transcription factor VP30 of the non-segmented RNA negative strand Ebola virus balances viral transcription and replication. Here, we comprehensively studied RNA binding by VP30. Using a novel VP30:RNA electrophoretic mobility shift assay, we tested truncated variants of 2 potential natural RNA substrates of VP30 - the genomic Ebola viral 3'-leader region and its complementary antigenomic counterpart (each ∼155 nt in length) - and a series of other non-viral RNAs. Based on oligonucleotide interference, the major VP30 binding region on the genomic 3'-leader substrate was assigned to the internal expanded single-stranded region (∼ nt 125-80). Best binding to VP30 was obtained with ssRNAs of optimally ∼ 40 nt and mixed base composition; underrepresentation of purines or pyrimidines was tolerated, but homopolymeric sequences impaired binding. A stem-loop structure, particularly at the 3'-end or positioned internally, supports stable binding to VP30. In contrast, dsRNA or RNAs exposing large internal loops flanked by entirely helical arms on both sides are not bound. Introduction of a 5´-Cap(0) structure impaired VP30 binding. Also, ssDNAs bind substantially weaker than isosequential ssRNAs and heparin competes with RNA for binding to VP30, indicating that ribose 2'-hydroxyls and electrostatic contacts of the phosphate groups contribute to the formation of VP30:RNA complexes. Our results indicate a rather relaxed RNA binding specificity of filoviral VP30, which largely differs from that of the functionally related transcription factor of the Paramyxoviridae which binds to ssRNAs as short as 13 nt with a preference for oligo(A) sequences.

  7. Life quality index revisited

    DEFF Research Database (Denmark)

    Ditlevsen, Ove Dalager

    2004-01-01

    The derivation of the life quality index (LQI) is revisited for a revision. This revision takes into account the unpaid but necessary work time needed to stay alive in clean and healthy conditions to be fit for effective wealth producing work and to enjoyable free time. Dimension analysis...... at birth should not vary between countries. Finally the distributional assumptions are relaxed as compared to the assumptions made in an earlier work by the author. These assumptions concern the calculation of the life expectancy change due to the removal of an accident source. Moreover a simple public...... consistency problems with the standard power function expression of the LQI are pointed out. It is emphasized that the combination coefficient in the convex differential combination between the relative differential of the gross domestic product per capita and the relative differential of the expected life...

  8. Automated Water Extraction Index

    DEFF Research Database (Denmark)

    Feyisa, Gudina Legese; Meilby, Henrik; Fensholt, Rasmus

    2014-01-01

    Classifying surface cover types and analyzing changes are among the most common applications of remote sensing. One of the most basic classification tasks is to distinguish water bodies from dry land surfaces. Landsat imagery is among the most widely used sources of data in remote sensing of water...... resources; and although several techniques of surface water extraction using Landsat data are described in the literature, their application is constrained by low accuracy in various situations. Besides, with the use of techniques such as single band thresholding and two-band indices, identifying...... an appropriate threshold yielding the highest possible accuracy is a challenging and time consuming task, as threshold values vary with location and time of image acquisition. The purpose of this study was therefore to devise an index that consistently improves water extraction accuracy in the presence...

  9. Refractive index based measurements

    DEFF Research Database (Denmark)

    2014-01-01

    A refractive index based measurement of a property of a fluid is measured in an apparatus comprising a variable wavelength coherent light source (16), a sample chamber (12), a wavelength controller (24), a light sensor (20), a data recorder (26) and a computation apparatus (28), by - directing...... coherent light having a wavelength along an input light path, - producing scattering of said light from each of a plurality of interfaces within said apparatus including interfaces between said fluid and a surface bounding said fluid, said scattering producing an interference pattern formed by said...... scattered light, - cyclically varying the wavelength of said light in said input light path over a 1 nm to 20nm wide range of wavelengths a rate of from 10Hz to 50 KHz, - recording variation of intensity of the interfering light with change in wavelength of the light at an angle of observation...

  10. Indexing contamination surveys

    International Nuclear Information System (INIS)

    Brown, R.L.

    1998-01-01

    The responsibility for safely managing the Tank Farms at Hanford belongs to Lockheed Martin Hanford Corporation which is part of the six company Project Hanford Management Team led by Fluor Daniel Hanford, Inc.. These Tank Farm Facilities contain numerous outdoor contamination areas which are surveyed at a periodicity consistent with the potential radiological conditions, occupancy, and risk of changes in radiological conditions. This document describes the survey documentation and data tracking method devised to track the results of contamination surveys this process is referred to as indexing. The indexing process takes a representative data set as an indicator for the contamination status of the facility. The data are further manipulated into a single value that can be tracked and trended using standard statistical methodology. To report meaningful data, the routine contamination surveys must be performed in a manner that allows the survey method and the data collection process to be recreated. Three key criteria are necessary to accomplish this goal: Accurate maps, consistent documentation, and consistent consolidation of data meeting these criteria provides data of sufficient quality to be tracked. Tracking of survey data is accomplished by converting the individual survey results into a weighted value, corrected for the actual number of survey points. This information can be compared over time using standard statistical analysis to identify trends. At the Tank Farms, the need to track and trend the facility's radiological status presents unique challenges. Many of these Tank Farm facilities date back to the second world war. The Tank Farm Facilities are exposed to weather extremes, plant and animal intrusion, as well as all of the normal challenges associated with handling radiological waste streams. Routine radiological surveys did not provide a radiological status adequate for continuing comparisons

  11. A comprehensive nuclear test ban

    International Nuclear Information System (INIS)

    1985-01-01

    The conclusion of a comprehensive nuclear test ban is of critical importance for the future of arms limitation and disarmament. As the 1980 report of the Secretary-General concluded, a comprehensive nuclear test ban is regarded as the first and most urgent step towards the cessation of the nuclear arms race and, in particular, of its qualitative aspects. It could serve as an important measure for the non-proliferation of nuclear weapons, both vertical and horizontal. It would have a major arms limitation impact in that it would make it difficult, if not impossible, to develop new designs of nuclear weapons and would also place constraints on the modification of existing weapon designs. The permanent cessation of all nuclear-weapon tests has long been sought by the world community and its achievement would be an event of great international significance

  12. Comprehensive numerical modelling of tokamaks

    International Nuclear Information System (INIS)

    Cohen, R.H.; Cohen, B.I.; Dubois, P.F.

    1991-01-01

    We outline a plan for the development of a comprehensive numerical model of tokamaks. The model would consist of a suite of independent, communicating packages describing the various aspects of tokamak performance (core and edge transport coefficients and profiles, heating, fueling, magnetic configuration, etc.) as well as extensive diagnostics. These codes, which may run on different computers, would be flexibly linked by a user-friendly shell which would allow run-time specification of packages and generation of pre- and post-processing functions, including workstation-based visualization of output. One package in particular, the calculation of core transport coefficients via gyrokinetic particle simulation, will become practical on the scale required for comprehensive modelling only with the advent of teraFLOP computers. Incremental effort at LLNL would be focused on gyrokinetic simulation and development of the shell

  13. Emergency preparedness: a comprehensive plan

    International Nuclear Information System (INIS)

    Wilson, R.H.

    1975-01-01

    The Atlantic Richfield Hanford Company (ARHCO) has developed comprehensive plans for coping with emergencies ranging from criticality to civil disturbance. A unique notification system provides for immediate contact with key personnel by using a central communications center, crash alarm warning networks, and a continuing telephone cascade notification system. There is also the capability of immediately contacting other contractor key personnel. Certain jobs have been predetermined as necessary for coping with an emergency. An emergency staff consisting of responsible management, with alternates, has been preselected to automatically fill these jobs when notified. Control centers for headquarters and ''field'' are established with telephone and radio communication capabilities and are also supplied with some source materials to assist initiating plans for containing an emergency for recovery. A comprehensive emergency procedures manual has been developed, which contains information of company-wide application and procedures for specific facilities covering almost all accident situations

  14. Evaluation of comprehensive environmental effect about coastal zone development activities in Liaoning Province and management advice.

    Science.gov (United States)

    Wang, Wei-Wei; Cai, Yue-Yin; Sun, Yong-Guang; Ma, Hong-Wei

    2015-07-01

    Using spatial analysis function of Arcgis software, the present study investigated the building environment impact evaluation index system of coastal development in Liaoning Province. The factors of it included of current state of environmental quality, environmental impact of marine development and marine environmental disaster. Weighted factor analysis and comprehensive index method were utilized. At the end, comprehensive environment effect of coastal development in Liaoning Province were evaluated successfully. The result showed that the environmental effect of development activity were most serious, along the Zhao Jiatun coast in north of Zhimao bay and coast of Mianhua island in Dalian bay.

  15. Colon cancer associated transcripts in human cancers.

    Science.gov (United States)

    Chen, Yincong; Xie, Haibiao; Gao, Qunjun; Zhan, Hengji; Xiao, Huizhong; Zou, Yifan; Zhang, Fuyou; Liu, Yuchen; Li, Jianfa

    2017-10-01

    Long non-coding RNAs serve as important regulators in complicated cellular activities, including cell differentiation, proliferation and death. Dysregulation of long non-coding RNAs occurs in the formation and progression of cancers. The family of colon cancer associated transcripts, long non-coding RNAs colon cancer associated transcript-1 and colon cancer associated transcript-2 are known as oncogenes involved in various cancers. Colon cancer associated transcript-1 is a novel lncRNA located in 8q24.2, and colon cancer associated transcript-2 maps to the 8q24.21 region encompassing rs6983267. Colon cancer associated transcripts have close associations with clinical characteristics, such as lymph node metastasis, high TNM stage and short overall survival. Knockdown of them can reverse the malignant phenotypes of cancer cells, including proliferation, migration, invasion and apoptosis. Moreover, they can increase the expression level of c-MYC and oncogenic microRNAs via activating a series of complex mechanisms. In brief, the family of colon cancer associated transcripts may serve as potential biomarkers or therapeutic targets for human cancers. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  16. Helping Students Develop Listening Comprehension

    Directory of Open Access Journals (Sweden)

    Cárdenas Beltrán Melba Libia

    2000-08-01

    Full Text Available Listening practice is often neglected or handled inappropriately in the teachinglearning process. This poses problem because listening is an integral part of conversations. Oral skills without equally welldeveloped listening abilities are of little practical value. In this article, I will take a look at issues related to the area of listening that may be considered when guiding students toward developing listening comprehension.

  17. Optimising Comprehensibility in Interlingual Translation

    DEFF Research Database (Denmark)

    Nisbeth Jensen, Matilde

    2015-01-01

    The increasing demand for citizen engagement in areas traditionally belonging exclusively to experts, such as health, law and technology has given rise to the necessity of making expert knowledge available to the general public through genres such as instruction manuals for consumer goods, patien...... the functional text type of Patient Information Leaflet. Finally, the usefulness of applying the principles of Plain Language and intralingual translation for optimising comprehensibility in interlingual translation is discussed....

  18. Cardiac rehabilitation: a comprehensive review

    OpenAIRE

    Lear, Scott A; Ignaszewski, Andrew

    2001-01-01

    Abstract Cardiac rehabilitation (CR) is a commonly used treatment for men and women with cardiovascular disease. To date, no single study has conclusively demonstrated a comprehensive benefit of CR. Numerous individual studies, however, have demonstrated beneficial effects such as improved risk-factor profile, slower disease progression, decreased morbidity, and decreased mortality. This paper will review the evidence for the use of CR and discuss the implications and limitations of these stu...

  19. Alarm management a comprehensive guide

    CERN Document Server

    Hollifield, Bill R

    2011-01-01

    In this second edition, Alarm Management: A Comprehensive Guide, various problems of alarm systems are covered with precise guidance on how they come about and how to effectively correct them. It is written by individuals with vast experience in the different plants, processes, and environments requiring effective alarm management. The second edition is filled with good examples and explanations of procedures, with practical lists and tips on how one should proceed. It is based on hundreds of successful projects.

  20. Comprehensive asymmetric dark matter model

    OpenAIRE

    Lonsdale, Stephen J.; Volkas, Raymond R.

    2018-01-01

    Asymmetric dark matter (ADM) is motivated by the similar cosmological mass densities measured for ordinary and dark matter. We present a comprehensive theory for ADM that addresses the mass density similarity, going beyond the usual ADM explanations of similar number densities. It features an explicit matter-antimatter asymmetry generation mechanism, has one fully worked out thermal history and suggestions for other possibilities, and meets all phenomenological, cosmological and astrophysical...

  1. A comprehensive radiology information system

    International Nuclear Information System (INIS)

    Jost, R.G.

    1985-01-01

    DECrad version II was recently tested by members of the Radiology Information System Consortium (RISC) and was found to meet the specifications prepared by the consortium. It is a comprehensive tailorable system that can be interfaced to practically any HIS. This paper provides an overall view of the major functions of the system which include registration, scheduling, tracking, film library management, reporting, statistics, and teaching modules. The evolution of the specification and user experiences is reported

  2. Neuronal basis of speech comprehension.

    Science.gov (United States)

    Specht, Karsten

    2014-01-01

    Verbal communication does not rely only on the simple perception of auditory signals. It is rather a parallel and integrative processing of linguistic and non-linguistic information, involving temporal and frontal areas in particular. This review describes the inherent complexity of auditory speech comprehension from a functional-neuroanatomical perspective. The review is divided into two parts. In the first part, structural and functional asymmetry of language relevant structures will be discus. The second part of the review will discuss recent neuroimaging studies, which coherently demonstrate that speech comprehension processes rely on a hierarchical network involving the temporal, parietal, and frontal lobes. Further, the results support the dual-stream model for speech comprehension, with a dorsal stream for auditory-motor integration, and a ventral stream for extracting meaning but also the processing of sentences and narratives. Specific patterns of functional asymmetry between the left and right hemisphere can also be demonstrated. The review article concludes with a discussion on interactions between the dorsal and ventral streams, particularly the involvement of motor related areas in speech perception processes, and outlines some remaining unresolved issues. This article is part of a Special Issue entitled Human Auditory Neuroimaging. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Comprehensive treatment of generalized parodontitis.

    Science.gov (United States)

    Mdinaradze, N

    2006-06-01

    The complexity of pathogenesis of periodontitis makes the use of comprehensive treatment necessary. We observed 60 patients, 20 women and 40 men among them aged from 20 to 50. In the course of parodontitis, we determined the intensity of inflammatory-destructive changes (Pi) in the course of periodontitis, the degree of fang denudation, the depth of gum and parodontal recesses, degree of the teeth becoming loose; we conducted the microbiological study of the oral cavity microflora and drew up an antibiotic graph. We included laser therapy in the comprehensive treatment course of generalized parodontitis. We divided the patients into two groups. The patients of the first group were treated in two stages. We used peridex, composed of chlorhexidine for antiseptic treatment of oral cavity. We used a combined solution of sage, eucalyptus, camomile and calendula to irrigate the oral cavity. At the second stage we used ointment applications with the composition of 3% indometacin, heparin, vitamins, sea-buckthorn oil and antibiotics. In the course of comprehensive treatment of the patients of the II group we included laser therapy. Our interest in the laser beam, as in the means of parodontitis treatment was stimulated by a number of properties of the laser beam and namely, its anti-inflammatory, desensitizing and antibacterial action promotes intensifying the reparation processes and does not entail any complications. The mentioned method has produced the best therapeutic results and has resulted in the reduced treatment period.

  4. Superconducting Super Collider: Final environmental impact statement: Volume 2, Comment/response document: Summary and index

    International Nuclear Information System (INIS)

    1988-12-01

    This volume is divided into five parts as follows: Summary and Index; Letters submitted by commenters in response to the Draft Environmental Impact Statement (DEIS) from date of issue through October 17, 1988; Transcripts of testimony at the public hearings conducted by the DOE in the vicinity of each site alternative; Letters postmarked after October 17, 1988; and Comment responses to both the letters and the testimony. This summary and index is published as a guide to the reader in reviewing this document. The summary is of the approximately 7000 comments received by the DOE from a total of about 5700 commenters. It was prepared as a general reference and guide to the readers of this volume. The Index follows the summary. The first index is an alphabetical listing of commenters (of both letters and transcripts) and indicates the number each commenter was assigned. The commenter numbers guide the reader to DOE comment responses in Volume 2B which are in numerical order

  5. Comprehensive Transcriptome Profiling and Functional Analysis of the Frog (Bombina maxima) Immune System

    Science.gov (United States)

    Zhao, Feng; Yan, Chao; Wang, Xuan; Yang, Yang; Wang, Guangyin; Lee, Wenhui; Xiang, Yang; Zhang, Yun

    2014-01-01

    Amphibians occupy a key phylogenetic position in vertebrates and evolution of the immune system. But, the resources of its transcriptome or genome are still little now. Bombina maxima possess strong ability to survival in very harsh environment with a more mature immune system. We obtained a comprehensive transcriptome by RNA-sequencing technology. 14.3% of transcripts were identified to be skin-specific genes, most of which were not isolated from skin secretion in previous works or novel non-coding RNAs. 27.9% of transcripts were mapped into 242 predicted KEGG pathways and 6.16% of transcripts related to human disease and cancer. Of 39 448 transcripts with the coding sequence, at least 1501 transcripts (570 genes) related to the immune system process. The molecules of immune signalling pathway were almost presented, several transcripts with high expression in skin and stomach. Experiments showed that lipopolysaccharide or bacteria challenge stimulated pro-inflammatory cytokine production and activation of pro-inflammatory caspase-1. These frog's data can remarkably expand the existing genome or transcriptome resources of amphibians, especially immunity data. The entity of the data provides a valuable platform for further investigation on more detailed immune response in B. maxima and a comparative study with other amphibians. PMID:23942912

  6. Viva the h-index

    OpenAIRE

    Waaijers, Leo

    2011-01-01

    In their article 'The inconsistency of the h-index' Ludo Waltman and Nees Jan van Neck give three examples to demonstrate the inconsistency of the h-index. As will be explained, a little extension of their examples just illustrate the opposite, a stable feature of the h-index. For starting authors it, the h-index that is, focusses on the number of articles; for experienced authors its focus shifts towards the citation scores. This feature may be liked or not but does not make the h-index an i...

  7. Research on comprehensive decision-making of PV power station connecting system

    Science.gov (United States)

    Zhou, Erxiong; Xin, Chaoshan; Ma, Botao; Cheng, Kai

    2018-04-01

    In allusion to the incomplete indexes system and not making decision on the subjectivity and objectivity of PV power station connecting system, based on the combination of improved Analytic Hierarchy Process (AHP), Criteria Importance Through Intercriteria Correlation (CRITIC) as well as grey correlation degree analysis (GCDA) is comprehensively proposed to select the appropriate system connecting scheme of PV power station. Firstly, indexes of PV power station connecting system are divided the recursion order hierarchy and calculated subjective weight by the improved AHP. Then, CRITIC is adopted to determine the objective weight of each index through the comparison intensity and conflict between indexes. The last the improved GCDA is applied to screen the optimal scheme, so as to, from the subjective and objective angle, select the connecting system. Comprehensive decision of Xinjiang PV power station is conducted and reasonable analysis results are attained. The research results might provide scientific basis for investment decision.

  8. Genome-wide investigation of transcription factors provides insights into transcriptional regulation in Plutella xylostella.

    Science.gov (United States)

    Zhao, Qian; Ma, Dongna; Huang, Yuping; He, Weiyi; Li, Yiying; Vasseur, Liette; You, Minsheng

    2018-04-01

    Transcription factors (TFs), which play a vital role in regulating gene expression, are prevalent in all organisms and characterization of them may provide important clues for understanding regulation in vivo. The present study reports a genome-wide investigation of TFs in the diamondback moth, Plutella xylostella (L.), a worldwide pest of crucifers. A total of 940 TFs distributed among 133 families were identified. Phylogenetic analysis of insect species showed that some of these families were found to have expanded during the evolution of P. xylostella or Lepidoptera. RNA-seq analysis showed that some of the TF families, such as zinc fingers, homeobox, bZIP, bHLH, and MADF_DNA_bdg genes, were highly expressed in certain tissues including midgut, salivary glands, fat body, and hemocytes, with an obvious sex-biased expression pattern. In addition, a number of TFs showed significant differences in expression between insecticide susceptible and resistant strains, suggesting that these TFs play a role in regulating genes related to insecticide resistance. Finally, we identified an expansion of the HOX cluster in Lepidoptera, which might be related to Lepidoptera-specific evolution. Knockout of this cluster using CRISPR/Cas9 showed that the egg cannot hatch, indicating that this cluster may be related to egg development and maturation. This is the first comprehensive study on identifying and characterizing TFs in P. xylostella. Our results suggest that some TF families are expanded in the P. xylostella genome, and these TFs may have important biological roles in growth, development, sexual dimorphism, and resistance to insecticides. The present work provides a solid foundation for understanding regulation via TFs in P. xylostella and insights into the evolution of the P. xylostella genome.

  9. Transcriptional mapping of rabies virus in vivo

    International Nuclear Information System (INIS)

    Flamand, A.; Delagneau, J.F.

    1978-01-01

    Synthesis of the proteins of rabies virus was studied in hamster cell infected with uv-irradiated virus. The uv target size of genes L, N, M 1 , and M 2 was measured during primary transcription. Except for N, the target size of the remaining genes was considerably larger than that of their physical sizes. The data fit the hypothesis that four genes occupy a single transcriptional unit and that transcription of rabies virus proceeds in the order N, M 1 , M 2 , and L

  10. CHD chromatin remodelers and the transcription cycle

    Science.gov (United States)

    Murawska, Magdalena

    2011-01-01

    It is well established that ATP-dependent chromatin remodelers modulate DNA access of transcription factors and RNA polymerases by “opening” or “closing” chromatin structure. However, this view is far too simplistic. Recent findings have demonstrated that these enzymes not only set the stage for the transcription machinery to act but also are actively involved at every step of the transcription process. As a consequence, they affect initiation, elongation, termination and RNA processing. In this review we will use the CHD family as a paradigm to illustrate the progress that has been made in revealing these new concepts. PMID:22223048

  11. NAC transcription factors: structurally distinct, functionally diverse

    DEFF Research Database (Denmark)

    Olsen, Addie Nina; Ernst, Heidi A; Leggio, Leila Lo

    2005-01-01

    level and localization, and to the first indications of NAC participation in transcription factor networks. The recent determination of the DNA and protein binding NAC domain structure offers insight into the molecular functions of the protein family. Research into NAC transcription factors has......NAC proteins constitute one of the largest families of plant-specific transcription factors, and the family is present in a wide range of land plants. Here, we summarize the biological and molecular functions of the NAC family, paying particular attention to the intricate regulation of NAC protein...

  12. Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses

    Directory of Open Access Journals (Sweden)

    Su Zhen

    2011-07-01

    Full Text Available Abstract Background Salt stress hinders the growth of plants and reduces crop production worldwide. However, different plant species might possess different adaptive mechanisms to mitigate salt stress. We conducted a detailed pathway analysis of transcriptional dynamics in the roots of Medicago truncatula seedlings under salt stress and selected a transcription factor gene, MtCBF4, for experimental validation. Results A microarray experiment was conducted using root samples collected 6, 24, and 48 h after application of 180 mM NaCl. Analysis of 11 statistically significant expression profiles revealed different behaviors between primary and secondary metabolism pathways in response to external stress. Secondary metabolism that helps to maintain osmotic balance was induced. One of the highly induced transcription factor genes was successfully cloned, and was named MtCBF4. Phylogenetic analysis revealed that MtCBF4, which belongs to the AP2-EREBP transcription factor family, is a novel member of the CBF transcription factor in M. truncatula. MtCBF4 is shown to be a nuclear-localized protein. Expression of MtCBF4 in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Transgenic Arabidopsis over-expressing MtCBF4 enhanced tolerance to drought and salt stress, and activated expression of downstream genes that contain DRE elements. Over-expression of MtCBF4 in M. truncatula also enhanced salt tolerance and induced expression level of corresponding downstream genes. Conclusion Comprehensive transcriptomic analysis revealed complex mechanisms exist in plants in response to salt stress. The novel transcription factor gene MtCBF4 identified here played an important role in response to abiotic stresses, indicating that it might be a good candidate gene for genetic improvement to produce stress-tolerant plants.

  13. A critique on nuclear factor-kappa B and signal transducer and activator of transcription 3: The key transcription factors in periodontal pathogenesis

    Directory of Open Access Journals (Sweden)

    Ranjith Ambili

    2017-01-01

    Full Text Available Periodontal disease is initiated by microorganisms in dental plaque, and host immunoinflammatory response to the microbial challenge helps in disease progression. Conventional periodontal therapy was mainly targeted on the elimination of microbial component. However, a better understanding of molecular aspects in host response will enable the clinicians to formulate effective host modulation therapy (HMT for the periodontal management. Inflammatory mediators were the main targets for HMT in the past. Transcription factors can regulate the production of multiple mediators simultaneously, and inhibition of these factors will be more beneficial than blocking individual molecule. Two important transcription factors implicated in chronic inflammatory diseases are nuclear factor kappa B (NF-κB and signal transducers and activators of transcription 3. The role of these factors in periodontal disease is a less explored area. This comprehensive review is aimed at unveiling the critical role of NF-κB and signal transducers and activators of transcription 3 in periodontal pathogenesis. An online search was performed using MEDLINE/PubMed database. All publications till 2016 related to NF-κB, signal transducer and activator of transcription 3 (STAT3, and inflammation were included in writing this review. A total of 27,390 references were published based on the search terms used. Out of these, 507 were related to the periodontal research published in English till 2016. Relevant papers were chosen after carefully reading the abstract. This review has attempted to comprehend the existing knowledge regarding the role of transcription factors NF-κB and STAT3 in periodontal disease. Moreover, it also provides a connecting molecular link for the periodontal medicine concept.

  14. Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses

    Science.gov (United States)

    2011-01-01

    Background Salt stress hinders the growth of plants and reduces crop production worldwide. However, different plant species might possess different adaptive mechanisms to mitigate salt stress. We conducted a detailed pathway analysis of transcriptional dynamics in the roots of Medicago truncatula seedlings under salt stress and selected a transcription factor gene, MtCBF4, for experimental validation. Results A microarray experiment was conducted using root samples collected 6, 24, and 48 h after application of 180 mM NaCl. Analysis of 11 statistically significant expression profiles revealed different behaviors between primary and secondary metabolism pathways in response to external stress. Secondary metabolism that helps to maintain osmotic balance was induced. One of the highly induced transcription factor genes was successfully cloned, and was named MtCBF4. Phylogenetic analysis revealed that MtCBF4, which belongs to the AP2-EREBP transcription factor family, is a novel member of the CBF transcription factor in M. truncatula. MtCBF4 is shown to be a nuclear-localized protein. Expression of MtCBF4 in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Transgenic Arabidopsis over-expressing MtCBF4 enhanced tolerance to drought and salt stress, and activated expression of downstream genes that contain DRE elements. Over-expression of MtCBF4 in M. truncatula also enhanced salt tolerance and induced expression level of corresponding downstream genes. Conclusion Comprehensive transcriptomic analysis revealed complex mechanisms exist in plants in response to salt stress. The novel transcription factor gene MtCBF4 identified here played an important role in response to abiotic stresses, indicating that it might be a good candidate gene for genetic improvement to produce stress-tolerant plants. PMID:21718548

  15. Review of Comprehensive Evaluation Methods for Power Quality and Its Trend in New Generation Energy System

    Science.gov (United States)

    Liu, Ruihua; Wang, Rong; Liu, Qunying; Yang, Li; Xi, Chuan; Wang, Wei; Li, Lingzhou; Zhao, Zhoufang; Zhou, Ying

    2018-02-01

    With China’s new energy generation grid connected capacity being in the forefront of the world and the uncertainty of new energy sources, such as wind energy and solar energy, it is be of great significance to study scientific and comprehensive assessment of power quality. On the foundation of analysizing the current power quality index systematically and objectively, the new energy grid power quality analysis method and comprehensive evaluation method, this paper tentatively explored the trend of the new generation of energy system power quality comprehensive evaluation.

  16. Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.

    Science.gov (United States)

    Chen, Huei-Mei; Rosebrock, Adam P; Khan, Sohail R; Futcher, Bruce; Leatherwood, Janet K

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the "unspliced" signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

  17. Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

    Science.gov (United States)

    Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression. PMID:22238674

  18. Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.

    Directory of Open Access Journals (Sweden)

    Huei-Mei Chen

    Full Text Available In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the "unspliced" signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

  19. Characterization and Improvement of RNA-Seq Precision in Quantitative Transcript Expression Profiling

    Energy Technology Data Exchange (ETDEWEB)

    Labaj, Pawel P.; Leparc, German G.; Linggi, Bryan E.; Markillie, Lye Meng; Wiley, H. S.; Kreil, David P.

    2011-07-01

    Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not. With the compilation of large scale RNA-Seq data sets with technical replicate samples, however, we can now, for the first time, perform a systematic analysis of the precision of expression level estimates from massively parallel sequencing technology. This then allows considerations for its improvement by computational or experimental means. Results: We report on a comprehensive study of target coverage and measurement precision, including their dependence on transcript expression levels, read depth and other parameters. In particular, an impressive target coverage of 84% of the estimated true transcript population could be achieved with 331 million 50 bp reads, with diminishing returns from longer read lengths and even less gains from increased sequencing depths. Most of the measurement power (75%) is spent on only 7% of the known transcriptome, however, making less strongly expressed transcripts harder to measure. Consequently, less than 30% of all transcripts could be quantified reliably with a relative error < 20%. Based on established tools, we then introduce a new approach for mapping and analyzing sequencing reads that yields substantially improved performance in gene expression profiling, increasing the number of transcripts that can reliably be quantified to over 40%. Extrapolations to higher sequencing depths highlight the need for efficient complementary steps. In discussion we outline possible experimental and computational strategies for further improvements in quantification precision.

  20. Modifiers of notch transcriptional activity identified by genome-wide RNAi

    Directory of Open Access Journals (Sweden)

    Firnhaber Christopher B

    2010-10-01

    Full Text Available Abstract Background The Notch signaling pathway regulates a diverse array of developmental processes, and aberrant Notch signaling can lead to diseases, including cancer. To obtain a more comprehensive understanding of the genetic network that integrates into Notch signaling, we performed a genome-wide RNAi screen in Drosophila cell culture to identify genes that modify Notch-dependent transcription. Results Employing complementary data analyses, we found 399 putative modifiers: 189 promoting and 210 antagonizing Notch activated transcription. These modifiers included several known Notch interactors, validating the robustness of the assay. Many novel modifiers were also identified, covering a range of cellular localizations from the extracellular matrix to the nucleus, as well as a large number of proteins with unknown function. Chromatin-modifying proteins represent a major class of genes identified, including histone deacetylase and demethylase complex components and other chromatin modifying, remodeling and replacement factors. A protein-protein interaction map of the Notch-dependent transcription modifiers revealed that a large number of the identified proteins interact physically with these core chromatin components. Conclusions The genome-wide RNAi screen identified many genes that can modulate Notch transcriptional output. A protein interaction map of the identified genes highlighted a network of chromatin-modifying enzymes and remodelers that regulate Notch transcription. Our results open new avenues to explore the mechanisms of Notch signal regulation and the integration of this pathway into diverse cellular processes.

  1. SUBJECT AND AUTHOR INDEXS

    Directory of Open Access Journals (Sweden)

    IJBE Volume 1

    2015-09-01

    Full Text Available SUBJECT INDEX IJBE VOLUME 1EPA, 1Agrotourism, 148AHP, 148balance scorecard, 63batik tulis Rolla Junior, 23Broiler, 90business model canvas, 137business performance,32capital structure, 81cashew industry,158CHAID,106CLI,42coal transportation service,63company’s characteristics, 81competitive advantage, 12competitive strategy, 127consumer satisfaction, 51CSI, 42customer loyalty, 42customer satisfaction,42decision of visitors, 72development strategy, 23development,158entrepreneurship, 32Feasibility studies, 90FEM, 81gap analysis, 1Indonesia Stock Exchange, 177Indosat, 137investor,177Kawah Putih, 72kedai sop durian lodaya (KSDL,51klassen typology, 96leading sector, 96less cash society, 137liquidity ratio, 165location quotient, 96logistic regression, 115market, 177marketing development strategy, 148Marketing mix, 72mobile payment, 137modern and Traditional cage, 90multiple regression analyse,165multiple regression, 177net working capital, 165organic tofu product, 115Padang, 106paired comparison, 63partnership, 1, 32Pecking Order Theory, 81PLS, 81Portfolio, 96power, 32product quality, 51profitability ratio, 165Prol Tape Primadona, 127purchase decision, 115purchase intention, 51purchasing interest,115QSPM, 23, 127refilled drinking water, 106seed,1segmentation, 106SEM, 42, 51service quality, 51SMEs, 96specialty coffee, 12stock,177strategic diagnosis,137strategy, 158Sukorambi Botanic Garden, 148SWOT, 23, 127, 148, 158SWOT-AHP, 12tourists,72UD. Primadona, 127value chain, 12VRIO,12 AUTHOR INDEX IJBE VOLUME 1Adiningsih, Kartika Puspitasari,42Aknesia, Vharessa,12Amalia, Firda Rachma,90Andati, Trias, 177Anggraeni, Lukytawati,23Asriani,158Daryanto, Arief,12, 90Djamaludin, MD., 42Djohar, Setiadi,96Fachrodji, Achmad,72Fahmi, Idqan,1, 63, 127Fasyni, Awisal,106Hubeis, Musa,148Iskandar, Dodi,51Juanda, Bambang, 165Kirbrandoko, 12, 106, 115Lumbantoruan, Dewi Margareth,96Maulana, TB Nur Ahmad,81Muksin, 148Mukti Soleh, Cecep,63Najib, Mukhamad,106Noor, Tajudin,81

  2. In silico and wet lab approaches to study transcriptional regulation

    NARCIS (Netherlands)

    Hestand, Matthew Scott

    2010-01-01

    Gene expression is a complicated process with multiple types of regulation, including binding of proteins termed transcription factors. This thesis looks at transcription factors and transcription factor binding site discovery through computational predictions and wet lab work to better elucidate

  3. CT-FC: more Comprehensive Traversal Focused Crawler

    Directory of Open Access Journals (Sweden)

    NFN Kuspriyanto

    2012-03-01

    Full Text Available In todays world, people depend more on the WWW information, including professionals who have to analyze the data according their domain to maintain and improve their business. A data analysis would require information that is comprehensive and relevant to their domain. Focused crawler as a topical based Web indexer agent is used to meet this applications information need. In order to increase the precision, focused crawler face the problem of low recall. The study on WWW hyperlink structure characteristics indicates that many Web documents are not strong connected but through co-citation & co-reference. Conventional focused crawler that uses forward crawling strategy could not visit the documents in these characteristics. This study proposes a more comprehensive traversal framework. As a proof, CT-FC (a focused crawler with the new traversal framework ran on DMOZ data that is representative to WWW characteristics. The results show that this strategy can increase the recall significantly.

  4. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

    Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

  5. Battles and hijacks: Noncoding transcription in plants

    KAUST Repository

    Ariel, Federico; Romero-Barrios, Natali; Jé gu, Teddy; Benhamed, Moussa; Crespi, Martin

    2015-01-01

    splicing, fine-tuning of miRNA activity, and the control of mRNA translation or accumulation. Recently, dual noncoding transcription by alternative RNA polymerases was implicated in epigenetic and chromatin conformation dynamics. This review integrates

  6. Salmonella Typhimurium transcription profiles in space flight

    Data.gov (United States)

    National Aeronautics and Space Administration — Salmonella transcription profiles were obtained from samples flown on space shuttle mission STS-115 and compared to profiles from Salmonella grown under identical...

  7. Transcript for Understanding Medical Words: A Tutorial

    Science.gov (United States)

    ... medlineplus.gov/medicalwordstranscript.html Transcript for Understanding Medical Words: A Tutorial To use the sharing features on ... get to what those mean in a minute. Word Roots Word Roots. Let's begin with body parts. ...

  8. Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale

    Directory of Open Access Journals (Sweden)

    Aifantis Iannis

    2011-02-01

    Full Text Available Abstract Background Pathway databases are becoming increasingly important and almost omnipresent in most types of biological and translational research. However, little is known about the quality and completeness of pathways stored in these databases. The present study conducts a comprehensive assessment of transcriptional regulatory pathways in humans for seven well-studied transcription factors: MYC, NOTCH1, BCL6, TP53, AR, STAT1, and RELA. The employed benchmarking methodology first involves integrating genome-wide binding with functional gene expression data to derive direct targets of transcription factors. Then the lists of experimentally obtained direct targets are compared with relevant lists of transcriptional targets from 10 commonly used pathway databases. Results The results of this study show that for the majority of pathway databases, the overlap between experimentally obtained target genes and targets reported in transcriptional regulatory pathway databases is surprisingly small and often is not statistically significant. The only exception is MetaCore pathway database which yields statistically significant intersection with experimental results in 84% cases. Additionally, we suggest that the lists of experimentally derived direct targets obtained in this study can be used to reveal new biological insight in transcriptional regulation and suggest novel putative therapeutic targets in cancer. Conclusions Our study opens a debate on validity of using many popular pathway databases to obtain transcriptional regulatory targets. We conclude that the choice of pathway databases should be informed by solid scientific evidence and rigorous empirical evaluation. Reviewers This article was reviewed by Prof. Wing Hung Wong, Dr. Thiago Motta Venancio (nominated by Dr. L Aravind, and Prof. Geoff J McLachlan.

  9. A unified architecture of transcriptional regulatory elements

    DEFF Research Database (Denmark)

    Andersson, Robin; Sandelin, Albin Gustav; Danko, Charles G.

    2015-01-01

    Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However...... and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements and the surrounding sequences determine local transcriptional output as well as the enhancer and promoter activities of individual elements....

  10. Transcriptional Waves in the Yeast Cell Cycle

    OpenAIRE

    Oliva, Anna; Rosebrock, Adam; Ferrezuelo, Francisco; Pyne, Saumyadipta; Chen, Haiying; Skiena, Steve; Futcher, Bruce; Leatherwood, Janet

    2005-01-01

    Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillat...

  11. The importance of causal connections in the comprehension of spontaneous spoken discourse.

    Science.gov (United States)

    Cevasco, Jazmin; van den Broek, Paul

    2008-11-01

    In this study, we investigated the psychological processes in spontaneous discourse comprehension through a network theory of discourse representation. Existing models of narrative comprehension describe the importance of causality processing for forming a representation of a text, but usually in the context of deliberately composed texts rather than in spontaneous, unplanned discourse. Our aim was to determine whether spontaneous discourse components with many causal connections are represented more strongly than components with few connections--similar to the findings in text comprehension literature--and whether any such effects depend on the medium in which the spontaneous discourse is presented (oral vs. written). Participants either listened to or read a transcription of a section of a radio transmission. They then recalled the spontaneous discourse material and answered comprehension questions. Results indicate that the processing of causal connections plays an important role in the comprehension of spontaneous spoken discourse, and do not indicate that their effects on recall are weaker in the comprehension of oral discourse than in the comprehension of written discourse.

  12. NUCKS Is a Positive Transcriptional Regulator of Insulin Signaling

    Directory of Open Access Journals (Sweden)

    Beiying Qiu

    2014-06-01

    Full Text Available Although much is known about the molecular players in insulin signaling, there is scant information about transcriptional regulation of its key components. We now find that NUCKS is a transcriptional regulator of the insulin signaling components, including the insulin receptor (IR. Knockdown of NUCKS leads to impaired insulin signaling in endocrine cells. NUCKS knockout mice exhibit decreased insulin signaling and increased body weight/fat mass along with impaired glucose tolerance and reduced insulin sensitivity, all of which are further exacerbated by a high-fat diet (HFD. Genome-wide ChIP-seq identifies metabolism and insulin signaling as NUCKS targets. Importantly, NUCKS is downregulated in individuals with a high body mass index and in HFD-fed mice, and conversely, its levels increase upon starvation. Altogether, NUCKS is a physiological regulator of energy homeostasis and glucose metabolism that works by regulating chromatin accessibility and RNA polymerase II recruitment to the promoters of IR and other insulin pathway modulators.

  13. 2012 Environmental Performance Index and Pilot Trend Environmental Performance Index

    Data.gov (United States)

    National Aeronautics and Space Administration — The 2012 Environmental Performance Index (EPI) ranks 132 countries on 22 performance indicators in the following 10 policy categories: environmental burden of...

  14. Genome-Wide Identification of the Target Genes of AP2-O, a Plasmodium AP2-Family Transcription Factor.

    Directory of Open Access Journals (Sweden)

    Izumi Kaneko

    2015-05-01

    Full Text Available Stage-specific transcription is a fundamental biological process in the life cycle of the Plasmodium parasite. Proteins containing the AP2 DNA-binding domain are responsible for stage-specific transcriptional regulation and belong to the only known family of transcription factors in Plasmodium parasites. Comprehensive identification of their target genes will advance our understanding of the molecular basis of stage-specific transcriptional regulation and stage-specific parasite development. AP2-O is an AP2 family transcription factor that is expressed in the mosquito midgut-invading stage, called the ookinete, and is essential for normal morphogenesis of this stage. In this study, we identified the genome-wide target genes of AP2-O by chromatin immunoprecipitation-sequencing and elucidate how this AP2 family transcription factor contributes to the formation of this motile stage. The analysis revealed that AP2-O binds specifically to the upstream genomic regions of more than 500 genes, suggesting that approximately 10% of the parasite genome is directly regulated by AP2-O. These genes are involved in distinct biological processes such as morphogenesis, locomotion, midgut penetration, protection against mosquito immunity and preparation for subsequent oocyst development. This direct and global regulation by AP2-O provides a model for gene regulation in Plasmodium parasites and may explain how these parasites manage to control their complex life cycle using a small number of sequence-specific AP2 transcription factors.

  15. Transcriptional analysis of phloem-associated cells of potato.

    Science.gov (United States)

    Lin, Tian; Lashbrook, Coralie C; Cho, Sung Ki; Butler, Nathaniel M; Sharma, Pooja; Muppirala, Usha; Severin, Andrew J; Hannapel, David J

    2015-09-03

    Numerous signal molecules, including proteins and mRNAs, are transported through the architecture of plants via the vascular system. As the connection between leaves and other organs, the petiole and stem are especially important in their transport function, which is carried out by the phloem and xylem, especially by the sieve elements in the phloem system. The phloem is an important conduit for transporting photosynthate and signal molecules like metabolites, proteins, small RNAs, and full-length mRNAs. Phloem sap has been used as an unadulterated source to profile phloem proteins and RNAs, but unfortunately, pure phloem sap cannot be obtained in most plant species. Here we make use of laser capture microdissection (LCM) and RNA-seq for an in-depth transcriptional profile of phloem-associated cells of both petioles and stems of potato. To expedite our analysis, we have taken advantage of the potato genome that has recently been fully sequenced and annotated. Out of the 27 k transcripts assembled that we identified, approximately 15 k were present in phloem-associated cells of petiole and stem with greater than ten reads. Among these genes, roughly 10 k are affected by photoperiod. Several RNAs from this day length-regulated group are also abundant in phloem cells of petioles and encode for proteins involved in signaling or transcriptional control. Approximately 22 % of the transcripts in phloem cells contained at least one binding motif for Pumilio, Nova, or polypyrimidine tract-binding proteins in their downstream sequences. Highlighting the predominance of binding processes identified in the gene ontology analysis of active genes from phloem cells, 78 % of the 464 RNA-binding proteins present in the potato genome were detected in our phloem transcriptome. As a reasonable alternative when phloem sap collection is not possible, LCM can be used to isolate RNA from specific cell types, and along with RNA-seq, provides practical access to expression profiles of

  16. TAF(II)250: a transcription toolbox.

    Science.gov (United States)

    Wassarman, D A; Sauer, F

    2001-08-01

    Activation of RNA-polymerase-II-dependent transcription involves conversion of signals provided by gene-specific activator proteins into the synthesis of messenger RNA. This conversion requires dynamic structural changes in chromatin and assembly of general transcription factors (GTFs) and RNA polymerase II at core promoter sequence elements surrounding the transcription start site of genes. One hallmark of transcriptional activation is the interaction of DNA-bound activators with coactivators such as the TATA-box binding protein (TBP)-associated factors (TAF(II)s) within the GTF TFIID. TAF(II)250 possesses a variety of activities that are likely to contribute to the initial steps of RNA polymerase II transcription. TAF(II)250 is a scaffold for assembly of other TAF(II)s and TBP into TFIID, TAF(II)250 binds activators to recruit TFIID to particular promoters, TAF(II)250 regulates binding of TBP to DNA, TAF(II)250 binds core promoter initiator elements, TAF(II)250 binds acetylated lysine residues in core histones, and TAF(II)250 possesses protein kinase, ubiquitin-activating/conjugating and acetylase activities that modify histones and GTFs. We speculate that these activities achieve two goals--(1) they aid in positioning and stabilizing TFIID at particular promoters, and (2) they alter chromatin structure at the promoter to allow assembly of GTFs--and we propose a model for how TAF(II)250 converts activation signals into active transcription.

  17. A biophysical model for transcription factories

    International Nuclear Information System (INIS)

    Canals-Hamann, Ana Z; Neves, Ricardo Pires das; Reittie, Joyce E; Iñiguez, Carlos; Soneji, Shamit; Enver, Tariq; Buckle, Veronica J; Iborra, Francisco J

    2013-01-01

    Transcription factories are nuclear domains where gene transcription takes place although the molecular basis for their formation and maintenance are unknown. In this study, we explored how the properties of chromatin as a polymer may contribute to the structure of transcription factories. We found that transcriptional active chromatin contains modifications like histone H4 acetylated at Lysine 16 (H4K16ac). Single fibre analysis showed that this modification spans the entire body of the gene. Furthermore, H4K16ac genes cluster in regions up to 500 Kb alternating active and inactive chromatin. The introduction of H4K16ac in chromatin induces stiffness in the chromatin fibre. The result of this change in flexibility is that chromatin could behave like a multi-block copolymer with repetitions of stiff-flexible (active-inactive chromatin) components. Copolymers with such structure self-organize through spontaneous phase separation into microdomains. Consistent with such model H4K16ac chromatin form foci that associates with nascent transcripts. We propose that transcription factories are the result of the spontaneous concentration of H4K16ac chromatin that are in proximity, mainly in cis

  18. Intrinsic terminators in Mycoplasma hyopneumoniae transcription.

    Science.gov (United States)

    Fritsch, Tiago Ebert; Siqueira, Franciele Maboni; Schrank, Irene Silveira

    2015-04-08

    Mycoplasma hyopneumoniae, an important pathogen of swine, exhibits a low guanine and cytosine (GC) content genome. M. hyopneumoniae genome is organised in long transcriptional units and promoter sequences have been mapped upstream of all transcription units. These analysis provided insights into the gene organisation and transcription initiation at the genome scale. However, the presence of transcriptional terminator sequences in the M. hyopneumoniae genome is poorly understood. In silico analyses demonstrated the presence of putative terminators in 82% of the 33 monocistronic units (mCs) and in 74% of the 116 polycistronic units (pCs) considering different classes of terminators. The functional activity of 23 intrinsic terminators was confirmed by RT-PCR and qPCR. Analysis of all terminators found by three software algorithms, combined with experimental results, allowed us to propose a pattern of RNA hairpin formation during the termination process and to predict the location of terminators in the M. hyopneumoniae genome sequence. The stem-loop structures of intrinsic terminators of mycoplasma diverge from the pattern of terminators found in other bacteria due the low content of guanine and cytosine. In M. hyopneumoniae, transcription can end after a transcriptional unit and before its terminator sequence and can also continue past the terminator sequence with RNA polymerases gradually releasing the RNA.

  19. MADS-box gene evolution - structure and transcription patterns

    DEFF Research Database (Denmark)

    Johansen, Bo; Pedersen, Louise Buchholt; Skipper, Martin

    2002-01-01

    Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs......Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs...

  20. A comprehensive outlook of Sannipata

    Science.gov (United States)

    Panja, Asit K; Chattopadhyaya, Abichal; Chaudhuri, Supriyo

    2011-01-01

    Nomenclature of the disease on the basis of vitiation of the body humors is stressed in ayurveda. Sannipatika, i.e., ‘conglomeration of vitiated tridosa’ is the final stage of process of manifestation of disease. In this specific state of pathogenesis, the disease becomes more advance and mostly irreversible. A detailed scientific study of Sannipatika-avastha has been documented in classics. Comprehensive analysis of sannipata-state and its ways of presentation is the main theme of the current article. PMID:22408295

  1. NRC comprehensive records disposition schedule

    International Nuclear Information System (INIS)

    1982-07-01

    Effective January 1, 1982, NRC will institute records retention and disposal practices in accordance with the approved Comprehensive Records Disposition Schedule (CRDS). CRDS is comprised of NRC Schedules (NRCS) 1 to 4 which apply to the agency's program or substantive records and General Records Schedules (GRS) 1 to 22 which apply to housekeeping or facilitative records. The schedules are assembled functionally/organizationally to facilitate their use. Preceding the records descriptions and disposition instructions for both NRCS and GRS, there are brief statements on the organizational units which accumulate the records in each functional area, and other information regarding the schedules' applicability

  2. A Comprehensive Theory of Integration.

    Science.gov (United States)

    Singer, Sara J; Kerrissey, Michaela; Friedberg, Mark; Phillips, Russell

    2018-03-01

    Efforts to transform health care delivery to improve care have increasingly focused on care integration. However, variation in how integration is defined has complicated efforts to design, synthesize, and compare studies of integration in health care. Evaluations of integration initiatives would be enhanced by describing them according to clear definitions of integration and specifying which empirical relationships they seek to test-whether among types of integration or between integration and outcomes of care. Drawing on previous work, we present a comprehensive theoretical model of relationships between types of integration and propose how to measure them.

  3. Comprehensive management of project changes

    Directory of Open Access Journals (Sweden)

    Aljaž Stare

    2010-06-01

    Full Text Available The goal of this research was to examine how project changes can be prevented, and how to reduce their negative impact. Theoretical research examined risk management, project control and change management. Based on the study a “Comprehensive Change Management Model” was developed and verified after conducting empirical research in Slovenian enterprises. The research confirmed that risk management identifies possible changes and reduces their impact; project control ensures the timely detection of changes and an efficient response, while formal change management ensures the effective implementation of changes. The combined functioning of all three areas ensures effective project execution.

  4. On the importance of listening comprehension.

    Science.gov (United States)

    Hogan, Tiffany P; Adlof, Suzanne M; Alonzo, Crystle N

    2014-06-01

    The simple view of reading highlights the importance of two primary components which account for individual differences in reading comprehension across development: word recognition (i.e., decoding) and listening comprehension. While assessments and interventions for decoding have been the focus of pedagogy in the past several decades, the importance of listening comprehension has received less attention. This paper reviews evidence showing that listening comprehension becomes the dominating influence on reading comprehension starting even in the elementary grades. It also highlights a growing number of children who fail to develop adequate reading comprehension skills, primarily due to deficient listening comprehension skills (i.e., poor comprehenders). Finally we discuss key language influences on listening comprehension for consideration during assessment and treatment of reading disabilities.

  5. Production Practice During Language Learning Improves Comprehension.

    Science.gov (United States)

    Hopman, Elise W M; MacDonald, Maryellen C

    2018-04-01

    Language learners often spend more time comprehending than producing a new language. However, memory research suggests reasons to suspect that production practice might provide a stronger learning experience than comprehension practice. We tested the benefits of production during language learning and the degree to which this learning transfers to comprehension skill. We taught participants an artificial language containing multiple linguistic dependencies. Participants were randomly assigned to either a production- or a comprehension-learning condition, with conditions designed to balance attention demands and other known production-comprehension differences. After training, production-learning participants outperformed comprehension-learning participants on vocabulary comprehension and on comprehension tests of grammatical dependencies, even when we controlled for individual differences in vocabulary learning. This result shows that producing a language during learning can improve subsequent comprehension, which has implications for theories of memory and learning, language representations, and educational practices.

  6. How Do We Motivate Reading Comprehension?

    Science.gov (United States)

    Shanahan, Timothy

    1982-01-01

    Considers the nature of motivation and its place in the development of reading comprehension. Uses A. Maslow's hierarchy of motivation as a heuristic for examining the motivational quality of several teaching methods commonly proposed for comprehension instruction. (FL)

  7. Ending reliance on nuclear and conventional arms. Edited transcripts of the disarmament week symposium

    International Nuclear Information System (INIS)

    1995-01-01

    This publication contains the edited transcripts of the two meetings held at the United Nations in 1994: the Disarmament Week Symposium, sponsored by the United Nations Centre for Disarmament Affairs and Department of Public Information and the NGO Committee on Disarmament, from 25 to 27 October, and a panel discussion on the land mines crisis, sponsored by the NGO Committee on Disarmament, on 16 November. Only the material concerning the first Symposium was indexed for INIS database

  8. SUBJECT AND AUTHOR INDEXS

    Directory of Open Access Journals (Sweden)

    IJBE Volume 2

    2016-09-01

    Full Text Available SUBJECT INDEX IJBE VOLUME 2access credit, 93acquisition, 177AHP, 61, 82, 165arena simulation,43BMC, 69Bojonegoro, 69brand choice, 208brand image, 208brand positioning, 208bullwhip effect, 43burger buns, 1business synergy and financial reports, 177capital structure, 130cluster, 151coal reserves, 130coffee plantation, 93competitiveness, 82consumer behaviour, 33consumer complaint behavior, 101cooking spices, 1crackers, 1cross sectional analytical, 139crosstab, 101CSI, 12direct selling, 122discriminant analysis, 33economic value added, 130, 187employee motivation, 112employee performance, 112employees, 139EOQ, 23farmer decisions, 93farmer group, 52financial performance evaluation, 187financial performance, 52, 177financial ratio, 187financial report, 187fiva food, 23food crops, 151horticulture, 151imports, 151improved capital structure, 177IPA, 12leading sector, 151life insurance, 165LotteMart, 43main product, 61marketing mix, 33, 165matrix SWOT, 69MPE, 61multiple linear regression, 122muslim clothing, 197Ogun, 139Pangasius fillet, 82Pati, 93pearson correlation, 101perceived value, 208performance suppy chain, 23PLS, 208POQ, 23portfolio analyzing, 1product, 101PT SKP, 122pulp and papers, 187purchase decision, 165purchase intention, 33remuneration, 112re-purchasing decisions, 197sales performance, 122sawmill, 52SCOR, 23sekolah peternakan rakyat, 69SEM, 112SERVQUAL, 12Sido Makmur farmer groups, 93SI-PUHH Online, 12small and medium industries (IKM, 61socio-demographic, 139sport drink, 208stress, 139supply chain, 43SWOT, 82the mix marketing, 197Tobin’s Q, 130trade partnership, 52uleg chili sauce, 1 AUTHOR INDEX IJBE VOLUME 2Achsani, Noer Azam, 177Andati, Trias, 52, 177Andihka, Galih, 208Arkeman, Yandra, 43Baga, Lukman M, 69Cahyanugroho, Aldi, 112Daryanto, Arief, 12David, Ajibade, 139Djoni, 122Fahmi, Idqan, 1Fattah, Muhammad Unggul Abdul, 61Hakim, Dedi Budiman, 187Harianto, 93Hartoyo, 101Homisah, 1Hubeis, Musa, 112Hutagaol, M. Parulian, 93Jaya, Stevana

  9. Transcriptional regulation of N-acetylaspartate metabolism in the 5xFAD model of Alzheimer's disease: evidence for neuron-glia communication during energetic crisis.

    Science.gov (United States)

    Zaroff, Samantha; Leone, Paola; Markov, Vladimir; Francis, Jeremy S

    2015-03-01

    N-acetylaspartate (NAA) provides a non-invasive clinical index of neuronal metabolic integrity across the entire neurodegenerative spectrum. While NAA function is not comprehensively defined, reductions in the brain are associated with compromised mitochondrial metabolism and are tightly linked to ATP. We have undertaken an analysis of abnormalities in NAA during early stage pathology in the 5xFAD mouse model of familial Alzheimer's disease and show here that dysregulated expression of the gene encoding for the rate-limiting NAA synthetic enzyme (Nat8L) is associated with deficits in mitochondrial oxidative phosphorylation in this model system. Downreguation of Nat8L is particularly pronounced in the 5xFAD hippocampus, and is preceded by a significant upregulation of oligodendrocytic aspartoacylase (aspa), which encodes for the sole known NAA-catabolizing enzyme in the brain. Reductions in 5xFAD NAA and Nat8L cannot be accounted for by discrepancies in either neuron content or activity of the substrate-providing malate-aspartate shuttle, thereby implicating transcriptional regulation in a coordinated response to pathological energetic crisis. A central role for ASPA in this response is supported by a parallel developmental analysis showing highly significant increases in Nat8L expression in an ASPA-null mouse model during a period of early postnatal development normally punctuated by the transcriptional upregulation of aspa. These results provide preliminary evidence of a signaling mechanism in Alzheimer's disease that involves cross talk between neurons and oligodendrocytes, and suggest that ASPA acts to negatively regulate Nat8L expression. This mechanism is proposed to be a fundamental means by which the brain conserves available substrate during energy crises. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Comprehensive framework for preventive maintenance priority of medical equipment.

    Science.gov (United States)

    Saleh, Neven; Balestra, Gabriella

    2015-08-01

    Throughout the medical equipment life cycle, preventive maintenance is considered one of the most important stages that should be managed properly. However, the need for better management and control by giving a reasonable prioritization for preventive maintenance becomes essential. The purpose of this study is to develop a comprehensive framework for preventive maintenance priority of medical equipment using Quality Function Deployment (QFD) and Fuzzy Logic (FL). The quality function deployment is proposed in order to identify the most important criteria that could impact preventive maintenance priority decision; meanwhile the role of the fuzzy logic is to generate a priority index of the list of equipment considering those criteria. The model validation was carried out on 140 pieces of medical equipment belonging to two hospitals. In application, we propose to classify the priority index into five classes. The results indicate that the strong correlation existence between risk-based criteria and preventive maintenance priority decision.

  11. Filter indexing for spectrophotometer system

    International Nuclear Information System (INIS)

    Chamran, M.M.; Scott, L.B.; Williams, P.B.

    1982-01-01

    A spectrophotometer system has an optical system for transmitting a beam from a source at select wavelengths onto a detector. A plurality of filters are positioned in a tray. A stepper mechanism indexes the tray along a path. A microcomputer controls the stepper mechanism and the optical system. The wavelength is successively changed over a range, the tray is indexed to move a select filter into the beam at a predetermined wavelength and the changing is discontinued during indexing

  12. Asset pricing with index investing

    OpenAIRE

    Georgy Chabakauri; Oleg Rytchkov

    2014-01-01

    We provide a novel theoretical analysis of how index investing affects capital market equilibrium. We consider a dynamic exchange economy with heterogeneous investors and two Lucas trees and find that indexing can either increase or decrease the correlation between stock returns and in general increases (decreases) volatilities and betas of stocks with larger (smaller) market capitalizations. Indexing also decreases market volatility and interest rates, although those effects are weak. The im...

  13. Dynamic analysis of stochastic transcription cycles.

    Directory of Open Access Journals (Sweden)

    Claire V Harper

    2011-04-01

    Full Text Available In individual mammalian cells the expression of some genes such as prolactin is highly variable over time and has been suggested to occur in stochastic pulses. To investigate the origins of this behavior and to understand its functional relevance, we quantitatively analyzed this variability using new mathematical tools that allowed us to reconstruct dynamic transcription rates of different reporter genes controlled by identical promoters in the same living cell. Quantitative microscopic analysis of two reporter genes, firefly luciferase and destabilized EGFP, was used to analyze the dynamics of prolactin promoter-directed gene expression in living individual clonal and primary pituitary cells over periods of up to 25 h. We quantified the time-dependence and cyclicity of the transcription pulses and estimated the length and variation of active and inactive transcription phases. We showed an average cycle period of approximately 11 h and demonstrated that while the measured time distribution of active phases agreed with commonly accepted models of transcription, the inactive phases were differently distributed and showed strong memory, with a refractory period of transcriptional inactivation close to 3 h. Cycles in transcription occurred at two distinct prolactin-promoter controlled reporter genes in the same individual clonal or primary cells. However, the timing of the cycles was independent and out-of-phase. For the first time, we have analyzed transcription dynamics from two equivalent loci in real-time in single cells. In unstimulated conditions, cells showed independent transcription dynamics at each locus. A key result from these analyses was the evidence for a minimum refractory period in the inactive-phase of transcription. The response to acute signals and the result of manipulation of histone acetylation was consistent with the hypothesis that this refractory period corresponded to a phase of chromatin remodeling which significantly

  14. The PAPAS index: a novel index for the prediction of hepatitis C-related fibrosis.

    Science.gov (United States)

    Ozel, Banu D; Poyrazoğlu, Orhan K; Karaman, Ahmet; Karaman, Hatice; Altinkaya, Engin; Sevinç, Eylem; Zararsiz, Gökmen

    2015-08-01

    Several noninvasive tests have been developed to determine the degree of hepatic fibrosis in patients with chronic hepatitis C (CHC) without performing liver biopsy. This study aimed to determine the performance of the PAPAS (Platelet/Age/Phosphatase/AFP/AST) index in patients with CHC for the prediction of significant fibrosis and cirrhosis and to compare it with other noninvasive tests. To date, no study has evaluated the application of the PAPAS index in CHC-associated liver fibrosis. This retrospective study included 137 consecutive patients with CHC who had undergone a percutaneous liver biopsy before treatment. The aspartate aminotransferase/platelet ratio (APRI), aspartate aminotransferase/alanine transaminase ratio (AAR), age-platelet index (API), FIB4, cirrhosis discriminate score (CDS), the Göteborg University cirrhosis index (GUCI), and PAPAS were calculated and compared with the diagnostic accuracies of all fibrosis indices between the groups F0-F2 (no-mild fibrosis) versus F3-F6 (significant fibrosis) and F0-F4 (no cirrhosis) versus F5-F6 (cirrhosis). To predict significant fibrosis, the area under curve (95% confidence interval) for FIB4 was 0.727 followed by GUCI (0.721), PAPAS≈APRI≈CDS (0.716), and API (0.68). To predict cirrhosis, the area under curve (95% confidence interval) for FIB4 was calculated to be 0.735, followed by GUCI (0.723), PAPAS≈APRI≈CDS≈(0.71), and API (0.66). No statistically significant difference was observed among these predictors to exclude both significant fibrosis and cirrhosis (P>0.05). The diagnostic capability of the PAPAS index has moderate efficiency and was not superior to other fibrosis markers for the identification of fibrosis in CHC patients. There is a need for more comprehensive prospective studies to help determine the diagnostic value of PAPAS for liver fibrosis.

  15. Text comprehension strategy instruction with poor readers

    NARCIS (Netherlands)

    Van den Bos, K.P.; Aarnoudse, C.C.; Brand-Gruwel, S.

    1998-01-01

    The goal of this study was to investigate the effects of teaching text comprehension strategies to children with decoding and reading comprehension problems and with a poor or normal listening ability. Two experiments are reported. Four text comprehension strategies, viz., question generation,

  16. Classroom Talk for Rigorous Reading Comprehension Instruction

    Science.gov (United States)

    Wolf, Mikyung Kim; Crosson, Amy C.; Resnick, Lauren B.

    2004-01-01

    This study examined the quality of classroom talk and its relation to academic rigor in reading-comprehension lessons. Additionally, the study aimed to characterize effective questions to support rigorous reading comprehension lessons. The data for this study included 21 reading-comprehension lessons in several elementary and middle schools from…

  17. Idiom Comprehension in Mandarin-Speaking Children

    Science.gov (United States)

    Hsieh, Shelley Ching-Yu; Hsu, Chun-Chieh Natalie

    2010-01-01

    This study examines the effect of familiarity, context, and linguistic convention on idiom comprehension in Mandarin speaking children. Two experiments (a comprehension task followed by a comprehension task coupled with a metapragmatic task) were administered to test participants in three age groups (6 and 9-year-olds, and an adult control group).…

  18. 18 CFR 801.5 - Comprehensive plan.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Comprehensive plan. 801... POLICIES § 801.5 Comprehensive plan. (a) The Compact requires that the Commission formulate and adopt a comprehensive plan for the immediate and long-range development and use of the water resources of the basin. (1...

  19. Comprehension or comprehending? Using Critical Language ...

    African Journals Online (AJOL)

    It is argued that the genre of the school reading comprehension exercise is a prime inculcator of thoughtless and non-interactive reading practices. Doing 'a comprehension' (the word is often nominalised in this manner) and answering the comprehension questions often 'counts as' reading and substitutes for other types of ...

  20. 16 CFR 1018.43 - Comprehensive review.

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Comprehensive review. 1018.43 Section 1018.43 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION GENERAL ADVISORY COMMITTEE MANAGEMENT Records, Annual Reports and Audits § 1018.43 Comprehensive review. A comprehensive review of all...

  1. Complete cumulative index (1963-1983)

    International Nuclear Information System (INIS)

    1983-01-01

    This complete cumulative index covers all regular and special issues and supplements published by Atomic Energy Review (AER) during its lifetime (1963-1983). The complete cumulative index consists of six Indexes: the Index of Abstracts, the Subject Index, the Title Index, the Author Index, the Country Index and the Table of Elements Index. The complete cumulative index supersedes the Cumulative Indexes for Volumes 1-7: 1963-1969 (1970), and for Volumes 1-10: 1963-1972 (1972); this Index also finalizes Atomic Energy Review, the publication of which has recently been terminated by the IAEA

  2. Prediction During Natural Language Comprehension.

    Science.gov (United States)

    Willems, Roel M; Frank, Stefan L; Nijhof, Annabel D; Hagoort, Peter; van den Bosch, Antal

    2016-06-01

    The notion of prediction is studied in cognitive neuroscience with increasing intensity. We investigated the neural basis of 2 distinct aspects of word prediction, derived from information theory, during story comprehension. We assessed the effect of entropy of next-word probability distributions as well as surprisal A computational model determined entropy and surprisal for each word in 3 literary stories. Twenty-four healthy participants listened to the same 3 stories while their brain activation was measured using fMRI. Reversed speech fragments were presented as a control condition. Brain areas sensitive to entropy were left ventral premotor cortex, left middle frontal gyrus, right inferior frontal gyrus, left inferior parietal lobule, and left supplementary motor area. Areas sensitive to surprisal were left inferior temporal sulcus ("visual word form area"), bilateral superior temporal gyrus, right amygdala, bilateral anterior temporal poles, and right inferior frontal sulcus. We conclude that prediction during language comprehension can occur at several levels of processing, including at the level of word form. Our study exemplifies the power of combining computational linguistics with cognitive neuroscience, and additionally underlines the feasibility of studying continuous spoken language materials with fMRI. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Mangrove vulnerability index using GIS

    Science.gov (United States)

    Yunus, Mohd Zulkifli Mohd; Ahmad, Fatimah Shafinaz; Ibrahim, Nuremira

    2018-02-01

    Climate change, particularly its associated sea level rise, is major threat to mangrove coastal areas, and it is essential to develop ways to reduce vulnerability through strategic management planning. Environmental vulnerability can be understood as a function of exposure to impacts and the sensitivity and adaptive capacity of ecological systems towards environmental tensors. Mangrove vulnerability ranking using up to 14 parameters found in study area, which is in Pulau Kukup and Sg Pulai, where 1 is low vulnerability and 5 is very high vulnerability. Mangrove Vulnerability Index (MVI) is divided into 3 main categories Physical Mangrove Index (PMI), Biological Mangrove Index (BMI) and Hazard Mangrove Index (HMI).

  4. Index Bioclimatic "Wind-Chill"

    Directory of Open Access Journals (Sweden)

    Teodoreanu Elena

    2015-05-01

    Full Text Available This paper presents an important bioclimatic index which shows the influence of wind on the human body thermoregulation. When the air temperature is high, the wind increases thermal comfort. But more important for the body is the wind when the air temperature is low. When the air temperature is lower and wind speed higher, the human body is threatening to freeze faster. Cold wind index is used in Canada, USA, Russia (temperature "equivalent" to the facial skin etc., in the weather forecast every day in the cold season. The index can be used and for bioclimatic regionalization, in the form of skin temperature index.

  5. 2008 Environmental Performance Index (EPI)

    Data.gov (United States)

    National Aeronautics and Space Administration — The 2008 Environmental Performance Index (EPI) centers on two broad environmental protection objectives: (1) reducing environmental stresses on human health, and (2)...

  6. 2002 Environmental Sustainability Index (ESI)

    Data.gov (United States)

    National Aeronautics and Space Administration — The 2002 Environmental Sustainability Index (ESI) measures overall progress toward environmental sustainability for 142 countries based on environmental systems,...

  7. Nelson-Farrar cost indexes

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    This paper discusses the Nelson-Farrar Cost Indexs. Topics covered include: economic analysis, petroleum refineries, petroleum industry, pumps, compressors, beat exchangers, cost estimation, productivity and wages

  8. A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

    KAUST Repository

    Kulakovskiy, Ivan V.; Belostotsky, A. A.; Kasianov, Artem S.; Esipova, Natalia G.; Medvedeva, Yulia; Eliseeva, Irina A.; Makeev, Vsevolod J.

    2011-01-01

    Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding

  9. Malaysian Education Index (MEI): An Online Indexing and Repository System

    Science.gov (United States)

    Kabilan, Muhammad Kamarul; Ismail, Hairul Nizam; Yaakub, Rohizani; Yusof, Najeemah Mohd; Idros, Sharifah Noraidah Syed; Umar, Irfan Naufal; Arshad, Muhammad Rafie Mohd.; Idrus, Rosnah; Rahman, Habsah Abdul

    2010-01-01

    This "Project Sheet" describes an on-going project that is being carried out by a group of educational researchers, computer science researchers and librarians from Universiti Sains Malaysia, Penang. The Malaysian Education Index (MEI) has two main functions--(1) Online Indexing System, and (2) Online Repository System. In this brief…

  10. Sprache und Sozio-Oekonomischer Index (Speech and Socioeconomic Index)

    Science.gov (United States)

    Bluhme, Hermann

    1976-01-01

    A comparison of the socioeconomic index of 77 speakers of Dutch, recorded in 40 places, revealed certain correlations between index and individual linguistic behavior, particularly in regard to the speed of articulation, quantity quotient (low vowels/short vowels), pitch modulation, number of relative clauses and passive construction. (Text is in…

  11. A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Tony Håndstad

    Full Text Available BACKGROUND: Transcription factors are important controllers of gene expression and mapping transcription factor binding sites (TFBS is key to inferring transcription factor regulatory networks. Several methods for predicting TFBS exist, but there are no standard genome-wide datasets on which to assess the performance of these prediction methods. Also, it is believed that information about sequence conservation across different genomes can generally improve accuracy of motif-based predictors, but it is not clear under what circumstances use of conservation is most beneficial. RESULTS: Here we use published ChIP-seq data and an improved peak detection method to create comprehensive benchmark datasets for prediction methods which use known descriptors or binding motifs to detect TFBS in genomic sequences. We use this benchmark to assess the performance of five different prediction methods and find that the methods that use information about sequence conservation generally perform better than simpler motif-scanning methods. The difference is greater on high-affinity peaks and when using short and information-poor motifs. However, if the motifs are specific and information-rich, we find that simple motif-scanning methods can perform better than conservation-based methods. CONCLUSIONS: Our benchmark provides a comprehensive test that can be used to rank the relative performance of transcription factor binding site prediction methods. Moreover, our results show that, contrary to previous reports, sequence conservation is better suited for predicting strong than weak transcription factor binding sites.

  12. The Pemberton Happiness Index

    Science.gov (United States)

    Paiva, Bianca Sakamoto Ribeiro; de Camargos, Mayara Goulart; Demarzo, Marcelo Marcos Piva; Hervás, Gonzalo; Vázquez, Carmelo; Paiva, Carlos Eduardo

    2016-01-01

    Abstract The Pemberton Happiness Index (PHI) is a recently developed integrative measure of well-being that includes components of hedonic, eudaimonic, social, and experienced well-being. The PHI has been validated in several languages, but not in Portuguese. Our aim was to cross-culturally adapt the Universal Portuguese version of the PHI and to assess its psychometric properties in a sample of the Brazilian population using online surveys. An expert committee evaluated 2 versions of the PHI previously translated into Portuguese by the original authors using a standardized form for assessment of semantic/idiomatic, cultural, and conceptual equivalence. A pretesting was conducted employing cognitive debriefing methods. In sequence, the expert committee evaluated all the documents and reached a final Universal Portuguese PHI version. For the evaluation of the psychometric properties, the data were collected using online surveys in a cross-sectional study. The study population included healthcare professionals and users of the social network site Facebook from several Brazilian geographic areas. In addition to the PHI, participants completed the Satisfaction with Life Scale (SWLS), Diener and Emmons’ Positive and Negative Experience Scale (PNES), Psychological Well-being Scale (PWS), and the Subjective Happiness Scale (SHS). Internal consistency, convergent validity, known-group validity, and test–retest reliability were evaluated. Satisfaction with the previous day was correlated with the 10 items assessing experienced well-being using the Cramer V test. Additionally, a cut-off value of PHI to identify a “happy individual” was defined using receiver-operating characteristic (ROC) curve methodology. Data from 1035 Brazilian participants were analyzed (health professionals = 180; Facebook users = 855). Regarding reliability results, the internal consistency (Cronbach alpha = 0.890 and 0.914) and test–retest (intraclass correlation coefficient = 0.814) were

  13. Evaluating energy saving system of data centers based on AHP and fuzzy comprehensive evaluation model

    Science.gov (United States)

    Jiang, Yingni

    2018-03-01

    Due to the high energy consumption of communication, energy saving of data centers must be enforced. But the lack of evaluation mechanisms has restrained the process on energy saving construction of data centers. In this paper, energy saving evaluation index system of data centers was constructed on the basis of clarifying the influence factors. Based on the evaluation index system, analytical hierarchy process was used to determine the weights of the evaluation indexes. Subsequently, a three-grade fuzzy comprehensive evaluation model was constructed to evaluate the energy saving system of data centers.

  14. A temporary index

    International Nuclear Information System (INIS)

    Thomson, Jon; Craighead, Alison

    2015-01-01

    The ongoing management of low, intermediate and high-level nuclear waste is an unresolved issue for humanity, not least because the time-frames in question when dealing with the hazards of radioactive wastes, range from as little as a few tens of years to more than 100 000 years. It is from this starting point that we are beginning the development of an ambitious multifaceted artwork aiming to help us consider our relationship with deep-time and our nuclear legacy. The expressed aim of Temporary Index is to raise general awareness about these long-term management issues, and in doing so, to embed this knowledge into our collective cultural memory so as to transmit useful information about our nuclear waste into the future. We wish to create a series of decorative, real-time numeric counters based on the probabilistic decay (including decay of daughter products) of existing nuclear waste that we identify from the earliest weapons' development programmes in the United States right through to contemporary wastes being produced by nuclear energy production today across the world. Each display will countdown in seconds, showing the time remaining before the given item of waste (or a particular site) is considered safe to humans. A hypothetical example of one counter could be a bottle of sludge containing plutonium discovered in 2004 during an attempted clean-up of the Hanford nuclear site in Washington State, United States. Another example might be the geological storage facility for vitrified nuclear waste at Horonobe in Japan, should it be established in the future. Accident sites, such as Chernobyl or Fukushima Daiichi could also be tagged with counters, as could low-level waste (LLW) repositories such as the one at Drigg near Sellafield in the United Kingdom. Whatever the items identified and this will be a complex process requiring collaboration with experts in the field, it is important that a wide range of short- and long-term counters are established to

  15. Listening Comprehension in Middle-Aged Adults.

    Science.gov (United States)

    Sommers, Mitchell S

    2015-06-01

    The purpose of this summary is to examine changes in listening comprehension across the adult lifespan and to identify factors associated with individual differences in listening comprehension. In this article, the author reports on both cross-sectional and longitudinal changes in listening comprehension. Despite significant declines in both sensory and cognitive abilities, listening comprehension remains relatively unchanged in middle-aged listeners (between the ages of 40 and 60 years) compared with young listeners. These results are discussed with respect to possible compensatory factors that maintain listening comprehension despite impaired hearing and reduced cognitive capacities.

  16. Role of Working Memory in Typically Developing Children's Complex Sentence Comprehension

    Science.gov (United States)

    Montgomery, James W.; Magimairaj, Beula M.; O'Malley, Michelle H.

    2008-01-01

    The influence of three mechanisms of working memory (phonological short-term memory (PSTM capacity), attentional resource control/allocation, and processing speed) on children's complex (and simple) sentence comprehension was investigated. Fifty two children (6-12 years) completed a nonword repetition task (indexing PSTM), concurrent verbal…

  17. Nursing supervision for care comprehensiveness.

    Science.gov (United States)

    Chaves, Lucieli Dias Pedreschi; Mininel, Vivian Aline; Silva, Jaqueline Alcântara Marcelino da; Alves, Larissa Roberta; Silva, Maria Ferreira da; Camelo, Silvia Helena Henriques

    2017-01-01

    To reflect on nursing supervision as a management tool for care comprehensiveness by nurses, considering its potential and limits in the current scenario. A reflective study based on discourse about nursing supervision, presenting theoretical and practical concepts and approaches. Limits on the exercise of supervision are related to the organization of healthcare services based on the functional and clinical model of care, in addition to possible gaps in the nurse training process and work overload. Regarding the potential, researchers emphasize that supervision is a tool for coordinating care and management actions, which may favor care comprehensiveness, and stimulate positive attitudes toward cooperation and contribution within teams, co-responsibility, and educational development at work. Nursing supervision may help enhance care comprehensiveness by implying continuous reflection on including the dynamics of the healthcare work process and user needs in care networks. refletir a supervisão de enfermagem como instrumento gerencial do enfermeiro para integralidade do cuidado, considerando suas potencialidades e limitações no cenário atual. estudo reflexivo baseado na formulação discursiva sobre a supervisão de enfermagem, apresentando conceitos e enfoques teóricos e/ou práticos. limitações no exercício da supervisão estão relacionadas à organização dos serviços de saúde embasada no modelo funcional e clínico de atenção, assim como possíveis lacunas no processo de formação do enfermeiro e sobrecarga de trabalho. Quanto às potencialidades, destaca-se a supervisão como instrumento de articulação de ações assistenciais e gerenciais, que pode favorecer integralidade da atenção, estimular atitudes de cooperação e colaboração em equipe, além da corresponsabilização e promoção da educação no trabalho. supervisão de enfermagem pode contribuir para fortalecimento da integralidade do cuidado, pressupondo reflexão cont

  18. Contribution Index Based on Green Building Certification Systems

    Directory of Open Access Journals (Sweden)

    Yuting Sun

    2015-05-01

    Full Text Available Green Building Certification Systems (GBCS are carried out in many countries due to the rising awareness of the importance of sustainability in the building industry. The intention should have motivated participants to construct and operate buildings sustainably, however, there is not yet a method developed to investigate the motivation of the participants. Based on the GBCS, this paper proposes the contribution index as a standard global method to analyze the performance of participants in the green building industry. Three contribution indices, namely Frequency Contribution Index (FCI, Intensity Contribution Index (ICI and Comprehensive Contribution Index (CCI that concern each different category of participant, have been formulated. Three further analyses based on the index were undertaken to investigate some features of the industry. A case study of Singapore was conducted to show how the contribution index could be used to extract industry patterns and trends and assess the participants’ performance in the green building industry. Interviews with experts provide some suggested applications and support for the findings.

  19. The Summary Index of Malaria Surveillance (SIMS: a stable index of malaria within India

    Directory of Open Access Journals (Sweden)

    Sharma Vinod P

    2010-02-01

    Full Text Available Abstract Background Malaria in India has been difficult to measure. Mortality and morbidity are not comprehensively reported, impeding efforts to track changes in disease burden. However, a set of blood measures has been collected regularly by the National Malaria Control Program in most districts since 1958. Methods Here, we use principal components analysis to combine these measures into a single index, the Summary Index of Malaria Surveillance (SIMS, and then test its temporal and geographic stability using subsets of the data. Results The SIMS correlates positively with all its individual components and with external measures of mortality and morbidity. It is highly consistent and stable over time (1995-2005 and regions of India. It includes measures of both vivax and falciparum malaria, with vivax dominant at lower transmission levels and falciparum dominant at higher transmission levels, perhaps due to ecological specialization of the species. Conclusions This measure should provide a useful tool for researchers looking to summarize geographic or temporal trends in malaria in India, and can be readily applied by administrators with no mathematical or scientific background. We include a spreadsheet that allows simple calculation of the index for researchers and local administrators. Similar principles are likely applicable worldwide, though further validation is needed before using the SIMS outside India.

  20. Information Transparency of the Statement of Comprehensive Income: The Reporting Practice of WIG30 and DAX Companies

    Directory of Open Access Journals (Sweden)

    Jacek Gad

    2016-01-01

    Full Text Available This article aims to identify changes in the form of the statement of comprehensive income in companies in the WIG30 and DAX indices. It also aims to identify and grade components of other comprehensive income, in terms of the information transparency of the presentation options. The article demonstrates also the impact of national cultural dimensions on the form of the statement of comprehensive income. The study found that most of the surveyed companies present their statement of comprehensive income in two statements, with the number of accounting notes regarding comprehensive income presented by companies in their financial statements increasing over the period under study. The study identified four options for the presentation of other comprehensive income components used by the surveyed companies in the years 2012-2014, with the particular option chosen reflecting the different information transparency of the statement of comprehensive income. The results show that the practice of reporting in the area of the statement of comprehensive income of the DAX index companies is ahead of that in the WIG30 index. The research results on information transparency of the statement of comprehensive income correspond to one of the national cultural dimensions.

  1. A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

    Directory of Open Access Journals (Sweden)

    Wenbin Mei

    2017-05-01

    Full Text Available Identifying and characterizing alternative splicing (AS enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 × Mo17 recombinant inbred lines (RILs identified splicing QTL (sQTL. The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.

  2. The dark side of SOX2: cancer - a comprehensive overview.

    Science.gov (United States)

    Wuebben, Erin L; Rizzino, Angie

    2017-07-04

    The pluripotency-associated transcription factor SOX2 is essential during mammalian embryogenesis and later in life, but SOX2 expression can also be highly detrimental. Over the past 10 years, SOX2 has been shown to be expressed in at least 25 different cancers. This review provides a comprehensive overview of the roles of SOX2 in cancer and focuses on two broad topics. The first delves into the expression and function of SOX2 in cancer focusing on the connection between SOX2 levels and tumor grade as well as patient survival. As part of this discussion, we address the developing connection between SOX2 expression and tumor drug resistance. We also call attention to an under-appreciated property of SOX2, its levels in actively proliferating tumor cells appear to be optimized to maximize tumor growth - too little or too much SOX2 dramatically alters tumor growth. The second topic of this review focuses on the exquisite array of molecular mechanisms that control the expression and transcriptional activity of SOX2. In addition to its complex regulation at the transcriptional level, SOX2 expression and activity are controlled carefully by microRNAs, long non-coding RNAs, and post-translational modifications. In the Conclusion and Future Perspectives section, we point out that there are still important unanswered questions. Addressing these questions is expected to lead to new insights into the functions of SOX2 in cancer, which will help design novels strategies for more effectively treating some of the most deadly cancers.

  3. Manuscript Transcription by Crowdsourcing: Transcribe Bentham

    Directory of Open Access Journals (Sweden)

    Martin Moyle

    2011-02-01

    Full Text Available Transcribe Bentham is testing the feasibility of outsourcing the work of manuscript transcription to members of the public. UCL Library Services holds 60,000 folios of manuscripts of the philosopher and jurist Jeremy Bentham (1748–1832. Transcribe Bentham will digitise 12,500 Bentham folios, and, through a wiki-based interface, allow volunteer transcribers to take temporary ownership of manuscript images and to create TEI-encoded transcription text for final approval by UCL experts. Approved transcripts will be stored and preserved, with the manuscript images, in UCL’s public Digital Collections repository. The project makes innovative use of traditional library material. It will stimulate public engagement with UCL’s scholarly archive collections and the challenges of palaeography and manuscript transcription; it will raise the profile of the work and thought of Jeremy Bentham; and it will create new digital resources for future use by professional researchers. Towards the end of the project, the transcription tool will be made available to other projects and services. This paper is based on a presentation given by the lead author at LIBER’s 39th Annual General Conference in Aarhus, Denmark, 2010.

  4. Structural Basis of Mitochondrial Transcription Initiation.

    Science.gov (United States)

    Hillen, Hauke S; Morozov, Yaroslav I; Sarfallah, Azadeh; Temiakov, Dmitry; Cramer, Patrick

    2017-11-16

    Transcription in human mitochondria is driven by a single-subunit, factor-dependent RNA polymerase (mtRNAP). Despite its critical role in both expression and replication of the mitochondrial genome, transcription initiation by mtRNAP remains poorly understood. Here, we report crystal structures of human mitochondrial transcription initiation complexes assembled on both light and heavy strand promoters. The structures reveal how transcription factors TFAM and TFB2M assist mtRNAP to achieve promoter-dependent initiation. TFAM tethers the N-terminal region of mtRNAP to recruit the polymerase to the promoter whereas TFB2M induces structural changes in mtRNAP to enable promoter opening and trapping of the DNA non-template strand. Structural comparisons demonstrate that the initiation mechanism in mitochondria is distinct from that in the well-studied nuclear, bacterial, or bacteriophage transcription systems but that similarities are found on the topological and conceptual level. These results provide a framework for studying the regulation of gene expression and DNA replication in mitochondria. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. HELP OPTIONS AND MULTIMEDIA LISTENING: STUDENTS’ USE OF SUBTITLES AND THE TRANSCRIPT

    Directory of Open Access Journals (Sweden)

    Maja Grgurović

    2007-02-01

    Full Text Available As multimedia language learning materials become prevalent in foreign and second language classrooms, their design is an important avenue of research in Computer-Assisted Language Learning (CALL. Some argue that the design of the pedagogical materials should be informed by theory such as the interactionist SLA theory, which suggests that input modification can help comprehension, but does not provide specific guidance regarding choices designers should make when they attempt to implement theory-based features like modified input. This empirical study was designed to provide evidence about one such issue: whether subtitles or transcripts are more effective in providing modified input to learners. A multimedia listening activity containing a video of an academic lecture was designed to offer help in the form of target language subtitles (captions and lecture transcripts in cases of comprehension breakdowns. Eighteen intermediate ESL students enrolled in an academic listening class at a research university participated in the study. Two tests and questionnaires in addition to screen recordings were used to analyze students' performance on the activity and their use of help. The results indicate that participants interacted with the subtitles more frequently and for longer periods of time than with the transcript. Also, the study identified four patterns of learner interaction with the help options. Since, overall, the participants interacted with help less than half of the time they opened help pages, an important challenge in investigating help options lies in finding ways to promote the use of help.

  6. The Carbon City Index (CCI)

    DEFF Research Database (Denmark)

    Boyd, Britta; Straatman, Bas; Mangalagiu, Diana

    This paper presents a consumption-based Carbon City Index for CO2 emissions in a city. The index is derived from regional consumption and not from regional production. It includes imports and exports of emissions, factual emission developments, green investments as well as low carbon city...

  7. Index Selection in Relational Databases

    NARCIS (Netherlands)

    Choenni, R.S.; Blanken, Henk; Chang, S.C.

    Intending to develop a tool which aims to support the physical design of relational databases can not be done without considering the problem of index selection. Generally the problem is split into a primary and secondary index selection problem and the selection is done per table. Whereas much

  8. A Tourism Financial Conditions Index

    NARCIS (Netherlands)

    C-L. Chang (Chia-Lin); H-K. Hsu (Hui-Kuang); M.J. McAleer (Michael)

    2014-01-01

    markdownabstract__Abstract__ The paper uses monthly data on financial stock index returns, tourism stock sub-index returns, effective exchange rate returns and interest rate differences from April 2005 – August 2013 for Taiwan that applies Chang’s (2014) novel approach for constructing a tourism

  9. Maslov index for Hamiltonian systems

    Directory of Open Access Journals (Sweden)

    Alessandro Portaluri

    2008-01-01

    Full Text Available The aim of this article is to give an explicit formula for computing the Maslov index of the fundamental solutions of linear autonomous Hamiltonian systems in terms of the Conley-Zehnder index and the map time one flow.

  10. Probability theory a comprehensive course

    CERN Document Server

    Klenke, Achim

    2014-01-01

    This second edition of the popular textbook contains a comprehensive course in modern probability theory. Overall, probabilistic concepts play an increasingly important role in mathematics, physics, biology, financial engineering and computer science. They help us in understanding magnetism, amorphous media, genetic diversity and the perils of random developments at financial markets, and they guide us in constructing more efficient algorithms.   To address these concepts, the title covers a wide variety of topics, many of which are not usually found in introductory textbooks, such as:   • limit theorems for sums of random variables • martingales • percolation • Markov chains and electrical networks • construction of stochastic processes • Poisson point process and infinite divisibility • large deviation principles and statistical physics • Brownian motion • stochastic integral and stochastic differential equations. The theory is developed rigorously and in a self-contained way, with the c...

  11. Understanding peace a comprehensive introduction

    CERN Document Server

    Fox, Michael Allen

    2013-01-01

    Understanding Peace: A Comprehensive Introduction fills the need for an original, contemporary examination of peace that is challenging, informative, and empowering. This well-researched, fully documented, and highly accessible textbook moves beyond fixation on war to highlight the human capacity for nonviolent cooperation in everyday life and in conflict situations. After deconstructing numerous ideas about war and explaining its heavy costs to humans, animals, and the environment, discussion turns to evidence for the existence of peaceful societies. Further topics include the role of nonviolence in history, the nature of violence and aggression, and the theory and practice of nonviolence. The book offers two new moral arguments against war, and concludes by defining peace carefully from different angles and then describing conditions for creating a culture of peace. Understanding Peace brings a fresh philosophical perspective to discussions of peace, and also addresses down-to-earth issues about effecting ...

  12. Building Information Modeling Comprehensive Overview

    Directory of Open Access Journals (Sweden)

    Sergey Kalinichuk

    2015-07-01

    Full Text Available The article is addressed to provide a comprehensive review on recently accelerated development of the Information Technology within project market such as industrial, engineering, procurement and construction. Author’s aim is to cover the last decades of the growth of the Information and Communication Technology in construction industry in particular Building Information Modeling and testifies that the problem of a choice of the effective project realization method not only has not lost its urgency, but has also transformed into one of the major condition of the intensive technology development. All of it has created a great impulse on shortening the project duration and has led to the development of various schedule compression techniques what becomes a focus of modern construction.

  13. Investigating reading comprehension through EEG

    Directory of Open Access Journals (Sweden)

    Luciane Baretta

    2012-12-01

    Full Text Available http://dx.doi.org/10.5007/2175-8026.2012n63p69   Experimental studies point that different factors can influence reading comprehension, such as the topic, text type, reading task, and others. The advances in technologies for the past decades have provided researchers with several possibilities to investigate what goes on in one’s brain since their eyes meet the page until comprehension is achieved. Since the mid-80’s, numerous studies have been conducted with the use of the electroencephalogram (EEG to investigate the process of reading, through the analysis of different components – n400, n100 or n1, P2, among others. These components reveal, for example, how the brain integrates the meaning of a specific word in the semantic context of a given sentence.  based on previous studies, which demonstrate that different types of words affect cognitive load, this paper aims at investigating how the brain processes function and content words inserted in expository and narrative texts with suitable / unsuitable conclusions. results showed that the type of text and word influence the cognitive load in different scalp areas (midline, right and left hemispheres. The  n1s were more pronounced to the content words inserted in narrative texts and to the function words inserted in the expository type of texts, corroborating former studies.

  14. The transcript release factor PTRF augments ribosomal gene transcription by facilitating reinitiation of RNA polymerase I

    Czech Academy of Sciences Publication Activity Database

    Jansa, Petr; Burek, C.; Sander, E. E.; Grummt, I.

    2001-01-01

    Roč. 29, č. 2 (2001), s. 423-429 ISSN 0305-1048 Institutional research plan: CEZ:AV0Z5052915 Keywords : rDNA transcription * PTRF * transcription reinitiation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.373, year: 2001

  15. Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription.

    Science.gov (United States)

    Gerasimova, N S; Pestov, N A; Kulaeva, O I; Clark, D J; Studitsky, V M

    2016-05-26

    RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.

  16. A New Index of Democracy

    Directory of Open Access Journals (Sweden)

    Jesús M. de Miguel

    2014-01-01

    Full Text Available The present paper analyses and revises the latest Democracy Index published by the Economist Intelligence Unit in the United Kingdom. We analyze the changes produced in the index from 2006 to 2011, as well as in the five basic factors that constitute the index: electoral process and pluralism; civil liberties; the functioning of government; political participation; and political culture. The analysis of these factors ?measured by sixty variables? has made it possible to develop a new index, based on the data from 167 countries, and calculate a revised ranking. Countries have been classified into four types: democracies, flawed democracies, mixed systems, and authoritarian/totalitarian regimes. The new index permits a better understanding of the impact of the crisis through variables such as economic growth, human development, quality of life, corruption, and violence.

  17. A new relative hazard index

    International Nuclear Information System (INIS)

    Smith, C.F.; Burnett, T.W.T; Kastenberg, W.E.

    1976-01-01

    Several indexes for the evaluation of relative radionuclide hazards have been previously developed. In this paper, a new relative hazard index is derived for use in the assessment of the future burden to mankind from the presence of radionuclides in the environment. Important features of this hazard index are that it takes into account multiple decay schemes, non-equilibrium conditions, and finite time periods. As an application of this hazard index, a comparison is made between thermal reactor radioactive waste and the uranium required as fuel with the following conclusions: (1) For short time intervals (d 234 U breaking the uranium decay chain. (3) For long time intervals of concern (d >= 500 000 years), the reactor waste and consumed uranium indexes are equal after a much shorter decay time (approximately 10 years.) (author)

  18. The Intertwined Roles of DNA Damage and Transcription

    OpenAIRE

    Di Palo, Giacomo

    2016-01-01

    DNA damage and transcription are two interconnected events. Transcription can induce damage and scheduled DNA damage can be required for transcription. Here, we analyzed genome-wide distribution of 8oxodG-marked oxidative DNA damage obtained by OxiDIP-Seq, and we found a correlation with transcription of protein coding genes.

  19. Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

    Directory of Open Access Journals (Sweden)

    Kevin M. Harlen

    2016-06-01

    Full Text Available Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II C-terminal domain (CTD and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7, we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3′ end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3′ splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes.

  20. Battles and hijacks: Noncoding transcription in plants

    KAUST Repository

    Ariel, Federico

    2015-06-01

    Noncoding RNAs have emerged as major components of the eukaryotic transcriptome. Genome-wide analyses revealed the existence of thousands of long noncoding RNAs (lncRNAs) in several plant species. Plant lncRNAs are transcribed by the plant-specific RNA polymerases Pol IV and Pol V, leading to transcriptional gene silencing, as well as by Pol II. They are involved in a wide range of regulatory mechanisms impacting on gene expression, including chromatin remodeling, modulation of alternative splicing, fine-tuning of miRNA activity, and the control of mRNA translation or accumulation. Recently, dual noncoding transcription by alternative RNA polymerases was implicated in epigenetic and chromatin conformation dynamics. This review integrates the current knowledge on the regulatory mechanisms acting through plant noncoding transcription. © 2015 Elsevier Ltd.

  1. Phonemic Transcriptions in British and American Dictionaries

    Directory of Open Access Journals (Sweden)

    Rastislav Šuštaršič

    2005-06-01

    Full Text Available In view of recent criticisms concerning vowel symbols in some British English dictionaries (in particular by J. Windsor Lewis in JIPA (Windsor Lewis, 2003, with regard to the Oxford Dictionary of Pronunciation (Upton, 2001, this article extends the discussion on English phonemic transcriptions by including those that typically occur in standard American dictionaries, and by comparing the most common conventions of British and American dictionaries. In addition to symbols for both vowels and consonants, the paper also deals with the different representations of word accentuation and the issue of consistency regarding application of phonemic (systemic, broad, rather than phonetic (allophonic, narrow transcription. The different transcriptions are assessed from the points of view of their departures from the International Phonetic Alphabet, their overlapping with orthographic representation (spelling and their appropriateness in terms of reflecting actual pronunciation in standard British and/or American pronunciation.

  2. Crowdsourcing for quantifying transcripts: An exploratory study.

    Science.gov (United States)

    Azzam, Tarek; Harman, Elena

    2016-02-01

    This exploratory study attempts to demonstrate the potential utility of crowdsourcing as a supplemental technique for quantifying transcribed interviews. Crowdsourcing is the harnessing of the abilities of many people to complete a specific task or a set of tasks. In this study multiple samples of crowdsourced individuals were asked to rate and select supporting quotes from two different transcripts. The findings indicate that the different crowdsourced samples produced nearly identical ratings of the transcripts, and were able to consistently select the same supporting text from the transcripts. These findings suggest that crowdsourcing, with further development, can potentially be used as a mixed method tool to offer a supplemental perspective on transcribed interviews. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Transcription regulatory networks analysis using CAGE

    KAUST Repository

    Tegnér, Jesper N.

    2009-10-01

    Mapping out cellular networks in general and transcriptional networks in particular has proved to be a bottle-neck hampering our understanding of biological processes. Integrative approaches fusing computational and experimental technologies for decoding transcriptional networks at a high level of resolution is therefore of uttermost importance. Yet, this is challenging since the control of gene expression in eukaryotes is a complex multi-level process influenced by several epigenetic factors and the fine interplay between regulatory proteins and the promoter structure governing the combinatorial regulation of gene expression. In this chapter we review how the CAGE data can be integrated with other measurements such as expression, physical interactions and computational prediction of regulatory motifs, which together can provide a genome-wide picture of eukaryotic transcriptional regulatory networks at a new level of resolution. © 2010 by Pan Stanford Publishing Pte. Ltd. All rights reserved.

  4. Runx transcription factors in neuronal development

    Directory of Open Access Journals (Sweden)

    Shiga Takashi

    2008-08-01

    Full Text Available Abstract Runt-related (Runx transcription factors control diverse aspects of embryonic development and are responsible for the pathogenesis of many human diseases. In recent years, the functions of this transcription factor family in the nervous system have just begun to be understood. In dorsal root ganglion neurons, Runx1 and Runx3 play pivotal roles in the development of nociceptive and proprioceptive sensory neurons, respectively. Runx appears to control the transcriptional regulation of neurotrophin receptors, numerous ion channels and neuropeptides. As a consequence, Runx contributes to diverse aspects of the sensory system in higher vertebrates. In this review, we summarize recent progress in determining the role of Runx in neuronal development.

  5. Transcriptional inhibition by the retinoblastoma protein

    DEFF Research Database (Denmark)

    Fattaey, A; Helin, K; Harlow, E

    1993-01-01

    The retinoblastoma protein, pRB, appears to play a key role in coordinating the regulation of cell cycle position and transcriptional events. pRB undergoes specific cell-cycle-dependent phosphorylation, being underphosphorylated in G1 and heavily phosphorylated in S, G2, and M. The underphosphory......The retinoblastoma protein, pRB, appears to play a key role in coordinating the regulation of cell cycle position and transcriptional events. pRB undergoes specific cell-cycle-dependent phosphorylation, being underphosphorylated in G1 and heavily phosphorylated in S, G2, and M......-mediated transcription would be lost by mutation in the retinoblastoma gene in human tumours, by pRB's interaction with DNA tumour virus oncoproteins, or by phosphorylation during the cell cycle....

  6. Deciphering the Innate Lymphoid Cell Transcriptional Program

    Directory of Open Access Journals (Sweden)

    Cyril Seillet

    2016-10-01

    Full Text Available Innate lymphoid cells (ILCs are enriched at mucosal surfaces, where they provide immune surveillance. All ILC subsets develop from a common progenitor that gives rise to pre-committed progenitors for each of the ILC lineages. Currently, the temporal control of gene expression that guides the emergence of these progenitors is poorly understood. We used global transcriptional mapping to analyze gene expression in different ILC progenitors. We identified PD-1 to be specifically expressed in PLZF+ ILCp and revealed that the timing and order of expression of the transcription factors NFIL3, ID2, and TCF-1 was critical. Importantly, induction of ILC lineage commitment required only transient expression of NFIL3 prior to ID2 and TCF-1 expression. These findings highlight the importance of the temporal program that permits commitment of progenitors to the ILC lineage, and they expand our understanding of the core transcriptional program by identifying potential regulators of ILC development.

  7. Transcription as a Threat to Genome Integrity.

    Science.gov (United States)

    Gaillard, Hélène; Aguilera, Andrés

    2016-06-02

    Genomes undergo different types of sporadic alterations, including DNA damage, point mutations, and genome rearrangements, that constitute the basis for evolution. However, these changes may occur at high levels as a result of cell pathology and trigger genome instability, a hallmark of cancer and a number of genetic diseases. In the last two decades, evidence has accumulated that transcription constitutes an important natural source of DNA metabolic errors that can compromise the integrity of the genome. Transcription can create the conditions for high levels of mutations and recombination by its ability to open the DNA structure and remodel chromatin, making it more accessible to DNA insulting agents, and by its ability to become a barrier to DNA replication. Here we review the molecular basis of such events from a mechanistic perspective with particular emphasis on the role of transcription as a genome instability determinant.

  8. Molecular imaging of transcriptional regulation during inflammation

    Directory of Open Access Journals (Sweden)

    Carlsen Harald

    2010-04-01

    Full Text Available Abstract Molecular imaging enables non-invasive visualization of the dynamics of molecular processes within living organisms in vivo. Different imaging modalities as MRI, SPECT, PET and optic imaging are used together with molecular probes specific for the biological process of interest. Molecular imaging of transcription factor activity is done in animal models and mostly in transgenic reporter mice, where the transgene essentially consists of a promoter that regulates a reporter gene. During inflammation, the transcription factor NF-κB is widely involved in orchestration and regulation of the immune system and almost all imaging studies in this field has revolved around the role and regulation of NF-κB. We here present a brief introduction to experimental use and design of transgenic reporter mice and a more extensive review of the various studies where molecular imaging of transcriptional regulation has been applied during inflammation.

  9. Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control.

    Science.gov (United States)

    Celton, Jean-Marc; Gaillard, Sylvain; Bruneau, Maryline; Pelletier, Sandra; Aubourg, Sébastien; Martin-Magniette, Marie-Laure; Navarro, Lionel; Laurens, François; Renou, Jean-Pierre

    2014-07-01

    Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined. Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3'UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21-23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants. © 2014 INRA. New Phytologist © 2014 New Phytologist Trust.

  10. Harnessing transcription for bioproduction in cyanobacteria

    DEFF Research Database (Denmark)

    Stensjö, Karin; Vavitsas, Konstantinos; Tyystjärvi, Taina

    2018-01-01

    Sustainable production of biofuels and other valuable compounds is one of our future challenges. One tempting possibility is to use photosynthetic cyanobacteria as production factories. Currently, tools for genetic engineering of cyanobacteria are yet not good enough to exploit the full potential...... of cyanobacteria. A wide variety of expression systems will be required to adjust both the expression of heterologous enzyme(s) and metabolic routes to the best possible balance, allowing the optimal production of a particular substance. In bacteria, transcription, especially the initiation of transcription, has...

  11. Transcription and the aspect ratio of DNA

    DEFF Research Database (Denmark)

    Olsen, Kasper Wibeck; Bohr, Jakob

    2013-01-01

    analysis of transcription. It is shown that under certain reasonable assumptions transcription is only possible if the aspect ratio is in the regime corresponding to further twisting. We find this constraint to be in agreement with long-established crystallographic studies of DNA.......Two separate regimes exist for the aspect ratio of DNA. A low aspect regime where DNA will twist further under strain and a high aspect regime where DNA will untwist under strain. The question of the overall geometry, i.e. the aspect ratio, of DNA is revisited from the perspective of a geometrical...

  12. Transcription instability in high-risk neuroblastoma is associated with a global perturbation of chromatin domains.

    Science.gov (United States)

    Zanon, Carlo; Tonini, Gian Paolo

    2017-11-01

    Chromosome instability has a pivotal role among the hallmarks of cancer, but its transcriptional counterpart is rarely considered a relevant factor in cell destabilization. To examine transcription instability (TIN), we first devised a metric we named TIN index and used it to evaluate TIN on a dataset containing more than 500 neuroblastoma samples. We found that metastatic tumors from high-risk (HR) patients are characterized by significantly different TIN index values compared to low/intermediate-risk patients. Our results indicate that the TIN index is a good predictor of neuroblastoma patient's outcome, and a related TIN index gene signature (TIN-signature) is also able to predict the neuroblastoma patient's outcome with high confidence. Interestingly, we find that TIN-signature genes have a strong positional association with superenhancers in neuroblastoma tumors. Finally, we show that TIN is linked to chromatin structural domains and interferes with their integrity in HR neuroblastoma patients. This novel approach to gene expression analysis broadens the perspective of genome instability investigations to include functional aspects. © 2017 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

  13. Cook Inlet and Kenai Peninsula, Alaska ESI: INDEX (Index Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains vector polygons representing the boundaries used in the creation of the Environmental Sensitivity Index (ESI) for Cook Inlet and Kenai...

  14. Negative index effects from a homogeneous positive index prism

    Science.gov (United States)

    Marcus, Sherman W.; Epstein, Ariel

    2017-12-01

    Cellular structured negative index metamaterials in the form of a right triangular prism have often been tested by observing the refraction of a beam across the prism hypotenuse which is serrated in order to conform to the cell walls. We show that not only can this negative index effect be obtained from a homogeneous dielectric prism having a positive index of refraction, but in addition, for sampling at the walls of the cellular structure, the phase in the material has the illusory appearance of moving in a negative direction. Although many previous reports relied on refraction direction and phase velocity of prism structures to verify negative index design, our investigation indicates that to unambiguously demonstrate material negativity additional empirical evidence is required.

  15. Louisiana ESI: LG_INDEX (Large Index Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains vector polygons representing the boundaries of all the hardcopy cartographic products produced as part of the Environmental Sensitivity Index...

  16. Bristol Bay, Alaska Subarea ESI: INDEX (Index Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains vector polygons representing the boundaries of all the hardcopy cartographic products produced as part of the Environmental Sensitivity Index...

  17. A new multi-sensor integrated index for drought monitoring

    Science.gov (United States)

    Jiao, W.; Wang, L.; Tian, C.

    2017-12-01

    Drought is perceived as one of the most expensive and least understood natural disasters. The remote-sensing-based integrated drought indices, which integrate multiple variables, could reflect the drought conditions more comprehensively than single drought indices. However, most of current remote-sensing-based integrated drought indices focus on agricultural drought (i.e., deficit in soil moisture), their application in monitoring meteorological drought (i.e., deficit in precipitation) was limited. More importantly, most of the remote-sensing-based integrated drought indices did not take into consideration of the spatially non-stationary nature of the related variables, so such indices may lose essential local details when integrating multiple variables. In this regard, we proposed a new mathematical framework for generating integrated drought index for meteorological drought monitoring. The geographically weighted regression (GWR) model and principal component analysis were used to composite Moderate-resolution Imaging Spectroradiometer (MODIS) based temperature condition index (TCI), the Vegetation Index based on the Universal Pattern Decomposition method (VIUPD) based vegetation condition index (VCI), tropical rainfall measuring mission (TRMM) based Precipitation Condition Index (PCI) and Advanced Microwave Scanning Radiometer-EOS (AMSR-E) based soil moisture condition index (SMCI). We called the new remote-sensing-based integrated drought index geographical-location-based integrated drought index (GLIDI). We examined the utility of the GLIDI for drought monitoring in various climate divisions across the continental United States (CONUS). GLIDI showed high correlations with in-situ drought indices and outperformed most other existing drought indices. The results also indicate that the performance of GLIDI is not affected by environmental factors such as land cover, precipitation, temperature and soil conditions. As such, the GLIDI has considerable potential for

  18. Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors.

    Directory of Open Access Journals (Sweden)

    Georgi K Marinov

    Full Text Available Mitochondria contain their own circular genome, with mitochondria-specific transcription and replication systems and corresponding regulatory proteins. All of these proteins are encoded in the nuclear genome and are post-translationally imported into mitochondria. In addition, several nuclear transcription factors have been reported to act in mitochondria, but there has been no comprehensive mapping of their occupancy patterns and it is not clear how many other factors may also be found in mitochondria. Here we address these questions by using ChIP-seq data from the ENCODE, mouseENCODE and modENCODE consortia for 151 human, 31 mouse and 35 C. elegans factors. We identified 8 human and 3 mouse transcription factors with strong localized enrichment over the mitochondrial genome that was usually associated with the corresponding recognition sequence motif. Notably, these sites of occupancy are often the sites with highest ChIP-seq signal intensity within both the nuclear and mitochondrial genomes and are thus best explained as true binding events to mitochondrial DNA, which exist in high copy number in each cell. We corroborated these findings by immunocytochemical staining evidence for mitochondrial localization. However, we were unable to find clear evidence for mitochondrial binding in ENCODE and other publicly available ChIP-seq data for most factors previously reported to localize there. As the first global analysis of nuclear transcription factors binding in mitochondria, this work opens the door to future studies that probe the functional significance of the phenomenon.

  19. Deterministic indexing for packed strings

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Skjoldjensen, Frederik Rye

    2017-01-01

    Given a string S of length n, the classic string indexing problem is to preprocess S into a compact data structure that supports efficient subsequent pattern queries. In the deterministic variant the goal is to solve the string indexing problem without any randomization (at preprocessing time...... or query time). In the packed variant the strings are stored with several character in a single word, giving us the opportunity to read multiple characters simultaneously. Our main result is a new string index in the deterministic and packed setting. Given a packed string S of length n over an alphabet σ...

  20. The Nurses' Well-Being Index and Factors Influencing This Index among Nurses in Central China: A Cross-Sectional Study.

    Directory of Open Access Journals (Sweden)

    Runtang Meng

    Full Text Available A discussion and analysis of factors that contribute to nurses' happiness index can be useful in developing effective interventions to improve nurses' enthusiasm, sense of honor and pride and to improve the efficiency and quality of medical services.In this study, 206 registered nurses at the 2011 annual encounter for 12 Hanchuan hospitals completed a questionnaire survey that covered three aspects of the well-being index and thus served as a comprehensive well-being and general information tool.Based on their index score, the nurses' overall happiness level was moderate. The dimensions of the happiness index are listed in descending order of their contribution to the nurses' comprehensive happiness levels: health concerns, friendly relationships, self-worth, altruism, vitality, positive emotions, personality development, life satisfaction and negative emotions. Four variables (positive emotion, life satisfaction, negative emotions, and friendly relationships jointly explained 47.80% of the total variance of the happiness index; positive emotions had the greatest impact on the happiness index.Appropriate nursing interventions can improve nurses' happiness index scores, thereby increasing nurses' motivation and promoting the development of their nursing practice.

  1. The Nurses’ Well-Being Index and Factors Influencing This Index among Nurses in Central China: A Cross-Sectional Study

    Science.gov (United States)

    Liu, Bing; Hu, Ying; Yu, Chuanhua

    2015-01-01

    Backgrounds/Objectives A discussion and analysis of factors that contribute to nurses’ happiness index can be useful in developing effective interventions to improve nurses’ enthusiasm, sense of honor and pride and to improve the efficiency and quality of medical services. Methods In this study, 206 registered nurses at the 2011 annual encounter for 12 Hanchuan hospitals completed a questionnaire survey that covered three aspects of the well-being index and thus served as a comprehensive well-being and general information tool. Results Based on their index score, the nurses’ overall happiness level was moderate. The dimensions of the happiness index are listed in descending order of their contribution to the nurses’ comprehensive happiness levels: health concerns, friendly relationships, self-worth, altruism, vitality, positive emotions, personality development, life satisfaction and negative emotions. Four variables (positive emotion, life satisfaction, negative emotions, and friendly relationships) jointly explained 47.80% of the total variance of the happiness index; positive emotions had the greatest impact on the happiness index. Conclusions Appropriate nursing interventions can improve nurses’ happiness index scores, thereby increasing nurses’ motivation and promoting the development of their nursing practice. PMID:26680594

  2. Intelligent indexing: a semi-automated, trainable system for field labeling

    Science.gov (United States)

    Clawson, Robert; Barrett, William

    2015-01-01

    We present Intelligent Indexing: a general, scalable, collaborative approach to indexing and transcription of non-machinereadable documents that exploits visual consensus and group labeling while harnessing human recognition and domain expertise. In our system, indexers work directly on the page, and with minimal context switching can navigate the page, enter labels, and interact with the recognition engine. Interaction with the recognition engine occurs through preview windows that allow the indexer to quickly verify and correct recommendations. This interaction is far superior to conventional, tedious, inefficient post-correction and editing. Intelligent Indexing is a trainable system that improves over time and can provide benefit even without prior knowledge. A user study was performed to compare Intelligent Indexing to a basic, manual indexing system. Volunteers report that using Intelligent Indexing is less mentally fatiguing and more enjoyable than the manual indexing system. Their results also show that it reduces significantly (30.2%) the time required to index census records, while maintaining comparable accuracy. (a video demonstration is available at http://youtube.com/gqdVzEPnBEw)

  3. Comprehension and production of idioms in dysphasia.

    Science.gov (United States)

    Bush, P G; Drummond, S S

    1985-10-01

    The comprehension and production of idioms was investigated in 10 dysphasic adults. Two different tasks, one comprehension and the other production, were developed. The production task required the subject to verbally explain 15 idioms. The comprehension task necessitated the selection of the correct figurative representation of the idiom from four illustrations: a literal, a literal variation, a figurative, and an unrelated picture. Results indicated no significant correlation between overall comprehension and production performances. No significant difference was found between the comprehension or the production of idioms when type or severity of dysphasia was considered. A significant difference was found, however, in the type of incorrect response, in that subjects selected the literal depiction more often than other foil representations for the comprehension.

  4. Comparison of pause predictions of two sequence-dependent transcription models

    International Nuclear Information System (INIS)

    Bai, Lu; Wang, Michelle D

    2010-01-01

    Two recent theoretical models, Bai et al (2004, 2007) and Tadigotla et al (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for pause locations, and different predictions on pause kinetics and mechanisms. Here we present a comprehensive comparison of the two models. We show that while they have comparable predictive power of pause locations at low NTP concentrations, the Bai et al model is more accurate than Tadigotla et al at higher NTP concentrations. The pausing kinetics predicted by Bai et al is also consistent with time-course transcription reactions, while Tadigotla et al is unsuited for this type of kinetic prediction. More importantly, the two models in general predict different pausing mechanisms even for the same pausing sites, and the Bai et al model provides an explanation more consistent with recent single molecule observations

  5. Swine Flu -A Comprehensive View

    Science.gov (United States)

    Singh, Vandana; Sood, Meenakshi

    2012-07-01

    The present article is aimed on comprehensive view of Swine flu. It was first isolated from pigs in 1930 in USA. Pandemic caused by H1N1 in 2009 brought it in limelight. Itís a viral respiratory disease caused by viruses that infects pigs, resulting in nasal secretions, barking cough, decreased appetite, and listless behavior. Swine virus consist of eight RNA strands, one strand derived from human flu strains, two from avian (bird) strains, and five from swine strains. Swine flu spreads from infected person to healthy person by inhalation or ingestion of droplets contaminated with virus while sneezing or coughing. Two antiviral agents have been reported to help prevent or reduce the effects of swine flu, flu shot and nasal spray. WHO recommended for pandemic period to prevent its future outbreaks through vaccines or non-vaccines means. Antiviral drugs effective against this virus are Tamiflu and Relenza. Rapid antigen testing (RIDT), DFA testing, viral culture, and molecular testing (RT-PCR) are used for its diagnosis in laboratory

  6. NRC comprehensive records disposition schedule

    International Nuclear Information System (INIS)

    1983-05-01

    Effective January 1, 1982, NRC will institute records retention and disposal practives in accordance with the approved Comprehensive Records Disposition Schedule (CRDS). CRDS is comprised of NRC Schedules (NRCS) 1 to 4 which apply to the agency's program or substantive records and General Records Schedules (GRS) 1 to 24 which apply to housekeeping or facilitative records. NRCS-I applies to records common to all or most NRC offices; NRCS-II applies to program records as found in the various offices of the Commission, Atomic Safety and Licensing Board Panel, and the Atomic Safety and Licensing Appeal Panel; NRCS-III applies to records accumulated by the Advisory Committee on Reactor Safeguards; and NRCS-IV applies to records accumulated in the various NRC offices under the Executive Director for Operations. The schedules are assembled functionally/organizationally to facilitate their use. Preceding the records descriptions and disposition instructions for both NRCS and GRS, there are brief statements on the organizational units which accumulate the records in each functional area, and other information regarding the schedules' applicability

  7. Comprehensive approach to diabetic nephropathy

    Directory of Open Access Journals (Sweden)

    Bancha Satirapoj

    2014-09-01

    Full Text Available Diabetic nephropathy (DN is a leading cause of mortality and morbidity in patients with diabetes. This complication reflects a complex pathophysiology, whereby various genetic and environmental factors determine susceptibility and progression to end-stage renal disease. DN should be considered in patients with type 1 diabetes for at least 10 years who have microalbuminuria and diabetic retinopathy, as well as in patients with type 1 or type 2 diabetes with macroalbuminuria in whom other causes for proteinuria are absent. DN may also present as a falling estimated glomerular filtration rate with albuminuria as a minor presenting feature, especially in patients taking renin–angiotensin–aldosterone system inhibitors (RAASi. The pathological characteristic features of disease are three major lesions: diffuse mesangial expansion, diffuse thickened glomerular basement membrane, and hyalinosis of arterioles. Functionally, however, the pathophysiology is reflected in dysfunction of the mesangium, the glomerular capillary wall, the tubulointerstitium, and the vasculature. For all diabetic patients, a comprehensive approach to management including glycemic and hypertensive control with RAASi combined with lipid control, dietary salt restriction, lowering of protein intake, increased physical activity, weight reduction, and smoking cessation can reduce the rate of progression of nephropathy and minimize the risk for cardiovascular events. This review focuses on the latest published data dealing with the mechanisms, diagnosis, and current treatment of DN.

  8. Abdominopelvic washings: A comprehensive review

    Directory of Open Access Journals (Sweden)

    Erika F Rodriguez

    2013-01-01

    Full Text Available Intraperitoneal spread may occur with gynecological epithelial neoplasms, as well as with non-gynecological malignancies, which may result in serosal involvement with or without concomitant effusion. Therefore, washings in patients with abdominopelvic tumors represent important specimens for cytologic examination. They are primarily utilized for staging ovarian cancers, although their role has decreased in staging of endometrial and cervical carcinoma. Abdominopelvic washings can be positive in a variety of pathologic conditions, including benign conditions, borderline neoplastic tumors, locally invasive tumors, or distant metastases. In a subset of cases, washings can be diagnostically challenging due to the presence of co-existing benign cells (e.g., mesothelial hyperplasia, endosalpingiosis, or endometriosis, lesions in which there is only minimal atypia (e.g., serous borderline tumors or scant atypical cells, and the rarity of specific tumor types (e.g., mesothelioma. Ancillary studies including immunocytochemistry and fluorescence in situ hybridization may be required in difficult cases to resolve the diagnosis. This article provides a comprehensive and contemporary review of abdominopelvic washings in the evaluation of gynecologic and non-gynecologic tumors, including primary peritoneal and mesothelial entities.

  9. CEDR: Comprehensive Epidemiologic Data Resource

    Energy Technology Data Exchange (ETDEWEB)

    1993-08-01

    The Department of Energy (DOE) and its predecessor agencies have a long history of epidemiologic research programs. The main focus of these programs has been the Health and Mortality Study of the DOE work force. This epidemiologic study began in 1964 with a feasibility study of workers at the Hanford facility. Studies of other populations exposed to radiation have also been supported, including the classic epidemiologic study of radium dial painters and studies of atomic bomb survivors. From a scientific perspective, these epidemiologic research program have been productive, highly credible, and formed the bases for many radiological protection standards. Recently, there has been concern that, although research results were available, the data on which these results were based were not easily obtained by interested investigators outside DOE. Therefore, as part of an effort to integrate and broaden access to its epidemiologic information, the DOE has developed the Comprehensive Epidemiologic Data Resource (CEDR) Program. Included in this effort is the development of a computer information system for accessing the collection of CEDR data and its related descriptive information. The epidemiologic data currently available through the CEDAR Program consist of analytic data sets, working data sets, and their associated documentation files. In general, data sets are the result of epidemiologic studies that have been conducted on various groups of workers at different DOE facilities during the past 30 years.

  10. The Comprehensive Emergent Literacy Model

    Directory of Open Access Journals (Sweden)

    Leigh Rohde

    2015-03-01

    Full Text Available The early skills of Emergent Literacy include the knowledge and abilities related to the alphabet, phonological awareness, symbolic representation, and communication. However, existing models of emergent literacy focus on discrete skills and miss the perspective of the surrounding environment. Early literacy skills, including their relationship to one another, and the substantial impact of the setting and context, are critical in ensuring that children gain all of the preliminary skills and awareness they will need to become successful readers and writers. Research findings over the last few decades have led to a fuller understanding of all that emergent literacy includes, resulting in a need for a new, more comprehensive model. A new model, described in this article, strives to explain how emergent literacy can be viewed as an interactive process of skills and context rather than a linear series of individual components. Early literacy learning opportunities are more likely to happen when teachers have a solid knowledge base of emergent literacy and child development. Research has shown that preschool teachers with limited knowledge about literacy development are significantly less able to provide such experiences for children. Teachers will be better able to facilitate all of the components of emergent literacy if they have access to, and understanding of, a model that describes the components, their interactions, and the importance of environmental factors in supporting children.

  11. A comprehensive computational mutation structure- function ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research is indexed by Science Citation Index (SciSearch), Scopus, ... proteinases are excellent substrates for drug ... Figure 1: Schematic representation of prioritization pipeline in identifying regions with ...

  12. Comprehensive energy management eco routing & velocity profiles

    CERN Document Server

    Brandstätter, Bernhard

    2017-01-01

    The book discusses the emerging topic of comprehensive energy management in electric vehicles from the viewpoint of academia and from the industrial perspective. It provides a seamless coverage of all relevant systems and control algorithms for comprehensive energy management, their integration on a multi-core system and their reliability assurance (validation and test). Relevant European projects contributing to the evolvement of comprehensive energy management in fully electric vehicles are also included.

  13. Mitochondrial transcription factor A protects human retinal ...

    African Journals Online (AJOL)

    Purpose: To investigate the impact of mitochondrial transcription factor A (TFAM), as a modulator of NF-κB, on proliferation of hypoxia-induced human retinal endothelial cell (HREC), and the probable mechanism. Methods: After exposure to hypoxia (1 % O2) for 5 days, cell proliferation and cell cycle of HREC were ...

  14. RNA Polymerase II–The Transcription Machine

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 3. RNA Polymerase II – The Transcription Machine - Nobel Prize in Chemistry 2006. Jiyoti Verma Aruna Naorem Anand Kumar Manimala Sen Parag Sadhale. General Article Volume 12 Issue 3 March 2007 pp 47-53 ...

  15. Polyphenol Compound as a Transcription Factor Inhibitor

    Directory of Open Access Journals (Sweden)

    Seyeon Park

    2015-10-01

    Full Text Available A target-based approach has been used to develop novel drugs in many therapeutic fields. In the final stage of intracellular signaling, transcription factor–DNA interactions are central to most biological processes and therefore represent a large and important class of targets for human therapeutics. Thus, we focused on the idea that the disruption of protein dimers and cognate DNA complexes could impair the transcriptional activation and cell transformation regulated by these proteins. Historically, natural products have been regarded as providing the primary leading compounds capable of modulating protein–protein or protein-DNA interactions. Although their mechanism of action is not fully defined, polyphenols including flavonoids were found to act mostly as site-directed small molecule inhibitors on signaling. There are many reports in the literature of screening initiatives suggesting improved drugs that can modulate the transcription factor interactions responsible for disease. In this review, we focus on polyphenol compound inhibitors against dimeric forms of transcription factor components of intracellular signaling pathways (for instance, c-jun/c-fos (Activator Protein-1; AP-1, c-myc/max, Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB and β-catenin/T cell factor (Tcf.

  16. Polyphenol Compound as a Transcription Factor Inhibitor.

    Science.gov (United States)

    Park, Seyeon

    2015-10-30

    A target-based approach has been used to develop novel drugs in many therapeutic fields. In the final stage of intracellular signaling, transcription factor-DNA interactions are central to most biological processes and therefore represent a large and important class of targets for human therapeutics. Thus, we focused on the idea that the disruption of protein dimers and cognate DNA complexes could impair the transcriptional activation and cell transformation regulated by these proteins. Historically, natural products have been regarded as providing the primary leading compounds capable of modulating protein-protein or protein-DNA interactions. Although their mechanism of action is not fully defined, polyphenols including flavonoids were found to act mostly as site-directed small molecule inhibitors on signaling. There are many reports in the literature of screening initiatives suggesting improved drugs that can modulate the transcription factor interactions responsible for disease. In this review, we focus on polyphenol compound inhibitors against dimeric forms of transcription factor components of intracellular signaling pathways (for instance, c-jun/c-fos (Activator Protein-1; AP-1), c-myc/max, Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and β-catenin/T cell factor (Tcf)).

  17. Cross-Family Transcription Factor Interactions

    NARCIS (Netherlands)

    Bemer, Marian; Dijk, van Aalt-Jan; Immink, Richard G.H.; Angenent, Gerco C.

    2017-01-01

    Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the expression of the corresponding gene in an additive fashion or cooperate by physical interactions, forming larger

  18. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

    Science.gov (United States)

    Le Billan, Florian; Amazit, Larbi; Bleakley, Kevin; Xue, Qiong-Yao; Pussard, Eric; Lhadj, Christophe; Kolkhof, Peter; Viengchareun, Say; Fagart, Jérôme; Lombès, Marc

    2018-05-07

    Mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) are two closely related hormone-activated transcription factors that regulate major pathophysiologic functions. High homology between these receptors accounts for the crossbinding of their corresponding ligands, MR being activated by both aldosterone and cortisol and GR essentially activated by cortisol. Their coexpression and ability to bind similar DNA motifs highlight the need to investigate their respective contributions to overall corticosteroid signaling. Here, we decipher the transcriptional regulatory mechanisms that underlie selective effects of MRs and GRs on shared genomic targets in a human renal cellular model. Kinetic, serial, and sequential chromatin immunoprecipitation approaches were performed on the period circadian protein 1 ( PER1) target gene, providing evidence that both receptors dynamically and cyclically interact at the same target promoter in a specific and distinct transcriptional signature. During this process, both receptors regulate PER1 gene by binding as homo- or heterodimers to the same promoter region. Our results suggest a novel level of MR-GR target gene regulation, which should be considered for a better and integrated understanding of corticosteroid-related pathophysiology.-Le Billan, F., Amazit, L., Bleakley, K., Xue, Q.-Y., Pussard, E., Lhadj, C., Kolkhof, P., Viengchareun, S., Fagart, J., Lombès, M. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

  19. Transcriptional networks in epithelial-mesenchymal transition.

    Directory of Open Access Journals (Sweden)

    Christo Venkov

    Full Text Available Epithelial-mesenchymal transition (EMT changes polarized epithelial cells into migratory phenotypes associated with loss of cell-cell adhesion molecules and cytoskeletal rearrangements. This form of plasticity is seen in mesodermal development, fibroblast formation, and cancer metastasis.Here we identify prominent transcriptional networks active during three time points of this transitional process, as epithelial cells become fibroblasts. DNA microarray in cultured epithelia undergoing EMT, validated in vivo, were used to detect various patterns of gene expression. In particular, the promoter sequences of differentially expressed genes and their transcription factors were analyzed to identify potential binding sites and partners. The four most frequent cis-regulatory elements (CREs in up-regulated genes were SRY, FTS-1, Evi-1, and GC-Box, and RNA inhibition of the four transcription factors, Atf2, Klf10, Sox11, and SP1, most frequently binding these CREs, establish their importance in the initiation and propagation of EMT. Oligonucleotides that block the most frequent CREs restrain EMT at early and intermediate stages through apoptosis of the cells.Our results identify new transcriptional interactions with high frequency CREs that modulate the stability of cellular plasticity, and may serve as targets for modulating these transitional states in fibroblasts.

  20. 2014 Environmental Performance Index (EPI)

    Data.gov (United States)

    National Aeronautics and Space Administration — The 2014 Environmental Performance Index (EPI) ranks 178 countries on 20 performance indicators in the following 9 policy categories: health impacts, air quality,...