Sample records for comprehensive transcript index

  1. Comprehensive transcriptional map of primate brain development (United States)

    Bakken, Trygve E.; Miller, Jeremy A.; Ding, Song-Lin; Sunkin, Susan M.; Smith, Kimberly A.; Ng, Lydia; Szafer, Aaron; Dalley, Rachel A.; Royall, Joshua J.; Lemon, Tracy; Shapouri, Sheila; Aiona, Kaylynn; Arnold, James; Bennett, Jeffrey L.; Bertagnolli, Darren; Bickley, Kristopher; Boe, Andrew; Brouner, Krissy; Butler, Stephanie; Byrnes, Emi; Caldejon, Shiella; Carey, Anita; Cate, Shelby; Chapin, Mike; Chen, Jefferey; Dee, Nick; Desta, Tsega; Dolbeare, Tim A.; Dotson, Nadia; Ebbert, Amanda; Fulfs, Erich; Gee, Garrett; Gilbert, Terri L.; Goldy, Jeff; Gourley, Lindsey; Gregor, Ben; Gu, Guangyu; Hall, Jon; Haradon, Zeb; Haynor, David R.; Hejazinia, Nika; Hoerder-Suabedissen, Anna; Howard, Robert; Jochim, Jay; Kinnunen, Marty; Kriedberg, Ali; Kuan, Chihchau L.; Lau, Christopher; Lee, Chang-Kyu; Lee, Felix; Luong, Lon; Mastan, Naveed; May, Ryan; Melchor, Jose; Mosqueda, Nerick; Mott, Erika; Ngo, Kiet; Nyhus, Julie; Oldre, Aaron; Olson, Eric; Parente, Jody; Parker, Patrick D.; Parry, Sheana; Pendergraft, Julie; Potekhina, Lydia; Reding, Melissa; Riley, Zackery L.; Roberts, Tyson; Rogers, Brandon; Roll, Kate; Rosen, David; Sandman, David; Sarreal, Melaine; Shapovalova, Nadiya; Shi, Shu; Sjoquist, Nathan; Sodt, Andy J.; Townsend, Robbie; Velasquez, Lissette; Wagley, Udi; Wakeman, Wayne B.; White, Cassandra; Bennett, Crissa; Wu, Jennifer; Young, Rob; Youngstrom, Brian L.; Wohnoutka, Paul; Gibbs, Richard A.; Rogers, Jeffrey; Hohmann, John G.; Hawrylycz, Michael J.; Hevner, Robert F.; Molnár, Zoltán; Phillips, John W.; Dang, Chinh; Jones, Allan R.; Amaral, David G.; Bernard, Amy; Lein, Ed S.


    The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high resolution transcriptional atlas of rhesus monkey brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical parcellation of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons, and cortical layers and areas acquire adult-like molecular profiles surprisingly late postnatally. Disparate cell populations exhibit distinct developmental timing but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, and approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny. PMID:27409810

  2. A new comprehensive index for drought monitoring with TM data (United States)

    Wang, Yuanyuan


    Drought is one of the most important and frequent natural hazards to agriculture production in North China Plain. To improve agriculture water management, accurate drought monitoring information is needed. This study proposed a method for comprehensive drought monitoring by combining a meteorological index and three satellite drought indices of TM data together. SPI (Standard Precipitation Index), the meteorological drought index, is used to measure precipitation deficiency. Three satellite drought indices (Temperature Vegetation Drought Index, Land Surface Water Index, Modified Perpendicular Drought Index) are used to evaluate agricultural drought risk by exploring data from various channels (VIS, NIR, SWIR, TIR). Considering disparities in data ranges of different drought indices, normalization is implemented before combination. First, SPI is normalized to 0 — 100 given that its normal range is -4 - +4. Then, the three satellite drought indices are normalized to 0 - 100 according to the maximum and minimum values in the image, and aggregated using weighted average method (the result is denoted as ADI, Aggregated drought index). Finally, weighed geometric mean of SPI and ADI are calculated (the result is denoted as DIcombined). A case study in North China plain using three TM images acquired during April-May 2007 show that the method proposed in this study is effective. In spatial domain, DIcombined demonstrates dramatically more details than SPI; in temporal domain, DIcombined shows more reasonable drought development trajectory than satellite indices that are derived from independent TM images.

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

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


    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 expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes

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    Kanai Akio


    Full Text Available Abstract Background Recent studies have identified thousands of sense-antisense gene pairs across different genomes by computational mapping of cDNA sequences. These studies have shown that approximately 25% of all transcriptional units in the human and mouse genomes are involved in cis-sense-antisense pairs. However, the number of known sense-antisense pairs remains limited because currently available cDNA sequences represent only a fraction of the total number of transcripts comprising the transcriptome of each cell type. Methods To discover novel antisense transcripts encoded in the antisense strand of important genes, such as cancer-related genes, we conducted expression analyses of antisense transcripts using our custom microarray platform along with 2376 probes designed specifically to detect the potential antisense transcripts of 501 well-known genes suitable for cancer research. Results Using colon cancer tissue and normal tissue surrounding the cancer tissue obtained from 6 patients, we found that antisense transcripts without poly(A tails are expressed from approximately 80% of these well-known genes. This observation is consistent with our previous finding that many antisense transcripts expressed in a cell are poly(A-. We also identified 101 and 71 antisense probes displaying a high level of expression specifically in normal and cancer tissues respectively. Conclusion Our microarray analysis identified novel antisense transcripts with expression profiles specific to cancer tissue, some of which might play a role in the regulatory networks underlying oncogenesis and thus are potential targets for further experimental validation. Our microarray data are available at

  5. Gastrointestinal Fibroblasts Have Specialized, Diverse Transcriptional Phenotypes: A Comprehensive Gene Expression Analysis of Human Fibroblasts.

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    Youichi Higuchi

    Full Text Available Fibroblasts are the principal stromal cells that exist in whole organs and play vital roles in many biological processes. Although the functional diversity of fibroblasts has been estimated, a comprehensive analysis of fibroblasts from the whole body has not been performed and their transcriptional diversity has not been sufficiently explored. The aim of this study was to elucidate the transcriptional diversity of human fibroblasts within the whole body.Global gene expression analysis was performed on 63 human primary fibroblasts from 13 organs. Of these, 32 fibroblasts from gastrointestinal organs (gastrointestinal fibroblasts: GIFs were obtained from a pair of 2 anatomical sites: the submucosal layer (submucosal fibroblasts: SMFs and the subperitoneal layer (subperitoneal fibroblasts: SPFs. Using hierarchical clustering analysis, we elucidated identifiable subgroups of fibroblasts and analyzed the transcriptional character of each subgroup.In unsupervised clustering, 2 major clusters that separate GIFs and non-GIFs were observed. Organ- and anatomical site-dependent clusters within GIFs were also observed. The signature genes that discriminated GIFs from non-GIFs, SMFs from SPFs, and the fibroblasts of one organ from another organ consisted of genes associated with transcriptional regulation, signaling ligands, and extracellular matrix remodeling.GIFs are characteristic fibroblasts with specific gene expressions from transcriptional regulation, signaling ligands, and extracellular matrix remodeling related genes. In addition, the anatomical site- and organ-dependent diversity of GIFs was also discovered. These features of GIFs contribute to their specific physiological function and homeostatic maintenance, and create a functional diversity of the gastrointestinal tract.

  6. Development and evaluation of a comprehensive drought index. (United States)

    Esfahanian, Elaheh; Nejadhashemi, A Pouyan; Abouali, Mohammad; Adhikari, Umesh; Zhang, Zhen; Daneshvar, Fariborz; Herman, Matthew R


    Droughts are known as the world's costliest natural disasters impacting a variety of sectors. Despite their wide range of impacts, no universal drought definition has been defined. The goal of this study is to define a universal drought index that considers drought impacts on meteorological, agricultural, hydrological, and stream health categories. Additionally, predictive drought models are developed to capture both categorical (meteorological, hydrological, and agricultural) and overall impacts of drought. In order to achieve these goals, thirteen commonly used drought indices were aggregated to develop a universal drought index named MASH. The thirteen drought indices consist of four drought indices from each meteorological, hydrological, and agricultural categories, and one from the stream health category. Cluster analysis was performed to find the three closest indices in each category. Then the closest drought indices were averaged in each category to create the categorical drought score. Finally, the categorical drought scores were simply averaged to develop the MASH drought index. In order to develop predictive drought models for each category and MASH, the ReliefF algorithm was used to rank 90 variables and select the best variable set. Using the best variable set, the adaptive neuro-fuzzy inference system (ANFIS) was used to develop drought predictive models and their accuracy was examined using the 10-fold cross validation technique. The models' predictabilities ranged from R 2  = 0.75 for MASH to R 2  = 0.98 for the hydrological drought model. The results of this study can help managers to better position resources to cope with drought by reducing drought impacts on different sectors. Copyright © 2016 Elsevier Ltd. All rights reserved.

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


    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.

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

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    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.

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

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    Deyholos Michael K


    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

  10. Comprehensive lipid tetrad index, atherogenic index and lipid peroxidation: Surrogate markers for increased cardiovascular risk in psoriasis

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    S Sunitha


    Full Text Available Background and Objectives: Recently, the concept of "psoriatic march" has come to the fore, in which chronic cutaneous inflammation in psoriasis leads to systemic inflammation which, in conjunction with increased oxidative stress, triggers a cascade of events resulting in increased cardiovascular risk in patients with severe psoriasis. We, therefore, decided to study the levels of some biochemical cardiovascular risk markers: lipid peroxidation (malondialdehyde, lipoprotein (a, lipid indices and atherogenic index, in patients with psoriasis and their association with disease severity. Methods: Fortyfive patients with psoriasis and 45 age and gender-matched healthy controls were included in this cross-sectional study. Disease severity was assessed by the Psoriasis Area Severity Index (PASI. Serum malondialdehyde, lipoprotein (a and fasting lipid profile were estimated in all study subjects. Lipoprotein ratios were computed using standard formulae. Atherogenic index was calculated as ratio of lipoprotein (a/high-density lipoprotein. Results: In psoriasis, we observed significantly higher levels of malondialdehyde, total cholesterol, low-density lipoprotein cholesterol, non-high-density lipoprotein cholesterol, lipoprotein (a, lipid ratios, atherogenic index and comprehensive lipid tetrad index, compared to controls. These levels were directly proportional to disease severity. Serum levels of malondialdehyde correlated positively with serum lipoprotein (a, comprehensive lipid tetrad index and atherogenic index. Limitations: Different morphological types of psoriasis were not included and follow-up post-therapy was not done. A larger sample size would have validated the results further. Conclusion: Our results indicate that psoriasis, especially the severe variants, are associated with increased oxidative stress and dyslipidemia, which correlate positively with atherogenic index and hence, an increased cardiovascular risk.

  11. Comprehensive lipid tetrad index, atherogenic index and lipid peroxidation: Surrogate markers for increased cardiovascular risk in psoriasis. (United States)

    Sunitha, S; Rajappa, Medha; Thappa, Devinder Mohan; Chandrashekar, Laxmisha; Munisamy, Malathi; Revathy, G; Priyadarssini, M


    Recently, the concept of "psoriatic march" has come to the fore, in which chronic cutaneous inflammation in psoriasis leads to systemic inflammation which, in conjunction with increased oxidative stress, triggers a cascade of events resulting in increased cardiovascular risk in patients with severe psoriasis. We, therefore, decided to study the levels of some biochemical cardiovascular risk markers: lipid peroxidation (malondialdehyde), lipoprotein (a), lipid indices and atherogenic index, in patients with psoriasis and their association with disease severity. Forty five patients with psoriasis and 45 age and gender-matched healthy controls were included in this cross-sectional study. Disease severity was assessed by the Psoriasis Area Severity Index (PASI). Serum malondialdehyde, lipoprotein (a) and fasting lipid profile were estimated in all study subjects. Lipoprotein ratios were computed using standard formulae. Atherogenic index was calculated as ratio of lipoprotein (a)/high-density lipoprotein. In psoriasis, we observed significantly higher levels of malondialdehyde, total cholesterol, low-density lipoprotein cholesterol, non-high-density lipoprotein cholesterol, lipoprotein (a), lipid ratios, atherogenic index and comprehensive lipid tetrad index, compared to controls. These levels were directly proportional to disease severity. Serum levels of malondialdehyde correlated positively with serum lipoprotein (a), comprehensive lipid tetrad index and atherogenic index. Different morphological types of psoriasis were not included and follow-up post-therapy was not done. A larger sample size would have validated the results further. Our results indicate that psoriasis, especially the severe variants, are associated with increased oxidative stress and dyslipidemia, which correlate positively with atherogenic index and hence, an increased cardiovascular risk.

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

    DEFF Research Database (Denmark)

    Sivertsen, Gunnar; Larsen, Birger


    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 chapte...

  13. A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear (United States)

    Corneveaux, Jason J.; Ohmen, Jeffrey; White, Cory; Allen, April N.; Lusis, Aldons J.; Van Camp, Guy; Huentelman, Matthew J.; Friedman, Rick A.


    The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at

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

    KAUST Repository

    Kulakovskiy, Ivan V.


    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,, 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.

  15. HOCOMOCO: a comprehensive collection of human transcription factor binding sites models (United States)

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


    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,, 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. Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. (United States)

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


    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.

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

    KAUST Repository

    Wenger, A. M.


    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.

  18. Comprehensive analysis of TCP transcription factors and their expression during cotton (Gossypium arboreum) fiber early development (United States)

    Ma, Jun; Liu, Fang; Wang, Qinglian; Wang, Kunbo; Jones, Don C.; Zhang, Baohong


    TCP proteins are plant-specific transcription factors implicated to perform a variety of physiological functions during plant growth and development. In the current study, we performed for the first time the comprehensive analysis of TCP gene family in a diploid cotton species, Gossypium arboreum, including phylogenetic analysis, chromosome location, gene duplication status, gene structure and conserved motif analysis, as well as expression profiles in fiber at different developmental stages. Our results showed that G. arboreum contains 36 TCP genes, distributing across all of the thirteen chromosomes. GaTCPs within the same subclade of the phylogenetic tree shared similar exon/intron organization and motif composition. In addition, both segmental duplication and whole-genome duplication contributed significantly to the expansion of GaTCPs. Many these TCP transcription factor genes are specifically expressed in cotton fiber during different developmental stages, including cotton fiber initiation and early development. This suggests that TCP genes may play important roles in cotton fiber development. PMID:26857372

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

  20. Comprehensive and comparative transcription analyses of the complement pathway in rainbow trout. (United States)

    Köbis, Judith M; Rebl, Alexander; Kühn, Carsten; Korytář, Tomáš; Köllner, Bernd; Goldammer, Tom


    The complement system is one of the most ancient and most essential innate immune cascades throughout the animal kingdom. Survival of aquatic animals, such as rainbow trout, depends on this early inducible, efficient immune cascade. Despite increasing research on genes coding for complement components in bony fish, some complement-related genes are still unknown in salmonid fish. In the present study, we characterize the genes encoding complement factor D (CFD), CD93 molecule (CD93), and C-type lectin domain family 4, member M (CLEC4M) from rainbow trout (Oncorhynchus mykiss). Subsequently, we performed comprehensive and comparative expression analyses of 36 complement genes including CFD, CD93, and CLEC4M and further putative complement-associated genes to obtain general information about the functional gene interaction within the complement pathway in fish. These quantification analyses were conducted in liver, spleen and gills of healthy fish of two rainbow trout strains, selected for survival (strain BORN) and growth (Import strain), respectively. The present expression study clearly confirms for rainbow trout that liver represents the primary site of complement expression. Spleen and gills also express most complement genes, although the mean transcript levels were generally lower than in liver. The transcription data suggest a contribution of spleen and gills to complement activity. The comparison of the two rainbow trout strains revealed a generally similar complement gene expression. However, a significantly lower expression of numerous genes especially in spleen seems characteristic for the BORN strain. This suggests a strain-specific complement pathway regulation under the selected rearing conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

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    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.

  2. The comprehensive aerospace index (CASI): Tracking the economic performance of the aerospace industry (United States)

    Mattedi, Adriana Prest; Mantegna, Rosario Nunzio; Ramos, Fernando Manuel; Rosa, Reinaldo Roberto


    In this paper, we described the Comprehensive AeroSpace Index (CASI), a financial index aimed at representing the economic performance of the aerospace industry. CASI is build upon a data set of approximately 20 years of daily close prices set, from January 1987 to June 2007, from a comprehensive sample of leading aerospace-related companies with stocks negotiated on the New York Exchange (NYSE) and on the over-the-counter (OTC) markets. We also introduced the sub-indices CASI-AERO, for aeronautical segment, and CASI-SAT, for satellite segment, and considered the relation between them. These three indices are compared to others aerospace indices and to more traditional general financial indices like DJIA, S&P500 and Nasdaq. Our results have shown that the CASI is an index that describes very well the aerospace sector behavior, since it is able to reflect the aeronautical segment comportment as well as the satellite one. Therefore, in this sense, it can be considered as a representative index of the aerospace sector. Moreover, the creation of two sub-indices, the CASI-AERO and the CASI-SAT, allows to elucidate capital movements within the aerospace sector, particularly those of speculative nature, like the bubble and crash of 1998-2001.

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

    Directory of Open Access Journals (Sweden)

    Argiles Angel


    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.

  4. [Comprehensive evaluation of multi-quality characteristic indexes of Chaenomeles speciosa and C. sinensis fruits]. (United States)

    Liu, Shiyao; Bai, Zhichuan; Li, Jiana


    To evaluate the 8 main quality characteristic indexes of fruit-using Chaenomeles speciosa and C. sinensis fruits produced in Chongqing and explore the comprehensive assessment for the fresh eating-quality of the samples based on the theory of fuzzy comprehensive. The total sugar content, titratable acid content, ascorbic acid content and superoxide dismutase (SOD) activity of fresh samples were determined, and the oleanolic acid, ursolic acid, total flavones and total saponins content of dried sample were determined by HPLC and colorimetry method. The fuzzy probability method was used to comprehensively evaluate their fresh eating-quality of the fruit-using C. speciosa and C. sinensis fruits produced in Chongqing. The mean SOD activity of C. speciosa and C. sinensis fresh fruits separately was 15.99 U x mg(-1) and 27.40 U x mg(-1), respectively. And the fresh fruit titratable acid content, total sugar content, ascorbic acid content separately was 0.357 g x L(-1), 0.854 mg x L(-1), 1.118 mg x L(-1) and 0.252 g x L(-1), 0.845 mg x L(-1), 1.260 mg x L(-1), respectively. The oleanolic acid, ursolic acid, total flavones and total saponins content was 0.320%, 0.461%, 43.90 mg x g(-1), 23.11 mg x g(-1) and 0.255%, 0.176%, 41.24 mg x g(-1), 15.01 mg x g(-1), respectively. The Chaenomeles speciosa and C. sinensis sample quality mean comprehensive evaluation value was 0.599 and 0.367 based on the fuzzy probability method. The edible quality of fruit-using C. speciosa fruits are better than C. sinensis fruits produced in Chongqing. And the fuzzy probability method could be used to quality comprehensive evaluation of samples containing many trait paramaters.

  5. A new comprehensive index for discriminating adulteration in bovine raw milk. (United States)

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


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

    International Nuclear Information System (INIS)

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


    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

  7. Comprehensive drought characteristics analysis based on a nonlinear multivariate drought index (United States)

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


    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.

  8. Teacher Talk: Transcript Analysis as a Method of Improving Effectiveness during Comprehension Strategies Instruction (United States)

    Robertson, Dana Andrew


    This mixed-methods study compared the outcomes of 5 general education teachers in a suburban, upper-middle-class elementary school engaged in transcript analysis during small-group reading strategies instruction to those obtained when engaged in audio analysis. Over a 5-month period, the teachers recorded one lesson per week and debriefed with the…

  9. The Comprehensive Complication Index: a New Measure of the Burden of Complications After Hyperthermic Intraperitoneal Chemotherapy. (United States)

    Dumitra, Sinziana; O'Leary, Michael; Raoof, Mustafa; Wakabayashi, Mark; Dellinger, Thanh H; Han, Ernest S; Lee, Stephen J; Lee, Byrne


    Cytoreduction and hyperthermic intraperitoneal chemotherapy (HIPEC) are complex surgeries with multiple comorbidities. The Clavien-Dindo classification (CDC) is the most commonly used method to report surgical morbidity, but limits it to the highest-grade complication. The Comprehensive Complication Index (CCI) is a score ranging from 0 to 100, calculated using all 30-day complications and their treatment after abdominal surgery. The aim of this study is to assess the CCI's validity in the HIPEC patient population. A review of our institutional cytoreduction database from 2009 to 2015 was undertaken. Patient demographics, pathology, Peritoneal Carcinomatosis Index (PCI), complications and their treatments, and length of stay (LOS) were reviewed. The CCI was calculated for each patient. Linear regression was used to assess whether the CCI and CDC were predictors of LOS. Of 157 patients reviewed, 110 (70.1%) underwent HIPEC. The majority were female (77, 66.9%), and the mean age was 53.7 years. Mean PCI was 13.2 [interquartile range (IQR) 7-18]. Median CDC was grade 2 (IQR 0-2), and only 9.8% had CDC of grade 4 or higher. Mean CCI was 21.4, while the median was 20.9 (IQR 0-30.8). Mean LOS was 16.2 days, while the median was 11 days (IQR 8-15 days). The CCI strongly correlated with LOS with coefficient of 0.46 [95% confidence interval (CI) 0.38-0.54, p = 0.000]. The CCI is an adequate tool to capture all complications and their overall burden in patients having undergone HIPEC. This study shows that the CCI can predict LOS and could be used to quantify and compare the burden of multiple complications.

  10. Comprehensive study in the inhibitory effect of berberine on gene transcription, including TATA box. (United States)

    Wang, Yugang; Kheir, Michael M; Chai, Yushuang; Hu, Jun; Xing, Dongming; Lei, Fan; Du, Lijun


    Berberine (BBR) is an established natural DNA intercalator with numerous pharmacological functions. However, currently there are neither detailed reports concerning the distribution of this alkaloid in living cells nor reports concerning the relationship between BBR's association with DNA and the function of DNA. Here we report that the distribution of BBR within the nucleus can be observed 30 minutes after drug administration, and that the content of berberine in the nucleus peaks at around 4 µmol, which is twelve hours after drug administration. The spatial conformation of DNA and chromatin was altered immediately after their association with BBR. Moreover, this association can effectively suppress the transcription of DNA in living cell systems and cell-free systems. Electrophoretic mobility shift assays (EMSA) demonstrated further that BBR can inhibit the association between the TATA binding protein (TBP) and the TATA box in the promoter, and this finding was also attained in living cells by chromatin immunoprecipitation (ChIP). Based on results from this study, we hypothesize that berberine can suppress the transcription of DNA in living cell systems, especially suppressing the association between TBP and the TATA box by binding with DNA and, thus, inhibiting TATA box-dependent gene expression in a non-specific way. This novel study has significantly expanded the sphere of knowledge concerning berberine's pharmacological effects, beginning at its paramount initial interaction with the TATA box.

  11. Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers (United States)

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


    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

  12. A comprehensive study design reveals treatment- and transcript abundance–dependent concordance between RNA-seq and microarray data (United States)

    Wang, Charles; Gong, Binsheng; Bushel, Pierre R.; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Xu, Joshua; Fang, Hong; Hong, Huixiao; Shen, Jie; Su, Zhenqiang; Meehan, Joe; Li, Xiaojin; Yang, Lu; Li, Haiqing; Łabaj, Paweł P.; Kreil, David P.; Megherbi, Dalila; Florian, Caiment; Gaj, Stan; van Delft, Joost; Kleinjans, Jos; Scherer, Andreas; Viswanath, Devanarayan; Wang, Jian; Yang, Yong; Qian, Hui-Rong; Lancashire, Lee J.; Bessarabova, Marina; Nikolsky, Yuri; Furlanello, Cesare; Chierici, Marco; Albanese, Davide; Jurman, Giuseppe; Riccadonna, Samantha; Filosi, Michele; Visintainer, Roberto; Zhang, Ke K.; Li, Jianying; Hsieh, Jui-Hua; Svoboda, Daniel L.; Fuscoe, James C.; Deng, Youping; Shi, Leming; Paules, Richard S.; Auerbach, Scott S.; Tong, Weida


    RNA-seq facilitates unbiased genome-wide gene-expression profiling. However, its concordance with the well-established microarray platform must be rigorously assessed for confident uses in clinical and regulatory application. Here we use a comprehensive study design to generate Illumina RNA-seq and Affymetrix microarray data from the same set of liver samples of rats under varying degrees of perturbation by 27 chemicals representing multiple modes of action (MOA). The cross-platform concordance in terms of differentially expressed genes (DEGs) or enriched pathways is highly correlated with treatment effect size, gene-expression abundance and the biological complexity of the MOA. RNA-seq outperforms microarray (90% versus 76%) in DEG verification by quantitative PCR and the main gain is its improved accuracy for low expressed genes. Nonetheless, predictive classifiers derived from both platforms performed similarly. Therefore, the endpoint studied and its biological complexity, transcript abundance, and intended application are important factors in transcriptomic research and for decision-making. PMID:25150839

  13. Tomato plants increase their tolerance to low temperature in a chilling acclimation process entailing comprehensive transcriptional and metabolic adjustments. (United States)

    Barrero-Gil, Javier; Huertas, Raúl; Rambla, José Luís; Granell, Antonio; Salinas, Julio


    Low temperature is a major environmental stress that seriously compromises plant development, distribution and productivity. Most crops are from tropical origin and, consequently, chilling sensitive. Interestingly, however, some tropical plants, are able to augment their chilling tolerance when previously exposed to suboptimal growth temperatures. Yet, the molecular and physiological mechanisms underlying this adaptive process, termed chilling acclimation, still remain practically unknown. Here, we demonstrate that tomato plants can develop a chilling acclimation response, which includes comprehensive transcriptomic and metabolic adjustments leading to increased chilling tolerance. More important, our results reveal strong resemblances between this response and cold acclimation, the process whereby plants from temperate regions raise their freezing tolerance after exposure to low, non-freezing temperatures. Both chilling and cold acclimation are regulated by a similar set of transcription factors and hormones, and share common defence mechanisms, including the accumulation of compatible solutes, the mobilization of antioxidant systems and the rearrangement of the photosynthetic machinery. Nonetheless, we have found some important divergences that may account for the freezing sensitivity of tomato plants. The data reported in this manuscript should foster new research into the chilling acclimation response with the aim of improving tomato tolerance to low temperature. © 2016 John Wiley & Sons Ltd.

  14. Reliability and Validity of a Simplified Comprehensive Assessment Tool for Feeding Support: Kuchi-Kara Taberu Index. (United States)

    Maeda, Keisuke; Shamoto, Hiroshi; Wakabayashi, Hidetaka; Enomoto, Junko; Takeichi, Mika; Koyama, Tamami


    To verify the reliability and validity and develop an English version of an instrument (Kuchi-Kara Taberu Index (KT Index)) to comprehensively assess and intervene in problems with eating and swallowing. Multicenter cross-sectional study. Nursing homes. Individuals aged 65 and older (mean age 88.3 ± 6.8; 80.0% female) who had lived in a nursing home for longer than 1 month (N = 115). The KT index consisted of 13 items: desire to eat, overall condition, respiratory condition, oral condition, cognitive function while eating, oral preparatory and propulsive phases, dysphagia severity, position and endurance while eating, eating, daily life, food intake level, food modification, and nutrition. Weighted kappa coefficients, Cronbach alpha, and Spearman rank correlation coefficients were determined. Weighted kappa values in the inter- and intrarater reliability tests ranged from 0.54 to 0.96 and 0.68 to 0.98, respectively. Cronbach alpha was 0.892. Spearman rank correlation coefficients (r) between the total KT index and external criteria were determined (Functional Oral Intake Scale, r = 0.790; Barthel Index, r = 0.830; Mini Nutritional Assessment Short Form, r = 0.582; Cognitive Performance Scale, r = -0.673; all P eating and swallowing conditions are needed. © 2016, Copyright the Authors Journal compilation © 2016, The American Geriatrics Society.

  15. CENTRAL, PEDro, PubMed, and EMBASE are the most comprehensive databases indexing randomized controlled trials of physical therapy interventions. (United States)

    Michaleff, Zoe A; Costa, Leonardo O P; Moseley, Anne M; Maher, Christopher G; Elkins, Mark R; Herbert, Robert D; Sherrington, Catherine


    Many bibliographic databases index research studies evaluating the effects of health care interventions. One study has concluded that the Physiotherapy Evidence Database (PEDro) has the most complete indexing of reports of randomized controlled trials of physical therapy interventions, but the design of that study may have exaggerated estimates of the completeness of indexing by PEDro. The purpose of this study was to compare the completeness of indexing of reports of randomized controlled trials of physical therapy interventions by 8 bibliographic databases. This study was an audit of bibliographic databases. Prespecified criteria were used to identify 400 reports of randomized controlled trials from the reference lists of systematic reviews published in 2008 that evaluated physical therapy interventions. Eight databases (AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO, and PubMed) were searched for each trial report. The proportion of the 400 trial reports indexed by each database was calculated. The proportions of the 400 trial reports indexed by the databases were as follows: CENTRAL, 95%; PEDro, 92%; PubMed, 89%; EMBASE, 88%; CINAHL, 53%; AMED, 50%; Hooked on Evidence, 45%; and PsycINFO, 6%. Almost all of the trial reports (99%) were found in at least 1 database, and 88% were indexed by 4 or more databases. Four trial reports were uniquely indexed by a single database only (2 in CENTRAL and 1 each in PEDro and PubMed). The results are only applicable to searching for English-language published reports of randomized controlled trials evaluating physical therapy interventions. The 4 most comprehensive databases of trial reports evaluating physical therapy interventions were CENTRAL, PEDro, PubMed, and EMBASE. Clinicians seeking quick answers to clinical questions could search any of these databases knowing that all are reasonably comprehensive. PEDro, unlike the other 3 most complete databases, is specific to physical therapy, so studies not

  16. Study on the calculating the second dimension retention index in comprehensive two-dimensional gas chromatography spectrometry

    International Nuclear Information System (INIS)

    Zhao Yaping; Zhang Jun; Wang Bing; Fang Aiqin; Zhang Xiang; Kim, Seong Ho; Bogdanov, Bogdan; McClain, Craig


    A method was developed to calculate the second dimension retention index of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC/TOF MS) data using n-alkanes as reference compounds. The retention times of the C 7 -C 31 alkanes acquired during 24 isothermal experiments cover the 0-6 s retention time area in the second dimension retention time space, which makes it possible to calculate the retention indices of target compounds from the corresponding retention time values without the extension of the retention space of the reference compounds. An empirical function was proposed to show the relationship among the second dimension retention time. the temperature of the second dimension column, and the carbon number of the n-alkanes. The proposed function is able to extend the second dimension retention time beyond the reference n-alkanes by increasing the carbon number. The extension of carbon numbers in reference n-alkanes up to two more carbon atoms introduces less than 10 retention index units (iu) of deviation. The effectiveness of using the proposed method was demonstrated by analyzing a mixture of compound standards in temperature programmed experiments using 6 different initial column temperatures. The standard deviation of the calculated retention index values of the compound standards fluctuated from 1 to 12 iu with a mean standard deviation of 5 iu. (authors)

  17. Treatment implications of predominant polarity and the polarity index: a comprehensive review. (United States)

    Carvalho, Andre F; Quevedo, João; McIntyre, Roger S; Soeiro-de-Souza, Márcio G; Fountoulakis, Konstantinos N; Berk, Michael; Hyphantis, Thomas N; Vieta, Eduard


    Bipolar disorder (BD) is a serious and recurring condition that affects approximately 2.4% of the global population. About half of BD sufferers have an illness course characterized by either a manic or a depressive predominance. This predominant polarity in BD may be differentially associated with several clinical correlates. The concept of a polarity index (PI) has been recently proposed as an index of the antimanic versus antidepressive efficacy of various maintenance treatments for BD. Notwithstanding its potential clinical utility, predominant polarity was not included in the DSM-5 as a BD course specifier. Here we searched computerized databases for original clinical studies on the role of predominant polarity for selection of and response to pharmacological treatments for BD. Furthermore, we systematically searched the Pubmed database for maintenance randomized controlled trials (RCTs) for BD to determine the PI of the various pharmacological agents for BD. We found support from naturalistic studies that bipolar patients with a predominantly depressive polarity are more likely to be treated with an antidepressive stabilization package, while BD patients with a manic-predominant polarity are more frequently treated with an antimanic stabilization package. Furthermore, predominantly manic BD patients received therapeutic regimens with a higher mean PI. The calculated PI varied from 0.4 (for lamotrigine) to 12.1 (for aripiprazole). This review supports the clinical relevance of predominant polarity as a course specifier for BD. Future studies should investigate the role of baseline, predominant polarity as an outcome predictor of BD maintenance RCTs. © The Author 2015. Published by Oxford University Press on behalf of CINP.

  18. The development of Japanese passive syntax as indexed by structural priming in comprehension. (United States)

    Arai, Manabu; Mazuka, Reiko


    A number of previous studies reported a phenomenon of syntactic priming with young children as evidence for cognitive representations required for processing syntactic structures. However, it remains unclear how syntactic priming reflects children's grammatical competence. The current study investigated structural priming of the Japanese passive structure with 5- and 6-year-old children in a visual-world setting. Our results showed a priming effect as anticipatory eye movements to an upcoming referent in these children but the effect was significantly stronger in magnitude in 6-year-olds than in 5-year-olds. Consistently, the responses to comprehension questions revealed that 6-year-olds produced a greater number of correct answers and more answers using the passive structure than 5-year-olds. We also tested adult participants who showed even stronger priming than the children. The results together revealed that language users with the greater linguistic competence with the passives exhibited stronger priming, demonstrating a tight relationship between the effect of priming and the development of grammatical competence. Furthermore, we found that the magnitude of the priming effect decreased over time. We interpret these results in the light of an error-based learning account. Our results also provided evidence for prehead as well as head-independent priming.

  19. The assessment of eco-design with a comprehensive index incorporating environmental impact and economic profit (United States)

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


    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.

  20. Water Quality Assessment for Deep-water Channel area of Guangzhou Port based on the Comprehensive Water Quality Identification Index Method (United States)

    Chen, Yi


    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.

  1. Comprehensive analysis of transcript start sites in ly49 genes reveals an unexpected relationship with gene function and a lack of upstream promoters. (United States)

    Gays, Frances; Koh, Alan S C; Mickiewicz, Katarzyna M; Aust, Jonathan G; Brooks, Colin G


    Comprehensive analysis of the transcription start sites of the Ly49 genes of C57BL/6 mice using the oligo-capping 5'-RACE technique revealed that the genes encoding the "missing self" inhibitory receptors, Ly49A, C, G, and I, were transcribed from multiple broad regions in exon 1, in the intron1/exon2 region, and upstream of exon -1b. Ly49E was also transcribed in this manner, and uniquely showed a transcriptional shift from exon1 to exon 2 when NK cells were activated in vitro with IL2. Remarkably, a large proportion of Ly49E transcripts was then initiated from downstream of the translational start codon. By contrast, the genes encoding Ly49B and Q in myeloid cells, the activating Ly49D and H receptors in NK cells, and Ly49F in activated T cells, were predominantly transcribed from a conserved site in a pyrimidine-rich region upstream of exon 1. An ∼200 bp fragment from upstream of the Ly49B start site displayed tissue-specific promoter activity in dendritic cell lines, but the corresponding upstream fragments from all other Ly49 genes lacked detectable tissue-specific promoter activity. In particular, none displayed any significant activity in a newly developed adult NK cell line that expressed multiple Ly49 receptors. Similarly, no promoter activity could be found in fragments upstream of intron1/exon2. Collectively, these findings reveal a previously unrecognized relationship between the pattern of transcription and the expression/function of Ly49 receptors, and indicate that transcription of the Ly49 genes expressed in lymphoid cells is achieved in a manner that does not require classical upstream promoters.

  2. Indexed

    CERN Document Server

    Hagy, Jessica


    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, 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.

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

    Ruggieri, Dominique G.; Bass, Sarah B.


    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…

  4. 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.

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


    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.

  6. Validity of the American Board of Orthodontics Discrepancy Index and the Peer Assessment Rating Index for comprehensive evaluation of malocclusion severity. (United States)

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


    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.

  7. Long-term prognostic value of a comprehensive assessment of cardiac magnetic resonance indexes after an ST-segment elevation myocardial infarction. (United States)

    Merlos, Pilar; López-Lereu, Maria P; Monmeneu, Jose V; Sanchis, Juan; Núñez, Julio; Bonanad, Clara; Valero, Ernesto; Miñana, Gema; Chaustre, Fabián; Gómez, Cristina; Oltra, Ricardo; Palacios, Lorena; Bosch, Maria J; Navarro, Vicente; Llácer, Angel; Chorro, Francisco J; Bodí, Vicente


    A variety of cardiac magnetic resonance indexes predict mid-term prognosis in ST-segment elevation myocardial infarction patients. The extent of transmural necrosis permits simple and accurate prediction of systolic recovery. However, its long-term prognostic value beyond a comprehensive clinical and cardiac magnetic resonance evaluation is unknown. We hypothesized that a simple semiquantitative assessment of the extent of transmural necrosis is the best resonance index to predict long-term outcome soon after a first ST-segment elevation myocardial infarction. One week after a first ST-segment elevation myocardial infarction we carried out a comprehensive quantification of several resonance parameters in 206 consecutive patients. A semiquantitative assessment (altered number of segments in the 17-segment model) of edema, baseline and post-dobutamine wall motion abnormalities, first pass perfusion, microvascular obstruction, and the extent of transmural necrosis was also performed. During follow-up (median 51 months), 29 patients suffered a major adverse cardiac event (8 cardiac deaths, 11 nonfatal myocardial infarctions, and 10 readmissions for heart failure). Major cardiac events were associated with more severely altered quantitative and semiquantitative resonance indexes. After a comprehensive multivariate adjustment, the extent of transmural necrosis was the only resonance index independently related to the major cardiac event rate (hazard ratio=1.34 [1.19-1.51] per each additional segment displaying>50% transmural necrosis, P<.001). A simple and non-time consuming semiquantitative analysis of the extent of transmural necrosis is the most powerful cardiac magnetic resonance index to predict long-term outcome soon after a first ST-segment elevation myocardial infarction. Copyright © 2013 Sociedad Española de Cardiología. Published by Elsevier Espana. All rights reserved.

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


    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

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

  10. 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


    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.

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

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


    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.

  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


    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. Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. (United States)

    Ramaprasad, Abhinay; Mourier, Tobias; Naeem, Raeece; Malas, Tareq B; Moussa, Ehab; Panigrahi, Aswini; Vermont, Sarah J; Otto, Thomas D; Wastling, Jonathan; Pain, Arnab


    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.

  14. Transportation cost index : a comprehensive performance measure for transportation and land and its application in OR, FL, and UT : final report. (United States)


    MAP-21 and state laws are placing increasing emphasis on using comprehensive transportation performance measures that include mobility, : safety, economy, livability, equity, and environmental to guide transportation decision-making. One of the tough...

  15. 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

  16. 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


    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

  17. Alternative staffing services. Contract transcription. (United States)

    Tessier, C


    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.

  18. Indexing from thesauri to the semantic web

    CERN Document Server

    de Keyser, Piet


    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

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

    Directory of Open Access Journals (Sweden)

    Margaret E Katz


    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.

  20. Patients Comprehension of Pharmaceutical Package Inserts ...

    African Journals Online (AJOL)

    Patients Comprehension of Pharmaceutical Package ... Tropical Journal of Pharmaceutical Research is indexed by Science Citation Index (SciSearch), Scopus, ... of problem in reading and understanding of PPI by patients [7-9]. It is imperative to know the perception of patients/consumers about PPI. Such type of.

  1. Afghanistan Index

    DEFF Research Database (Denmark)

    Linnet, Poul Martin


    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...... information on progress or lack of progress in the reconstruction of the post Taliban Afghanistan. The index is mainly based on information collected on the internet in order to provide quick access to the original source. The index is under development and thus new information will be added on a continuous...

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

    International Nuclear Information System (INIS)

    Burchsted, C.A.


    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

  3. AP Index (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...

  4. AA Index (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,...

  5. Diversity Index (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...

  6. Walkability Index (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...

  7. Intelligent indexing

    International Nuclear Information System (INIS)

    Farkas, J.


    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

  8. HIV-1 reverse transcription. (United States)

    Hu, Wei-Shau; Hughes, Stephen H


    Reverse transcription and integration are the defining features of the Retroviridae; the common name "retrovirus" derives from the fact that these viruses use a virally encoded enzyme, reverse transcriptase (RT), to convert their RNA genomes into DNA. Reverse transcription is an essential step in retroviral replication. This article presents an overview of reverse transcription, briefly describes the structure and function of RT, provides an introduction to some of the cellular and viral factors that can affect reverse transcription, and discusses fidelity and recombination, two processes in which reverse transcription plays an important role. In keeping with the theme of the collection, the emphasis is on HIV-1 and HIV-1 RT.

  9. Isaac Asimov's library of the universe. Index. (United States)

    Asimov, Isaac

    A comprehensive index to the complete set of Isaac Asimov's thirty-two volume Library of the Universe, a series of space science books that introduce young readers to the facts and mysteries of the cosmos.

  10. Index of international publications in aerospace medicine. (United States)


    The 5th edition of the Index of International Publications in Aerospace Medicine is a comprehensive : listing of international publications in clinical aerospace medicine, operational aerospace medicine, : aerospace physiology, environmental medicine...

  11. Validation of the prosthetic esthetic index

    DEFF Research Database (Denmark)

    Özhayat, Esben B; Dannemand, Katrine


    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...

  12. Index of international publications in aerospace medicine (United States)


    The Index of International Publications in Aerospace Medicine is a comprehensive listing of international publications in clinical aerospace medicine, operational aerospace medicine, aerospace physiology, environmental medicine/physiology, diving med...

  13. Indexing mechanisms

    International Nuclear Information System (INIS)

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


    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.)

  14. HIV-1 Reverse Transcription


    Hu, Wei-Shau; Hughes, Stephen H.


    Reverse transcription and integration are the defining features of the Retroviridae; the common name “retrovirus” derives from the fact that these viruses use a virally encoded enzyme, reverse transcriptase (RT), to convert their RNA genomes into DNA. Reverse transcription is an essential step in retroviral replication. This article presents an overview of reverse transcription, briefly describes the structure and function of RT, provides an introduction to some of the cellular and viral fact...

  15. Author Index

    Indian Academy of Sciences (India)

    Author Index. Alshaary, A. A. see Sharaf, M. A., 9. Banajh, M. A. see Sharaf, M. A., 9. Burbidge Geoffrey see Narlikar Jayant, V., 67. Chen, H. D. see Li, K. J., 147. Chen, Y. Q. see Huang, C., 139. Cui Wenyuan Evolution of the Distribution of Neutron Exposures in the Galaxy. Disc: An Analytical Model, 55. Dhurde Samir see ...

  16. Author Index

    Indian Academy of Sciences (India)

    Author Index. Alecian, E. see Samadhi, R., 171; see Goupil, M.-J., 249. Antia, H. M. Helioseismology, 161. Ashoka, B. N. see Seetha, S., 301. Baudin, F. see Samadhi, R., 171. Boehm, T. see Goupil, M.-J., 249. Catala, C. see Goupil, M.-J., 249. Cunha Margarida S. Asteroseismic Theory of Rapidly Oscillating Ap Stars, 213.


    Indian Academy of Sciences (India)


    SUBJECT INDEX. Absorption. Effect of NaCl on the spectral and kinetic properties of cresyl violet (CV)-sodium dodecyl sulphate (SDS) complex. 299. Acid catalysts. Temperature-programmed desorption of water and ammonia on sulphated zirconia catalysts for measuring their strong acidity and acidity distribution. 281.

  18. Author Index

    Indian Academy of Sciences (India)

    J. Astrophys. Astr. (2008) 29, 405–409. Author Index. Aggarwal Malini see Jain Rajmal, 125; X-ray Emission Characteristics of Flares. Associated with CMEs, 195. Alyana Radharani see Rathod Jatin, 293; see Reddy Chandrasekhar, A., 313. Ambastha Ashok Helioseismic Effects of Energetic Transients, 93; see Maurya.


    Indian Academy of Sciences (India)


    SUBJECT INDEX. Ab initio calculations. Basis set effects on energy and hardness profiles of the hydrogen fluoride dimer. 549. Activation by calcinations. Highly active and reusable catalyst from Fe-Mg- hydrotalcite anionic clay for Friedel–Crafts type benzyla- tion reactions. 635. Adsorption. Adsorption studies of iron(III) on ...

  20. Author Index

    Indian Academy of Sciences (India)

    Author Index. Aggarwal Malini see Jain Rajmal, 155. Aghaee, A. Determination of the Mean Hi Absorption of the Intergalactic. Medium, 59. Agrawal, S. P. see Singh Ambika, 89. Biesiada Marek Could the Optical Transient SCP 06F6 be due to Micro- lensing?, 213. C¸ aliskan, S . see Küçük, ˙I., 135. Evans Lloyd, T. Carbon ...

  1. Author Index

    Indian Academy of Sciences (India)

    Author Index. Ahmad Farooq see Iqbal Naseer, 373. Ali Syed Salman Study of a Large Helical Eruptive Prominence Associated with. Double CME on 21 April 2001, 347; see Uddin Wahab, 267. Ali, A. Chemistry of Carbon Rich Star IRAS 15194–5115, 399. Ambastha Ashok Photospheric, Chromospheric and Helioseismic ...

  2. Subject Index

    Indian Academy of Sciences (India)

    J. Astrophys. Astr. (2006) 27, 469–472. Subject Index. Astrophysical Processes. Spatial Damping of Linear Compressional Magnetoacoustic Waves in Quiescent. Prominences (K. A. P. Singh), 321. Report on the Dynamical Evolution of an Axially Symmetric Quasar Model. (N. J. Papadopoulos & N. D. Caranicolas), 389.


    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    SUBJECT INDEX. 1D inversion. A direct inversion scheme for deep resistivity sound- ing data using artificial neural networks. 49. 40. Ar-. 39. Ar thermochronology. Tectono-thermal evolution of the India-Asia colli- sion zone based on. 40. Ar-. 39. Ar thermochronology in. Ladakh, India. 737. ANN. Artificial neural network ...

  4. Index Fossils

    Indian Academy of Sciences (India)

    stricted geologic time range, easily preservable, of short species duration and found in multiple environment. Index fossils are used by geologists and palaeontologists as significant aids to determine the correlation and age of rock sequences [2]. Geologists use both large fossils or 'macrofossils' and microscopic fossils or ...

  5. Author Index

    Indian Academy of Sciences (India)


    Yan, X. L. see Deng, L. H., 221. Phase Relationship Between Sunspot Number, Flare Index and Solar Radio. Flux, 387. ZANINETTI, L. Revisiting the Cosmological Principle in a Cellular Framework, 399. ZHAO XIAN-FENG. Constraints on the Moment of Inertia of a Proto Neutron Star from the Hyperon Coupling Constants, ...

  6. Index Fossils

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 10. Index Fossils - Evidences from Plant Sources. Dipanjan Ghosh. General Article ... Author Affiliations. Dipanjan Ghosh1. Biological Science Department Kirnahar Shib Chandra High School Kirnahar, Birbhum 731302, West Bengal, India.

  7. Ptolemaic indexing

    Directory of Open Access Journals (Sweden)

    Magnus Lie Hetland


    Full Text Available This paper discusses a new family of bounds for use in similarity search, related to those used in metric indexing, but based on Ptolemy's inequality, rather than the metric axioms. Ptolemy's inequality holds for the well-known Euclidean distance, but is also shown here to hold for quadratic form metrics in general, with Mahalanobis distance as an important special case. The inequality is examined empirically on both synthetic and real-world data sets and is also found to hold approximately, with a very low degree of error, for important distances such as the angular pseudometric and several Lp norms. Indexing experiments are performed on several data sets, demonstrating a highly increased filtering power when using certain forms of Ptolemaic filtering, compared to existing, triangular methods. It is also shown that combining the Ptolemaic and triangular filtering can lead to better results than using either approach on its own.

  8. The Transcription Factor Encyclopedia

    NARCIS (Netherlands)

    Yusuf, Dimas; Butland, Stefanie L.; Swanson, Magdalena I.; Bolotin, Eugene; Ticoll, Amy; Cheung, Warren A.; Zhang, Xiao Yu Cindy; Dickman, Christopher T. D.; Fulton, Debra L.; Lim, Jonathan S.; Schnabl, Jake M.; Ramos, Oscar H. P.; Vasseur-Cognet, Mireille; de Leeuw, Charles N.; Simpson, Elizabeth M.; Ryffel, Gerhart U.; Lam, Eric W.-F.; Kist, Ralf; Wilson, Miranda S. C.; Marco-Ferreres, Raquel; Brosens, Jan J.; Beccari, Leonardo L.; Bovolenta, Paola; Benayoun, Bérénice A.; Monteiro, Lara J.; Schwenen, Helma D. C.; Grontved, Lars; Wederell, Elizabeth; Mandrup, Susanne; Veitia, Reiner A.; Chakravarthy, Harini; Hoodless, Pamela A.; Mancarelli, M. Michela; Torbett, Bruce E.; Banham, Alison H.; Reddy, Sekhar P.; Cullum, Rebecca L.; Liedtke, Michaela; Tschan, Mario P.; Vaz, Michelle; Rizzino, Angie; Zannini, Mariastella; Frietze, Seth; Farnham, Peggy J.; Eijkelenboom, Astrid; Brown, Philip J.; Laperrière, David; Leprince, Dominique; de Cristofaro, Tiziana; Prince, Kelly L.; Putker, Marrit; del Peso, Luis; Camenisch, Gieri; Wenger, Roland H.; Mikula, Michal; Rozendaal, Marieke; Mader, Sylvie; Ostrowski, Jerzy; Rhodes, Simon J.; van Rechem, Capucine; Boulay, Gaylor; Olechnowicz, Sam W. Z.; Breslin, Mary B.; Lan, Michael S.; Nanan, Kyster K.; Wegner, Michael; Hou, Juan; Mullen, Rachel D.; Colvin, Stephanie C.; Noy, Peter John; Webb, Carol F.; Witek, Matthew E.; Ferrell, Scott; Daniel, Juliet M.; Park, Jason; Waldman, Scott A.; Peet, Daniel J.; Taggart, Michael; Jayaraman, Padma-Sheela; Karrich, Julien J.; Blom, Bianca; Vesuna, Farhad; O'Geen, Henriette; Sun, Yunfu; Gronostajski, Richard M.; Woodcroft, Mark W.; Hough, Margaret R.; Chen, Edwin; Europe-Finner, G. Nicholas; Karolczak-Bayatti, Magdalena; Bailey, Jarrod; Hankinson, Oliver; Raman, Venu; Lebrun, David P.; Biswal, Shyam; Harvey, Christopher J.; Debruyne, Jason P.; Hogenesch, John B.; Hevner, Robert F.; Héligon, Christophe; Luo, Xin M.; Blank, Marissa Cathleen; Millen, Kathleen Joyce; Sharlin, David S.; Forrest, Douglas; Dahlman-Wright, Karin; Zhao, Chunyan; Mishima, Yuriko; Sinha, Satrajit; Chakrabarti, Rumela; Portales-Casamar, Elodie; Sladek, Frances M.; Bradley, Philip H.; Wasserman, Wyeth W.


    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 mini review

  9. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik


    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 codi...

  10. Mechanical Properties of Transcription (United States)

    Sevier, Stuart A.; Levine, Herbert


    The mechanical properties of transcription have recently been shown to play a central role in gene expression. However, a full physical characterization of this central biological process is lacking. In this Letter, we introduce a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase rotation, and DNA supercoiling are coupled. The resulting framework describes the relative amount of RNA polymerase rotation and DNA supercoiling that occurs during RNA elongation. Asymptotic behavior is derived and can be used to experimentally extract unknown mechanical parameters of transcription. Mechanical limits to transcription are incorporated through the addition of a DNA supercoiling-dependent RNA polymerase velocity. This addition can lead to transcriptional stalling and resulting implications for gene expression, chromatin structure and genome organization are discussed.

  11. Deciphering Transcriptional Regulation

    DEFF Research Database (Denmark)

    Valen, Eivind

    RNA); and ii) translation, in which the mRNA is translated into a protein. This thesis focus on the ¿rst of these steps, transcription, and speci¿cally the initiation of this. Simpli¿ed, initiation is preceded by the binding of several proteins, known as transcription factors (TFs), to DNA. This takes place...... published providing an unbiased overview of the transcription start site (TSS) usage in a tissue. We have paired this method with high-throughput sequencing technology to produce a library of unprecedented depth (DeepCAGE) for the mouse hippocampus. We investigated this in detail and focused particularly...... control spanning the range from completely muted to cranked up to maximum. The volume, in this case, is the production rate of proteins. This production is the result of a two step procedure: i) transcription, in which a small part of DNA from the genome (a gene) is transcribed into an RNA molecule (an m...

  12. Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. (United States)

    Meers, Michael P; Adelman, Karen; Duronio, Robert J; Strahl, Brian D; McKay, Daniel J; Matera, A Gregory


    High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis. The data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly, a sub-class of these unannotated TSSs overlaps with functionally validated enhancer elements, consistent with a regulatory role for "enhancer RNAs" (eRNAs) in defining developmental transcription programs. High-depth TSS mapping is a powerful strategy for identifying and characterizing low-abundance and/or low-stability RNAs. Global analysis of transcription initiation patterns in a developing organism reveals a vast number of novel initiation events that identify potential eRNAs as well as other non-coding transcripts critical for animal development.

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

    International Nuclear Information System (INIS)

    Zhu Yiming; Liu Yuan; Fan Huixian


    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. Transcriptional regulation of secondary growth and wood formation. (United States)

    Du, Juan; Groover, Andrew


    Secondary growth and wood formation are products of the vascular cambium, a lateral meristem. Although the mechanisms have only recently begun to be uncovered, transcriptional regulation appears increasingly central to the regulation of secondary growth. The importance of transcriptional regulation is illustrated by the correlation of expression of specific classes of genes with related biological processes occurring at specific stages of secondary growth, including cell division, cell expansion, and cell differentiation. At the same time, transcription factors have been characterized that affect specific aspects of secondary growth, including regulation of the cambium and differentiation of cambial daughter cells. In the present review, we summarize evidence pointing to transcription as a major mechanism for regulation of secondary growth, and outline future approaches for comprehensively describing transcriptional networks underlying secondary growth.

  15. Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. (United States)

    Brown, Thomas; Howe, Françoise S; Murray, Struan C; Wouters, Meredith; Lorenz, Philipp; Seward, Emily; Rata, Scott; Angel, Andrew; Mellor, Jane


    Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript degradation. At GAL1 , high levels of antisense transcription alter sense transcription dynamics, reducing rates of transcript production and processing, while increasing transcript stability. This relationship with transcript stability is also observed as a genome-wide association. Establishing the antisense transcription-associated chromatin signature through disruption of the Set3C histone deacetylase activity is sufficient to similarly change these rates even in the absence of antisense transcription. Thus, antisense transcription alters sense transcription dynamics in a chromatin-dependent manner. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  16. An index of financial safety of China

    Directory of Open Access Journals (Sweden)

    Xiaojun Jia


    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

  17. Informed consent comprehension in African research settings. (United States)

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


    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

  18. Transcriptional landscape of the human cell cycle. (United States)

    Liu, Yin; Chen, Sujun; Wang, Su; Soares, Fraser; Fischer, Martin; Meng, Feilong; Du, Zhou; Lin, Charles; Meyer, Clifford; DeCaprio, James A; Brown, Myles; Liu, X Shirley; He, Housheng Hansen


    Steady-state gene expression across the cell cycle has been studied extensively. However, transcriptional gene regulation and the dynamics of histone modification at different cell-cycle stages are largely unknown. By applying a combination of global nuclear run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and histone-modification Chip sequencing (ChIP-seq), we depicted a comprehensive transcriptional landscape at the G0/G1, G1/S, and M phases of breast cancer MCF-7 cells. Importantly, GRO-seq and RNA-seq analysis identified different cell-cycle-regulated genes, suggesting a lag between transcription and steady-state expression during the cell cycle. Interestingly, we identified genes actively transcribed at early M phase that are longer in length and have low expression and are accompanied by a global increase in active histone 3 lysine 4 methylation (H3K4me2) and histone 3 lysine 27 acetylation (H3K27ac) modifications. In addition, we identified 2,440 cell-cycle-regulated enhancer RNAs (eRNAs) that are strongly associated with differential active transcription but not with stable expression levels across the cell cycle. Motif analysis of dynamic eRNAs predicted Kruppel-like factor 4 (KLF4) as a key regulator of G1/S transition, and this identification was validated experimentally. Taken together, our combined analysis characterized the transcriptional and histone-modification profile of the human cell cycle and identified dynamic transcriptional signatures across the cell cycle.

  19. SoyDB: a knowledge database of soybean transcription factors

    Directory of Open Access Journals (Sweden)

    Valliyodan Babu


    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

  20. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

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


    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...... and vetted by experts in the field. TFe is available at

  1. The transcription factor encyclopedia. (United States)

    Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I; Bolotin, Eugene; Ticoll, Amy; Cheung, Warren A; Zhang, Xiao Yu Cindy; Dickman, Christopher T D; Fulton, Debra L; Lim, Jonathan S; Schnabl, Jake M; Ramos, Oscar H P; Vasseur-Cognet, Mireille; de Leeuw, Charles N; Simpson, Elizabeth M; Ryffel, Gerhart U; Lam, Eric W-F; Kist, Ralf; Wilson, Miranda S C; Marco-Ferreres, Raquel; Brosens, Jan J; Beccari, Leonardo L; Bovolenta, Paola; Benayoun, Bérénice A; Monteiro, Lara J; Schwenen, Helma D C; Grontved, Lars; Wederell, Elizabeth; Mandrup, Susanne; Veitia, Reiner A; Chakravarthy, Harini; Hoodless, Pamela A; Mancarelli, M Michela; Torbett, Bruce E; Banham, Alison H; Reddy, Sekhar P; Cullum, Rebecca L; Liedtke, Michaela; Tschan, Mario P; Vaz, Michelle; Rizzino, Angie; Zannini, Mariastella; Frietze, Seth; Farnham, Peggy J; Eijkelenboom, Astrid; Brown, Philip J; Laperrière, David; Leprince, Dominique; de Cristofaro, Tiziana; Prince, Kelly L; Putker, Marrit; del Peso, Luis; Camenisch, Gieri; Wenger, Roland H; Mikula, Michal; Rozendaal, Marieke; Mader, Sylvie; Ostrowski, Jerzy; Rhodes, Simon J; Van Rechem, Capucine; Boulay, Gaylor; Olechnowicz, Sam W Z; Breslin, Mary B; Lan, Michael S; Nanan, Kyster K; Wegner, Michael; Hou, Juan; Mullen, Rachel D; Colvin, Stephanie C; Noy, Peter John; Webb, Carol F; Witek, Matthew E; Ferrell, Scott; Daniel, Juliet M; Park, Jason; Waldman, Scott A; Peet, Daniel J; Taggart, Michael; Jayaraman, Padma-Sheela; Karrich, Julien J; Blom, Bianca; Vesuna, Farhad; O'Geen, Henriette; Sun, Yunfu; Gronostajski, Richard M; Woodcroft, Mark W; Hough, Margaret R; Chen, Edwin; Europe-Finner, G Nicholas; Karolczak-Bayatti, Magdalena; Bailey, Jarrod; Hankinson, Oliver; Raman, Venu; LeBrun, David P; Biswal, Shyam; Harvey, Christopher J; DeBruyne, Jason P; Hogenesch, John B; Hevner, Robert F; Héligon, Christophe; Luo, Xin M; Blank, Marissa Cathleen; Millen, Kathleen Joyce; Sharlin, David S; Forrest, Douglas; Dahlman-Wright, Karin; Zhao, Chunyan; Mishima, Yuriko; Sinha, Satrajit; Chakrabarti, Rumela; Portales-Casamar, Elodie; Sladek, Frances M; Bradley, Philip H; Wasserman, Wyeth W


    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 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 and vetted by experts in the field. TFe is available at

  2. 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...

  3. Teaching reading comprehension strategies

    Directory of Open Access Journals (Sweden)

    Majlinda Lika


    Full Text Available The academic debate nowadays is focused on producing an applied science of learning, aiming to teach students how to learn and be strategic in their acquisition. The aim of the study is to identify and discuss the reading comprehension instruction approach applied in the Albanian system of education. Findings from 10 classes of Albanian language and literature with students of third grade were directly observed and analyzed, in order to gather evidence based on indicators and instruments that assess the way of reading comprehension. Findings were categorized according to strategy use; the frequency of their application in different classes was counted and represented in percentages. In this paper we will try to respond to questions like: What are students' main barriers of comprehending? Does the instructional approach respond to students’ needs and level of comprehension? Are teachers prepared to teach comprehension strategies? Furthermore, examples of procedures on how to deliver instruction of comprehension strategies in natural contexts will be represented. Results from teacher practices during lessons of reading comprehension confirmed that teachers use limited teaching strategies to deliver lessons. They mainly use strategies to test comprehension; while the approach of teaching students to read independently and strategically is an unknown practice.

  4. Interruptions disrupt reading comprehension. (United States)

    Foroughi, Cyrus K; Werner, Nicole E; Barragán, Daniela; Boehm-Davis, Deborah A


    Previous research suggests that being interrupted while reading a text does not disrupt the later recognition or recall of information from that text. This research is used as support for Ericsson and Kintsch's (1995) long-term working memory (LT-WM) theory, which posits that disruptions while reading (e.g., interruptions) do not impair subsequent text comprehension. However, to fully comprehend a text, individuals may need to do more than recognize or recall information that has been presented in the text at a later time. Reading comprehension often requires individuals to connect and synthesize information across a text (e.g., successfully identifying complex topics such as themes and tones) and not just make a familiarity-based decision (i.e., recognition). The goal for this study was to determine whether interruptions while reading disrupt reading comprehension when the questions assessing comprehension require participants to connect and synthesize information across the passage. In Experiment 1, interruptions disrupted reading comprehension. In Experiment 2, interruptions disrupted reading comprehension but not recognition of information from the text. In Experiment 3, the addition of a 15-s time-out prior to the interruption successfully removed these negative effects. These data suggest that the time it takes to process the information needed to successfully comprehend text when reading is greater than that required for recognition. Any interference (e.g., an interruption) that occurs during the comprehension process may disrupt reading comprehension. This evidence supports the need for transient activation of information in working memory for successful text comprehension and does not support LT-WM theory. (c) 2015 APA, all rights reserved).

  5. Quotient-Comprehension Chains

    Directory of Open Access Journals (Sweden)

    Kenta Cho


    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 benefit analysis of regional water resources based on multi-objective evaluation (United States)

    Chi, Yixia; Xue, Lianqing; Zhang, Hui


    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.

  7. Machine Dictation and Transcription. (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…

  8. Automatic Music Transcription (United States)

    Klapuri, Anssi; Virtanen, Tuomas

    Written musical notation describes music in a symbolic form that is suitable for performing a piece using the available musical instruments. Traditionally, musical notation indicates the pitch, target instrument, timing, and duration of each sound to be played. The aim of music transcription either by humans or by a machine is to infer these musical parameters, given only the acoustic recording of a performance.

  9. Bayesian Music Transcription

    NARCIS (Netherlands)

    Cemgil, A.T.


    Music transcription refers to extraction of a human readable and interpretable description from a recording of a music performance. The final goal is to implement a program that can automatically infer a musical notation that lists the pitch levels of notes and corresponding score positions in any

  10. Comprehension in "Hyperlexic" Readers. (United States)

    Snowling, Maggie; Frith, Uta


    The reading comprehension of hyperlexic children, mentally retarded children who can read aloud written words better than one would expect from their Mental Age, was investigated in four experiments involving both autistic and nonautistic children. (Author/NH)

  11. Features of Instructional Talk Predictive of Reading Comprehension (United States)

    Michener, Catherine J.; Patrick Proctor, C.; Silverman, Rebecca D.


    Increasingly, reading research has begun to address how students' linguistic environments may explain their reading achievement. In this exploratory analysis, we investigated how the rates of specific instructional talk moves predicted student reading comprehension achievement. Transcripts from third-, fourth-, and fifth-grade classrooms (teacher…

  12. 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


    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...

  13. NRC comprehensive records disposition schedule

    International Nuclear Information System (INIS)


    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

  14. Metacognition in Reading Comprehension


    Ceylan, Eda; Harputlu, Leyla


    Metacognition is defined basically as thinking about thinking. It is a significant factor that affects many activities related to language use. Reading comprehension, which is an indispensable part of daily life and language classrooms, is affected by metacognition, too. Hence, this paper aims to present an overview of the recent theoretical and empirical studies about metacognition and reading comprehension. Firstly, it provides the definitions and the importance of metacognition. Secondly, ...

  15. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager


    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....

  16. A comprehensive analysis of immunoglobulin heavy chain genes in the Bactrian camel (Camelus bactrianus

    Directory of Open Access Journals (Sweden)

    Zuoxiang LIANG,Tao WANG,Yi SUN,Wenlong YANG,Zhihong LIU,Jing FEI,Ying GUO,Qingwei MA,Qingjie PAN,Liming REN


    Full Text Available Heavy chain only antibodies (HCAbs represent a rare type of antibody that is devoid of light chains and the CH1 domain that have been reported in cartilaginous fish and camelids. By analyzing transcript data and genome sequences, we conducted a comprehensive analysis of Bactrian camel immunoglobulin heavy chain genes. Based on the transcript data, one μ gene, five γ genes, one α gene and one ε gene were found. Additionally, the variable region of HCAbs (VHH and the conventional antibodies (VH sequences associated with the γ3, γ1a/b and μ genes were amplified. Based on these genome sequences, seven DH, six JH, μ, γ2a, γ2c, α, and ε genes and a portion of a γ3 gene were observed. Different Kozak sequences within different VH families were found in our analysis, and the variability index differed between the VHH3 and VH3 families. Phylogenetic analysis of the constant regions of the camelid immunoglobulin genes indicates that these genes appeared before the evolutionary divergence of Bactrian camels and dromedaries.

  17. Eukaryotic transcription factors

    DEFF Research Database (Denmark)

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


    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...... them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions...

  18. Spanish dialects: phonetic transcription


    Moreno Bilbao, M. Asunción; Mariño Acebal, José Bernardo


    It is well known that canonical Spanish, the dialectal variant `central' of Spain, so called Castilian, can be transcribed by rules. This paper deals with the automatic grapheme to phoneme transcription rules in several Spanish dialects from Latin America. Spanish is a language spoken by more than 300 million people, has an important geographical dispersion compared among other languages and has been historically influenced by many native languages. In this paper authors expand the Castilian ...

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

    DEFF Research Database (Denmark)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal


    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......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...... 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.e. cerebellum versus heart for differential variation at the gene...

  20. Comprehensive cardiac rehabilitation

    DEFF Research Database (Denmark)

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


    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...... for the situation at hand. Due to challenging circumstances, the cost assessment turned out to be ex-post and top-down. RESULTS: Cost per treatment sequence is estimated to be approximately euro 976, whereas the incremental cost (compared with usual care) is approximately euro 682. The cost estimate is uncertain...... 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....

  1. Co-transcriptional folding is encoded within RNA genes

    Directory of Open Access Journals (Sweden)

    Miklós István


    Full Text Available Abstract Background Most of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription. Methods The main aim of this work is to study if and how co-transcriptional folding is encoded within the primary and secondary structure of RNA genes. In order to achieve this, we study the known primary and secondary structures of a comprehensive data set of 361 RNA genes as well as a set of 48 RNA sequences that are known to differ from the originally transcribed sequence units. We detect co-transcriptional folding by defining two measures of directedness which quantify the extend of asymmetry between alternative helices that lie 5' and those that lie 3' of the known helices with which they compete. Results We show with statistical significance that co-transcriptional folding strongly influences RNA sequences in two ways: (1 alternative helices that would compete with the formation of the functional structure during co-transcriptional folding are suppressed and (2 the formation of transient structures which may serve as guidelines for the co-transcriptional folding pathway is encouraged. Conclusions These findings have a number of implications for RNA secondary structure prediction methods and the detection of RNA genes.

  2. Multiple circadian transcriptional elements cooperatively regulate cell-autonomous transcriptional oscillation ofPeriod3, a mammalian clock gene. (United States)

    Matsumura, Ritsuko; Akashi, Makoto


    Cell-autonomous oscillation in clock gene expression drives circadian rhythms. The development of comprehensive analytical techniques, such as bioinformatics and ChIP-sequencing, has enabled the genome-wide identification of potential circadian transcriptional elements that regulate the transcriptional oscillation of clock genes. However, detailed analyses using traditional biochemical and molecular-biological approaches, such as binding and reporter assays, are still necessary to determine whether these potential circadian transcriptional elements are actually functional and how significantly they contribute to driving transcriptional oscillation. Here, we focused on the molecular mechanism of transcriptional oscillations in the mammalian clock gene Period3 ( Per3 ). The PER3 protein is essential for robust peripheral clocks and is a key component in circadian output processes. We found three E box-like elements located upstream of human Per3 transcription start sites that additively contributed to cell-autonomous transcriptional oscillation. However, we also found that Per3 is still expressed in a circadian manner when all three E box-like elements are functionally impaired. We noted that Per3 transcription was activated by the synergistic actions of two D box-like elements and the three E box-like elements, leading to a drastic increase in circadian amplitude. Interestingly, circadian expression of Per3 was completely disrupted only when all five transcriptional elements were functionally impaired. These results indicate that three E box-like and two D box-like elements cooperatively and redundantly regulate cell-autonomous transcriptional oscillation of Per3 . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. EJSCREEN Indexes 2015 Public (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:...

  4. EJSCREEN Indexes 2016 Public (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:...




  6. Painless reading comprehension

    CERN Document Server

    Jones, EdD, Darolyn "Lyn"


    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.

  7. Comprehension Strategy Gloves. (United States)

    Newman, Gayle


    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…

  8. Comprehensive metabolic panel (United States)

    Metabolic panel - comprehensive; Chem-20; SMA20; Sequential multi-channel analysis with computer-20; SMAC20; Metabolic panel 20 ... Normal values for the panel tests are: Albumin : 3.4 to 5.4 g/dL (34 to 54 g/L) Alkaline phosphatase : 44 to 147 ...

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

    DEFF Research Database (Denmark)

    Fang, Xin; Sastry, Anand; Mih, Nathan


    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...... 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...

  10. Cognitive Correlates of Listening Comprehension (United States)

    Kim, Young-Suk; Phillips, Beth


    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…

  11. Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Sophie H. Adjalley


    Full Text Available A comprehensive map of transcription start sites (TSSs across the highly AT-rich genome of P. falciparum would aid progress toward deciphering the molecular mechanisms that underlie the timely regulation of gene expression in this malaria parasite. Using high-throughput sequencing technologies, we generated a comprehensive atlas of transcription initiation events at single-nucleotide resolution during the parasite intra-erythrocytic developmental cycle. This detailed analysis of TSS usage enabled us to define architectural features of plasmodial promoters. We demonstrate that TSS selection and strength are constrained by local nucleotide composition. Furthermore, we provide evidence for coordinate and stage-specific TSS usage from distinct sites within the same transcription unit, thereby producing transcript isoforms, a subset of which are developmentally regulated. This work offers a framework for further investigations into the interactions between genomic sequences and regulatory factors governing the complex transcriptional program of this major human pathogen.

  12. [Journal selection and indexing for Index Medicus and Chinese periodicals indexed in Index Medicus]. (United States)

    Zhou, Qing-Hui; Ling, Chang-Quan; Bai, Yu-Jin; Yin, Hui-Xia


    Index Medicus/MEDLINE/PubMed published by U. S. National Library of Medicine (NLM) is the most important and commonly used biomedical literature retrieval system in the world. According to the"List of Journals Indexed in Index Medicus (2004)", 4,098 journals are indexed for Index Medicus, including 70 journals from mainland China and Hong Kong and 9 journals from Taiwan. Journal of Chinese Integrative Medicine established in May, 2003 is indexed in Index Medicus in 2004. This article outlines the critical elements of journal selection for Index Medicus/MEDLINE and the journal selection process for indexing at NLM, and introduces some measures for the Journal of Chinese Integrative Medicine being indexed in Index Medicus/MEDLINE.

  13. Comprehensive evaluation on urban competitiveness - A Case of Xinjiang Province


    Wan, Qiu-cheng


    This paper constructs the index system and econometric model of comprehensive evaluation on urban competitiveness, then adopts the factor analysis method to measure the urban competitiveness of 22 prefecture-level cities in Xinjiang Province. The 22 prefecture-level cities are divided into four levels according to the measurement result. Comprehensive analysis of the advantages and disadvantages of the cities in each level is carried out. And related countermeasures and proposals on how to im...

  14. Comprehensive hard materials

    CERN Document Server


    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...

  15. 501 reading comprehension questions

    CERN Document Server


    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.

  16. Transcriptional Regulation in Haematopoiesis:

    DEFF Research Database (Denmark)

    Lauridsen, Felicia K B

    Haematopoietic stem cells (HSCs) are responsible for the formation of all of the distinct mature cell types found in the blood. HSCs can – as the only cells of the haematopoietic system – regenerate all of the blood cells when transplanted into a irradiated host, because they are endowed...... of distinct lineage affiliated genes in the otherwise highly purified HSCs. Taken together, these studies demonstrate the use of our model as a tool for isolating superior HSCs, and show that low-level expression of mature lineage markers is inherent in the highly purified stem cell compartment. In the second...... in transplantation studies. Consistent with this, transcriptome profiling revealed very low expression of cell cycle genes in these reporter-dim HSCs. Sequencing of >1200 single HSCs confirmed that the main source of transcriptional heterogeneity was the cell cycle. It also revealed a low-level expression...

  17. Euglena Transcript Processing. (United States)

    McWatters, David C; Russell, Anthony G


    RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism. More recent efforts to examine mitochondrial genome structure and RNA maturation have been stimulated by the discovery of unusual processing pathways in other Euglenozoans such as kinetoplastids and diplonemids. Eukaryotes containing large genomes are now known to typically contain large collections of introns and regulatory RNAs involved in RNA processing events, and Euglena gracilis in particular has a relatively large genome for a protist. Studies examining the structure of nuclear genes and the mechanisms involved in nuclear RNA processing have revealed that indeed Euglena contains large numbers of introns in the limited set of genes so far examined and also possesses large numbers of specific classes of regulatory and processing RNAs, such as small nucleolar RNAs (snoRNAs). Most interestingly, these studies have also revealed that Euglena possesses novel processing pathways generating highly fragmented cytosolic ribosomal RNAs and subunits and non-conventional intron classes removed by unknown splicing mechanisms. This unexpected diversity in RNA processing pathways emphasizes the importance of identifying the components involved in these processing mechanisms and their evolutionary emergence in Euglena species.

  18. To Index or Not To Index. (United States)

    Veenema, Fred


    Describes an experiment comparing the performance of an automatic full-text indexing software for personal computers (i.e., the Quick-Finder facility in WordPerfect 6.1 for Windows) with the human intellectual assignment of indexing terms to each document in a collection. Results are discussed in terms of ease of use, the time factor, and recall…

  19. Initiation of HIV Reverse Transcription

    Directory of Open Access Journals (Sweden)

    Roland Marquet


    Full Text Available Reverse transcription of retroviral genomes into double stranded DNA is a key event for viral replication. The very first stage of HIV reverse transcription, the initiation step, involves viral and cellular partners that are selectively packaged into the viral particle, leading to an RNA/protein complex with very specific structural and functional features, some of which being, in the case of HIV-1, linked to particular isolates. Recent understanding of the tight spatio-temporal regulation of reverse transcription and its importance for viral infectivity further points toward reverse transcription and potentially its initiation step as an important drug target.

  20. Research on Comprehensive Evaluation Method for Heating Project Based on Analytic Hierarchy Processing (United States)

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


    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.

  1. Emergent Comprehension: Understanding Comprehension Development among Young Literacy Learners (United States)

    McMunn Dooley, Caitlin; Matthews, Mona W.


    This article hones what is meant by "emergent comprehension". The authors define emergent comprehension as the period when young children, prior to conventional reading, engage in meaningful experiences that stimulate the development and use of meaning-making strategies with potential to affect later reading comprehension. The construct "emergent…

  2. A comprehensive psychiatric service

    DEFF Research Database (Denmark)

    Wang, A G


    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......, and an outpatient service. The number of chronic patients has not decreased, due to an influx of unruly senile patients. The close proximity of the service to the community has increased the pressure with regard to the care of such patients. Other services, such as outpatient treatment of alcoholics and neurotics...

  3. A comprehensive French grammar

    CERN Document Server

    Price, Glanville


    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


    Directory of Open Access Journals (Sweden)

    G. Kharlamova


    Full Text Available Ecological security of the state – is a complex and multifaceted category that requires deep study. A comprehensive assessment of environmental security in terms of national security in Ukraine is not exercised. The paper summarizes the theoretical aspects of ecological safety of Ukraine and its components, contains the analysis of environmental safety indexes compiled by international organizations, including the Commission on Sustainable Development UN, the International Institute for Sustainable Development (IISD, the Scientific Committee on Problems of the Environment (SCOPE, Yale University. Analyses of such indexes as Environmental Sustainability Index, Environmental Performance Index, Human Development Index, Environmental Vulnerability Index, Enabling Environment Index had shown that despite all of them represent the level of ecological security, there is a lack of adapted for Ukraine method to assess domestic ecological situation and to compare it with global tendencies. On the basis of statistical data, a concept of evaluation of Environmental Safety Index (ESfIof Ukraine is proposed for subsequent adequate science-based assessment of the current level of ecological situation in Ukraine in comparison with other countries. Its main feature is that it takes into account in addition to the most important environmental indicators also economic and demographic indicators as threats/risks components. The rating of more than 150 countries according to ESfI is evaluated.

  5. Analysis in indexing

    DEFF Research Database (Denmark)

    Mai, Jens Erik


    The paper discusses the notion of steps in indexing and reveals that the document-centered approach to indexing is prevalent and argues that the document-centered approach is problematic because it blocks out context-dependent factors in the indexing process. A domain-centered approach to indexing...... 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...

  6. Supersymmetry and index theory

    International Nuclear Information System (INIS)

    Alvarez-Gaume, L.


    The author presents information mainly concerned with the fact that many of the ingredients and results in index theory have very simple analogs in supersymmetric quantum mechanical systems so that using elementary quantum mechanics one can obtain new proofs of the Atiyah-Singer index theorem and related results. Simple ideas on index theorems and characteristic classes are reviewed; simple results on fermion functional integrals are outlined; supersymmetric quantum mechanical systems which appear naturally in dealing with index problems are analyzed; proof of the classical index theorem is presented; the character valued index theorem is derived; and applications of the methods developed here for the computation of anomalies are presented

  7. 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.

  8. Idiom Comprehension in Aphasic Patients (United States)

    Papagno, Costanza; Tabossi, Patrizia; Colombo, Maria Rosa; Zampetti, Patrizia


    Idiom comprehension was assessed in 10 aphasic patients with semantic deficits by means of a string-to-picture matching task. Patients were also submitted to an oral explanation of the same idioms, and to a word comprehension task. The stimuli of this last task were the words following the verb in the idioms. Idiom comprehension was severely…

  9. Cultural Knowledge in News Comprehension

    DEFF Research Database (Denmark)

    Mathieu, David


    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...

  10. Comprehensive national energy strategy

    Energy Technology Data Exchange (ETDEWEB)



    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. Comprehensive overview of prostatitis. (United States)

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


    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.

  12. Mitotic bookmarking by transcription factors. (United States)

    Kadauke, Stephan; Blobel, Gerd A


    Mitosis is accompanied by dramatic changes in chromatin organization and nuclear architecture. Transcription halts globally and most sequence-specific transcription factors and co-factors are ejected from mitotic chromatin. How then does the cell maintain its transcriptional identity throughout the cell division cycle? It has become clear that not all traces of active transcription and gene repression are erased within mitotic chromatin. Many histone modifications are stable or only partially diminished throughout mitosis. In addition, some sequence-specific DNA binding factors have emerged that remain bound to select sites within mitotic chromatin, raising the possibility that they function to transmit regulatory information through the transcriptionally silent mitotic phase, a concept that has been termed "mitotic bookmarking." Here we review recent approaches to studying potential bookmarking factors with regards to their mitotic partitioning, and summarize emerging ideas concerning the in vivo functions of mitotically bound nuclear factors.

  13. Towards a Road Safety Development Index (RSDI) : Development of an International Index to Measure Road Safety Performance


    Al Haji, Ghazwan


    Aim. This study suggests a set of methodologies to combine different indicators of road safety into a single index. The RSDI is a simple and quick composite index, which may become a significant measurement in comparing, ranking and determining road safety levels in different countries and regions worldwide. Design. One particular concern in designing a Road Safety Development Index (RSDI) is to come up with a comprehensive set of exposure and risk indicators which includes as far as possible...

  14. Transcriptional Landscape of the Prenatal Human Brain (United States)

    Miller, Jeremy A.; Ding, Song-Lin; Sunkin, Susan M.; Smith, Kimberly A; Ng, Lydia; Szafer, Aaron; Ebbert, Amanda; Riley, Zackery L.; Aiona, Kaylynn; Arnold, James M.; Bennet, Crissa; Bertagnolli, Darren; Brouner, Krissy; Butler, Stephanie; Caldejon, Shiella; Carey, Anita; Cuhaciyan, Christine; Dalley, Rachel A.; Dee, Nick; Dolbeare, Tim A.; Facer, Benjamin A. C.; Feng, David; Fliss, Tim P.; Gee, Garrett; Goldy, Jeff; Gourley, Lindsey; Gregor, Benjamin W.; Gu, Guangyu; Howard, Robert E.; Jochim, Jayson M.; Kuan, Chihchau L.; Lau, Christopher; Lee, Chang-Kyu; Lee, Felix; Lemon, Tracy A.; Lesnar, Phil; McMurray, Bergen; Mastan, Naveed; Mosqueda, Nerick F.; Naluai-Cecchini, Theresa; Ngo, Nhan-Kiet; Nyhus, Julie; Oldre, Aaron; Olson, Eric; Parente, Jody; Parker, Patrick D.; Parry, Sheana E.; Player, Allison Stevens; Pletikos, Mihovil; Reding, Melissa; Royall, Joshua J.; Roll, Kate; Sandman, David; Sarreal, Melaine; Shapouri, Sheila; Shapovalova, Nadiya V.; Shen, Elaine H.; Sjoquist, Nathan; Slaughterbeck, Clifford R.; Smith, Michael; Sodt, Andy J.; Williams, Derric; Zöllei, Lilla; Fischl, Bruce; Gerstein, Mark B.; Geschwind, Daniel H.; Glass, Ian A.; Hawrylycz, Michael J.; Hevner, Robert F.; Huang, Hao; Jones, Allan R.; Knowles, James A.; Levitt, Pat; Phillips, John W.; Sestan, Nenad; Wohnoutka, Paul; Dang, Chinh; Bernard, Amy; Hohmann, John G.; Lein, Ed S.


    Summary The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe. Finally, many neurodevelopmental disorder and human evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development. PMID:24695229

  15. Western Alaska ESI: INDEX (Index Polygons) (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. IndexCat (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...

  17. Body Mass Index Table (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 ...

  18. Human Use Index (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...

  19. Master Veteran Index (MVI) (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,...

  20. Human Use Index (Future) (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...

  1. Indexing Executive Compensation Contracts

    NARCIS (Netherlands)

    I. Dittmann (Ingolf); E.G. Maug (Ernst); O.G. Spalt (Oliver)


    textabstractWe analyze the efficiency of indexing executive pay by calibrating the standard model of executive compensation to a large sample of US CEOs. The benefits from linking the strike price of stock options to an index are small and fully indexing all options would increase compensation costs

  2. The Europe 2020 Index (United States)

    Pasimeni, Paolo


    This paper presents a new index to quantify, measure and monitor the progress towards the objectives of the Europe 2020 strategy. This index is based on a set of relevant, accepted, credible, easy to monitor and robust indicators presented by the European Commission at the time the strategy was launched. The internal analysis of the index shows…

  3. The Validity of Reading Comprehension Rate: Reading Speed, Comprehension, and Comprehension Rates (United States)

    Skinner, Christopher H.; Williams, Jacqueline L.; Morrow, Jennifer Ann; Hale, Andre D.; Neddenriep, Christine E.; Hawkins, Renee O.


    This article describes a secondary analysis of a brief reading comprehension rate measure, percent comprehension questions correct per minute spent reading (%C/M). This measure includes reading speed (seconds to read) in the denominator and percentage of comprehension questions answered correctly in the numerator. Participants were 22 4th-, 29…

  4. Reporting comprehensive income: reasons for reporting choices and investor reactions

    NARCIS (Netherlands)

    Turktas, B.; Georgakopoulos, G.; Sotiropoulos, I.; Vasileiou, K.Z.


    This paper aims to investigate whether the reporting way of comprehensive income is influenced by some factors mentioned by the Positive Accounting Theory and whether the investors value their choice by looking at stock returns (measured in different ways) for firms in the S&P 350 Europe Index. The

  5. 21 CFR 12.98 - Official transcript. (United States)


    ..., participants, and counsel have 30 days from the time the transcript becomes available to propose corrections in the transcript of oral testimony. Corrections are permitted only for transcription errors. The... a verbatim stenographic transcript of oral testimony and for necessary copies of the transcript. (b...

  6. Comprehensive Environmental Management Plan

    International Nuclear Information System (INIS)

    Hjeresen, D.L.


    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

  7. Comprehensive nuclear materials

    CERN Document Server

    Allen, Todd; Stoller, Roger; Yamanaka, Shinsuke


    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.

  8. Psychodermatology: A comprehensive review

    Directory of Open Access Journals (Sweden)

    Savita Yadav


    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.

  9. Measuring Financial Inclusion: A Multidimensional Index


    Noelia Camara; David Tuesta


    We rely on demand and supply-side information to measure the extent of financial inclusion at country level for eighty-two developed and less-developed countries. We postulate that the degree of financial inclusion is determined by three dimensions: usage, barriers and access to financial inclusion. Weights assigned to the dimensions are determined endogenously by employing a two-stage Principal Component Analysis. Our composite index offers a comprehensive measure of the degree of financial ...

  10. Frequency shifting approach towards textual transcription of heartbeat sounds

    Directory of Open Access Journals (Sweden)

    Safar Khorasani Ehsan


    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.

  11. Frequency shifting approach towards textual transcription of heartbeat sounds (United States)


    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. PMID:21970368

  12. Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters. (United States)

    Erb, Ionas; van Nimwegen, Erik


    The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of 6 'proximal promoter motifs' (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1) occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters.

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

    Directory of Open Access Journals (Sweden)

    Steven Grant Hussey


    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.

  14. Chromosomal contact permits transcription between coregulated genes

    CSIR Research Space (South Africa)

    Fanucchi, Stephanie


    Full Text Available Transcription of coregulated genes occurs in the context of long-range chromosomal contacts that form multigene complexes. Such contacts and transcription are lost in knockout studies of transcription factors and structural chromatin proteins...

  15. A Brassica exon array for whole-transcript gene expression profiling.

    Directory of Open Access Journals (Sweden)

    Christopher G Love


    Full Text Available Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18, and categorisation by Gene Ontologies (GO based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at

  16. Transcriptional control of megakaryocyte development. (United States)

    Goldfarb, A N


    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.

  17. Transcriptional Silencing of Retroviral Vectors

    DEFF Research Database (Denmark)

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


    Although retroviral vector systems have been found to efficiently transduce a variety of cell types in vitro, the use of vectors based on murine leukemia virus in preclinical models of somatic gene therapy has led to the identification of transcriptional silencing in vivo as an important problem....... 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...

  18. RNA-guided transcriptional regulation (United States)

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


    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.

  19. Initiation of HIV Reverse Transcription


    Isel, Catherine; Ehresmann, Chantal; Marquet, Roland


    Reverse transcription of retroviral genomes into double stranded DNA is a key event for viral replication. The very first stage of HIV reverse transcription, the initiation step, involves viral and cellular partners that are selectively packaged into the viral particle, leading to an RNA/protein complex with very specific structural and functional features, some of which being, in the case of HIV-1, linked to particular isolates. Recent understanding of the tight spatio-temporal regulation of...

  20. Glycemic index, insulinemic index, and satiety index of kefir. (United States)

    Kong, Kai Ling; Hendrich, Suzanne


    To determine glycemic, insulinemic, and satiety indices of 3 types of kefir. This study was divided into 3 phases. In phase 1, 50 g of available carbohydrate from low-fat strawberry kefir or orange kefir was tested, and in phase 2, low-fat plain kefir containing 25 g of available carbohydrates was tested for glycemic index (GI), in both cases compared with an equivalent amount of glucose. In phase 3, 1000-kJ portions of all 3 types of kefirs were compared with white bread with the same energy content to determine the insulinemic index (II) and satiety index (SI) of all 3 kefirs. In all phases, a single-meal, randomized crossover design was performed in which the test meals were given to healthy adults, 5 men and 5 women. The total incremental plasma glucose area under the curve (iAUC) for strawberry, orange, and plain kefirs was significantly lower compared with the respective high-GI control food, which was glucose solution. However, the IIs and SIs of kefir did not differ significantly from the white bread. Kefir is a low- to moderate-GI food; however, its II was high. Although kefir had higher water content, the SI of kefir was not significantly different from white bread.

  1. An anatomically comprehensive atlas of the adult human brain transcriptome (United States)

    Guillozet-Bongaarts, Angela L.; Shen, Elaine H.; Ng, Lydia; Miller, Jeremy A.; van de Lagemaat, Louie N.; Smith, Kimberly A.; Ebbert, Amanda; Riley, Zackery L.; Abajian, Chris; Beckmann, Christian F.; Bernard, Amy; Bertagnolli, Darren; Boe, Andrew F.; Cartagena, Preston M.; Chakravarty, M. Mallar; Chapin, Mike; Chong, Jimmy; Dalley, Rachel A.; David Daly, Barry; Dang, Chinh; Datta, Suvro; Dee, Nick; Dolbeare, Tim A.; Faber, Vance; Feng, David; Fowler, David R.; Goldy, Jeff; Gregor, Benjamin W.; Haradon, Zeb; Haynor, David R.; Hohmann, John G.; Horvath, Steve; Howard, Robert E.; Jeromin, Andreas; Jochim, Jayson M.; Kinnunen, Marty; Lau, Christopher; Lazarz, Evan T.; Lee, Changkyu; Lemon, Tracy A.; Li, Ling; Li, Yang; Morris, John A.; Overly, Caroline C.; Parker, Patrick D.; Parry, Sheana E.; Reding, Melissa; Royall, Joshua J.; Schulkin, Jay; Sequeira, Pedro Adolfo; Slaughterbeck, Clifford R.; Smith, Simon C.; Sodt, Andy J.; Sunkin, Susan M.; Swanson, Beryl E.; Vawter, Marquis P.; Williams, Derric; Wohnoutka, Paul; Zielke, H. Ronald; Geschwind, Daniel H.; Hof, Patrick R.; Smith, Stephen M.; Koch, Christof; Grant, Seth G. N.; Jones, Allan R.


    Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of ~900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography— the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function. PMID:22996553

  2. National Capital Planning Commission Meeting Transcripts (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...

  3. 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 ...

  4. Comprehensive facilities plan

    Energy Technology Data Exchange (ETDEWEB)



    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.

  5. Comprehensive test ban negotiations (United States)

    Grab, G. Allen; Heckrotte, Warren


    Although it has been a stated policy goal of American and Soviet leaders since 1958 (with the exception of Ronald Reagan), the world today is still without a Comprehensive Test Ban Treaty. Throughout their history, test an negotiatins have been plagued by a number of persistent problems. Chief among these is East-West differences on the verification question, with the United States concerned about the problem of possible Soviet cheating and the USSR concerned about the protection of its national sovereignty. In addition, internal bureaucratic politics have played a major role in preventing the successful conclusion of an agreement. Despite these problems, the superpowers have concluded several significant partial meausres: a brief (1958-1961) total moratorium on nuclear weapons tests; the Limited Test Ban Treaty of 1963, banning tests in the air, water and outer space; the Threshold Test Ban Treaty of 1974 (150 KT limit on underground explosions); and the Peaceful Nuclear Explosions Treaty of 1976 (150 KT limit on individal PNEs). Today, the main U.S. objections to a CTBT center is the nuclear weapons laboratories, the Department of Energy, and the Pentagon, who all stress the issues of stockpile reliability and verification. Those who remain committed to a CTBT emphasize and the potential political leverage it offers in checking both horizontal and vertical proliferation.

  6. Neural activity tied to reading predicts individual differences in extended-text comprehension. (United States)

    Mossbridge, Julia A; Grabowecky, Marcia; Paller, Ken A; Suzuki, Satoru


    Reading comprehension depends on neural processes supporting the access, understanding, and storage of words over time. Examinations of the neural activity correlated with reading have contributed to our understanding of reading comprehension, especially for the comprehension of sentences and short passages. However, the neural activity associated with comprehending an extended text is not well-understood. Here we describe a current-source-density (CSD) index that predicts individual differences in the comprehension of an extended text. The index is the difference in CSD-transformed event-related potentials (ERPs) to a target word between two conditions: a comprehension condition with words from a story presented in their original order, and a scrambled condition with the same words presented in a randomized order. In both conditions participants responded to the target word, and in the comprehension condition they also tried to follow the story in preparation for a comprehension test. We reasoned that the spatiotemporal pattern of difference-CSDs would reflect comprehension-related processes beyond word-level processing. We used a pattern-classification method to identify the component of the difference-CSDs that accurately (88%) discriminated good from poor comprehenders. The critical CSD index was focused at a frontal-midline scalp site, occurred 400-500 ms after target-word onset, and was strongly correlated with comprehension performance. Behavioral data indicated that group differences in effort or motor preparation could not explain these results. Further, our CSD index appears to be distinct from the well-known P300 and N400 components, and CSD transformation seems to be crucial for distinguishing good from poor comprehenders using our experimental paradigm. Once our CSD index is fully characterized, this neural signature of individual differences in extended-text comprehension may aid the diagnosis and remediation of reading comprehension deficits.

  7. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) (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...

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

    Directory of Open Access Journals (Sweden)

    Jose L. Pruneda-Paz


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


    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.

  10. Supplement: Commodity Index Report (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...

  11. The Role of Reading Time Complexity and Reading Speed in Text Comprehension (United States)

    Wallot, Sebastian; O'Brien, Beth A.; Haussmann, Anna; Kloos, Heidi; Lyby, Marlene S.


    Reading speed is commonly used as an index of reading fluency. However, reading speed is not a consistent predictor of text comprehension, when speed and comprehension are measured on the same text within the same reader. This might be due to the somewhat ambiguous nature of reading speed, which is sometimes regarded as a feature of the reading…

  12. Transcriptional Profiling of Caudal Fin Regeneration in Zebrafish

    Directory of Open Access Journals (Sweden)

    Michael Schebesta


    Full Text Available Regeneration of severed limbs in adult animals is restricted to urodele amphibians. Mammals, including humans, have very limited regenerative capabilities and even with proper treatment, only the tips of our digits can grow back. Teleost fish can regenerate amputated fins, the evolutionary ancestors of limbs. To elucidate the principles of limb-fin regeneration, we performed an Affymetrix microarray screen on regenerating caudal fins 12, 24, 48, and 72 h post amputation. Approximately 15,000 zebrafish transcripts were analyzed, identifying 829 transcripts as differentially expressed during regeneration. Of those, 563 were up-regulated and 266 were down-regulated. We constructed a comprehensive database containing expression data, functional assignment, and background information from the literature for each differentially expressed transcript. In order to validate our findings, we employed three approaches: (1 microarray expression analysis of genes previously implicated in fin regeneration, (2 RT-PCR analysis of genes newly identified as differentially expressed during regeneration, and (3 in situ hybridization of the up-regulated genes bambi, dlx5A, and her6. Moreover, we show that Smad 1/5/8 proteins, effector molecules of Bmp signaling, are phosphorylated during fin regeneration. Taken together, we provide a comprehensive database of fin regeneration that will serve as an important tool for understanding the molecular mechanisms of regeneration.

  13. What can digital transcript profiling reveal about human cancers?

    Directory of Open Access Journals (Sweden)

    J.M. Cerutti


    Full Text Available Important biological and clinical features of malignancy are reflected in its transcript pattern. Recent advances in gene expression technology and informatics have provided a powerful new means to obtain and interpret these expression patterns. A comprehensive approach to expression profiling is serial analysis of gene expression (SAGE, which provides digital information on transcript levels. SAGE works by counting transcripts and storing these digital values electronically, providing absolute gene expression levels that make historical comparisons possible. SAGE produces a comprehensive profile of gene expression and can be used to search for candidate tumor markers or antigens in a limited number of samples. The Cancer Genome Anatomy Project has created a SAGE database of human gene expression levels for many different tumors and normal reference tissues and provides online tools for viewing, comparing, and downloading expression profiles. Digital expression profiling using SAGE and informatics have been useful for identifying genes that have a role in tumor invasion and other aspects of tumor progression.

  14. Reading comprehension in Parkinson's disease. (United States)

    Murray, Laura L; Rutledge, Stefanie


    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.

  15. Pragmatic Comprehension Development through Telecollaboration (United States)

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


    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…

  16. Artificial Intelligence and Language Comprehension. (United States)

    National Inst. of Education (DHEW), Washington, DC. Basic Skills Group. Learning Div.

    The three papers in this volume concerning artificial intelligence and language comprehension were commissioned by the National Institute of Education to further the understanding of the cognitive processes that enable people to comprehend what they read. The first paper, "Artificial Intelligence and Language Comprehension," by Terry Winograd,…

  17. Comprehensive mathematics for computer scientists

    CERN Document Server

    Mazzola, Guerino; Weissmann, Jody


    This two-volume textbook Comprehensive Mathematics for the Working Computer Scientist is a self-contained comprehensive presentation of mathematics including sets, numbers, graphs, algebra, logic, grammars, machines, linear geometry, calculus, ODEs, and special themes such as neural networks, Fourier theory, wavelets, numerical.

  18. EJSCREEN Supplementary Indexes 2015 Public (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...

  19. Ankle-Brachial Index (United States)

    ... measured at your arm. A low ankle-brachial index number can indicate narrowing or blockage of the arteries in ... tell your doctor so that he or she can continue to monitor your risk. Blockage (0.9 or less). An ankle-brachial index number less than 1.0 indicates narrowing of ...

  20. Global Ecosystem Restoration Index

    DEFF Research Database (Denmark)

    Fernandez, Miguel; Garcia, Monica; Fernandez, Nestor


    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...

  1. Rethinking image indexing?

    DEFF Research Database (Denmark)

    Christensen, Hans Dam


    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...

  2. Browse Title Index

    African Journals Online (AJOL)

    Browse Title Index. Journal Home > Advanced Search > Browse Title Index. Log in or Register to get access to full text downloads. ... Vol 2, No 1 (1978), Weakly Nonlinear Waves with Slowly-Varying Speed, Abstract PDF. SC Chikwendu. Vol 33, No 2 (2014), Web Portal Usability among Nigerian University Students: A Case ...

  3. ParkIndex

    DEFF Research Database (Denmark)

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


    , 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...... 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...... summary variables were used to create a raster surface (ParkIndex) representing the probability of park use for all 100m×100m cells in KCMO. Two park summary variables were positively associated with park use - the number of parks and the average park quality index within 1 mile. The ParkIndex probability...

  4. 16 CFR 1502.36 - Official transcript. (United States)


    ... the time the transcript becomes available to propose corrections in the transcript of oral testimony. Corrections are permitted only for transcription errors. The presiding officer shall promptly order justified... presiding officer will arrange for a verbatim stenographic transcript of oral testimony and for necessary...

  5. Browse Title Index

    African Journals Online (AJOL)

    Items 401 - 450 of 452 ... Vol 13, No 2 (2012), Simultaneous detection of respiratory syncytial virus types A and B and influenza virus types A and B in community-acquired pneumonia by reverse transcription-multiplex PCR, Abstract PDF. TE Deraz, MGE Mansour, S Albendary, AM Abdelwahab. Vol 16, No 2 (2015), SIRT1 ...

  6. Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions.

    Directory of Open Access Journals (Sweden)

    Chieh-Chun Chen

    Full Text Available Despite explosive growth in genomic datasets, the methods for studying epigenomic mechanisms of gene regulation remain primitive. Here we present a model-based approach to systematically analyze the epigenomic functions in modulating transcription factor-DNA binding. Based on the first principles of statistical mechanics, this model considers the interactions between epigenomic modifications and a cis-regulatory module, which contains multiple binding sites arranged in any configurations. We compiled a comprehensive epigenomic dataset in mouse embryonic stem (mES cells, including DNA methylation (MeDIP-seq and MRE-seq, DNA hydroxymethylation (5-hmC-seq, and histone modifications (ChIP-seq. We discovered correlations of transcription factors (TFs for specific combinations of epigenomic modifications, which we term epigenomic motifs. Epigenomic motifs explained why some TFs appeared to have different DNA binding motifs derived from in vivo (ChIP-seq and in vitro experiments. Theoretical analyses suggested that the epigenome can modulate transcriptional noise and boost the cooperativity of weak TF binding sites. ChIP-seq data suggested that epigenomic boost of binding affinities in weak TF binding sites can function in mES cells. We showed in theory that the epigenome should suppress the TF binding differences on SNP-containing binding sites in two people. Using personal data, we identified strong associations between H3K4me2/H3K9ac and the degree of personal differences in NFκB binding in SNP-containing binding sites, which may explain why some SNPs introduce much smaller personal variations on TF binding than other SNPs. In summary, this model presents a powerful approach to analyze the functions of epigenomic modifications. This model was implemented into an open source program APEG (Affinity Prediction by Epigenome and Genome,

  7. Transcriptional networks of TCP transcription factors in Arabidopsis development

    NARCIS (Netherlands)

    Danisman, S.D.


    Leaves are a plant’s main organs of photosynthesis and hence the development of this organ is under strict control. The different phases of leaf development are under the control of both endogenous and exogenous influences. In this work we were interested in a particular class of transcription

  8. Chromatin and Transcription in Yeast (United States)

    Rando, Oliver J.; Winston, Fred


    Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field. PMID:22345607

  9. Reading comprehension in autism spectrum disorders: the role of oral language and social functioning. (United States)

    Ricketts, Jessie; Jones, Catherine R G; Happé, Francesca; Charman, Tony


    Reading comprehension is an area of difficulty for many individuals with autism spectrum disorders (ASD). According to the Simple View of Reading, word recognition and oral language are both important determinants of reading comprehension ability. We provide a novel test of this model in 100 adolescents with ASD of varying intellectual ability. Further, we explore whether reading comprehension is additionally influenced by individual differences in social behaviour and social cognition in ASD. Adolescents with ASD aged 14-16 years completed assessments indexing word recognition, oral language, reading comprehension, social behaviour and social cognition. Regression analyses show that both word recognition and oral language explain unique variance in reading comprehension. Further, measures of social behaviour and social cognition predict reading comprehension after controlling for the variance explained by word recognition and oral language. This indicates that word recognition, oral language and social impairments may constrain reading comprehension in ASD.

  10. 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. (United States)

    Lee, Byron H


    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.

  11. 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.


    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

  12. The post-transcriptional operon

    DEFF Research Database (Denmark)

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


    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...

  13. NAC transcription factors in senescence

    DEFF Research Database (Denmark)

    Podzimska-Sroka, Dagmara; O'Shea, Charlotte; Gregersen, Per L.


    Within the last decade, NAC transcription factors have been shown to play essential roles in senescence, which is the focus of this review. Transcriptome analyses associate approximately one third of Arabidopsis NAC genes and many crop NAC genes with senescence, thereby implicating NAC genes as i...

  14. Transcription factor-based biosensor (United States)

    Dietrich, Jeffrey A; Keasling, Jay D


    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.

  15. HDG1 transcription factor targets

    NARCIS (Netherlands)

    Horstman, A.; Boutilier, K.A.; Sanchez Perez, Gabino


    The AIL transcription factor BABY BOOM (BBM) is required together with the related PLETHORA proteins for embryo and root meristem development and its expression is sufficient to confer pluripotency and totipotency to somatic tissues. We show that BBM and other AIL proteins interact with multiple

  16. Development and implementation of a business continuity management risk index. (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.

  17. Pesticide Use Site Index (United States)

    The Pesticide Use Site Index will help a company (or other applicant) identify which data requirements are needed to register a pesticide product. It provides information on pesticide use sites and pesticide major use patterns.

  18. Palmer Drought Severity Index (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...

  19. VT Nitrate Leaching Index (United States)

    Vermont Center for Geographic Information — (Link to Metadata) Nitrate Leaching Index data for the state of Vermont. This is a derivative product based on the SSURGO soils data for all counties except Essex...

  20. National Death Index (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...

  1. Regional Snowfall Index (RSI) (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...

  2. TOMS Absorbing Aerosol Index (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...

  3. Comprehensive Error Rate Testing (CERT) (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...

  4. Does classroom amplification aid comprehension? (United States)

    Arnold, P; Canning, D


    Many classrooms are noisy and this interferes with listening and teaching. FM soundfield (FM) amplification systems have been developed which provide a uniform soundfield throughout the classroom and increase the speech-signal:noise ratio. The effect on comprehension of such a system was investigated. Forty-nine pupils (comprising the two top classes of a mainstream primary school) participated in this study, with a mean age of 9.92 years (range 8.58-11.42 years). The Neale Analysis of Reading Ability (Neale, 1988a, b) was modified and administered as a spoken comprehension test. Tests of nonverbal intelligence, auditory memory and a questionnaire were given. The passages spoken though the FM amplification system were understood better than the comparable unamplified passages. Auditory memory, sex and non-verbal intelligence had no effect on improved comprehension. FM amplification significantly improved comprehension and could be considered for use in other schools.

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

    DEFF Research Database (Denmark)

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


    RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed...

  6. Indexing for summary queries

    DEFF Research Database (Denmark)

    Yi, Ke; Wang, Lu; Wei, Zhewei


    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....



    Suprajitno Suprajitno


    Introduction: Nurses have some variables, which can be used as basic of the remuneration. The aim of the study was to develop nursing remuneration index in the hospital of Ngudi Waluyo Wlingi using statistics approach. Methods: Research design was descriptive, study that is divided into two levels. The fi rst level was surveying and focus group discussion and the second level was assessing the remuneration index formula by simulation. The subject for surveying was the whole nurses who have st...

  8. Modeling transcriptional networks regulating secondary growth and wood formation in forest trees. (United States)

    Liu, Lijun; Filkov, Vladimir; Groover, Andrew


    The complex interactions among the genes that underlie a biological process can be modeled and presented as a transcriptional network, in which genes (nodes) and their interactions (edges) are shown in a graphical form similar to a wiring diagram. A large number of genes have been identified that are expressed during the radial woody growth of tree stems (secondary growth), but a comprehensive understanding of how these genes interact to influence woody growth is currently lacking. Modeling transcriptional networks has recently been made tractable by next-generation sequencing-based technologies that can comprehensively catalog gene expression and transcription factor-binding genome-wide, but has not yet been extensively applied to undomesticated tree species or woody growth. Here we discuss basic features of transcriptional networks, approaches for modeling biological networks, and examples of biological network models developed for forest trees to date. We discuss how transcriptional network research is being developed in the model forest tree genus, Populus, and how this research area can be further developed and applied. Transcriptional network models for forest tree secondary growth and wood formation could ultimately provide new predictive models to accelerate hypothesis-driven research and develop new breeding applications. © 2013 Scandinavian Plant Physiology Society.

  9. Burkholderia pseudomallei transcriptional adaptation in macrophages

    Directory of Open Access Journals (Sweden)

    Chieng Sylvia


    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.

  10. 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.

  11. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 169 ... Vol 8, No 1-2 (2009), Some psycho cultural and physiological factors as predictors of in-school adolescents' response to HIV/AIDS preventive ... Vol 10, No 2 (2011), Students' perception of teacher's knowledge of subject matter and reading comprehension performance of SS 3 students in Cross River ...

  12. 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.

  13. Browse Title Index

    African Journals Online (AJOL)

    Items 301 - 350 of 483 ... Vol 48, No 1 (2005), Pattern of First-Aid Measures Used by Snake-bite Patients and Clinical Outcome at Zamko Comprehensive Health Centre, Langtang, ... Vol 45, No 5 (2004), Perceptions of Health Students of the Lagos University Teaching Hospital to Gender Based Issues related to Reproductive ...

  14. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 399 ... JD Seffah, KA Ampofo, EK Srofenyoh, IO Korenteng. Vol 44, No 3 (2010), A case report of intracranial vertebral-basilar artery hypoplasia presenting with episodic dizziness, Abstract PDF. JJ Chen, DL Chen. Vol 46, No 2 (2012): Supplementary, A comprehensive review of the policy and programmatic ...

  15. Browse Title Index

    African Journals Online (AJOL)

    Items 401 - 450 of 1732 ... Vol 18, No 4 (2015), Comprehensive dental management in a Hallermann–Streiff syndrome patient with unusual radiographic appearance of teeth, Abstract ... Vol 11, No 4 (2008), Correlating Antibiotic ConsumptionWith Antimicrobial Resistance Of Uropathogens In A University Teaching Hospital In ...

  16. Browse Title Index

    African Journals Online (AJOL)

    Items 551 - 600 of 670 ... Vol 4 (2007), The effect of listening comprehension skills on students' performance in oral English language test, Abstract ... Vol 10, No 2 (2013), The Impact of Emotional Intelligence and Self-Efficacy on the Malleability of Job Performance and Job Involvement of Prison Personnel in Nigeria, Abstract.

  17. 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 ...

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

    Energy Technology Data Exchange (ETDEWEB)

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


    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

  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


    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. Comprehensive evaluation system of intelligent urban growth (United States)

    Li, Lian-Yan; Ren, Xiao-Bin


    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.

  1. Gradient-index optics fundamentals and applications

    CERN Document Server

    Gomez-Reino, Carlos; Bao, Carmen


    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.

  2. Memory mechanisms supporting syntactic comprehension. (United States)

    Caplan, David; Waters, Gloria


    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.

  3. Sustainability index for Taipei

    International Nuclear Information System (INIS)

    Lee, Y.-J.; Huang Chingming


    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

  4. Calculate Your Body Mass Index (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 ...

  5. Transcriptional control of t lymphocyte differentiation

    NARCIS (Netherlands)

    F.J.T. Staal (Frank); F. Weerkamp (Floor); A.W. Langerak (Anton); R.W. Hendriks (Rudi); H.C. Clevers (Hans)


    textabstractInitiation of gene transcription by transcription factors (TFs) is an important regulatory step in many developmental processes. The differentiation of T cell progenitors in the thymus is tightly controlled by signaling molecules, ultimately activating

  6. 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)


    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.

  7. [Comprehensive traditional Chinese medicine intervention for perimenopausal syndrome in women: a community study]. (United States)

    Zheng, Jin; Li, Ji; Song, Lin-Yi; Ni, Shuang; Chen, Ying-Chao; Huang, Shan-di


    As perimenopausal syndrome is a particularly disturbing condition to the patient, it is practical and necessary to establish a program of comprehensive traditional Chinese medicine therapy for women with perimenopausal syndrome. To observe the therapeutic effects of a comprehensive traditional Chinese medicine therapy for women with perimenopausal syndrome in the community. Women with perimenopausal syndrome who met the inclusion criteria in 3 communities of Shanghai were selected for this study. Comprehensive traditional Chinese medicine therapy, including administration of Chinese herbs, auricular point therapy, psychological counseling and the practice of Tai Chi, was applied for these women. The modified Kupperman index was measured once every 4 weeks for 12 weeks; the indexes of menopause-specific quality of life (MENQOL) questionnaire were measured before and after the treatment. There was no significant difference in 4 groups of negative conversion ratio of the modified Kupperman index at the 4th, 8th and 12th week, respectively. The indexes of the MENQOL questionnaire showed significant differences in 4 groups before and after the treatment. The overall efficacy rate of the comprehensive traditional Chinese medicine therapy in women with perimenopausal syndrome achieved 97.84% at the 8th and the 12th week. The comprehensive traditional Chinese medicine therapy can achieve significant improvements in women with perimenopausal syndrome who exhibit both physical and psychological symptoms. With such significant clinical effects, the comprehensive traditional Chinese medicine therapy should be promoted in the community.

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

    NARCIS (Netherlands)

    Lin, Y.F.; Severing, E.I.; Lintel Hekkert, te B.; Schijlen, E.G.W.M.; Aarts, M.G.M.


    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

  9. Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing

    NARCIS (Netherlands)

    Rienksma, R.A.; Suarez Diez, M.; Mollenkopf, H.J.; Dolganov, G.M.; Dorhoi, A.; Schoolnik, G.K.; Martins Dos Santos, V.A.P.; Kaufmann, S.; Schaap, P.J.; Gengenbacher, M.


    BackgroundThe human pathogen Mycobacterium tuberculosis has the capacity to escape eradication by professional phagocytes. During infection, M. tuberculosis resists the harsh environment of phagosomes and actively manipulates macrophages and dendritic cells to ensure prolonged intracellular

  10. 2005 Environmental Sustainability Index (ESI) (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...

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

    Directory of Open Access Journals (Sweden)

    Sun Tongda


    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.

  12. Sales concentration index in the Iranian car market

    Directory of Open Access Journals (Sweden)

    Kazemzadeh Emad


    Full Text Available Concentration is among the key indicators of market structure. The number of manufacturers and distribution of market between firms with different sizes can be examined using concentration index. In this paper, the concentration ratio, Herfindahl-Hirschman Index, Hall-Tiedman Index, comprehensive industrial concentration index, entropy and Hannah-Kay index were used during 1996, 2011, 2006 and 2011. The main objective of the present study is to measure concentration in the Iranian car market and show its changes during 1996-2011. The results indicated a high concentration in the Iranian automotive industry. Even with the advent of new firms to the Iranian automotive industry and increased total production, there has been a constant concentration in the automotive industry.

  13. Optimising Comprehensibility in Interlingual Translation

    DEFF Research Database (Denmark)

    Nisbeth Jensen, Matilde


    information on medication and tax information. Such texts are often written by experts and received by lay people, and, in today’s globalised world, they are often translated as well. In these functional texts, the receiver is not a mere recipient of information, but s/he needs to be able to act upon it....... Action requires understanding, and these texts consequently need to be optimally comprehensible. The aim of this paper is therefore to provide a framework for optimising comprehensibility in translation. In order to do so, the concept of intralingual translation is argued for as a useful starting point...

  14. Conceptual Combination During Sentence Comprehension (United States)

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


    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

  15. Constraint Programming for Context Comprehension

    DEFF Research Database (Denmark)

    Christiansen, Henning


    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...... of knowledge. The language of Constraint Handling Rules, CHR, is suggested for defining constraint solvers that reflect “world knowledge” for the given domain, and driver algorithms may be ex- pressed in Prolog or additional rules of CHR. It is argued that this way of doing context comprehension is an instance...

  16. Conservation Priority Index for Estuarine Fish (COPIEF) (United States)

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


    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.

  17. Generation of a large catalog of unique transcripts for whole-genome expression analysis in nonmodel species. (United States)

    Bellin, Diana; Ferrarini, Alberto; Delledonne, Massimo


    Next-generation sequencing technologies have allowed new tools to be developed for transcriptome characterization. We describe here the methods for the preparation of a library from pooled RNAs for 454 sequencing of 3'-cDNA fragments. We also describe how the read sequences obtained can be used to generate, through de novo reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence is not available. Finally, this catalog can be used efficiently to design oligonucleotide probes for setting up a comprehensive microarray for global analysis of gene expression.

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

    KAUST Repository

    Alam, Tanvir


    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:

  19. Browse Title Index

    African Journals Online (AJOL)

    Items 301 - 312 of 312 ... Vol 30, No 1-2 (2015), Vitamin C Prevents Sleep Deprivation-induced Elevation in Cortisol and Lipid Peroxidation in the Rat Plasma, Abstract PDF. Olayaki L A, Sulaiman S O, Anoba N B. Vol 25, No 2 (2010), Waist circumference, waist to hip ratio, and body mass index in the diagnosis of metabolic ...

  20. 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 ...

  1. Indexes to Volume 56

    Indian Academy of Sciences (India)

    Subject Index. Unsharp spin observables, non-locality and Fry, Walther and Li experiment. Sisir Roy. 189–198. Backward causation, hidden variables and the meaning of completeness. Huw Price. 199–210. An experiment to distinguish between de Broglie-Bohm and standard quan- tum mechanics. Partha Ghose. 211–216.

  2. 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 ...

  3. Refractive index based measurements

    DEFF Research Database (Denmark)


    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...

  4. Refractive index based measurements

    DEFF Research Database (Denmark)


    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...

  5. Refractive index based measurements

    DEFF Research Database (Denmark)


    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...

  6. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 379 ... Vol 52, No 1 (2016), Effects of adherence to antiretroviral therapy on body mass index, immunological and virological status of Nigerians living with HIV/AIDS ... Vol 51, No 2 (2015), Efficacy of biofeedback-assisted pelvic floor muscle training in females with pelvic floor dysfunction, Abstract PDF.

  7. Browse Title Index

    African Journals Online (AJOL)

    Items 101 - 150 of 183 ... Vol 10, No 1 (2005), Influence Of Specialized Mathematical Language On Secondary School Students Mathematical Achievement In Kenya, Abstract ... Vol 6, No 1 (2001), Maternal education, age and household head gender associated with weight for age index of preschool children in Imo state ...

  8. Nitrate leaching index (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...

  9. Browse Title Index

    African Journals Online (AJOL)

    Items 301 - 350 of 577 ... Vol 25, No 2 (2008), Maternal Serum Triglycerides at Midpregnancy and Term Neonate Weight in Non-Diabetic Women with Normal Body Mass Index, Abstract PDF. L Sekhavat, F Zare. Vol 25, No 1 (2008), MDGs & SOGON: Mortality, The Media & Corporate Nigeria - The Third Olusola Adewole Ojo ...

  10. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 68 of 68 ... Vol 11, No 2 (2013), Some Haematological Parameters in Posttraumatic Stress Disorder Patients in Nassarawa Gwom Following the 2010 Jos Crisis ... Vol 10, No 2 (2012), The comparative study of the body mass index of Hausa and Yoruba children aged 2-5 in Jos, Plateau state, Nigeria, Abstract.

  11. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 338 ... Vol 17, No 2 (2005), A successful cognitive-behavioural intervention that failed: a case study of adolescent conduct disorder at a school for the disadvantaged, Abstract. E Mashalaba, D Edwards. Vol 27, No 3 (2015), A validational study of the Ironson–Woods Spirituality/ Religiousness Index in Nigerian ...

  12. Browse Title Index

    African Journals Online (AJOL)

    Items 851 - 900 of 1255 ... Vol 10, No 4 (2004), Occurrence of Parasites in Pseudotolithus elongatus and Cynoglossus seneglensis in Cross River Estuary, Nigeria, Abstract PDF. JT Abraham, PA ... P C Chikezie. Vol 9, No 1 (2003), Parasitic contamination of leafy vegetables: a function of the leaf area index (lai), Abstract PDF.

  13. Browse Title Index

    African Journals Online (AJOL)

    Items 151 - 200 of 775 ... Vol 9, No 2 (2016), Biosynthesis, characterization and antimicrobial study of silver nanoparticles (agNPs), Abstract PDF. Aminu A. Hamisu, Maryam Abdullahi, U. Abubakar, S. Bilal, A.J. Abbas. Vol 2, No 2 (2009), Body mass index variations among adolescents from Kano Metropolis, Nigeria, Abstract ...

  14. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 100 of 242 ... ... No 2 (2008), Effect of Body Mass Index (BMI) On Degree of Angular Knee Deformity in Children with Blount\\'s Disease. Abstract. A Bafor, AO Ogbemudia, PFA Umebese. Vol 11, No 2 (2012), Efficacy of Six Weeks Skin Traction in the Management of Chronic Pain from Lumber Spondylosis, Abstract.

  15. Indexes to Volume 77

    Indian Academy of Sciences (India)


    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.

  16. Life quality index revisited

    DEFF Research Database (Denmark)

    Ditlevsen, Ove Dalager


    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 consist...

  17. Browse Title Index

    African Journals Online (AJOL)

    Items 251 - 300 of 1011 ... Issue, Title. Vol 31, No 2 (2012), Design and Development of a Soap Stamping and Tableting Machine for Small Scale Soap Manufacturer, Abstract PDF. BN Nwankwojike. Vol 36, No 3 (2017), DESIGN AND FABRICATION OF A DISCOMFORT INDEX METER FOR DETERMINATION OF STRESS IN ...

  18. A Tourism Conditions Index

    NARCIS (Netherlands)

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


    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

  19. Indexical Hybrid Tense Logic

    DEFF Research Database (Denmark)

    Blackburn, Patrick Rowan; Jørgensen, Klaus Frovin


    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...

  20. Browse Title Index

    African Journals Online (AJOL)

    Items 151 - 162 of 162 ... Issue, Title. Vol 2, No 2 (2003), The Significance Of Adaptive Changes In Rat Haemoglobin Micro-environment And Electophoretic Fractions During Barocamera Hypoxia, Abstract. BO Ekpo. Vol 5, No 1 (2006), The study of conicity index and waist hip ratio in Nigerian children and adolescents, Abstract.

  1. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 708 ... Vol 37, No 1 (2012), A comparative assessment of the health status of feral populations of Clarias gariepinus from three dams in the Limpopo and Olifants river systems, Limpopo province, South Africa, using the fish health assessment index protocol, Abstract. GN Madanire-Moyo, WJ Luus-Powell, ...

  2. Browse Title Index

    African Journals Online (AJOL)

    Items 51 - 100 of 273 ... AMS Nyomora. Vol 38, No 2 (2012), Distribution and Potential Impact of Feral Cotton on the Reintroduction of Cotton in the Southern Highlands, Tanzania, Abstract PDF. O Shilla, TP Hauser, FI Tibazarwa. Vol 31 (2005):, Distribution of hourly variability index of sky clearness, Abstract PDF. A Madhlopa.

  3. Browse Title Index

    African Journals Online (AJOL)

    Items 201 - 245 of 245 ... Vol 13, No 2 (2014), Sewage disposal methods in a sub-urban community in Edo state, Nigeria, Abstract PDF. AR Isara, AQ Aigbokhaode. Vol 16, No 1 (2017), Sleep deprivation and coffee consumption induced changes in blood pressure, body mass index and blood glucose in male Wistar albino rats ...

  4. Indexing Moving Points

    DEFF Research Database (Denmark)

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


    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...

  5. Montessori Index. Third Edition. (United States)

    Fleege, Virginia B.; And Others

    This volume, the result of 2 years of work, is an index to 24 volumes on Montessori theory and practice. The books were read and analyzed a minimum of six times. Sixteen of the volumes are authored by Maria Montessori. (DR)

  6. Browse Title Index

    African Journals Online (AJOL)

    Items 401 - 450 of 483 ... Vol 41, No 2 (2014), Serum zinc levels in HIV infected children attending the University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria. ... Vol 43, No 1 (2016), Subacute combined degeneration of the spinal cord in a Nigerian child: a need for a high index of suspicion, Abstract PDF.

  7. Automated Water Extraction Index

    DEFF Research Database (Denmark)

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


    of various sorts of environmental noise and at the same time offers a stable threshold value. Thus we introduced a new Automated Water Extraction Index (AWEI) improving classification accuracy in areas that include shadow and dark surfaces that other classification methods often fail to classify correctly...

  8. 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.

  9. 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.

  10. Browse Title Index

    African Journals Online (AJOL)

    Items 151 - 200 of 229 ... Journal Home > Advanced Search > Browse Title Index. Log in or Register to get ... KM Lawal, MN Umego, SB Ojo. Vol 17, No 1 (2005), Obtaining the green's function for electromagnetic waves propagating in layered in-homogeneous thin film media of spherical particles on a substrate, Abstract.

  11. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 48 of 48 ... Journal Home > Advanced Search > Browse Title Index. Log in or Register to get access to full text ... Vol 1 (2000), Measurement of Ground Electrical Conductivity for Planning Medium Wave Radio Broadcast Stations in South Western Nigeria, Abstract PDF. Moses Oludare Ajewole, Adeseye Muyiwa ...

  12. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 45 of 45 ... Vol 7, No 1 (2015), On The Relationship between Illiquidity, Aggregate Market Return and Conditional Volatility of the NIFTY Index, Abstract PDF. Som Sankar Sen. Vol 2, No 2 (2009), Opportunities for Micro and Small Scale Businesses in the Tourism Sector: The Case of The Kenya Coast1, Abstract PDF.

  13. Browse Title Index

    African Journals Online (AJOL)

    Vol 6, No 4 (2000), Solar energy as a viable pathway toward ecologically sustainable, Details ... Vol 18, No 3-4 (2012), Source Apportionment and distribution of Polycyclic Aromatic Hydrocarbons in Imo River Sediments near Afam Power Station, S.E. Nigeria: Molecular index and Multi-Variate Approaches, Abstract PDF.

  14. Browse Title Index

    African Journals Online (AJOL)

    Items 1 - 50 of 58 ... Vol 6, No 10 (2009), An Analysis of Alternative Weighting System on the National Price Index in Tanzania: The Implication to Poverty Analysis, Abstract PDF. AF Mkenda, W ... Vol 5, No 7 (2008), Exchange Rate Volatility, Currency Substitution and Monetary Policy in Nigeria, Abstract. DO Yinusa, AE Akinlo.

  15. Browse Title Index

    African Journals Online (AJOL)

    Items 251 - 300 of 390 ... Vol 46, No 3 (2005), Pattern of fertility and perception of population concerns in Kwara State, Nigeria, Abstract. MO Araoye .... Vol 54, No 3 (2013), Prevalence of obesity among adolescents in Ile‑Ife, Osun state, Nigeria using body mass index and waist hip ratio: A comparative study, Abstract. Adedayo ...

  16. Browse Title Index

    African Journals Online (AJOL)

    Items 951 - 1000 of 1329 ... ... Physicochemical Characteristics of Soil from Selected Solid Waste Dump Sites in Port Harcourt, Rivers State, Nigeria, Abstract PDF. FU Obianefo, IO Agbagwa, F.B.G. Tanee. Vol 19, No 3 (2015), Physico-Chemical Characterization and Pollution Index Determination of Leachates from Warri Waste ...

  17. Transport and transcriptional regulation of oil production in plants. (United States)

    Manan, Sehrish; Chen, Beibei; She, Guangbiao; Wan, Xiaochun; Zhao, Jian


    Triacylglycerol (TAG) serves as an energy reservoir and phospholipids as build blocks of biomembrane to support plant life. They also provide human with foods and nutrients. Multi-compartmentalized biosynthesis, trafficking or cross-membrane transport of lipid intermediates or precursors and their regulatory mechanisms are not fully understood. Recent progress has aided our understanding of how fatty acids (FAs) and phospholipids are transported between the chloroplast, the cytoplasm, and the endoplasmic reticulum (ER), and how the ins and outs of lipids take place in the peroxisome and other organelles for lipid metabolism and function. In addition, information regarding the transcriptional regulation network associated with FA and TAG biosynthesis has been further enriched. Recent breakthroughs made in lipid transport and transcriptional regulation has provided significant insights into our comprehensive understanding of plant lipid biology. This review attempts to highlight the recent progress made on lipid synthesis, transport, degradation, and their regulatory mechanisms. Metabolic engineering, based on these knowledge-powered technologies for production of edible oils or biofuels, is reviewed. The biotechnological application of metabolic enzymes, transcription factors and transporters, for oil production and composition improvement, are discussed in a broad context in order to provide a fresh scenario for researchers and to guide future research and applications.

  18. Transcript expression profiling for adventitious roots of Panax ginseng Meyer. (United States)

    Subramaniyam, Sathiyamoorthy; Mathiyalagan, Ramya; Natarajan, Sathishkumar; Kim, Yu-Jin; Jang, Moon-Gi; Park, Jun-Hyung; Yang, Deok Chun


    Panax ginseng Meyer is one of the major medicinal plants in oriental countries belonging to the Araliaceae family which are the primary source for ginsenosides. However, very few genes were characterized for ginsenoside pathway, due to the limited genome information. Through this study, we obtained a comprehensive transcriptome from adventitious roots, which were treated with methyl jasmonic acids for different time points (control, 2h, 6h, 12h, and 24h) and sequenced by RNA 454 pyrosequencing technology. Reference transcriptome 39,304,529 (0.04GB) was obtained from 5,724,987,880 bases (5.7GB) of 22 libraries by de novo assembly and 35,266 (58.5%) transcripts were annotated with biological schemas (GO and KEGG). The digital gene expression patterns were obtained from in vitro grown adventitious root sequences which mapped to reference, from that, 3813 (6.3%) unique transcripts were involved in ≥2 fold up and downregulations. Finally, candidates for ginsenoside pathway genes were predicted from observed expression patterns. Among them, 30 transcription factors, 20 cytochromes, and 11 glycosyl transferases were predicted as ginsenoside candidates. These data can remarkably expand the existing transcriptome resources of Panax, especially to predict existence of gene networks in P. ginseng. The entity of the data provides a valuable platform to reveal more on secondary metabolism and abiotic stresses from P. ginseng in vitro grown adventitious roots. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Elin Lehrmann


    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.

  20. The Springer index of viruses

    National Research Council Canada - National Science Library

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


    ... 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...

  1. Innovation Learning in Comprehensive Education? (United States)

    Lindfors, Eila; Hilmola, Antti


    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…

  2. Steam generator comprehensive testing facility

    International Nuclear Information System (INIS)

    Chen Changbing


    The main system and equipment of a capacity of 30 MW steam generator testing rig is briefly introduced. The thermal performance of steam generator simulator has been verified with a steam generator model comprehensive testing. The application and function of the Facility are analyzed. And the effective use of the equipment of the Facility is also proposed

  3. Planning for Change: Comprehensive Planning. (United States)

    Temkin, Sanford

    This speech draws a distinction between a priori and a posteriori planning, and relates these two types of planning in coping with the various problems faced by local school districts. The author describes the comprehensive planning process, the development of information required by the process, and how this process is supported in the local…

  4. A Comprehensive General Chemistry Demonstration (United States)

    Sweeder, Ryan D.; Jeffery, Kathleen A.


    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…

  5. Electroconvulsive Therapy: A Comprehensive Assessment

    Directory of Open Access Journals (Sweden)

    Tayfun Zeren


    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

  6. Neuroimaging Evidence of Comprehension Monitoring

    Directory of Open Access Journals (Sweden)

    Linda Baker


    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.

  7. Comprehensive dictionary of electrical engineering

    CERN Document Server

    Laplante, Philip A


    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.


    African Journals Online (AJOL)

    reading comprehension research and in linguistic pragmatics, and to assess its significance for both reading .... metaphorical or ironical interpretation; (vii) the meaning of any stylistic effects. The basic problem for ..... the speaker's emotional state and assumptions about other speakers' perception of your emotional state.

  9. Children's Comprehension of Live Theatre. (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…

  10. Eagle syndrome : A comprehensive review

    NARCIS (Netherlands)

    Badhey, Arvind; Jategaonkar, Ameya; Kovacs, Alexander Joseph Anglin; Kadakia, Sameep; De Deyn, Peter Paul; Ducic, Yadranko; Schantz, Stimson; Shin, Edward

    The objective of this report is to summarize the symptoms, diagnostic workup, necessary imaging, and management of Eagle syndrome. A comprehensive literature review was conducted on peer-reviewed publications of Eagle syndrome across multiple disciplines in order to gain a thorough understanding of

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

    KAUST Repository

    Zhang, Runxuan


    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.

  12. The Journey of a Transcription Factor

    DEFF Research Database (Denmark)

    Pireyre, Marie

    in their regulation at multiple steps of their activation. Plant signaling in connection with transcription factor regulation is an exciting field, allowing research on multiple regulatory mechanisms. This thesis shed light on the importance of integrating all steps of transcription factor activation in a regulatory......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...... MYBs to activate transcription of GLS biosynthetic genes. A lot is known about transcriptional regulation of these nine GLS regulators. This thesis aimed at identifying regulatory mechanisms at the protein level, allowing rapid and specific regulation of transcription factors using GLS as a model...

  13. Scientific Journal Indexing

    Directory of Open Access Journals (Sweden)

    Getulio Teixeira Batista


    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 - 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 ( 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

  14. Site index comparisons among hardwoods (United States)

    Richard M. Godman


    Site index is one of the more easily measured indicators of the productive capacity of an area for a given species. In mixed stands, the site index of one species can be used to predict the site index of another. Site index also illustrates growth differences among species.

  15. Transcriptional ontogeny of the developing liver

    Directory of Open Access Journals (Sweden)

    Lee Janice S


    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.

  16. Likelihood for transcriptions in a genetic regulatory system under asymmetric stable Lévy noise (United States)

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


    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.

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

    DEFF Research Database (Denmark)

    Stolc, Viktor; Li, Lei; Wang, Xiangfeng


    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...... 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...

  18. A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. (United States)

    Blitz, Ira L; Paraiso, Kitt D; Patrushev, Ilya; Chiu, William T Y; Cho, Ken W Y; Gilchrist, Michael J


    Gene regulatory networks (GRNs) involve highly combinatorial interactions between transcription factors and short sequence motifs in cis-regulatory modules of target genes to control cellular phenotypes. The GRNs specifying most cell types are largely unknown and are the subject of wide interest. A catalog of transcription factors is a valuable tool toward obtaining a deeper understanding of the role of these critical effectors in any biological setting. Here we present a comprehensive catalog of the transcription factors for the diploid frog Xenopus tropicalis. We identify 1235 genes encoding DNA-binding transcription factors, comparable to the numbers found in typical mammalian species. In detail, the repertoire of X. tropicalis transcription factor genes is nearly identical to human and mouse, with the exception of zinc finger family members, and a small number of species/lineage-specific gene duplications and losses relative to the mammalian repertoires. We applied this resource to the identification of transcription factors differentially expressed in the early gastrula stage embryo. We find transcription factor enrichment in Spemann's organizer, the ventral mesoderm, ectoderm and endoderm, and report 218 TFs that show regionalized expression patterns at this stage. Many of these have not been previously reported as expressed in the early embryo, suggesting thus far unappreciated roles for many transcription factors in the GRNs regulating early development. We expect our transcription factor catalog will facilitate myriad studies using Xenopus as a model system to understand basic biology and human disease. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Selective dissemination and indexing of scientific information. (United States)

    Schneider, J H


    and recombined to synthesize the original concept during search and retrieval. Such systems tend to involve imprecise indexing, with a high level of "noise" in retrieved documents, difficult search strategy involving extensive post-coordination, and lengthy, complex computer manipulations. This situation reflects the fact that many producers of indexed data originally focused the design of their systems on the production of a published product with entries printed under short, concise index headings. Production of magnetic tapes as a by-product of the publication process, and their use for retrospective searching or for SDI services, was a much later development, almost an afterthought. Yet use of these tapes is growing so rapidly that it may be time to redesign the tape-producing systems, with ease of tape use for SDI services and retrospective searching as the primary consideration, and with publication of abstract and index bulletins or title listings relegated to secondary importance (49). The use of keywords to index documents creates a high degree of disorganization in information search and retrieval operations: Information is scattered under the many different terms that can be used to index different aspects of a concept. If the large-scale, comprehensive abstracting and indexing services were based on enumerative classifications with assignment of documents to logical hierarchical categories at the time of initial indexing, then many of the specialized information centers (50) and the 1300 abstracting and indexing services (3) would be unnecessary, and much of the reindexing and reprocessing of documents, the repackaging and reworking of abstracts and index data, and the resulting overlap and duplication characteristic of current information processing could be terminated. Partly because of the disorganization resulting from keyword indexing, the cost of a 5-year retrospective search of information on just one data base on magnetic tapes is a major

  20. Biodiversity intactness index

    CSIR Research Space (South Africa)

    Scholes, RJ


    Full Text Available range from complete protection to extreme trans- formation, such as urbanization. All activities are expressed on the basis of the area affected. The index is aggregated by weighting by the area subject to each activity and the number of species... pastures and fallow, or recently abandoned cultivated areas. Orchards and vineyards. SADC Landcover Data set36, filled with GLC2000 (ref. 37) for Namibia and Botswana. Plantation Natural land cover permanently replaced by dense plantations of trees...

  1. 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 ...

  2. Gene transcription and electromagnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, A.S.


    Our overall aim is to obtain sufficient information to allow us to ultimately determine whether ELF EM field exposure is an initiating factor in neoplastic transformation and/or if exposure can mimic characteristics of the second-step counterpart in neoplastic disease. This aim is based on our previous findings that levels of some transcripts are increased in cells exposed to EM fields. While the research is basic in nature, the ramifications have bearing on the general safety of exposure to EM fields in industrial and everyday life. A large array of diverse biological effects are reported to occur as the result of exposure to elf EM fields, suggesting that the cell response to EM fields is at a basic level, presumably initiated by molecular and/or biophysical events at the cell membrane. The hypothesized route is a signal transduction pathway involving membrane calcium fluxes. Information flow resulting from signal transduction can mediate the induction of regulatory factors in the cell, and directly affect how transcription is regulated.

  3. Transcript catalogs of human chromosome 21 and orthologous chimpanzee and mouse regions. (United States)

    Sturgeon, Xiaolu; Gardiner, Katheleen J


    A comprehensive representation of the gene content of the long arm of human chromosome 21 (Hsa21q) remains of interest for the study of Down syndrome, its associated phenotypic features, and mouse models. Here we compare transcript catalogs for Hsa21q, chimpanzee chromosome 21 (Ptr21q), and orthologous regions of mouse chromosomes 16, 17, and 10 for open reading frame (ORF) characteristics and conservation. The Hsa21q and mouse catalogs contain 552 and 444 gene models, respectively, of which only 162 are highly conserved. Hsa21q transcripts were used to identify orthologous exons in Ptr21q and assemble 533 putative transcripts. Transcript catalogs for all three organisms are searchable for nucleotide and amino acid sequence features of ORF length, repeat content, experimental support, gene structure, and conservation. For human and mouse comparisons, three additional summaries are provided: (1) the chromosomal distribution of novel ORF transcripts versus potential functional RNAs, (2) the distribution of species-specific transcripts within Hsa21q and mouse models of Down syndrome, and (3) the organization of sense-antisense and putative sense-antisense structures defining potential regulatory mechanisms. Catalogs, summaries, and nucleotide and amino acid sequences of all composite transcripts are available and searchable at These data sets provide comprehensive information useful for evaluation of candidate genes and mouse models of Down syndrome and for identification of potential functional RNA genes and novel regulatory mechanisms involving Hsa21q genes. These catalogs and search tools complement and extend information available from other gene annotation projects.

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

    International Nuclear Information System (INIS)

    Xiang Yuanyuan; Chen Xukun; Xu Rongbin


    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. Early-adolescents' reading comprehension and the stability of the middle school classroom-language environment. (United States)

    Gámez, Perla B; Lesaux, Nonie K


    This study examined teachers' language use across the school year in 6th grade urban middle-school classrooms (n = 24) and investigated the influence of this classroom-based linguistic input on the reading comprehension skills of the students (n = 851; 599 language minority learners and 252 English-only) in the participating classrooms. Analysis of speech transcripts revealed substantial variability in teachers' use of sophisticated vocabulary and total amount of talk and that individual teacher's language use was consistent across the school year. Analyses using Hierarchical Linear Modeling showed that when controlling for students' reading comprehension and vocabulary knowledge at the start of the year, teachers' use of sophisticated vocabulary was significantly related to students' reading comprehension outcomes, as was the time spent on vocabulary instruction. These findings suggest that the middle school classroom language environment plays a significant role in the reading comprehension of adolescent learners. (c) 2015 APA, all rights reserved).

  6. Emotion simulation during language comprehension. (United States)

    Havas, David A; Glenberg, Arthur M; Rinck, Mike


    We report a novel finding on the relation of emotion and language. Covert manipulation of emotional facial posture interacts with sentence valence when measuring the amount of time to judge valence (Experiment 1) and sensibility (Experiment 2) of the sentence. In each case, an emotion-sentence compatibility effect is found: Judgment times are faster when facial posture and sentence valence match than when they mismatch. We interpret the finding using a simulation account; that is, emotional systems contribute to language comprehension much as they do in social interaction. Because the effect was not observed on a lexical decision task using emotion-laden words (Experiment 3), we suggest that the emotion simulation affects comprehension processes beyond initial lexical access.

  7. Emergency preparedness: a comprehensive plan

    International Nuclear Information System (INIS)

    Wilson, R.H.


    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

  8. Comprehensive numerical modelling of tokamaks

    International Nuclear Information System (INIS)

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


    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

  9. A comprehensive nuclear test ban

    International Nuclear Information System (INIS)


    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

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


    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.

  11. Alarm management a comprehensive guide

    CERN Document Server

    Hollifield, Bill R


    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.

  12. Neuronal basis of speech comprehension. (United States)

    Specht, Karsten


    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.

  13. Evaluation of comprehensive environmental effect about coastal zone development activities in Liaoning Province and management advice. (United States)

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


    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.

  14. A data discovery index for the social sciences. (United States)

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


    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.

  15. Study on Evaluation Index System of Green mine construction (United States)

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


    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.

  16. Specificity and robustness in transcription control networks. (United States)

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


    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

  17. Heart rate index

    DEFF Research Database (Denmark)

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


    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...

  18. Transcription factors: Time to deliver. (United States)

    Ulasov, Alexey V; Rosenkranz, Andrey A; Sobolev, Alexander S


    Transcription factors (TFs) are at the center of the broad regulatory network orchestrating gene expression programs that elicit different biological responses. For a long time, TFs have been considered as potent drug targets due to their implications in the pathogenesis of a variety of diseases. At the same time, TFs, located at convergence points of cellular regulatory pathways, are powerful tools providing opportunities both for cell type change and for managing the state of cells. This task formulation requires the TF modulation problem to come to the fore. We review several ways to manage TF activity (small molecules, transfection, nanocarriers, protein-based approaches), analyzing their limitations and the possibilities to overcome them. Delivery of TFs could revolutionize the biomedical field. Whether this forecast comes true will depend on the ability to develop convenient technologies for targeted delivery of TFs. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Transcriptional regulation by cyclic AMP. (United States)

    Montminy, M


    A number of hormones and growth factors have been shown to stimulate target cells via second messenger pathways that in turn regulate the phosphorylation of specific nuclear factors. The second messenger cyclic AMP, for example, regulates a striking number of physiologic processes, including intermediary metabolism, cellular proliferation, and neuronal signaling, by altering basic patterns of gene expression. Our understanding of cyclic AMP signaling in the nucleus has expanded considerably over the past decade, owing in large part to the characterization of cyclic AMP-responsive promoter elements, transcription factors that bind them, and signal-dependent coactivators that mediate target gene induction. More importantly, these studies have revealed new insights into biological problems as diverse as biological clocks and long-term memory. The purpose of this review is to describe the components of the cyclic AMP response unit and to analyze how these components cooperate to induce target gene expression in response to hormonal stimulation.

  20. Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. (United States)

    Kaikkonen, Minna U; Niskanen, Henri; Romanoski, Casey E; Kansanen, Emilia; Kivelä, Annukka M; Laitalainen, Jarkko; Heinz, Sven; Benner, Christopher; Glass, Christopher K; Ylä-Herttuala, Seppo


    Vascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using genome-wide global run-on sequencing (GRO-Seq). We demonstrate that half of VEGF-A-regulated gene promoters are characterized by a transcriptionally competent paused RNA polymerase II (Pol II). We show that transition into productive elongation is a major mechanism of gene activation of virtually all VEGF-regulated genes, whereas only ∼40% of the genes are induced at the level of initiation. In addition, we report a comprehensive chromatin interaction map generated in HUVECs using tethered conformation capture (TCC) and characterize chromatin interactions in relation to transcriptional activity. We demonstrate that sites of active transcription are more likely to engage in chromatin looping and cell type-specific transcriptional activity reflects the boundaries of chromatin interactions. Furthermore, we identify large chromatin compartments with a tendency to be coordinately transcribed upon VEGF-A stimulation. We provide evidence that these compartments are enriched for clusters of regulatory regions such as super-enhancers and for disease-associated single nucleotide polymorphisms (SNPs). Collectively, these findings provide new insights into mechanisms behind VEGF-A-regulated transcriptional programs in endothelial cells. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. The role of the DNA-binding One Zinc Finger (DOF) transcription factor family in plants. (United States)

    Noguero, Mélanie; Atif, Rana Muhammad; Ochatt, Sergio; Thompson, Richard D


    The DOF (DNA-binding One Zinc Finger) family of transcription factors is involved in many fundamental processes in higher plants, including responses to light and phytohormones as well as roles in seed maturation and germination. DOF transcription factor genes are restricted in their distribution to plants, where they are in many copies in both gymnosperms and angiosperms and also present in lower plants such as the moss Physcomitrella patens and in the alga Chlamydomonas reinhardtii which possesses a single DOF gene. DOF transcription factors bind to their promoter targets at the consensus sequence AAAG. This binding depends upon the presence of the highly conserved DOF domain in the protein. Depending on the target gene, DOF factor binding may activate or repress transcription. DOF factors are expressed in most if not all tissues of higher plants, but frequently appear to be functionally redundant. Recent next-generation sequencing data provide a more comprehensive survey of the distribution of DOF sequence classes among plant species and within tissue types, and clues as to the evolution of functions assumed by this transcription factor family. DOFs do not appear to be implicated in the initial differentiation of the plant body plan into organs via the resolution of meristematic zones, in contrast to MADS-box and homeobox transcription factors, which are found in other non-plant eukaryotes, and this may reflect a more recent evolutionary origin. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Antonio Federico


    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.

  3. Impact coverage of the success-index


    EGGHE, Leo


    We show mathematically that the success-index can be any of the following impact indices, dependent on the value of the threshold used in the definition of the success-index: Hirsch-index (h-index), g-index, generalized Wu- and Kosmulski-indices, the average. success-index; Hirsch-index; h-Index; g-Index; Wu-index; Kosmulski-index

  4. Review of Comprehensive Evaluation Methods for Power Quality and Its Trend in New Generation Energy System (United States)

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


    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.

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

    DEFF Research Database (Denmark)

    Troelsgård, Christian


    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....

  6. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne


    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....

  7. CT-FC: more Comprehensive Traversal Focused Crawler

    Directory of Open Access Journals (Sweden)

    NFN Kuspriyanto


    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.

  8. 2001 Environmental Sustainability Index (ESI) (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...

  9. 2016 Traffic Safety Culture Index (United States)

    ... 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 behaviors ...

  10. The dynamic of poverty measurement indexes, from HDI to MPI

    Directory of Open Access Journals (Sweden)

    Anila Nanaj


    Full Text Available This study is focused on the dynamic poverty measurement from Human Development Index (HDI to Multi Dimensional Poverty (MPI, as poverty indicators from Sen to Foster-Alkire indexes. The HDI takes into consideration three dimensions and four indexes, the MPI goes further. The dimensions and indicators exceed the limits of classical measurements of poverty, creates the possibilities of measuring and comparing multidimensional poverty. Multidimensional Poverty Index helps to analyze the spectrum of poverty, understanding of sustainable development emergency, as well as it is a great help for reading poverty phenomenon on a three dimensional aspect and under the sub-meaning of 10 different indicators. MPI calculation off ers further comparative analyses of MPI Albania and Eastern Balkan countries. Comprehensive indexes are generated and applied, but doesn’t mean their conclusions are translated (converted into comprehensive policies as well. The data and the indicators for poverty measurement in Albania are not frequently generated and calculated due to LSMS missing a> er 2012. So there is a big gap in poverty reports. Finally, we argue how the measures chosen to use in poverty measurement of course can lead or mislead towards the process of policy making due to the great practical relevance of measurement methodologies.

  11. 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


    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...

  12. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. (United States)

    Hah, Nasun; Danko, Charles G; Core, Leighton; Waterfall, Joshua J; Siepel, Adam; Lis, John T; Kraus, W Lee


    We report the immediate effects of estrogen signaling on the transcriptome of breast cancer cells using global run-on and sequencing (GRO-seq). The data were analyzed using a new bioinformatic approach that allowed us to identify transcripts directly from the GRO-seq data. We found that estrogen signaling directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. In addition to protein-coding genes, estrogen regulates the distribution and activity of all three RNA polymerases and virtually every class of noncoding RNA that has been described to date. We also identified a large number of previously undetected estrogen-regulated intergenic transcripts, many of which are found proximal to estrogen receptor binding sites. Collectively, our results provide the most comprehensive measurement of the primary and immediate estrogen effects to date and a resource for understanding rapid signal-dependent transcription in other systems. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. Transcriptional programs that control expression of the autoimmune regulator gene Aire. (United States)

    Herzig, Yonatan; Nevo, Shir; Bornstein, Chamutal; Brezis, Miriam R; Ben-Hur, Sharon; Shkedy, Aya; Eisenberg-Bord, Michal; Levi, Ben; Delacher, Michael; Goldfarb, Yael; David, Eyal; Weinberger, Leehee; Viukov, Sergey; Ben-Dor, Shifra; Giraud, Matthieu; Hanna, Jacob H; Breiling, Achim; Lyko, Frank; Amit, Ido; Feuerer, Markus; Abramson, Jakub


    Aire is a transcriptional regulator that induces promiscuous expression of thousands of genes encoding tissue-restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs that regulate its own expression have remained elusive. Here we comprehensively analyzed both cis-acting and trans-acting regulatory mechanisms and found that the Aire locus was insulated by the global chromatin organizer CTCF and was hypermethylated in cells and tissues that did not express Aire. In mTECs, however, Aire expression was facilitated by concurrent eviction of CTCF, specific demethylation of exon 2 and the proximal promoter, and the coordinated action of several transcription activators, including Irf4, Irf8, Tbx21, Tcf7 and Ctcfl, which acted on mTEC-specific accessible regions in the Aire locus.

  14. A comprehensive outlook of Sannipata (United States)

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


    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

  15. NRC comprehensive records disposition schedule

    International Nuclear Information System (INIS)


    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

  16. A Comprehensive Theory of Integration. (United States)

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


    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.

  17. Production Practice During Language Learning Improves Comprehension. (United States)

    Hopman, Elise W M; MacDonald, Maryellen C


    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.

  18. Teaching Language Clues to Reading Comprehension (United States)

    Miller, John W.


    Proposes a teaching viewpoint on comprehension which removes some of the abstraction; the final product is a teaching sequence for comprehension skills that is parallel in form to the teaching sequences commonly used for word recognition. (JM)

  19. How Do We Motivate Reading Comprehension? (United States)

    Shanahan, Timothy


    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)

  20. 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.

  1. Genome-Wide Dynamics of Nascent Noncoding RNA Transcription in Porcine Heart After Myocardial Infarction. (United States)

    Kaikkonen, Minna U; Halonen, Paavo; Liu, Oscar Hsin-Fu; Turunen, Tiia A; Pajula, Juho; Moreau, Pierre; Selvarajan, Ilakya; Tuomainen, Tomi; Aavik, Einari; Tavi, Pasi; Ylä-Herttuala, Seppo


    Microarrays and RNA sequencing are widely used to profile transcriptome remodeling during myocardial ischemia. However, the steady-state RNA analysis lacks in sensitivity to detect all noncoding RNA species and does not provide separation between transcriptional and post-transcriptional regulations. Here, we provide the first comprehensive analysis of nascent RNA profiles of mRNAs, primary micro-RNAs, long noncoding RNAs, and enhancer RNAs in a large animal model of acute infarction. Acute infarction was induced by cardiac catheterization of domestic swine. Nuclei isolated from healthy, border zone, and ischemic regions of the affected heart were subjected to global run-on sequencing. Global run-on sequencing analysis indicated that half of affected genes are regulated at the level of transcriptional pausing. A gradient of induction of inflammatory mediators and repression of peroxisome proliferator-activated receptor signaling and oxidative phosphorylation was detected when moving from healthy toward infarcted area. In addition, we interrogated the transcriptional regulation of primary micro-RNAs and provide evidence that several arrhythmia-related target genes exhibit repression at post-transcriptional level. We identified 450 long noncoding RNAs differently regulated by ischemia, including novel conserved long noncoding RNAs expressed in antisense orientation to myocardial transcription factors GATA-binding protein 4, GATA-binding protein 6, and Krüppel-like factor 6. Finally, characterization of enhancers exhibiting differential expression of enhancer RNAs pointed a central role for Krüppel-like factor, MEF2C, ETS, NFY, ATF, E2F2, and NRF1 transcription factors in determining transcriptional responses to ischemia. Global run-on sequencing allowed us to follow the gradient of gene expression occurring in the ischemic heart and identify novel noncoding RNAs regulated by oxygen deprivation. These findings highlight potential new targets for diagnosis and

  2. Text comprehension dependence on reading experience


    Tilmantaitė, Kamilė


    In bachelor thesis „Text comprehension dependence on reading experience“ – is researching, how students text comprehension is dependent on reading experience. In theoretical part discussed the reading conception and reading methods are discussed as well as the text comprehension, models and reading capacity. The practical part contains of pupils of eighth and tenth classes text comprehension test analysis, questionnaire about reading experience analysis and how they both interdependent. In th...

  3. Transcriptional profiling of putative human epithelial stem cells. (United States)

    Koçer, Salih S; Djurić, Petar M; Bugallo, Mónica F; Simon, Sanford R; Matic, Maja


    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. 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-kappaB are downregulated/inhibited in MHC negative basal cells. 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 may be enriched for stem cells. This study is the first

  4. Transcriptional profiling of putative human epithelial stem cells

    Directory of Open Access Journals (Sweden)

    Koçer Salih S


    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

  5. Developing a Global Cancer Stigma Index

    Directory of Open Access Journals (Sweden)

    Maria Orlando Edelen


    Full Text Available Despite increasing recognition about the stigma associated with cancer screening, diagnosis, and treatment-seeking behaviors, there has been relatively little attention paid to how to assess and intervene to reduce that stigma. An index to measure cancer stigma could empower health program developers and policymakers by identifying the key areas in which a population could benefit from education to change perceptions and address misinformation. The index also could be used to rank countries and communities based on their level of cancer stigma to assess where interventions are needed. We used structured literature review and expert review to generate a cancer stigma item pool. The item pool was subject to cognitive interviews for cultural appropriateness and comprehension; and data from initial pilot testing were used to reduce the pool of items for translation and field testing. The field test was conducted using a web-based survey in four samples representing two regions and three languages—English and Arabic speakers in Jordan and Egypt, and English and Mandarin Chinese speakers in China. Factor analyses and item response theory were applied to finalize the index. The analyses resulted in a 12-item cancer stigma index (CSI that was reliable across all four samples. The CSI scores were highly correlated with a general illness stigma scale, and operated as expected noting higher cancer stigma among men and those with lower income. The CSI can be used to inform initial cancer education efforts, identifying overall stigma levels in a country or community and particular issue areas requiring intervention.

  6. Indexing contamination surveys

    International Nuclear Information System (INIS)

    Brown, R.L.


    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

  7. Development of Comprehension Monitoring in Beginner Readers (United States)

    Yeomans-Maldonado, Gloria


    The current study was designed to understand the development of comprehension monitoring among beginner readers from first to third grade, and to determine the extent to which first graders' comprehension monitoring predicts reading comprehension in grade three. Participants were 113 children (57% female) from four US states who were followed from…

  8. 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 ...

  9. Comprehensive Approach Workshop: Hard Problem First Steps (United States)


    solving hard problems in general. The workshop participants agreed that the Comprehensive Approach is about entities working together towards the...généralement des conflits humains . Ils ont conclu que des problèmes difficiles ce qui utiliser « Comprehensive Approach » sont similaires au problème...Comprehensive Approach Solution .......................................................................................... 6 3.1 Working Definition

  10. 33 CFR 238.5 - Comprehensive planning. (United States)


    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Comprehensive planning. 238.5... Comprehensive planning. Coordinated comprehensive planning at the regional or river basin level, or for an urban.... This planning is particularly important in areas where significant portions of a watershed are expected...

  11. Text comprehension strategy instruction with poor readers

    NARCIS (Netherlands)

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


    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,

  12. Comprehensive framework for preventive maintenance priority of medical equipment. (United States)

    Saleh, Neven; Balestra, Gabriella


    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.

  13. 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.

  14. Regulation of transcription in hyperthermophilic archaea

    NARCIS (Netherlands)

    Brinkman, A.B.


    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

  15. 40 CFR 179.94 - Transcripts. (United States)


    ... of particular oral testimony first becomes available to propose corrections in the transcript of that testimony. Corrections are permitted only for transcription errors. The presiding officer shall promptly... have all oral testimony stenographically reported or recorded and transcribed, with evidence that is...

  16. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    Remodeling of chromatin confers it the ability for dynamic change. Remodeling is essential for transcriptional regulation, the first step of gene expression. Chromatin Structure and Gene Expression. Transcription is the first step of gene expression in which RNA synthesis occurs from the DNA (gene) template in a series of.

  17. Overlapping transcription structure of human cytomegalovirus ...

    Indian Academy of Sciences (India)


    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.

  18. NAC transcription factors: structurally distinct, functionally diverse

    DEFF Research Database (Denmark)

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


    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...

  19. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    In this article, we discuss the dynamic organization of eukaryotic genes into chromatin. Remodeling of chromatin confers it the ability for dynamic change. Remodeling is essential for transcriptional regulation, the first step of gene expression. Chromatin Structure and Gene Expression. Transcription is the first step of gene ...

  20. 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 ...

  1. Review of Cohesion in Indexing

    Directory of Open Access Journals (Sweden)

    Hasan Ashrafi Rizi


    Full Text Available Indexers often disagree on judging terms that best reflect the content of a document. Difference of opinion highlights one of the characteristics of indexing which is indexing cohesion. Also known as consistency, little study of the subject matter has been undertaken in the past few years. However, its importance has been recently acknowledged in effective information retrieval and expansion of access points to the document content. The present paper investigates cohesion in indexing. In addition of presenting the definitions offered by experts, it takes note of the factors influencing indexing cohesion. Methods for measuring cohesion are offered.

  2. Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice. (United States)

    Smita, Shuchi; Katiyar, Amit; Chinnusamy, Viswanathan; Pandey, Dev M; Bansal, Kailash C


    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 50 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 response in rice

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

    Directory of Open Access Journals (Sweden)

    Shuchi eSmita


    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

  4. Solar index generation and delivery

    Energy Technology Data Exchange (ETDEWEB)

    Lantz, L.J.


    The Solar Index, or, more completely defined as the Service Hot Water Solar Index, was conceptualized during the spring of 1978. The purpose was to enhance public awareness to solar energy usability. Basically, the Solar Index represents the percentage of energy that solar would provide in order to heat an 80 gallon service hot water load for a given location and day. The Index is computed by utilizing SOLCOST, a computer program, which also has applications to space heating, cooling, and heat pump systems and which supplies economic analyses for such solar energy systems. The Index is generated for approximately 68 geographic locations in the country on a daily basis. The definition of the Index, how the project came to be, what it is at the present time and a plan for the future are described. Also presented are the models used for the generation of the Index, a discussion of the primary tool of implementation (the SOLCOST program) and future efforts.

  5. RNA binding specificity of Ebola virus transcription factor VP30. (United States)

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


    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.

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

    Directory of Open Access Journals (Sweden)

    Dmitry A Rodionov


    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.

  7. Nursing supervision for care comprehensiveness. (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


    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


    Directory of Open Access Journals (Sweden)

    IJBE Volume 1


    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

  9. Evaluating energy saving system of data centers based on AHP and fuzzy comprehensive evaluation model (United States)

    Jiang, Yingni


    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.

  10. Role of Working Memory in Typically Developing Children's Complex Sentence Comprehension (United States)

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


    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…

  11. Happy life-expectancy. A comprehensive measure of quality-of-life in nations

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)


    One of the aims of social indicator research is to develop a comprehensive measure of quality-of-life in nations that is analogous to GNP in economic indicator research. For that purpose, several multi dimensional indexes have been proposed. In addition to economic

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

    Directory of Open Access Journals (Sweden)

    Jacek Gad


    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.

  13. Transcription-dependent degradation controls the stability of the SREBP family of transcription factors. (United States)

    Sundqvist, Anders; Ericsson, Johan


    Cholesterol metabolism is tightly controlled by members of the sterol regulatory element-binding protein (SREBP) family of transcription factors. Here we demonstrate that the ubiquitination and degradation of SREBPs depend on their transcriptional activity. Mutations in the transactivation or DNA-binding domains of SREBPs inhibit their transcriptional activity and stabilize the proteins. The transcriptional activity and degradation of these mutants are restored when fused to heterologous transactivation or DNA-binding domains. When SREBP1a was fused to the DBD of Gal4, the ubiquitination and degradation of the fusion protein depended on coexpression of a promoter-reporter gene containing Gal4-binding sites. In addition, disruption of the interaction between WT SREBP and endogenous p300/CBP resulted in inhibition of SREBP-dependent transcription and stabilization of SREBP. Chemical inhibitors of transcription reduced the degradation of transcriptionally active SREBP1a, whereas they had no effect on the stability of transcriptionally inactive mutants, demonstrating that transcriptional activation plays an important role in the degradation of SREBPs. Thus, transcription-dependent degradation of SREBP constitutes a feedback mechanism to regulate the expression of genes involved in cholesterol metabolism and may represent a general mechanism to regulate the duration of transcriptional responses.

  14. The Comprehensive Antibiotic Resistance Database (United States)

    McArthur, Andrew G.; Waglechner, Nicholas; Nizam, Fazmin; Yan, Austin; Azad, Marisa A.; Baylay, Alison J.; Bhullar, Kirandeep; Canova, Marc J.; De Pascale, Gianfranco; Ejim, Linda; Kalan, Lindsay; King, Andrew M.; Koteva, Kalinka; Morar, Mariya; Mulvey, Michael R.; O'Brien, Jonathan S.; Pawlowski, Andrew C.; Piddock, Laura J. V.; Spanogiannopoulos, Peter; Sutherland, Arlene D.; Tang, Irene; Taylor, Patricia L.; Thaker, Maulik; Wang, Wenliang; Yan, Marie; Yu, Tennison


    The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD; The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment. PMID:23650175

  15. Stereo Visualization and Map Comprehension (United States)

    Rapp, D. N.; Culpepper, S.; Kirkby, K.; Morin, P.


    In this experiment, we assessed the use of stereo visualizations as effective tools for topographic map learning. In most Earth Science courses, students spend extended time learning how to read topographic maps, relying on the lines of the map as indicators of height and accompanying distance. These maps often necessitate extended training for students to acquire an understanding of what they represent, how they are to be used, and the implementation of these maps to solve problems. In fact instructors often comment that students fail to adequately use such maps, instead relying on prior spatial knowledge or experiences which may be inappropriate for understanding topographic displays. We asked participants to study maps that provided 3-dimensional or 2-dimensional views, and then answer a battery of questions about features and processes associated with the maps. The results will be described with respect to the cognitive utility of visualizations as tools for map comprehension tasks.

  16. Probability theory a comprehensive course

    CERN Document Server

    Klenke, Achim


    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...

  17. Building Information Modeling Comprehensive Overview

    Directory of Open Access Journals (Sweden)

    Sergey Kalinichuk


    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.

  18. Understanding peace a comprehensive introduction

    CERN Document Server

    Fox, Michael Allen


    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 ...

  19. Investigating reading comprehension through EEG

    Directory of Open Access Journals (Sweden)

    Luciane Baretta


    Full Text Available   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.

  20. 2012 Environmental Performance Index and Pilot Trend Environmental Performance Index (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...

  1. 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


    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.

  2. 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


    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.

  3. Colon cancer associated transcripts in human cancers. (United States)

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


    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.

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

    Directory of Open Access Journals (Sweden)

    Firnhaber Christopher B


    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.

  5. A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

    Directory of Open Access Journals (Sweden)

    Wenbin Mei


    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.

  6. Optogenetic control of transcription in zebrafish.

    Directory of Open Access Journals (Sweden)

    Hongtao Liu

    Full Text Available Light inducible protein-protein interactions are powerful tools to manipulate biological processes. Genetically encoded light-gated proteins for controlling precise cellular behavior are a new and promising technology, called optogenetics. Here we exploited the blue light-induced transcription system in yeast and zebrafish, based on the blue light dependent interaction between two plant proteins, blue light photoreceptor Cryptochrome 2 (CRY2 and the bHLH transcription factor CIB1 (CRY-interacting bHLH 1. We demonstrate the utility of this system by inducing rapid transcription suppression and activation in zebrafish.

  7. Transcriptional mapping of rabies virus in vivo

    International Nuclear Information System (INIS)

    Flamand, A.; Delagneau, J.F.


    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

  8. Enhancer RNAs: the new molecules of transcription. (United States)

    Lai, Fan; Shiekhattar, Ramin


    In the past few years, technological advances in nucleotide sequencing have culminated in a greater understanding of the complexity of the human transcriptome. Notably, the discovery that distal regulatory elements known as enhancers are transcribed and such enhancer-derived transcripts (eRNAs) serve a critical function in transcriptional activation has added a new dimension to transcriptional regulation. Here we review recent insights into the tissue-specific and temporal-specific gene regulation brought about by the discovery of eRNAs. Copyright © 2013 Elsevier Ltd. All rights reserved.


    Directory of Open Access Journals (Sweden)

    IJBE Volume 2


    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

  10. Equiseparability on Terminal Wiener Index

    DEFF Research Database (Denmark)

    Deng, Xiaotie; Zhang, Jie


    The aim of this work is to explore the properties of the terminal Wiener index, which was recently proposed by Gutman et al. (2004) [3], and to show the fact that there exist pairs of trees and chemical trees which cannot be distinguished by using it. We give some general methods for constructing...... equiseparable pairs and compare the methods with the case for the Wiener index. More specifically, we show that the terminal Wiener index is degenerate to some extent....

  11. Asset pricing with index investing


    Georgy Chabakauri; Oleg Rytchkov


    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...

  12. Mangrove vulnerability index using GIS (United States)

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


    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).

  13. 2002 Environmental Sustainability Index (ESI) (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,...

  14. 2008 Environmental Performance Index (EPI) (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)...

  15. Index Bioclimatic "Wind-Chill"

    Directory of Open Access Journals (Sweden)

    Teodoreanu Elena


    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.

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


    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…

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

    NARCIS (Netherlands)

    Hestand, Matthew Scott


    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

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

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


    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.

  19. Contribution Index Based on Green Building Certification Systems

    Directory of Open Access Journals (Sweden)

    Yuting Sun


    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.

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

    Directory of Open Access Journals (Sweden)

    Kevin M. Harlen


    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.

  1. NUCKS Is a Positive Transcriptional Regulator of Insulin Signaling

    Directory of Open Access Journals (Sweden)

    Beiying Qiu


    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.

  2. High throughput assays for analyzing transcription factors. (United States)

    Li, Xianqiang; Jiang, Xin; Yaoi, Takuro


    Transcription factors are a group of proteins that modulate the expression of genes involved in many biological processes, such as cell growth and differentiation. Alterations in transcription factor function are associated with many human diseases, and therefore these proteins are attractive potential drug targets. A key issue in the development of such therapeutics is the generation of effective tools that can be used for high throughput discovery of the critical transcription factors involved in human diseases, and the measurement of their activities in a variety of disease or compound-treated samples. Here, a number of innovative arrays and 96-well format assays for profiling and measuring the activities of transcription factors will be discussed.

  3. Characterization of BRCA2 Transcriptional Regulation

    National Research Council Canada - National Science Library

    Couch, Fergus


    .... Initially, reagents for transcriptional studies were generated. The promoter was cloned into luciferase reporter vectors, and expression constructs of BRCA2, BRCA1, p53, p21, p27 and a number of other cell cycle regulating genes were generated...

  4. Salmonella Typhimurium transcription profiles in space flight (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...

  5. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam


    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.

  6. The Pemberton Happiness Index (United States)

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


    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

  7. Relationship between Prior Knowledge and Reading Comprehension

    Directory of Open Access Journals (Sweden)

    Noureldin Mohamed Abdelaal


    Full Text Available This study investigates the relationship between prior knowledge and reading comprehension in second language among postgraduate students in UPM. Participants in the study were 20 students who have the same level in English as a second language from several faculties. On the basis of a prior-knowledge questionnaire and test, students were selected; they were asked to sit a two-passage reading comprehension exam. According to the questionnaire and the short prior quiz, students had high prior knowledge in one of the two passages, and low prior knowledge in the other. The result showed significantly high relationship between the high prior knowledge and reading comprehension. However, the results showed significantly low relationship between low prior knowledge and reading comprehension. Yet the performance of students in a reading comprehension with high prior knowledge was significantly better than reading comprehension with low prior knowledge.

  8. The role of reading time complexity and reading speed in text comprehension

    DEFF Research Database (Denmark)

    Wallot, Sebastian; O'Brien, Beth; Haussmann, Anna


    Reading speed is commonly used as an index of reading fluency. However, reading speed is not a consistent predictor of text comprehension, when speed and comprehension are measured on the same text within the same reader. This might be due to the somewhat ambiguous nature of reading speed, which...... is sometimes regarded as a feature of the reading process, and sometimes as a product of that process. We argue that both reading speed and comprehension should be seen as the result of the reading process, and that the process of fluent text reading can instead be described by complexity metrics that quantify...... aspects of the stability of the reading process. In this article, we introduce complexity metrics in the context of reading and apply them to data from a self-paced reading study. In this study, children and adults read a text silently or aloud and answered comprehension questions after reading. Our...

  9. Biophysical models of transcription in cells (United States)

    Choubey, Sandeep

    Cells constantly face environmental challenges and deal with them by changing their gene expression patterns. They make decisions regarding which genes to express and which genes not to express based on intra-cellular and environmental cues. These decisions are often made by regulating the process of transcription. While the identities of the different molecules that take part in regulating transcription have been determined for a number of different genes, their dynamics inside the cell are still poorly understood. One key feature of these regulatory dynamics is that the numbers of the bio-molecules involved is typically small, resulting in large temporal fluctuations in transcriptional outputs (mRNA and protein). In this thesis I show that measurements of the cell-to-cell variability of the distribution of transcribing RNA polymerases along a gene provide a previously unexplored method for deciphering the mechanism of its transcription in vivo. First, I propose a simple kinetic model of transcription initiation and elongation from which I calculate transcribing RNA polymerase copy-number fluctuations. I test my theory against published data obtained for yeast genes and propose a novel mechanism of transcription. Rather than transcription being initiated through a single rate-limiting step, as was previously proposed, my single-cell analysis reveals the presence of at least two rate limiting steps. Second, I compute the distribution of inter-polymerase distance distribution along a gene and propose a method for analyzing inter-polymerase distance distributions acquired in experiments. By applying this method to images of polymerases transcribing ribosomal genes in E.coli I show that one model of regulation of these genes is consistent with inter-polymerase distance data while a number of other models are not. The analytical framework described in this thesis can be used to extract quantitative information about the dynamics of transcription from single

  10. Specificity in ROS Signaling and Transcript Signatures


    Vaahtera, Lauri; Brosché, Mikael; Wrzaczek, Michael; Kangasjärvi, Jaakko


    Significance: Reactive oxygen species (ROS), important signaling molecules in plants, are involved in developmental control and stress adaptation. ROS production can trigger broad transcriptional changes; however, it is not clear how specificity in transcriptional regulation is achieved. Recent Advances: A large collection of public transcriptome data from the model plant Arabidopsis thaliana is available for analysis. These data can be used for the analysis of biological processes that are a...

  11. CEDR: Comprehensive Epidemiologic Data Resource

    Energy Technology Data Exchange (ETDEWEB)


    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.

  12. The Comprehensive Emergent Literacy Model

    Directory of Open Access Journals (Sweden)

    Leigh Rohde


    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.

  13. Abdominopelvic washings: A comprehensive review

    Directory of Open Access Journals (Sweden)

    Erika F Rodriguez


    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.

  14. Swine Flu -A Comprehensive View (United States)

    Singh, Vandana; Sood, Meenakshi


    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

  15. Comprehensive approach to diabetic nephropathy

    Directory of Open Access Journals (Sweden)

    Bancha Satirapoj


    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.

  16. NRC comprehensive records disposition schedule

    International Nuclear Information System (INIS)


    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

  17. A temporary index

    International Nuclear Information System (INIS)

    Thomson, Jon; Craighead, Alison


    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



    Eduardo Andrés Sandoval Forero


    In this chapter we present some ideas about comprehensive peace, sustainability and durability. Addressed the relationship of comprehensive peace education, understood as a subsystem in which conflicts arise, violence, courtly and dynamics of respect and implementation of human rights, tolerance varieties appreciation for diversity and a culture of peace praxis. Decolonize peace is another approach leading to the comprehensiveness of peace, and finally outline a conception of education for pe...


    Directory of Open Access Journals (Sweden)

    Eduardo Andrés Sandoval Forero


    Full Text Available In this chapter we present some ideas about comprehensive peace, sustainability and durability. Addressed the relationship of comprehensive peace education, understood as a subsystem in which conflicts arise, violence, courtly and dynamics of respect and implementation of human rights, tolerance varieties appreciation for diversity and a culture of peace praxis. Decolonize peace is another approach leading to the comprehensiveness of peace, and finally outline a conception of education for peace and harmonious school life.

  20. Comprehensive energy management eco routing & velocity profiles

    CERN Document Server

    Brandstätter, Bernhard


    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.

  1. 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


    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

  2. The regulation of transcriptional repression in hypoxia. (United States)

    Cavadas, Miguel A S; Cheong, Alex; Taylor, Cormac T


    A sufficient supply molecular oxygen is essential for the maintenance of physiologic metabolism and bioenergetic homeostasis for most metazoans. For this reason, mechanisms have evolved for eukaryotic cells to adapt to conditions where oxygen demand exceeds supply (hypoxia). These mechanisms rely on the modification of pre-existing proteins, translational arrest and transcriptional changes. The hypoxia inducible factor (HIF; a master regulator of gene induction in response to hypoxia) is responsible for the majority of induced gene expression in hypoxia. However, much less is known about the mechanism(s) responsible for gene repression, an essential part of the adaptive transcriptional response. Hypoxia-induced gene repression leads to a reduction in energy demanding processes and the redirection of limited energetic resources to essential housekeeping functions. Recent developments have underscored the importance of transcriptional repressors in cellular adaptation to hypoxia. To date, at least ten distinct transcriptional repressors have been reported to demonstrate sensitivity to hypoxia. Central among these is the Repressor Element-1 Silencing Transcription factor (REST), which regulates over 200 genes. In this review, written to honor the memory and outstanding scientific legacy of Lorenz Poellinger, we provide an overview of our existing knowledge with respect to transcriptional repressors and their target genes in hypoxia. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Proofreading of misincorporated nucleotides in DNA transcription

    International Nuclear Information System (INIS)

    Voliotis, Margaritis; Liverpool, Tanniemola B; Cohen, Netta; Molina-París, Carmen


    The accuracy of DNA transcription is crucial for the proper functioning of the cell. Although RNA polymerases demonstrate selectivity for correct nucleotides, additional active mechanisms of transcriptional error correction are required to achieve observed levels of fidelity. Recent experimental findings have shed light on a particular mechanism of transcriptional error correction involving: (i) diffusive translocation of the RNA polymerase along the DNA (backtracking) and (ii) irreversible RNA cleavage. This mechanism achieves preferential cleavage of misincorporated nucleotides by biasing the local rates of translocation. Here, we study how misincorporated nucleotides affect backtracking dynamics and how this effect determines the level of transcriptional fidelity. We consider backtracking as a diffusive process in a periodic, one-dimensional energy landscape, which at a coarse-grained level gives rise to a hopping process between neighbouring local minima. We propose a model for how misincorporated nucleotides deform this energy landscape and hence affect the hopping rates. In particular, we show that this model can be used to derive both the theoretical limit on the fidelity (i.e. the minimum fraction of misincorporated nucleotides) and the actual fidelity relative to this optimum, achieved for specific combinations of the cleavage and polymerization rates. Finally, we study how external factors influencing backtracking dynamics affect transcriptional fidelity. We show that biologically relevant loads, similar to those exerted by nucleosomes or other transcriptional barriers, increase error correction. (paper)

  4. Lineage-specific partitions in archaeal transcription

    Directory of Open Access Journals (Sweden)

    Richard M. R. Coulson


    Full Text Available The phylogenetic distribution of the components comprising the transcriptional machinery in the crenarchaeal and euryarchaeal lineages of the Archaea was analyzed in a systematic manner by genome-wide profiling of transcription complements in fifteen complete archaeal genome sequences. Initially, a reference set of transcription-associated proteins (TAPs consisting of sequences functioning in all aspects of the transcriptional process, and originating from the three domains of life, was used to query the genomes. TAP-families were detected by sequence clustering of the TAPs and their archaeal homologues, and through extensive database searching, these families were assigned a function. The phylogenetic origins of archaeal genes matching hidden Markov model profiles of protein domains associated with transcription, and those encoding the TAP-homologues, showed there is extensive lineage-specificity of proteins that function as regulators of transcription: most of these sequences are present solely in the Euryarchaeota, with nearly all of them homologous to bacterial DNA-binding proteins. Strikingly, the hidden Markov model profile searches revealed that archaeal chromatin and histone-modifying enzymes also display extensive taxon-restrictedness, both across and within the two phyla.

  5. The effects of cocaine on HIV transcription. (United States)

    Tyagi, Mudit; Weber, Jaime; Bukrinsky, Michael; Simon, Gary L


    Illicit drug users are a high-risk population for infection with the human immunodeficiency virus (HIV). A strong correlation exists between prohibited drug use and an increased rate of HIV transmission. Cocaine stands out as one of the most frequently abused illicit drugs, and its use is correlated with HIV infection and disease progression. The central nervous system (CNS) is a common target for both drugs of abuse and HIV, and cocaine intake further accelerates neuronal injury in HIV patients. Although the high incidence of HIV infection in illicit drug abusers is primarily due to high-risk activities such as needle sharing and unprotected sex, several studies have demonstrated that cocaine enhances the rate of HIV gene expression and replication by activating various signal transduction pathways and downstream transcription factors. In order to generate mature HIV genomic transcript, HIV gene expression has to pass through both the initiation and elongation phases of transcription, which requires discrete transcription factors. In this review, we will provide a detailed analysis of the molecular mechanisms that regulate HIV transcription and discuss how cocaine modulates those mechanisms to upregulate HIV transcription and eventually HIV replication.

  6. Intrinsic terminators in Mycoplasma hyopneumoniae transcription. (United States)

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


    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.

  7. Transcriptional tools: Small molecules for modulating CBP KIX-dependent transcriptional activators. (United States)

    Bates, Caleb A; Pomerantz, William C; Mapp, Anna K


    Previously it was demonstrated that amphipathic isoxazolidines are able to functionally replace the transcriptional activation domains of endogenous transcriptional activators. In addition, in vitro binding studies suggested that a key binding partner of these molecules is the CREB Binding Protein (CBP), more specifically the KIX domain within this protein. Here we show that CBP plays an essential role in the ability of isoxazolidine transcriptional activation domains to activate transcription in cells. Consistent with this model, isoxazolidines are able to function as competitive inhibitors of the activators MLL and Jun, both of which utilize a binding interaction with KIX to up-regulate transcription. Further, modification of the N2 side chain produced three analogs with enhanced potency against Jun-mediated transcription, although increased cytotoxicity was also observed. Collectively these small KIX-binding molecules will be useful tools for dissecting the role of the KIX domain in a variety of pathological processes. 2010 Wiley Periodicals, Inc.

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

    DEFF Research Database (Denmark)

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


    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...

  9. Implementing Comprehensive Reform: Implications for Practice (United States)

    Stout, Karen A.


    This chapter describes the challenges and practical barriers community colleges face when implementing comprehensive reform, exploring how reforms are leading to some improvements but not often scaled improvements.

  10. Beyond Comprehension Strategy Instruction: What's Next? (United States)

    Elleman, Amy M; Compton, Donald L


    In this article, we respond to Catts and Kamhi's (2017) argument that reading comprehension is not a single ability. We provide a brief review of the impact of strategy instruction, the importance of knowledge in reading comprehension, and possible avenues for future research and practice. We agree with Catts and Kamhi's argument that reading comprehension is a complex endeavor and that current recommended practices do not reflect the complexity of the construct. Knowledge building, despite its important role in comprehension, has been relegated to a back seat in reading comprehension instruction. In the final section of the article, we outline possible avenues for research and practice (e.g., generative language instruction, dialogic approaches to knowledge building, analogical reasoning and disciplinary literacy, the use of graphics and media, inference instruction) for improving reading-comprehension outcomes. Reading comprehension is a complex ability, and comprehension instruction should reflect this complexity. If we want to have an impact on long-term growth in reading comprehension, we will need to expand our current repertoire of instructional methods to include approaches that support the acquisition and integration of knowledge across a variety of texts and topics.

  11. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - NPL Sites (United States)

    U.S. Environmental Protection Agency — National Priorities List (NPL) Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access...

  12. 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.

  13. Simplifying the Water Poverty Index (United States)

    Cho, Danny I.; Ogwang, Tomson; Opio, Christopher


    In this paper, principal components methodology is used to derive simplified and cost effective indexes of water poverty. Using a well known data set for 147 countries from which an earlier five-component water poverty index comprising of "Resources," "Access," "Capacity," "Use" and "Environment" was constructed, we find that a simplified…

  14. A Tourism Financial Conditions Index

    NARCIS (Netherlands)

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


    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

  15. Maslov index for Hamiltonian systems

    Directory of Open Access Journals (Sweden)

    Alessandro Portaluri


    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.

  16. National index of radioactive wastes

    International Nuclear Information System (INIS)


    According to the 30 th december 1991 law, ANDRA is the public authority in charge of indexing the state and localisation of all the nuclear wastes existing on national territory. This index is the third edition of the resulting file. (D.L.)

  17. 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...

  18. TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics. (United States)

    Mochida, Keiichi; Yoshida, Takuhiro; Sakurai, Tetsuya; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo; Tran, Lam-Son Phan


    Crop plants, whose productivity is affected by a wide range of growing and environmental conditions, are grown for economic purposes. Transcription factors (TFs) play central role in regulation of many biological processes, including plant development and responses to environmental stimuli, by activating or repressing spatiotemporal gene expression. Here, we describe the TreeTFDB ( that houses the TF repertoires of six economically important tree crop species: Jatropha curcas, papaya, cassava, poplar, castor bean and grapevine. Among these, the TF repertoire of J. curcas has not been reported by any other TF databases. In addition to their basic information, such as sequence and domain features, domain alignments, gene ontology assignment and sequence comparison, information on available full-length cDNAs, identity and positions of all types of known cis-motifs found in the promoter regions, gene expression data are provided. With its newly designed and friendly interface and its unique features, TreeTFDB will enable research community to predict the functions and provide access to available genetic resources for performing comparative and functional genomics of the crop TFs, either individually or at whole family level, in a comprehensive and convenient manner.

  19. A New Index of Democracy

    Directory of Open Access Journals (Sweden)

    Jesús M. de Miguel


    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.

  20. Dynamic analysis of stochastic transcription cycles.

    Directory of Open Access Journals (Sweden)

    Claire V Harper


    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

  1. Dynamic regulation of genes involved in mitochondrial DNA replication and transcription during mouse brown fat cell differentiation and recruitment

    DEFF Research Database (Denmark)

    Murholm, Maria; Dixen, Karen; Qvortrup, Klaus


    ) and a remarkably higher mitochondrial abundance in brown adipocytes. METHODOLOGY/PRINCIPAL FINDINGS: Here we report a comprehensive characterisation of gene expression linked to mitochondrial DNA replication, transcription and function during white and brown fat cell differentiation in vitro as well as in white...... and brown fat, brown adipose tissue fractions and in selected adipose tissues during cold exposure. We find a massive induction of the majority of such genes during brown adipocyte differentiation and recruitment, e.g. of the mitochondrial transcription factors A (Tfam) and B2 (Tfb2m), whereas only a subset...

  2. A new multi-sensor integrated index for drought monitoring (United States)

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


    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

  3. Extraction of transcript diversity from scientific literature.

    Directory of Open Access Journals (Sweden)

    Parantu K Shah


    Full Text Available Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term "alternative splicing" to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts is publicly available at

  4. The Nurses’ Well-Being Index and Factors Influencing This Index among Nurses in Central China: A Cross-Sectional Study (United States)

    Liu, Bing; Hu, Ying; Yu, Chuanhua


    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

  5. 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.

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

  7. Guam and the Northern Mariana Islands ESI: INDEX (Index Polygons) (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...

  8. Reading comprehension interaction – a conversation analysis ...

    African Journals Online (AJOL)

    Such reading comprehension interactions display both a pedagogical structure, with the teacher 'teaching for comprehension', and a conversational structure, with participants interacting and conversing about the text. The focus of this article is on the conversational dimensions of such interactions. The purpose is to use ...

  9. A Dynamic Developmental Link between Verbal Comprehension-Knowledge (Gc) and Reading Comprehension: Verbal Comprehension-Knowledge Drives Positive Change in Reading Comprehension (United States)

    Reynolds, Matthew R.; Turek, Joshua J.


    Intelligence and general academic achievement have a well-established relation, but the interrelated development of the two constructs over time is less well-known. In this study, the dynamic developmental relation between verbal comprehension-knowledge (Gc) and reading comprehension was examined by applying bivariate dual change score models…

  10. Does Monitoring Event Changes Improve Comprehension? (United States)

    Bohn-Gettler, Catherine M.


    During narrative comprehension, reading times increase for changes in time, space, characters, goals, and causation. This study examined the extent to which instructional manipulations modify dimension monitoring during reading and whether this affects comprehension. Sixty-seven participants read three narratives (pretest). Half of the…


    Directory of Open Access Journals (Sweden)

    Інна Шимків


    Full Text Available This article reveals the basic features of listening comprehensive that are very constituent of communicative activity; listening comprehensive is analyzed, and attention is concentrated on the importance of its development in the teaching of future specialists. The nature of listening comprehension as a foreign-language skill is considered. Essential features of neuro-linguistic programming strategies used to teach listening are outlined. The system of teaching listening and its major levels are analyzed within the framework of communicative language teaching. The structural characteristics of listening comprehension on the basis of its psychophysiological mechanisms are elucidated. Listening comprehension difficulties caused by the physical settings are determined. Phonetic, lexical and grammatical problems encountered in listening are identified. It has been proved that both linguistic and non-linguistic types of knowledge, as well as various factors of communicative situation are essential for efficient listening comprehension. The characteristic features of handouts and worksheets used to overcome listening comprehension difficulties are defined. The study concludes with the integral part of listening comprehension in second language instruction and the need to improve the receptive mechanisms ensuring the efficiency of teaching listening.

  12. University Students with Poor Reading Comprehension (United States)

    Georgiou, George K.; Das, J. P.


    The present study aimed to examine the nature of the working memory and general cognitive ability deficits experienced by university students with a specific reading comprehension deficit. A total of 32 university students with poor reading comprehension but average word-reading skills and 60 age-word-matched controls with no comprehension…

  13. Comprehensive Teacher Education: A Handbook of Knowledge. (United States)

    American Association of Colleges for Teacher Education, Washington, DC.

    Since 1992, AACTE and the DeWitt Wallace-Reader's Digest Fund have worked in partnership to advance the knowledge base of comprehensive teacher education. The AACTE/DeWitt Wallace-Reader's Digest Fund's Comprehensive Teacher Education National Demonstration Project is grounded in the mutual belief that preparation of classroom teachers must…

  14. Reading Comprehension in Children with Down Syndrome (United States)

    Laws, Glynis; Brown, Heather; Main, Elizabeth


    Two studies aimed to investigate the reading comprehension abilities of 14 readers with Down syndrome aged 6 years 8 months to 13 years relative to those of typically developing children matched on word reading ability, and to investigate how these abilities were associated with reading accuracy, listening comprehension, phonological awareness and…

  15. Changing Student Teachers' Views of Comprehension Instruction ...

    African Journals Online (AJOL)

    At the same time research shows that little, if any, explicit and continuous strategy instruction takes place in classrooms. Reasons seem ... This article reports on the effect of a reading comprehension instruction course on university student teachers' lesson planning, strategy use and views about comprehension instruction.

  16. Tests of Reading Comprehension (TORCH) Pilot Study. (United States)

    Burgon, J. R.

    A New Zealand pilot study examined Tests of Reading Comprehension (TORCH) scores compared to PAT: Reading Comprehension scores and compared with teacher ratings. TORCH is a reading test package published in 1987 by the Australian Council for Educational Research. It consists of 14 untimed passages intended to assess the extent to which readers in…

  17. Comprehensive Education Portfolio with a Career Focus (United States)

    Kruger, Evonne J.; Holtzman, Diane M.; Dagavarian, Debra A.


    There are many types of student portfolios used within academia: the prior learning portfolio, credentialing portfolio, developmental portfolio, capstone portfolio, individual course portfolio, and the comprehensive education portfolio. The comprehensive education portfolio (CEP), as used by the authors, is a student portfolio, developed over…

  18. Teaching Comprehension Skills in the Middle Schools. (United States)

    Roehler, Laura R.

    This paper presents procedures and techniques for teaching comprehension skills to middle school students. Comprehension is described in terms of four skill areas: word meaning, structure, literal and inferential thinking, and critical reading. To help students think as they read, a strategy is proposed which involves a logical sequencing of all…

  19. Reading Comprehension Instruction Practices in Sierra Leone

    NARCIS (Netherlands)

    Hersbach, S.; Denessen, E.J.P.G.; Droop, W.


    Aim: In this study an attempt was made to give insight in the way reading comprehension is taught in Sierra Leone. Attention was paid to the didactical strategies and the materials used during reading comprehension instruction. Methodology: Primary school teachers in Sierra Leone (N=43) were

  20. Financial planning on a comprehensive scale. (United States)

    Mishra, Simita


    Hospitals and health systems that wish to explore the shift to comprehensive care management should: Assess the investments in infrastructure necessary to support comprehensive care management, Gauge the financial implications and set quality and financial goals, Monitor performance using metrics such as patient satisfaction, avoidable admissions, out-of-group referrals, and average length of stay.

  1. Teaching Listening Comprehension: Bottom-Up Approach (United States)

    Khuziakhmetov, Anvar N.; Porchesku, Galina V.


    Improving listening comprehension skills is one of the urgent contemporary educational problems in the field of second language acquisition. Understanding how L2 listening comprehension works can have a serious influence on language pedagogy. The aim of the paper is to discuss the practical and methodological value of the notion of the perception…

  2. Building Effective Collaboration in a Comprehensive Approach

    NARCIS (Netherlands)

    Essens, P.J.M.D.; Thompson, M.T.; Karrasch, A.; Jermalavičius, J.


    The Comprehensive Approach (CA) to crisis management operations is an essential element in NATO’s transformation in modern operations. At the Bucharest Summit in April 2008, Allied leaders endorsed an Action Plan for the development and implementation of NATO’s contribution to a Comprehensive

  3. Profiling classroom reading comprehension development practices ...

    African Journals Online (AJOL)

    Of specific concern is the lack of representation of the sampled South African learners at the PIRLS international benchmarks, revealing a distinct lack of their development of thinking and reasoning abilities for reading comprehension. To shed light on potential reasons for learners' reading comprehension difficulties, this ...

  4. Firm Sustainability Performance Index Modeling

    Directory of Open Access Journals (Sweden)

    Che Wan Jasimah Bt Wan Mohamed Radzi


    Full Text Available The main objective of this paper is to bring a model for firm sustainability performance index by applying both classical and Bayesian structural equation modeling (parametric and semi-parametric modeling. Both techniques are considered to the research data collected based on a survey directed to the China, Taiwan, and Malaysia food manufacturing industry. For estimating firm sustainability performance index we consider three main indicators include knowledge management, organizational learning, and business strategy. Based on the both Bayesian and classical methodology, we confirmed that knowledge management and business strategy have significant impact on firm sustainability performance index.

  5. The Selection of Trade Integration Indicators: Intraregional Share, Intensity, Homogeneous Intensity, and Introversion Index


    Hamanaka, Shintaro


    This paper attempts to provide a clear and comprehensive picture of trade integration in Asia, using a trade linkage diagram. The paper reviews four types of indicators (share, intensity, homogeneous intensity, and introversion index) and argues that the introversion index is the most suitable indicator for the comparison of the level of trade integration, both in terms of cross-regional comparisons and time series analyses. Next, since Asia is a group of heterogeneous economies and the level...

  6. Facilitating pictorial comprehension with color highlighting. (United States)

    McDougald, Brannan R; Wogalter, Michael S


    Pictorials can aid in communicating warning information, but viewers may not always correctly comprehend them. Two experiments focused on whether the use of relevant highlighting could benefit pictorial comprehension. A set of warning-related pictorials were manipulated according to three-color highlighting conditions: highlighting areas more relevant to correct comprehension, highlighting areas less relevant to comprehension, and no highlighting. Participants were asked to describe the purpose and meaning of each pictorial presented to them. The findings from both experiments indicate that comprehension of warning pictorials is higher for the relevant highlighting condition than the other two conditions. The highlighting of less relevant areas reduced comprehension compared to no highlighting. Use of appropriately placed highlighting could benefit the design of a complex symbol by pointing out pertinent areas to aid in determining its intended conceptual meaning. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  7. Uncertainty result of biotic index in analysing the water quality of Cikapundung river catchment area, Bandung (United States)

    Surtikanti, Hertien Koosbandiah


    The Biotic Index was developed in Western Countries in response to the need in water quality evaluation. This method analysis is based on the classification of aquatic macrobenthos as a bioindicator for clean and polluted water. The aim of this study is to compare the analysis of Cikapundung river using 6 different Biotic Indexes. BI Shannon-Weiner, Belgian Biological Index (BBI), Family Biotic Index (FBI), Biological Monitoring Working Party (BMWP), Biological Monitoring Working Party-Average Score Per Taxon (BMWP-ASPT), and A Scoring System for Macroinvertebrate in Australian River (A SIGNAL). Those analysis are compared with Physical Water Index (CPI) which is developed in Indonesia. The result shows that a decreasing water quality is detected upstream to downstream of Cikapundung River. However, based on the CPI analysis result, the BMWP-ASPT biotic index analysis is more comprehensive than other BI in explaining Cikapundung water quality.

  8. Towards a Comprehensive Catalog of Volcanic Seismicity (United States)

    Thompson, G.


    Catalogs of earthquakes located using differential travel-time techniques are a core product of volcano observatories, and while vital, they represent an incomplete perspective of volcanic seismicity. Many (often most) earthquakes are too small to locate accurately, and are omitted from available catalogs. Low frequency events, tremor and signals related to rockfalls, pyroclastic flows and lahars are not systematically catalogued, and yet from a hazard management perspective are exceedingly important. Because STA/LTA detection schemes break down in the presence of high amplitude tremor, swarms or dome collapses, catalogs may suggest low seismicity when seismicity peaks. We propose to develop a workflow and underlying software toolbox that can be applied to near-real-time and offline waveform data to produce comprehensive catalogs of volcanic seismicity. Existing tools to detect and locate phaseless signals will be adapted to fit within this framework. For this proof of concept the toolbox will be developed in MATLAB, extending the existing GISMO toolbox (an object-oriented MATLAB toolbox for seismic data analysis). Existing database schemas such as the CSS 3.0 will need to be extended to describe this wider range of volcano-seismic signals. WOVOdat may already incorporate many of the additional tables needed. Thus our framework may act as an interface between volcano observatories (or campaign-style research projects) and WOVOdat. We aim to take the further step of reducing volcano-seismic catalogs to sets of continuous metrics that are useful for recognizing data trends, and for feeding alarm systems and forecasting techniques. Previous experience has shown that frequency index, peak frequency, mean frequency, mean event rate, median event rate, and cumulative magnitude (or energy) are potentially useful metrics to generate for all catalogs at a 1-minute sample rate (directly comparable with RSAM and similar metrics derived from continuous data). Our framework

  9. Transcription of the T4 late genes

    Directory of Open Access Journals (Sweden)

    Kassavetis George A


    Full Text Available Abstract This article reviews the current state of understanding of the regulated transcription of the bacteriophage T4 late genes, with a focus on the underlying biochemical mechanisms, which turn out to be unique to the T4-related family of phages or significantly different from other bacterial systems. The activator of T4 late transcription is the gene 45 protein (gp45, the sliding clamp of the T4 replisome. Gp45 becomes topologically linked to DNA through the action of its clamp-loader, but it is not site-specifically DNA-bound, as other transcriptional activators are. Gp45 facilitates RNA polymerase recruitment to late promoters by interacting with two phage-encoded polymerase subunits: gp33, the co-activator of T4 late transcription; and gp55, the T4 late promoter recognition protein. The emphasis of this account is on the sites and mechanisms of actions of these three proteins, and on their roles in the formation of transcription-ready open T4 late promoter complexes.

  10. Transcriptional features of genomic regulatory blocks. (United States)

    Akalin, Altuna; Fredman, David; Arner, Erik; Dong, Xianjun; Bryne, Jan Christian; Suzuki, Harukazu; Daub, Carsten O; Hayashizaki, Yoshihide; Lenhard, Boris


    Genomic regulatory blocks (GRBs) are chromosomal regions spanned by highly conserved non-coding elements (HCNEs), most of which serve as regulatory inputs of one target gene in the region. The target genes are most often transcription factors involved in embryonic development and differentiation. GRBs often contain extensive gene deserts, as well as additional 'bystander' genes intertwined with HCNEs but whose expression and function are unrelated to those of the target gene. The tight regulation of target genes, complex arrangement of regulatory inputs, and the differential responsiveness of genes in the region call for the examination of fundamental rules governing transcriptional activity in GRBs. Here we use extensive CAGE tag mapping of transcription start sites across different human tissues and differentiation stages combined with expression data and a number of sequence and epigenetic features to discover these rules and patterns. We show evidence that GRB target genes have properties that set them apart from their bystanders as well as other genes in the genome: longer CpG islands, a higher number and wider spacing of alternative transcription start sites, and a distinct composition of transcription factor binding sites in their core/proximal promoters. Target gene expression correlates with the acetylation state of HCNEs in the region. Additionally, target gene promoters have a distinct combination of activating and repressing histone modifications in mouse embryonic stem cell lines. GRB targets are genes with a number of unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances.

  11. Alu-directed transcriptional regulation of some novel miRNAs

    Directory of Open Access Journals (Sweden)

    Zhao Xi W


    Full Text Available Abstract Background Despite many studies on the biogenesis, molecular structure and biological functions of microRNAs, little is known about the transcriptional regulatory mechanisms controlling the spatiotemporal expression pattern of human miRNA gene loci. Several lines of experimental results have indicated that both polymerase II (Pol-II and polymerase III (Pol-III may be involved in transcribing miRNAs. Here, we assessed the genomic evidence for Alu-directed transcriptional regulation of some novel miRNA genes in humans. Our data demonstrate that the expression of these Alu-related miRNAs may be modulated by Pol-III. Results We present a comprehensive exploration of the Alu-directed transcriptional regulation of some new miRNAs. Using a new computational approach, a variety of Alu-related sequences from multiple sources were pooled and filtered to obtain a subset containing Alu elements and characterized miRNA genes for which there is clear evidence of full-length transcription (embedded in EST. We systematically demonstrated that 73 miRNAs including five known ones may be transcribed by Pol-III through Alu or MIR. Among the new miRNAs, 33 were determined by high-throughput Solexa sequencing. Real-time TaqMan PCR and Northern blotting verified that three newly identified miRNAs could be induced to co-express with their upstream Alu transcripts by heat shock or cycloheximide. Conclusion Through genomic analysis, Solexa sequencing and experimental validation, we have identified candidate sequences for Alu-related miRNAs, and have found that the transcription of these miRNAs could be governed by Pol-III. Thus, this study may elucidate the mechanisms by which the expression of a class of small RNAs may be regulated by their upstream repeat elements.

  12. Var transcription profiling of Plasmodium falciparum 3D7: assignment of cytoadherent phenotypes to dominant transcripts

    Directory of Open Access Journals (Sweden)

    Wunderlich Gerhard


    Full Text Available Abstract Background Cytoadherence of Plasmodium falciparum-infected red blood cells is mediated by var gene-encoded P. falciparum erythrocyte membrane protein-1 and host receptor preference depends in most cases on which of the 50–60 var genes per genome is expressed. Enrichment of phenotypically homogenous parasites by panning on receptor expressing cells is fundamental for the identification of the corresponding var transcript. Methods P. falciparum 3D7 parasites were panned on several transfected CHO-cell lines and their var transcripts analysed by i reverse transcription/PCR/cloning/sequencing using a universal DBLα specific oligonucleotide pair and ii by reverse transcription followed by quantitative PCR using 57 different oligonucleotide pairs. Results Each cytoadherence selected parasite line also adhered to untransfected CHO-745 cells and upregulation of the var gene PFD995/PFD1000c was consistently associated with cytoadherence to all but one CHO cell line. In addition, parasites panned on different CHO cell lines revealed candidate var genes which reproducibly associated to the respective cytoadherent phenotype. The transcription profile obtained by RT-PCR/cloning/sequencing differed significantly from that of RT-quantitative PCR. Conclusion Transfected CHO cell lines are of limited use for the creation of monophenotypic cytoadherent parasite lines. Nevertheless, 3D7 parasites can be reproducibly selected for the transcription of different determined var genes without genetic manipulation. Most importantly, var transcription analysis by RT-PCR/cloning/sequencing may lead to erroneous interpretation of var transcription profiles.

  13. 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.


    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

  14. Transcription factor, promoter, and enhancer utilization in human myeloid cells

    NARCIS (Netherlands)

    Joshi, Anagha; Pooley, Christopher; Freeman, Tom C.; Lennartsson, Andreas; Babina, Magda; Schmidl, Christian; Geijtenbeek, Teunis; Michoel, Tom; Severin, Jessica; Itoh, Masayoshi; Lassmann, Timo; Kawaji, Hideya; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R. R.; Rehli, Michael; Hume, David A.


    The generation of myeloid cells from their progenitors is regulated at the level of transcription by combinatorial control of key transcription factors influencing cell-fate choice. To unravel the global dynamics of this process at the transcript level, we generated transcription profiles for 91

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