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Sample records for exploring temporal transcription

  1. Attribute Exploration of Discrete Temporal Transitions

    CERN Document Server

    Wollbold, Johannes

    2007-01-01

    Discrete temporal transitions occur in a variety of domains, but this work is mainly motivated by applications in molecular biology: explaining and analyzing observed transcriptome and proteome time series by literature and database knowledge. The starting point of a formal concept analysis model is presented. The objects of a formal context are states of the interesting entities, and the attributes are the variable properties defining the current state (e.g. observed presence or absence of proteins). Temporal transitions assign a relation to the objects, defined by deterministic or non-deterministic transition rules between sets of pre- and postconditions. This relation can be generalized to its transitive closure, i.e. states are related if one results from the other by a transition sequence of arbitrary length. The focus of the work is the adaptation of the attribute exploration algorithm to such a relational context, so that questions concerning temporal dependencies can be asked during the exploration pr...

  2. Gene length as a biological timer to establish temporal transcriptional regulation.

    Science.gov (United States)

    Kirkconnell, Killeen S; Magnuson, Brian; Paulsen, Michelle T; Lu, Brian; Bedi, Karan; Ljungman, Mats

    2017-02-01

    Transcriptional timing is inherently influenced by gene length, thus providing a mechanism for temporal regulation of gene expression. While gene size has been shown to be important for the expression timing of specific genes during early development, whether it plays a role in the timing of other global gene expression programs has not been extensively explored. Here, we investigate the role of gene length during the early transcriptional response of human fibroblasts to serum stimulation. Using the nascent sequencing techniques Bru-seq and BruUV-seq, we identified immediate genome-wide transcriptional changes following serum stimulation that were linked to rapid activation of enhancer elements. We identified 873 significantly induced and 209 significantly repressed genes. Variations in gene size allowed for a large group of genes to be simultaneously activated but produce full-length RNAs at different times. The median length of the group of serum-induced genes was significantly larger than the median length of all expressed genes, housekeeping genes, and serum-repressed genes. These gene length relationships were also observed in corresponding mouse orthologs, suggesting that relative gene size is evolutionarily conserved. The sizes of transcription factor and microRNA genes immediately induced after serum stimulation varied dramatically, setting up a cascade mechanism for temporal expression arising from a single activation event. The retention and expansion of large intronic sequences during evolution have likely played important roles in fine-tuning the temporal expression of target genes in various cellular response programs.

  3. Spatial-temporal transcriptional dynamics of long non-coding RNAs in human brain.

    Science.gov (United States)

    Zhang, Xiao-Qin; Wang, Ze-Lin; Poon, Ming-Wai; Yang, Jian-Hua

    2017-08-15

    The functional architecture of the human brain is greatly determined by the temporal and spatial regulation of the transcription process. However, the spatial and temporal transcriptional landscape of long non-coding RNAs (lncRNAs) during human brain development remains poorly understood. Here, we report the genome-wide lncRNA transcriptional analysis in an extensive series of 1340 post-mortem human brain specimens collected from 16 regions spanning the period from early embryo development to late adulthood. We discovered that lncRNA transcriptome dramatically changed during fetal development, while transited to a surprisingly relatively stable state after birth till the late adulthood. We also discovered that the transcription map of lncRNAs was spatially different, and that this spatial difference was developmentally regulated. Of the 16 brain regions explored (cerebellar cortex, thalamus, striatum, amygdala, hippocampus and 11 neocortex areas), cerebellar cortex showed the most distinct lncRNA expression features from all remaining brain regions throughout the whole developmental period, reflecting its unique developmental and functional features. Furthermore, by characterizing the functional modules and cellular processes of the spatial-temporal dynamic lncRNAs, we found that they were significantly associated with the RNA processing, neuron differentiation and synaptic signal transportation processes. Furthermore, we found that many lncRNAs associated with the neurodegenerative Alzheimer and Parkinson diseases were co-expressed in the fetal development of the human brain, and affected the convergent biological processes. In summary, our study provides a comprehensive map for lncRNA transcription dynamics in human brain development, which might shed light on the understanding of the molecular underpinnings of human brain function and disease. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. Extracting Temporal Information from Open Domain Text: A Comparative Exploration

    NARCIS (Netherlands)

    Ahn, D.D.; Fissaha Adafre, S.; de Rijke, M.

    2005-01-01

    The utility of data-driven techniques in the end-to-end problem of temporal information extraction is unclear. Recognition of temporal expressions yields readily to machine learning, but normalization seems to call for a rule-based approach. We explore two aspects of the (potential) utility of

  5. Temporal Modulations of Contact Force during Haptic Surface Exploration

    National Research Council Canada - National Science Library

    Mueller, Stephanie; Martin, Sven; Schwarz, Michael; Grunwald, Martin

    2016-01-01

    .... Perception depends on the exploratory movements as well as influencing them. While this seems to be common sense, scientifically we know very little about the temporal dynamics during haptic exploration...

  6. Transcriptional Regulation and Transport of Terpenoid Indole Alkaloid in Catharanthus roseus: Exploration of New Research Directions.

    Science.gov (United States)

    Liu, Jiaqi; Cai, Junjun; Wang, Rui; Yang, Shihai

    2016-12-28

    As one of the model medicinal plants for exploration of biochemical pathways and molecular biological questions on complex metabolic pathways, Catharanthus roseus synthesizes more than 100 terpenoid indole alkaloids (TIAs) used for clinical treatment of various diseases and for new drug discovery. Given that extensive studies have revealed the major metabolic pathways and the spatial-temporal biosynthesis of TIA in C. roseus plant, little is known about subcellular and inter-cellular trafficking or long-distance transport of TIA end products or intermediates, as well as their regulation. While these transport processes are indispensable for multi-organelle, -tissue and -cell biosynthesis, storage and their functions, great efforts have been made to explore these dynamic cellular processes. Progress has been made in past decades on transcriptional regulation of TIA biosynthesis by transcription factors as either activators or repressors; recent studies also revealed several transporters involved in subcellular and inter-cellular TIA trafficking. However, many details and the regulatory network for controlling the tissue-or cell-specific biosynthesis, transport and storage of serpentine and ajmalicine in root, catharanthine in leaf and root, vindoline specifically in leaf and vinblastine and vincristine only in green leaf and their biosynthetic intermediates remain to be determined. This review is to summarize the progress made in biosynthesis, transcriptional regulation and transport of TIAs. Based on analysis of organelle, tissue and cell-type specific biosynthesis and progresses in transport and trafficking of similar natural products, the transporters that might be involved in transport of TIAs and their synthetic intermediates are discussed; according to transcriptome analysis and bioinformatic approaches, the transcription factors that might be involved in TIA biosynthesis are analyzed. Further discussion is made on a broad context of transcriptional and

  7. Transcriptional Regulation and Transport of Terpenoid Indole Alkaloid in Catharanthus roseus: Exploration of New Research Directions

    Directory of Open Access Journals (Sweden)

    Jiaqi Liu

    2016-12-01

    Full Text Available As one of the model medicinal plants for exploration of biochemical pathways and molecular biological questions on complex metabolic pathways, Catharanthus roseus synthesizes more than 100 terpenoid indole alkaloids (TIAs used for clinical treatment of various diseases and for new drug discovery. Given that extensive studies have revealed the major metabolic pathways and the spatial-temporal biosynthesis of TIA in C. roseus plant, little is known about subcellular and inter-cellular trafficking or long-distance transport of TIA end products or intermediates, as well as their regulation. While these transport processes are indispensable for multi-organelle, -tissue and -cell biosynthesis, storage and their functions, great efforts have been made to explore these dynamic cellular processes. Progress has been made in past decades on transcriptional regulation of TIA biosynthesis by transcription factors as either activators or repressors; recent studies also revealed several transporters involved in subcellular and inter-cellular TIA trafficking. However, many details and the regulatory network for controlling the tissue-or cell-specific biosynthesis, transport and storage of serpentine and ajmalicine in root, catharanthine in leaf and root, vindoline specifically in leaf and vinblastine and vincristine only in green leaf and their biosynthetic intermediates remain to be determined. This review is to summarize the progress made in biosynthesis, transcriptional regulation and transport of TIAs. Based on analysis of organelle, tissue and cell-type specific biosynthesis and progresses in transport and trafficking of similar natural products, the transporters that might be involved in transport of TIAs and their synthetic intermediates are discussed; according to transcriptome analysis and bioinformatic approaches, the transcription factors that might be involved in TIA biosynthesis are analyzed. Further discussion is made on a broad context of

  8. The temporally regulated transcription factor sel-7 controls developmental timing in C. elegans.

    Science.gov (United States)

    Xia, Dan; Huang, Xinxin; Zhang, Hong

    2009-08-15

    The temporal sequence of cell division and differentiation is explicitly controlled for succession and synchrony of developmental events. In this study we describe how the Caenorhabditis elegans gene sel-7 specifies the L3 stage-specific fate of seam cells, which adopt temporal specificities at each of four larval stages. Loss of function of sel-7 causes reiteration of the L2 stage fate at the L3 stage. sel-7 is involved in regulating the temporal expression pattern of hbl-1, which is a key factor in specifying the L2/L3 progression. We also show that sel-7 functions redundantly with other retarded heterochronic genes, including lin-46, daf-12 and the let-7 family miRNAs, in preventing adoption of the L2 fate at later stages. Expression of sel-7 in seam cells is temporally regulated through an evolutionarily conserved regulatory element located in intron 4 of sel-7. We further demonstrate that reiteration of the L2 proliferative seam cell division at the L3 stage in sel-7 mutants requires activity of the transcriptional mediator complex. Our study reveals that sel-7 functions as a novel heterochronic gene in controlling temporal cell identities and also demonstrates a role of the transcriptional mediator complex in integrating temporal information to specify seam cell division patterns in C. elegans.

  9. Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling.

    Science.gov (United States)

    Spealman, Pieter; Wang, Hao; May, Gemma; Kingsford, Carl; McManus, C Joel

    2016-01-01

    Recent technological advances (e.g., microarrays and massively parallel sequencing) have facilitated genome-wide measurement of many aspects of gene regulation. Ribosome profiling is a high-throughput sequencing method used to measure gene expression at the level of translation. This is accomplished by quantifying both the number of translating ribosomes and their locations on mRNA transcripts. The inventors of this approach have published several methods papers detailing its implementation and addressing the basics of ribosome profiling data analysis. Here we describe our lab's procedure, which differs in some respects from those published previously. In addition, we describe a data analysis pipeline, Ribomap, for ribosome profiling data. Ribomap allocates sequence reads to alternative mRNA isoforms, normalizes sequencing bias along transcripts using RNA-seq data, and outputs count vectors of per-codon ribosome occupancy for each transcript.

  10. Exploring the robustness of the transcriptional response to dosage ...

    Indian Academy of Sciences (India)

    VEITIA Reiner

    2Université Paris-Diderot, Paris, France. Correspondence to Prof. Reiner A. Veitia: reiner.veitia@ijm.fr. Abstract. The classical Hill equation is the simplest way to model sharp transcriptional responses (TR) to changing concentrations of an activator. Such steep sigmoidal transitions of the TR are often involved in the creation ...

  11. Exploring cellular memory molecules marking competent and active transcriptions

    Directory of Open Access Journals (Sweden)

    Liu De-Pei

    2007-05-01

    Full Text Available Abstract Background Development in higher eukaryotes involves programmed gene expression. Cell type-specific gene expression is established during this process and is inherited in succeeding cell cycles. Higher eukaryotes have evolved elegant mechanisms by which committed gene-expression states are transmitted through numerous cell divisions. Previous studies have shown that both DNase I-sensitive sites and the basal transcription factor TFIID remain on silenced mitotic chromosomes, suggesting that certain trans-factors might act as bookmarks, maintaining the information and transmitting it to the next generation. Results We used the mouse globin gene clusters as a model system to examine the retention of active information on M-phase chromosomes and its contribution to the persistence of transcriptional competence of these gene clusters in murine erythroleukemia cells. In cells arrested in mitosis, the erythroid-specific activator NF-E2p45 remained associated with its binding sites on the globin gene loci, while the other major erythroid factor, GATA-1, was removed from chromosome. Moreover, despite mitotic chromatin condensation, the distant regulatory regions and promoters of transcriptionally competent globin gene loci are marked by a preserved histone code consisting in active histone modifications such as H3 acetylation, H3-K4 dimethylation and K79 dimethylation. Further analysis showed that other active genes are also locally marked by the preserved active histone code throughout mitotic inactivation of transcription. Conclusion Our results imply that certain kinds of specific protein factors and active histone modifications function as cellular memory markers for both competent and active genes during mitosis, and serve as a reactivated core for the resumption of transcription when the cells exit mitosis.

  12. Exploring the spatio-temporal neural basis of face learning.

    Science.gov (United States)

    Yang, Ying; Xu, Yang; Jew, Carol A; Pyles, John A; Kass, Robert E; Tarr, Michael J

    2017-06-01

    Humans are experts at face individuation. Although previous work has identified a network of face-sensitive regions and some of the temporal signatures of face processing, as yet, we do not have a clear understanding of how such face-sensitive regions support learning at different time points. To study the joint spatio-temporal neural basis of face learning, we trained subjects to categorize two groups of novel faces and recorded their neural responses using magnetoencephalography (MEG) throughout learning. A regression analysis of neural responses in face-sensitive regions against behavioral learning curves revealed significant correlations with learning in the majority of the face-sensitive regions in the face network, mostly between 150-250 ms, but also after 300 ms. However, the effect was smaller in nonventral regions (within the superior temporal areas and prefrontal cortex) than that in the ventral regions (within the inferior occipital gyri (IOG), midfusiform gyri (mFUS) and anterior temporal lobes). A multivariate discriminant analysis also revealed that IOG and mFUS, which showed strong correlation effects with learning, exhibited significant discriminability between the two face categories at different time points both between 150-250 ms and after 300 ms. In contrast, the nonventral face-sensitive regions, where correlation effects with learning were smaller, did exhibit some significant discriminability, but mainly after 300 ms. In sum, our findings indicate that early and recurring temporal components arising from ventral face-sensitive regions are critically involved in learning new faces.

  13. Temporal and spatial transcriptional fingerprints by antipsychotic or propsychotic drugs in mouse brain.

    Directory of Open Access Journals (Sweden)

    Kensuke Sakuma

    Full Text Available Various types of antipsychotics have been developed for the treatment of schizophrenia since the accidental discovery of the antipsychotic activity of chlorpromazine. Although all clinically effective antipsychotic agents have common properties to interact with the dopamine D2 receptor (D2R activation, their precise mechanisms of action remain elusive. Antipsychotics are well known to induce transcriptional changes of immediate early genes (IEGs, raising the possibility that gene expressions play an essential role to improve psychiatric symptoms. Here, we report that while different classes of antipsychotics have complex pharmacological profiles against D2R, they share common transcriptome fingerprint (TFP profile of IEGs in the murine brain in vivo by quantitative real-time PCR (qPCR. Our data showed that various types of antipsychotics with a profound interaction of D2R including haloperidol (antagonist, olanzapine (antagonist, and aripiprazole (partial agonist all share common spatial TFPs closely homologous to those of D2R antagonist sulpiride, and elicited greater transcriptional responses in the striatum than in the nucleus accumbens. Meanwhile, D2R agonist quinpirole and propsychotic NMDA antagonists such as MK-801 and phencyclidine (PCP exhibited the contrasting TFP profiles. Clozapine and propsychotic drug methamphetamine (MAP displayed peculiar TFPs that reflect their unique pharmacological property. Our results suggest that transcriptional responses are conserved across various types of antipsychotics clinically effective in positive symptoms of schizophrenia and also show that temporal and spatial TFPs may reflect the pharmacological features of the drugs. Thus, we propose that a TFP approach is beneficial to evaluate novel drug candidates for antipsychotic development.

  14. Sequence mining and transcript profiling to explore cyst nematode parasitism

    Directory of Open Access Journals (Sweden)

    Recknor Justin

    2009-01-01

    currently known 6,860 H. glycines genes to a pool of 788 most promising candidate genes (including known parasitism genes and documented their expression profiles. Using our approach to pre-select genes likely involved in parasitism now allows detailed functional analyses in a manner not feasible for larger numbers of genes. The generation of the candidate pool described here is an important enabling advance because it will significantly facilitate the unraveling of fascinating plant-animal interactions and deliver knowledge that can be transferred to other pathogen-host systems. Ultimately, the exploration of true parasitism genes verified from the gene pool delineated here will identify weaknesses in the nematode life cycle that can be exploited by novel anti-nematode efforts.

  15. Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli.

    Science.gov (United States)

    Yang, Chi; Chang, Chuan-Hsiung

    2015-11-23

    Modeling the binding of transcription factors helps to decipher the control logic behind transcriptional regulatory networks. Position weight matrix is commonly used to describe a binding motif but assumes statistical independence between positions. Although current approaches take within-motif dependence into account for better predictive performance, these models usually rely on prior knowledge and incorporate simple positional dependence to describe binding motifs. The inability to take complex within-motif dependence into account may result in an incomplete representation of binding motifs. In this work, we applied association rule mining techniques and constructed models to explore within-motif dependence for transcription factors in Escherichia coli. Our models can reflect transcription factor-DNA recognition where the explored dependence correlates with the binding specificity. We also propose a graphical representation of the explored within-motif dependence to illustrate the final binding configurations. Understanding the binding configurations also enables us to fine-tune or design transcription factor binding sites, and we attempt to present the configurations through exploring within-motif dependence.

  16. Transcriptional Analysis of the Genetic Element pSSVx: Differential and Temporal Regulation of Gene Expression Reveals Correlation between Transcription and Replication

    DEFF Research Database (Denmark)

    Contursi, Patrizia; Cannio, Raffaele; Prato, Santina

    2007-01-01

    was differentially and temporally regulated over the growth cycle of S. islandicus. The map positions of the RNAs as well as the clockwise and the anticlockwise directions of their transcription were determined. Some genes were clustered and appeared to be transcribed as polycistronic messengers, among which one......pSSVx from Sulfolobus islandicus strain REY15/4 is a hybrid between a plasmid and a fusellovirus. A systematic study performed by a combination of Northern blot analysis, primer extension, and reverse transcriptase PCR revealed the presence of nine major transcripts whose expression...... long transcriptional unit comprised the genes for the plasmid copy number control protein ORF60 (CopG), ORF91, and the replication protein ORF892 (RepA). We propose that a termination readthrough mechanism might be responsible for the formation of more than one RNA species from a single 5' end...

  17. Exploring the roles of basal transcription factor 3 in eukaryotic growth and development.

    Science.gov (United States)

    Jamil, Muhammad; Wang, Wenyi; Xu, Mengyun; Tu, Jumin

    2015-01-01

    Basal transcription factor 3 (BTF3) has been reported to play a significant part in the transcriptional regulation linking with eukaryotes growth and development. Alteration in the BTF3 gene expression patterns or variation in their activities adds to the explanation of different signaling pathways and regulatory networks. Moreover, BTF3s often respond to numerous stresses, and subsequently they are involved in regulation of various mechanisms. BTF3 proteins also function through protein-protein contact, which can assist us to identify the multifaceted processes of signaling and transcriptional regulation controlled by BTF3 proteins. In this review, we discuss current advances made in starting to explore the roles of BTF3 transcription factors in eukaryotes especially in plant growth and development.

  18. Temporal embryonic transcription of chicken fast skeletal myosin heavy chain isoforms in the single comb white leghorn.

    Science.gov (United States)

    Griffin, J; St-Pierre, N; Lilburn, M S; Wick, M

    2016-05-01

    There are numerous factors that can significantly influence embryonic development in poultry and thus make simple days of incubation (chronological age) a less than perfect metric for studying embryonic physiology. The developmental fast skeletal muscle myosin (MyHC), the predominant protein in the Pectoralis major (PM), is temporally expressed as a cadre of highly specific developmental isoforms. In the study described herein, a novel molecular technology (NanoString) was used to characterize the myosin isoform transcriptional patterns in the PM of Single Comb White Leghorn (SCWL) embryos. NanoString technology is based on quantitative analysis of the transcriptome through digital detection and quantification of target mRNA transcripts. Total RNA was isolated and gene transcription quantified using NanoString in embryonic muscle samples collected daily from 6 through 19 days of incubation. Data were analyzed using the LOESS smoothing function at a 95% confidence level. The temporal transcription of MyHC isoforms obtained in this study was consistent with the literature at higher specificity and resolution, thus validating NanoString for use in gene transcription analyses. The results support a hypothesis that the transcription patterns of the embryonic MyHC isoforms may be used as molecular clocks to further investigate the developmental relationships underlying embryonic fast skeletal muscle growth and development. © The Author 2016. Published by Oxford University Press on behalf of Poultry Science Association.

  19. Exploring spatio-temporal patterns in traffic congestion data

    DEFF Research Database (Denmark)

    Kveladze, Irma; Agerholm, Niels; Reinau, Kristian Hegner

    2017-01-01

    in two years, an intensive exploration and analysis of complex transport data is considered. Based on the information such as location, time, segment length and road categories, the average time and speed required to cover each route segment will be calculated. The used visualization methods should lead......An efficient infrastructure is essential for economic development. However, economic growth has been closely connected to the increasing road transport. This increases traffic congestions significantly, and road network gets near or at its capacity limits. Hence, congestion has become a central...... problem in modern cities. Existing traffic information systems do rarely provide optimized information for both users and operators to make quick decisions on alternative routes, and to optimize the capacity of the road network. Therefore, development of an effective and efficient system that will enhance...

  20. Clustering-Based Approaches to the Exploration of Spatio-Temporal Data

    Science.gov (United States)

    Wu, X.; Zurita-Milla, R.; Kraak, M.-J.; Izquierdo-Verdiguier, E.

    2017-09-01

    As one spatio-temporal data mining task, clustering helps the exploration of patterns in the data by grouping similar elements together. However, previous studies on spatial or temporal clustering are incapable of analysing complex patterns in spatio-temporal data. For instance, concurrent spatio-temporal patterns in 2D or 3D datasets. In this study we present two clustering algorithms for complex pattern analysis: (1) the Bregman block average co-clustering algorithm with I-divergence (BBAC_I) which enables the concurrent analysis of spatio-temporal patterns in 2D data matrix, and (2) the Bregman cube average tri-clustering algorithm with I-divergence (BCAT_I) which enables the complete partitional analysis in 3D data cube. Here the use of the two clustering algorithms is illustrated by Dutch daily average temperature dataset from 28 weather stations from 1992 to 2011. For BBAC_I, it is applied to the averaged yearly dataset to identify station-year co-clusters which contain similar temperatures along stations and years, thus revealing patterns along both spatial and temporal dimensions. For BCAT_I, it is applied to the temperature dataset organized in a data cube with one spatial (stations) and two nested temporal dimensions (years and days). By partitioning the whole dataset into clusters of stations and years with similar within-year temperature similarity, BCATI explores the spatio-temporal patterns of intra-annual variability in the daily temperature dataset. As such, both BBACI and BCATI algorithms, combined with suitable geovisualization techniques, allow the exploration of complex spatial and temporal patterns, which contributes to a better understanding of complex patterns in spatio-temporal data.

  1. Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores.

    Directory of Open Access Journals (Sweden)

    Marcin Dembek

    Full Text Available Clostridium difficile is the leading cause of hospital acquired diarrhoea in industrialised countries. Under conditions that are not favourable for growth, the pathogen produces metabolically dormant endospores via asymmetric cell division. These are extremely resistant to both chemical and physical stress and provide the mechanism by which C. difficile can evade the potentially fatal consequences of exposure to heat, oxygen, alcohol, and certain disinfectants. Spores are the primary infective agent and must germinate to allow for vegetative cell growth and toxin production. While spore germination in Bacillus is well understood, little is known about C. difficile germination and outgrowth. Here we use genome-wide transcriptional analysis to elucidate the temporal gene expression patterns in C. difficile 630 endospore germination. We have optimized methods for large scale production and purification of spores. The germination characteristics of purified spores have been characterized and RNA extraction protocols have been optimized. Gene expression was highly dynamic during germination and outgrowth, and was found to involve a large number of genes. Using this genome-wide, microarray approach we have identified 511 genes that are significantly up- or down-regulated during C. difficile germination (p≤0.01. A number of functional groups of genes appeared to be co-regulated. These included transport, protein synthesis and secretion, motility and chemotaxis as well as cell wall biogenesis. These data give insight into how C. difficile re-establishes its metabolism, re-builds the basic structures of the vegetative cell and resumes growth.

  2. MicroRNA filters Hox temporal transcription noise to confer boundary formation in the spinal cord

    Science.gov (United States)

    Li, Chung-Jung; Hong, Tian; Tung, Ying-Tsen; Yen, Ya-Ping; Hsu, Ho-Chiang; Lu, Ya-Lin; Chang, Mien; Nie, Qing; Chen, Jun-An

    2017-03-01

    The initial rostrocaudal patterning of the neural tube leads to differential expression of Hox genes that contribute to the specification of motor neuron (MN) subtype identity. Although several 3' Hox mRNAs are expressed in progenitors in a noisy manner, these Hox proteins are not expressed in the progenitors and only become detectable in postmitotic MNs. MicroRNA biogenesis impairment leads to precocious expression and propagates the noise of Hoxa5 at the protein level, resulting in an imprecise Hoxa5-Hoxc8 boundary. Here we uncover, using in silico simulation, two feed-forward Hox-miRNA loops accounting for the precocious and noisy Hoxa5 expression, as well as an ill-defined boundary phenotype in Dicer mutants. Finally, we identify mir-27 as a major regulator coordinating the temporal delay and spatial boundary of Hox protein expression. Our results provide a novel trans Hox-miRNA circuit filtering transcription noise and controlling the timing of protein expression to confer robust individual MN identity.

  3. Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

    Science.gov (United States)

    Teber, Erdahl T; Crawford, Edward; Bolton, Kent B; Van Dyk, Derek; Schofield, Peter R; Kapoor, Vimal; Church, W Bret

    2006-01-01

    Background There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sources, designed to identify a myriad of sequence patterns considered to have potential biological importance within inter-genic regions, genes, transcripts, and proteins. However, biologists require easy to use, uncomplicated tools to integrate this information, visualise and print gene annotations. Integrating this information usually requires considerable informatics skills, and comprehensive knowledge of the data format to make full use of this information. Tools are needed to explore gene model variants by allowing users the ability to create alternative transcript models using novel combinations of exons not necessarily represented in current database deposits of mRNA/cDNA sequences. Results Djinn Lite is designed to be an intuitive program for storing and visually exploring of custom annotations relating to a eukaryotic gene sequence and its modelled gene products. In particular, it is helpful in developing hypothesis regarding alternate splicing of transcripts by allowing the construction of model transcripts and inspection of their resulting translations. It facilitates the ability to view a gene and its gene products in one synchronised graphical view, allowing one to drill down into sequence related data. Colour highlighting of selected sequences and added annotations further supports exploration, visualisation of sequence regions and motifs known or predicted to be biologically significant. Conclusion Gene annotating remains an ongoing and challengingtask that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become moreprecisely defined. Djinn Lite offers an accessible interface to help accumulate, enrich, and individualise sequence annotations relating to a gene, its

  4. Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

    Directory of Open Access Journals (Sweden)

    Van Dyk Derek

    2006-01-01

    Full Text Available Abstract Background There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sources, designed to identify a myriad of sequence patterns considered to have potential biological importance within inter-genic regions, genes, transcripts, and proteins. However, biologists require easy to use, uncomplicated tools to integrate this information, visualise and print gene annotations. Integrating this information usually requires considerable informatics skills, and comprehensive knowledge of the data format to make full use of this information. Tools are needed to explore gene model variants by allowing users the ability to create alternative transcript models using novel combinations of exons not necessarily represented in current database deposits of mRNA/cDNA sequences. Results Djinn Lite is designed to be an intuitive program for storing and visually exploring of custom annotations relating to a eukaryotic gene sequence and its modelled gene products. In particular, it is helpful in developing hypothesis regarding alternate splicing of transcripts by allowing the construction of model transcripts and inspection of their resulting translations. It facilitates the ability to view a gene and its gene products in one synchronised graphical view, allowing one to drill down into sequence related data. Colour highlighting of selected sequences and added annotations further supports exploration, visualisation of sequence regions and motifs known or predicted to be biologically significant. Conclusion Gene annotating remains an ongoing and challengingtask that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become moreprecisely defined. Djinn Lite offers an accessible interface to help accumulate, enrich, and individualise sequence

  5. The prolactin gene: a paradigm of tissue-specific gene regulation with complex temporal transcription dynamics.

    Science.gov (United States)

    Featherstone, K; White, M R H; Davis, J R E

    2012-07-01

    Transcription of numerous mammalian genes is highly pulsatile, with bursts of expression occurring with variable duration and frequency. The presence of this stochastic or 'noisy' expression pattern has been relatively unexplored in tissue systems. The prolactin gene provides a model of tissue-specific gene regulation resulting in pulsatile transcription dynamics in both cell lines and endocrine tissues. In most cell culture models, prolactin transcription appears to be highly variable between cells, with differences in transcription pulse duration and frequency. This apparently stochastic transcription is constrained by a transcriptional refractory period, which may be related to cycles of chromatin remodelling. We propose that prolactin transcription dynamics result from the summation of oscillatory cellular inputs and by regulation through chromatin remodelling cycles. Observations of transcription dynamics in cells within pituitary tissue show reduced transcriptional heterogeneity and can be grouped into a small number of distinct patterns. Thus, it appears that the tissue environment is able to reduce transcriptional noise to enable coordinated tissue responses to environmental change. We review the current knowledge on the complex tissue-specific regulation of the prolactin gene in pituitary and extra-pituitary sites, highlighting differences between humans and rodent experimental animal models. Within this context, we describe the transcription dynamics of prolactin gene expression and how this may relate to specific processes occurring within the cell. © 2012 The Authors. Journal of Neuroendocrinology © 2012 Blackwell Publishing Ltd.

  6. Temporal and Spatial Coexistence of Archaeal and Bacterial amoA Genes and Gene Transcripts in Lake Lucerne

    Directory of Open Access Journals (Sweden)

    Elisabeth W. Vissers

    2013-01-01

    Full Text Available Despite their crucial role in the nitrogen cycle, freshwater ecosystems are relatively rarely studied for active ammonia oxidizers (AO. This study of Lake Lucerne determined the abundance of both amoA genes and gene transcripts of ammonia-oxidizing archaea (AOA and bacteria (AOB over a period of 16 months, shedding more light on the role of both AO in a deep, alpine lake environment. At the surface, at 42 m water depth, and in the water layer immediately above the sediment, AOA generally outnumbered AOB. However, in the surface water during summer stratification, when both AO were low in abundance, AOB were more numerous than AOA. Temporal distribution patterns of AOA and AOB were comparable. Higher abundances of amoA gene transcripts were observed at the onset and end of summer stratification. In summer, archaeal amoA genes and transcripts correlated negatively with temperature and conductivity. Concentrations of ammonium and oxygen did not vary enough to explain the amoA gene and transcript dynamics. The observed herbivorous zooplankton may have caused a hidden flux of mineralized ammonium and a change in abundance of genes and transcripts. At the surface, AO might have been repressed during summer stratification due to nutrient limitation caused by active phytoplankton.

  7. Temporal profile of gene transcription noise modulated by cross-talking signal transduction pathways.

    Science.gov (United States)

    Sun, Qiwen; Tang, Moxun; Yu, Jianshe

    2012-02-01

    Gene transcription is a central cellular process and is stochastic in nature. The stochasticity has been studied in real cells and in theory, but often for the transcription activated by a single signaling pathway at steady-state. As transcription of many genes is involved with multiple pathways, we investigate how the transcription efficiency and noise is modulated by cross-talking pathways. We model gene transcription as a renewal process for which the gene can be turned on by different pathways. We determine the transcription efficiency by solving a system of differential equations, and obtain the mathematical formula of the noise strength by the Laplace transform and standard techniques in renewal theory. Our numerical examples demonstrate that cross-talking pathways are capable of inducing more cells to transcribe than the steady-state level after a short time period of signal transduction, and creating exceedingly high stationary transcription noise strength. In contrast, it is shown that one signaling pathway alone is unable to do so. Very strikingly, it is observed that the noise strength varies gradually over most values of the system parameters, but changes abruptly over a narrow range in the neighborhoods of some critical parameter values.

  8. Identification and exploration of pollen tube small proteins encoded by pollination-induced transcripts.

    Science.gov (United States)

    Huang, Jong-Chin; Chang, Liang-Chi; Wang, Min-Long; Guo, Cian-Ling; Chung, Mei-Chu; Jauh, Guang-Yuh

    2011-09-01

    Pollination is composed of cell-cell communication and complicated signaling cascades that regulate pollen tube growth and guidance toward the ovules for double fertilization, and is critical for successful sexual reproduction. Exploring expression profiles of in vivo grown pollen tubes is important. Nevertheless, it is difficult to obtain accessible pollen tubes for profiling studies in most model plants. By taking advantage of the hollow styles of lily (Lilium longiflorum), in vivo pollen tubes harvested from pollinated styles which had been cut open were used here to study their protein and transcript profiles. Pollination quantitatively and qualitatively altered the total protein composition of elongating pollen tubes. cDNAs generated and amplified from total RNAs of 24 h in vivo grown and 12 h in vitro cultured pollen tubes were used for suppression subtractive hybridization analyses and preparation of home-made array chips. Microarray analyses conducted with different probe sets revealed 16 transcripts specifically present and/or enriched in in vivo pollen tubes. Reverse transcription-PCR (RT-PCR), in situ hybridization and Northern blotting were applied to validate their unique pollination-induced expression features. Interestingly, several transcripts were simultaneously detected on the stylar transmitting tract epidermis, where in vivo pollen tubes tightly adhered during pollination. Their deduced amino acid sequences showed that most of them encoded small proteins and could be classified into several families. Transient assay revealed filament-like structures decorated by these proteins and one probably localized in the generative cell. These small peptides might be critical for pollen tube growth during pollination, and further exploration of their biological functions and mechanisms of action are of great interest.

  9. Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions.

    Science.gov (United States)

    Beaume, Marie; Hernandez, David; Farinelli, Laurent; Deluen, Cécile; Linder, Patrick; Gaspin, Christine; Romby, Pascale; Schrenzel, Jacques; Francois, Patrice

    2010-05-20

    Staphylococcus aureus is a versatile bacterial opportunist responsible for a wide spectrum of infections. The severity of these infections is highly variable and depends on multiple parameters including the genome content of the bacterium as well as the condition of the infected host. Clinically and epidemiologically, S. aureus shows a particular capacity to survive and adapt to drastic environmental changes including the presence of numerous antimicrobial agents. Mechanisms triggering this adaptation remain largely unknown despite important research efforts. Most studies evaluating gene content have so far neglected to analyze the so-called intergenic regions as well as potential antisense RNA molecules. Using high-throughput sequencing technology, we performed an inventory of the whole transcriptome of S. aureus strain N315. In addition to the annotated transcription units, we identified more than 195 small transcribed regions, in the chromosome and the plasmid of S. aureus strain N315. The coding strand of each transcript was identified and structural analysis enabled classification of all discovered transcripts. RNA purified at four time-points during the growth phase of the bacterium allowed us to define the temporal expression of such transcripts. A selection of 26 transcripts of interest dispersed along the intergenic regions was assessed for expression changes in the presence of various stress conditions including pH, temperature, oxidative shocks and growth in a stringent medium. Most of these transcripts showed expression patterns specific for the defined stress conditions that we tested. These RNA molecules potentially represent important effectors of S. aureus adaptation and more generally could support some of the epidemiological characteristics of the bacterium.

  10. Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network.

    Science.gov (United States)

    Jakobsen, Janus S; Braun, Martina; Astorga, Jeanette; Gustafson, E Hilary; Sandmann, Thomas; Karzynski, Michal; Carlsson, Peter; Furlong, Eileen E M

    2007-10-01

    Smooth muscle plays a prominent role in many fundamental processes and diseases, yet our understanding of the transcriptional network regulating its development is very limited. The FoxF transcription factors are essential for visceral smooth muscle development in diverse species, although their direct regulatory role remains elusive. We present a transcriptional map of Biniou (a FoxF transcription factor) and Bagpipe (an Nkx factor) activity, as a first step to deciphering the developmental program regulating Drosophila visceral muscle development. A time course of chromatin immunoprecipitatation followed by microarray analysis (ChIP-on-chip) experiments and expression profiling of mutant embryos reveal a dynamic map of in vivo bound enhancers and direct target genes. While Biniou is broadly expressed, it regulates enhancers driving temporally and spatially restricted expression. In vivo reporter assays indicate that the timing of Biniou binding is a key trigger for the time span of enhancer activity. Although bagpipe and biniou mutants phenocopy each other, their regulatory potential is quite different. This network architecture was not apparent from genetic studies, and highlights Biniou as a universal regulator in all visceral muscle, regardless of its developmental origin or subsequent function. The regulatory connection of a number of Biniou target genes is conserved in mice, suggesting an ancient wiring of this developmental program.

  11. Spatio-temporal Visualisation and Data Exploration of Traditional Ecological Knowledge/Indigenous Knowledge

    Directory of Open Access Journals (Sweden)

    Kierin Mackenzie

    2017-01-01

    Full Text Available Traditional Ecological Knowledge (TEK has been at the centre of mapping efforts for decades. Indigenous knowledge (IK is a critical subset of TEK, and Indigenous peoples utilise a wide variety of techniques for keeping track of time. Although techniques for mapping and visualising the temporal aspects of TEK/IK have been utilised, the spatio-temporal dimensions of TEK are not well explored visually outside of seasonal data and narrative approaches. Existing spatio-temporal models can add new visualisation approaches for TEK but are limited by ontological constraints regarding time, particularly the poor support for multi-cyclical data and localised timing. For TEK to be well represented, flexible systems are needed for modelling and mapping time that correspond well with traditional conceptions of time and space being supported. These approaches can take cues from previous spatio-temporal visualisation work in the Geographic(al Information System(s/Science(s GIS community, and from temporal depictions extant in existing cultural traditions.

  12. Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions.

    Science.gov (United States)

    Moscou, Matthew J; Lauter, Nick; Caldo, Rico A; Nettleton, Dan; Wise, Roger P

    2011-06-01

    Barley Mildew resistance locus a (Mla) is a major determinant of immunity to the powdery mildew pathogen, Blumeria graminis f. sp. hordei. Alleles of Mla encode cytoplasmic- and membrane-localized coiled-coil, nucleotide binding site, leucine-rich repeat proteins that mediate resistance when complementary avirulence effectors (AVR(a)) are present in the pathogen. Presence of an appropriate AVR(a) protein triggers nuclear relocalization of MLA, in which MLA binds repressing host transcription factors. Timecourse expression profiles of plants harboring Mla1, Mla6, and Mla12 wild-type alleles versus paired loss-of-function mutants were compared to discover conserved transcriptional targets of MLA and downstream signaling cascades. Pathogen-dependent gene expression was equivalent or stronger in susceptible plants at 20 h after inoculation (HAI) and was attenuated at later timepoints, whereas resistant plants exhibited a time-dependent strengthening of the transcriptional response, increasing in both fold change and the number of genes differentially expressed. Deregulation at 20 HAI implicated 16 HAI as a crucial point in determining the future trajectory of this interaction and was interrogated by quantitative analysis. In total, 28 potential transcriptional targets of the MLA regulon were identified. These candidate targets possess a diverse set of predicted functions, suggesting that multiple pathways are required to mediate the hypersensitive reaction.

  13. The Hunchback temporal transcription factor establishes, but is not required to maintain, early-born neuronal identity.

    Science.gov (United States)

    Hirono, Keiko; Kohwi, Minoree; Clark, Matt Q; Heckscher, Ellie S; Doe, Chris Q

    2017-01-31

    Drosophila and mammalian neural progenitors typically generate a diverse family of neurons in a stereotyped order. Neuronal diversity can be generated by the sequential expression of temporal transcription factors. In Drosophila, neural progenitors (neuroblasts) sequentially express the temporal transcription factors Hunchback (Hb), Kruppel, Pdm, and Castor. Hb is necessary and sufficient to specify early-born neuronal identity in multiple lineages, and is maintained in the post-mitotic neurons produced during each neuroblast expression window. Surprisingly, nothing is currently known about whether Hb acts in neuroblasts or post-mitotic neurons (or both) to specify first-born neuronal identity. Here we selectively remove Hb from post-mitotic neurons, and assay the well-characterized NB7-1 and NB1-1 lineages for defects in neuronal identity and function. We find that loss of Hb from embryonic and larval post-mitotic neurons does not affect neuronal identity. Furthermore, removing Hb from post-mitotic neurons throughout the entire CNS has no effect on larval locomotor velocity, a sensitive assay for motor neuron and pre-motor neuron function. We conclude that Hb functions in progenitors (neuroblasts/GMCs) to establish heritable neuronal identity that is maintained by a Hb-independent mechanism. We suggest that Hb acts in neuroblasts to establish an epigenetic state that is permanently maintained in early-born neurons.

  14. Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data

    Energy Technology Data Exchange (ETDEWEB)

    Song, Mingzhou (Joe) [New Mexico State University, Las Cruces; Lewis, Chris K. [New Mexico State University, Las Cruces; Lance, Eric [New Mexico State University, Las Cruces; Chesler, Elissa J [ORNL; Kirova, Roumyana [Bristol-Myers Squibb Pharmaceutical Research & Development, NJ; Langston, Michael A [University of Tennessee, Knoxville (UTK); Bergeson, Susan [Texas Tech University, Lubbock

    2009-01-01

    The problem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from high-throughput transcriptomic data is addressed. A network reconstruction algorithm was developed that uses the statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. Using temporal gene expression data collected from the brains of alcohol-treated mice in an analysis of the molecular response to alcohol, this algorithm identified genes from a major neuronal pathway as putative components of the alcohol response mechanism. Three of these genes have known associations with alcohol in the literature. Several other potentially relevant genes, highlighted and agreeing with independent results from literature mining, may play a role in the response to alcohol. Additional, previously-unknown gene interactions were discovered that, subject to biological verification, may offer new clues in the search for the elusive molecular mechanisms of alcoholism.

  15. Transcript, protein and metabolite temporal dynamics in the CAM plant Agave

    OpenAIRE

    Abraham, PE; Yin, H; Borland, AM; Weighill, D; Lim, SD; De Paoli, HC; Engle, N; Jones, PC; Agh, R; Weston, DJ; Wullschleger, SD; Tschaplinski, T; Jacobson, D; Cushman, JC; Hettich, RL

    2016-01-01

    © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Already a proven mechanism for drought resilience, crassulacean acid metabolism (CAM) is a specialized type of photosynthesis that maximizes water-use efficiency by means of an inverse (compared to C 3 and C 4 photosynthesis) day/night pattern of stomatal closure/opening to shift CO 2 uptake to the night, when evapotranspiration rates are low. A systems-level understanding of temporal molecular and metaboli...

  16. Exploring spatial-temporal dynamics of fire regime features in mainland Spain

    Science.gov (United States)

    Jiménez-Ruano, Adrián; Rodrigues Mimbrero, Marcos; de la Riva Fernández, Juan

    2017-10-01

    This paper explores spatial-temporal dynamics in fire regime features, such as fire frequency, burnt area, large fires and natural- and human-caused fires, as an essential part of fire regime characterization. Changes in fire features are analysed at different spatial - regional and provincial/NUTS3 - levels, together with summer and winter temporal scales, using historical fire data from Spain for the period 1974-2013. Temporal shifts in fire features are investigated by means of change point detection procedures - Pettitt test, AMOC (at most one change), PELT (pruned exact linear time) and BinSeg (binary segmentation) - at a regional level to identify changes in the time series of the features. A trend analysis was conducted using the Mann-Kendall and Sen's slope tests at both the regional and NUTS3 level. Finally, we applied a principal component analysis (PCA) and varimax rotation to trend outputs - mainly Sen's slope values - to summarize overall temporal behaviour and to explore potential links in the evolution of fire features. Our results suggest that most fire features show remarkable shifts between the late 1980s and the first half of the 1990s. Mann-Kendall outputs revealed negative trends in the Mediterranean region. Results from Sen's slope suggest high spatial and intra-annual variability across the study area. Fire activity related to human sources seems to be experiencing an overall decrease in the northwestern provinces, particularly pronounced during summer. Similarly, the Hinterland and the Mediterranean coast are gradually becoming less fire affected. Finally, PCA enabled trends to be synthesized into four main components: winter fire frequency (PC1), summer burnt area (PC2), large fires (PC3) and natural fires (PC4).

  17. Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Lodowski Kerrie H

    2009-01-01

    Full Text Available Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from transcriptomic data is addressed. A network reconstruction algorithm was developed that uses statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. The multinomial hypothesis testing-based network reconstruction allows for explicit specification of the false-positive rate, unique from all extant network inference algorithms. The method is superior to dynamic Bayesian network modeling in a simulation study. Temporal gene expression data from the brains of alcohol-treated mice in an analysis of the molecular response to alcohol are used for modeling. Genes from major neuronal pathways are identified as putative components of the alcohol response mechanism. Nine of these genes have associations with alcohol reported in literature. Several other potentially relevant genes, compatible with independent results from literature mining, may play a role in the response to alcohol. Additional, previously unknown gene interactions were discovered that, subject to biological verification, may offer new clues in the search for the elusive molecular mechanisms of alcoholism.

  18. Cryopreservation induces temporal DNA methylation epigenetic changes and differential transcriptional activity in Ribes germplasm.

    Science.gov (United States)

    Johnston, Jason W; Benson, Erica E; Harding, Keith

    2009-02-01

    The physiological and molecular mechanisms associated with acclimation and survival have been examined in four Ribes genotypes displaying differential cryotolerance. Changes in DNA methylation, nucleic acid and nucleoside composition were determined during acclimation and recovery of in vitro shoot-meristems from cryopreservation. DNA methylation was induced in the tolerant genotype, while demethylation was evident in sensitive genotypes. This response initially occurred during sucrose simulated acclimation, with progressive changes as shoots recovered from successive stages of the encapsulation-dehydration protocol. These methylation patterns existed in the initial vegetative cycle but regressed to control values following subculture, indicating the changes in DNA methylation to be a reversible epigenetic mechanism. RNA levels indicating transcriptional activity during the acclimation of nodal tissue are inversely linked to methylation changes, where activity appears to be up-regulated in the cryosensitive genotypes. Conversely, cryopreserved shoots show increased levels of both RNA and DNA methylation in the cryotolerant genotypes. Other nucleosides show post-transcriptional activity corresponds with tolerance during acclimation and cryopreservation. These observations connect physiological attributes to differential molecular changes in Ribes, the implications of which are discussed in relation to cryopreservation-induced apoptosis and genetic stability.

  19. Exploring the temporal effects of seasonal water availability on the snail kite of Florida: Part III

    Science.gov (United States)

    Mooij, Wolf M.; Martin, Julien; Kitchens, Wiley M.; DeAngelis, Donald L.; Bissonette, John A.; Storch, Ilse

    2007-01-01

    The Florida snail kite (Rostrhamus sociabilis) is an endangered raptor that occurs as an isolated population, currently of about 2,000 birds, in the wetlands of southern and central Florida, USA. Its exclusive prey species, the apple snail (Pomacea paludosa) is strongly influenced by seasonal changes in water abundance. Droughts during the snail kite breeding season have a direct negative effect on snail kite survival and reproduction, but droughts are also needed to maintain aquatic vegetation types favorable to snail kite foraging for snails. We used a spatially explicit matrix model to explore the effects of temporal variation in water levels on the viability of the snail kite population under different temporal drought regimes in its wetland breeding habitat. We focused on three aspects of variations in water levels that were likely to affect kites: (1) drought frequency; (2) drought duration; and (3) drought timing within the year. We modeled a 31-year historical scenario using four different scenarios in which the average water level was maintained constant, but the amplitude of water level fluctuations was modified. Our results reveal the complexity of the effects of temporal variation in water levels on snail kite population dynamics. Management implications of these results are discussed. In particular, management decisions should not be based on annual mean water levels alone, but must consider the intra-annual variability.

  20. TimeSpan: Using Visualization to Explore Temporal Multi-dimensional Data of Stroke Patients.

    Science.gov (United States)

    Loorak, Mona Hosseinkhani; Perin, Charles; Kamal, Noreen; Hill, Michael; Carpendale, Sheelagh

    2016-01-01

    We present TimeSpan, an exploratory visualization tool designed to gain a better understanding of the temporal aspects of the stroke treatment process. Working with stroke experts, we seek to provide a tool to help improve outcomes for stroke victims. Time is of critical importance in the treatment of acute ischemic stroke patients. Every minute that the artery stays blocked, an estimated 1.9 million neurons and 12 km of myelinated axons are destroyed. Consequently, there is a critical need for efficiency of stroke treatment processes. Optimizing time to treatment requires a deep understanding of interval times. Stroke health care professionals must analyze the impact of procedures, events, and patient attributes on time-ultimately, to save lives and improve quality of life after stroke. First, we interviewed eight domain experts, and closely collaborated with two of them to inform the design of TimeSpan. We classify the analytical tasks which a visualization tool should support and extract design goals from the interviews and field observations. Based on these tasks and the understanding gained from the collaboration, we designed TimeSpan, a web-based tool for exploring multi-dimensional and temporal stroke data. We describe how TimeSpan incorporates factors from stacked bar graphs, line charts, histograms, and a matrix visualization to create an interactive hybrid view of temporal data. From feedback collected from domain experts in a focus group session, we reflect on the lessons we learned from abstracting the tasks and iteratively designing TimeSpan.

  1. Eukaryotic and prokaryotic promoter databases as valuable tools in exploring the regulation of gene transcription: a comprehensive overview.

    Science.gov (United States)

    Majewska, Małgorzata; Wysokińska, Halina; Kuźma, Łukasz; Szymczyk, Piotr

    2017-11-02

    The complete exploration of the regulation of gene expression remains one of the top-priority goals for researchers. As the regulation is mainly controlled at the level of transcription by promoters, study on promoters and findings are of great importance. This review summarizes forty selected databases that centralize experimental and theoretical knowledge regarding the organization of promoters, interacting transcription factors (TFs) and microRNAs (miRNAs) in many eukaryotic and prokaryotic species. The presented databases offer researchers valuable support in elucidating the regulation of gene transcription. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription

    Directory of Open Access Journals (Sweden)

    Newton Paul N

    2011-08-01

    Full Text Available Abstract Background Artemisinin resistance in Plasmodium falciparum malaria has emerged in Western Cambodia. This is a major threat to global plans to control and eliminate malaria as the artemisinins are a key component of antimalarial treatment throughout the world. To identify key features associated with the delayed parasite clearance phenotype, we employed DNA microarrays to profile the physiological gene expression pattern of the resistant isolates. Results In the ring and trophozoite stages, we observed reduced expression of many basic metabolic and cellular pathways which suggests a slower growth and maturation of these parasites during the first half of the asexual intraerythrocytic developmental cycle (IDC. In the schizont stage, there is an increased expression of essentially all functionalities associated with protein metabolism which indicates the prolonged and thus increased capacity of protein synthesis during the second half of the resistant parasite IDC. This modulation of the P. falciparum intraerythrocytic transcriptome may result from differential expression of regulatory proteins such as transcription factors or chromatin remodeling associated proteins. In addition, there is a unique and uniform copy number variation pattern in the Cambodian parasites which may represent an underlying genetic background that contributes to the resistance phenotype. Conclusions The decreased metabolic activities in the ring stages are consistent with previous suggestions of higher resilience of the early developmental stages to artemisinin. Moreover, the increased capacity of protein synthesis and protein turnover in the schizont stage may contribute to artemisinin resistance by counteracting the protein damage caused by the oxidative stress and/or protein alkylation effect of this drug. This study reports the first global transcriptional survey of artemisinin resistant parasites and provides insight to the complexities of the molecular basis

  3. Spatio-Temporal Feature Exploration in Combined Particle/Volume Reference Frames.

    Science.gov (United States)

    Sauer, Franz; Ma, Kwan-Liu

    2017-06-01

    The use of large-scale scientific simulations that can represent physical systems using both particle and volume data simultaneously is gaining popularity as each of these reference frames has an inherent set of advantages when studying different phenomena. Furthermore, being able to study the dynamic evolution of these time varying data types is an integral part of nearly all scientific endeavors. However, the techniques available to scientists generally limit them to studying each reference frame separately making it difficult to draw connections between the two. In this work we present a novel method of feature exploration that can be used to investigate spatio-temporal patterns in both data types simultaneously. More specifically, we focus on how spatio-temporal subsets can be identified from both reference frames, and develop new ways of visually presenting the embedded information to a user in an intuitive manner. We demonstrate the effectiveness of our method using case studies of real world scientific datasets and illustrate the new types of exploration and analyses that can be achieved through this technique.

  4. Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.

    Science.gov (United States)

    Wan, Cen; Lees, Jonathan G; Minneci, Federico; Orengo, Christine A; Jones, David T

    2017-10-01

    Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but struggle to provide useful annotations relating to biological process functions due to the limited power of sequence-based features in that functional domain. In this work, we systematically evaluate the predictive power of temporal transcription expression profiles for protein function prediction in Drosophila melanogaster. Our results show significantly better performance on predicting protein function when transcription expression profile-based features are integrated with sequence-derived features, compared with the sequence-derived features alone. We also observe that the combination of expression-based and sequence-based features leads to further improvement of accuracy on predicting all three domains of gene function. Based on the optimal feature combinations, we then propose a novel multi-classifier-based function prediction method for Drosophila melanogaster proteins, FFPred-fly+. Interpreting our machine learning models also allows us to identify some of the underlying links between biological processes and developmental stages of Drosophila melanogaster.

  5. Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Cen Wan

    2017-10-01

    Full Text Available Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but struggle to provide useful annotations relating to biological process functions due to the limited power of sequence-based features in that functional domain. In this work, we systematically evaluate the predictive power of temporal transcription expression profiles for protein function prediction in Drosophila melanogaster. Our results show significantly better performance on predicting protein function when transcription expression profile-based features are integrated with sequence-derived features, compared with the sequence-derived features alone. We also observe that the combination of expression-based and sequence-based features leads to further improvement of accuracy on predicting all three domains of gene function. Based on the optimal feature combinations, we then propose a novel multi-classifier-based function prediction method for Drosophila melanogaster proteins, FFPred-fly+. Interpreting our machine learning models also allows us to identify some of the underlying links between biological processes and developmental stages of Drosophila melanogaster.

  6. Rationalizing spatial exploration patterns of wild animals and humans through a temporal discounting framework.

    Science.gov (United States)

    Namboodiri, Vijay Mohan K; Levy, Joshua M; Mihalas, Stefan; Sims, David W; Hussain Shuler, Marshall G

    2016-08-02

    Understanding the exploration patterns of foragers in the wild provides fundamental insight into animal behavior. Recent experimental evidence has demonstrated that path lengths (distances between consecutive turns) taken by foragers are well fitted by a power law distribution. Numerous theoretical contributions have posited that "Lévy random walks"-which can produce power law path length distributions-are optimal for memoryless agents searching a sparse reward landscape. It is unclear, however, whether such a strategy is efficient for cognitively complex agents, from wild animals to humans. Here, we developed a model to explain the emergence of apparent power law path length distributions in animals that can learn about their environments. In our model, the agent's goal during search is to build an internal model of the distribution of rewards in space that takes into account the cost of time to reach distant locations (i.e., temporally discounting rewards). For an agent with such a goal, we find that an optimal model of exploration in fact produces hyperbolic path lengths, which are well approximated by power laws. We then provide support for our model by showing that humans in a laboratory spatial exploration task search space systematically and modify their search patterns under a cost of time. In addition, we find that path length distributions in a large dataset obtained from free-ranging marine vertebrates are well described by our hyperbolic model. Thus, we provide a general theoretical framework for understanding spatial exploration patterns of cognitively complex foragers.

  7. A temporal gate for viral enhancers to co-opt Toll-like-receptor transcriptional activation pathways upon acute infection.

    Directory of Open Access Journals (Sweden)

    Kai A Kropp

    2015-04-01

    Full Text Available Viral engagement with macrophages activates Toll-Like-Receptors (TLRs and viruses must contend with the ensuing inflammatory responses to successfully complete their replication cycle. To date, known counter-strategies involve the use of viral-encoded proteins that often employ mimicry mechanisms to block or redirect the host response to benefit the virus. Whether viral regulatory DNA sequences provide an opportunistic strategy by which viral enhancer elements functionally mimic innate immune enhancers is unknown. Here we find that host innate immune genes and the prototypical viral enhancer of cytomegalovirus (CMV have comparable expression kinetics, and positively respond to common TLR agonists. In macrophages but not fibroblasts we show that activation of NFκB at immediate-early times of infection is independent of virion-associated protein, M45. We find upon virus infection or transfection of viral genomic DNA the TLR-agonist treatment results in significant enhancement of the virus transcription-replication cycle. In macrophage time-course infection experiments we demonstrate that TLR-agonist stimulation of the viral enhancer and replication cycle is strictly delimited by a temporal gate with a determined half-maximal time for enhancer-activation of 6 h; after which TLR-activation blocks the viral transcription-replication cycle. By performing a systematic siRNA screen of 149 innate immune regulatory factors we identify not only anticipated anti-viral and pro-viral contributions but also new factors involved in the CMV transcription-replication cycle. We identify a central convergent NFκB-SP1-RXR-IRF axis downstream of TLR-signalling. Activation of the RXR component potentiated direct and indirect TLR-induced activation of CMV transcription-replication cycle; whereas chromatin binding experiments using wild-type and enhancer-deletion virus revealed IRF3 and 5 as new pro-viral host transcription factor interactions with the CMV enhancer in

  8. Interactive visual exploration of a large spatio-temporal dataset: reflections on a geovisualization mashup.

    Science.gov (United States)

    Wood, Jo; Dykes, Jason; Slingsby, Aidan; Clarke, Keith

    2007-01-01

    Exploratory visual analysis is useful for the preliminary investigation of large structured, multifaceted spatio-temporaldatasets. This process requires the selection and aggregation of records by time, space and attribute, the ability to transform data and the flexibility to apply appropriate visual encodings and interactions. We propose an approach inspired by geographical 'mashups' in which freely-available functionality and data are loosely but flexibly combined using de facto exchange standards. Our case study combines MySQL, PHP and the LandSerf GIS to allow Google Earth to be used for visual synthesis and interaction with encodings described in KML. This approach is applied to the exploration of a log of 1.42 million requests made of a mobile directory service. Novel combinations of interaction and visual encoding are developed including spatial 'tag clouds', 'tag maps', 'data dials' and multi-scale density surfaces. Four aspects of the approach are informally evaluated: the visual encodings employed, their success in the visual exploration of the dataset, the specific tools used and the 'mashup' approach. Preliminary findings will be beneficial to others considering using mashups for visualization. The specific techniques developed may be more widely applied to offer insights into the structure of multifarious spatio-temporal data of the type explored here.

  9. Analysis of Transcriptional Signatures in Response to Listeria monocytogenes Infection Reveals Temporal Changes That Result from Type I Interferon Signaling

    Science.gov (United States)

    Potempa, Krzysztof; Graham, Christine M.; Moreira-Teixeira, Lucia; McNab, Finlay W.; Howes, Ashleigh; Stavropoulos, Evangelos; Pascual, Virginia; Banchereau, Jacques; Chaussabel, Damien; O’Garra, Anne

    2016-01-01

    Analysis of the mouse transcriptional response to Listeria monocytogenes infection reveals that a large set of genes are perturbed in both blood and tissue and that these transcriptional responses are enriched for pathways of the immune response. Further we identified enrichment for both type I and type II interferon (IFN) signaling molecules in the blood and tissues upon infection. Since type I IFN signaling has been reported widely to impair bacterial clearance we examined gene expression from blood and tissues of wild type (WT) and type I IFNαβ receptor-deficient (Ifnar1-/-) mice at the basal level and upon infection with L. monocytogenes. Measurement of the fold change response upon infection in the absence of type I IFN signaling demonstrated an upregulation of specific genes at day 1 post infection. A less marked reduction of the global gene expression signature in blood or tissues from infected Ifnar1-/- as compared to WT mice was observed at days 2 and 3 after infection, with marked reduction in key genes such as Oasg1 and Stat2. Moreover, on in depth analysis, changes in gene expression in uninfected mice of key IFN regulatory genes including Irf9, Irf7, Stat1 and others were identified, and although induced by an equivalent degree upon infection this resulted in significantly lower final gene expression levels upon infection of Ifnar1-/- mice. These data highlight how dysregulation of this network in the steady state and temporally upon infection may determine the outcome of this bacterial infection and how basal levels of type I IFN-inducible genes may perturb an optimal host immune response to control intracellular bacterial infections such as L. monocytogenes. PMID:26918359

  10. Analysis of Transcriptional Signatures in Response to Listeria monocytogenes Infection Reveals Temporal Changes That Result from Type I Interferon Signaling.

    Directory of Open Access Journals (Sweden)

    Jonathan M Pitt

    Full Text Available Analysis of the mouse transcriptional response to Listeria monocytogenes infection reveals that a large set of genes are perturbed in both blood and tissue and that these transcriptional responses are enriched for pathways of the immune response. Further we identified enrichment for both type I and type II interferon (IFN signaling molecules in the blood and tissues upon infection. Since type I IFN signaling has been reported widely to impair bacterial clearance we examined gene expression from blood and tissues of wild type (WT and type I IFNαβ receptor-deficient (Ifnar1-/- mice at the basal level and upon infection with L. monocytogenes. Measurement of the fold change response upon infection in the absence of type I IFN signaling demonstrated an upregulation of specific genes at day 1 post infection. A less marked reduction of the global gene expression signature in blood or tissues from infected Ifnar1-/- as compared to WT mice was observed at days 2 and 3 after infection, with marked reduction in key genes such as Oasg1 and Stat2. Moreover, on in depth analysis, changes in gene expression in uninfected mice of key IFN regulatory genes including Irf9, Irf7, Stat1 and others were identified, and although induced by an equivalent degree upon infection this resulted in significantly lower final gene expression levels upon infection of Ifnar1-/- mice. These data highlight how dysregulation of this network in the steady state and temporally upon infection may determine the outcome of this bacterial infection and how basal levels of type I IFN-inducible genes may perturb an optimal host immune response to control intracellular bacterial infections such as L. monocytogenes.

  11. A grounded visualization approach to explore sociospatial and temporal complexities of older adults' mobility.

    Science.gov (United States)

    Franke, Thea; Winters, Meghan; McKay, Heather; Chaudhury, Habib; Sims-Gould, Joanie

    2017-11-01

    In the past decade, there has been an increasing interest in older adults' mobility. Most often, mobility is measured quantitatively as physical movement (e.g. physical activity) or travel behavior (e.g. trips, modes, and distances). There is a need to integrate both quantitative and qualitative data over time to visualize both context and content in a spatial and temporal dimension and discover patterns and explanations for their underlying processes. We aim to address this gap by demonstrating how a grounded visualization approach can be used to explore sociospatial and temporal complexities of older adults' mobility. We present two cases of active community (urban) dwelling older adults with low incomes (age > 65) who live in Metro Vancouver, Canada, over a period of 4 years. Geographical Position Systems (GPS) (QStarz Datalogger BT-Q1000x) data is used to capture the destinations participants travel to and the routes they take to get there. Survey data provides socio-demographic characteristics and neighborhood environments. Interview data capture perceptions, attitudes, and motivations of destinations and route choices over time. Integration of the methods identified the following themes: spatial perceptions of neighborhood, consistency in travel patterns, changes in physical health, familiarity with place and access over time. Our grounded visualization approach demonstrates how georeferenced qualitative data can be combined with quantitative spatial data to provide a deeper understanding of the complexity of older adults' mobility experiences over time. Findings illustrate that time is a necessary component of older adults' engagement with place; familiarity influences spatial perceptions of local and distant 'neighbourhoods'; and older adults prioritize destinations that allow them to engage in multiple activities. By integrating methods we are able to gain a better understanding of challenges faced by older adults at multiple systems levels, and uncover

  12. Towards operational hydrology for a thorough spatio-temporal exploration of the Critical Zone

    Science.gov (United States)

    Chatton, Eliot; Labasque, Thierry; Guillou, Aurélie; Aquilina, Luc; Bour, Olivier; Le Borgne, Tanguy; Longuevergne, Laurent

    2017-04-01

    Over the last century, the Critical Zone faced remarkable climate and land use changes increasing the pressures on the Hydrosphere and giving rise to numerous environmental consequences in terms of water quantity and quality. From now on, the Critical Zone must face the challenge to supply 9 billion people with quality food and safe drinking water in a context of global warming. For the Hydrosphere, this challenge could be addressed with a better understanding of the dynamics and resilience of aquatic environments (rivers, lakes, groundwaters, oceans). In view of the spatial and temporal variety and variability of flow dynamics and biogeochemical reactions occurring in the Hydrosphere a new investigation method is needed. This study approaches the concept of "operational hydrology" aiming to enhance either the spatio-temporal distribution and the quality of environmental data for a thorough exploration of the Hydrosphere. To illustrate our approach, we present natural and anthropogenic dissolved gas data (He, Ne, Ar, Kr, Xe, N2, O2, CO2, CH4, N2O, H2, BTEX, and some VOCs) measured in situ with a CF-MIMS (Chatton et al, 2016) installed in a mobile laboratory arranged in an all-terrain truck (CRITEX-Lab). This ongoing work focuses on groundwater and the field investigation of residence time distributions, recharge processes (origins), water flow paths and mixing, biogeochemical reactivity and contamination (sources). The rationale behind "operational hydrology" could be applied to the field measurement at high-frequency of many other environmental parameters (temperature, cations, anions, isotopes, micro-organisms) not only for the investigation of groundwaters but also rivers, lakes and oceans. Eliot Chatton, Thierry Labasque, Jérôme de La Bernardie, Nicolas Guihéneuf, Olivier Bour and Luc Aquilina; Field Continuous Measurement of Dissolved Gases with a CF-MIMS: Applications to the Physics and Biogeochemistry of Groundwater Flow; Environmental Science

  13. The influence of forest cover on landslide occurrence explored with spatio-temporal information

    Science.gov (United States)

    Schmaltz, Elmar M.; Steger, Stefan; Glade, Thomas

    2017-08-01

    Multi-temporal landslide inventories in widely forested landscapes are scarce and further studies are required to face the challenges of producing reliable inventories in woodland areas. An elaboration of valuable empirical relationships between shallow landslides and forest cover based on recent remote sensing data alone is often hampered due to constant land cover changes, differing ages of landslides within a landslide inventory and the fact that usage of different data sets for mapping might lead to various systematic mapping biases. Within this study, we attempted to overcome these difficulties in order to explore the effect of forest cover on shallow landslide occurrences. Thus, forest dynamics were examined on the basis of 9 orthophoto series from 1950s to 2015, distinguishing 3 forest classes, based on the wood type. These classes were furthermore distinguished in 12 subclasses, considering stand density and age. A multi-temporal landslide inventory was compiled for the same period based on the aerial photography, 2 airborne LiDAR imageries, 8 field surveys and archive data. We derived topographical parameters (slope, topographical positioning index and convergency index) from the digital elevation model for areal correction and accounting for topographical confounders within a logistic regression model. Empirical relationships were assessed by means of (a) areal changes of forests and logged areas, (b) spatio-temporal distribution of shallow translational landslides, (c) frequency ratios and (d) logistic regression analysis. The findings revealed that forests increased by 16.2% from 1950s to 2015. 311 landslides of 351 in total that where mapped in total could be assigned to the observed time series and were considered for our analyses. Frequency ratios and odds ratios indicated a stabilising effect of all forest classes on landslide occurrences. Odds ratios observed for the models based on aggregated data sets (3 forest classes) indicated provided

  14. Transcript profiles uncover temporal and stress-induced changes of metabolic pathways in germinating sugar beet seeds

    Directory of Open Access Journals (Sweden)

    Windhövel Andrea

    2008-12-01

    Full Text Available Abstract Background With a cultivation area of 1.75 Mio ha and sugar yield of 16.7 Mio tons in 2006, sugar beet is a crop of great economic importance in Europe. The productivity of sugar beet is determined significantly by seed vigour and field emergence potential; however, little is known about the molecular mechanisms underlying these traits. Both traits exhibit large variations within sugar beet germplasm that have been difficult to ascribe to either environmental or genetic causes. Among potential targets for trait improvement, an enhancement of stress tolerance is considered because of the high negative influence of environmental stresses on trait parameters. Extending our knowledge of genetic and molecular determinants of sugar beet germination, stress response and adaptation mechanisms would facilitate the detection of new targets for breeding crop with an enhanced field emergence potential. Results To gain insight into the sugar beet germination we initiated an analysis of gene expression in a well emerging sugar beet hybrid showing high germination potential under various environmental conditions. A total of 2,784 ESTs representing 2,251 'unigenes' was generated from dry mature and germinating seeds. Analysis of the temporal expression of these genes during germination under non-stress conditions uncovered drastic transcriptional changes accompanying a shift from quiescent to metabolically active stages of the plant life cycle. Assay of germination under stressful conditions revealed 157 genes showing significantly different expression patterns in response to stress. As deduced from transcriptome data, stress adaptation mechanisms included an alteration in reserve mobilization pathways, an accumulation of the osmoprotectant glycine betaine, late embryogenesis abundant proteins and detoxification enzymes. The observed transcriptional changes are supposed to be regulated by ABA-dependent signal transduction pathway. Conclusion This study

  15. Exploring the structure and function of temporal networks with dynamic graphlets

    Science.gov (United States)

    Hulovatyy, Y.; Chen, H.; Milenković, T.

    2015-01-01

    Motivation: With increasing availability of temporal real-world networks, how to efficiently study these data? One can model a temporal network as a single aggregate static network, or as a series of time-specific snapshots, each being an aggregate static network over the corresponding time window. Then, one can use established methods for static analysis on the resulting aggregate network(s), but losing in the process valuable temporal information either completely, or at the interface between different snapshots, respectively. Here, we develop a novel approach for studying a temporal network more explicitly, by capturing inter-snapshot relationships. Results: We base our methodology on well-established graphlets (subgraphs), which have been proven in numerous contexts in static network research. We develop new theory to allow for graphlet-based analyses of temporal networks. Our new notion of dynamic graphlets is different from existing dynamic network approaches that are based on temporal motifs (statistically significant subgraphs). The latter have limitations: their results depend on the choice of a null network model that is required to evaluate the significance of a subgraph, and choosing a good null model is non-trivial. Our dynamic graphlets overcome the limitations of the temporal motifs. Also, when we aim to characterize the structure and function of an entire temporal network or of individual nodes, our dynamic graphlets outperform the static graphlets. Clearly, accounting for temporal information helps. We apply dynamic graphlets to temporal age-specific molecular network data to deepen our limited knowledge about human aging. Availability and implementation: http://www.nd.edu/∼cone/DG. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072480

  16. Temporal transcription of the lactococcal temperate phage TP901-1 and DNA sequence of the early promoter region

    DEFF Research Database (Denmark)

    Madsen, Hans Peter Lynge; Hammer, Karin

    1998-01-01

    , of which at least two (the integrase gene and putative repressor) are needed for lysogeny, and the divergent and longer transcriptional unit from PL, presumably encoding functions required for the lytic life cycle. ORFs with homology to proteins involved in DNA replication were identified on the latter......Transcriptional analysis by Northern blotting identified clusters of early, middle and late transcribed regions of the temperate lactococcal bacteriophage TP901-1 during one-step growth experiments. The latent period was found to be 65 min and the burst size 40 +/- 10. The eight early transcripts...

  17. A Review Paper On Exploring Text Link And Spacial-Temporal Information In Social Media Networks

    Directory of Open Access Journals (Sweden)

    Dr. Mamta Madan

    2015-03-01

    Full Text Available ABSTRACT The objective of this paper is to have a literature review on the various methods to mine the knowledge from the social media by taking advantage of embedded heterogeneous information. Specifically we are trying to review different types of mining framework which provides us useful information from these networks that have heterogeneous data types including text spacial-temporal and data association LINK information. Firstly we will discuss the link mining to study the link structure with respect to Social Media SM. Secondly we summarize the various text mining models thirdly we shall review spacial as well the temporal models to extract or detect the frequent related topics from SM. Fourthly we will try to figure out few improvised models that take advantage of the link textual temporal and spacial information which motivates to discover progressive principles and fresh methodologies for DM Data Mining in social media networks SMNs.

  18. RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

    Science.gov (United States)

    Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

    2013-11-01

    bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.

  19. Exploring the Ecological Coherence between the Spatial and Temporal Patterns of Bacterioplankton in Boreal Lakes

    Directory of Open Access Journals (Sweden)

    Juan Pablo Niño-García

    2017-04-01

    Full Text Available One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydrology-mediated dispersal along the aquatic network or environmental selection mechanisms within lakes. Here, we test whether this categorization derived from the spatial distribution of taxa is maintained over time, by analyzing the temporal dynamics of the operational taxonomic units (OTUs within those spatially derived categories along an annual cycle in the oligotrophic lake Croche (Québec, Canada, and assessing the coherence in the patterns of abundance, occurrence, and environmental range of these OTUs over space and time. We report that the temporal dynamics of most taxa within a single lake are largely coherent with those derived from their spatial distribution over large spatial scales, suggesting that these properties must be intrinsic of particular taxa. We also identified a set of rare taxa cataloged as having a random occupancy based on their spatial distribution, but which showed clear seasonality and abundance peaks along the year, yet these comprised a very small fraction of the total rare OTUs. We conclude that the presence of most rare bacterioplankton taxa in boreal lakes is random, since both their temporal and spatial dynamics suggest links to passive downstream transport and persistence in freshwater networks, rather than environmental selection.

  20. Exploring spatial and temporal trends in the soundscape of an ecologically significant embayment.

    Science.gov (United States)

    Putland, R L; Constantine, R; Radford, C A

    2017-07-18

    The Hauraki Gulf, a shallow embayment in north-eastern New Zealand, provides an interesting environment for ecological soundscape research. It is situated on a tectonic plate boundary, contains one of the busiest ports in the southern hemisphere and is home to a diverse range of soniferous animals. The underwater soundscape was monitored for spatial and temporal trends at six different listening stations using passive acoustic recorders. The RMS sound pressure level of ambient sound (50-24,000 Hz) at the six listening stations was similar, ranging from 90-110 dB re 1 μPa throughout the recording period. Biophony had distinct temporal patterns and biological choruses of urchins were significantly correlated to temperature. Geophony and biophony followed the acoustic niche hypothesis, where each sound exhibited both temporal and frequency partitioning. Vessel passage sound were identified in 1.9-35.2% of recordings from the different listening stations. Vessel sound recorded in the Hauraki Gulf has the potential to mask concurrent geophony and biophony, sounds that may be important to marine life. This study provides a baseline of ambient sound, useful for future management strategies in shallow embayments where anthropogenic pressure is likewise increasing.

  1. Temporal analysis and spatial mapping of Lymantria dispar nuclear polyhedrosis virus transcripts and in-vitro translation products

    Science.gov (United States)

    James M. Slavicek; Nancy Hayes-Plazolles

    1991-01-01

    The Lymantria dispar nuclear polyhedrosis virus LdNPV) is being used as a biopesticide against the gypsy moth. We are attempting to enhance the potency of the LdNPV through recombinant DNA technology. As a prerequisite to genetic manipulation, we have characterized LdNPV gene expression in cell culture through the generation of transcription and...

  2. An exploration of conceptual and temporal fallacies in international health law and promotion of global public health preparedness.

    Science.gov (United States)

    Bhattacharya, Dhrubajyoti

    2007-01-01

    In February 2007, Indonesia withheld sharing H5N1 viral samples in order to compel the World Health Organization and Member States to guarantee future access to vaccines for States disproportionately burdened by infectious diseases. This article explores conceptual and temporal fallacies in the International Health Regulations (2005) and the Doha Declaration on the TRIPS Agreement and Public Health, as relates to global public health preparedness. Recommendations include adopting laws to facilitate non-pharmaceutical interventions; securing the rights of affected populations; and fostering inter-State collaborations to promote intra-State public health capacity building.

  3. Temporal embryonic transcription of chicken fast skeletal myosin heavy chain isoforms in the single comb white leghorn

    OpenAIRE

    Griffin, J.; St-Pierre, N.; Lilburn, M. S.; Wick, M.

    2016-01-01

    There are numerous factors that can significantly influence embryonic development in poultry and thus make simple days of incubation (chronological age) a less than perfect metric for studying embryonic physiology. The developmental fast skeletal muscle myosin (MyHC), the predominant protein in the Pectoralis major (PM), is temporally expressed as a cadre of highly specific developmental isoforms. In the study described herein, a novel molecular technology (NanoString) was used to characteriz...

  4. Explore spatial-temporal relations: transient super-resolution with PMD sensors

    Science.gov (United States)

    Han, Chaosheng; Lin, Xing; Lin, Jingyu; Yan, Chenggang; Dai, Qionghai

    2014-11-01

    Transient imaging provides a direct view of how light travel in the scene, which leads to exciting applications such as looking around corners. Low-budget transient imagers, adapted from Time-of-Fight (ToF) cameras, reduce the barrier of entry for performing research of this new imaging modality. However, the image quality is far from satisfactory due to the limited resolution of PMD sensors. In this paper, we improve the resolution of transient images by modulating the illumination. We capture the scene under three linearly independent lighting conditions, and derive a theoretical model for the relationship between the time-profile and the corresponding 3D details of each pixel. Our key idea is that the light flight time in each pixel patch is proportional to the cross product of the illuminating direction and the surface normal. First we capture and reconstruct transient images by Fourier analysis at multiple illumination locations, and then fuse the data of acquired low-spatial resolution images to calculate the surface normal. Afterwards, we use an optimization procedure to split the pixels and finally enhance the image quality. We show that we can not only reveal the fine structure of the object but may also uncover the reflectance properties of different materials. We hope the idea of utilizing spatial-temporal relations will give new insights to the research and applications of transient imaging.

  5. Exploring differences between left and right hand motor imagery via spatio-temporal EEG microstate.

    Science.gov (United States)

    Liu, Weifeng; Liu, Xiaoming; Dai, Ruomeng; Tang, Xiaoying

    2017-12-01

    EEG-based motor imagery is very useful in brain-computer interface. How to identify the imaging movement is still being researched. Electroencephalography (EEG) microstates reflect the spatial configuration of quasi-stable electrical potential topographies. Different microstates represent different brain functions. In this paper, microstate method was used to process the EEG-based motor imagery to obtain microstate. The single-trial EEG microstate sequences differences between two motor imagery tasks - imagination of left and right hand movement were investigated. The microstate parameters - duration, time coverage and occurrence per second as well as the transition probability of the microstate sequences were obtained with spatio-temporal microstate analysis. The results were shown significant differences (P < 0.05) with paired t-test between the two tasks. Then these microstate parameters were used as features and a linear support vector machine (SVM) was utilized to classify the two tasks with mean accuracy 89.17%, superior performance compared to the other methods. These indicate that the microstate can be a promising feature to improve the performance of the brain-computer interface classification.

  6. Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks

    Science.gov (United States)

    Miranda, Gisele Helena Barboni; Machicao, Jeaneth; Bruno, Odemir Martinez

    2016-11-01

    Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability.

  7. Exploring the isotopic niche: isotopic variance, physiological incorporation, and the temporal dynamics of foraging

    Directory of Open Access Journals (Sweden)

    Justin Douglas Yeakel

    2016-01-01

    Full Text Available Consumer foraging behaviors are dynamic, changing in response to prey availability, seasonality, competition, and even the consumer's physiological state. The isotopic composition of a consumer is a product of these factors as well as the isotopic `landscape' of its prey, i.e. the isotopic mixing space. Stable isotope mixing models are used to back-calculate the most likely proportional contribution of a set of prey to a consumer's diet based on their respective isotopic distributions, however they are disconnected from ecological process. Here we build a mechanistic framework that links the ecological and physiological processes of an individual consumer to the isotopic distribution that describes its diet, and ultimately to the isotopic composition of its own tissues, defined as its `isotopic niche’. By coupling these processes, we systematically investigate under what conditions the isotopic niche of a consumer changes as a function of both the geometric properties of its mixing space and foraging strategies that may be static or dynamic over time. Results of our derivations reveal general insight into the conditions impacting isotopic niche width as a function of consumer specialization on prey, as well as the consumer's ability to transition between diets over time. We show analytically that moderate specialization on isotopically unique prey can serve to maximize a consumer's isotopic niche width, while temporally dynamic diets will tend to result in peak isotopic variance during dietary transitions. We demonstrate the relevance of our theoretical findings by examining a marine system composed of nine invertebrate species commonly consumed by sea otters. In general, our analytical framework highlights the complex interplay of mixing space geometry and consumer dietary behavior in driving expansion and contraction of the isotopic niche. Because this approach is established on ecological mechanism, it is well-suited for enhancing the

  8. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion

    Science.gov (United States)

    Dekhang, Rigzin; Wu, Cheng; Smith, Kristina M.; Lamb, Teresa M.; Peterson, Matthew; Bredeweg, Erin L.; Ibarra, Oneida; Emerson, Jillian M.; Karunarathna, Nirmala; Lyubetskaya, Anna; Azizi, Elham; Hurley, Jennifer M.; Dunlap, Jay C.; Galagan, James E.; Freitag, Michael; Sachs, Matthew S.; Bell-Pedersen, Deborah

    2016-01-01

    Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Toward understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa. A large proportion of ADV-1 targets were found to be light- and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion. We show that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion. However, while ADV-1 targets are altered in predictable ways in Δadv-1 cells in response to light, this is not always the case for rhythmic target gene expression. These data suggest that a complex regulatory network downstream of ADV-1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism. PMID:27856696

  9. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion

    Directory of Open Access Journals (Sweden)

    Rigzin Dekhang

    2017-01-01

    Full Text Available Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Toward understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa. A large proportion of ADV-1 targets were found to be light- and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion. We show that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion. However, while ADV-1 targets are altered in predictable ways in Δadv-1 cells in response to light, this is not always the case for rhythmic target gene expression. These data suggest that a complex regulatory network downstream of ADV-1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism.

  10. Exploring the spatio-temporal interrelation between groundwater and surface water by using the self-organizing maps

    Science.gov (United States)

    Chen, I.-Ting; Chang, Li-Chiu; Chang, Fi-John

    2018-01-01

    In this study, we propose a soft-computing methodology to visibly explore the spatio-temporal groundwater variations of the Kuoping River basin in southern Taiwan. The self-organizing map (SOM) is implemented to investigate the interactive mechanism between surface water and groundwater over the river basin based on large high-dimensional data sets coupled with their occurrence times. We find that extracting the occurrence time from each 30-day moving average data set in the clustered neurons of the SOM is a crucial step to learn the spatio-temporal interaction between surface water and groundwater. We design 2-D Topological Bubble Map to summarize all the groundwater values of four aquifers in a neuron, which can visibly explore the major features of the groundwater in the vertical direction. The constructed SOM topological maps nicely display that: (1) the groundwater movement, in general, extends from the eastern area to the western, where groundwater in the eastern area can be easily recharged from precipitation in wet seasons and discharged into streams during dry seasons due to the high permeability in this area; (2) the water movements in the four aquifers of the study area are quite different, and the seasonal variations of groundwater in the second and third aquifers are larger than those of the others; and (3) the spatial distribution and seasonal variations of groundwater and surface water are comprehensively linked together over the constructed maps to present groundwater characteristics and the interrelation between groundwater and surface water. The proposed modeling methodology not only can classify the large complex high-dimensional data sets into visible topological maps to effectively facilitate the quantitative status of regional groundwater resources but can also provide useful elaboration for future groundwater management.

  11. Exploring the temporal development of childhood IgE profiles to allergen components

    Directory of Open Access Journals (Sweden)

    Önell Annica

    2012-12-01

    Full Text Available Abstract Background Children often develop allergies that may or not persist into adulthood. Although the different allergic symptoms over time have been well documented, the underlying pattern of sensitization to various proteins and subsequent allergy development is unexplored. The aim was to study the sensitization pattern to allergen components over time from infancy to adulthood in a group of infants with heredity for allergic diseases. Methods IgE profiles were monitored in a group of 67 children from 6 months to 18 years using a microarray chip (ImmunoCAP® ISAC containing 103 allergen components derived from 47 allergen sources. The chip IgE profile was compared with clinical history, skin prick test results and diagnoses (atopic dermatitis, asthma and allergic rhinoconjunctivitis at each time point for each child. Results IgE profiles were unique for each child and showed broad agreement with the results of skin prick tests and doctors’ diagnoses. In addition, close examination of the IgE profiles often revealed early indication of subsequent allergies. IgE profiles also facilitated the examination of cross-reactivity contra co-sensitization, thereby greatly enhancing the possibility for managing patients. Conclusion This explorative description indicates that sensitization pattern to allergen components differs over time as well as among allergic individuals when examined with microarray technology.

  12. The Prader-Willi syndrome murine imprinting center is not involved in the spatio-temporal transcriptional regulation of the Necdin gene

    Directory of Open Access Journals (Sweden)

    Dandolo Luisa

    2005-01-01

    Full Text Available Abstract Background The human Prader-Willi syndrome (PWS domain and its mouse orthologue include a cluster of paternally expressed genes which imprinted expression is co-ordinately regulated by an imprinting center (IC closely associated to the Snurf-Snrpn gene. Besides their co-regulated imprinted expression, two observations suggest that the spatio-temporal expression of these genes could also be co-regulated. First, the PWS genes have all been reported to be expressed in the mouse nervous system. Second, Snurf-Snrpn and its associated IC are the most ancient elements of the domain which later acquired additional functional genes by retrotransposition. Although located at least 1.5 megabases from the IC, these retroposons acquired the same imprinted regulation as Snurf-Snrpn. In this study, we ask whether the IC, in addition to its function in imprinting, could also be involved in the spatio-temporal regulation of genes in the PWS domain. Results We compared the expression pattern of Snurf-Snrpn and C/D-box small nucleolar RNAs (snoRNAs MBII-85 and MBII-52 to the expression pattern of the two evolutionary related retroposons Ndn and Magel2, in the developing mouse embryo. We show that these genes have highly similar expression patterns in the central nervous system, suggesting that they share a common central nervous system-specific regulatory element. Among these genes, Ndn and Magel2 display the most similar expression patterns. Using transgenic mice containing the Ndn and Magel2 genes, we show that the transgenic Ndn gene whereas not imprinted is correctly expressed. Search for DNase I hypersensitive sites in the Ndn-Magel2 genomic region and comparative genomic analyses were performed in order to identify potential transcriptional cis-regulatory elements. Conclusions These results strongly suggest that paternally expressed genes of the PWS domain share a common central nervous system-specific regulatory element. We proposed that this

  13. Exploring the effect of drought extent and interval on the Florida snail kite: Interplay between spatial and temporal scales

    Science.gov (United States)

    Mooij, Wolf M.; Bennetts, Robert E.; Kitchens, Wiley M.; DeAngelis, Donald L.

    2002-01-01

    The paper aims at exploring the viability of the Florida snail kite population under various drought regimes in its wetland habitat. The population dynamics of snail kites are strongly linked with the hydrology of the system due to the dependence of this bird species on one exclusive prey species, the apple snail, which is negatively affected by a drying out of habitat. Based on empirical evidence, it has been hypothesised that the viability of the snail kite population critically depends not only on the time interval between droughts, but also on the spatial extent of these droughts. A system wide drought is likely to result in reduced reproduction and increased mortality, whereas the birds can respond to local droughts by moving to sites where conditions are still favourable. This paper explores the implications of this hypothesis by means of a spatially-explicit individual-based model. The specific aim of the model is to study in a factorial design the dynamics of the kite population in relation to two scale parameters, the temporal interval between droughts and the spatial correlation between droughts. In the model high drought frequencies led to reduced numbers of kites. Also, habitat degradation due to prolonged periods of inundation led to lower predicted numbers of kites. Another main result was that when the spatial correlation between droughts was low, the model showed little variability in the predicted numbers of kites. But when droughts occurred mostly on a system wide level, environmental stochasticity strongly increased the stochasticity in kite numbers and in the worst case the viability of the kite population was seriously threatened.

  14. Exploration of G-quadruplex function in c-Myb gene and its transcriptional regulation by topotecan.

    Science.gov (United States)

    Li, Fangyuan; Zhou, Jiang; Xu, Ming; Yuan, Gu

    2017-10-05

    Our bioinformatics research shows that there are four G-rich sequences (S1-S4) in the upstream region of the transcription start site of c-Myb gene, and we have proved that these sequences have the ability to form G-quadruplex structures. This work mainly focuses on G-quadruplex function, recognition and transcription regulation in c-Myb gene, revealing a novel regulatory element in c-Myb proximal promoter region, and its transcription regulation by G-quadruplex binder. The research has identified that the enhancer effect in c-Myb transcription was primarily affected by the G-quadruplex formed by S1 sequence, and the up-regulation effect may due to the removal of repressive progress of MZF-1 by stabilizing G-quadruplex. Attentions were being paid to the development of G-quadruplex binders for selective recognition, and topotecan was found to have high binding affinity in vitro and could effectively affect the c-Myb transcription activities in cells. The regulation of G-quadruplex with binders in transcriptional, translational levels by Q-RT-PCR and western blot was in expectation of providing a strategy for gene expression modulation. In conclusion, our study revealed a G-quadruplex structure in c-Myb proximal promoter region, which was of great importance in the regulation of c-Myb function. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Exploration

    Science.gov (United States)

    Wilburn, D.R.

    2001-01-01

    Part of an annual review of mines and mineral resources in the U.S. An overview of nonfuel-mineral exploration in 2000 is presented. Principal exploration target was gold exploration in Latin America, Australia, and the U.S. There was a decrease of 18 percent in the exploration budget for gold as compared with the budget for 1999. Statistical information on nonfuel-mineral exploration worldwide is presented, analyzed, and interpreted.

  16. Transcriptionally Less Active Prodynorphin Promoter Alleles are Associated with Temporal Lobe Epilepsy: A Case-Control Study and Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Marcelo A. Kauffman

    2008-01-01

    Full Text Available We performed an association study in a population of patients with Mesial Temporal Lobe Epilepsy (TLE with Hippocampal Sclerosis (MTEHS together with a systematic revision of the literature to investigate the role of transcriptionally less active polymorphic alleles of Prodynorphin (PDYN gene in this pathology. We included 102 patients with a diagnosis of MTEHS and 86 healthy controls. The positive antecedent of family history for epileptic events defined a TLE subgroup with familial predisposition for epileptic disorders. The PDYN promoter polymorphism was genotyped by means of a PCR assay. For meta-analysis, we identified case-control association studies between TLE and PDYN by searching PUBMED. The pooled OR was estimated using a fixed effects model under dominant and co-dominant heredity models. No differences in genotypic and allelic frequencies were found between cases and controls (p = 0.61 in our population, neither in the whole cohort nor in the analysis limited to TLE with familial predisposition (p = 0.71. The Meta-Analysis included 591 TLE patients and 1117 healthy controls. We found an association between L allele (p = 0.003; OR = 1.40; IC 95 = 1.12–1.74 and a modestly higher risk to develop TLE in the group of patients with familial predisposition. Therefore, functional allelic variants in the PDYN promoter might modify the risk to develop TLE in subjects with familial predisposition.

  17. Exploring Google Earth Engine platform for big data processing: classification of multi-temporal satellite imagery for crop mapping

    Science.gov (United States)

    Shelestov, Andrii; Lavreniuk, Mykola; Kussul, Nataliia; Novikov, Alexei; Skakun, Sergii

    2017-02-01

    Many applied problems arising in agricultural monitoring and food security require reliable crop maps at national or global scale. Large scale crop mapping requires processing and management of large amount of heterogeneous satellite imagery acquired by various sensors that consequently leads to a “Big Data” problem. The main objective of this study is to explore efficiency of using the Google Earth Engine (GEE) platform when classifying multi-temporal satellite imagery with potential to apply the platform for a larger scale (e.g. country level) and multiple sensors (e.g. Landsat-8 and Sentinel-2). In particular, multiple state-of-the-art classifiers available in the GEE platform are compared to produce a high resolution (30 m) crop classification map for a large territory ( 28,100 km2 and 1.0 M ha of cropland). Though this study does not involve large volumes of data, it does address efficiency of the GEE platform to effectively execute complex workflows of satellite data processing required with large scale applications such as crop mapping. The study discusses strengths and weaknesses of classifiers, assesses accuracies that can be achieved with different classifiers for the Ukrainian landscape, and compares them to the benchmark classifier using a neural network approach that was developed in our previous studies. The study is carried out for the Joint Experiment of Crop Assessment and Monitoring (JECAM) test site in Ukraine covering the Kyiv region (North of Ukraine) in 2013. We found that Google Earth Engine (GEE) provides very good performance in terms of enabling access to the remote sensing products through the cloud platform and providing pre-processing; however, in terms of classification accuracy, the neural network based approach outperformed support vector machine (SVM), decision tree and random forest classifiers available in GEE.

  18. Brief Report: Which Came First? Exploring Crossmodal Temporal Order Judgements and Their Relationship with Sensory Reactivity in Autism and Neurotypicals

    Science.gov (United States)

    Poole, Daniel; Gowen, Emma; Warren, Paul A.; Poliakoff, Ellen

    2017-01-01

    Previous studies have indicated that visual-auditory temporal acuity is reduced in children with autism spectrum conditions (ASC) in comparison to neurotypicals. In the present study we investigated temporal acuity for all possible bimodal pairings of visual, tactile and auditory information in adults with ASC (n = 18) and a matched control group…

  19. Exploring the mialome of ticks: an annotated catalogue of midgut transcripts from the hard tick, Dermacentor variabilis (Acari: Ixodidae

    Directory of Open Access Journals (Sweden)

    Valenzuela Jesus G

    2008-11-01

    Full Text Available Abstract Background Ticks are obligate blood feeders. The midgut is the first major region of the body where blood and microbes ingested with the blood meal come in contact with the tick's internal tissues. Little is known about protein expression in the digestive tract of ticks. In this study, for analysis of global gene expression during tick attachment and feeding, we generated and sequenced 1,679 random transcripts (ESTs from cDNA libraries from the midguts of female ticks at varying stages of feeding. Results Sequence analysis of the 1,679 ESTs resulted in the identification of 835 distinct transcripts, from these, a total of 82 transcripts were identified as proteins putatively directly involved in blood meal digestion, including enzymes involved in oxidative stress reduction/antimicrobial activity/detoxification, peptidase inhibitors, protein digestion (cysteine-, aspartic-, serine-, and metallo-peptidases, cell, protein and lipid binding including mucins and iron/heme metabolism and transport. A lectin-like protein with a high match to lectins in other tick species, allergen-like proteins and surface antigens important in pathogen recognition and/or antimicrobial activity were also found. Furthermore, midguts collected from the 6-day-fed ticks expressed twice as many transcripts involved in bloodmeal processing as midguts from unfed/2-day-fed ticks. Conclusion This tissue-specific transcriptome analysis provides an opportunity to examine the global expression of transcripts in the tick midgut and to compare the gut response to host attachment versus blood feeding and digestion. In contrast to those in salivary glands of other Ixodid ticks, most proteins in the D. variabilis midgut cDNA library were intracellular. Of the total ESTs associated with a function, an unusually large number of transcripts were associated with peptidases, cell, lipid and protein binding, and oxidative stress or detoxification. Presumably, this is consistent with

  20. Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice

    Directory of Open Access Journals (Sweden)

    Li Xianghua

    2009-06-01

    Full Text Available Abstract Background Rice transcription regulator OsWRKY13 influences the functioning of more than 500 genes in multiple signalling pathways, with roles in disease resistance, redox homeostasis, abiotic stress responses, and development. Results To determine the putative transcriptional regulation mechanism of OsWRKY13, the putative cis-acting elements of OsWRKY13-influenced genes were analyzed using the whole genome expression profiling of OsWRKY13-activated plants generated with the Affymetrix GeneChip Rice Genome Array. At least 39 transcription factor genes were influenced by OsWRKY13, and 30 of them were downregulated. The promoters of OsWRKY13-upregulated genes were overrepresented with W-boxes for WRKY protein binding, whereas the promoters of OsWRKY13-downregulated genes were enriched with cis-elements putatively for binding of MYB and AP2/EREBP types of transcription factors. Consistent with the distinctive distribution of these cis-elements in up- and downregulated genes, nine WRKY genes were influenced by OsWRKY13 and the promoters of five of them were bound by OsWRKY13 in vitro; all seven differentially expressed AP2/EREBP genes and six of the seven differentially expressed MYB genes were suppressed by in OsWRKY13-activated plants. A subset of OsWRKY13-influenced WRKY genes were involved in host-pathogen interactions. Conclusion These results suggest that OsWRKY13-mediated signalling pathways are partitioned by different transcription factors. WRKY proteins may play important roles in the monitoring of OsWRKY13-upregulated genes and genes involved in pathogen-induced defence responses, whereas MYB and AP2/EREBP proteins may contribute most to the control of OsWRKY13-downregulated genes.

  1. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

    Directory of Open Access Journals (Sweden)

    Fabrice Lopez

    Full Text Available BACKGROUND: As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data. METHODOLOGY: We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484. This approach led to the definition of 18,250 transcriptional signatures (TS that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%. We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/. User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs or associated with a set of functional terms. CONCLUSIONS/SIGNIFICANCE: As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.

  2. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

    Science.gov (United States)

    Lopez, Fabrice; Textoris, Julien; Bergon, Aurélie; Didier, Gilles; Remy, Elisabeth; Granjeaud, Samuel; Imbert, Jean; Nguyen, Catherine; Puthier, Denis

    2008-01-01

    As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data. We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/). User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms. As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.

  3. Co-clustering geo-referenced time series: exploring spatio-temporal patterns in Dutch temperature data

    NARCIS (Netherlands)

    Wu, X.; Zurita-Milla, R.; Kraak, M.J.

    2015-01-01

    Clustering allows considering groups of similar data elements at a higher level of abstraction. This facilitates the extraction of patterns and useful information from large amounts of spatio-temporal data. Till now, most studies have focused on the extraction of patterns from a spatial or a

  4. Time and Temporality in Early Childhood Educators' Work

    Science.gov (United States)

    Nuttall, Joce; Thomas, Louise

    2015-01-01

    This article reports on the persistence and significance of notions of time and temporality in interviews with early childhood educators in Victoria and Queensland, Australia, in two studies designed to explore the concept of "pedagogical leadership". Interpretive analysis of the interview transcripts of the 19 participants identified…

  5. Transcripts involved in hemostasis: Exploring salivary complexes from Haementeria vizottoi leeches through transcriptomics, phylogenetic studies and structural features.

    Science.gov (United States)

    Amorim, Adriane Michele Xavier Prado; de Oliveira, Ursula Castro; Faria, Fernanda; Pasqualoto, Kerly Fernanda Mesquita; Junqueira-de-Azevedo, Inácio de L M; Chudzinski-Tavassi, Ana Marisa

    2015-11-01

    Throughout evolution, parasites have adapted in order to successfully intervene in the host defense, producing specific peptides and proteins. Interestingly, these peptides and proteins have been exploited as potential drug candidates against several diseases. Furthermore, biotechnology studies and cDNA libraries have remarkably contributed to identify potentially bioactive molecules. In this regard, herein, a cDNA library of salivary complexes from Haementeria vizottoi leeches was constructed, the transcriptome was characterized and a phylogenetic analysis was performed considering antistasin-like and antiplatelet-like proteins. Hundred twenty three transcripts were identified coding for putative proteins involved in animal feeding (representing about 10% of the expression level). These sequences showed similarities with myohemerythrins, carbonic anhydrases, anticoagulants, antimicrobials, proteases and protease inhibitors. The phylogenetic analysis, regarding antistasin-like and antiplatetlet-like proteins, revealed two main clades in the Rhynchobdellida leeches. As expected, the sequences from H. vizottoi have presented high similarities with those types of proteins. Thus, our findings could be helpful not only to identify new coagulation inhibitors, but also to better understand the biological composition of the salivary complexes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Use of a handheld low-cost sensor to explore the effect of urban design features on local-scale spatial and temporal air quality variability.

    Science.gov (United States)

    Miskell, Georgia; Salmond, Jennifer A; Williams, David E

    2018-04-01

    Portable low-cost instruments have been validated and used to measure ambient nitrogen dioxide (NO2) at multiple sites over a small urban area with 20min time resolution. We use these results combined with land use regression (LUR) and rank correlation methods to explore the effects of traffic, urban design features, and local meteorology and atmosphere chemistry on small-scale spatio-temporal variations. We measured NO2 at 45 sites around the downtown area of Vancouver, BC, in spring 2016, and constructed four different models: i) a model based on averaging concentrations observed at each site over the whole measurement period, and separate temporal models for ii) morning, iii) midday, and iv) afternoon. Redesign of the temporal models using the average model predictors as constants gave three 'hybrid' models that used both spatial and temporal variables. These accounted for approximately 50% of the total variation with mean absolute error±5ppb. Ranking sites by concentration and by change in concentration across the day showed a shift of high NO2 concentrations across the central city from morning to afternoon. Locations could be identified in which NO2 concentration was determined by the geography of the site, and others as ones in which the concentration changed markedly from morning to afternoon indicating the importance of temporal controls. Rank correlation results complemented LUR in identifying significant urban design variables that impacted NO2 concentration. High variability across a relatively small space was partially described by predictor variables related to traffic (bus stop density, speed limits, traffic counts, distance to traffic lights), atmospheric chemistry (ozone, dew point), and environment (land use, trees). A high-density network recording continuously would be needed fully to capture local variations. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Tier-Scalable Reconnaissance Missions for Autonomous Exploration and Spatio-Temporal Monitoring of Climate Change with Particular Application to Glaciers and their Environs

    Science.gov (United States)

    Fink, W.; Tarbell, M. A.; Furfaro, R.; Kargel, J. S.

    2010-12-01

    Spatio-temporal monitoring of climate change and its impacts is needed globally and thus requires satellite-based observations and analysis. However, needed ground truth can only be obtained in situ. In situ exploration of extreme and often hazardous environments can pose a significant challenge to human access. We propose the use of a disruptive exploration paradigm that has earlier been introduced with autonomous robotic space exploration, termed Tier-Scalable Reconnaissance (PSS 2005; SCIENCE 2010). Tier-scalable reconnaissance utilizes orbital, aerial, and surface/subsurface robotic platforms working in concert, enabling event-driven and integrated global to regional to local reconnaissance capabilities. We report on the development of a robotic test bed for Tier-scalable Reconnaissance at the University of Arizona and Caltech (SCIENCE 2010) for distributed and science-driven autonomous exploration, mapping, and spatio-temporal monitoring of climate change in hazardous or inaccessible environments. We focus in particular on glaciers and their environs, especially glacier lakes. Such glacier lakes can pose a significant natural hazard to inhabited areas and economies downstream. The test bed currently comprises several robotic surface vehicles: rovers equipped with cameras, and boats equipped with cameras and side-scanning sonar technology for bathymetry and the characterization of subsurface structures in glacier lakes and other water bodies. To achieve a fully operational Tier-scalable Reconnaissance test bed, aerial platforms will be integrated in short order. Automated mapping and spatio-temporal monitoring of glaciers and their environs necessitate increasing degrees of operational autonomy: (1) Automatic mapping of an operational area from different vantages (i.e., airborne, surface, subsurface); (2) automatic sensor deployment and sensor data gathering; (3) automatic feature extraction and region-of-interest/anomaly identification within the mapped

  8. Project Temporalities

    DEFF Research Database (Denmark)

    Tryggestad, Kjell; Justesen, Lise; Mouritsen, Jan

    2013-01-01

    Purpose – The purpose of this paper is to explore how animals can become stakeholders in interaction with project management technologies and what happens with project temporalities when new and surprising stakeholders become part of a project and a recognized matter of concern to be taken...... into account. Design/methodology/approach – The paper is based on a qualitative case study of a project in the building industry. The authors use actor-network theory (ANT) to analyze the emergence of animal stakeholders, stakes and temporalities. Findings – The study shows how project temporalities can...... multiply in interaction with project management technologies and how conventional linear conceptions of project time may be contested with the emergence of new non-human stakeholders and temporalities. Research limitations/implications – The study draws on ANT to show how animals can become stakeholders...

  9. Accidental hazardous material releases with human impacts in the United States: exploration of geographical distribution and temporal trends.

    Science.gov (United States)

    Sengul, Hatice; Santella, Nicholas; Steinberg, Laura J; Chermak, Christina

    2010-09-01

    To investigate the circumstances and geographic and temporal distributions of hazardous material releases and resulting human impacts in the United States. Releases with fatalities, injuries, and evacuations were identified from reports to the National Response Center between 1990 and 2008, correcting for data quality issues identified in previous studies. From more than 550,000 reports, 861 deaths, 16,348 injuries and 741,427 evacuations were identified. Injuries from releases of chemicals at fixed facilities and natural gas from pipelines have decreased whereas evacuations from petroleum releases at fixed facilities have increased. Results confirm recent advances in chemical and pipeline safety and suggest directions for further improvement including targeted training and inspections and adoption of inherently safer design principles.

  10. Exploring the effect of drought extent and interval on the Florida snail kite: interplay between spatial and temporal scales

    NARCIS (Netherlands)

    Mooij, W.M.; Bennetts, R.E.; Kitchens, W.M.; DeAngelis, D.L.

    2002-01-01

    The paper aims at exploring the viability of the Florida snail kite population under various drought regimes in its wetland habitat. The population dynamics of snail kites are strongly linked with the hydrology of the system due to the dependence of this bird species on one exclusive prey species,

  11. An Online Atlas for Exploring Spatio-Temporal Patterns of Cancer Mortality (1972-2011) and Incidence (1995-2008) in Taiwan.

    Science.gov (United States)

    Ku, Wen-Yuan; Liaw, Yung-Po; Huang, Jing-Yang; Nfor, Oswald Ndi; Hsu, Shu-Yi; Ko, Pei-Chieh; Lee, Wen-Chung; Chen, Chien-Jen

    2016-05-01

    Public health mapping and Geographical Information Systems (GIS) are already being used to locate the geographical spread of diseases. This study describes the construction of an easy-to-use online atlas of cancer mortality (1972-2011) and incidence (1995-2008) in Taiwan.Two sets of color maps were made based on "age-adjusted mortality by rate" and "age-adjusted mortality by rank." AJAX (Asynchronous JavaScript and XML), JSON (JavaScript Object Notation), and SVG (Scaling Vector Graphic) were used to create the online atlas. Spatio-temporal patterns of cancer mortality and incidence in Taiwan over the period from 1972 to 2011 and from 1995 to 2008.The constructed online atlas contains information on cancer mortality and incidence (http://taiwancancermap.csmu-liawyp.tw/). The common GIS functions include zoom and pan and identity tools. Users can easily customize the maps to explore the spatio-temporal trends of cancer mortality and incidence using different devices (such as personal computers, mobile phone, or pad). This study suggests an easy- to-use, low-cost, and independent platform for exploring cancer incidence and mortality. It is expected to serve as a reference tool for cancer prevention and risk assessment.This online atlas is a cheap and fast tool that integrates various cancer maps. Therefore, it can serve as a powerful tool that allows users to examine and compare spatio-temporal patterns of various maps. Furthermore, it is an-easy-to use tool for updating data and assessing risk factors of cancer in Taiwan.

  12. Exploring the determinants of phylogenetic diversity and assemblage structure in conifers across temporal, spatial, and taxonomic scales

    DEFF Research Database (Denmark)

    Eiserhardt, Wolf L.; Borchsenius, Finn; Sandel, Brody Steven

    -environmental models are important elements in this framework. Here, we integrate both types of data in order to explore the determinants of forest tree diversity using the conifers as a model group. Conifers are an old, diverse (ca. 650 spp. in 6 families) and widespread group of woody plants of high ecological...... and economic importance. They are better studied than most other globally distributed groups of forest trees, allowing integrative studies with high phylogenetic and spatial resolution. We analyse phylogenetic diversity, assemblage structure, and diversification rates for regional conifer assemblages...... throughout the natural range of the group (269 TDWG3 “botanical countries”) to infer the effects of current and past climate . To explore the effects of taxonomic and spatial scale, we deconstruct the overall pattern into families and perform a fine-scale analysis for one particular lineage (the genus Pinus...

  13. Exploring the spatio-temporal relationship between two key aeroallergens and meteorological variables in the United Kingdom.

    Science.gov (United States)

    Khwarahm, Nabaz; Dash, Jadunandan; Atkinson, Peter M; Newnham, R M; Skjøth, C A; Adams-Groom, B; Caulton, Eric; Head, K

    2014-05-01

    Constructing accurate predictive models for grass and birch pollen in the air, the two most important aeroallergens, for areas with variable climate conditions such as the United Kingdom, require better understanding of the relationships between pollen count in the air and meteorological variables. Variations in daily birch and grass pollen counts and their relationship with daily meteorological variables were investigated for nine pollen monitoring sites for the period 2000-2010 in the United Kingdom. An active pollen count sampling method was employed at each of the monitoring stations to sample pollen from the atmosphere. The mechanism of this method is based on the volumetric spore traps of Hirst design (Hirst in Ann Appl Biol 39(2):257-265, 1952). The pollen season (start date, finish date) for grass and birch were determined using a first derivative method. Meteorological variables such as daily rainfall; maximum, minimum and average temperatures; cumulative sum of Sunshine duration; wind speed; and relative humidity were related to the grass and birch pollen counts for the pre-peak, post peak and the entire pollen season. The meteorological variables were correlated with the pollen count data for the following temporal supports: same-day, 1-day prior, 1-day mean prior, 3-day mean prior, 7-day mean prior. The direction of influence (positive/negative) of meteorological variables on pollen count varied for birch and grass, and also varied when the pollen season was treated as a whole season, or was segmented into the pre-peak and post-peak seasons. Maximum temperature, sunshine duration and rainfall were the most important variables influencing the count of grass pollen in the atmosphere. Both maximum temperature (pre-peak) and sunshine produced a strong positive correlation, and rain produced a strong negative correlation with grass pollen count in the air. Similarly, average temperature, wind speed and rainfall were the most important variables influencing

  14. Endo-(1,4-β-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes1

    Directory of Open Access Journals (Sweden)

    Buchanan Margaret

    2012-12-01

    Full Text Available Abstract Background Endo-(1,4-β-glucanase (cellulase glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4-β-glucosyl residues, and wall loosening during cell elongation. Results The endo-(1,4-β-glucanase gene families from barley (Hordeum vulgare, maize (Zea mays, sorghum (Sorghum bicolor, rice (Oryza sativa and Brachypodium (Brachypodium distachyon range in size from 23 to 29 members. Phylogenetic analyses show variations in clade structure between the grasses and Arabidopsis, and indicate differential gene loss and gain during evolution. Map positions and comparative studies of gene structures allow orthologous genes in the five species to be identified and synteny between the grasses is found to be high. It is also possible to differentiate between homoeologues resulting from ancient polyploidizations of the maize genome. Transcript analyses using microarray, massively parallel signature sequencing and quantitative PCR data for barley, rice and maize indicate that certain members of the endo-(1,4-β-glucanase gene family are transcribed across a wide range of tissues, while others are specifically transcribed in particular tissues. There are strong correlations between transcript levels of several members of the endo-(1,4-β-glucanase family and the data suggest that evolutionary conservation of transcription exists between orthologues across the grass family. There are also strong correlations between certain members of the endo-(1,4-β-glucanase family and other genes known to be involved in cell wall loosening and cell expansion, such as expansins and xyloglucan endotransglycosylases. Conclusions The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re

  15. Precipitation stable isotope analysis for exploring temporal characteristics of tropical cyclones: A case study in Hong Kong

    Science.gov (United States)

    Chun, K. P.; Klaus, J.

    2016-12-01

    Hurricanes (or typhoons) play an important role in tropical and subtropical synoptic climates. Although increasing global temperatures in the 20th and 21st centuries are proposed to be linked to changing characteristics of hurricanes, results from previous studies are contradictory and changing environmental conditions affecting hurricanes are somewhat poorly conceptualised. In this investigation, stable precipitation isotope data are used to explore how hurricane properties change with variations of monsoon and regional climate patterns (e.g. the El Niño-Southern Oscillations). As a case study, a new approach using precipitation isotopes to analyse Hong Kong tropical cyclone time series is proposed. First, the variance of precipitation stable isotopes is decomposed to understand the influence of monsoons, southern oscillations and other regional climate conditions on Hong Kong precipitation isotopic signatures. Then, using decomposed precipitation isotope results, a frequency analysis of tropical hurricanes is performed to identify climatic controls and quantify their effects. Results from this study are expected to be valuable because they will provide an example which illustrates how local isotope data can be linked to the regional climate patterns. A framework to investigate Asian tropical cyclone change using stable precipitation isotopes is also proposed.

  16. Expresso: A database and web server for exploring the interaction of transcription factors and their target genes inArabidopsis thalianausing ChIP-Seq peak data.

    Science.gov (United States)

    Aghamirzaie, Delasa; Raja Velmurugan, Karthik; Wu, Shuchi; Altarawy, Doaa; Heath, Lenwood S; Grene, Ruth

    2017-01-01

    Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. Results: We present Expresso (database and webserver) as a tool for the collection and integration of available Arabidopsis ChIP-Seq peak data, which in turn can be linked to a user's gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Availability : Expresso is freely available at http://bioinformatics.cs.vt.edu/expresso/.

  17. Exploring changes of land use and mangrove distribution in the economic area of Sidoarjo District, East Java using multi-temporal Landsat images

    Directory of Open Access Journals (Sweden)

    Norida Maryantika

    2017-12-01

    Full Text Available Remotely sensed data are capable of providing spatial and temporal information on land use land cover (LULC over a large extent of land. The Sidoarjo District in East Java Province has recently been extensively explored for economic development opportunities. This paper examines the use of multi-temporal Landsat images in deriving information for LULC maps, changes of land development and natural ecosystems such as mangrove forest within particular economic reform areas. Results suggest a minimum accuracy (baseline for LULC mapping using Landsat multispectral reflectance data of 74% for the overall accuracy (OA and 0.70 for the kappa coefficient of agreement (kappa. On average an acceptable accuracy (OA = 88% and kappa = 0.86 can be achieved by integrating multispectral reflectance and green normalized difference vegetation index (GNDVI to support vector machine classification. The economic reform in the Sidoarjo District made a significant change to LULC and mangrove distribution. From 1995 to 2015, 25% of crop land and 15% of bare land changed to become built-up areas, and 8% of wetland and 22% of mangroves changed to crop land. A remarkable decrease of mangrove forest occurred in the interior land along the river systems over the whole district. Fortunately, the coastal mangroves areas saw a significant increase due to the Lumpur Sidoarjo (LUSI-caused mud flow sediments near the estuary of the river. The impact of extensive economic activities and development on the natural mangrove forests was partially compensated for by the LUSI events and also newly developed local community oriented conservative management. Keywords: Mangroves, Land use land cover changes, Support vector machine (SVM, Vegetation index, Lumpur Sidoarjo (LUSI

  18. Initiation of HIV Reverse Transcription

    Directory of Open Access Journals (Sweden)

    Roland Marquet

    2010-01-01

    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.

  19. Exploiting the potential of three dimensional spatial wavelet analysis to explore nesting of temporal oscillations and spatial variance in simultaneous EEG-fMRI data.

    Science.gov (United States)

    Schultze-Kraft, Matthias; Becker, Robert; Breakspear, Michael; Ritter, Petra

    2011-03-01

    Synchronization of the activity in neural networks is a fundamental mechanism of brain function, putatively serving the integration of computations on multiple spatial and temporal scales. Time scales are thought to be nested within distinct spatial scales, so that whereas fast oscillations may integrate local networks, slow oscillations might integrate computations across distributed brain areas. We here describe a newly developed approach that provides potential for the further substantiation of this hypothesis in future studies. We demonstrate the feasibility and important caveats of a novel wavelet-based means of relating time series of three-dimensional spatial variance (energy) of fMRI data to time series of temporal variance of EEG. The spatial variance of fMRI data was determined by employing the three-dimensional dual-tree complex wavelet transform. The temporal variance of EEG data was estimated by using traditional continuous complex wavelets. We tested our algorithm on artificial signals with known signal-to-noise ratios and on empirical resting state EEG-fMRI data obtained from four healthy human subjects. By employing the human posterior alpha rhythm as an exemplar, we demonstrated face validity of the approach. We believe that the proposed method can serve as a suitable tool for future research on the spatiotemporal properties of brain dynamics, hence moving beyond analyses based exclusively in one domain or the other. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Normalization Strategies for Enhancing Spatio-Temporal Analysis of Social Media Responses during Extreme Events: A Case Study based on Analysis of Four Extreme Events using Socio-Environmental Data Explorer (SEDE)

    Science.gov (United States)

    Ajayakumar, J.; Shook, E.; Turner, V. K.

    2017-10-01

    With social media becoming increasingly location-based, there has been a greater push from researchers across various domains including social science, public health, and disaster management, to tap in the spatial, temporal, and textual data available from these sources to analyze public response during extreme events such as an epidemic outbreak or a natural disaster. Studies based on demographics and other socio-economic factors suggests that social media data could be highly skewed based on the variations of population density with respect to place. To capture the spatio-temporal variations in public response during extreme events we have developed the Socio-Environmental Data Explorer (SEDE). SEDE collects and integrates social media, news and environmental data to support exploration and assessment of public response to extreme events. For this study, using SEDE, we conduct spatio-temporal social media response analysis on four major extreme events in the United States including the "North American storm complex" in December 2015, the "snowstorm Jonas" in January 2016, the "West Virginia floods" in June 2016, and the "Hurricane Matthew" in October 2016. Analysis is conducted on geo-tagged social media data from Twitter and warnings from the storm events database provided by National Centers For Environmental Information (NCEI) for analysis. Results demonstrate that, to support complex social media analyses, spatial and population-based normalization and filtering is necessary. The implications of these results suggests that, while developing software solutions to support analysis of non-conventional data sources such as social media, it is quintessential to identify the inherent biases associated with the data sources, and adapt techniques and enhance capabilities to mitigate the bias. The normalization strategies that we have developed and incorporated to SEDE will be helpful in reducing the population bias associated with social media data and will be useful

  1. Direct Exploration of the Role of the Ventral Anterior Temporal Lobe in Semantic Memory: Cortical Stimulation and Local Field Potential Evidence From Subdural Grid Electrodes.

    Science.gov (United States)

    Shimotake, Akihiro; Matsumoto, Riki; Ueno, Taiji; Kunieda, Takeharu; Saito, Satoru; Hoffman, Paul; Kikuchi, Takayuki; Fukuyama, Hidenao; Miyamoto, Susumu; Takahashi, Ryosuke; Ikeda, Akio; Lambon Ralph, Matthew A

    2015-10-01

    Semantic memory is a crucial higher cortical function that codes the meaning of objects and words, and when impaired after neurological damage, patients are left with significant disability. Investigations of semantic dementia have implicated the anterior temporal lobe (ATL) region, in general, as crucial for multimodal semantic memory. The potentially crucial role of the ventral ATL subregion has been emphasized by recent functional neuroimaging studies, but the necessity of this precise area has not been selectively tested. The implantation of subdural electrode grids over this subregion, for the presurgical assessment of patients with partial epilepsy or brain tumor, offers the dual yet rare opportunities to record cortical local field potentials while participants complete semantic tasks and to stimulate the functionally identified regions in the same participants to evaluate the necessity of these areas in semantic processing. Across 6 patients, and utilizing a variety of semantic assessments, we evaluated and confirmed that the anterior fusiform/inferior temporal gyrus is crucial in multimodal, receptive, and expressive, semantic processing. © The Author 2014. Published by Oxford University Press.

  2. Functional Integration of Transcriptional and RNA Processing Machineries

    OpenAIRE

    Pandit, Shatakshi; Wang, Dong; Fu, Xiang-Dong

    2008-01-01

    Co-transcriptional RNA processing not only permits temporal RNA processing before the completion of transcription, but also allows sequential recognition of RNA processing signals on nascent transcripts threading out from the elongating RNAPII complex. Rapid progress in recent years has established multiple contacts that physically connect the transcription and RNA processing machineries, which centers on the C-terminal domain (CTD) of the largest subunit of RNAPII. While co-transcriptional R...

  3. Uncertainty and temporal aspects in long-term explorations of sustainable land use : with reference to the Northern Atlantic Zone of Costa Rica

    NARCIS (Netherlands)

    Bessembinder, J.

    1997-01-01


    Long-term explorations serve to widen the perspectives of decision makers. Biophysical and technical possibilities and constraints are confronted with the valuedriven objectives of stakeholders in Multiple Goal Linear Programming (MGLP) models. Two methodological aspects of long-term

  4. Spatio-temporal distribution of Oklahoma earthquakes: Exploring relationships using a nearest-neighbor approach: Nearest-neighbor analysis of Oklahoma

    Energy Technology Data Exchange (ETDEWEB)

    Vasylkivska, Veronika S. [National Energy Technology Lab. (NETL), Albany, OR (United States); Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); Huerta, Nicolas J. [National Energy Technology Lab. (NETL), Albany, OR (United States)

    2017-06-24

    Determining the spatiotemporal characteristics of natural and induced seismic events holds the opportunity to gain new insights into why these events occur. Linking the seismicity characteristics with other geologic, geographic, natural, or anthropogenic factors could help to identify the causes and suggest mitigation strategies that reduce the risk associated with such events. The nearest-neighbor approach utilized in this work represents a practical first step toward identifying statistically correlated clusters of recorded earthquake events. Detailed study of the Oklahoma earthquake catalog’s inherent errors, empirical model parameters, and model assumptions is presented. We found that the cluster analysis results are stable with respect to empirical parameters (e.g., fractal dimension) but were sensitive to epicenter location errors and seismicity rates. Most critically, we show that the patterns in the distribution of earthquake clusters in Oklahoma are primarily defined by spatial relationships between events. This observation is a stark contrast to California (also known for induced seismicity) where a comparable cluster distribution is defined by both spatial and temporal interactions between events. These results highlight the difficulty in understanding the mechanisms and behavior of induced seismicity but provide insights for future work.

  5. Normalization Strategies for Enhancing Spatio-Temporal Analysis of Social Media Responses during Extreme Events: A Case Study based on Analysis of Four Extreme Events using Socio-Environmental Data Explorer (SEDE

    Directory of Open Access Journals (Sweden)

    J. Ajayakumar

    2017-10-01

    Full Text Available With social media becoming increasingly location-based, there has been a greater push from researchers across various domains including social science, public health, and disaster management, to tap in the spatial, temporal, and textual data available from these sources to analyze public response during extreme events such as an epidemic outbreak or a natural disaster. Studies based on demographics and other socio-economic factors suggests that social media data could be highly skewed based on the variations of population density with respect to place. To capture the spatio-temporal variations in public response during extreme events we have developed the Socio-Environmental Data Explorer (SEDE. SEDE collects and integrates social media, news and environmental data to support exploration and assessment of public response to extreme events. For this study, using SEDE, we conduct spatio-temporal social media response analysis on four major extreme events in the United States including the “North American storm complex” in December 2015, the “snowstorm Jonas” in January 2016, the “West Virginia floods” in June 2016, and the “Hurricane Matthew” in October 2016. Analysis is conducted on geo-tagged social media data from Twitter and warnings from the storm events database provided by National Centers For Environmental Information (NCEI for analysis. Results demonstrate that, to support complex social media analyses, spatial and population-based normalization and filtering is necessary. The implications of these results suggests that, while developing software solutions to support analysis of non-conventional data sources such as social media, it is quintessential to identify the inherent biases associated with the data sources, and adapt techniques and enhance capabilities to mitigate the bias. The normalization strategies that we have developed and incorporated to SEDE will be helpful in reducing the population bias associated with

  6. Determining DNA Sequence Specificity of Natural and Artificial Transcription Factors by Cognate Site Identifier Analysis

    Science.gov (United States)

    Ozers, Mary S.; Warren, Christopher L.; Ansari, Aseem Z.

    Artificial transcription factors (ATFs) are designed to mimic natural transcription factors in the control of gene expression and are comprised of domains for DNA binding and gene regulation. ATF domains are modular, interchangeable, and can be composed of protein-based or nonpeptidic moieties, yielding DNA-interacting regulatory molecules that can either activate or inhibit transcription. Sequence-specific targeting is a key determinant in ATF activity, and DNA-binding domains such as natural zinc fingers and synthetic polyamides have emerged as useful DNA targeting molecules. Defining the comprehensive DNA binding specificity of these targeting molecules for accurate manipulations of the genome can be achieved using cognate site identifier DNA microarrays to explore the entire sequence space of binding sites. Design of ATFs that regulate gene expression with temporal control will generate important molecular tools to probe cell- and tissue-specific gene regulation and to function as potential therapeutic agents.

  7. Synthetic in vitro transcription circuits.

    Science.gov (United States)

    Weitz, Maximilian; Simmel, Friedrich C

    2012-01-01

    With the help of only two enzymes--an RNA polymerase and a ribonuclease--reduced versions of transcriptional regulatory circuits can be implemented in vitro. These circuits enable the emulation of naturally occurring biochemical networks, the exploration of biological circuit design principles and the biochemical implementation of powerful computational models.

  8. Temporal naturalism

    Science.gov (United States)

    Smolin, Lee

    2015-11-01

    Two people may claim both to be naturalists, but have divergent conceptions of basic elements of the natural world which lead them to mean different things when they talk about laws of nature, or states, or the role of mathematics in physics. These disagreements do not much affect the ordinary practice of science which is about small subsystems of the universe, described or explained against a background, idealized to be fixed. But these issues become crucial when we consider including the whole universe within our system, for then there is no fixed background to reference observables to. I argue here that the key issue responsible for divergent versions of naturalism and divergent approaches to cosmology is the conception of time. One version, which I call temporal naturalism, holds that time, in the sense of the succession of present moments, is real, and that laws of nature evolve in that time. This is contrasted with timeless naturalism, which holds that laws are immutable and the present moment and its passage are illusions. I argue that temporal naturalism is empirically more adequate than the alternatives, because it offers testable explanations for puzzles its rivals cannot address, and is likely a better basis for solving major puzzles that presently face cosmology and physics. This essay also addresses the problem of qualia and experience within naturalism and argues that only temporal naturalism can make a place for qualia as intrinsic qualities of matter.

  9. ADHD and temporality

    DEFF Research Database (Denmark)

    Nielsen, Mikka

    According to the official diagnostic manual, ADHD is defined by symptoms of inattention, hyperactivity, and impulsivity and patterns of behaviour are characterized as failure to pay attention to details, excessive talking, fidgeting, or inability to remain seated in appropriate situations (DSM-5......). In this paper, however, I will ask if we can understand what we call ADHD in a different way than through the symptom descriptions and will advocate for a complementary, phenomenological understanding of ADHD as a certain being in the world – more specifically as a matter of a phenomenological difference...... in temporal experience and/or rhythm. Inspired by both psychiatry’s experiments with people diagnosed with ADHD and their assessment of time and phenomenological perspectives on mental disorders and temporal disorientation I explore the experience of ADHD as a disruption in the phenomenological experience...

  10. Deciphering the Innate Lymphoid Cell Transcriptional Program

    Directory of Open Access Journals (Sweden)

    Cyril Seillet

    2016-10-01

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

  11. Innocence and Nostalgia in Conversation Analysis: The Dynamic Relations of Tape and Transcript

    Directory of Open Access Journals (Sweden)

    Malcolm Ashmore

    2000-12-01

    Full Text Available This paper attempts an analysis of some of the methodological practices of Conversation Analysis (CA; in particular, tape recording and transcription. The paper starts from the observation that, in the CA literature, these practices, and the analytic objects they create (the tape and the transcript, are accorded different treatment: simply put, for CA the tape is a "realist" object, while the transcript is a "constructivist" one. The significance of this difference is explored through an analysis of the dynamics of CA practice. We argue that the "constructivist transcript" is premised on an understanding of CA as predominantly concerned with maximising its "analytic utility": a concern of one distinct temporal stage of CA work: that of the "innocent" apprehension of objects in the "first time through". The "realist tape", in contrast, is based on a different aspect of the work of CA: its quest for greater "evidential utility", achieved by the "nostalgic" revisiting of previously produced objects for purposes of checking them against each other; work done in the "next time through". We further argue that both the ontology and the epistemology of CA's objects are changed in any next time encounter. We conclude with a cautionary speculation on the currently-projected, transcript-free, digital future of CA. URN: urn:nbn:de:0114-fqs000335

  12. The effect of temporal manipulation of transforming growth factor beta 3 and fibroblast growth factor 2 on the derivation of proliferative chondrocytes from mensenchymal stem cells-A study monitored by quantitative reverse transcription polymerase chain reaction and molecular beacon based nanosensors.

    Science.gov (United States)

    Tay, Li Min; Wiraja, Christian; Wu, Yingnan; Yang, Zheng; Lee, Eng Hin; Xu, Chenjie

    2017-11-06

    Proliferative chondrocytes are critical to realize regeneration of damaged epiphyseal growth plate. However, acquiring autologous replacement cells involves highly invasive procedures and often results in limited cell quantity. Mesenchymal stem cells (MSCs) are a potential source of chondrogenic cells for the treatment of cartilage disorders and injuries. The temporal effect of transforming growth factor beta 3 (TGFβ3) and fibroblast growth factor 2 (FGF2) on the derivation of proliferative chondrocytes from MSCs in three-dimensional agarose was investigated by manipulating the duration of TGFβ3 and FGF2 treatment. The differentiation process was monitored by quantitative reverse transcription polymerase chain reaction (qRT-PCR) as well as nanosensors containing two molecular beacons that target critical biomarkers for proliferative chondrocytes (i.e., collagen type-II messenger ribonucleic acid [mRNA] and Ki67 mRNA). The molecular beacon-based nanosensors were found to be comparable to qRT-PCR in measuring mRNA expression and thus providing a noninvasive mean to screen and monitor culture samples. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2017. © 2017 Wiley Periodicals, Inc.

  13. WRKY transcription factors.

    Science.gov (United States)

    Rushton, Paul J; Somssich, Imre E; Ringler, Patricia; Shen, Qingxi J

    2010-05-01

    WRKY transcription factors are one of the largest families of transcriptional regulators in plants and form integral parts of signalling webs that modulate many plant processes. Here, we review recent significant progress in WRKY transcription factor research. New findings illustrate that WRKY proteins often act as repressors as well as activators, and that members of the family play roles in both the repression and de-repression of important plant processes. Furthermore, it is becoming clear that a single WRKY transcription factor might be involved in regulating several seemingly disparate processes. Mechanisms of signalling and transcriptional regulation are being dissected, uncovering WRKY protein functions via interactions with a diverse array of protein partners, including MAP kinases, MAP kinase kinases, 14-3-3 proteins, calmodulin, histone deacetylases, resistance proteins and other WRKY transcription factors. WRKY genes exhibit extensive autoregulation and cross-regulation that facilitates transcriptional reprogramming in a dynamic web with built-in redundancy. 2010 Elsevier Ltd. All rights reserved.

  14. High-density transcriptional initiation signals underline genomic islands in bacteria.

    Directory of Open Access Journals (Sweden)

    Qianli Huang

    Full Text Available Genomic islands (GIs, frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these "exotic" regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased "non-optimal" codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for "alien" regions, but also provide hints to the special

  15. Optogenetic Modulation of Intracellular Signalling and Transcription: Focus on Neuronal Plasticity

    Directory of Open Access Journals (Sweden)

    Cyril Eleftheriou

    2017-04-01

    Full Text Available Several fields in neuroscience have been revolutionized by the advent of optogenetics, a technique that offers the possibility to modulate neuronal physiology in response to light stimulation. This innovative and far-reaching tool provided unprecedented spatial and temporal resolution to explore the activity of neural circuits underlying cognition and behaviour. With an exponential growth in the discovery and synthesis of new photosensitive actuators capable of modulating neuronal networks function, other fields in biology are experiencing a similar re-evolution. Here, we review the various optogenetic toolboxes developed to influence cellular physiology as well as the diverse ways in which these can be engineered to precisely modulate intracellular signalling and transcription. We also explore the processes required to successfully express and stimulate these photo-actuators in vivo before discussing how such tools can enlighten our understanding of neuronal plasticity at the systems level.

  16. Extensive polycistronism and antisense transcription in the mammalian Hox clusters.

    Directory of Open Access Journals (Sweden)

    Gaëll Mainguy

    Full Text Available The Hox clusters play a crucial role in body patterning during animal development. They encode both Hox transcription factor and micro-RNA genes that are activated in a precise temporal and spatial sequence that follows their chromosomal order. These remarkable collinear properties confer functional unit status for Hox clusters. We developed the TranscriptView platform to establish high resolution transcriptional profiling and report here that transcription in the Hox clusters is far more complex than previously described in both human and mouse. Unannotated transcripts can represent up to 60% of the total transcriptional output of a cluster. In particular, we identified 14 non-coding Transcriptional Units antisense to Hox genes, 10 of which (70% have a detectable mouse homolog. Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional. Hox clusters also display at least seven polycistronic clusters, i.e., different genes being co-transcribed on long isoforms (up to 30 kb. This work provides a reevaluated framework for understanding Hox gene function and dys-function. Such extensive transcriptions may provide a structural explanation for Hox clustering.

  17. Towards General Temporal Aggregation

    DEFF Research Database (Denmark)

    Boehlen, Michael H.; Gamper, Johann; Jensen, Christian Søndergaard

    2008-01-01

    Most database applications manage time-referenced, or temporal, data. Temporal data management is difficult when using conventional database technology, and many contributions have been made for how to better model, store, and query temporal data. Temporal aggregation illustrates well the problem...

  18. Filovirus replication and transcription

    OpenAIRE

    Mühlberger, Elke

    2007-01-01

    The highly pathogenic filoviruses, Marburg and Ebola virus, belong to the nonsegmented negative-sense RNA viruses of the order Mononegavirales. The mode of replication and transcription is similar for these viruses. On one hand, the negative-sense RNA genome serves as a template for replication, to generate progeny genomes, and, on the other hand, for transcription, to produce mRNAs. Despite the similarities in the replication/transcription strategy, filoviruses have evolved structural and fu...

  19. WRKY transcription factors

    Science.gov (United States)

    Bakshi, Madhunita; Oelmüller, Ralf

    2014-01-01

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

  20. Biophysical models of transcription in cells

    Science.gov (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

  1. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

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

    2012-01-01

    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...

  2. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein codi...

  3. Temporal Cyber Attack Detection.

    Energy Technology Data Exchange (ETDEWEB)

    Ingram, Joey Burton [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Draelos, Timothy J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Galiardi, Meghan [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Doak, Justin E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-11-01

    Rigorous characterization of the performance and generalization ability of cyber defense systems is extremely difficult, making it hard to gauge uncertainty, and thus, confidence. This difficulty largely stems from a lack of labeled attack data that fully explores the potential adversarial space. Currently, performance of cyber defense systems is typically evaluated in a qualitative manner by manually inspecting the results of the system on live data and adjusting as needed. Additionally, machine learning has shown promise in deriving models that automatically learn indicators of compromise that are more robust than analyst-derived detectors. However, to generate these models, most algorithms require large amounts of labeled data (i.e., examples of attacks). Algorithms that do not require annotated data to derive models are similarly at a disadvantage, because labeled data is still necessary when evaluating performance. In this work, we explore the use of temporal generative models to learn cyber attack graph representations and automatically generate data for experimentation and evaluation. Training and evaluating cyber systems and machine learning models requires significant, annotated data, which is typically collected and labeled by hand for one-off experiments. Automatically generating such data helps derive/evaluate detection models and ensures reproducibility of results. Experimentally, we demonstrate the efficacy of generative sequence analysis techniques on learning the structure of attack graphs, based on a realistic example. These derived models can then be used to generate more data. Additionally, we provide a roadmap for future research efforts in this area.

  4. Mechanical Properties of Transcription.

    Science.gov (United States)

    Sevier, Stuart A; Levine, Herbert

    2017-06-30

    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.

  5. How Would You Like to Aggregate Your Temporal Data?

    DEFF Research Database (Denmark)

    Böhlen, M. H.; Gamper, J.; Jensen, Christian Søndergaard

    2006-01-01

    and query languages have been proposed. Motivated in part by the emergence of non-traditional data management applications and the increasing proliferation of temporal data, this paper puts focus on the aggregation of temporal data. In particular, it provides a general framework of temporal aggregation...... concepts, and it discusses the abilities of five approaches to the design of temporal query languages with respect to temporal aggregation. Rather than providing focused, polished results, the paper?s aim is to explore the inherent support for temporal aggregation in an informal manner that may serve...

  6. Semantics of Temporal Models with Multiple Temporal Dimensions

    DEFF Research Database (Denmark)

    Kraft, Peter; Sørensen, Jens Otto

    Semantics of temporal models with multi temporal dimensions are examined progressing from non-temporal models unto uni-temporal, and further unto bi- and tri-temporal models. An example of a uni-temporal model is the valid time model, an example of a bi-temporal model is the valid time/transactio...

  7. Analysis of BMP4 and BMP7 signaling in breast cancer cells unveils time-dependent transcription patterns and highlights a common synexpression group of genes

    Directory of Open Access Journals (Sweden)

    Rodriguez-Martinez Alejandra

    2011-11-01

    Full Text Available Abstract Background Bone morphogenetic proteins (BMPs are members of the TGF-beta superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP4 and BMP7, in particular, have been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We explored the effects of BMP4 and BMP7 treatment on global gene transcription in seven breast cancer cell lines during a 6-point time series, using a whole-genome oligo microarray. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data. Results Both ligands had a strong effect on gene expression, although the response to BMP4 treatment was more pronounced. The cellular functions most strongly affected by BMP signaling were regulation of transcription and development. The observed transcriptional response, as well as its functional outcome, followed a temporal sequence, with regulation of gene expression and signal transduction leading to changes in metabolism and cell proliferation. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMPs, but also highlighted a synexpression group of genes for both ligands. Interestingly, the majority of the genes within these synexpression groups were shared by the two ligands, probably representing the core molecular responses common to BMP4 and BMP7 signaling pathways. Conclusions All in all, we show that BMP signaling has a remarkable effect on gene transcription in breast cancer cells and that the functions affected follow a logical temporal pattern. Our results also uncover components of the common cellular transcriptional response to BMP4 and BMP7. Most importantly, this study provides a list of potential novel BMP target

  8. Temporal Coding of Volumetric Imagery

    Science.gov (United States)

    Llull, Patrick Ryan

    'Image volumes' refer to realizations of images in other dimensions such as time, spectrum, and focus. Recent advances in scientific, medical, and consumer applications demand improvements in image volume capture. Though image volume acquisition continues to advance, it maintains the same sampling mechanisms that have been used for decades; every voxel must be scanned and is presumed independent of its neighbors. Under these conditions, improving performance comes at the cost of increased system complexity, data rates, and power consumption. This dissertation explores systems and methods capable of efficiently improving sensitivity and performance for image volume cameras, and specifically proposes several sampling strategies that utilize temporal coding to improve imaging system performance and enhance our awareness for a variety of dynamic applications. Video cameras and camcorders sample the video volume (x,y,t) at fixed intervals to gain understanding of the volume's temporal evolution. Conventionally, one must reduce the spatial resolution to increase the framerate of such cameras. Using temporal coding via physical translation of an optical element known as a coded aperture, the compressive temporal imaging (CACTI) camera emonstrates a method which which to embed the temporal dimension of the video volume into spatial (x,y) measurements, thereby greatly improving temporal resolution with minimal loss of spatial resolution. This technique, which is among a family of compressive sampling strategies developed at Duke University, temporally codes the exposure readout functions at the pixel level. Since video cameras nominally integrate the remaining image volume dimensions (e.g. spectrum and focus) at capture time, spectral (x,y,t,lambda) and focal (x,y,t,z) image volumes are traditionally captured via sequential changes to the spectral and focal state of the system, respectively. The CACTI camera's ability to embed video volumes into images leads to exploration

  9. Eukaryotic transcription factors

    DEFF Research Database (Denmark)

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

    2017-01-01

    Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains...

  10. Navigability of multiplex temporal network

    Science.gov (United States)

    Wang, Yan; Song, Qiao-Zhen

    2017-01-01

    Real world complex systems have multiple levels of relationships and in many cases, they need to be modeled as multiplex networks where the same nodes can interact with each other in different layers, such as social networks. However, social relationships only appear at prescribed times so the temporal structures of edge activations can also affect the dynamical processes located above them. To consider both factors are simultaneously, we introduce multiplex temporal networks and propose three different walk strategies to investigate the concurrent dynamics of random walks and the temporal structure of multiplex networks. Thus, we derive analytical results for the multiplex centrality and coverage function in multiplex temporal networks. By comparing them with the numerical results, we show how the underlying topology of the layers and the walk strategy affect the efficiency when exploring the networks. In particular, the most interesting result is the emergence of a super-diffusion process, where the time scale of the multiplex is faster than that of both layers acting separately.

  11. Transcriptional regulation of metabolism.

    Science.gov (United States)

    Desvergne, Béatrice; Michalik, Liliane; Wahli, Walter

    2006-04-01

    Our understanding of metabolism is undergoing a dramatic shift. Indeed, the efforts made towards elucidating the mechanisms controlling the major regulatory pathways are now being rewarded. At the molecular level, the crucial role of transcription factors is particularly well-illustrated by the link between alterations of their functions and the occurrence of major metabolic diseases. In addition, the possibility of manipulating the ligand-dependent activity of some of these transcription factors makes them attractive as therapeutic targets. The aim of this review is to summarize recent knowledge on the transcriptional control of metabolic homeostasis. We first review data on the transcriptional regulation of the intermediary metabolism, i.e., glucose, amino acid, lipid, and cholesterol metabolism. Then, we analyze how transcription factors integrate signals from various pathways to ensure homeostasis. One example of this coordination is the daily adaptation to the circadian fasting and feeding rhythm. This section also discusses the dysregulations causing the metabolic syndrome, which reveals the intricate nature of glucose and lipid metabolism and the role of the transcription factor PPARgamma in orchestrating this association. Finally, we discuss the molecular mechanisms underlying metabolic regulations, which provide new opportunities for treating complex metabolic disorders.

  12. A biophysical model for transcription factories

    Directory of Open Access Journals (Sweden)

    Canals-Hamann Ana Z

    2013-02-01

    Full Text Available Summary 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.

  13. 21 CFR 12.98 - Official transcript.

    Science.gov (United States)

    2010-04-01

    ... a verbatim stenographic transcript of oral testimony and for necessary copies of the transcript. (b... the transcript of oral testimony. Corrections are permitted only for transcription errors. The...

  14. Regulation of Transcript Elongation

    Science.gov (United States)

    Belogurov, Georgiy A.; Artsimovitch, Irina

    2015-01-01

    Bacteria lack subcellular compartments and harbor a single RNA polymerase that synthesizes both structural and protein-coding RNAs, which are cotranscriptionally processed by distinct pathways. Nascent rRNAs fold into elaborate secondary structures and associate with ribosomal proteins, whereas nascent mRNAs are translated by ribosomes. During elongation, nucleic acid signals and regulatory proteins modulate concurrent RNA-processing events, instruct RNA polymerase where to pause and terminate transcription, or act as roadblocks to the moving enzyme. Communications among complexes that carry out transcription, translation, repair, and other cellular processes ensure timely execution of the gene expression program and survival under conditions of stress. This network is maintained by auxiliary proteins that act as bridges between RNA polymerase, ribosome, and repair enzymes, blurring boundaries between separate information-processing steps and making assignments of unique regulatory functions meaningless. Understanding the regulation of transcript elongation thus requires genome-wide approaches, which confirm known and reveal new regulatory connections. PMID:26132790

  15. Deciphering Transcriptional Regulation

    DEFF Research Database (Denmark)

    Valen, Eivind

    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 mRNA...... prediction and provide tools that help investigators use these. In addition, a de novo motif discovery tool was developed that locates these patterns in DNA sequences. This compared favorably to many contemporary methods. A novel experimental method, cap-analysis of gene expression (CAGE), was recently......); 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...

  16. Dynamic Mechanism for the Transcription Apparatus Orchestrating Reliable Responses to Activators

    Science.gov (United States)

    Wang, Yaolai; Liu, Feng; Wang, Wei

    2012-05-01

    The transcription apparatus (TA) is a huge molecular machine. It detects the time-varying concentrations of transcriptional activators and initiates mRNA transcripts at appropriate rates. Based on the general structural organizations of the TA, we propose how the TA dynamically orchestrates transcriptional responses. The activators rapidly cycle in and out of a clamp-like space temporarily formed between the enhancer and the Mediator, with the concentration of activators encoded as their temporal occupancy rate (RTOR) within the space. The entry of activators into this space induces allostery in the Mediator, resulting in a facilitated circumstance for transcriptional reinitiation. The reinitiation rate is much larger than the cycling rate of activators, thereby RTOR guiding the amount of transcripts. Based on this mechanism, stochastic simulations can qualitatively reproduce and interpret multiple features of gene expression, e.g., transcriptional bursting is not mere noise as traditionally believed, but rather the basis of reliable transcriptional responses.

  17. Inductive Temporal Logic Programming

    OpenAIRE

    Kolter, Robert

    2009-01-01

    We study the extension of techniques from Inductive Logic Programming (ILP) to temporal logic programming languages. Therefore we present two temporal logic programming languages and analyse the learnability of programs from these languages from finite sets of examples. In first order temporal logic the following topics are analysed: - How can we characterize the denotational semantics of programs? - Which proof techniques are best suited? - How complex is the learning task? In propositional ...

  18. Negotiating Transcription as a Relative Insider: Implications for Rigor

    Directory of Open Access Journals (Sweden)

    Chad S. G. Witcher MA

    2010-06-01

    Full Text Available Despite the prevalence of the transcription of language data in qualitative research, few published studies provide insight into how the transcription process is negotiated. The purpose of this article is to describe unique challenges to quality transcription faced by a “relative insider” by reflexively exploring the research process (in particular the researcher's position and to explicate the implications for transcription quality and research rigor/trustworthiness. Inaccuracies within transcripts created by discrepancies between participants' intended meaning and the researcher's/transcriptionist's interpretation can compromise the rigor of one's findings. Therefore, when conducting research among speakers of regional dialects, researchers/transcriptionists should plan how issues related to interviewing and particularly to transcription will be negotiated.

  19. Measuring temporal trends in biodiversity

    OpenAIRE

    Buckland, S. T.; Yuan, Y.; Marcon, Eric

    2017-01-01

    Yuan was part-funded by EPSRC/NERC Grant EP/1000917/1 and Marcon by ANR-10-LABX-25-01. In 2002, nearly 200 nations signed up to the 2010 target of the Convention for Biological Diversity, ‘to significantly reduce the rate of biodiversity loss by 2010’. In order to assess whether the target was met, it became necessary to quantify temporal trends in measures of diversity. This resulted in a marked shift in focus for biodiversity measurement. We explore the developments in measuring biodiver...

  20. Ethnographies of Youth and Temporality

    DEFF Research Database (Denmark)

    Dalsgård, Anne Line; Frederiksen, Martin Demant; Højlund, Susanne

    and Temporality, have provided a diverse collection of ethnographic studies and theoretical explorations of youth experiencing time in a variety of contemporary socio-cultural settings. The essays in this volume focus on time as an external and often troubling factor in young people’s lives, and show how...... emotional unrest and violence but also creativity and hope are responses to troubling times. The chapters discuss notions of time and its “objectification” in diverse locales including the Georgian Republic, Brazil, Denmark, and Uganda. Based on long-term ethnographic fieldwork, the essays in Ethnographies...

  1. Indeterministic Temporal Logic

    Directory of Open Access Journals (Sweden)

    Trzęsicki Kazimierz

    2015-09-01

    Full Text Available The questions od determinism, causality, and freedom have been the main philosophical problems debated since the beginning of temporal logic. The issue of the logical value of sentences about the future was stated by Aristotle in the famous tomorrow sea-battle passage. The question has inspired Łukasiewicz’s idea of many-valued logics and was a motive of A. N. Prior’s considerations about the logic of tenses. In the scheme of temporal logic there are different solutions to the problem. In the paper we consider indeterministic temporal logic based on the idea of temporal worlds and the relation of accessibility between them.

  2. Full-fledged temporal processing: bridging the gap between deep linguistic processing and temporal extraction

    Directory of Open Access Journals (Sweden)

    Francisco Costa

    2013-07-01

    Full Text Available The full-fledged processing of temporal information presents specific challenges. These difficulties largely stem from the fact that the temporal meaning conveyed by grammatical means interacts with many extra-linguistic factors (world knowledge, causality, calendar systems, reasoning. This article proposes a novel approach to this problem, based on a hybrid strategy that explores the complementarity of the symbolic and probabilistic methods. A specialized temporal extraction system is combined with a deep linguistic processing grammar. The temporal extraction system extracts eventualities, times and dates mentioned in text, and also temporal relations between them, in line with the tasks of the recent TempEval challenges; and uses machine learning techniques to draw from different sources of information (grammatical and extra-grammatical even if it is not explicitly known how these combine to produce the final temporal meaning being expressed. In turn, the deep computational grammar delivers richer truth-conditional meaning representations of input sentences, which include a principled representation of temporal information, on which higher level tasks, including reasoning, can be based. These deep semantic representations are extended and improved according to the output of the aforementioned temporal extraction module. The prototype implemented shows performance results that increase the quality of the temporal meaning representations and are better than the performance of each of the two components in isolation.

  3. Rhythm quantization for transcription

    NARCIS (Netherlands)

    Cemgil, A.T.; Desain, P.W.M.; Kappen, H.J.

    1999-01-01

    Automatic Music Transcription is the extraction of an acceptable notation from performed music. One important task in this problem is rhythm quantization which refers to categorization of note durations. Although quantization of a pure mechanical performance is rather straightforward, the task

  4. Actinomycin and DNA transcription.

    OpenAIRE

    Sobell, H M

    1985-01-01

    Recent advances in understanding how actinomycin binds to DNA have suggested its mechanism of action. Actinomycin binds to a premelted DNA conformation present within the transcriptional complex. This immobilizes the complex, interfering with the elongation of growing RNA chains. The model has a number of implications for understanding RNA synthesis.

  5. Actinomycin and DNA transcription.

    Science.gov (United States)

    Sobell, H M

    1985-01-01

    Recent advances in understanding how actinomycin binds to DNA have suggested its mechanism of action. Actinomycin binds to a premelted DNA conformation present within the transcriptional complex. This immobilizes the complex, interfering with the elongation of growing RNA chains. The model has a number of implications for understanding RNA synthesis. Images PMID:2410919

  6. transcriptional regulatory element

    African Journals Online (AJOL)

    ARL

    2012-06-12

    Jun 12, 2012 ... Further test of the effect of WPRE on plasmid-mediated gene expression with two therapeutic proteins showed substantial ... promoter-independent, and provide valuable information to improve vectors for efficient and stable gene expression in ... transcriptional events concerning the recombinant. mRNA.

  7. Bayesian Music Transcription

    NARCIS (Netherlands)

    Cemgil, A.T.

    2004-01-01

    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

  8. Actinomycin and DNA transcription

    Energy Technology Data Exchange (ETDEWEB)

    Sobell, H.M.

    1985-08-01

    Recent advances in understanding how actinomycin binds to DNA have suggested its mechanism of action. Actinomycin binds to a premelted DNA conformation present within the transcriptional complex. This immobilizes the complex, interfering with the elongation of growing RNA chains. The model has a number of implications for understanding RNA synthesis.

  9. Class-C SOX Transcription Factors Control GnRH Gene Expression via the Intronic Transcriptional Enhancer

    Science.gov (United States)

    Kim, Hee-Dae; Choe, Han Kyoung; Chung, Sooyoung; Kim, Myungjin; Seong, Jae Young

    2011-01-01

    GnRH is a pivotal hypothalamic neurohormone governing reproduction and sexual development. Because transcriptional regulation is crucial for the spatial and temporal expression of the GnRH gene, a region approximately 3.0 kb upstream of the mammalian GnRH promoter has been extensive studied. In the present study, we demonstrate a transcription-enhancer located in the first intron (intron A) region of the GnRH gene. This transcriptional enhancer harbors putative sex-determining region Y-related high-mobility-group box (SOX) family transcription factor-binding sites, which are well conserved across many mammalian species. The class-C SOX member proteins (SOX-C) (SOX4 and SOX11) specifically augment this transcriptional activation by binding to these SOX-binding sites. In accordance, SOX11 is highly enriched in immortalized GnRH-producing GT1-1 cells, and suppression of its expression significantly decreases GnRH gene expression as well as GnRH secretion. Chromatin immunoprecipitation shows that endogenous SOX-C factors recognize and bind to the intronic enhancer in GT1-1 cells and the hypothalamus. Accompanying immunohistochemical analysis demonstrates that SOX4 or SOX11 are highly expressed in the majority of hypothalamic GnRH neurons in adult mice. Taken together, these findings demonstrate that SOX-C transcription factors function as important transcriptional regulators of cell type-specific GnRH gene expression by acting on the intronic transcriptional enhancer. PMID:21527504

  10. spacetime : Spatio-Temporal Data in R

    Directory of Open Access Journals (Sweden)

    Edzer Pebesma

    2012-11-01

    Full Text Available This document describes classes and methods designed to deal with different types of spatio-temporal data in R implemented in the R package spacetime, and provides examples for analyzing them. It builds upon the classes and methods for spatial data from package sp, and for time series data from package xts. The goal is to cover a number of useful representations for spatio-temporal sensor data, and results from predicting (spatial and/or temporal interpolation or smoothing, aggregating, or subsetting them, and to represent trajectories. The goals of this paper is to explore how spatio-temporal data can be sensibly represented in classes, and to find out which analysis and visualisation methods are useful and feasible. We discuss the time series convention of representing time intervals by their starting time only. This document is the main reference for the R package spacetime, and is available (in updated form as a vignette in this package.

  11. Temporal properties of stereopsis

    NARCIS (Netherlands)

    Gheorghiu, E.

    2005-01-01

    The goal of the research presented in this thesis was to investigate temporal properties of disparity processing and depth perception in human subjects, in response to dynamic stimuli. The results presented in various chapters, reporting findings about different temporal aspects of disparity

  12. Temporal Linear System Structure

    NARCIS (Netherlands)

    Willigenburg, van L.G.; Koning, de W.L.

    2008-01-01

    Piecewise constant rank systems and the differential Kalman decomposition are introduced in this note. Together these enable the detection of temporal uncontrollability/unreconstructability of linear continuous-time systems. These temporal properties are not detected by any of the four conventional

  13. Temporal Context, Preference, and Resistance to Change

    Science.gov (United States)

    Podlesnik, Christopher A.; Jimenez-Gomez, Corina; Thrailkill, Eric A.; Shahan, Timothy A.

    2011-01-01

    According to behavioral momentum theory, preference and relative resistance to change in concurrent chains schedules are correlated and reflect the relative conditioned value of discriminative stimuli. In the present study, we explore the generality of this relation by manipulating the temporal context within a concurrent-chains procedure through…

  14. Temporal Photon Differentials

    DEFF Research Database (Denmark)

    Schjøth, Lars; Frisvad, Jeppe Revall; Erleben, Kenny

    2010-01-01

    , constituting a temporal smoothing of rapidly changing illumination. In global illumination temporal smoothing can be achieved with distribution ray tracing (Cook et al., 1984). Unfortunately, this, and resembling methods, requires a high temporal resolution as samples has to be drawn from in-between frames. We...... present a novel method which is able to produce high quality temporal smoothing for indirect illumination without using in-between frames. Our method is based on ray differentials (Igehy, 1999) as it has been extended in (Sporring et al., 2009). Light rays are traced as bundles creating footprints, which......The finite frame rate also used in computer animated films is cause of adverse temporal aliasing effects. Most noticeable of these is a stroboscopic effect that is seen as intermittent movement of fast moving illumination. This effect can be mitigated using non-zero shutter times, effectively...

  15. Temporal properties of stereopsis

    Science.gov (United States)

    Gheorghiu, E.

    2005-03-01

    The goal of the research presented in this thesis was to investigate temporal properties of disparity processing and depth perception in human subjects, in response to dynamic stimuli. The results presented in various chapters, reporting findings about different temporal aspects of disparity processing, are based on psychophysical experiments and computational model analysis. In chapter 1 we investigated which processes of binocular depth perception in dynamic random-dot stereograms (DRS), i.e., tolerance for interocular delays and temporal integration of correlation, are responsible for the temporal flexibility of the stereoscopic system. Our results demonstrate that (i) disparities from simultaneous monocular inputs dominate those from interocular delayed inputs; (ii) stereopsis is limited by temporal properties of monocular luminance mechanisms; (iii) depth perception in DRS results from cross-correlation-like operation on two simultaneous monocular inputs that represent the retinal images after having been subjected to a process of monocular temporal integration of luminance. In chapter 2 we examined what temporal information is exploited by the mechanisms underlying stereoscopic motion in depth. We investigated systematically the influence of temporal frequency on binocular depth perception in temporally correlated and temporally uncorrelated DRS. Our results show that disparity-defined depth is judged differently in temporally correlated and uncorrelated DRS above a temporal frequency of about 3 Hz. The results and simulations indicate that: (i) above about 20 Hz, the complete absence of stereomotion is caused by temporal integration of luminance; (ii) the difference in perceived depth in temporally correlated and temporally uncorrelated DRS for temporal frequencies between 20 and 3 Hz, is caused by temporal integration of disparity. In chapter 3 we investigated temporal properties of stereopsis at different spatial scales in response to sustained and

  16. Exploration Review

    Science.gov (United States)

    Wilburn, D.R.; Stanley, K.A.

    2013-01-01

    This summary of international mineral exploration activities for 2012 draws upon information from industry sources, published literature and U.S. Geological Survey (USGS) specialists. The summary provides data on exploration budgets by region and mineral commodity, identifies significant mineral discoveries and areas of mineral exploration, discusses government programs affecting the mineral exploration industry and presents analyses of exploration activities performed by the mineral industry. Three sources of information are reported and analyzed in this annual review of international exploration for 2012: 1) budgetary statistics expressed in U.S. nominal dollars provided by SNL Metals Economics Group (MEG) of Halifax, Nova Scotia; 2) regional and site-specific exploration activities that took place in 2012 as compiled by the USGS and 3) regional events including economic, social and political conditions that affected exploration activities, which were derived from published sources and unpublished discussions with USGS and industry specialists.

  17. Exploration technology

    Energy Technology Data Exchange (ETDEWEB)

    Roennevik, H.C. [Saga Petroleum A/S, Forus (Norway)

    1996-12-31

    The paper evaluates exploration technology. Topics discussed are: Visions; the subsurface challenge; the creative tension; the exploration process; seismic; geology; organic geochemistry; seismic resolution; integration; drilling; value creation. 4 refs., 22 figs.

  18. Transcriptional and post-transcriptional regulation of nucleotide excision repair genes in human cells

    Energy Technology Data Exchange (ETDEWEB)

    Lefkofsky, Hailey B. [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Veloso, Artur [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Bioinformatics Program, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI (United States); Ljungman, Mats, E-mail: ljungman@umich.edu [Translational Oncology Program, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI (United States); Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI (United States)

    2015-06-15

    Nucleotide excision repair (NER) removes DNA helix-distorting lesions induced by UV light and various chemotherapeutic agents such as cisplatin. These lesions efficiently block the elongation of transcription and need to be rapidly removed by transcription-coupled NER (TC-NER) to avoid the induction of apoptosis. Twenty-nine genes have been classified to code for proteins participating in nucleotide excision repair (NER) in human cells. Here we explored the transcriptional and post-transcriptional regulation of these NER genes across 13 human cell lines using Bru-seq and BruChase-seq, respectively. Many NER genes are relatively large in size and therefore will be easily inactivated by UV-induced transcription-blocking lesions. Furthermore, many of these genes produce transcripts that are rather unstable. Thus, these genes are expected to rapidly lose expression leading to a diminished function of NER. One such gene is ERCC6 that codes for the CSB protein critical for TC-NER. Due to its large gene size and high RNA turnover rate, the ERCC6 gene may act as dosimeter of DNA damage so that at high levels of damage, ERCC6 RNA levels would be diminished leading to the loss of CSB expression, inhibition of TC-NER and the promotion of cell death.

  19. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager

    2015-01-01

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

  20. Mechanisms of temporal identity regulation in mouse retinal progenitor cells.

    Science.gov (United States)

    Mattar, Pierre; Cayouette, Michel

    2015-01-01

    While much progress has been made in recent years toward elucidating the transcription factor codes controlling how neural progenitor cells generate the various glial and neuronal cell types in a particular spatial domain, much less is known about how these progenitors alter their output over time. In the past years, work in the developing mouse retina has provided evidence that a transcriptional cascade similar to the one used in Drosophila neuroblasts might control progenitor temporal identity in vertebrates. The zinc finger transcription factor Ikzf1 (Ikaros), an ortholog of Drosophila hunchback, was reported to confer early temporal identity in retinal progenitors and, more recently, the ortholog of Drosophila castor, Casz1, was found to function as a mid/late temporal identity factor that is negatively regulated by Ikzf1. The molecular mechanisms by which these temporal identity factors function in retinal progenitors, however, remain unknown. Here we briefly review previous work on the vertebrate temporal identity factors in the retina, and propose a model by which they might operate.

  1. An index guiding temporal planting policies for wind erosion reduction

    NARCIS (Netherlands)

    Zhao, C.X.; Zheng, D.W.; Stigter, C.J.; He, W.Q.; Tuo, D.B.; Zhao, P.

    2006-01-01

    Vegetation cover has spatial as well as temporal characteristics, but the latter are often neglected. Temporal cover characteristics were explored to recommend planting policies for returning arable land into land better protected from serious wind erosion during late autumn, winter, and

  2. Spanish dialects: phonetic transcription

    OpenAIRE

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

    1998-01-01

    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 ...

  3. Towards Temporal Graph Databases

    OpenAIRE

    Campos, Alexander; Mozzino, Jorge; Vaisman, Alejandro

    2016-01-01

    In spite of the extensive literature on graph databases (GDBs), temporal GDBs have not received too much attention so far. Temporal GBDs can capture, for example, the evolution of social networks across time, a relevant topic in data analysis nowadays. In this paper we propose a data model and query language (denoted TEG-QL) for temporal GDBs, based on the notion of attribute graphs. This allows a straightforward translation to Neo4J, a well-known GBD. We present extensive examples of the use...

  4. Mechanochemical ATPases and transcriptional activation

    National Research Council Canada - National Science Library

    Zhang, X; Chaney, M; Wigneshweraraj, Siva R; Schumacher, J; Bordes, P; Cannon, W; Buck, M

    2002-01-01

    ... transcription from other ATP‐independent activation mechanisms that rely on the recruitment of RNAP by transcription factors. As described below, productive interactions between σ 54 and its a...

  5. Nucleocytoplasmic shuttling of transcription factors

    DEFF Research Database (Denmark)

    Cartwright, P; Helin, K

    2000-01-01

    To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation of the t......To elicit the transcriptional response following intra- or extracellular stimuli, the signals need to be transmitted to their site of action within the nucleus. The nucleocytoplasmic shuttling of transcription factors is a mechanism mediating this process. The activation and inactivation...... transcription factor families are regulated by similar mechanisms, there are several differences that allow for the specific activation of each transcription factor. This review discusses the general import and export pathways found to be common amongst many different transcription factors, and highlights...... a select group of transcription factors that demonstrate the diversity displayed in their mode of activation and inactivation....

  6. Transcriptional networks controlling adipocyte differentiation

    DEFF Research Database (Denmark)

    Siersbæk, R; Mandrup, Susanne

    2011-01-01

    Adipocyte differentiation is regulated by a complex cascade of signals that drive the transcriptional reprogramming of the fibroblastic precursors. Genome-wide analyses of chromatin accessibility and binding of adipogenic transcription factors make it possible to generate "snapshots" of the trans......Adipocyte differentiation is regulated by a complex cascade of signals that drive the transcriptional reprogramming of the fibroblastic precursors. Genome-wide analyses of chromatin accessibility and binding of adipogenic transcription factors make it possible to generate "snapshots...

  7. Temporal Lobe Seizure

    Science.gov (United States)

    ... pregnancy Temporal lobe seizure Symptoms & causes Diagnosis & treatment Advertisement Mayo Clinic does not endorse companies or products. ... a Job Site Map About This Site Twitter Facebook Google YouTube Pinterest Mayo Clinic is a not- ...

  8. Temporal Lobe Seizure

    Science.gov (United States)

    ... functions, including having odd feelings — such as euphoria, deja vu or fear. During a temporal lobe seizure, you ... include: A sudden sense of unprovoked fear A deja vu experience — a feeling that what's happening has happened ...

  9. Multisensory temporal numerosity judgment

    NARCIS (Netherlands)

    Philippi, T.; Erp, J.B.F. van; Werkhoven, P.J.

    2008-01-01

    In temporal numerosity judgment, observers systematically underestimate the number of pulses. The strongest underestimations occur when stimuli are presented with a short interstimulus interval (ISI) and are stronger for vision than for audition and touch. We investigated if multisensory

  10. Neocortical Temporal Lobe Epilepsy

    Science.gov (United States)

    Bercovici, Eduard; Kumar, Balagobal Santosh; Mirsattari, Seyed M.

    2012-01-01

    Complex partial seizures (CPSs) can present with various semiologies, while mesial temporal lobe epilepsy (mTLE) is a well-recognized cause of CPS, neocortical temporal lobe epilepsy (nTLE) albeit being less common is increasingly recognized as separate disease entity. Differentiating the two remains a challenge for epileptologists as many symptoms overlap due to reciprocal connections between the neocortical and the mesial temporal regions. Various studies have attempted to correctly localize the seizure focus in nTLE as patients with this disorder may benefit from surgery. While earlier work predicted poor outcomes in this population, recent work challenges those ideas yielding good outcomes in part due to better localization using improved anatomical and functional techniques. This paper provides a comprehensive review of the diagnostic workup, particularly the application of recent advances in electroencephalography and functional brain imaging, in neocortical temporal lobe epilepsy. PMID:22953057

  11. Massive temporal lobe cholesteatoma

    National Research Council Canada - National Science Library

    Waidyasekara, Pasan; Dowthwaite, Samuel A; Stephenson, Ellison; Bhuta, Sandeep; McMonagle, Brent

    2015-01-01

    .... There had been no relevant symptoms in the interim until 6 weeks prior to this presentation. Imaging demonstrated a large right temporal lobe mass contiguous with the middle ear and mastoid cavity with features consistent with cholesteatoma...

  12. Massive Temporal Lobe Cholesteatoma

    National Research Council Canada - National Science Library

    Waidyasekara, Pasan; Dowthwaite, Samuel A; Stephenson, Ellison; Bhuta, Sandeep; McMonagle, Brent

    2015-01-01

    .... There had been no relevant symptoms in the interim until 6 weeks prior to this presentation. Imaging demonstrated a large right temporal lobe mass contiguous with the middle ear and mastoid cavity with features consistent with cholesteatoma...

  13. Temporal Processing in Audition: Insights from Music.

    Science.gov (United States)

    Rajendran, Vani G; Teki, Sundeep; Schnupp, Jan W H

    2017-11-03

    Music is a curious example of a temporally patterned acoustic stimulus, and a compelling pan-cultural phenomenon. This review strives to bring some insights from decades of music psychology and sensorimotor synchronization (SMS) literature into the mainstream auditory domain, arguing that musical rhythm perception is shaped in important ways by temporal processing mechanisms in the brain. The feature that unites these disparate disciplines is an appreciation of the central importance of timing, sequencing, and anticipation. Perception of musical rhythms relies on an ability to form temporal predictions, a general feature of temporal processing that is equally relevant to auditory scene analysis, pattern detection, and speech perception. By bringing together findings from the music and auditory literature, we hope to inspire researchers to look beyond the conventions of their respective fields and consider the cross-disciplinary implications of studying auditory temporal sequence processing. We begin by highlighting music as an interesting sound stimulus that may provide clues to how temporal patterning in sound drives perception. Next, we review the SMS literature and discuss possible neural substrates for the perception of, and synchronization to, musical beat. We then move away from music to explore the perceptual effects of rhythmic timing in pattern detection, auditory scene analysis, and speech perception. Finally, we review the neurophysiology of general timing processes that may underlie aspects of the perception of rhythmic patterns. We conclude with a brief summary and outlook for future research. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes.

    Science.gov (United States)

    Basnet, Ram Kumar; Moreno-Pachon, Natalia; Lin, Ke; Bucher, Johan; Visser, Richard G F; Maliepaard, Chris; Bonnema, Guusje

    2013-12-01

    Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed. Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 "gene modules", of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways. This is the first study of genome-wide profiling of transcript abundance during seed development in B

  15. Temporal network epidemiology

    CERN Document Server

    Holme, Petter

    2017-01-01

    This book covers recent developments in epidemic process models and related data on temporally varying networks. It is widely recognized that contact networks are indispensable for describing, understanding, and intervening to stop the spread of infectious diseases in human and animal populations; “network epidemiology” is an umbrella term to describe this research field. More recently, contact networks have been recognized as being highly dynamic. This observation, also supported by an increasing amount of new data, has led to research on temporal networks, a rapidly growing area. Changes in network structure are often informed by epidemic (or other) dynamics, in which case they are referred to as adaptive networks. This volume gathers contributions by prominent authors working in temporal and adaptive network epidemiology, a field essential to understanding infectious diseases in real society.

  16. Laminar and Temporal Expression Dynamics of Coding and Noncoding RNAs in the Mouse Neocortex

    Directory of Open Access Journals (Sweden)

    Sofia Fertuzinhos

    2014-03-01

    Full Text Available The hallmark of the cerebral neocortex is its organization into six layers, each containing a characteristic set of cell types and synaptic connections. The transcriptional events involved in laminar development and function still remain elusive. Here, we employed deep sequencing of mRNA and small RNA species to gain insights into transcriptional differences among layers and their temporal dynamics during postnatal development of the mouse primary somatosensory neocortex. We identify a number of coding and noncoding transcripts with specific spatiotemporal expression and splicing patterns. We also identify signature trajectories and gene coexpression networks associated with distinct biological processes and transcriptional overlap between these processes. Finally, we provide data that allow the study of potential miRNA and mRNA interactions. Overall, this study provides an integrated view of the laminar and temporal expression dynamics of coding and noncoding transcripts in the mouse neocortex and a resource for studies of neurodevelopment and transcriptome.

  17. Vivienda temporal para refugiados

    OpenAIRE

    Amonarraiz Gutiérrez, Ana

    2015-01-01

    El proyecto se centra en el diseño y desarrollo de un espacio destinado a vivienda temporal para dar hogar a personas que han perdido su casa. Este tipo de vivienda es fundamental dentro del proceso de recuperación post-desastre ya que la construcción inmediata de viviendas permanentes es utópica. El objetivo principal es la construcción de una vivienda temporal formada por elementos prefabricados, logrando así una mayor rapidez en su montaje. Esto también permitirá que cualquier component...

  18. Transcriptional Regulation in Haematopoiesis:

    DEFF Research Database (Denmark)

    Lauridsen, Felicia K B

    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...... 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...... study we profiled the global DNA binding sites of two major players in myeloid differentiation – PU.1 and C/EBPα - together with histone modifications in four successive stages of myeloid differentiation (LSK, preGM, GMP and mature granulocytes). Consistent with their haematopoietic expression patterns...

  19. Exploration into the spatial and temporal mechanisms of bacterial polarity

    DEFF Research Database (Denmark)

    Ebersbach, Gitte; Jacobs-Wagner, Christine; Charbon, Gitte Ebersbach

    2007-01-01

    The recognition of bacterial asymmetry is not new: the first high-resolution microscopy studies revealed that bacteria come in a multitude of shapes and sometimes carry asymmetrically localized external structures such as flagella on the cell surface. Even so, the idea that bacteria could have...... an inherent overall polarity, which affects not only their outer appearance but also many of their vital processes, has only recently been appreciated. In this review, we focus on recent advances in our understanding of the molecular mechanisms underlying the establishment of polarized functions and cell...

  20. Euglena Transcript Processing.

    Science.gov (United States)

    McWatters, David C; Russell, Anthony G

    2017-01-01

    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.

  1. Marking Time, Making Methods: Temporality and Untimely Dilemmas in the Sociology of Youth and Educational Change

    Science.gov (United States)

    McLeod, Julie

    2017-01-01

    This article explores how temporality and temporal regimes might be engaged in qualitative research in the sociology of education, proposing that such questions matter in relation to how research is done, not only to the topics and themes researched. The article shows how temporality enters into research designs, practices and imaginaries, arguing…

  2. Space exploration

    National Research Council Canada - National Science Library

    Chris Moore

    2012-01-01

      Here, Moore presents a year in review on space exploration programs. This 2012 NASA's strategy of stimulating the development of commercial capabilities to launch crew and cargo to the ISS began to pay off...

  3. Promoter-mediated transcriptional dynamics.

    Science.gov (United States)

    Zhang, Jiajun; Zhou, Tianshou

    2014-01-21

    Genes in eukaryotic cells are typically regulated by complex promoters containing multiple binding sites for a variety of transcription factors, but how promoter dynamics affect transcriptional dynamics has remained poorly understood. In this study, we analyze gene models at the transcriptional regulation level, which incorporate the complexity of promoter structure (PS) defined as transcriptional exits (i.e., ON states of the promoter) and the transition pattern (described by a matrix consisting of transition rates among promoter activity states). We show that multiple exits of transcription are the essential origin of generating multimodal distributions of mRNA, but promoters with the same transition pattern can lead to multimodality of different modes, depending on the regulation of transcriptional factors. In turn, for similar mRNA distributions in the models, the mean ON or OFF time distributions may exhibit different characteristics, thus providing the supplemental information on PS. In addition, we demonstrate that the transcriptional noise can be characterized by a nonlinear function of mean ON and OFF times. These results not only reveal essential characteristics of promoter-mediated transcriptional dynamics but also provide signatures useful for inferring PS based on characteristics of transcriptional outputs. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. The post-transcriptional operon

    DEFF Research Database (Denmark)

    2011-01-01

    A post-transcriptional operon is a set of monocistronic mRNAs encoding functionally related proteins that are co-regulated by a group of RNA-binding proteins and/or small non-coding RNAs so that protein expression is coordinated at the post-transcriptional level. The post-transcriptional operon...... 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...

  5. Characterizing dynamic changes in the human blood transcriptional network.

    Directory of Open Access Journals (Sweden)

    Jun Zhu

    2010-02-01

    Full Text Available Gene expression data generated systematically in a given system over multiple time points provides a source of perturbation that can be leveraged to infer causal relationships among genes explaining network changes. Previously, we showed that food intake has a large impact on blood gene expression patterns and that these responses, either in terms of gene expression level or gene-gene connectivity, are strongly associated with metabolic diseases. In this study, we explored which genes drive the changes of gene expression patterns in response to time and food intake. We applied the Granger causality test and the dynamic Bayesian network to gene expression data generated from blood samples collected at multiple time points during the course of a day. The simulation result shows that combining many short time series together is as powerful to infer Granger causality as using a single long time series. Using the Granger causality test, we identified genes that were supported as the most likely causal candidates for the coordinated temporal changes in the network. These results show that PER1 is a key regulator of the blood transcriptional network, in which multiple biological processes are under circadian rhythm regulation. The fasted and fed dynamic Bayesian networks showed that over 72% of dynamic connections are self links. Finally, we show that different processes such as inflammation and lipid metabolism, which are disconnected in the static network, become dynamically linked in response to food intake, which would suggest that increasing nutritional load leads to coordinate regulation of these biological processes. In conclusion, our results suggest that food intake has a profound impact on the dynamic co-regulation of multiple biological processes, such as metabolism, immune response, apoptosis and circadian rhythm. The results could have broader implications for the design of studies of disease association and drug response in clinical

  6. Temporal compressive sensing systems

    Energy Technology Data Exchange (ETDEWEB)

    Reed, Bryan W.

    2017-12-12

    Methods and systems for temporal compressive sensing are disclosed, where within each of one or more sensor array data acquisition periods, one or more sensor array measurement datasets comprising distinct linear combinations of time slice data are acquired, and where mathematical reconstruction allows for calculation of accurate representations of the individual time slice datasets.

  7. Temporal Concurrent Constraint Programming

    DEFF Research Database (Denmark)

    Nielsen, Mogens; Palamidessi, Catuscia; Valencia, Frank Dan

    2002-01-01

    The ntcc calculus is a model of non-deterministic temporal concurrent constraint programming. In this paper we study behavioral notions for this calculus. In the underlying computational model, concurrent constraint processes are executed in discrete time intervals. The behavioral notions studied...

  8. Temporal Concurrent Constraint Programming

    DEFF Research Database (Denmark)

    Valencia, Frank Dan

    Concurrent constraint programming (ccp) is a formalism for concurrency in which agents interact with one another by telling (adding) and asking (reading) information in a shared medium. Temporal ccp extends ccp by allowing agents to be constrained by time conditions. This dissertation studies...

  9. Mesial temporal sclerosis

    African Journals Online (AJOL)

    Kurt

    2005-07-29

    Jul 29, 2005 ... Introduction. Mesial temporal sclerosis is the commonest cause of partial complex seizures. The aetiology of this condi- tion is controversial, but it is postulat- ed that both acquired and develop- mental processes may be involved. Familial cases have also been reported. Magnetic resonance imaging. (MRI) ...

  10. Temporal bone imaging

    Energy Technology Data Exchange (ETDEWEB)

    Lemmerling, Marc [Algemeen Ziekenhuis Sint-Lucas, Gent (Belgium). Dept. of Radiology; Foer, Bert de (ed.) [Sint-Augustinus Ziekenhuis, Wilrijk (Belgium). Dept. of Radiology

    2015-04-01

    Complete overview of imaging of normal and diseased temporal bone. Straightforward structure to facilitate learning. Detailed consideration of newer imaging techniques, including the hot topic of diffusion-weighted imaging. Includes a chapter on anatomy that will be of great help to the novice interpreter of imaging findings. Excellent illustrations throughout. This book provides a complete overview of imaging of normal and diseased temporal bone. After description of indications for imaging and the cross-sectional imaging anatomy of the area, subsequent chapters address the various diseases and conditions that affect the temporal bone and are likely to be encountered regularly in clinical practice. The classic imaging methods are described and discussed in detail, and individual chapters are included on newer techniques such as functional imaging and diffusion-weighted imaging. There is also a strong focus on postoperative imaging. Throughout, imaging findings are documented with the aid of numerous informative, high-quality illustrations. Temporal Bone Imaging, with its straightforward structure based essentially on topography, will prove of immense value in daily practice.

  11. Communication, Technology, Temporality

    Directory of Open Access Journals (Sweden)

    Mark A. Martinez

    2012-08-01

    Full Text Available This paper proposes a media studies that foregrounds technological objects as communicative and historical agents. Specifically, I take the digital computer as a powerful catalyst of crises in communication theories and certain key features of modernity. Finally, the computer is the motor of “New Media” which is at once a set of technologies, a historical epoch, and a field of knowledge. As such the computer shapes “the new” and “the future” as History pushes its origins further in the past and its convergent quality pushes its future as a predominate medium. As treatment of information and interface suggest, communication theories observe computers, and technologies generally, for the mediated languages they either afford or foreclose to us. My project describes the figures information and interface for the different ways they can be thought of as aspects of communication. I treat information not as semantic meaning, formal or discursive language, but rather as a physical organism. Similarly an interface is not a relationship between a screen and a human visual intelligence, but is instead a reciprocal, affective and physical process of contact. I illustrate that historically there have been conceptions of information and interface complimentary to mine, fleeting as they have been in the face of a dominant temporality of mediation. I begin with a theoretically informed approach to media history, and extend it to a new theory of communication. In doing so I discuss a model of time common to popular, scientific, and critical conceptions of media technologies especially in theories of computer technology. This is a predominate model with particular rules of temporal change and causality for thinking about mediation, and limits the conditions of possibility for knowledge production about communication. I suggest a new model of time as integral to any event of observation and analysis, and that human mediation does not exhaust the

  12. Preparing for opening night: temporal boundary objects in textually-mediated professional practice

    Directory of Open Access Journals (Sweden)

    Elisabeth Davies

    2004-01-01

    Full Text Available The authors report on two projects in which the role of documents as temporal boundary objects mediating information practices across multiple timelines was explored. It has been suggested that studying workplace documents will uncover the information practices of professionals beyond traditional information needs and uses studies. Two workplaces were studied: a professional theatre production and a midwifery clinic. Both settings are communities constructed partly through textual dynamics and both have a pre-production phase leading to an opening night. In the theatre setting, qualitative interviews with the cast and crew and document analysis of the prompt book were the means of data collection. The midwifery clinic setting was investigated by means of interviews and follow-ups with sixteen midwife-client pairs and document analysis of the antenatal record. Preliminary thematic analysis pertaining to time and information was conducted on interview transcripts and the relevant documents. It was possible to show several instances of both the prompt book and the antenatal record being treated as a timeline by the various professionals using them. The authors conclude with a discussion of the temporal aspects of professionals' information practices as revealed by these two projects and encourage further document-focused research.

  13. Synthetic transcription elongation factors license transcription across repressive chromatin.

    Science.gov (United States)

    Erwin, Graham S; Grieshop, Matthew P; Ali, Asfa; Qi, Jun; Lawlor, Matthew; Kumar, Deepak; Ahmad, Istaq; McNally, Anna; Teider, Natalia; Worringer, Katie; Sivasankaran, Rajeev; Syed, Deeba N; Eguchi, Asuka; Ashraf, Md; Jeffery, Justin; Xu, Mousheng; Park, Paul M C; Mukhtar, Hasan; Srivastava, Achal K; Faruq, Mohammed; Bradner, James E; Ansari, Aseem Z

    2017-11-30

    Releasing a paused RNA polymerase II into productive elongation is tightly-regulated, especially at genes that impact human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators. We present Syn-TEF1, a molecule that actively enables transcription across repressive GAA repeats that silence frataxin expression in Friedreich's ataxia, a terminal neurodegenerative disease with no effective therapy. Furthermore, the modular design of Syn-TEF1 defines a general framework for developing a class of molecules that license transcription elongation at targeted genomic loci. Copyright © 2017, American Association for the Advancement of Science.

  14. Subgenic Pol II interactomes identify region-specific transcription elongation regulators.

    Science.gov (United States)

    Harlen, Kevin M; Churchman, L Stirling

    2017-01-02

    Transcription, RNA processing, and chromatin-related factors all interact with RNA polymerase II (Pol II) to ensure proper timing and coordination of transcription and co-transcriptional processes. Many transcription elongation regulators must function simultaneously to coordinate these processes, yet few strategies exist to explore the complement of factors regulating specific stages of transcription. To this end, we developed a strategy to purify Pol II elongation complexes from subgenic regions of a single gene, namely the 5' and 3' regions, using sequences in the nascent RNA. Applying this strategy to Saccharomyces cerevisiae, we determined the specific set of factors that interact with Pol II at precise stages during transcription. We identify many known region-specific factors as well as determine unappreciated associations of regulatory factors during early and late stages of transcription. These data reveal a role for the transcription termination factor, Rai1, in regulating the early stages of transcription genome-wide and support the role of Bye1 as a negative regulator of early elongation. We also demonstrate a role for the ubiquitin ligase, Bre1, in regulating Pol II dynamics during the latter stages of transcription. These data and our approach to analyze subgenic transcription elongation complexes will shed new light on the myriad factors that regulate the different stages of transcription and coordinate co-transcriptional processes. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

  15. Coordinated Evolution of Transcriptional and Post-Transcriptional Regulation for Mitochondrial Functions in Yeast Strains.

    Directory of Open Access Journals (Sweden)

    Xuepeng Sun

    Full Text Available Evolution of gene regulation has been proposed to play an important role in environmental adaptation. Exploring mechanisms underlying coordinated evolutionary changes at various levels of gene regulation could shed new light on how organism adapt in nature. In this study, we focused on regulatory differences between a laboratory Saccharomyces cerevisiae strain BY4742 and a pathogenic S. cerevisiae strain, YJM789. The two strains diverge in many features, including growth rate, morphology, high temperature tolerance, and pathogenicity. Our RNA-Seq and ribosomal footprint profiling data showed that gene expression differences are pervasive, and genes functioning in mitochondria are mostly divergent between the two strains at both transcriptional and translational levels. Combining functional genomics data from other yeast strains, we further demonstrated that significant divergence of expression for genes functioning in the electron transport chain (ETC was likely caused by differential expression of a transcriptional factor, HAP4, and that post-transcriptional regulation mediated by an RNA-binding protein, PUF3, likely led to expression divergence for genes involved in mitochondrial translation. We also explored mito-nuclear interactions via mitochondrial DNA replacement between strains. Although the two mitochondrial genomes harbor substantial sequence divergence, neither growth nor gene expression were affected by mitochondrial DNA replacement in both fermentative and respiratory growth media, indicating compatible mitochondrial and nuclear genomes between these two strains in the tested conditions. Collectively, we used mitochondrial functions as an example to demonstrate for the first time that evolution at both transcriptional and post-transcriptional levels could lead to coordinated regulatory changes underlying strain specific functional variations.

  16. Isolation, classification and transcription profiles of the AP2/ERF transcription factor superfamily in citrus.

    Science.gov (United States)

    Xie, Xiu-lan; Shen, Shu-ling; Yin, Xue-ren; Xu, Qian; Sun, Chong-de; Grierson, Donald; Ferguson, Ian; Chen, Kun-song

    2014-07-01

    The AP2/ERF gene family encodes plant-specific transcription factors. In model plants, AP2/ERF genes have been shown to be expressed in response to developmental and environmental stimuli, and many function downstream of the ethylene, biotic, and abiotic stress signaling pathways. In citrus, ethylene is effective in regulation citrus fruit quality, such as degreening and aroma. However, information about the citrus AP2/ERF family is limited, and would enhance our understanding of fruit responses to environmental stress, fruit development and quality. CitAP2/ERF genes were isolated using the citrus genome database, and their expression patterns analyzed by real-time PCR using various orange organs and samples from a fruit developmental series. 126 sequences with homologies to AP2/ERF proteins were identified from the citrus genome, and, on the basis of their structure and sequence, assigned to the ERF family (102), AP2 family (18), RAV family (4) and Soloist (2). MEME motif analysis predicted the defining AP2/ERF domain and EAR repressor domains. Analysis of transcript accumulation in Citrus sinensis cv. 'Newhall' indicated that CitAP2/ERF genes show organ-specific and temporal expression, and provided a framework for understanding the transcriptional regulatory roles of AP2/ERF gene family members in citrus. Hierarchical cluster analysis and t tests identified regulators that potentially function during orange fruit growth and development.

  17. Farside explorer

    DEFF Research Database (Denmark)

    Mimoun, David; Wieczorek, Mark A.; Alkalai, Leon

    2012-01-01

    Farside Explorer is a proposed Cosmic Vision medium-size mission to the farside of the Moon consisting of two landers and an instrumented relay satellite. The farside of the Moon is a unique scientific platform in that it is shielded from terrestrial radio-frequency interference, it recorded...... the primary differentiation and evolution of the Moon, it can be continuously monitored from the Earth-Moon L2 Lagrange point, and there is a complete lack of reflected solar illumination from the Earth. Farside Explorer will exploit these properties and make the first radio-astronomy measurements from...... the most radio-quiet region of near-Earth space, determine the internal structure and thermal evolution of the Moon, from crust to core, and quantify impact hazards in near-Earth space by the measurement of flashes generated by impact events. The Farside Explorer flight system includes two identical solar...

  18. Adaptation with transcriptional regulation

    Science.gov (United States)

    Shi, Wenjia; Ma, Wenzhe; Xiong, Liyang; Zhang, Mingyue; Tang, Chao

    2017-02-01

    Biochemical adaptation is one of the basic functions that are widely implemented in biological systems for a variety of purposes such as signal sensing, stress response and homeostasis. The adaptation time scales span from milliseconds to days, involving different regulatory machineries in different processes. The adaptive networks with enzymatic regulation (ERNs) have been investigated in detail. But it remains unclear if and how other forms of regulation will impact the network topology and other features of the function. Here, we systematically studied three-node transcriptional regulatory networks (TRNs), with three different types of gene regulation logics. We found that the topologies of adaptive gene regulatory networks can still be grouped into two general classes: negative feedback loop (NFBL) and incoherent feed-forward loop (IFFL), but with some distinct topological features comparing to the enzymatic networks. Specifically, an auto-activation loop on the buffer node is necessary for the NFBL class. For IFFL class, the control node can be either a proportional node or an inversely-proportional node. Furthermore, the tunability of adaptive behavior differs between TRNs and ERNs. Our findings highlight the role of regulation forms in network topology, implementation and dynamics.

  19. Dynamic usage of transcription start sites within core promoters

    DEFF Research Database (Denmark)

    Kawaji, Hideya; Frith, Martin C; Katayama, Shintaro

    2006-01-01

    BACKGROUND: Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously characterized the static structures of transcription start site usage within promoters at the base pair level......, based on large-scale sequencing of transcript 5' ends. RESULTS: In the present study we begin to explore the internal dynamics of mammalian promoters, and demonstrate that start site selection within many mouse core promoters varies among tissues. We also show that this dynamic usage of start sites...... is associated with CpG islands, broad and multimodal promoter structures, and imprinting. CONCLUSION: Our results reveal a new level of biologic complexity within promoters--fine-scale regulation of transcription starting events at the base pair level. These events are likely to be related to epigenetic...

  20. First Exon Length Controls Active Chromatin Signatures and Transcription

    Directory of Open Access Journals (Sweden)

    Nicole I. Bieberstein

    2012-07-01

    Full Text Available Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

  1. Discontent with content analysis of online transcripts

    Directory of Open Access Journals (Sweden)

    Judith Guevarra Enriquez

    2009-12-01

    Full Text Available Content analysis has dominated computer-mediated communication and educational technology studies for some time, and a review of its practices applied to online corpus of data or messages is overdue. We are confronted with complexity given the various foci, nuances and models for theorising learning and applying methods. One common suggestion to deal with the complexity in content analysis is a call for standardisation by replication or systematic research studies. This article presents its ‘discontent' with content analysis, discussing the issues and concerns that surround the analysis of online transcripts. It does not attempt to resolve nor provide a definitive answer. Instead, it is an open inquiry into another way of looking at online content. It presents an alternative or perhaps an extension of what we have come to know as content analysis. It argues for the notion of genres as another way of conceptualising online transcripts. It proposes two things: first that in performing transcript analysis, it is worthwhile to think how messages relate to a system of interactions that persists even beyond the online environment; secondly, there is an emergent and recurring metastructuring that is at work in online environments that is worth exploring, instead of imposing structures – models and frameworks that do not fit the emerging communicative practices of participants.

  2. Mitotic bookmarking by transcription factors.

    Science.gov (United States)

    Kadauke, Stephan; Blobel, Gerd A

    2013-04-02

    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.

  3. Temporal lobe epilepsy semiology.

    Science.gov (United States)

    Blair, Robert D G

    2012-01-01

    Epilepsy represents a multifaceted group of disorders divided into two broad categories, partial and generalized, based on the seizure onset zone. The identification of the neuroanatomic site of seizure onset depends on delineation of seizure semiology by a careful history together with video-EEG, and a variety of neuroimaging technologies such as MRI, fMRI, FDG-PET, MEG, or invasive intracranial EEG recording. Temporal lobe epilepsy (TLE) is the commonest form of focal epilepsy and represents almost 2/3 of cases of intractable epilepsy managed surgically. A history of febrile seizures (especially complex febrile seizures) is common in TLE and is frequently associated with mesial temporal sclerosis (the commonest form of TLE). Seizure auras occur in many TLE patients and often exhibit features that are relatively specific for TLE but few are of lateralizing value. Automatisms, however, often have lateralizing significance. Careful study of seizure semiology remains invaluable in addressing the search for the seizure onset zone.

  4. Different Phases of Long-Term Memory Require Distinct Temporal Patterns of PKA Activity after Single-Trial Classical Conditioning

    Science.gov (United States)

    Michel, Maximilian; Kemenes, Ildiko; Muller, Uli; Kemenes, Gyorgy

    2008-01-01

    The cAMP-dependent protein kinase (PKA) is known to play a critical role in both transcription-independent short-term or intermediate-term memory and transcription-dependent long-term memory (LTM). Although distinct phases of LTM already have been demonstrated in some systems, it is not known whether these phases require distinct temporal patterns…

  5. Transcriptional regulation of inflammatory genes associated with severe asthma.

    Science.gov (United States)

    Clifford, Rachel L; Coward, William R; Knox, Alan J; John, Alison E

    2011-01-01

    The 10% of patients with the most severe asthma are responsible for a large part of healthcare expenditure and morbidity. Understanding the processes involved is key if new therapeutic approaches are to be developed. Evidence is accumulating that chronic diseases such as asthma are associated with temporal and spatial alterations in the pattern of inflammatory gene expression within the airways. Expression of these genes can be regulated by transcriptional, posttranscriptional, translational and epigenetic mechanisms. It is well established that binding of activated transcription factors to specific inducible gene promoter sites is tightly controlled by chromatin state as a result of histone modifications, particularly the balance between histone acetylation and deacetylation [1]. The interaction between transcription factors and the promoter is key to the diversification of gene expression in a time dependent manner leading to altered gene expression profiles. Alterations of the accessibility of transcription factors to the DNA can have residing effects upon gene transcription. This review will focus on the regulation of several groups of key genes which are involved in chronic airway inflammation and remodelling in asthma drawing mainly from our experience of studying these processes in airway smooth muscle cells. An overview is shown in figure 1.

  6. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

    Directory of Open Access Journals (Sweden)

    Nick D.L. Owens

    2016-01-01

    Full Text Available Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions. By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude. Ordering genes by expression dynamics, we find that “temporal synexpression” predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.

  7. 7 CFR 614.12 - Transcripts.

    Science.gov (United States)

    2010-01-01

    ... verbatim transcript must pay for the transcription service and provide a copy of the transcript to NRCS at... participant may obtain a verbatim transcript as provided in paragraph (b) of this section. (b) Any party to an informal hearing appeal under § 614.9 may request that a verbatim transcript is made of the hearing...

  8. Exploring quadrangulations

    KAUST Repository

    Peng, Chihan

    2014-01-01

    Here we presented a framework to explore quad mesh topologies. The core of our work is a systematic enumeration algorithm that can generate all possible quadrangular meshes inside a defined boundary with an upper limit of v3-v5 pairs. The algorithm is orders of magnitude more efficient than previous work. The combination of topological enumeration and shape-space exploration demonstrates that mesh topology has a powerful influence on geometry. The Fig. 18. A gallery of different quadrilateral meshes for a Shuriken. The quadrilaterals of the model were colored in a postprocess. Topological variations have distinctive, interesting patterns of mesh lines. © 2014 ACM 0730-0301/2014/01-ART3 15.00.

  9. Tc-MYBPA an Arabidopsis TT2-like transcription factor and functions in the regulation of proanthocyanidin synthesis in Theobroma cacao.

    Science.gov (United States)

    Liu, Yi; Shi, Zi; Maximova, Siela N; Payne, Mark J; Guiltinan, Mark J

    2015-06-25

    The flavan-3-ols catechin and epicatechin, and their polymerized oligomers, the proanthocyanidins (PAs, also called condensed tannins), accumulate to levels of up to 15 % of the total weight of dry seeds of Theobroma cacao L. These compounds have been associated with several health benefits in humans. They also play important roles in pest and disease defense throughout the plant. In Arabidopsis, the R2R3 type MYB transcription factor TT2 regulates the major genes leading to the synthesis of PA. To explore the transcriptional regulation of the PA synthesis pathway in cacao, we isolated and characterized an R2R3 type MYB transcription factor MYBPA from cacao. We examined the spatial and temporal gene expression patterns of the Tc-MYBPA gene and found it to be developmentally expressed in a manner consistent with its involvement in PAs and anthocyanin synthesis. Functional complementation of an Arabidopsis tt2 mutant with Tc-MYBPA suggested that it can functionally substitute the Arabidopsis TT2 gene. Interestingly, in addition to PA accumulation in seeds of the Tc-MYBPA expressing plants, we also observed an obvious increase of anthocyanidin accumulation in hypocotyls. We observed that overexpression of the Tc-MYBPA gene resulted in increased expression of several key genes encoding the major structural enzymes of the PA and anthocyanidin pathway, including DFR (dihydroflavanol reductase), LDOX (leucoanthocyanidin dioxygenase) and BAN (ANR, anthocyanidin reductase). We conclude that the Tc-MYBPA gene that encodes an R2R3 type MYB transcription factor is an Arabidopsis TT2 like transcription factor, and may be involved in the regulation of both anthocyanin and PA synthesis in cacao. This research may provide molecular tools for breeding of cacao varieties with improved disease resistance and enhanced flavonoid profiles for nutritional and pharmaceutical applications.

  10. Transcriptional regulation of flavonoid biosynthesis in nectarine (Prunus persica) by a set of R2R3 MYB transcription factors.

    Science.gov (United States)

    Ravaglia, Daniela; Espley, Richard V; Henry-Kirk, Rebecca A; Andreotti, Carlo; Ziosi, Vanina; Hellens, Roger P; Costa, Guglielmo; Allan, Andrew C

    2013-04-25

    Flavonoids such as anthocyanins, flavonols and proanthocyanidins, play a central role in fruit colour, flavour and health attributes. In peach and nectarine (Prunus persica) these compounds vary during fruit growth and ripening. Flavonoids are produced by a well studied pathway which is transcriptionally regulated by members of the MYB and bHLH transcription factor families. We have isolated nectarine flavonoid regulating genes and examined their expression patterns, which suggests a critical role in the regulation of flavonoid biosynthesis. In nectarine, expression of the genes encoding enzymes of the flavonoid pathway correlated with the concentration of proanthocyanidins, which strongly increases at mid-development. In contrast, the only gene which showed a similar pattern to anthocyanin concentration was UDP-glucose-flavonoid-3-O-glucosyltransferase (UFGT), which was high at the beginning and end of fruit growth, remaining low during the other developmental stages. Expression of flavonol synthase (FLS1) correlated with flavonol levels, both temporally and in a tissue specific manner. The pattern of UFGT gene expression may be explained by the involvement of different transcription factors, which up-regulate flavonoid biosynthesis (MYB10, MYB123, and bHLH3), or repress (MYB111 and MYB16) the transcription of the biosynthetic genes. The expression of a potential proanthocyanidin-regulating transcription factor, MYBPA1, corresponded with proanthocyanidin levels. Functional assays of these transcription factors were used to test the specificity for flavonoid regulation. MYB10 positively regulates the promoters of UFGT and dihydroflavonol 4-reductase (DFR) but not leucoanthocyanidin reductase (LAR). In contrast, MYBPA1 trans-activates the promoters of DFR and LAR, but not UFGT. This suggests exclusive roles of anthocyanin regulation by MYB10 and proanthocyanidin regulation by MYBPA1. Further, these transcription factors appeared to be responsive to both

  11. Traverse Planning with Temporal-Spatial Constraints

    Science.gov (United States)

    Bresina, John L.; Morris, Paul H.; Deans, Mathew C.; Cohen, Tamar E.; Lees, David S.

    2017-01-01

    We present an approach to planning rover traverses in a domain that includes temporal-spatial constraints. We are using the NASA Resource Prospector mission as a reference mission in our research. The objective of this mission is to explore permanently shadowed regions at a Lunar pole. Most of the time the rover is required to avoid being in shadow. This requirement depends on where the rover is located and when it is at that location. Such a temporal-spatial constraint makes traverse planning more challenging for both humans and machines. We present a mixed-initiative traverse planner which addresses this challenge. This traverse planner is part of the Exploration Ground Data Systems (xGDS), which we have enhanced with new visualization features, new analysis tools, and new automation for path planning, in order to be applicable to the Re-source Prospector mission. The key concept that is the basis of the analysis tools and that supports the automated path planning is reachability in this dynamic environment due to the temporal-spatial constraints.

  12. Differential turnover of the multiple processed transcripts of the Escherichia coli focA-pflB operon.

    Science.gov (United States)

    Sawers, R Gary

    2006-08-01

    the focA-pflB operon was restricted to exponentially growing cells. Expression of transcript 7 peaked in early to mid-exponential phase, while the levels of transcript 6 steadily accumulated toward the late-exponential phase of growth. Taken together, these findings indicate that although subject to common positive control by ArcA approximately P and FNR, the transcripts generated by promoters 6 and 7 are subject to differential temporal and post-transcriptional regulation.

  13. Longitudinal evaluation of leukocyte transcripts in killer whales (Orcinus Orca).

    Science.gov (United States)

    Sitt, Tatjana; Bowen, Lizabeth; Lee, Chia-Shan; Blanchard, Myra T; McBain, James; Dold, Christopher; Stott, Jeffrey L

    2016-07-01

    Early identification of illness and/or presence of environmental and/or social stressors in free-ranging and domestic cetaceans is a priority for marine mammal health care professionals. Incorporation of leukocyte gene transcript analysis into the diagnostic tool kit has the potential to augment classical diagnostics based upon ease of sample storage and shipment, inducible nature and well-defined roles of transcription and associated downstream actions. Development of biomarkers that could serve to identify "insults" and potentially differentiate disease etiology would be of great diagnostic value. To this end, a modest number of peripheral blood leukocyte gene transcripts were selected for application to a domestic killer whale population with a focus on broad representation of inducible immunologically relevant genes. Normalized leukocyte transcript values, longitudinally acquired from 232 blood samples derived from 26 clinically healthy whales, were not visibly influenced temporally nor by sex or the specific Park in which they resided. Stability in leukocyte transcript number during periods of health enhances their potential use in diagnostics through identification of outliers. Transcript levels of two cytokine genes, IL-4 and IL-17, were highly variable within the group as compared to the other transcripts. IL-4 transcripts were typically absent. Analysis of transcript levels on the other genes of interest, on an individual animal basis, identified more outliers than were visible when analyzed in the context of the entire population. The majority of outliers (9 samples) were low, though elevated transcripts were identified for IL-17 from 2 animals and one each for Cox-2 and IL-10. The low number of outliers was not unexpected as sample selection was intentionally directed towards animals that were clinically healthy at the time of collection. Outliers may reflect animals experiencing subclinical disease that is transient and self-limiting. The immunologic

  14. Longitudinal evaluation of leukocyte transcripts in killer whales (Orcinus Orca)

    Science.gov (United States)

    Sitt, Tatjana; Bowen, Lizabeth; Lee, Chia-Shan; Blanchard, Myra; McBain, James; Dold, Christopher; Stott, Jeffrey L.

    2016-01-01

    Early identification of illness and/or presence of environmental and/or social stressors in free-ranging and domestic cetaceans is a priority for marine mammal health care professionals. Incorporation of leukocyte gene transcript analysis into the diagnostic tool kit has the potential to augment classical diagnostics based upon ease of sample storage and shipment, inducible nature and well-defined roles of transcription and associated downstream actions. Development of biomarkers that could serve to identify “insults” and potentially differentiate disease etiology would be of great diagnostic value. To this end, a modest number of peripheral blood leukocyte gene transcripts were selected for application to a domestic killer whale population with a focus on broad representation of inducible immunologically relevant genes. Normalized leukocyte transcript values, longitudinally acquired from 232 blood samples derived from 26 clinically healthy whales, were not visibly influenced temporally nor by sex or the specific Park in which they resided. Stability in leukocyte transcript number during periods of health enhances their potential use in diagnostics through identification of outliers. Transcript levels of two cytokine genes, IL-4 and IL-17, were highly variable within the group as compared to the other transcripts. IL-4 transcripts were typically absent. Analysis of transcript levels on the other genes of interest, on an individual animal basis, identified more outliers than were visible when analyzed in the context of the entire population. The majority of outliers (9 samples) were low, though elevated transcripts were identified for IL-17 from 2 animals and one each for Cox-2 and IL-10. The low number of outliers was not unexpected as sample selection was intentionally directed towards animals that were clinically healthy at the time of collection. Outliers may reflect animals experiencing subclinical disease that is transient and self-limiting. The

  15. RNA-guided transcriptional regulation

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-23

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

  16. Spatio-Temporal Rule Mining

    DEFF Research Database (Denmark)

    Gidofalvi, Gyozo; Pedersen, Torben Bach

    2005-01-01

    Recent advances in communication and information technology, such as the increasing accuracy of GPS technology and the miniaturization of wireless communication devices pave the road for Location-Based Services (LBS). To achieve high quality for such services, spatio-temporal data mining techniques...... are needed. In this paper, we describe experiences with spatio-temporal rule mining in a Danish data mining company. First, a number of real world spatio-temporal data sets are described, leading to a taxonomy of spatio-temporal data. Second, the paper describes a general methodology that transforms...... the spatio-temporal rule mining task to the traditional market basket analysis task and applies it to the described data sets, enabling traditional association rule mining methods to discover spatio-temporal rules for LBS. Finally, unique issues in spatio-temporal rule mining are identified and discussed....

  17. Endometrial transcriptional profiling of a bovine fertility model by Next-Generation Sequencing

    Directory of Open Access Journals (Sweden)

    F.S. Mesquita

    2016-03-01

    Full Text Available Studying the multitude of molecular networks and pathways that are potentially involved in a complex trait such as fertility requires an equally complex and broad strategy. Here, we used Next-Generation Sequencing for the characterization of the transcriptional signature of the bovine endometrial tissue. Periovulatory endocrine environments were manipulated to generate two distinctly different fertility phenotypes. Cycling, non-lactating, multiparous Nelore cows were manipulated to ovulate larger (>13 mm; LF group; high fertility phenotype or smaller (<12 mm; SF group follicles. As a result, greater proestrus estrogen concentrations, corpora lutea and early diestrus progesterone concentrations were also observed in LF group in comparison to SF group. Endometrial cell proliferation was estimated by the protein marker MKI67 on tissues collected 4 (D4 and 7 (D7 days after induction of ovulation. Total RNA extracts from D7 were sequenced and compared according to the transcriptional profile of each experimental group (LF versus SF. Functional enrichment analysis revealed that LF and SF endometria were asynchronous in regards to their phenotype manifestation. Major findings indicated an LF endometrium that was switching phenotypes earlier than the SF one. More specifically, a proliferating SF endometrium was observed on D7, whereas the LF tissue, which expressed a proliferative phenotype earlier at D4, seemed to have already shifted towards a biosynthetically and metabolically active endometrium on D7. Data on MKI67 support the transcriptomic results. RNA-Seq-derived transcriptional profile of the endometrial tissue indicated a temporal effect of the periovulatory endocrine environment, suggesting that the moment of the endometrial exposure to the ovarian steroids, E2 and P4, regulates the timing of phenotype manifestation. Gene expression profiling revealed molecules that may be targeted to elucidate ovarian steroid-dependent mechanisms that

  18. Transcript Analysis of Stem Cells

    OpenAIRE

    Alison V. Nairn; Rosa, Mitche dela; Moremen, Kelley W.

    2010-01-01

    Quantitative real-time polymerase chain reaction (qRT-PCR) is a flexible and scalable method for analyzing transcript abundance that can be used at a single gene or high-throughput (>100 genes) level. Information obtained from this technique can be used as an indicator of potential regulation of glycosylation at the transcript level when combined with glycan structural or protein abundance data. This chapter describes detailed methods to design and perform qRT-PCR analyses and provides exampl...

  19. Space exploration

    CERN Document Server

    2009-01-01

    Space Exploration, is one book in the Britannica Illustrated Science Library Series that is correlated to the science curriculum in grades 5-8. The Britannica Illustrated Science Library is a visually compelling set that covers earth science, life science, and physical science in 16 volumes.  Created for ages 10 and up, each volume provides an overview on a subject and thoroughly explains it through detailed and powerful graphics-more than 1,000 per volume-that turn complex subjects into information that students can grasp.  Each volume contains a glossary with full definitions for vocabulary help and an index.

  20. Text Dependent Speaker Verification Using Un-supervised HMM-UBM and Temporal GMM-UBM

    DEFF Research Database (Denmark)

    Sarkar, Achintya Kumar; Tan, Zheng-Hua

    2016-01-01

    In this paper, we investigate the Hidden Markov Model (HMM) and the temporal Gaussian Mixture Model (GMM) systems based on the Universal Background Model (UBM) concept to capture temporal information of speech for Text Dependent (TD) Speaker Verification (SV). In TD-SV, target speakers...... are constrained to use only predefined fixed sentence/s during both the enrollment and the test process. The temporal information is therefore important in the sense of utterance verification, i.e. whether the test utterance has the same sequence of textual content as the utterance used during the target...... enrollment. However, the temporal information is not considered in the classical GMM-UBM based TD-SV system. Moreover, no transcription knowledge of the speech is required in the HMM-UBM and temporal GMM-UBM based systems. We also study the fusion of the HMM-UBM, the temporal GMM-UBM and the classical GMM...

  1. Neural correlates of audiovisual temporal processing--comparison of temporal order and simultaneity judgments.

    Science.gov (United States)

    Binder, M

    2015-08-06

    Multisensory integration is one of the essential features of perception. Though the processing of spatial information is an important clue to understand its mechanisms, a complete knowledge cannot be achieved without taking into account the processing of temporal information. Simultaneity judgments (SJs) and temporal order judgments (TOJs) are the two most widely used procedures for explicit estimation of temporal relations between sensory stimuli. Behavioral studies suggest that both tasks recruit different sets of cognitive operations. On the other hand, empirical evidence related to their neuronal underpinnings is still scarce, especially with regard to multisensory stimulation. The aim of the current fMRI study was to explore neural correlates of both tasks using paradigm with audiovisual stimuli. Fifteen subjects performed TOJ and SJ tasks grouped in 18-second blocks. Subjects were asked to estimate onset synchrony or temporal order of onsets of non-semantic auditory and visual stimuli. Common areas of activation elicited by both tasks were found in the bilateral fronto-parietal network, including regions whose activity can be also observed in tasks involving spatial selective attention. This can be regarded as an evidence for the hypothesis that tasks involving selection based on temporal information engage the similar regions as the attentional tasks based on spatial information. The direct contrast between the SJ task and the TOJ task did not reveal any regions showing stronger activity for SJ task than in TOJ task. The reverse contrast revealed a number of left hemisphere regions which were more active during the TOJ task than the SJ task. They were found in the prefrontal cortex, the parietal lobules (superior and inferior) and in the occipito-temporal regions. These results suggest that the TOJ task requires recruitment of additional cognitive operations in comparison to SJ task. They are probably associated with forming representations of stimuli as

  2. Genome maintenance and transcription integrity in ageing and disease

    Directory of Open Access Journals (Sweden)

    Stefanie eWolters

    2013-02-01

    Full Text Available DNA Damage contributes to cancer development and ageing. Congenital syndromes that affect DNA repair processes are characterized by cancer susceptibility, developmental defects, and accelerated ageing (Schumacher et al., 2008. DNA damage interferes with DNA metabolism by blocking replication and transcription. DNA polymerase blockage leads to replication arrest and can gives rise to genome instability. Transcription, on the other hand, is an essential process for utilizing the information encoded in the genome. DNA damage that interferes with transcription can lead to apoptosis and cellular senescence. Both processes are powerful tumor suppressors (Bartek and Lukas, 2007. Cellular response mechanisms to stalled RNA polymerase (RNAP II complexes have only recently started to be uncovered. Transcription-coupled DNA damage responses might thus play important roles for the adjustments to DNA damage accumulation in the ageing organism (Garinis et al., 2009. Here we review human disorders that are caused by defects in genome stability to explore the role of DNA damage in ageing and disease. We discuss how the nucleotide excision repair (NER system functions at the interface of transcription and repair and conclude with concepts how therapeutic targeting of transcription might be utilized in the treatment of cancer.

  3. Temporal Convergence for Knowledge Management

    Directory of Open Access Journals (Sweden)

    Christopher Phillip Martin

    2008-05-01

    Full Text Available Time and knowledge have tended to be conceptualised in conventional knowledge management systems as either ‘timeless’ recordings of procedures, or time-stamped records of past events and states. The concept of temporal convergence was previously developed to help apply knowledge-management theory to complex military processes such as commander’s intent, shared situation awareness, and self-synchronisation. This paper clarifies the concept and introduces several others in forming a framework to assist discussion and exploration of the types of knowledge required for complex endeavours, such as warfighting, characterised by opposition and uncertainty. The approach is grounded in a pragmatist philosophy and constructivist epistemology. Argument proceeds along mathematical lines from a basis that the types of knowledge most valuable to goal-directed agents in uncertain environments can be modelled as directed graph topologies. The framework is shown to be useful in describing and reasoning about the knowledge requirements and prerequisites for distributed decision-making through the sharing of situational knowledge and common intentions, with practical application to the planning and execution of operations. To the designers of knowledge management systems seeking to address this space, it presents a challenge that cannot be addressed merely by construction, storage, search and retrieval of documents and records pertaining to the past.

  4. Discovering metric temporal constraint networks on temporal databases.

    Science.gov (United States)

    Álvarez, Miguel R; Félix, Paulo; Cariñena, Purificación

    2013-07-01

    In this paper, we propose the ASTPminer algorithm for mining collections of time-stamped sequences to discover frequent temporal patterns, as represented in the simple temporal problem (STP) formalism: a representation of temporal knowledge as a set of event types and a set of metric temporal constraints among them. To focus the mining process, some initial knowledge can be provided by the user, also expressed as an STP, that acts as a seed pattern for the searching procedure. In this manner, the mining algorithm will search for those frequent temporal patterns consistent with the initial knowledge. Health organisations demand, for multiple areas of activity, new computational tools that will obtain new knowledge from huge collections of data. Temporal data mining has arisen as an active research field that provides new algorithms for discovering new temporal knowledge. An important point in defining different proposals is the expressiveness of the resulting temporal knowledge, which is commonly found in the bibliography in a qualitative form. ASTPminer develops an Apriori-like strategy in an iterative algorithm where, as a result of each iteration i, a set of frequent temporal patterns of size i is found that incorporates three distinctive mechanisms: (1) use of a clustering procedure over distributions of temporal distances between events to recognise similar occurrences as temporal patterns; (2) consistency checking of every combination of temporal patterns, which ensures the soundness of the resultant patterns; and (3) use of seed patterns to allow the user to drive the mining process. To validate our proposal, several experiments were conducted over a database of time-stamped sequences obtained from polysomnography tests in patients with sleep apnea-hypopnea syndrome. ASTPminer was able to extract well-known temporal patterns corresponding to different manifestations of the syndrome. Furthermore, the use of seed patterns resulted in a reduction in the size of

  5. Time matters: Temporal harmony and dissonance in nanotechnology networks

    DEFF Research Database (Denmark)

    Selin, Cynthia Lea

    2006-01-01

    the coding mediations that occur in the nanotechnology arena. The case of nanotechnology – due to its emergent properties, affinity with science fiction and inexhaustible promises – is taken up with an analytic exploration of network participants’ perspectives on time. Departing from empirical evidence...... within the nanotechnology arena, the focus is to explore the meanings and dilemmas implicated in disparate temporal horizons. Particular emphasis is placed on the effects of temporal diversity latent in discourses of the future as they relate to the formulation of a new technological domain....

  6. The ets-related transcription factor GABP directs bidirectional transcription.

    Directory of Open Access Journals (Sweden)

    Patrick J Collins

    2007-11-01

    Full Text Available Approximately 10% of genes in the human genome are distributed such that their transcription start sites are located less than 1 kb apart on opposite strands. These divergent gene pairs have a single intergenic segment of DNA, which in some cases appears to share regulatory elements, but it is unclear whether these regions represent functional bidirectional promoters or two overlapping promoters. A recent study showed that divergent promoters are enriched for consensus binding sequences of a small group of transcription factors, including the ubiquitous ets-family transcription factor GA-binding protein (GABP. Here we show that GABP binds to more than 80% of divergent promoters in at least one cell type. Furthermore, we demonstrate that GABP binding is correlated and associated with bidirectional transcriptional activity in a luciferase transfection assay. In addition, we find that the addition of a strict consensus GABP site into a set of promoters that normally function in only one direction significantly increases activity in the opposite direction in 67% of cases. Our findings demonstrate that GABP regulates the majority of divergent promoters and suggest that bidirectional transcriptional activity is mediated through GABP binding and transactivation at both divergent and nondivergent promoters.

  7. Geoelectrical exploration

    Directory of Open Access Journals (Sweden)

    Mostafa Said Barseem

    2015-12-01

    Full Text Available Sinai development is a goal of successive governments in Egypt. The present study is a geoelectrical exploration to find appropriate solutions of the problems affecting the land of a Research Station in Southeast Al Qantara. This research station is one of the Desert Research Center stations to facilitate the development of desert land for agriculture by introducing applied research. It suffers from some problems which can be summarized in the shortage of irrigation water and water logging. The appropriate solutions of these problems have been delineated by the results of 1D and 2D geoelectrical measurements. Electrical resistivity (ER revealed the subsurface sedimentary sequences and extension of subsurface layers in the horizontal and vertical directions, especially, the water bearing layer. Additionally it helped to choose the most suitable places to drill productive wells with a good condition.

  8. Exploring ESASky

    Science.gov (United States)

    De Marchi, Guido; ESASky Team

    2017-06-01

    ESASky is a science-driven discovery portal for all ESA space astronomy missions. It also includes missions from international partners such as Suzaku and Chandra. The first public release of ESASky features interfaces for sky exploration and for single and multiple target searches. Using the application requires no prior-knowledge of any of the missions involved and gives users world-wide simplified access to high-level science-ready data products from space-based Astronomy missions, plus a number of ESA-produced source catalogues, including the Gaia Data Release 1 catalogue. We highlight here the latest features to be developed, including one that allows the user to project onto the sky the footprints of the JWST instruments, at any chosen position and orientation. This tool has been developed to aid JWST astronomers when they are defining observing proposals. We aim to include other missions and instruments in the near future.

  9. Dynamic mechanism for the transcription apparatus orchestrating reliable responses to activators

    National Research Council Canada - National Science Library

    Wang, Yaolai; Liu, Feng; Wang, Wei

    2012-01-01

    ... between the enhancer and the Mediator, with the concentration of activators encoded as their temporal occupancy rate (RTOR) within the space. The entry of activators into this space induces allostery in theMediator, resulting in a facilitated circumstance for transcriptional reinitiation. The reinitiation rate is much larger than the cycling rate of...

  10. Transcription termination in the plasmid/virus hybrid pSSVx from Sulfolobus islandicus

    DEFF Research Database (Denmark)

    Contursi, Patrizia; Cannio, Raffaele; She, Qunxin

    2010-01-01

    The pSSVx from Sulfolobus islandicus, strain REY15/4, is a hybrid between a plasmid and a fusellovirus. A systematic study previously performed revealed the presence of nine major transcripts, the expression of which was differentially and temporally regulated over the growth cycle of S. islandic...

  11. In silico comparative genomic analysis of GABAA receptor transcriptional regulation

    Directory of Open Access Journals (Sweden)

    Joyce Christopher J

    2007-06-01

    Full Text Available Abstract Background Subtypes of the GABAA receptor subunit exhibit diverse temporal and spatial expression patterns. In silico comparative analysis was used to predict transcriptional regulatory features in individual mammalian GABAA receptor subunit genes, and to identify potential transcriptional regulatory components involved in the coordinate regulation of the GABAA receptor gene clusters. Results Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π subunit genes. Putative core elements and proximal transcriptional factors were identified within these predicted promoters, and within the experimentally determined promoters of other subunit genes. Conserved intergenic regions of sequence in the mammalian GABAA receptor gene cluster comprising the α1, β2, γ2 and α6 subunits were identified as potential long range transcriptional regulatory components involved in the coordinate regulation of these genes. A region of predicted DNase I hypersensitive sites within the cluster may contain transcriptional regulatory features coordinating gene expression. A novel model is proposed for the coordinate control of the gene cluster and parallel expression of the α1 and β2 subunits, based upon the selective action of putative Scaffold/Matrix Attachment Regions (S/MARs. Conclusion The putative regulatory features identified by genomic analysis of GABAA receptor genes were substantiated by cross-species comparative analysis and now require experimental verification. The proposed model for the coordinate regulation of genes in the cluster accounts for the head-to-head orientation and parallel expression of the α1 and β2 subunit genes, and for the disruption of transcription caused by insertion of a neomycin gene in the close vicinity of the α6 gene, which is proximal to a putative critical S/MAR.

  12. Transcriptional Auto-Regulation of RUNX1 P1 Promoter.

    Directory of Open Access Journals (Sweden)

    Milka Martinez

    Full Text Available RUNX1 a member of the family of runt related transcription factors (RUNX, is essential for hematopoiesis. The expression of RUNX1 gene is controlled by two promoters; the distal P1 promoter and the proximal P2 promoter. Several isoforms of RUNX1 mRNA are generated through the use of both promoters and alternative splicing. These isoforms not only differs in their temporal expression pattern but also exhibit differences in tissue specificity. The RUNX1 isoforms derived from P2 are expressed in a variety of tissues, but expression of P1-derived isoform is restricted to cells of hematopoietic lineage. However, the control of hematopoietic-cell specific expression is poorly understood. Here we report regulation of P1-derived RUNX1 mRNA by RUNX1 protein. In silico analysis of P1 promoter revealed presence of two evolutionary conserved RUNX motifs, 0.6kb upstream of the transcription start site, and three RUNX motifs within 170bp of the 5'UTR. Transcriptional contribution of these RUNX motifs was studied in myeloid and T-cells. RUNX1 genomic fragment containing all sites show very low basal activity in both cell types. Mutation or deletion of RUNX motifs in the UTR enhances basal activity of the RUNX1 promoter. Chromatin immunoprecipitation revealed that RUNX1 protein is recruited to these sites. Overexpression of RUNX1 in non-hematopoietic cells results in a dose dependent activation of the RUNX1 P1 promoter. We also demonstrate that RUNX1 protein regulates transcription of endogenous RUNX1 mRNA in T-cell. Finally we show that SCL transcription factor is recruited to regions containing RUNX motifs in the promoter and the UTR and regulates activity of the RUNX1 P1 promoter in vitro. Thus, multiple lines of evidence show that RUNX1 protein regulates its own gene transcription.

  13. Genome-wide transcriptional reprogramming under drought stress

    KAUST Repository

    Chen, Hao

    2012-01-01

    Soil water deficit is one of the major factors limiting plant productivity. Plants cope with this adverse environmental condition by coordinating the up- or downregulation of an array of stress responsive genes. Reprogramming the expression of these genes leads to rebalanced development and growth that are in concert with the reduced water availability and that ultimately confer enhanced stress tolerance. Currently, several techniques have been employed to monitor genome-wide transcriptional reprogramming under drought stress. The results from these high throughput studies indicate that drought stress-induced transcriptional reprogramming is dynamic, has temporal and spatial specificity, and is coupled with the circadian clock and phytohormone signaling pathways. © 2012 Springer-Verlag Berlin Heidelberg. All rights are reserved.

  14. Phylogenetic and Transcription Analysis of Chrysanthemum WRKY Transcription Factors

    Science.gov (United States)

    Song, Aiping; Li, Peiling; Jiang, Jiafu; Chen, Sumei; Li, Huiyun; Zeng, Jun; Shao, Yafeng; Zhu, Lu; Zhang, Zhaohe; Chen, Fadi

    2014-01-01

    WRKY transcription factors are known to function in a number of plant processes. Here we have characterized 15 WRKY family genes of the important ornamental species chrysanthemum (Chrysanthemum morifolium). A total of 15 distinct sequences were isolated; initially internal fragments were amplified based on transcriptomic sequence, and then the full length cDNAs were obtained using RACE (rapid amplification of cDNA ends) PCR. The transcription of these 15 genes in response to a variety of phytohormone treatments and both biotic and abiotic stresses was characterized. Some of the genes behaved as would be predicted based on their homology with Arabidopsis thaliana WRKY genes, but others showed divergent behavior. PMID:25196345

  15. Transcriptional profiles of plasticity for desiccation stress in drosophila.

    Science.gov (United States)

    Clemson, Allannah S; Sgrò, Carla M; Telonis-Scott, Marina

    2017-11-08

    We examined the transcriptional responses of desiccation resistance candidate genes in populations of Drosophila melanogaster divergent for desiccation resistance and in capacity to improve resistance via phenotypic plasticity. Adult females from temperate and tropical eastern Australian populations were exposed to a rapid desiccation hardening (RDH) treatment, and groups without RDH to acute desiccation stress, and temporally profiled transcript expression of 12 candidate desiccation genes during, and in recovery from stress. We found that desiccation exposure resulted in largely transitory, stress-specific transcriptional changes in all but one gene. However linking the expression profiles to the population-level phenotypic divergence was difficult given subtle, and time-point specific population expression variation. Nonetheless, rapid desiccation hardening had the largest effect on gene expression, resulting in distinct molecular profiles. We report a hitherto uncharacterised desiccation molecular hardening response where prior exposure essentially 'primes' genes to respond to subsequent stress without discernible transcript changes prior to stress. This, taken together with some population gene expression variation of several bona fide desiccation candidates associated with different water balance strategies speaks of the complexity of natural desiccation resistance and plasticity and provides new avenues for understanding the molecular basis of a trait of ecological significance. Copyright © 2017. Published by Elsevier Inc.

  16. [Temporal meaning of suffering].

    Science.gov (United States)

    Porée, J

    2015-09-01

    If we had to find a few simple words to express what a suffering human being experiences, no matter what ills are causing the suffering and no matter what circumstances underlie the ills themselves, we could unmistakably say that it is the experience of not being able to go on like this. Suffering can be described, in this same sense, as an alteration in temporality. However, describing suffering as such only makes sense if we already have a conception of normal temporality. Yet for this, philosophical tradition offers not one but four competing conceptions. In the present article, we begin by briefly presenting these different conceptions. We then show how each one sheds light, by way of contrast, on a phenomenon whose meaning thus appears to be essentially negative. But does this phenomenon have a negative meaning only? Doesn't it correspond as much to a transformation as an alteration of temporality? This is what we will strive to establish in the third part of the article by relating suffering to hope, in a paradoxical sense of the term. Of the four conceptions of time likely to shed a contrasting light on the upheavals that suffering introduces into our life experience, the one described by Aristotle in Physics is historically the first. In particular, the notion of succession originates therein. But this conception does not account for what makes time the unit of a past, a present, and a future. In Book XI of Confessions, St. Augustine situated this unit not in nature but in the human mind. Hence, his definition of time as a distension of the soul and the necessary division into physical time and psychic time it entails. Husserl's Lessons on the phenomenology of the consciousness of internal time lend credit to this division, but they illuminate only the internal constitution of the "present", which is at the heart of the psychological conception of time. In Being and Time, Heidegger breaks away from this long-standing tradition; in his view, physical time

  17. Processivity and coupling in messenger RNA transcription.

    Directory of Open Access Journals (Sweden)

    Stuart Aitken

    2010-01-01

    Full Text Available The complexity of messenger RNA processing is now being uncovered by experimental techniques that are capable of detecting individual copies of mRNA in cells, and by quantitative real-time observations that reveal the kinetics. This processing is commonly modelled by permitting mRNA to be transcribed only when the promoter is in the on state. In this simple on/off model, the many processes involved in active transcription are represented by a single reaction. These processes include elongation, which has a minimum time for completion and processing that is not captured in the model.In this paper, we explore the impact on the mRNA distribution of representing the elongation process in more detail. Consideration of the mechanisms of elongation leads to two alternative models of the coupling between the elongating polymerase and the state of the promoter: Processivity allows polymerases to complete elongation irrespective of the promoter state, whereas coupling requires the promoter to be active to produce a full-length transcript. We demonstrate that these alternatives have a significant impact on the predicted distributions. Models are simulated by the Gillespie algorithm, and the third and fourth moments of the resulting distribution are computed in order to characterise the length of the tail, and sharpness of the peak. By this methodology, we show that the moments provide a concise summary of the distribution, showing statistically-significant differences across much of the feasible parameter range.We conclude that processivity is not fully consistent with the on/off model unless the probability of successfully completing elongation is low--as has been observed. The results also suggest that some form of coupling between the promoter and a rate-limiting step in transcription may explain the cell's inability to maintain high mRNA levels at low noise--a prediction of the on/off model that has no supporting evidence.

  18. Temporal Representation in Semantic Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Levandoski, J J; Abdulla, G M

    2007-08-07

    A wide range of knowledge discovery and analysis applications, ranging from business to biological, make use of semantic graphs when modeling relationships and concepts. Most of the semantic graphs used in these applications are assumed to be static pieces of information, meaning temporal evolution of concepts and relationships are not taken into account. Guided by the need for more advanced semantic graph queries involving temporal concepts, this paper surveys the existing work involving temporal representations in semantic graphs.

  19. Spatio temporal media components for neurofeedback

    DEFF Research Database (Denmark)

    Jensen, Camilla Birgitte Falk; Petersen, Michael Kai; Larsen, Jakob Eg

    2013-01-01

    A class of Brain Computer Interfaces (BCI) involves interfaces for neurofeedback training, where a user can learn to self-regulate brain activity based on real-time feedback. These particular interfaces are constructed from audio-visual components and temporal settings, which appear to have...... a strong influence on the ability to control brain activity. Therefore, identifying the different interface components and exploring their individual effects might be key for constructing new interfaces that support more efficient neurofeedback training. We discuss experiments involving two different...

  20. 7 CFR 780.13 - Verbatim transcripts.

    Science.gov (United States)

    2010-01-01

    ... of the hearing. The party requesting a verbatim transcript shall pay for the transcription service... 7 Agriculture 7 2010-01-01 2010-01-01 false Verbatim transcripts. 780.13 Section 780.13... AGRICULTURE SPECIAL PROGRAMS APPEAL REGULATIONS § 780.13 Verbatim transcripts. (a) Appellants and their...

  1. Circadian Control of Global Transcription

    Science.gov (United States)

    Li, Shujing; Zhang, Luoying

    2015-01-01

    Circadian rhythms exist in most if not all organisms on the Earth and manifest in various aspects of physiology and behavior. These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs). CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. The transcription of CCGs is tuned by rhythmic actions of transcription factors and circadian alterations in chromatin. Here, we review the circadian control of CCG transcription in five model organisms that are widely used, including cyanobacterium, fungus, plant, fruit fly, and mouse. Comparing the similarity and differences in the five organisms could help us better understand the function of the circadian clock, as well as its output mechanisms adapted to meet the demands of diverse environmental conditions. PMID:26682214

  2. Circadian Control of Global Transcription

    Directory of Open Access Journals (Sweden)

    Shujing Li

    2015-01-01

    Full Text Available Circadian rhythms exist in most if not all organisms on the Earth and manifest in various aspects of physiology and behavior. These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs. CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. The transcription of CCGs is tuned by rhythmic actions of transcription factors and circadian alterations in chromatin. Here, we review the circadian control of CCG transcription in five model organisms that are widely used, including cyanobacterium, fungus, plant, fruit fly, and mouse. Comparing the similarity and differences in the five organisms could help us better understand the function of the circadian clock, as well as its output mechanisms adapted to meet the demands of diverse environmental conditions.

  3. Mitochondrial transcription in mammalian cells.

    Science.gov (United States)

    Shokolenko, Inna N; Alexeyev, Mikhail F

    2017-01-01

    As a consequence of recent discoveries of intimate involvement of mitochondria with key cellular processes, there has been a resurgence of interest in all aspects of mitochondrial biology, including the intricate mechanisms of mitochondrial DNA maintenance and expression. Despite four decades of research, there remains a lot to be learned about the processes that enable transcription of genetic information from mitochondrial DNA to RNA, as well as their regulation. These processes are vitally important, as evidenced by the lethality of inactivating the central components of mitochondrial transcription machinery. Here, we review the current understanding of mitochondrial transcription and its regulation in mammalian cells. We also discuss key theories in the field and highlight controversial subjects and future directions as we see them.

  4. Auditory temporal processing in patients with temporal lobe epilepsy.

    Science.gov (United States)

    Lavasani, Azam Navaei; Mohammadkhani, Ghassem; Motamedi, Mahmoud; Karimi, Leyla Jalilvand; Jalaei, Shohreh; Shojaei, Fereshteh Sadat; Danesh, Ali; Azimi, Hadi

    2016-07-01

    Auditory temporal processing is the main feature of speech processing ability. Patients with temporal lobe epilepsy, despite their normal hearing sensitivity, may present speech recognition disorders. The present study was carried out to evaluate the auditory temporal processing in patients with unilateral TLE. The present study was carried out on 25 patients with epilepsy: 11 patients with right temporal lobe epilepsy and 14 with left temporal lobe epilepsy with a mean age of 31.1years and 18 control participants with a mean age of 29.4years. The two experimental and control groups were evaluated via gap-in-noise and duration pattern sequence tests. One-way ANOVA was run to analyze the data. The mean of the threshold of the GIN test in the control group was observed to be better than that in participants with LTLE and RTLE. Also, it was observed that the percentage of correct responses on the DPS test in the control group and in participants with RTLE was better than that in participants with LTLE. Patients with TLE have difficulties in temporal processing. Difficulties are more significant in patients with LTLE, likely because the left temporal lobe is specialized for the processing of temporal information. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Chromatin and Transcription in Yeast

    Science.gov (United States)

    Rando, Oliver J.; Winston, Fred

    2012-01-01

    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

  6. Dynamic CRM occupancy reflects a temporal map of developmental progression.

    Science.gov (United States)

    Wilczyński, Bartek; Furlong, Eileen E M

    2010-06-22

    Development is driven by tightly coordinated spatio-temporal patterns of gene expression, which are initiated through the action of transcription factors (TFs) binding to cis-regulatory modules (CRMs). Although many studies have investigated how spatial patterns arise, precise temporal control of gene expression is less well understood. Here, we show that dynamic changes in the timing of CRM occupancy is a prevalent feature common to all TFs examined in a developmental ChIP time course to date. CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves. The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development. Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression. Systematic measurement of dynamic CRM occupancy may therefore serve as a powerful method to decode dynamic changes in gene expression driving developmental progression.

  7. Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries

    DEFF Research Database (Denmark)

    Jakobsen, Janus Schou; Waage, Johannes; Rapin, Nicolas

    2013-01-01

    Dynamic shifts in transcription factor binding are central to the regulation of biological processes by allowing rapid changes in gene transcription. However, very few genome-wide studies have examined how transcription factor occupancy is coordinated temporally in vivo in higher animals. Here, w......-renewal of differentiated cells. Taken together, our work emphasizes the power of global temporal analyses of transcription factor occupancy to elucidate mechanisms regulating dynamic biological processes in complex higher organisms....... polymerase II binding data, we find three temporal classes of transcription factor binding to be associated with distinct sets of regulated genes involved in the acute phase response, metabolic/homeostatic functions, or cell cycle progression. Moreover, we demonstrate a previously unrecognized early phase...

  8. Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures

    Directory of Open Access Journals (Sweden)

    DuBois Debra C

    2010-10-01

    Full Text Available Abstract Background Comprehensively understanding corticosteroid pharmacogenomic effects is an essential step towards an insight into the underlying molecular mechanisms for both beneficial and detrimental clinical effects. Nevertheless, even in a single tissue different methods of corticosteroid administration can induce different patterns of expression and regulatory control structures. Therefore, rich in vivo datasets of pharmacological time-series with two dosing regimens sampled from rat liver are examined for temporal patterns of changes in gene expression and their regulatory commonalities. Results The study addresses two issues, including (1 identifying significant transcriptional modules coupled with dynamic expression patterns and (2 predicting relevant common transcriptional controls to better understand the underlying mechanisms of corticosteroid adverse effects. Following the orientation of meta-analysis, an extended computational approach that explores the concept of agreement matrix from consensus clustering has been proposed with the aims of identifying gene clusters that share common expression patterns across multiple dosing regimens as well as handling challenges in the analysis of microarray data from heterogeneous sources, e.g. different platforms and time-grids in this study. Six significant transcriptional modules coupled with typical patterns of expression have been identified. Functional analysis reveals that virtually all enriched functions (gene ontologies, pathways in these modules are shown to be related to metabolic processes, implying the importance of these modules in adverse effects under the administration of corticosteroids. Relevant putative transcriptional regulators (e.g. RXRF, FKHD, SP1F are also predicted to provide another source of information towards better understanding the complexities of expression patterns and the underlying regulatory mechanisms of those modules. Conclusions We have proposed a

  9. Transcription factor co-repressors in cancer biology: roles and targeting.

    Science.gov (United States)

    Battaglia, Sebastiano; Maguire, Orla; Campbell, Moray J

    2010-06-01

    Normal transcription displays a high degree of flexibility over the choice, timing and magnitude of mRNA expression levels that tend to oscillate and cycle. These processes allow for combinatorial actions, feedback control and fine-tuning. A central role has emerged for the transcriptional co-repressor proteins such as NCOR1, NCOR2/SMRT, CoREST and CTBPs, to control the actions of many transcriptional factors, in large part, by recruitment and activation of a range of chromatin remodeling enzymes. Thus, co-repressors and chromatin remodeling factors are recruited to transcription factors at specific promoter/enhancer regions and execute changes in the chromatin structure. The specificity of this recruitment is controlled in a spatial-temporal manner. By playing a central role in transcriptional control, as they move and target transcription factors, co-repressors act as a key driver in the epigenetic economy of the nucleus. Co-repressor functions are selectively distorted in malignancy, by both loss and gain of function and contribute to the generation of transcriptional rigidity. Features of transcriptional rigidity apparent in cancer cells include the distorted signaling of nuclear receptors and the WNTs/beta-catenin axis. Understanding and predicting the consequences of altered co-repressor expression patterns in cancer cells has diagnostic and prognostic significance, and also have the capacity to be targeted through selective epigenetic therapies.

  10. Discriminative identification of transcriptional responses of promoters and enhancers after stimulus

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2016-10-17

    Promoters and enhancers regulate the initiation of gene expression and maintenance of expression levels in spatial and temporal manner. Recent findings stemming from the Cap Analysis of Gene Expression (CAGE) demonstrate that promoters and enhancers, based on their expression profiles after stimulus, belong to different transcription response subclasses. One of the most promising biological features that might explain the difference in transcriptional response between subclasses is the local chromatin environment. We introduce a novel computational framework, PEDAL, for distinguishing effectively transcriptional profiles of promoters and enhancers using solely histone modification marks, chromatin accessibility and binding sites of transcription factors and co-activators. A case study on data from MCF-7 cell-line reveals that PEDAL can identify successfully the transcription response subclasses of promoters and enhancers from two different stimulations. Moreover, we report subsets of input markers that discriminate with minimized classification error MCF-7 promoter and enhancer transcription response subclasses. Our work provides a general computational approach for identifying effectively cell-specific and stimulation-specific promoter and enhancer transcriptional profiles, and thus, contributes to improve our understanding of transcriptional activation in human.

  11. Quantifying temporal change in biodiversity: challenges and opportunities

    Science.gov (United States)

    Dornelas, Maria; Magurran, Anne E.; Buckland, Stephen T.; Chao, Anne; Chazdon, Robin L.; Colwell, Robert K.; Curtis, Tom; Gaston, Kevin J.; Gotelli, Nicholas J.; Kosnik, Matthew A.; McGill, Brian; McCune, Jenny L.; Morlon, Hélène; Mumby, Peter J.; Øvreås, Lise; Studeny, Angelika; Vellend, Mark

    2013-01-01

    Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions. PMID:23097514

  12. Spatial-temporal forecasting the sunspot diagram

    Science.gov (United States)

    Covas, Eurico

    2017-09-01

    Aims: We attempt to forecast the Sun's sunspot butterfly diagram in both space (i.e. in latitude) and time, instead of the usual one-dimensional time series forecasts prevalent in the scientific literature. Methods: We use a prediction method based on the non-linear embedding of data series in high dimensions. We use this method to forecast both in latitude (space) and in time, using a full spatial-temporal series of the sunspot diagram from 1874 to 2015. Results: The analysis of the results shows that it is indeed possible to reconstruct the overall shape and amplitude of the spatial-temporal pattern of sunspots, but that the method in its current form does not have real predictive power. We also apply a metric called structural similarity to compare the forecasted and the observed butterfly cycles, showing that this metric can be a useful addition to the usual root mean square error metric when analysing the efficiency of different prediction methods. Conclusions: We conclude that it is in principle possible to reconstruct the full sunspot butterfly diagram for at least one cycle using this approach and that this method and others should be explored since just looking at metrics such as sunspot count number or sunspot total area coverage is too reductive given the spatial-temporal dynamical complexity of the sunspot butterfly diagram. However, more data and/or an improved approach is probably necessary to have true predictive power.

  13. Feature extraction using multi-temporal fully polarimetric SAR data

    Science.gov (United States)

    Ramya, M. N. S.; Kumar, Shashi

    2016-05-01

    The main objective of this study was to explore the potential of the multi-temporal PolSAR data in LULC mapping and to evaluate the accuracy of classification using single date and multi-temporal data. Multi-temporal data acquired on three different dates were used. Advanced classification techniques Support Vector Machine and Rule Based Hierarchical approaches were performed on multitemporal ALOS PALSAR data to classify features at different temporal combinations. In this study, SVM classification was applied on the derived output of Yamaguchi decomposition model, for which kernel approach of second order polynomial was used. In Rule Based Hierarchical approach, Backscattering coefficients, Yamaguchi and H/A/Alpha decomposition statistics are computed and analyzed to estimate the decision boundaries of the features to separate feature at different hierarchical levels. SVM classified the PolSAR data efficiently of single data, highest overall accuracy and kappa statistics achieved was 67.65% and 0.61 from the individual image. Rule based classified map of single date, highest overall accuracy and kappa statistics achieved was 68% and 0.67. Based on the accuracy assessment, SVM and Rule Based classification both are approximately of same accuracy but comparatively Rule Based classification was accurate temporally. Rule Based classification was further considered for multi-temporal classification and achieved high overall accuracy and kappa statistics of 80% and 0.76. This proves that multi-temporal PolSAR data helps to increase the accuracy of classification in LULC mapping.

  14. Temporal nonlinear beam dynamics in infiltrated photonic crystal fibers

    DEFF Research Database (Denmark)

    Bennet, Francis; Rosberg, Christian Romer; Neshev, Dragomir N.

    -sensing as well as active devices for all-optical switching at low (mW) laser powers. Commercially available PCFs infiltrated with liquids also provide a versatile and compact tool for exploration of the fundamentals of nonlinear beam propagation in periodic photonic structures. To explore the full scientific...... and technological potential of liquid-infiltrated PCFs it is important to understand the temporal dynamics of nonlinear beam propagation in such structures. In this work we consider thermally induced spatial nonlinear effects in infiltrated photonic crystal fibers. We experimentally study the temporal dynamics...... of nonlinear beam reshaping occurring on a short time scale before the establishment of a steady state regime. In experiment, a 532nm laser beam can be injected into a single hole of an infiltrated PCF cladding structure, and the temporal dynamics of the nonlinear response is measured by monitoring...

  15. Spatio-temporal models of synthetic genetic oscillators.

    Science.gov (United States)

    Macnamara, Cicely K; Chaplain, Mark A J

    2017-02-01

    Signal transduction pathways play a major role in many important aspects of cellular function e.g. cell division, apoptosis. One important class of signal transduction pathways is gene regulatory networks (GRNs). In many GRNs, proteins bind to gene sites in the nucleus thereby altering the transcription rate. Such proteins are known as transcription factors. If the binding reduces the transcription rate there is a negative feedback leading to oscillatory behaviour in mRNA and protein levels, both spatially (e.g. by observing fluorescently labelled molecules in single cells) and temporally (e.g. by observing protein/mRNA levels over time). Recent computational modelling has demonstrated that spatial movement of the molecules is a vital component of GRNs and may cause the oscillations. These numerical findings have subsequently been proved rigorously i.e. the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf bifurcation. In this paper we first present a model of the canonical GRN (the Hes1 protein) and show the effect of varying the spatial location of gene and protein production sites on the oscillations. We then extend the approach to examine spatio-temporal models of synthetic gene regulatory networks e.g. n-gene repressilators and activator-repressor systems.

  16. Massive Temporal Lobe Cholesteatoma

    Directory of Open Access Journals (Sweden)

    Pasan Waidyasekara

    2015-01-01

    Full Text Available Introduction. Intracranial extension of cholesteatoma is rare. This may occur de novo or recur some time later either contiguous with or separate to the site of the original cholesteatoma. Presentation of Case. A 63-year-old female presented to a tertiary referral hospital with a fluctuating level of consciousness, fever, headache, and right-sided otorrhoea, progressing over several days. Her past medical history included surgery for right ear cholesteatoma and drainage of intracranial abscess 23 years priorly. There had been no relevant symptoms in the interim until 6 weeks prior to this presentation. Imaging demonstrated a large right temporal lobe mass contiguous with the middle ear and mastoid cavity with features consistent with cholesteatoma. The patient underwent a combined transmastoid/middle fossa approach for removal of the cholesteatoma and repair of the tegmen dehiscence. The patient made an uneventful recovery and remains well over 12 months later. Conclusion. This case presentation details a large intracranial cholesteatoma which had extended through a tegmen tympani dehiscence from recurrent right ear cholesteatoma treated by modified radical mastoidectomy over two decades priorly. There was a completely asymptomatic progression of disease until several weeks prior to this presentation.

  17. Ivory Osteoma Of Temporal Bone

    Directory of Open Access Journals (Sweden)

    Ravi Meher

    2006-03-01

    Full Text Available Osteomas are slow growing bony tumors common in fronto-ethmoid regions and rare in temporal bone. These are usually asymptomatic and require treatment mainly for cosmetic reasons. We describe a case of temporal bone osteoma in a female.

  18. Spatial Grouping Determines Temporal Integration

    Science.gov (United States)

    Hermens, Frouke; Scharnowski, Frank; Herzog, Michael H.

    2009-01-01

    To make sense out of a continuously changing visual world, people need to integrate features across space and time. Despite more than a century of research, the mechanisms of features integration are still a matter of debate. To examine how temporal and spatial integration interact, the authors measured the amount of temporal fusion (a measure of…

  19. Model Checking Discounted Temporal Properties

    NARCIS (Netherlands)

    de Alfaro, Luca; Faella, Marco; Henzinger, Thomas A.; Majumdar, Rupak; Stoelinga, Mariëlle Ida Antoinette; Jensen, K; Podelski, A.

    2004-01-01

    Temporal logic is two-valued: a property is either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a

  20. Model Checking Discounted Temporal Properties

    NARCIS (Netherlands)

    de Alfaro, Luca; Faella, Marco; Henzinger, Thomas A.; Majumdar, Rupak; Stoelinga, Mariëlle Ida Antoinette

    2005-01-01

    Temporal logic is two-valued: a property is either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a

  1. Temporal Processing and Reading Disability.

    Science.gov (United States)

    Share, David L.; Jorm, Anthony F.; Maclean, Rod; Matthews, Russell

    2002-01-01

    Examines the hypothesis that early auditory temporal processing deficits cause later specific reading disability by impairing phonological processing. Suggests that auditory temporal deficits in dyslexics may be associated with dysphasic-type symptoms observed by Tallal and her colleagues in specific language-impaired populations, but do not cause…

  2. Epigenetics regulates transcription and pathogenesis in the parasite Trichomonas vaginalis.

    Science.gov (United States)

    Pachano, Tomas; Nievas, Yesica R; Lizarraga, Ayelen; Johnson, Patricia J; Strobl-Mazzulla, Pablo H; de Miguel, Natalia

    2017-06-01

    Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogenital tract. Infections range from asymptomatic to highly inflammatory, depending on the host and the parasite strain. Different T. vaginalis strains vary greatly in their adherence and cytolytic capacities. These phenotypic differences might be attributed to differentially expressed genes as a consequence of extra-genetic variation, such as epigenetic modifications. In this study, we explored the role of histone acetylation in regulating gene transcription and pathogenesis in T. vaginalis. Here, we show that histone 3 lysine acetylation (H3KAc) is enriched in nucleosomes positioned around the transcription start site of active genes (BAP1 and BAP2) in a highly adherent parasite strain; compared with the low acetylation abundance in contrast to that observed in a less-adherent strain that expresses these genes at low levels. Additionally, exposition of less-adherent strain with a specific histone deacetylases inhibitor, trichostatin A, upregulated the transcription of BAP1 and BAP2 genes in concomitance with an increase in H3KAc abundance and chromatin accessibility around their transcription start sites. Moreover, we demonstrated that the binding of initiator binding protein, the transcription factor responsible for the initiation of transcription of ~75% of known T. vaginalis genes, depends on the histone acetylation state around the metazoan-like initiator to which initiator binding protein binds. Finally, we found that trichostatin A treatment increased parasite aggregation and adherence to host cells. Our data demonstrated for the first time that H3KAc is a permissive histone modification that functions to mediate both transcription and pathogenesis of the parasite T. vaginalis. © 2017 John Wiley & Sons Ltd.

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

    Directory of Open Access Journals (Sweden)

    Steven Grant Hussey

    2013-08-01

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

  4. Temporality and Identity in Danish Historical Discourse, 1900–45

    DEFF Research Database (Denmark)

    Jørgensen, Claus Møller

    2014-01-01

    The chapter explores how temporality, identity, and modernity were conceptualized in Danish history-writing from 1900 to 1945. The first part of the chapter deals with the conceptualizations of historical change, its causes, and its direction. The second part focuses primarily on the way in which...

  5. Unemployment in South Africa: Building a Spatio-temporal ...

    African Journals Online (AJOL)

    The spatial understanding of unemployment in South Africa is often limited to provinces. This paper explores ways to integrate unemployment data from 1991 to 2007 to obtain a spatially more detailed understanding of the phenomenon. Creating such a temporal GIS is challenging because of the changing administrative ...

  6. Transcriptional Silencing of Retroviral Vectors

    DEFF Research Database (Denmark)

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

    1996-01-01

    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...

  7. Transcription factors in alkaloid biosynthesis.

    Science.gov (United States)

    Yamada, Yasuyuki; Sato, Fumihiko

    2013-01-01

    Higher plants produce a large variety of low-molecular weight secondary compounds. Among them, nitrogen-containing alkaloids are the most biologically active and are often used pharmaceutically. Whereas alkaloid chemistry has been intensively investigated, alkaloid biosynthesis, including the relevant biosynthetic enzymes, genes and their regulation, and especially transcription factors, is largely unknown, as only a limited number of plant species produce certain types of alkaloids and they are difficult to study. Recently, however, several groups have succeeded in isolating the transcription factors that are involved in the biosynthesis of several types of alkaloids, including bHLH, ERF, and WRKY. Most of them show Jasmonate (JA) responsiveness, which suggests that the JA signaling cascade plays an important role in alkaloid biosynthesis. Here, we summarize the types and functions of transcription factors that have been isolated in alkaloid biosynthesis, and characterize their similarities and differences compared to those in other secondary metabolite pathways, such as phenylpropanoid and terpenoid biosyntheses. The evolution of this biosynthetic pathway and regulatory network, as well as the application of these transcription factors to metabolic engineering, is discussed. © 2013, Elsevier Inc. All Rights Reserved.

  8. Medical transcription outsourcing greased lightning?

    Science.gov (United States)

    Bikman, Jeremy; Whiting, Stacilee

    2007-06-01

    As medical transcription volume grows, providers need to decide whether to outsource the work, and if so, whether to retain offshore or onshore firms. There are benefits and drawbacks to both. To avoid problems, providers need to make sure the details are spelled out in the contract and that their expectations are understood and met by the outsource firm.

  9. Hedgehog signaling acts with the temporal cascade to promote neuroblast cell cycle exit.

    Directory of Open Access Journals (Sweden)

    Phing Chian Chai

    Full Text Available In Drosophila postembryonic neuroblasts, transition in gene expression programs of a cascade of transcription factors (also known as the temporal series acts together with the asymmetric division machinery to generate diverse neurons with distinct identities and regulate the end of neuroblast proliferation. However, the underlying mechanism of how this "temporal series" acts during development remains unclear. Here, we show that Hh signaling in the postembryonic brain is temporally regulated; excess (earlier onset of Hh signaling causes premature neuroblast cell cycle exit and under-proliferation, whereas loss of Hh signaling causes delayed cell cycle exit and excess proliferation. Moreover, the Hh pathway functions downstream of Castor but upstream of Grainyhead, two components of the temporal series, to schedule neuroblast cell cycle exit. Interestingly, hh is likely a target of Castor. Hence, Hh signaling provides a link between the temporal series and the asymmetric division machinery in scheduling the end of neurogenesis.

  10. Control of cell cycle transcription during G1 and S phases.

    Science.gov (United States)

    Bertoli, Cosetta; Skotheim, Jan M; de Bruin, Robertus A M

    2013-08-01

    The accurate transition from G1 phase of the cell cycle to S phase is crucial for the control of eukaryotic cell proliferation, and its misregulation promotes oncogenesis. During G1 phase, growth-dependent cyclin-dependent kinase (CDK) activity promotes DNA replication and initiates G1-to-S phase transition. CDK activation initiates a positive feedback loop that further increases CDK activity, and this commits the cell to division by inducing genome-wide transcriptional changes. G1-S transcripts encode proteins that regulate downstream cell cycle events. Recent work is beginning to reveal the complex molecular mechanisms that control the temporal order of transcriptional activation and inactivation, determine distinct functional subgroups of genes and link cell cycle-dependent transcription to DNA replication stress in yeast and mammals.

  11. Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

    Science.gov (United States)

    Johard, Helena; Mahdessian, Diana; Fedr, Radek; Marks, Carolyn; Medalová, Jiřina; Souček, Karel; Lundberg, Emma; Linnarsson, Sten; Bryja, Vítězslav; Sekyrova, Petra; Altun, Mikael; Andäng, Michael

    2017-01-01

    The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development. PMID:29228002

  12. Feed-forward transcriptional programming by nuclear receptors: regulatory principles and therapeutic implications.

    Science.gov (United States)

    Sasse, Sarah K; Gerber, Anthony N

    2015-01-01

    Nuclear receptors (NRs) are widely targeted to treat a range of human diseases. Feed-forward loops are an ancient mechanism through which single cell organisms organize transcriptional programming and modulate gene expression dynamics, but they have not been systematically studied as a regulatory paradigm for NR-mediated transcriptional responses. Here, we provide an overview of the basic properties of feed-forward loops as predicted by mathematical models and validated experimentally in single cell organisms. We review existing evidence implicating feed-forward loops as important in controlling clinically relevant transcriptional responses to estrogens, progestins, and glucocorticoids, among other NR ligands. We propose that feed-forward transcriptional circuits are a major mechanism through which NRs integrate signals, exert temporal control over gene regulation, and compartmentalize client transcriptomes into discrete subunits. Implications for the design and function of novel selective NR ligands are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Phylogenetic and Transcription Analysis of Chrysanthemum WRKY Transcription Factors

    Directory of Open Access Journals (Sweden)

    Aiping Song

    2014-08-01

    Full Text Available WRKY transcription factors are known to function in a number of plant processes. Here we have characterized 15 WRKY family genes of the important ornamental species chrysanthemum (Chrysanthemum morifolium. A total of 15 distinct sequences were isolated; initially internal fragments were amplified based on transcriptomic sequence, and then the full length cDNAs were obtained using RACE (rapid amplification of cDNA ends PCR. The transcription of these 15 genes in response to a variety of phytohormone treatments and both biotic and abiotic stresses was characterized. Some of the genes behaved as would be predicted based on their homology with Arabidopsis thaliana WRKY genes, but others showed divergent behavior.

  14. Identification of temporal association rules from time-series microarray data sets.

    Science.gov (United States)

    Nam, Hojung; Lee, KiYoung; Lee, Doheon

    2009-03-19

    One of the most challenging problems in mining gene expression data is to identify how the expression of any particular gene affects the expression of other genes. To elucidate the relationships between genes, an association rule mining (ARM) method has been applied to microarray gene expression data. However, a conventional ARM method has a limit on extracting temporal dependencies between gene expressions, though the temporal information is indispensable to discover underlying regulation mechanisms in biological pathways. In this paper, we propose a novel method, referred to as temporal association rule mining (TARM), which can extract temporal dependencies among related genes. A temporal association rule has the form [gene A upward arrow, gene B downward arrow] --> (7 min) [gene C upward arrow], which represents that high expression level of gene A and significant repression of gene B followed by significant expression of gene C after 7 minutes. The proposed TARM method is tested with Saccharomyces cerevisiae cell cycle time-series microarray gene expression data set. In the parameter fitting phase of TARM, the fitted parameter set [threshold = +/- 0.8, support >or= 3 transactions, confidence >or= 90%] with the best precision score for KEGG cell cycle pathway has been chosen for rule mining phase. With the fitted parameter set, numbers of temporal association rules with five transcriptional time delays (0, 7, 14, 21, 28 minutes) are extracted from gene expression data of 799 genes, which are pre-identified cell cycle relevant genes. From the extracted temporal association rules, associated genes, which play same role of biological processes within short transcriptional time delay and some temporal dependencies between genes with specific biological processes are identified. In this work, we proposed TARM, which is an applied form of conventional ARM. TARM showed higher precision score than Dynamic Bayesian network and Bayesian network. Advantages of TARM are

  15. Transcription Blockage Leads to New Beginnings

    Science.gov (United States)

    Andrade-Lima, Leonardo C.; Veloso, Artur; Ljungman, Mats

    2015-01-01

    Environmental agents are constantly challenging cells by damaging DNA, leading to the blockage of transcription elongation. How do cells deal with transcription-blockage and how is transcription restarted after the blocking lesions are removed? Here we review the processes responsible for the removal of transcription-blocking lesions, as well as mechanisms of transcription restart. We also discuss recent data suggesting that blocked RNA polymerases may not resume transcription from the site of the lesion following its removal but, rather, are forced to start over from the beginning of genes. PMID:26197343

  16. Temporal selection is suppressed, delayed, and diffused during the attentional blink

    NARCIS (Netherlands)

    Vul, Edward; Nieuwenstein, Mark; Kanwisher, Nancy

    2008-01-01

    How does temporal selection work, and along what dimensions does it vary from one instance to the next? We explored these questions using a phenomenon in which temporal selection goes awry. In the attentional blink, subjects fail to report the second of a pair of targets (T1 and T2) when they are

  17. Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription

    OpenAIRE

    Dumay-Odelot, Hélène; Durrieu-Gaillard, Stéphanie; El Ayoubi, Leyla; Parrot, Camila; Teichmann, Martin

    2014-01-01

    Human RNA polymerase III transcribes small untranslated RNAs that contribute to the regulation of essential cellular processes, including transcription, RNA processing and translation. Analysis of this transcription system by in vitro transcription techniques has largely contributed to the discovery of its transcription factors and to the understanding of the regulation of human RNA polymerase III transcription. Here we review some of the key steps that led to the identification of transcript...

  18. Transcriptional oscillation of canonical clock genes in mouse peripheral tissues

    Directory of Open Access Journals (Sweden)

    Nakahata Yasukazu

    2004-10-01

    Full Text Available Abstract Background The circadian rhythm of about 24 hours is a fundamental physiological function observed in almost all organisms from prokaryotes to humans. Identification of clock genes has allowed us to study the molecular bases for circadian behaviors and temporal physiological processes such as hormonal secretion, and has prompted the idea that molecular clocks reside not only in a central pacemaker, the suprachiasmatic nuclei (SCN of hypothalamus in mammals, but also in peripheral tissues, even in immortalized cells. Furthermore, previous molecular dissection revealed that the mechanism of circadian oscillation at a molecular level is based on transcriptional regulation of clock and clock-controlled genes. Results We systematically analyzed the mRNA expression of clock and clock-controlled genes in mouse peripheral tissues. Eight genes (mBmal1, mNpas2, mRev-erbα, mDbp, mRev-erbβ, mPer3, mPer1 and mPer2; given in the temporal order of the rhythm peak showed robust circadian expressions of mRNAs in all tissues except testis, suggesting that these genes are core molecules of the molecular biological clock. The bioinformatics analysis revealed that these genes have one or a combination of 3 transcriptional elements (RORE, DBPE, and E-box, which are conserved among human, mouse, and rat genome sequences, and indicated that these 3 elements may be responsible for the biological timing of expression of canonical clock genes. Conclusions The observation of oscillatory profiles of canonical clock genes is not only useful for physiological and pathological examination of the circadian clock in various organs but also important for systematic understanding of transcriptional regulation on a genome-wide basis. Our finding of the oscillatory expression of canonical clock genes with a temporal order provides us an interesting hypothesis, that cyclic timing of all clock and clock-controlled genes may be dependent on several transcriptional elements

  19. Dispersal Ability Determines the Role of Environmental, Spatial and Temporal Drivers of Metacommunity Structure

    NARCIS (Netherlands)

    Padial, André A.; Ceschin, Fernanda; Declerck, Steven A. J.; De Meester, Luc; Bonecker, Cláudia C.; Lansac-Tôha, Fabio A.; Rodrigues, Liliana; Rodrigues, Luzia C.; Train, Sueli; Velho, Luiz F. M.; Bini, Luis M.

    2014-01-01

    Recently, community ecologists are focusing on the relative importance of local environmental factors and proxies to dispersal limitation to explain spatial variation in community structure. Albeit less explored, temporal processes may also be important in explaining species composition variation in

  20. Join Operations in Temporal Databases

    DEFF Research Database (Denmark)

    Gao, D.; Jensen, Christian Søndergaard; Snodgrass, R.T.

    2005-01-01

    Joins are arguably the most important relational operators. Poor implementations are tantamount to computing the Cartesian product of the input relations. In a temporal database, the problem is more acute for two reasons. First, conventional techniques are designed for the evaluation of joins wit...... to implementation, is on non-index-based join algorithms. Such algorithms do not rely on auxiliary access paths but may exploit sort orderings to achieve efficiency......., if any, comparison of the various operators. We then address evaluation algorithms, comparing the applicability of various algorithms to the temporal join operators and describing a performance study involving algorithms for one important operator, the temporal equijoin. Our focus, with respect...

  1. Building a Synthetic Transcriptional Oscillator.

    Science.gov (United States)

    Schwarz-Schilling, Matthaeus; Kim, Jongmin; Cuba, Christian; Weitz, Maximilian; Franco, Elisa; Simmel, Friedrich C

    2016-01-01

    Reaction circuits mimicking genetic oscillators can be realized with synthetic, switchable DNA genes (so-called genelets), and two enzymes only, an RNA polymerase and a ribonuclease. The oscillatory behavior of the genelets is driven by the periodic production and degradation of RNA effector molecules. Here, we describe the preparation, assembly, and testing of a synthetic, transcriptional two-node negative-feedback oscillator, whose dynamics can be followed in real-time by fluorescence read-out.

  2. The transcriptional regulators, the immune system and the the circadian clock.

    Science.gov (United States)

    Vinciguerra, M; Borghesan, M; Pazienza, V; Piepoli, A; Palmieri, O; Tarquini, R; Tevy, M F; De Cata, A; Mazzoccoli, G

    2013-01-01

    The immune system function oscillates with a 24-hour period driving circadian rhythmicity of immune responses. A circadian timing system comprising central and peripheral oscillators entrains body rhythmicity of physiology and behavior to environmental cues by means of humoral signals and autonomic neural outputs. In every single cell an oscillator goes ticking through a molecular clock operated by transcriptional/translational feedback loops driven by the rhythmic expression of circadian genes. This clock gene machinery steers daily oscillations in the regulation of immune cell activity, driving the periodicity in immune system function. The transcriptional networks that regulate temporal variation in gene expression in immunocompetent cells and tissues respond to diverse physiological clues, addressing well-timed adjustments of transcription and translation processes. Nuclear receptors comprise a unique class of transcriptional regulators that are capable of gauging hormones, metabolites, endobiotics and xenobiotics, linking ligand sensing to transcriptional responses in various cell types through switching between coactivator and corepressor recruitment. The expression of coregulators is highly responsive to physiological signals, and plays an important role in the control of rhythmic patterns of gene expression, optimizing the switch between nycthemeral patterns, and synchronizing circadian rhythmicity with changing physiological demands across the light-dark cycle. The nuclear receptors and transcription factors expressed in the immune components contribute to the cross-talk between the circadian timing system, the clock gene machinery and the immune system, influencing transcriptional activities and directing cell-type specific gene expression programs linked to innate and adaptive immune responses.

  3. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    Elongation. Residual Promoter Complex. Elongation complex. Figure 2. Assembly of Transcription initiation complex on a TATA containing promoter: The single line with boxes represent promoter DNA and the +1 indicates the transcription start ...

  4. 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)

    2001-01-01

    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

  5. 16 CFR 1502.36 - Official transcript.

    Science.gov (United States)

    2010-01-01

    ... presiding officer will arrange for a verbatim stenographic transcript of oral testimony and for necessary.... Corrections are permitted only for transcription errors. The presiding officer shall promptly order justified...

  6. Functionality of intergenic transcription: an evolutionary comparison.

    Directory of Open Access Journals (Sweden)

    Philipp Khaitovich

    2006-10-01

    Full Text Available Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis, and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression, which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by widespread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts.

  7. Treatment of Temporal Bone Fractures.

    Science.gov (United States)

    Diaz, Rodney C; Cervenka, Brian; Brodie, Hilary A

    2016-10-01

    Traumatic injury to the temporal bone can lead to significant morbidity or mortality and knowledge of the pertinent anatomy, pathophysiology of injury, and appropriate management strategies is critical for successful recovery and rehabilitation of such injured patients. Most temporal bone fractures are caused by motor vehicle accidents. Temporal bone fractures are best classified as either otic capsule sparing or otic capsule disrupting-type fractures, as such classification correlates well with risk of concomitant functional complications. The most common complications of temporal bone fractures are facial nerve injury, cerebrospinal fluid (CSF) leak, and hearing loss. Assessment of facial nerve function as soon as possible following injury greatly facilitates clinical decision making. Use of prophylactic antibiotics in the setting of CSF leak is controversial; however, following critical analysis and interpretation of the existing classic and contemporary literature, we believe its use is absolutely warranted.

  8. Treatment of Temporal Bone Fractures

    Science.gov (United States)

    Diaz, Rodney C.; Cervenka, Brian; Brodie, Hilary A.

    2016-01-01

    Traumatic injury to the temporal bone can lead to significant morbidity or mortality and knowledge of the pertinent anatomy, pathophysiology of injury, and appropriate management strategies is critical for successful recovery and rehabilitation of such injured patients. Most temporal bone fractures are caused by motor vehicle accidents. Temporal bone fractures are best classified as either otic capsule sparing or otic capsule disrupting-type fractures, as such classification correlates well with risk of concomitant functional complications. The most common complications of temporal bone fractures are facial nerve injury, cerebrospinal fluid (CSF) leak, and hearing loss. Assessment of facial nerve function as soon as possible following injury greatly facilitates clinical decision making. Use of prophylactic antibiotics in the setting of CSF leak is controversial; however, following critical analysis and interpretation of the existing classic and contemporary literature, we believe its use is absolutely warranted. PMID:27648399

  9. Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max Embryos

    Directory of Open Access Journals (Sweden)

    Ruth Grene

    2013-05-01

    Full Text Available Soybean (Glycine max seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.

  10. Microarray analysis of Paramecium bursaria chlorella virus 1 transcription.

    Science.gov (United States)

    Yanai-Balser, Giane M; Duncan, Garry A; Eudy, James D; Wang, Dong; Li, Xiao; Agarkova, Irina V; Dunigan, David D; Van Etten, James L

    2010-01-01

    Paramecium bursaria chlorella virus 1 (PBCV-1), a member of the family Phycodnaviridae, is a large double-stranded DNA, plaque-forming virus that infects the unicellular green alga Chlorella sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)-containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: (i) the PBCV-1 replication cycle is temporally programmed and regulated; (ii) 360 (99%) of the arrayed PBCV-1 CDSs were expressed at some time in the virus life cycle in the laboratory; (iii) 227 (62%) of the CDSs were expressed before virus DNA synthesis begins; (iv) these 227 CDSs were grouped into two classes: 127 transcripts disappeared prior to initiation of virus DNA synthesis (considered early), and 100 transcripts were still detected after virus DNA synthesis begins (considered early/late); (v) 133 (36%) of the CDSs were expressed after virus DNA synthesis begins (considered late); and (vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor, aphidicolin, prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 life cycle.

  11. Retroviral transcriptional regulation and embryonic stem cells: war and peace.

    Science.gov (United States)

    Schlesinger, Sharon; Goff, Stephen P

    2015-03-01

    Retroviruses have evolved complex transcriptional enhancers and promoters that allow their replication in a wide range of tissue and cell types. Embryonic stem (ES) cells, however, characteristically suppress transcription of proviruses formed after infection by exogenous retroviruses and also of most members of the vast array of endogenous retroviruses in the genome. These cells have unusual profiles of transcribed genes and are poised to make rapid changes in those profiles upon induction of differentiation. Many of the transcription factors in ES cells control both host and retroviral genes coordinately, such that retroviral expression patterns can serve as markers of ES cell pluripotency. This overlap is not coincidental; retrovirus-derived regulatory sequences are often used to control cellular genes important for pluripotency. These sequences specify the temporal control and perhaps "noisy" control of cellular genes that direct proper cell gene expression in primitive cells and their differentiating progeny. The evidence suggests that the viral elements have been domesticated for host needs, reflecting the wide-ranging exploitation of any and all available DNA sequences in assembling regulatory networks. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. Analytical Computation of the Epidemic Threshold on Temporal Networks

    Directory of Open Access Journals (Sweden)

    Eugenio Valdano

    2015-04-01

    Full Text Available The time variation of contacts in a networked system may fundamentally alter the properties of spreading processes and affect the condition for large-scale propagation, as encoded in the epidemic threshold. Despite the great interest in the problem for the physics, applied mathematics, computer science, and epidemiology communities, a full theoretical understanding is still missing and currently limited to the cases where the time-scale separation holds between spreading and network dynamics or to specific temporal network models. We consider a Markov chain description of the susceptible-infectious-susceptible process on an arbitrary temporal network. By adopting a multilayer perspective, we develop a general analytical derivation of the epidemic threshold in terms of the spectral radius of a matrix that encodes both network structure and disease dynamics. The accuracy of the approach is confirmed on a set of temporal models and empirical networks and against numerical results. In addition, we explore how the threshold changes when varying the overall time of observation of the temporal network, so as to provide insights on the optimal time window for data collection of empirical temporal networked systems. Our framework is of both fundamental and practical interest, as it offers novel understanding of the interplay between temporal networks and spreading dynamics.

  13. Mutual interdependence of splicing and transcription elongation.

    Science.gov (United States)

    Brzyżek, Grzegorz; Świeżewski, Szymon

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-09-01

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

  15. Stereopsis after anterior temporal lobectomy.

    Science.gov (United States)

    Verhoef, Bram-Ernst; Decramer, Thomas; van Loon, Johannes; Goffin, Jan; Van Paesschen, Wim; Janssen, Peter; Theys, Tom

    2016-09-01

    Brain areas critical for stereopsis have been investigated in non-human primates but are largely unknown in the human brain. Microelectrode recordings and functional MRI (fMRI) studies in monkeys have shown that in monkeys the inferior temporal cortex is critically involved in 3D shape categorization. Furthermore, some human fMRI studies similarly suggest an involvement of visual areas in the temporal lobe in depth perception. We aimed to investigate the role of the human anterior temporal neocortex in stereopsis by assessing stereoscopic depth perception before and after anterior temporal lobectomy. Eighteen epilepsy surgery patients were tested, pre- and postoperatively, in 3 different depth discrimination tasks. Sensitivity for local and global disparity was tested in a near-far discrimination task and sensitivity for 3D curvature was assessed in a convex-concave discrimination task, where 3D shapes were presented at different positions in depth. We found no evidence that temporal lobe epilepsy surgery has a significant effect on stereopsis. In contrast with earlier findings, we conclude that local as well as global stereopsis is maintained after unilateral resection of the temporal pole in epilepsy surgery patients. Our findings, together with previous studies, suggest that in humans more posterior visual regions underlie depth perception. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. The grounding of temporal metaphors.

    Science.gov (United States)

    Lai, Vicky T; Desai, Rutvik H

    2016-03-01

    Grounded cognition suggests that the processing of conceptual knowledge cued by language relies on the sensory-motor regions. Does temporal language similarly engage brain areas involved in time perception? Participants read sentences that describe the temporal extent of events with motion verbs (The hours crawled until the release of the news) and their static controls. Comparison conditions were fictive motion (The trail crawled until the end of the hills) and literal motion (The caterpillar crawled towards the top of the tree), along with their static controls. Several time sensitive locations, identified using a meta-analysis, showed activation specific to temporal metaphors, including in the left insula, right claustrum, and bilateral posterior superior temporal sulci. Fictive and literal motion contrasts did not show this difference. Fictive motion contrast showed activation in a conceptual motion sensitive area of the left posterior inferior temporal sulcus (ITS). These data suggest that language of time is at least partially grounded in experiential time. In addition, motion semantics has different consequences for events and objects: temporal events become animate, while static entities become motional. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Polymyalgia rheumatica and temporal arthritis.

    Science.gov (United States)

    Epperly, T D; Moore, K E; Harrover, J D

    2000-08-15

    Polymyalgia rheumatica and temporal arteritis are closely related inflammatory conditions that affect different cellular targets in genetically predisposed persons. Compared with temporal arteritis, polymyalgla rheumatica is much more common, affecting one in 200 persons older than 50 years. Temporal arteritis, however, is more dangerous and can lead to sudden blindness. The diagnosis of polymyalgia rheumatica is based on the presence of a clinical syndrome consisting of fever, nonspecific somatic complaints, pain and stiffness in the shoulder and pelvic girdles, and an elevated erythrocyte sedimentation rate. Temporal arteritis typically presents with many of the same findings as polymyalgia rheumatica, but patients also have headaches and tenderness to palpation over the involved artery. Arterial biopsy usually confirms the diagnosis of temporal arteritis. Early diagnosis and treatment of polymyalgia rheumatica or temporal arteritis can dramatically improve patients' lives and return them to previous functional status. Corticosteroid therapy provides rapid and dramatic improvement of the clinical features of both conditions. Therapy is generally continued for six to 24 months. Throughout treatment, clinical condition is assessed periodically. Patients are instructed to see their physician immediately if symptoms recur or they develop new headache, jaw claudication or visual problems.

  18. Remote temporal camouflage: contextual flicker disrupts perceived visual temporal order.

    Science.gov (United States)

    Cass, John; Van der Burg, Erik

    2014-10-01

    Correctly perceiving the temporal order of events is essential to many tasks. Despite this, the factors constraining our ability to make timing judgments remain largely unspecified. Here we present a new phenomenon demonstrating that perceived timing of visual events may be profoundly impaired by the mere presence of irrelevant events elsewhere in the visual field. Human observers saw two abrupt luminance events presented across a range of onset asynchronies. Temporal order judgment (TOJ) just noticeable differences (JNDs) provided a behavioural index of temporal precision. When target events were presented in isolation or in static distractor environments temporal resolution was very precise (JNDs ∼20ms). However, when surrounded by dynamic distractor events, performance deteriorated more than a factor of four. This contextual effect we refer to as Remote Temporal Camouflage (RTC) operates across large spatial and temporal distances and possesses a unique spatial distribution conforming to neither the predictions of attentional capture by transient events, nor by stimulus dependencies associated with other contextual phenomena such as surround suppression, crowding, object-substitution masking or motion-induced blindness. We propose that RTC is a consequence of motion-related masking whereby irrelevant motion signals evoked by dynamic distractors interfere with TOJ-relevant target-related apparent motion. Consistent with this we also show that dynamic visual distractors do not interfere with audio-visual TOJs. Not only is RTC the most spatially extensive contextual effect ever reported, it offers vision science a new technique with which to investigate temporal order performance, free of motion-related sensory contributions. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Grievous Temporal and Occipital Injury Caused by a Bear Attack

    Directory of Open Access Journals (Sweden)

    Sampath Chandra Prasad

    2013-01-01

    Full Text Available Bear attacks are reported from nearly every part of the world. The chance of a human encountering a bear increases as the remote bear territory diminishes. The sloth bear is one of the three species of bears found in India, which inhabits the forests of India and its neighboring countries. Here we describe a teenager who came to us with a critical injury involving the face, temporal and occipital bones inflicted by a sloth bear attack. He underwent a temporal exploration, facial nerve decompression, pinna reconstruction, and occipital bone repair to save him from fatality.

  20. Spatio-temporal data analytics for wind energy integration

    CERN Document Server

    Yang, Lei; Zhang, Junshan

    2014-01-01

    This SpringerBrief presents spatio-temporal data analytics for wind energy integration using stochastic modeling and optimization methods. It explores techniques for efficiently integrating renewable energy generation into bulk power grids. The operational challenges of wind, and its variability are carefully examined. A spatio-temporal analysis approach enables the authors to develop Markov-chain-based short-term forecasts of wind farm power generation. To deal with the wind ramp dynamics, a support vector machine enhanced Markov model is introduced. The stochastic optimization of economic di

  1. Statistical analysis of spatial and spatio-temporal point patterns

    CERN Document Server

    Diggle, Peter J

    2013-01-01

    Written by a prominent statistician and author, the first edition of this bestseller broke new ground in the then emerging subject of spatial statistics with its coverage of spatial point patterns. Retaining all the material from the second edition and adding substantial new material, Statistical Analysis of Spatial and Spatio-Temporal Point Patterns, Third Edition presents models and statistical methods for analyzing spatially referenced point process data. Reflected in the title, this third edition now covers spatio-temporal point patterns. It explores the methodological developments from th

  2. Mammalian transcription-coupled excision repair

    NARCIS (Netherlands)

    W. Vermeulen (Wim); M.I. Fousteri (Maria)

    2013-01-01

    textabstractTranscriptional arrest caused by DNA damage is detrimental for cells and organisms as it impinges on gene expression and thereby on cell growth and survival. To alleviate transcrip-tional arrest, cells trigger a transcription-dependent genome surveillance pathway, termed

  3. Hydra constitutively expresses transcripts involved in vertebrate ...

    Indian Academy of Sciences (India)

    Unknown

    conserved glycolytic pathway. Noggin is expressed in the Spemann organizer in the. Xenopus embryo and is required for neural induction. Figure 1. Noggin- and goosecoid-like transcripts in P. oligactis. (a) Noggin-like transcripts in the hypostomal region (hp) and basal disc (bp) in an adult hydra. (b) Noggin-like transcripts ...

  4. CYCLOPS reveals human transcriptional rhythms in health and disease.

    Science.gov (United States)

    Anafi, Ron C; Francey, Lauren J; Hogenesch, John B; Kim, Junhyong

    2017-05-16

    Circadian rhythms modulate many aspects of physiology. Knowledge of the molecular basis of these rhythms has exploded in the last 20 years. However, most of these data are from model organisms, and translation to clinical practice has been limited. Here, we present an approach to identify molecular rhythms in humans from thousands of unordered expression measurements. Our algorithm, cyclic ordering by periodic structure (CYCLOPS), uses evolutionary conservation and machine learning to identify elliptical structure in high-dimensional data. From this structure, CYCLOPS estimates the phase of each sample. We validated CYCLOPS using temporally ordered mouse and human data and demonstrated its consistency on human data from two independent research sites. We used this approach to identify rhythmic transcripts in human liver and lung, including hundreds of drug targets and disease genes. Importantly, for many genes, the circadian variation in expression exceeded variation from genetic and other environmental factors. We also analyzed hepatocellular carcinoma samples and show these solid tumors maintain circadian function but with aberrant output. Finally, to show how this method can catalyze medical translation, we show that dosage time can temporally segregate efficacy from dose-limiting toxicity of streptozocin, a chemotherapeutic drug. In sum, these data show the power of CYCLOPS and temporal reconstruction in bridging basic circadian research and clinical medicine.

  5. Regulation of Chlamydia Gene Expression by Tandem Promoters with Different Temporal Patterns.

    Science.gov (United States)

    Rosario, Christopher J; Tan, Ming

    2015-11-02

    Chlamydia is a genus of pathogenic bacteria with an unusual intracellular developmental cycle marked by temporal waves of gene expression. The three main temporal groups of chlamydial genes are proposed to be controlled by separate mechanisms of transcriptional regulation. However, we have noted genes with discrepancies, such as the early gene dnaK and the midcycle genes bioY and pgk, which have promoters controlled by the late transcriptional regulators EUO and σ(28). To resolve this issue, we analyzed the promoters of these three genes in vitro and in Chlamydia trachomatis bacteria grown in cell culture. Transcripts from the σ(28)-dependent promoter of each gene were detected only at late times in the intracellular infection, bolstering the role of σ(28) RNA polymerase in late gene expression. In each case, however, expression prior to late times was due to a second promoter that was transcribed by σ(66) RNA polymerase, which is the major form of chlamydial polymerase. These results demonstrate that chlamydial genes can be transcribed from tandem promoters with different temporal profiles, leading to a composite expression pattern that differs from the expression profile of a single promoter. In addition, tandem promoters allow a gene to be regulated by multiple mechanisms of transcriptional regulation, such as DNA supercoiling or late regulation by EUO and σ(28). We discuss how tandem promoters broaden the repertoire of temporal gene expression patterns in the chlamydial developmental cycle and can be used to fine-tune the expression of specific genes. Chlamydia is a pathogenic bacterium that is responsible for the majority of infectious disease cases reported to the CDC each year. It causes an intracellular infection that is characterized by coordinated expression of chlamydial genes in temporal waves. Chlamydial transcription has been shown to be regulated by DNA supercoiling, alternative forms of RNA polymerase, and transcription factors, but the number

  6. Perceptual Training Enhances Temporal Acuity for Multisensory Speech.

    Science.gov (United States)

    De Niear, Matthew A; Gupta, Pranjal B; Baum, Sarah H; Wallace, Mark T

    2017-10-28

    The temporal relationship between auditory and visual cues is a fundamental feature in the determination of whether these signals will be integrated. The window of perceived simultaneity (TBW) is a construct that describes the epoch of time during which asynchronous auditory and visual stimuli are likely to be perceptually bound. Recently, a number of studies have demonstrated the capacity for perceptual training to enhance temporal acuity for audiovisual stimuli (i.e., narrow the TBW). These studies, however, have only examined multisensory perceptual learning that develops in response to feedback that is provided when making judgments on simple, low-level audiovisual stimuli (i.e., flashes and beeps). Here we sought to determine if perceptual training was capable of altering temporal acuity for audiovisual speech. Furthermore, we also explored whether perceptual training with simple or complex audiovisual stimuli generalized across levels of stimulus complexity. Using a simultaneity judgment (SJ) task, we measured individuals' temporal acuity (as estimated by the TBW) prior to, immediately following, and one week after four consecutive days of perceptual training. We report that temporal acuity for audiovisual speech stimuli is enhanced following perceptual training using speech stimuli. Additionally, we find that changes in temporal acuity following perceptual training do not generalize across the levels of stimulus complexity in this study. Overall, the results suggest that perceptual training is capable of enhancing temporal acuity for audiovisual speech in adults, and that the dynamics of the changes in temporal acuity following perceptual training differ between simple audiovisual stimuli and more complex audiovisual speech stimuli. Copyright © 2017. Published by Elsevier Inc.

  7. Coding of multisensory temporal patterns in human superior temporal sulcus

    Directory of Open Access Journals (Sweden)

    Toemme eNoesselt

    2012-08-01

    Full Text Available Philosophers, psychologists, and neuroscientists have long been interested in how the temporal aspects of perception are represented in the brain. In the present study, we investigated the neural basis of the temporal perception of synchrony/asynchrony for audiovisual speech stimuli using functional magnetic imaging (fMRI. Subjects judged the temporal relation of (asynchronous audiovisual speech streams, and indicated any changes in their perception of the stimuli over time. Differential hemodynamic responses for synchronous versus asynchronous stimuli were observed in the multisensory superior temporal sulcus complex (mSTS-c and prefrontal cortex. Within mSTS-c we found adjacent regions expressing an enhanced BOLD-response to the different physical (asynchrony conditions. These regions were further modulated by the subjects’ perceptual state. By calculating the distances between the modulated regions within mSTS-c in single-subjects we demonstrate that the ‘auditory’ and ‘visual leading areas’ lie closer to ‘synchrony areas’ than to each other. Moreover, analysis of interregional connectivity indicates a stronger functional connection between multisensory prefrontal cortex and mSTS-c during the perception of asynchrony. Taken together, these results therefore suggest the presence of distinct sub-regions within the human STS-c for the maintenance of temporal relations for audiovisual speech stimuli plus differential functional connectivity with prefrontal regions. The respective local activity in mSTS-c is dependent both upon the physical properties of the stimuli presented and upon the subjects’ perception of (asynchrony.

  8. Mortality in Danish Swine herds: Spatio-temporal clusters and risk factors

    DEFF Research Database (Denmark)

    Lopes Antunes, Ana Carolina; Ersbøll, Annette Kjær; Bihrmann, Kristine

    2017-01-01

    The aim of this study was to explore spatio-temporal mortality patterns in Danish swine herds from December 2013 to October 2015, and to discuss the use of mortality data for syndromic surveillance in Denmark. Although it has previously been assessed within the context of syndromic surveillance......-temporal analysis included data description for spatial, temporal, and spatio-temporal cluster analysis for three age groups: weaners (up to 30 kg), sows and finishers. Logistic regression models were used to assess the potential factors associated with finisher and weaner herds being included within multiple...

  9. Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

    Directory of Open Access Journals (Sweden)

    Emanuel Gonçalves

    2017-01-01

    Full Text Available Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt and pheromone stimulation and developed a machine learning approach to explore regulatory associations between metabolism and signal transduction. Existing phosphoproteomics measurements under the same conditions and kinase-substrate regulatory interactions were used to in silico estimate the enzymatic activity of signalling kinases. Our approach identified informative associations between kinases and metabolic enzymes capable of predicting metabolic changes. We extended our analysis to two studies containing transcriptomics, phosphoproteomics and metabolomics measurements across a comprehensive panel of kinases/phosphatases knockouts and time-resolved perturbations to the nitrogen metabolism. Changes in activity of transcription factors, kinases and phosphatases were estimated in silico and these were capable of building predictive models to infer the metabolic adaptations of previously unseen conditions across different dynamic experiments. Time-resolved experiments were significantly more informative than genetic perturbations to infer metabolic adaptation. This difference may be due to the indirect nature of the associations and of general cellular states that can hinder the identification of causal relationships. This work provides a novel genome-scale integrative analysis to propose putative transcriptional and post-translational regulatory mechanisms of metabolic processes.

  10. Negative transcriptional regulation of mitochondrial transcription factor A (TFAM) by nuclear TFAM

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eun Jin; Kang, Young Cheol; Park, Wook-Ha; Jeong, Jae Hoon; Pak, Youngmi Kim, E-mail: ykpak@khu.ac.kr

    2014-07-18

    Highlights: • TFAM localizes in nuclei and mitochondria of neuronal cells. • Nuclear TFAM does not bind the Tfam promoter. • Nuclear TFAM reduced the Tfam promoter activity via suppressing NRF-1 activity. • A novel self-negative feedback regulation of Tfam gene expression is explored. • FAM may play different roles depending on its subcellular localizations. - Abstract: The nuclear DNA-encoded mitochondrial transcription factor A (TFAM) is synthesized in cytoplasm and transported into mitochondria. TFAM enhances both transcription and replication of mitochondrial DNA. It is unclear, however, whether TFAM plays a role in regulating nuclear gene expression. Here, we demonstrated that TFAM was localized to the nucleus and mitochondria by immunostaining, subcellular fractionation, and TFAM-green fluorescent protein hybrid protein studies. In HT22 hippocampal neuronal cells, human TFAM (hTFAM) overexpression suppressed human Tfam promoter-mediated luciferase activity in a dose-dependent manner. The mitochondria targeting sequence-deficient hTFAM also repressed Tfam promoter activity to the same degree as hTFAM. It indicated that nuclear hTFAM suppressed Tfam expression without modulating mitochondrial activity. The repression required for nuclear respiratory factor-1 (NRF-1), but hTFAM did not bind to the NRF-1 binding site of its promoter. TFAM was co-immunoprecipitated with NRF-1. Taken together, we suggest that nuclear TFAM down-regulate its own gene expression as a NRF-1 repressor, showing that TFAM may play different roles depending on its subcellular localizations.

  11. TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions

    KAUST Repository

    Schmeier, Sebastian

    2016-10-17

    Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.

  12. Transcription of nuclear organellar DNA in a model plant system.

    Science.gov (United States)

    Wang, Dong; Qu, Zhipeng; Adelson, David L; Zhu, Jian-Kang; Timmis, Jeremy N

    2014-05-27

    Endosymbiotic gene transfer from cytoplasmic organelles (chloroplasts and mitochondria) to the nucleus is an ongoing process in land plants. Although the frequency of organelle DNA migration is high, functional gene transfer is rare because a nuclear promoter is thought necessary for activity in the nucleus. Here we show that a chloroplast promoter, 16S rrn, drives nuclear transcription, suggesting that a transferred organellar gene may become active without obtaining a nuclear promoter. Examining the chromatin status of a known de novo chloroplast integrant indicates that plastid DNA inserts into open chromatin and that this relaxed condition is maintained after integration. Transcription of nuclear organelle DNA integrants was explored at the whole genome level by analyzing RNA-seq data of Oryza sativa subsp. japonica, and utilizing sequence polymorphisms to unequivocally discriminate nuclear organelle DNA transcripts from those of bona fide cytoplasmic organelle DNA. Nuclear copies of organelle DNA that are transcribed show a spectrum of transcriptional activity but at comparatively low levels compared with the majority of other nuclear genes. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Transcription-dependent association of HDAC2 with active chromatin.

    Science.gov (United States)

    Jahan, Sanzida; Sun, Jian-Min; He, Shihua; Davie, James R

    2018-02-01

    Histone deacetylase 2 (HDAC2) catalyzes deacetylation of histones at the promoter and coding regions of transcribed genes and regulates chromatin structure and transcription. To explore the role of HDAC2 and phosphorylated HDAC2 in gene regulation, we studied the location along transcribed genes, the mode of recruitment and the associated proteins with HDAC2 and HDAC2S394ph in chicken polychromatic erythrocytes. We show that HDAC2 and HDAC2S394ph are associated with transcriptionally active chromatin and located in the interchromatin channels. HDAC2S394ph was present primarly at the upstream promoter region of the transcribed CA2 and GAS41 genes, while total HDAC2 was also found within the coding region of the CA2 gene. Recruitment of HDAC2 to these genes was partially dependent upon on-going transcription. Unmodified HDAC2 was associated with RNA binding proteins and interacted with RNA bound to the initiating and elongating forms of RNA polymerase II. HDAC2S394ph was not associated with RNA polymerase II. These results highlight the differential properties of unmodified and phosphorylated HDAC2 and the organization of acetylated transcriptionally active chromatin in the chicken polychromatic erythrocyte. © 2017 Wiley Periodicals, Inc.

  14. Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription.

    Science.gov (United States)

    Dumay-Odelot, Hélène; Durrieu-Gaillard, Stéphanie; El Ayoubi, Leyla; Parrot, Camila; Teichmann, Martin

    2014-01-01

    Human RNA polymerase III transcribes small untranslated RNAs that contribute to the regulation of essential cellular processes, including transcription, RNA processing and translation. Analysis of this transcription system by in vitro transcription techniques has largely contributed to the discovery of its transcription factors and to the understanding of the regulation of human RNA polymerase III transcription. Here we review some of the key steps that led to the identification of transcription factors and to the definition of minimal promoter sequences for human RNA polymerase III transcription.

  15. Temporal discounting and inter-temporal choice in rhesus monkeys

    Directory of Open Access Journals (Sweden)

    Jaewon Hwang

    2009-06-01

    Full Text Available Humans and animals are more likely to take an action leading to an immediate reward than actions with delayed rewards of similar magnitudes. Although such devaluation of delayed rewards has been almost universally described by hyperbolic discount functions, the rate of this temporal discounting varies substantially among different animal species. This might be in part due to the differences in how the information about reward is presented to decision makers. In previous animal studies, reward delays or magnitudes were gradually adjusted across trials, so the animals learned the properties of future rewards from the rewards they waited for and consumed previously. In contrast, verbal cues have been used commonly in human studies. In the present study, rhesus monkeys were trained in a novel inter-temporal choice task in which the magnitude and delay of reward were indicated symbolically using visual cues and varied randomly across trials. We found that monkeys could extract the information about reward delays from visual symbols regardless of the number of symbols used to indicate the delay. The rate of temporal discounting observed in the present study was comparable to the previous estimates in other mammals, and the animal’s choice behavior was largely consistent with hyperbolic discounting. Our results also suggest that the rate of temporal discounting might be influenced by contextual factors, such as the novelty of the task. The flexibility furnished by this new inter-temporal choice task might be useful for future neurobiological investigations on inter-temporal choice in non-human primates.

  16. Mammalian Transcription-Coupled Excision Repair

    Science.gov (United States)

    Vermeulen, Wim; Fousteri, Maria

    2013-01-01

    Transcriptional arrest caused by DNA damage is detrimental for cells and organisms as it impinges on gene expression and thereby on cell growth and survival. To alleviate transcriptional arrest, cells trigger a transcription-dependent genome surveillance pathway, termed transcription-coupled nucleotide excision repair (TC-NER) that ensures rapid removal of such transcription-impeding DNA lesions and prevents persistent stalling of transcription. Defective TC-NER is causatively linked to Cockayne syndrome, a rare severe genetic disorder with multisystem abnormalities that results in patients’ death in early adulthood. Here we review recent data on how damage-arrested transcription is actively coupled to TC-NER in mammals and discuss new emerging models concerning the role of TC-NER-specific factors in this process. PMID:23906714

  17. The Journey of a Transcription Factor

    DEFF Research Database (Denmark)

    Pireyre, Marie

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

  18. Temporal Ventriloquism in Sensorimotor Synchronization

    Science.gov (United States)

    Parker, Melody Kay

    Perception of time is multisensory and therefore requires integration of the auditory and visual systems. Temporal ventriloquism is a phenomenon in which discrepant temporal aspects of multisensory stimuli are resolved through auditory dominance. Numerous prior experiments have demonstrated temporal ventriloquism using simple flash and click stimuli. The experiment presented herein employed a sensorimotor synchronization task to examine the effect of visual stimulus type across a range of stimulus onset asynchronies (SOA). This study compared sensorimotor response to three visual stimuli: a flash, a baton swinging, and a mallet striking a block. The results of the experiment indicated that the influence of SOA was greatly dependent on stimulus type. In contrast with the transient flash stimulus, the oscillatory visual stimuli provided more spatiotemporal information. This could explain the significantly reduced effect of temporal ventriloquism observed in response to the baton and mallet relative to the flash. Multisensory integration did not absolutely bias the auditory system; predictive visual dynamics proved useful in the unified perception of temporal occurrence.

  19. Envelhecimento do processamento temporal auditivo

    Directory of Open Access Journals (Sweden)

    Vera Tôrres das Neves

    Full Text Available O presente artigo faz uma revisão breve da literatura sobre envelhecimento auditivo, abordando os estudos sobre o envelhecimento do processamento temporal auditivo, especificamente, estudos sobre detecção de interrupções em sons, por sujeitos adultos de mais idade. São apresentadas definições e descrições da presbiacusia, suas conseqüências, e sua prevalência. São descritos os procedimentos experimentais para estudo de processamento temporal envolvendo a detecção de interrupções em ruídos com faixas amplas de freqüência, a discriminação de sons com reversão temporal, a detecção de mudanças na amplitude de sons, a detecção de interrupções em sons com faixas estreitas de freqüências, a detecção de diferenças de duração entre dois estímulos, bem como a discriminação da ordem temporal de diferentes canais de freqüência componentes de tons complexos. São revisados, adicionalmente, estudos que descrevem as características psicofísicas do processamento auditivo temporal em idosos. Finalmente, são apresentadas sugestões sobre direções futuras para pesquisa.

  20. Envelhecimento do processamento temporal auditivo

    Directory of Open Access Journals (Sweden)

    Neves Vera Tôrres das

    2002-01-01

    Full Text Available O presente artigo faz uma revisão breve da literatura sobre envelhecimento auditivo, abordando os estudos sobre o envelhecimento do processamento temporal auditivo, especificamente, estudos sobre detecção de interrupções em sons, por sujeitos adultos de mais idade. São apresentadas definições e descrições da presbiacusia, suas conseqüências, e sua prevalência. São descritos os procedimentos experimentais para estudo de processamento temporal envolvendo a detecção de interrupções em ruídos com faixas amplas de freqüência, a discriminação de sons com reversão temporal, a detecção de mudanças na amplitude de sons, a detecção de interrupções em sons com faixas estreitas de freqüências, a detecção de diferenças de duração entre dois estímulos, bem como a discriminação da ordem temporal de diferentes canais de freqüência componentes de tons complexos. São revisados, adicionalmente, estudos que descrevem as características psicofísicas do processamento auditivo temporal em idosos. Finalmente, são apresentadas sugestões sobre direções futuras para pesquisa.

  1. Temporal tendinitis: a modified Levandoski panoramic analysis of 21 cases.

    Science.gov (United States)

    Shankland, Wesley E

    2011-07-01

    In 1993, Levandoski published the details of a system to analyze panoramic radiographs and especially, the temporomandibular joints. Piedra expanded the work of Levandoski to analyze facial and dental asymmetries. In this brief treatise, the disorder of temporal tendinitis was explored. A modified Levandoski technique was used to compare the lengths of the coronoid and condylar processes in an attempt to demonstrate how the panoramic radiograph can be simply used in the diagnosis of temporal tendinitis in the retrospective study of 21 such cases. a total of 18 of the 21 coronoid processes (85%) were equal to or longer than their condylar process counterparts, thus indicating that a panoramic radiograph may be useful in the diagnosis of temporal tendinitis.

  2. Level and Temporal Trend of Perfluoroalkyl Acids in Greenlandic Inuit

    DEFF Research Database (Denmark)

    Long, Manhai; Bossi, Rossana; Bonefeld-Jørgensen, Eva Cecilie

    bears. However, until now, no data have been reported for PFAAs in Greenlandic Inuit. This study assesses the level and temporal trend of serum PFAAs in Greenlandic Inuit. Study design: Cross-section and temporal time trend survey. Methods: Serum PFAA levels were determined in 284 Inuit from different...... Greenlandic districts using liquid chromatography-tandem mass spectrometry with electrospray ionization. The temporal time trend of serum PFAAs in Nuuk Inuit during 19982005 and the correlation between serum PFAAs and legacy persistent organic pollutants (POPs) were explored. Results: Serum PFAA levels were...... higher in Nuuk Inuit than in non-Nuuk Inuit. Within the same district, higher PFAA levels were observed for males. An age-dependent, increasing trend of serum PFAA levels in the period from 19982005 was observed for Nuuk Inuit. For the pooled gender data, no significant association between PFAAs...

  3. Level and temporal trend of perfluoroalkyl acids in Greenlandic Inuit

    DEFF Research Database (Denmark)

    Long, Manhai; Bossi, Rossana; Bonefeld-Jørgensen, Eva Cecilie

    2012-01-01

    bears. However, until now, no data have been reported for PFAAs in Greenlandic Inuit. This study assesses the level and temporal trend of serum PFAAs in Greenlandic Inuit. Study design: Cross-section and temporal time trend survey. Methods: Serum PFAA levels were determined in 284 Inuit from different...... Greenlandic districts using liquid chromatography-tandem mass spectrometry with electrospray ionization. The temporal time trend of serum PFAAs in Nuuk Inuit during 19982005 and the correlation between serum PFAAs and legacy persistent organic pollutants (POPs) were explored. Results: Serum PFAA levels were...... higher in Nuuk Inuit than in non-Nuuk Inuit. Within the same district, higher PFAA levels were observed for males. An age-dependent, increasing trend of serum PFAA levels in the period from 19982005 was observed for Nuuk Inuit. For the pooled gender data, no significant association between PFAAs...

  4. Data from selective harvests underestimate temporal trends in quantitative traits.

    Science.gov (United States)

    Pelletier, Fanie; Festa-Bianchet, Marco; Jorgenson, Jon T

    2012-10-23

    Human harvests can select against phenotypes favoured by natural selection, and natural resource managers should evaluate possible artificial selection on wild populations. Because the required genetic data are extremely difficult to gather, however, managers typically rely on harvested animals to document temporal trends. It is usually unknown whether these data are unbiased. We explore our ability to detect a decline in horn size of bighorn sheep (Ovis canadensis) by comparing harvested males with all males in a population where evolutionary changes owing to trophy hunting were previously reported. Hunting records underestimated the temporal decline, partly because of an increasing proportion of rams that could not be harvested because their horns were smaller than the threshold set by hunting regulations. If harvests are selective, temporal trends measured from harvest records will underestimate the magnitude of changes in wild populations.

  5. Declarative Programming with Temporal Constraints, in the Language CG

    Science.gov (United States)

    2015-01-01

    Specifying and interpreting temporal constraints are key elements of knowledge representation and reasoning, with applications in temporal databases, agent programming, and ambient intelligence. We present and formally characterize the language CG, which tackles this issue. In CG, users are able to develop time-dependent programs, in a flexible and straightforward manner. Such programs can, in turn, be coupled with evolving environments, thus empowering users to control the environment's evolution. CG relies on a structure for storing temporal information, together with a dedicated query mechanism. Hence, we explore the computational complexity of our query satisfaction problem. We discuss previous implementation attempts of CG and introduce a novel prototype which relies on logic programming. Finally, we address the issue of consistency and correctness of CG program execution, using the Event-B modeling approach. PMID:25893212

  6. Declarative Programming with Temporal Constraints, in the Language CG.

    Science.gov (United States)

    Negreanu, Lorina

    2015-01-01

    Specifying and interpreting temporal constraints are key elements of knowledge representation and reasoning, with applications in temporal databases, agent programming, and ambient intelligence. We present and formally characterize the language CG, which tackles this issue. In CG, users are able to develop time-dependent programs, in a flexible and straightforward manner. Such programs can, in turn, be coupled with evolving environments, thus empowering users to control the environment's evolution. CG relies on a structure for storing temporal information, together with a dedicated query mechanism. Hence, we explore the computational complexity of our query satisfaction problem. We discuss previous implementation attempts of CG and introduce a novel prototype which relies on logic programming. Finally, we address the issue of consistency and correctness of CG program execution, using the Event-B modeling approach.

  7. Do temporal processes underlie left hemisphere dominance in speech perception?

    Science.gov (United States)

    Scott, Sophie K; McGettigan, Carolyn

    2013-10-01

    It is not unusual to find it stated as a fact that the left hemisphere is specialized for the processing of rapid, or temporal aspects of sound, and that the dominance of the left hemisphere in the perception of speech can be a consequence of this specialization. In this review we explore the history of this claim and assess the weight of this assumption. We will demonstrate that instead of a supposed sensitivity of the left temporal lobe for the acoustic properties of speech, it is the right temporal lobe which shows a marked preference for certain properties of sounds, for example longer durations, or variations in pitch. We finish by outlining some alternative factors that contribute to the left lateralization of speech perception. Copyright © 2013. Published by Elsevier Inc.

  8. Declarative Programming with Temporal Constraints, in the Language CG

    Directory of Open Access Journals (Sweden)

    Lorina Negreanu

    2015-01-01

    Full Text Available Specifying and interpreting temporal constraints are key elements of knowledge representation and reasoning, with applications in temporal databases, agent programming, and ambient intelligence. We present and formally characterize the language CG, which tackles this issue. In CG, users are able to develop time-dependent programs, in a flexible and straightforward manner. Such programs can, in turn, be coupled with evolving environments, thus empowering users to control the environment’s evolution. CG relies on a structure for storing temporal information, together with a dedicated query mechanism. Hence, we explore the computational complexity of our query satisfaction problem. We discuss previous implementation attempts of CG and introduce a novel prototype which relies on logic programming. Finally, we address the issue of consistency and correctness of CG program execution, using the Event-B modeling approach.

  9. Gene transcription and electromagnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, A.S.

    1992-01-01

    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.

  10. Temporal Lobe Epilepsy in Children

    Science.gov (United States)

    Nickels, Katherine C.; Wong-Kisiel, Lily C.; Moseley, Brian D.; Wirrell, Elaine C.

    2012-01-01

    The temporal lobe is a common focus for epilepsy. Temporal lobe epilepsy in infants and children differs from the relatively homogeneous syndrome seen in adults in several important clinical and pathological ways. Seizure semiology varies by age, and the ictal EEG pattern may be less clear cut than what is seen in adults. Additionally, the occurrence of intractable seizures in the developing brain may impact neurocognitive function remote from the temporal area. While many children will respond favorably to medical therapy, those with focal imaging abnormalities including cortical dysplasia, hippocampal sclerosis, or low-grade tumors are likely to be intractable. Expedient workup and surgical intervention in these medically intractable cases are needed to maximize long-term developmental outcome. PMID:22957247

  11. Temporal Lobe Epilepsy in Children

    Directory of Open Access Journals (Sweden)

    Katherine C. Nickels

    2012-01-01

    Full Text Available The temporal lobe is a common focus for epilepsy. Temporal lobe epilepsy in infants and children differs from the relatively homogeneous syndrome seen in adults in several important clinical and pathological ways. Seizure semiology varies by age, and the ictal EEG pattern may be less clear cut than what is seen in adults. Additionally, the occurrence of intractable seizures in the developing brain may impact neurocognitive function remote from the temporal area. While many children will respond favorably to medical therapy, those with focal imaging abnormalities including cortical dysplasia, hippocampal sclerosis, or low-grade tumors are likely to be intractable. Expedient workup and surgical intervention in these medically intractable cases are needed to maximize long-term developmental outcome.

  12. SILAC-Based Temporal Phosphoproteomics

    DEFF Research Database (Denmark)

    Francavilla, Chiara; Hekmat, Omid; Blagoev, Blagoy

    2014-01-01

    In recent years, thanks to advances in Mass Spectrometry (MS)-based quantitative proteomics, studies on signaling pathways have moved from a detailed description of individual components to system-wide analysis of entire signaling cascades, also providing spatio-temporal views of intracellular...... tyrosines by immunoaffinity and then further enriched for phosphorylated serine/threonine peptides by strong cation exchange in combination with titanium dioxide-beads chromatography. Analysis of enriched peptides on Orbitrap-based MS results in comprehensive and accurate reconstruction of temporal changes...... signaling events. Here we provide an optimized SILAC-based proteomic workflow to analyze temporal changes in phosphoproteomes, which involve a generic three step enrichment protocol for phosphopeptides. SILAC-labeled peptides from digested whole cell lysates are as a first step enriched for phosphorylated...

  13. Heart morphogenesis gene regulatory networks revealed by temporal expression analysis.

    Science.gov (United States)

    Hill, Jonathon T; Demarest, Bradley; Gorsi, Bushra; Smith, Megan; Yost, H Joseph

    2017-10-01

    During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks (GRNs) driving this phase of heart development, during which many congenital heart disease malformations likely arise, we conducted an RNA-seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern, identified transcription factor binding motifs enriched in each cluster, and generated a model GRN for the major gene batteries in heart morphogenesis. This approach predicted hundreds of regulatory interactions and found batteries enriched in specific cell and tissue types, indicating that the approach can be used to narrow the search for novel genetic markers and regulatory interactions. Subsequent analyses confirmed the GRN using two mutants, Tbx5 and nkx2-5, and identified sets of duplicated zebrafish genes that do not show temporal subfunctionalization. This dataset provides an essential resource for future studies on the genetic/epigenetic pathways implicated in congenital heart defects and the mechanisms of cardiac transcriptional regulation. © 2017. Published by The Company of Biologists Ltd.

  14. [Temporal orientation and cognitive impairment].

    Science.gov (United States)

    Fernandez-Turrado, T; Pascual-Millan, L F; Aguilar-Palacio, I; Burriel-Rosello, A; Santolaria-Martinez, L; Perez-Lazaro, C

    2011-03-16

    Temporal orientation is a component of most screening tests for diagnosing cognitive impairment. Correct temporal orientation involves activating both semantic information (concepts of the calendar date) and episodic information (remembering the current date). The aim of this study was to assess the diagnostic usefulness of a technique for evaluating temporal orientation, which was open-ended, and scoring the semantic and episodic information thus generated (0-10 points). A total of 24 subjects without impairment, 77 patients with mild cognitive impairment (MCI) and 62 patients with dementia were evaluated by means of a 30-point mini-mental/mini-examination, semantic verbal fluency test, global deterioration scale, mini-mental-type temporal orientation and open-ended temporal orientation tests. The areas under the curve (aROC), sensitivity and specificity for dementia and cognitive impairment at any degree (MCI and dementia) were analysed. Open-ended temporal orientation presented a greater area under the curve (aROC: 0.90) for discrimination between patients with dementia and without dementia (MCI and without impairment) and an aROC of 0.83 for discrimination between patients with MCI or dementia and without impairment. For dementia, with a cut-off point equal to or below 6, sensitivity was 0.96 and specificity was 0.68, and for MCI with dementia, with a cut-off point equal to or below 7, sensitivity was 0.72 and specificity was 0.92. The usefulness, conciseness and strategic position of this technique in examining mental status make it suitable as an instrument for screening for cognitive impairment. It has a high level of sensitivity with low specificity for dementia and low sensitivity with high specificity for any degree of impairment.

  15. 10 CFR 9.108 - Certification, transcripts, recordings and minutes.

    Science.gov (United States)

    2010-01-01

    ... transcription as provided in § 9.14. The Secretary shall maintain a complete verbatim copy of the transcript, a...). Copies of such transcript, or minutes, or a transcription of such recording disclosing the identity of...

  16. Optical noise and temporal coherence

    Science.gov (United States)

    Chavel, P.

    1980-08-01

    Previous articles have been devoted to the study of optical noise as a function of spatial coherence. The present one completes this study by considering temporal coherence. Noise arising from defects in the pupil plane and affecting the high spatial frequencies of an image is notably reduced by white-light illumination. Temporal coherence has little effect on noise arising from defects in the object plane. However, impulse noise due to small isolated defects is reduced in size. Physical arguments are presented to explain these phenomena and a mathematical study of partially coherent imaging in the presence of random defects is given.

  17. Temporal context for authorship attribution

    DEFF Research Database (Denmark)

    Hansen, Niels Dalum; Lioma, Christina; Larsen, Birger

    2014-01-01

    A study of temporal aspects of authorship attribution - a task which aims to distinguish automatically between texts written by different authors by measuring textual features. This task is important in a number of areas, including plagiarism detection in secondary education, which we study...... in this work. As the academic abilities of students evolve during their studies, so does their writing style. These changes in writing style form a type of temporal context, which we study for the authorship attribution process by focussing on the students’ more recent writing samples. Experiments with real...

  18. Emotions are temporal interpersonal systems.

    Science.gov (United States)

    Butler, Emily A

    2017-10-01

    Several characteristics of emotions are that they: first, evolve dynamically over time, second, extend beyond the individual to incorporate multiple people, and third, function as a system. In other words, emotions can be seen as temporal interpersonal systems. This review summarizes current models for temporal interpersonal emotion systems (TIES), evidence they matter beyond levels of emotional responding, their connections with relationship quality and interpersonal regulation, and some of the challenges for studying them. Important directions for future research include distinguishing between different patterns of interpersonal emotional dynamics and extending theory and experimental work to uncover mechanisms for altering harmful TIES and promoting beneficial ones. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Translation with frameshifting of ribosome along mRNA transcript

    CERN Document Server

    Li, Jingwei

    2015-01-01

    Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been developed to determine the biochemical mechanism of translation. However, to simplify the majority of the existing models, the frameshifting of ribosome along the mRNA transcript is neglected, which actually occurs in real cells and has been extensively experimentally studied. The frameshifting of ribosome evidently influences the efficiency and speed of translation, considering that the peptide chains synthesized by shifted ribosomes will not fold into functional proteins and will degrade rapidly. In this study, a theoretical model is presented to describe the translational process based on the model for totally asymmetric simple exclusion process. In this model, the frameshifting of the ribosome along the mRNA transcript and the attachment/detachment of the ribosome to/from the ...

  20. Transcriptional response of polycomb group genes to status epilepticus in mice is modified by prior exposure to epileptic preconditioning

    Directory of Open Access Journals (Sweden)

    James eReynolds

    2015-03-01

    Full Text Available Exposure of the brain to brief, non-harmful seizures can activate protective mechanisms that temporarily generate a damage-refractory state. This process, termed epileptic tolerance, is associated with large-scale down-regulation of gene expression. Polycomb group proteins are master controllers of gene silencing during development that are re-activated by injury to the brain. Here we explored the transcriptional response of genes associated with polycomb repressor complex (PRC 1 (Ring1A and Ring1B and Bmi1 and PRC2 (Ezh1, Ezh2 and Suz12, as well as additional transcriptional regulators Sirt1, Yy1 and Yy2, in a mouse model of status epilepticus. Findings were contrasted to changes after status epilepticus in mice previously given brief seizures to evoke tolerance. Real-time quantitative PCR showed status epilepticus prompted an early (1 h increase in expression of several genes in PRC1 and PRC2 in the hippocampus, followed by down-regulation of many of the same genes at later times points (4 , 8 and 24 h. Spatio-temporal differences were found among PRC2 genes in epileptic tolerance, including increased expression of Ezh2, Suz12 and Yy2 relative to the normal injury response to status epilepticus. In contrast, PRC1 complex genes including Ring 1B and Bmi1 displayed differential down-regulation in epileptic tolerance. The present study characterizes polycomb group gene expression following status epilepticus and shows prior seizure exposure produces select changes to PRC1 and PRC2 composition that may influence differential gene expression in epileptic tolerance.

  1. Automatic Drums Transcription for polyphonic music using Non-Negative Matrix Factor Deconvolution

    OpenAIRE

    Pons i Puig, Jordi

    2014-01-01

    [ANGLÈS] This thesis presents an automatic procedure for the detection and classification of percussive sounds in polyphonic audio mixes. The proposed method uses an extension of Non-negative Matrix Factorization (NMF) [1] which is capable to identify patterns with a temporal structure: Non-negative Matrix Factor Deconvolution (NMD) [2]. A complete drum transcription aims to be achieved with the time localization of the onsets and the identification of the percussive sounds. This work is focu...

  2. Temporality of Features in Near-Death Experience Narratives

    Directory of Open Access Journals (Sweden)

    Charlotte Martial

    2017-06-01

    Full Text Available Background: After an occurrence of a Near-Death Experience (NDE, Near-Death Experiencers (NDErs usually report extremely rich and detailed narratives. Phenomenologically, a NDE can be described as a set of distinguishable features. Some authors have proposed regular patterns of NDEs, however, the actual temporality sequence of NDE core features remains a little explored area.Objectives: The aim of the present study was to investigate the frequency distribution of these features (globally and according to the position of features in narratives as well as the most frequently reported temporality sequences of features.Methods: We collected 154 French freely expressed written NDE narratives (i.e., Greyson NDE scale total score ≥ 7/32. A text analysis was conducted on all narratives in order to infer temporal ordering and frequency distribution of NDE features.Results: Our analyses highlighted the following most frequently reported sequence of consecutive NDE features: Out-of-Body Experience, Experiencing a tunnel, Seeing a bright light, Feeling of peace. Yet, this sequence was encountered in a very limited number of NDErs.Conclusion: These findings may suggest that NDEs temporality sequences can vary across NDErs. Exploring associations and relationships among features encountered during NDEs may complete the rigorous definition and scientific comprehension of the phenomenon.

  3. Single-molecule RNA observation in vivo reveals dynamics of co-transcriptional splicing

    Science.gov (United States)

    Ferguson, M. L.; Coulon, A.; de Turris, V.; Palangat, M.; Chow, C. C.; Singer, R. H.; Larson, D. R.

    2013-03-01

    The synthesis of pre-mRNA and the splicing of that pre-mRNA to form completed transcripts requires coordination between two large multi-subunit complexes (the transcription elongation complex and the spliceosome). How this coordination occurs in vivo is unknown. Here we report the first experimental observation of transcription and splicing occurring at the same gene in living cells. By utilizing the PP7/MS2 fluorescent RNA reporter system, we can directly observe two distinct regions of the nascent RNA, allowing us to measure the rise and fall time of the intron and exon of a reporter gene stably integrated into a human cell line. The reporter gene consists of a beta globin gene where we have inserted a 24 RNA hairpin cassette into the intron/exon. Upon synthesis, the RNA hairpins are tightly bound by fluorescently-labeled PP7/MS2 bacteriophage coat proteins. After gene induction, a single locus of active transcription in the nucleus shows fluorescence intensity changes characteristic of the synthesis and excision of the intron/exon. Using fluctuation analysis, we determine the elongation rate to be 1.5 kb/min. From the temporal cross correlation function, we determine that splicing of this gene must be co-transcriptional with a splicing time of ~100 seconds before termination and a ~200 second pause at termination. We propose that dual-color RNA imaging may be extended to investigate other mechanisms of transcription, gene regulation, and RNA processing.

  4. Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis.

    Science.gov (United States)

    Chow, Brenda Y; Sanchez, Sabrina E; Breton, Ghislain; Pruneda-Paz, Jose L; Krogan, Naden T; Kay, Steve A

    2014-07-07

    Circadian clocks allow organisms to anticipate daily changes in the environment to enhance overall fitness. Transcription factors (TFs) play a prominent role in the molecular mechanism but are incompletely described possibly due to functional redundancy, gene family proliferation, and/or lack of context-specific assays. To overcome these, we performed a high-throughput yeast one-hybrid screen using the LUX ARRYHTHMO (LUX) gene promoter as bait against an Arabidopsis TF library. LUX is a unique gene because its mutation causes severe clock defects and transcript maintains high-amplitude cycling in the cold. We report the well-characterized cold-inducible C-repeat (CRT)/drought-responsive element (DRE) binding factor CBF1/DREB1b is a transcriptional regulator of LUX. We show that CBF1 binds the CRT in the LUX promoter, and both genes overlap in temporal and spatial expression. CBF1 overexpression causes upregulation of LUX and also alters other clock gene transcripts. LUX promoter regions including the CRT and Evening Element (EE) are sufficient for high-amplitude transcriptional cycling in the cold, and cold-acclimated lux seedlings are sensitive to freezing stress. Our data show cold signaling is integrated into the clock by CBF-mediated regulation of LUX expression, thereby defining a new transcriptional mechanism for temperature input to the circadian clock. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Temporal hypometabolism at the onset of cryptogenic temporal lobe epilepsy

    Energy Technology Data Exchange (ETDEWEB)

    Matheja, P.; Kuwert, T.; Weckesser, M.; Schober, O. [Dept. of Nuclear Medicine, Muenster Univ. (Germany); Luedemann, P.; Kellinghaus, C.; Diehl, B.; Ringelstein, E.B. [Dept. of Neurology, Muenster Univ. (Germany); Schuierer, G. [Dept. of Clinical Radiology, Muenster Univ. (Germany)

    2001-05-01

    Most patients with intractable temporal lobe epilepsy (TLE) exhibit temporal glucose hypometabolism. The reasons for the development of this abnormality are as yet unclear. The current notion is that an initial injury causes seizures, which in turn give rise to hypometabolism. The aim of this study was to assess whether temporal reductions in glucose metabolism in non-lesional TLE are the result of repeated seizures or whether hypometabolism represents an initial disturbance at the onset of disease. Glucose consumption was assessed with fluorine-18 fluorodeoxyglucose positron emission tomography ({sup 18}F-FDG PET) in 62 patients with cryptogenic non-refractory TLE in different stages of disease. Twelve subjects without neurological illness served as controls. Patients with onset of epilepsy at least 3 years prior to the PET scan were defined as having chronic TLE. Using this criterion, the whole patient cohort included 27 patients with de novo TLE and 35 patients with chronic TLE. The groups were matched for age and sex. The appearance of high-resolution magnetic resonance images of the brain was unremarkable in all patients. In the total cohort, number, duration and frequency of seizures had a significant relation to the magnitude of hypometabolism. Temporal hypometabolism was exhibited by 26 of the 62 patients (42%), including 8 out of 27 (30%) with newly diagnosed TLE and 18 out of 35 (51%) with chronic TLE. The disturbances were more extensive and more severe in patients with chronic TLE. It is concluded that temporal hypometabolism may already be present at the onset of TLE, but is less frequent and less severe in newly diagnosed than in chronic TLE. The metabolic disturbance correlates with the number of seizures. These findings suggest that an initial dysfunction is present in a considerable number of patients and that hypometabolism is worsened by continuing epileptic activity. (orig.)

  6. Coding of multisensory temporal patterns in human superior temporal sulcus.

    Science.gov (United States)

    Noesselt, Tömme; Bergmann, Daniel; Heinze, Hans-Jochen; Münte, Thomas; Spence, Charles

    2012-01-01

    Philosophers, psychologists, and neuroscientists have long been interested in how the temporal aspects of perception are represented in the brain. In the present study, we investigated the neural basis of the temporal perception of synchrony/asynchrony for audiovisual speech stimuli using functional magnetic resonance imaging (fMRI). Subjects judged the temporal relation of (a)synchronous audiovisual speech streams, and indicated any changes in their perception of the stimuli over time. Differential hemodynamic responses for synchronous versus asynchronous stimuli were observed in the multisensory superior temporal sulcus complex (mSTS-c) and prefrontal cortex. Within mSTS-c we found adjacent regions expressing an enhanced BOLD-response to the different physical (a)synchrony conditions. These regions were further modulated by the subjects' perceptual state. By calculating the distances between the modulated regions within mSTS-c in single-subjects we demonstrate that the "auditory leading (A(L))" and "visual leading (V(L)) areas" lie closer to "synchrony areas" than to each other. Moreover, analysis of interregional connectivity indicates a stronger functional connection between multisensory prefrontal cortex and mSTS-c during the perception of asynchrony. Taken together, these results therefore suggest the presence of distinct sub-regions within the human STS-c for the maintenance of temporal relations for audiovisual speech stimuli plus differential functional connectivity with prefrontal regions. The respective local activity in mSTS-c is dependent both upon the physical properties of the stimuli presented and upon the subjects' perception of (a)synchrony.

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

    Science.gov (United States)

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

    2015-11-05

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

  8. Aerobic glycolysis tunes YAP/TAZ transcriptional activity.

    Science.gov (United States)

    Enzo, Elena; Santinon, Giulia; Pocaterra, Arianna; Aragona, Mariaceleste; Bresolin, Silvia; Forcato, Mattia; Grifoni, Daniela; Pession, Annalisa; Zanconato, Francesca; Guzzo, Giulia; Bicciato, Silvio; Dupont, Sirio

    2015-05-12

    Increased glucose metabolism and reprogramming toward aerobic glycolysis are a hallmark of cancer cells, meeting their metabolic needs for sustained cell proliferation. Metabolic reprogramming is usually considered as a downstream consequence of tumor development and oncogene activation; growing evidence indicates, however, that metabolism on its turn can support oncogenic signaling to foster tumor malignancy. Here, we explored how glucose metabolism regulates gene transcription and found an unexpected link with YAP/TAZ, key transcription factors regulating organ growth, tumor cell proliferation and aggressiveness. When cells actively incorporate glucose and route it through glycolysis, YAP/TAZ are fully active; when glucose metabolism is blocked, or glycolysis is reduced, YAP/TAZ transcriptional activity is decreased. Accordingly, glycolysis is required to sustain YAP/TAZ pro-tumorigenic functions, and YAP/TAZ are required for the full deployment of glucose growth-promoting activity. Mechanistically we found that phosphofructokinase (PFK1), the enzyme regulating the first committed step of glycolysis, binds the YAP/TAZ transcriptional cofactors TEADs and promotes their functional and biochemical cooperation with YAP/TAZ. Strikingly, this regulation is conserved in Drosophila, where phosphofructokinase is required for tissue overgrowth promoted by Yki, the fly homologue of YAP. Moreover, gene expression regulated by glucose metabolism in breast cancer cells is strongly associated in a large dataset of primary human mammary tumors with YAP/TAZ activation and with the progression toward more advanced and malignant stages. These findings suggest that aerobic glycolysis endows cancer cells with particular metabolic properties and at the same time sustains transcription factors with potent pro-tumorigenic activities such as YAP/TAZ. © 2015 The Authors.

  9. Microsurgical treatment of temporal lobe arachnoid cysts complicated with epilepsy

    Directory of Open Access Journals (Sweden)

    Yong-qin KUANG

    2011-02-01

    Full Text Available Objective To explore the technique and precautions of microsurgical treatment of temporal lobe arachnoid cysts complicated with spilepsy.Methods The clinical data of 32 patients with temporal lobe arachnoid cysts complicated with epilepsy,admitted from Nov.2007 to Apr.2010,were analyzed retrospectively.The diagnosis of temporal lobe arachnoid cysts was confirmed before surgical operation by cranial MRI or CT.Continual video-electroencephalogram monitoring with sphenoidal electrodes were employed in all patients,and spike-wave,polyspike-wave and/or sharp-slow-wave was detected at arachnoid cyst side.Craniotomy was performed under general anesthesia,the temporal lobe arachnoid cysts were treated by microsurgical excision.Besides,partial anterior temporal lobectomy,hippocampectomy,amygdalotomy and bipolar electrogulation on functional cortex were conducted in all cases.Intraoperative electroencephalography(EEG monitoring was used in all patients.And an one year follow-up after surgery was carried out.Results No postoperative death occurred.Transient aphasia and hemiplegia were found in 14 patients(10 in left and 4 in right and recovered 7-10 days after treatment.A one-year MRI follow-up showed the temporal lobe arachnoid cysts disappeared in 12 patients(37.5%,shrank in 8(25.0%,and unchanged in 12(37.5%.Epileptic symptom disappeared in 27 cases(84.4% and temporary symptoms could be observed in 5 cases(15.6%.Continual video-electroencephalogram monitoring with sphenoidal electrodes showed no spike-wave,but sharp wave was detected in 8 cases and sharp-slow wave complexes were detected in 4 cases.Conclusion Microsurgery used in resection of the cysts and epileptic foci may achieve good therapeutic effects for temporal lobe arachnoid cysts complicated with epilepsy.

  10. Temporally remote destabilization of prediction after rare breaches of expectancy.

    Science.gov (United States)

    Kühn, Anne B; Schubotz, Ricarda I

    2012-08-01

    While neural signatures of breaches of expectancy and their immediate effects have been investigated, thus far, temporally more remote effects have been neglected. The present fMRI study explored neural correlates of temporally remote destabilization of prediction following rare breaches of expectancy with a mean delay of 14 s. We hypothesized temporally remote destabilization to be reflected either in an attenuation of areas related to long-term memory or in an increase of lateral fronto-parietal loops related to the encoding of new stimuli. Monitoring a deterministic 24-digit sequence, subjects were asked to indicate occasional sequential omissions by key press. Temporally remote destabilization of prediction was expected to be revealed by contrasting sequential events whose equivalent was omitted in the preceding sequential run n-1 (destabilized events) with sequential events without such history (nondestabilized events). Temporally remote destabilization of prediction was reflected in an attenuation of activity in the dorsal frontomedian cortex (Brodmann Area (BA) 9) bilaterally. Moreover, activation of the left medial BA 9 was enhanced by contrasting nondestabilized events with breaches. The decrease of dorsal frontomedian activation in the case of destabilized events might be interpreted as a top-down modulation on perception causing a less expectation-restricted encoding of the current stimulus and hence enabling the adaptation of expectation and prediction in the long run. Copyright © 2011 Wiley Periodicals, Inc.

  11. Dissociable spatial and temporal effects of inhibition of return.

    Directory of Open Access Journals (Sweden)

    Zhiguo Wang

    Full Text Available Inhibition of return (IOR refers to the relative suppression of processing at locations that have recently been attended. It is frequently explored using a spatial cueing paradigm and is characterized by slower responses to cued than to uncued locations. The current study investigates the impact of IOR on overt visual orienting involving saccadic eye movements. Using a spatial cueing paradigm, our experiments have demonstrated that at a cue-target onset asynchrony (CTOA of 400 ms saccades to the vicinity of cued locations are not only delayed (temporal cost but also biased away (spatial effect. Both of these effects are basically no longer present at a CTOA of 1200 ms. At a shorter 200 ms CTOA, the spatial effect becomes stronger while the temporal cost is replaced by a temporal benefit. These findings suggest that IOR has a spatial effect that is dissociable from its temporal effect. Simulations using a neural field model of the superior colliculus (SC revealed that a theory relying on short-term depression (STD of the input pathway can explain most, but not all, temporal and spatial effects of IOR.

  12. Birth Control Explorer

    Science.gov (United States)

    ... STIs Media Facebook Twitter Tumblr Shares · 579 Birth Control Explorer Sort by all methods most effective methods ... You are here Home » Birth Control Explorer Birth Control Explorer If you’re having sex —or if ...

  13. Bile Duct Exploration

    Science.gov (United States)

    ... Departments Home / Health Library / Articles / Bile Duct Exploration Bile Duct Exploration The CBD is a tube connecting the ... liver and gallbladder to the intestine. When is bile duct exploration performed? If something is blocking the bile ...

  14. Spatial and Temporal Ray Differentials

    DEFF Research Database (Denmark)

    Sporring, Jon; Schjøth, Lars; Erleben, Kenny

    We consider ray bundles emanating from a source such as a camera or light source. We derive the full spatial and temporal structure to ¿rst order of the intersection of ray bundles with scene geometry, where scene geometry given as any implicit function. Further, we present the full details of 2...

  15. Temporal structures in shell models

    DEFF Research Database (Denmark)

    Okkels, F.

    2001-01-01

    The intermittent dynamics of the turbulent Gledzer, Ohkitani, and Yamada shell-model is completely characterized by a single type of burstlike structure, which moves through the shells like a front. This temporal structure is described by the dynamics of the instantaneous configuration of the shell...

  16. Temporal Processing Dysfunction in Schizophrenia

    Science.gov (United States)

    Carroll, Christine A.; Boggs, Jennifer; O'Donnell, Brian F.; Shekhar, Anantha; Hetrick, William P.

    2008-01-01

    Schizophrenia may be associated with a fundamental disturbance in the temporal coordination of information processing in the brain, leading to classic symptoms of schizophrenia such as thought disorder and disorganized and contextually inappropriate behavior. Despite the growing interest and centrality of time-dependent conceptualizations of the…

  17. Temporal Structures in Shell Models

    OpenAIRE

    Okkels, Fridolin

    2000-01-01

    The intermittent dynamics of the turbulent GOY shell-model is characterised by a single type of burst-like structure, which moves through the shells like a front. This temporal structure is described by the dynamics of the instantaneous configuration of the shell-amplitudes revealing a approximative chaotic attractor of the dynamics.

  18. Semiology of temporal lobe epilepsies.

    Science.gov (United States)

    Abou-Khalil, Bassel W

    2003-07-01

    Temporal lobe epilepsies (TLE) represent the majority of the partial symptomatic/cryptogenic epilepsies. Excellent results of epilepsy surgery in well-selected patients have encouraged a search for localizing and lateralizing signs that could assist in the identification of the best surgical candidates. Seizure types in TLE include simple partial, complex partial and secondarily generalized seizures. Temporal lobe seizures most often arise in the amygdalo-hippocampal region. More than 90% of patients with mesial TLE report an aura, most commonly an epigastric sensation that often has a rising character. Other autonomic symptoms, psychic symptoms, and certain sensory phenomena (such as olfactory) also occur. The complex partial seizures of mesial TLE often involve motor arrest, oroalimentary automatisms or non-specific extremity automatisms at onset. Ictal manifestations that have lateralizing value include dystonic posturing (contralateral), early head turning (usually ipsilateral), and adversive head turning in transition to generalization (contralateral). Well-formed ictal language favors right temporal localization. Ictal vomiting, spitting, and drinking tend to be right sided. The duration of TLE complex partial seizures is generally greater than one minute and postictal confusion usually occurs. When postictal aphasia is noted a left-sided lateralization is favored. A lateral temporal onset is less common in TLE, and is most often suggested by an auditory aura. Somatosensory and visual auras are highly unlikely with TLE, and suggest neocortical extratemporal localization. A cephalic aura is non-specific, but is more common in frontal lobe epilepsy.

  19. Temporal scaling in information propagation.

    Science.gov (United States)

    Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi

    2014-06-18

    For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.

  20. Temporal scaling in information propagation

    Science.gov (United States)

    Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi

    2014-06-01

    For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.

  1. Temporal form in interaction design

    DEFF Research Database (Denmark)

    Vallgårda, Anna; Winther, Morten Trøstrup; Mørch, Nina

    2015-01-01

    temporal forms by letting a series of expert designers reflect upon them. We borrow a framework from Boorstin’s film theory in which he distinguishes between the voyeuristic, the vicarious, and the visceral experience. We show how to use rhythms, complexity, gentle or forceful behavior, etc., to create...

  2. Osteoradionecrosis of the temporal bone

    Energy Technology Data Exchange (ETDEWEB)

    Fujimori, Masato; Koyama, Yukiko; Enomoto, Fuyuki; Ichikawa, Ginichiro [Juntendo Univ., Tokyo (Japan). School of Medicine

    2002-08-01

    We report a case of temporal bone necrosis that emerged after radiotherapy for epipharyngeal carcinoma performed 13 years ago. The patient was a 51-year-old male. His major complaint was left facial swelling. The patient underwent chemotherapy and radiotherapy (Co 60, 6120 rad), as the treatment of that period, for epipharyngeal carcinoma from September 30, 1986 to January 31, 1987. He also underwent lobectomy of the left temporal lobe in brain surgery for left temporal lobe necrosis in August, 1989. After that operation, we saw constriction in his left external acoustic meatus and continued the follow-up. On October 22, 1999 he felt a left facial swelling. We found skin defects and ulcer formation in the front part of his left ear. Although we administered an antiseptic and antibiotic to the diseased area, his condition did not improve. He was hospitalized for the purpose of undergoing medical treatment on January 6, 2000. We found extensive skin necrosis and defects in his left auricular area. The corrupted temporal bone reached the zygomatic, the bone department external acoustic meatus and the mastoid process was exposing. We performed debridement of the diseased area on January 19, 2000. On February 23, we performed reconstruction by left trapezius muscle flap after debridement once again. One year after the operation, the flap was completely incorporated. (author)

  3. Algorithms for Simple Temporal Reasoning

    NARCIS (Netherlands)

    Planken, L.R.

    2013-01-01

    This dissertation describes research into new methods for automated temporal reasoning. For this purpose, several frameworks are available in literature. Chapter 1 presents a concise literature survey that provides a new overview of their interrelation. In the remainder of the dissertation, the

  4. Updating representations of temporal intervals.

    Science.gov (United States)

    Danckert, James; Anderson, Britt

    2015-12-01

    Effectively engaging with the world depends on accurate representations of the regularities that make up that world-what we call mental models. The success of any mental model depends on the ability to adapt to changes-to 'update' the model. In prior work, we have shown that damage to the right hemisphere of the brain impairs the ability to update mental models across a range of tasks. Given the disparate nature of the tasks we have employed in this prior work (i.e. statistical learning, language acquisition, position priming, perceptual ambiguity, strategic game play), we propose that a cognitive module important for updating mental representations should be generic, in the sense that it is invoked across multiple cognitive and perceptual domains. To date, the majority of our tasks have been visual in nature. Given the ubiquity and import of temporal information in sensory experience, we examined the ability to build and update mental models of time. We had healthy individuals complete a temporal prediction task in which intervals were initially drawn from one temporal range before an unannounced switch to a different range of intervals. Separate groups had the second range of intervals switch to one that contained either longer or shorter intervals than the first range. Both groups showed significant positive correlations between perceptual and prediction accuracy. While each group updated mental models of temporal intervals, those exposed to shorter intervals did so more efficiently. Our results support the notion of generic capacity to update regularities in the environment-in this instance based on temporal information. The task developed here is well suited to investigations in neurological patients and in neuroimaging settings.

  5. Transcriptional architecture of the mammalian circadian clock.

    Science.gov (United States)

    Takahashi, Joseph S

    2017-03-01

    Circadian clocks are endogenous oscillators that control 24-hour physiological and behavioural processes in organisms. These cell-autonomous clocks are composed of a transcription-translation-based autoregulatory feedback loop. With the development of next-generation sequencing approaches, biochemical and genomic insights into circadian function have recently come into focus. Genome-wide analyses of the clock transcriptional feedback loop have revealed a global circadian regulation of processes such as transcription factor occupancy, RNA polymerase II recruitment and initiation, nascent transcription, and chromatin remodelling. The genomic targets of circadian clocks are pervasive and are intimately linked to the regulation of metabolism, cell growth and physiology.

  6. A brain-specific transcription activator.

    Science.gov (United States)

    Korner, M; Rattner, A; Mauxion, F; Sen, R; Citri, Y

    1989-11-01

    We have identified a DNA binding protein, named BETA, that interacts with the same (B) transcriptional regulatory sequence as the known transcription factor NF-kappa B. BETA is found only in gray matter throughout the brain, and not in a variety of other rat tissues. Two binding sites for BETA are present adjacent to the promoter of the rat proenkephalin gene. Transfection of primary brain cultures that express BETA, with a reporter gene driven by the SV40 promoter linked to BETA DNA binding sites, results in transcriptional activation. We infer that BETA is a brain-specific transcription activator.

  7. Heritable change caused by transient transcription errors.

    Directory of Open Access Journals (Sweden)

    Alasdair J E Gordon

    2013-06-01

    Full Text Available Transmission of cellular identity relies on the faithful transfer of information from the mother to the daughter cell. This process includes accurate replication of the DNA, but also the correct propagation of regulatory programs responsible for cellular identity. Errors in DNA replication (mutations and protein conformation (prions can trigger stable phenotypic changes and cause human disease, yet the ability of transient transcriptional errors to produce heritable phenotypic change ('epimutations' remains an open question. Here, we demonstrate that transcriptional errors made specifically in the mRNA encoding a transcription factor can promote heritable phenotypic change by reprogramming a transcriptional network, without altering DNA. We have harnessed the classical bistable switch in the lac operon, a memory-module, to capture the consequences of transient transcription errors in living Escherichia coli cells. We engineered an error-prone transcription sequence (A9 run in the gene encoding the lac repressor and show that this 'slippery' sequence directly increases epigenetic switching, not mutation in the cell population. Therefore, one altered transcript within a multi-generational series of many error-free transcripts can cause long-term phenotypic consequences. Thus, like DNA mutations, transcriptional epimutations can instigate heritable changes that increase phenotypic diversity, which drives both evolution and disease.

  8. Temporal aspects of copper homeostasis and its crosstalk with hormones

    Directory of Open Access Journals (Sweden)

    Lola ePeñarrubia

    2015-04-01

    Full Text Available To cope with the dual nature of copper as being essential and toxic for cells, plants temporarily adapt the expression of copper homeostasis components to assure its delivery to cuproproteins while avoiding the interference of potential oxidative damage derived from both copper uptake and photosynthetic reactions during light hours. The circadian clock participates in the temporal organization of coordination of plant nutrition adapting metabolic responses to the daily oscillations. This timely control improves plant fitness and reproduction and holds biotechnological potential to drive increased crop yields. Hormonal pathways, including those of abscisic acid, gibberellins, ethylene, auxins, and jasmonates are also under direct clock and light control, both in mono and dicotyledons. In this review, we focus on copper transport in Arabidopsis thaliana and Oryza sativa and the presumable role of hormones in metal homeostasis matching nutrient availability to growth requirements and preventing metal toxicity. The presence of putative hormone-dependent regulatory elements in the promoters of copper transporters genes suggests hormonal regulation to match special copper requirements during plant development. Spatial and temporal processes that can be affected by hormones include the regulation of copper uptake into roots, intracellular trafficking and compartmentalisation, and long-distance transport to developing vegetative and reproductive tissues. In turn, hormone biosynthesis and signalling are also influenced by copper availability, which suggests reciprocal regulation subjected to temporal control by the central oscillator of the circadian clock. This transcriptional regulatory network, coordinates environmental and hormonal signalling with developmental pathways to allow enhanced micronutrient acquisition efficiency.

  9. Temporal specification and bilaterality of human neocortical topographic gene expression.

    Science.gov (United States)

    Pletikos, Mihovil; Sousa, André M M; Sedmak, Goran; Meyer, Kyle A; Zhu, Ying; Cheng, Feng; Li, Mingfeng; Kawasawa, Yuka Imamura; Sestan, Nenad

    2014-01-22

    Transcriptional events involved in the development of human cerebral neocortex are poorly understood. Here, we analyzed the temporal dynamics and laterality of gene expression in human and macaque monkey neocortex. We found that interareal differences exhibit a temporal hourglass pattern, dividing the human neocortical development into three major phases. The first phase, corresponding to prenatal development, is characterized by the highest number of differential expressed genes among areas and gradient-like expression patterns, including those that are different between human and macaque. The second, preadolescent phase, is characterized by lesser interareal expression differences and by an increased synchronization of areal transcriptomes. During the third phase, from adolescence onward, differential expression among areas increases again driven predominantly by a subset of areas, without obvious gradient-like patterns. Analyses of left-right gene expression revealed population-level global symmetry throughout the fetal and postnatal time span. Thus, human neocortical topographic gene expression is temporally specified and globally symmetric. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. The Temporality of Power and the Power of Temporality

    DEFF Research Database (Denmark)

    Costas, Jana; Grey, Christopher

    2014-01-01

    This paper extends existing understandings of power, resistance and subjectivity in professional service organizations by developing an analysis of how these relate to temporality. Drawing in particular on Hoy’s reading of the Foucauldian account of temporality, we conceive of disciplinary power...... regimes and resistance as inherently future-oriented, or, to use Ybema’s term, postalgic. In moving beyond the extant research focus on self-disciplined and/or counter-resistant professional selves, we draw attention to the imaginary future self as an employee response to disciplinary power. In contrast...... to the future orientation of disciplinary power, this response envisages the future as a discontinuous break with the present which we examine as a form of resistant postalgia. Building on in-depth qualitative data gathered at two professional service firms, we explain how imaginary future selves can shed new...

  11. ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.

    Science.gov (United States)

    Minas, Giorgos; Momiji, Hiroshi; Jenkins, Dafyd J; Costa, Maria J; Rand, David A; Finkenstädt, Bärbel

    2017-06-26

    Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to researchers. The ReTrOS toolbox (Reconstructing Transcription Open Software) provides MATLAB-based implementations of two related methods, namely ReTrOS-Smooth and ReTrOS-Switch, for reconstructing the temporal transcriptional activity profile of a gene from given mRNA expression time series or protein reporter time series. The methods are based on fitting a differential equation model incorporating the processes of transcription, translation and degradation. The toolbox provides a framework for model fitting along with statistical analyses of the model with a graphical interface and model visualisation. We highlight several applications of the toolbox, including the reconstruction of the temporal cascade of transcriptional activity inferred from mRNA expression data and protein reporter data in the core circadian clock in Arabidopsis thaliana, and how such reconstructed transcription profiles can be used to study the effects of different cell lines and conditions. The ReTrOS toolbox allows users to analyse gene and/or protein expression time series where, with appropriate formulation of prior information about a minimum of kinetic parameters, in particular rates of degradation, users are able to infer timings of changes in transcriptional activity. Data from any organism and obtained from a range of technologies can be used as input due to the flexible and generic nature of the model and implementation. The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation.

  12. Methods and tools for temporal knowledge harvesting

    OpenAIRE

    Wang, Yafang

    2013-01-01

    To extend the traditional knowledge base with temporal dimension, this thesis offers methods and tools for harvesting temporal facts from both semi-structured and textual sources. Our contributions are briefly summarized as follows. 1. Timely YAGO: A temporal knowledge base called Timely YAGO (T-YAGO) which extends YAGO with temporal attributes is built. We define a simple RDF-style data model to support temporal knowledge. 2. PRAVDA: To be able to harvest as many temporal facts from free...

  13. Transcriptional atlas of cardiogenesis maps congenital heart disease interactome.

    Science.gov (United States)

    Li, Xing; Martinez-Fernandez, Almudena; Hartjes, Katherine A; Kocher, Jean-Pierre A; Olson, Timothy M; Terzic, Andre; Nelson, Timothy J

    2014-07-01

    Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, knowledge of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Mapping the dynamic transcriptional landscape of cardiogenesis from a genomic perspective is essential to integrate the knowledge of heart development into translational applications that accelerate disease discovery efforts toward mechanistic-based treatment strategies. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide dynamic expression landscape of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, revealed stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling known genetic underpinnings of CHD, we deconstructed a disease-centric dynamic interactome encoded within this cardiogenic atlas to identify stage-specific developmental disturbances clustered on regulation of epithelial-to-mesenchymal transition (EMT), BMP signaling, NF-AT signaling, TGFb-dependent EMT, and Notch signaling. Collectively, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease. Copyright © 2014 the American Physiological Society.

  14. Post-fasting olfactory, transcriptional, and feeding responses in Drosophila.

    Science.gov (United States)

    Farhadian, Shelli F; Suárez-Fariñas, Mayte; Cho, Christine E; Pellegrino, Maurizio; Vosshall, Leslie B

    2012-01-18

    The sensation of hunger after a period of fasting and of satiety after eating is crucial to behavioral regulation of food intake, but the biological mechanisms regulating these sensations are incompletely understood. We studied the behavioral and physiological adaptations to fasting in the vinegar fly (Drosophila melanogaster). Here we show that both male and female flies increased their rate of food intake transiently in the post-fasted state. Although the basal feeding rate was higher in females than males, the magnitude of the post-fasting feeding response was the same in both sexes. Flies returned to a stable baseline feeding rate within 12 h after return to food for males and 24 h for females. This modulation in feeding was accompanied by a significant increase in the size of the crop organ of the digestive system, suggesting that fasted flies responded both by increasing their food intake and storing reserve food in their crop. Flies demonstrated increased behavioral attraction to an attractive odor when food-deprived. Expression profiling of head, body, and chemosensory tissues by microarray analysis revealed 415 genes regulated by fasting after 24 h and 723 genes after 48 h, with downregulated genes outnumbering upregulated genes in each tissue and fasting time point. These transcriptional changes showed rich temporal dynamics and affected genes across multiple functional gene ontology categories. These observations suggest that a coordinated transcriptional response to internal physiological state may regulate both ingestive behaviors and chemosensory perception of food. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.

    Science.gov (United States)

    Askovich, Peter S; Ramsey, Stephen A; Diercks, Alan H; Kennedy, Kathleen A; Knijnenburg, Theo A; Aderem, Alan

    2017-01-01

    The innate immune response to pathogenic challenge is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of this response have been identified, the temporal complexity of gene expression changes in response to pathogen-associated molecular pattern receptor stimulation strongly suggest that additional layers of regulation remain to be uncovered. The evolved pathogen response program in mammalian innate immune cells is understood to reflect a compromise between the probability of clearing the infection and the extent of tissue damage and inflammatory sequelae it causes. Because of that, a key challenge to delineating the regulators that control the temporal inflammatory response is that an innate immune regulator that may confer a selective advantage in the wild may be dispensable in the lab setting. In order to better understand the complete transcriptional response of primary macrophages to the bacterial endotoxin lipopolysaccharide (LPS), we designed a method that integrates temporally resolved gene expression and chromatin-accessibility measurements from mouse macrophages. By correlating changes in transcription factor binding site motif enrichment scores, calculated within regions of accessible chromatin, with the average temporal expression profile of a gene cluster, we screened for transcriptional factors that regulate the cluster. We have validated our predictions of LPS-stimulated transcriptional regulators using ChIP-seq data for three transcription factors with experimentally confirmed functions in innate immunity. In addition, we predict a role in the macrophage LPS response for several novel transcription factors that have not previously been implicated in immune responses. This method is applicable to any experimental situation where temporal gene expression and chromatin-accessibility data are available.

  16. Imaging memory in temporal lobe epilepsy: predicting the effects of temporal lobe resection

    National Research Council Canada - National Science Library

    Bonelli, Silvia B; Powell, Robert H W; Yogarajah, Mahinda; Samson, Rebecca S; Symms, Mark R; Thompson, Pamela J; Koepp, Matthias J; Duncan, John S

    2010-01-01

    .... In patients with refractory temporal lobe epilepsy, evaluation of preoperative verbal and visual memory function is important as anterior temporal lobe resections may result in material specific...

  17. Temporal interpolation in Meteosat images

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Hansen, Johan Dore; Ersbøll, Bjarne Kjær

    The geostationary weather satellite Meteosat supplies us with a visual and an infrared image of the earth every 30 minutes. However, due to transmission error s some images may be missing. European TV weather reports are often supported by such infrared image sequences. The cloud movements...... in such animated films are perceived as being jerky due to t he low temporal sampling rate in general and missing images in particular. In order to perform a satisfactory temporal interpolation we estimate and use the optical flow corresponding to every image in the sequenc e. The estimation of the optical flow...... is based on images sequences where the clouds are segmented from the land/water that might a lso be visible in the images. Because the pixel values measured correspond directly to temperature and because clouds (normally) are colder than land/water we use an estimated lan d temperature map to perform...

  18. Transcriptional regulatory proteins as biosensing tools.

    Science.gov (United States)

    Turner, Kendrick; Joel, Smita; Feliciano, Jessika; Feltus, Agatha; Pasini, Patrizia; Wynn, Daniel; Dau, Peter; Dikici, Emre; Deo, Sapna K; Daunert, Sylvia

    2017-06-22

    We have developed sensing systems employing different classes of transcriptional regulatory proteins genetically and chemically modified to incorporate a fluorescent reporter molecule for detection of arsenic, hydroxylated polychlorinated biphenyls (OH-PCBs), and cyclic AMP (cAMP). These are the first examples of optical sensing systems based on transcriptional regulatory proteins.

  19. Transcriptional regulation of the cell cycle

    NARCIS (Netherlands)

    Stahl, M.

    2006-01-01

    Transcriptional regulators play an important role during cell cycle progression. A subset of these even seems to have a critical function in regulating cell cycle transitions. In this thesis, I have addressed the importance of transcriptional control in the regulation of cell cycle progression, in

  20. Overlapping transcription structure of human cytomegalovirus ...

    Indian Academy of Sciences (India)

    2013-01-21

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

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

    DEFF Research Database (Denmark)

    Troelsgård, Christian

    2007-01-01

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

  2. Speech Transcript Evaluation for Information Retrieval

    NARCIS (Netherlands)

    van der Werff, Laurens Bastiaan; Kraaij, Wessel; de Jong, Franciska M.G.

    Speech recognition transcripts are being used in various fields of research and practical applications, putting various demands on their accuracy. Traditionally ASR research has used intrinsic evaluation measures such as word error rate to determine transcript quality. In non-dictation-type

  3. DNA dynamically directs its own transcription initiation

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, K. O. (Kim O.); Kalosakas, G. (George); Bishop, A. R. (Alan R.); Choi, C. H. (Chu H.); Usheva, A. (Anny)

    2004-01-01

    Initiation of DNA gene transcription requires a transient opening in the double helix at the transcriptional start site. It is generally assumed that the location of this 'transcriptional bubble' is determined by sequence-specific protein binding, and that the energy required for unwinding the double helix comes from torsional strain. Physical twisting should cause DNA to open consistently in weakly bonded A/T rich stretches, however, simple base-pairing energetics alone can not account for the variety of observed transcriptional start sites. Applying the Peyrard-Bishop nonlinear cooperativity model to DNA, we are able to predict that thermally-induced DNA bubbles, similar in size to transcription bubbles, form at specific locations on DNA promoters. These predicted openings agree remarkably well with experiment, and that they correlate exactly with known transcription start sites and important regulatory sites on three different promoters. We propose that the sequence-specific location of the transcriptional start site is predetermined by the inherent opening patterns of specific DNA sequences. As DNA bubble formation is independent of protein binding, it appears that DNA is not only a passive carrier of information, but its dynamics plays an important role in directing the transcription and regulation of the genes it contains.

  4. 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 ...

  5. Temporal Windowing of Trapped States

    OpenAIRE

    Castellano, L. M.; Gonzalez, D. M.

    2001-01-01

    Trapped state definition for 3-level atoms in Lambda configuration, is a very restrictive one, and for the case of unpolarized beams, this definition no longer holds.We introduce a more general definition by using a reference frame rotating with the frequency of the control field, obtaining a temporal windowing for the trapped population.This amounts to a time quantization of the coherent population transfer, making possible to study the phase coherence in trapped light.

  6. Evolution of general transcription factors.

    Science.gov (United States)

    Gunbin, K V; Ruvinsky, A

    2013-02-01

    Three genes GTF2IRD1, GTF2I, and GTF2IRD2, which encode members of the GTF2I (or TFII-I) family of so-called general transcription factors, were discovered and studied during the last two decades. Chromosome location and similarity of exon-intron structures suggest that the family evolved by duplications. The initial duplication of ancestral proto-GTF2IRD1 gene likely occurred in early vertebrates prior to origin of cartilaginous fish and led to formation of GTF2I (>450 MYA), which was later lost in bony fish but successfully evolved in the land vertebrates. The second duplication event, which created GTF2IRD2, occurred prior to major radiation events of eutherian mammalian evolution (>100 MYA). During recent steps of primate evolution there was another duplication which led to formation of GTF2IRD2B (evolution of the genes. The atypical substitutions are often located on secondary structures joining α-helices and affect 3D arrangement of the protein globule. Such substitutions are commonly traced at the early stages of evolution in Tetrapoda, Amniota, and Mammalia.

  7. Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

    Science.gov (United States)

    Tsou, Ann-Ping; Sun, Yi-Ming; Liu, Chia-Lin; Huang, Hsien-Da; Horng, Jorng-Tzong; Tsai, Meng-Feng; Liu, Baw-Juine

    2006-07-01

    Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.

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

    Science.gov (United States)

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

    2012-04-01

    The WRKY transcription factors function in plant growth and development, and response to the biotic and abiotic stresses. Although many studies have focused on the functional identification of the WRKY transcription factors, much less is known about molecular phylogenetic and global expression analysis of the complete WRKY family in maize. In this study, we identified 136 WRKY proteins coded by 119 genes in the B73 inbred line from the complete genome and named them in an orderly manner. Then, a comprehensive phylogenetic analysis of five species was performed to explore the origin and evolutionary patterns of these WRKY genes, and the result showed that gene duplication is the major driving force for the origin of new groups and subgroups and functional divergence during evolution. Chromosomal location analysis of maize WRKY genes indicated that 20 gene clusters are distributed unevenly in the genome. Microarray-based expression analysis has revealed that 131 WRKY transcripts encoded by 116 genes may participate in the regulation of maize growth and development. Among them, 102 transcripts are stably expressed with a coefficient of variation (CV) value of transcripts produced by 25 WRKY genes with the CV value of >15% are further analysed to discover new organ- or tissue-specific genes. In addition, microarray analyses of transcriptional responses to drought stress and fungal infection showed that maize WRKY proteins are involved in stress responses. All these results contribute to a deep probing into the roles of WRKY transcription factors in maize growth and development and stress tolerance.

  9. Model-based redesign of global transcription regulation

    Science.gov (United States)

    Carrera, Javier; Rodrigo, Guillermo; Jaramillo, Alfonso

    2009-01-01

    Synthetic biology aims to the design or redesign of biological systems. In particular, one possible goal could be the rewiring of the transcription regulation network by exchanging the endogenous promoters. To achieve this objective, we have adapted current methods to the inference of a model based on ordinary differential equations that is able to predict the network response after a major change in its topology. Our procedure utilizes microarray data for training. We have experimentally validated our inferred global regulatory model in Escherichia coli by predicting transcriptomic profiles under new perturbations. We have also tested our methodology in silico by providing accurate predictions of the underlying networks from expression data generated with artificial genomes. In addition, we have shown the predictive power of our methodology by obtaining the gene profile in experimental redesigns of the E. coli genome, where rewiring the transcriptional network by means of knockouts of master regulators or by upregulating transcription factors controlled by different promoters. Our approach is compatible with most network inference methods, allowing to explore computationally future genome-wide redesign experiments in synthetic biology. PMID:19188257

  10. Temporal ecology in the Anthropocene.

    Science.gov (United States)

    Wolkovich, E M; Cook, B I; McLauchlan, K K; Davies, T J

    2014-11-01

    Two fundamental axes - space and time - shape ecological systems. Over the last 30 years spatial ecology has developed as an integrative, multidisciplinary science that has improved our understanding of the ecological consequences of habitat fragmentation and loss. We argue that accelerating climate change - the effective manipulation of time by humans - has generated a current need to build an equivalent framework for temporal ecology. Climate change has at once pressed ecologists to understand and predict ecological dynamics in non-stationary environments, while also challenged fundamental assumptions of many concepts, models and approaches. However, similarities between space and time, especially related issues of scaling, provide an outline for improving ecological models and forecasting of temporal dynamics, while the unique attributes of time, particularly its emphasis on events and its singular direction, highlight where new approaches are needed. We emphasise how a renewed, interdisciplinary focus on time would coalesce related concepts, help develop new theories and methods and guide further data collection. The next challenge will be to unite predictive frameworks from spatial and temporal ecology to build robust forecasts of when and where environmental change will pose the largest threats to species and ecosystems, as well as identifying the best opportunities for conservation. © 2014 John Wiley & Sons Ltd/CNRS.

  11. Temporality and modes of language.

    Science.gov (United States)

    Denis, A

    1995-12-01

    After reviewing some literary, philosophical and psychoanalytic conceptions of time, the author distinguishes between the sensation of time, in which rhythm is all-important, and its representation. The timeless unconscious, which can, however, be rendered temporal through the transference, is contrasted with the sequential chronology of preconscious and conscious functioning. Language, and in particular metaphorical language, is deemed to play a vital part in the structuring of the psyche, and is mediated by the object; the contingency of metaphor is held to be essential because otherwise the object will impose itself too directly, causing the previously undifferentiated death drive to predominate. A primal temporality must, in the author's view, have been laid down in the form of an unrepresentable auto-erotic datum before the individual can perceive himself as a living subject and conceive of lineal and irreversible time with its implications of castration and death; there is no such thing as a timeless subject. All pathologies of temporality are considered by the author to be at the same time pathologies of subjectivation and of language. The paper ends with a clinical illustration in which a key time-related defence of the patient is overcome by an intervention outside the strict time frame of the setting that proves mutative and enables her to recover her personal rhythm as a subject.

  12. Temporal compressive imaging for video

    Science.gov (United States)

    Zhou, Qun; Zhang, Linxia; Ke, Jun

    2018-01-01

    In many situations, imagers are required to have higher imaging speed, such as gunpowder blasting analysis and observing high-speed biology phenomena. However, measuring high-speed video is a challenge to camera design, especially, in infrared spectrum. In this paper, we reconstruct a high-frame-rate video from compressive video measurements using temporal compressive imaging (TCI) with a temporal compression ratio T=8. This means that, 8 unique high-speed temporal frames will be obtained from a single compressive frame using a reconstruction algorithm. Equivalently, the video frame rates is increased by 8 times. Two methods, two-step iterative shrinkage/threshold (TwIST) algorithm and the Gaussian mixture model (GMM) method, are used for reconstruction. To reduce reconstruction time and memory usage, each frame of size 256×256 is divided into patches of size 8×8. The influence of different coded mask to reconstruction is discussed. The reconstruction qualities using TwIST and GMM are also compared.

  13. Transcription Factor Networks in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    David Y. Rhee

    2014-09-01

    Full Text Available Specific cellular fates and functions depend on differential gene expression, which occurs primarily at the transcriptional level and is controlled by complex regulatory networks of transcription factors (TFs. TFs act through combinatorial interactions with other TFs, cofactors, and chromatin-remodeling proteins. Here, we define protein-protein interactions using a coaffinity purification/mass spectrometry method and study 459 Drosophila melanogaster transcription-related factors, representing approximately half of the established catalog of TFs. We probe this network in vivo, demonstrating functional interactions for many interacting proteins, and test the predictive value of our data set. Building on these analyses, we combine regulatory network inference models with physical interactions to define an integrated network that connects combinatorial TF protein interactions to the transcriptional regulatory network of the cell. We use this integrated network as a tool to connect the functional network of genetic modifiers related to mastermind, a transcriptional cofactor of the Notch pathway.

  14. Histone variants in plant transcriptional regulation.

    Science.gov (United States)

    Jiang, Danhua; Berger, Frédéric

    2017-01-01

    Chromatin based organization of eukaryotic genome plays a profound role in regulating gene transcription. Nucleosomes form the basic subunits of chromatin by packaging DNA with histone proteins, impeding the access of DNA to transcription factors and RNA polymerases. Exchange of histone variants in nucleosomes alters the properties of nucleosomes and thus modulates DNA exposure during transcriptional regulation. Growing evidence indicates the important function of histone variants in programming transcription during developmental transitions and stress response. Here we review how histone variants and their deposition machineries regulate the nucleosome stability and dynamics, and discuss the link between histone variants and transcriptional regulation in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Transcription Factor Pathways and Congenital Heart Disease

    Science.gov (United States)

    McCulley, David J.; Black, Brian L.

    2013-01-01

    Congenital heart disease is a major cause of morbidity and mortality throughout life. Mutations in numerous transcription factors have been identified in patients and families with some of the most common forms of cardiac malformations and arrhythmias. This review discusses factor pathways known to be important for normal heart development and how abnormalities in these pathways have been linked to morphological and functional forms of congenital heart defects. A comprehensive, current list of known transcription factor mutations associated with congenital heart disease is provided, but the review focuses primarily on three key transcription factors, Nkx2-5, GATA4, and Tbx5, and their known biochemical and genetic partners. By understanding the interaction partners, transcriptional targets, and upstream activators of these core cardiac transcription factors, additional information about normal heart formation and further insight into genes and pathways affected in congenital heart disease should result. PMID:22449847

  16. Chromosomal organization of transcription: in a nutshell.

    Science.gov (United States)

    Meyer, Sam; Reverchon, Sylvie; Nasser, William; Muskhelishvili, Georgi

    2017-11-28

    Early studies of transcriptional regulation focused on individual gene promoters defined specific transcription factors as central agents of genetic control. However, recent genome-wide data propelled a different view by linking spatially organized gene expression patterns to chromosomal dynamics. Therefore, the major problem in contemporary molecular genetics concerned with transcriptional gene regulation is to establish a unifying model that reconciles these two views. This problem, situated at the interface of polymer physics and network theory, requires development of an integrative methodology. In this review, we discuss recent achievements in classical model organism E. coli and provide some novel insights gained from studies of a bacterial plant pathogen, D. dadantii. We consider DNA topology and the basal transcription machinery as key actors of regulation, in which activation of functionally relevant genes is coupled to and coordinated with the establishment of extended chromosomal domains of coherent transcription. We argue that the spatial organization of genome plays a fundamental role in its own regulation.

  17. Transcriptional Activation of Virulence Genes of Rhizobium etli.

    Science.gov (United States)

    Wang, Luyao; Lacroix, Benoît; Guo, Jianhua; Citovsky, Vitaly

    2017-03-15

    Recently, Rhizobium etli, in addition to Agrobacterium spp., has emerged as a prokaryotic species whose genome encodes a functional machinery for DNA transfer to plant cells. To understand this R. etli-mediated genetic transformation, it would be useful to define how its vir genes respond to the host plants. Here, we explored the transcriptional activation of the vir genes contained on the R. etli p42a plasmid. Using a reporter construct harboring lacZ under the control of the R. etli virE promoter, we show that the signal phenolic molecule acetosyringone (AS) induces R. etli vir gene expression both in an R. etli background and in an Agrobacterium tumefaciens background. Furthermore, in both bacterial backgrounds, the p42a plasmid also promoted plant genetic transformation with a reporter transfer DNA (T-DNA). Importantly, the R. etli vir genes were transcriptionally activated by AS in a bacterial species-specific fashion in regard to the VirA/VirG signal sensor system, and this activation was induced by signals from the natural host species of this bacterium but not from nonhost plants. The early kinetics of transcriptional activation of the major vir genes of R. etli also revealed several features distinct from those known for A. tumefaciens: the expression of the virG gene reached saturation relatively quickly, and virB2, which in R. etli is located outside the virB operon, was expressed only at low levels and did not respond to AS. These differences in vir gene transcription may contribute to the lower efficiency of T-DNA transfer of R. etli p42a than of T-DNA transfer of pTiC58 of A. tumefaciensIMPORTANCE The region encoding homologs of Agrobacterium tumefaciens virulence genes in the Rhizobium etli CE3 p42a plasmid was the first endogenous virulence system encoded by the genome of a non-Agrobacterium species demonstrated to be functional in DNA transfer and stable integration into the plant cell genome. In this study, we explored the transcriptional

  18. Differential splicing using whole-transcript microarrays

    Directory of Open Access Journals (Sweden)

    Robinson Mark D

    2009-05-01

    Full Text Available Abstract Background The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative splicing genome-wide. The Exon 1.0 ST (sense target platform, with versions for Human, Mouse and Rat, is designed primarily to probe every known or predicted exon. The smaller Gene 1.0 ST array is designed as an expression microarray but still interrogates expression with probes along the full length of each well-characterized transcript. We explore the possibility of using the Gene 1.0 ST platform to identify differential splicing events. Results We propose a strategy to score differential splicing by using the auxiliary information from fitting the statistical model, RMA (robust multichip analysis. RMA partitions the probe-level data into probe effects and expression levels, operating robustly so that if a small number of probes behave differently than the rest, they are downweighted in the fitting step. We argue that adjacent poorly fitting probes for a given sample can be evidence of differential splicing and have designed a statistic to search for this behaviour. Using a public tissue panel dataset, we show many examples of tissue-specific alternative splicing. Furthermore, we show that evidence for putative alternative splicing has a strong correspondence between the Gene 1.0 ST and Exon 1.0 ST platforms. Conclusion We propose a new approach, FIRMAGene, to search for differentially spliced genes using the Gene 1.0 ST platform. Such an analysis complements the search for differential expression. We validate the method by illustrating several known examples and we note some of the challenges in interpreting the probe-level data. Software implementing our methods is freely available as an R package.

  19. Brain SPECT imaging in temporal lobe epilepsy

    Energy Technology Data Exchange (ETDEWEB)

    Krausz, Y.; Yaffe, S.; Atlan, H. (Hadassah Univ. Hospital, Jerusalem (Israel). Dept. of Medical Biophysics and Nuclear Medicine); Cohen, D. (Hadassah Univ. Hospital, Jerusalem (Israel). Dept. of Radiology); Konstantini, S. (Hadassah Univ. Hospital, Jerusalem (Israel). Dept. of Neurosurgery); Meiner, Z. (Hadassah Univ. Hospital, Jerusalem (Israel). Dept. of Neurology)

    1991-06-01

    Temporal lobe epilepsy is diagnosed by clinical symptoms and signs and by localization of an epileptogenic focus. A brain SPECT study of two patients with temporal lobe epilepsy, using {sup 99m}Tc-HMPAO, was used to demonstrate a perfusion abnormality in the temporal lobe, while brain CT and MRI were non-contributory. The electroencephalogram, though abnormal, did not localize the diseased area. The potential role of the SPECT study in diagnosis and localization of temporal lobe epilepsy is discussed. (orig.).

  20. Epilepsia temporal: relato de caso = Temporal epilepsy: case report

    Directory of Open Access Journals (Sweden)

    Souza, Taís Amara da Costa de

    2006-01-01

    Full Text Available Este trabalho tem o objetivo de divulgar um recurso terapêutico da epilepsia do lobo temporal por esclerose hipocampal: a cirurgia. Aproximadamente vinte e cinco mil pacientes com esta patologia são refratários aos tratamentos medicamentosos no sul do país e muitos chegam ao neurocirurgião com 30-40 anos de evolução, muitas vezes já mutilados em conseqüência das crises. Convulsões parciais originadas no lobo temporal são comuns, e grande parte originam-se em estruturas mesiais (esclerose mesial temporal – EMT. Como aí se encontram a sede de funções nobres do sistema nervoso – memória, aprendizagem, comportamento, entre outras –, os sintomas podem apresentar-se como alterações em qualquer uma delas. Ressaltamos a necessidade do correto diagnóstico e dos métodos para fazê-lo: através da anamnese, da ressonância magnética, do eletroencefalograma (EEG, do vídeo-EEG e por vezes através de sensores intracranianos (strips. Apesar de existirem métodos confiáveis para realizar o diagnóstico e tratamento cirúrgico com grande índice de sucesso, a desinformação dos profissionais que atendem pacientes com EMT acerca do assunto leva ao prolongamento de tratamentos clínico ineficiente e conseqüente seqüelas físicas, psicológicas e sociais

  1. Topology and Control of the Cell-Cycle-Regulated Transcriptional Circuitry

    Science.gov (United States)

    Haase, Steven B.; Wittenberg, Curt

    2014-01-01

    Nearly 20% of the budding yeast genome is transcribed periodically during the cell division cycle. The precise temporal execution of this large transcriptional program is controlled by a large interacting network of transcriptional regulators, kinases, and ubiquitin ligases. Historically, this network has been viewed as a collection of four coregulated gene clusters that are associated with each phase of the cell cycle. Although the broad outlines of these gene clusters were described nearly 20 years ago, new technologies have enabled major advances in our understanding of the genes comprising those clusters, their regulation, and the complex regulatory interplay between clusters. More recently, advances are being made in understanding the roles of chromatin in the control of the transcriptional program. We are also beginning to discover important regulatory interactions between the cell-cycle transcriptional program and other cell-cycle regulatory mechanisms such as checkpoints and metabolic networks. Here we review recent advances and contemporary models of the transcriptional network and consider these models in the context of eukaryotic cell-cycle controls. PMID:24395825

  2. Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component.

    Science.gov (United States)

    Kadener, Sebastian; Stoleru, Dan; McDonald, Michael; Nawathean, Pipat; Rosbash, Michael

    2007-07-01

    Many organisms use circadian clocks to keep temporal order and anticipate daily environmental changes. In Drosophila, the master clock gene Clock promotes the transcription of several key target genes. Two of these gene products, PER and TIM, repress CLK-CYC-mediated transcription. To recognize additional direct CLK target genes, we designed a genome-wide approach and identified clockwork orange (cwo) as a new core clock component. cwo encodes a transcriptional repressor that synergizes with PER and inhibits CLK-mediated activation. Consistent with this function, the mRNA profiles of CLK direct target genes in cwo mutant flies manifest high trough values and low amplitude oscillations. Because behavioral rhythmicity fails to persist in constant darkness (DD) with little or no effect on average mRNA levels in flies lacking cwo, transcriptional oscillation amplitude appears to be linked to rhythmicity. Moreover, the mutant flies are long period, consistent with the late repression indicated by the RNA profiles. These findings suggest that CWO acts preferentially in the late night to help terminate CLK-CYC-mediated transcription of direct target genes including cwo itself. The presence of mammalian homologs with circadian expression features (Dec1 and Dec2) suggests that a similar feedback mechanism exists in mammalian clocks.

  3. LocExpress: a web server for efficiently estimating expression of novel transcripts.

    Science.gov (United States)

    Hou, Mei; Tian, Feng; Jiang, Shuai; Kong, Lei; Yang, Dechang; Gao, Ge

    2016-12-22

    The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it's still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently. Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible. To the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn .

  4. Temporal Phenomena in the Korean Conjunctive Constructions

    Science.gov (United States)

    Kim, Dongmin

    2015-01-01

    The goal of this study is to characterize the temporal phenomena in the Korean conjunctive constructions. These constructions consist of three components: a verbal stem, a clause medial temporal suffix, and a clause terminal suffix. This study focuses on both the temporality of the terminal connective suffixes and the grammatical meanings of the…

  5. Temporal integration and instrumental conditioned reinforcement

    OpenAIRE

    Thrailkill, Eric A.; Shahan, Timothy A.

    2014-01-01

    Stimuli associated with primary reinforcement for instrumental behavior are widely believed to acquire the capacity to function as conditioned reinforcers via Pavlovian conditioning. Some Pavlovian conditioning studies suggest that animals learn the important temporal relations between stimuli and integrate such temporal information over separate experiences to form a temporal map. The present experiment examined whether Pavlovian conditioning can establish a positive instrumental conditioned...

  6. Querying temporal databases via OWL 2 QL

    CSIR Research Space (South Africa)

    Klarman, S

    2014-06-01

    Full Text Available practical approach to querying the SQL:2011-based temporal data model via the semantic layer of OWL 2 QL. The interval-based temporal query language (TQL), which we propose for this task, is based on naturally characterizable combinations of temporal logic...

  7. Spatial-Temporal Epidemiology of Tuberculosis in Mainland China: An Analysis Based on Bayesian Theory

    OpenAIRE

    Kai Cao; Kun Yang; Chao Wang; Jin Guo; Lixin Tao; Qingrong Liu; Mahara Gehendra; Yingjie Zhang; Xiuhua Guo

    2016-01-01

    Objective: To explore the spatial-temporal interaction effect within a Bayesian framework and to probe the ecological influential factors for tuberculosis. Methods: Six different statistical models containing parameters of time, space, spatial-temporal interaction and their combination were constructed based on a Bayesian framework. The optimum model was selected according to the deviance information criterion (DIC) value. Coefficients of climate variables were then estimated using the best f...

  8. Transcriptional profiling of the soil invertebrate Folsomia candida in pentachlorophenol-contaminated soil

    NARCIS (Netherlands)

    Min, Qiao; Wang, Guang-Peng; Zhang, Cai; Roelofs, D.; van Straalen, N.M.; Zhu, Yong-Guan

    2015-01-01

    Pentachlorophenol (PCP), a widely used pesticide, is considered to be an endocrine disruptor. The molecular effects of chemicals with endocrine-disrupting potential on soil invertebrates are largely unknown. In the present study, the authors explored the transcriptional expression changes of

  9. Microarray analysis of gender- and parasite-specific gene transcription in Strongyloides ratti

    NARCIS (Netherlands)

    Evans, Helen; Mello, Luciane V.; Fang, Yongxiang; Wit, Ernst; Thompson, Fiona J.; Viney, Mark E.; Paterson, Steve

    2008-01-01

    The molecular mechanisms by which parasitic nematodes reproduce and have adapted to life within a host are unclear. In the present study, microarray analysis was used to explore differential transcription among the different stages and sexes of Strongyloides ratti, a parasitic nematode of brown

  10. a Simple Spatially Weighted Measure of Temporal Stability for Data with Limited Temporal Observations

    Science.gov (United States)

    Piburn, J.; Stewart, R.; Morton, A.

    2017-10-01

    Identifying erratic or unstable time-series is an area of interest to many fields. Recently, there have been successful developments towards this goal. These new developed methodologies however come from domains where it is typical to have several thousand or more temporal observations. This creates a challenge when attempting to apply these methodologies to time-series with much fewer temporal observations such as for socio-cultural understanding, a domain where a typical time series of interest might only consist of 20-30 annual observations. Most existing methodologies simply cannot say anything interesting with so few data points, yet researchers are still tasked to work within in the confines of the data. Recently a method for characterizing instability in a time series with limitedtemporal observations was published. This method, Attribute Stability Index (ASI), uses an approximate entropy based method tocharacterize a time series' instability. In this paper we propose an explicitly spatially weighted extension of the Attribute StabilityIndex. By including a mechanism to account for spatial autocorrelation, this work represents a novel approach for the characterizationof space-time instability. As a case study we explore national youth male unemployment across the world from 1991-2014.

  11. A SIMPLE SPATIALLY WEIGHTED MEASURE OF TEMPORAL STABILITY FOR DATA WITH LIMITED TEMPORAL OBSERVATIONS

    Directory of Open Access Journals (Sweden)

    J. Piburn

    2017-10-01

    Full Text Available Identifying erratic or unstable time-series is an area of interest to many fields. Recently, there have been successful developments towards this goal. These new developed methodologies however come from domains where it is typical to have several thousand or more temporal observations. This creates a challenge when attempting to apply these methodologies to time-series with much fewer temporal observations such as for socio-cultural understanding, a domain where a typical time series of interest might only consist of 20-30 annual observations. Most existing methodologies simply cannot say anything interesting with so few data points, yet researchers are still tasked to work within in the confines of the data. Recently a method for characterizing instability in a time series with limitedtemporal observations was published. This method, Attribute Stability Index (ASI, uses an approximate entropy based method tocharacterize a time series’ instability. In this paper we propose an explicitly spatially weighted extension of the Attribute StabilityIndex. By including a mechanism to account for spatial autocorrelation, this work represents a novel approach for the characterizationof space-time instability. As a case study we explore national youth male unemployment across the world from 1991-2014.

  12. Transcription-dependent degradation controls the stability of the SREBP family of transcription factors.

    Science.gov (United States)

    Sundqvist, Anders; Ericsson, Johan

    2003-11-25

    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.

  13. Explore with Us

    Science.gov (United States)

    Morales, Lester

    2012-01-01

    The fundamental goal of this vision is to advance U.S. scientific, security and economic interest through a robust space exploration program. Implement a sustained and affordable human and robotic program to explore the solar system and beyond. Extend human presence across the solar system, starting with a human return to the Moon by the year 2020, in preparation for human exploration of Mars and other destinations. Develop the innovative technologies, knowledge, and infrastructures both to explore and to support decisions about the destinations for human exploration. Promote international and commercial participation in exploration to further U.S. scientific, security, and economic interests.

  14. Binaural interference: effects of temporal interferer fringe and interstimulus interval.

    Science.gov (United States)

    Camalier, Corrie R; Grantham, D Wesley; Bernstein, Leslie R

    2014-02-01

    Binaural interference refers to the phenomenon in which the potency of binaural cues conveyed by a "target" stimulus occupying one spectral region is degraded by the presence of an "interferer" stimulus occupying a spectral region remote from the target. It is typified by conditions in which thresholds for detection of interaural temporal difference conveyed by a high-frequency target are elevated when the target is accompanied by a spectrally remote low-frequency interferer. This study explored effects of temporal relations between targets and interferers on binaural interference. In the first experiment, duration by which the interferer preceded and/or trailed the target (onset and offset "fringes") was varied. Results indicated binaural interference decreased with total duration of the temporal fringe, but did not depend on whether that duration was composed of onset, offset, or onset + offset fringes. In the second experiment, binaural interference was measured as a function of the interstimulus interval (ISI) between the two presentations of the target. Results indicated that shorter ISIs increased thresholds in both the interferer and no-interferer conditions, but did not affect binaural interference. These results suggest that the mechanisms underlying the effects of manipulations of the interferer temporal fringe and manipulation of the ISI are essentially independent.

  15. Does Temporal Integration Occur for Unrecognizable Words in Visual Crowding?

    Directory of Open Access Journals (Sweden)

    Jifan Zhou

    Full Text Available Visual crowding-the inability to see an object when it is surrounded by flankers in the periphery-does not block semantic activation: unrecognizable words due to visual crowding still generated robust semantic priming in subsequent lexical decision tasks. Based on the previous finding, the current study further explored whether unrecognizable crowded words can be temporally integrated into a phrase. By showing one word at a time, we presented Chinese four-word idioms with either a congruent or incongruent ending word in order to examine whether the three preceding crowded words can be temporally integrated to form a semantic context so as to affect the processing of the ending word. Results from both behavioral (Experiment 1 and Event-Related Potential (Experiment 2 and 3 measures showed congruency effect in only the non-crowded condition, which does not support the existence of unconscious multi-word integration. Aside from four-word idioms, we also found that two-word (modifier + adjective combination integration-the simplest kind of temporal semantic integration-did not occur in visual crowding (Experiment 4. Our findings suggest that integration of temporally separated words might require conscious awareness, at least under the timing conditions tested in the current study.

  16. Spectral-temporal dynamics of multipulse mode-locking

    Science.gov (United States)

    Yu, Ying; Li, Bowen; Wei, Xiaoming; Xu, Yiqing; Tsia, Kevin K. M.; Wong, Kenneth K. Y.

    2017-05-01

    In addition to stable pulse generation, passively mode-locked fiber lasers can easily run into an unstable regime of multipulse mode-locking. The birth and dynamic behaviors of multipulse mode-locking so far have rarely been experimentally explored, particularly in the spectral domain. In this letter, several kinds of multipulse spectral-temporal dynamics of a passively mode-locked fiber laser are observed in a single-shot manner, e.g., energy quantization, self-phase modulation spectral broadening, wavelength shifting, spectral interfering, and ultraweak pulse interaction. This study is enabled by the high temporal resolution of spectral-temporal technology, i.e., 50 ps in the time domain and tens of nanoseconds in the spectral domain. Moreover, a wide observing time span of our spectral-temporal analyzing system, i.e., >6 ms—equivalent to 100 000 round trips, enables evolutionary characterization of individual pulses. The results will have a significant impact on optimizing the performance of mode-locked fiber lasers and understanding the nonlinear physics in a dissipative system.

  17. Papercraft temporal bone in the first step of anatomy education.

    Science.gov (United States)

    Hiraumi, Harukazu; Sato, Hiroaki; Ito, Juichi

    2017-06-01

    (1) To compare temporal bone anatomy comprehension taught to speech therapy students with or without a papercraft model. (2) To explore the effect of papercraft simulation on the understanding of surgical approaches in first-year residents. (1) One-hundred and ten speech therapy students were divided into three classes. The first class was taught with a lecture only. The students in the second class were given a lecture and a papercraft modeling task without instruction. The third class modeled a papercraft with instruction after the lecture. The students were tested on their understanding of temporal bone anatomy. (2) A questionnaire on the understanding of surgical approaches was completed by 10 residents before and after the papercraft modeling. The papercraft models were cut with scissors to simulate surgical approaches. (1) The average scores were 4.4/8 for the first class, 4.3/8 for the second class, and 6.3/8 for the third class. The third class had significantly better results than the other classes (panatomy using a papercraft temporal bone model is effective in the first step of learning temporal bone anatomy and surgical approaches. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. 5 CFR 1632.10 - Transcripts, recordings, and minutes.

    Science.gov (United States)

    2010-01-01

    ... actual cost of duplication or transcription. (d) A complete verbatim copy of the transcript, a complete copy of the minutes, or a complete electronic recording or verbatim copy of a transcription thereof of... maintain a complete transcript or electronic recording or transcription thereof adequate to record fully...

  19. Modernization as Temporalization. History of Concepts and Epochal Change in Reinhart Koselleck’s Reflection

    Directory of Open Access Journals (Sweden)

    Luca Scuccimarra

    2016-12-01

    Full Text Available Reconstructing the conception of historical change inside Reinhart Koselleck’s reflection, the essay deals with the affirmation and crisis of modern temporal order. If modernization has been intended as overcoming and abandonment of tradition, it becomes involved in the discovery of a multiplicity of temporal layers, that the formulation «contemporaneity of the non-contemporaneous» is designated to describe. Consequently, the essay explores the possibility of a new Sattelzeit, able to motivate the acceleration of contemporary time or the new regimes of historicity that it reveals. The split between modernization and temporalization might point out the necessity to formulate a new conceptual history.

  20. Nuclear Actin in Development and Transcriptional Reprogramming.

    Science.gov (United States)

    Misu, Shinji; Takebayashi, Marina; Miyamoto, Kei

    2017-01-01

    Actin is a highly abundant protein in eukaryotic cells and dynamically changes its polymerized states with the help of actin-binding proteins. Its critical function as a constituent of cytoskeleton has been well-documented. Growing evidence demonstrates that actin is also present in nuclei, referred to as nuclear actin, and is involved in a number of nuclear processes, including transcriptional regulation and chromatin remodeling. The contribution of nuclear actin to transcriptional regulation can be explained by its direct interaction with transcription machineries and chromatin remodeling factors and by controlling the activities of transcription factors. In both cases, polymerized states of nuclear actin affect the transcriptional outcome. Nuclear actin also plays an important role in activating strongly silenced genes in somatic cells for transcriptional reprogramming. When these nuclear functions of actin are considered, it is plausible to speculate that nuclear actin is also implicated in embryonic development, in which numerous genes need to be activated in a well-coordinated manner. In this review, we especially focus on nuclear actin's roles in transcriptional activation, reprogramming and development, including stem cell differentiation and we discuss how nuclear actin can be an important player in development and cell differentiation.

  1. Temporal MDS Plots for Analysis of Multivariate Data.

    Science.gov (United States)

    Jäckle, Dominik; Fischer, Fabian; Schreck, Tobias; Keim, Daniel A

    2016-01-01

    Multivariate time series data can be found in many application domains. Examples include data from computer networks, healthcare, social networks, or financial markets. Often, patterns in such data evolve over time among multiple dimensions and are hard to detect. Dimensionality reduction methods such as PCA and MDS allow analysis and visualization of multivariate data, but per se do not provide means to explore multivariate patterns over time. We propose Temporal Multidimensional Scaling (TMDS), a novel visualization technique that computes temporal one-dimensional MDS plots for multivariate data which evolve over time. Using a sliding window approach, MDS is computed for each data window separately, and the results are plotted sequentially along the time axis, taking care of plot alignment. Our TMDS plots enable visual identification of patterns based on multidimensional similarity of the data evolving over time. We demonstrate the usefulness of our approach in the field of network security and show in two case studies how users can iteratively explore the data to identify previously unknown, temporally evolving patterns.

  2. Spatial and temporal variability of chlorophyll in Bay of Bengal.

    Science.gov (United States)

    Jutla, A.; Akanda, S.; Islam, S.

    2009-04-01

    The Bay of Bengal (BoB) receives approximately 628 km3/ year of freshwater discharge from the Ganges and Brahmaputra rivers. Freshwater discharge from rivers increases the nutrient load and thereby enhances phytoplankton production in the BoB. Cholera, an infectious water-borne disease caused by bacterium Vibrio cholerae, remains endemic in the BoB region. Phytoplankton provides favorable environment for survival of cholera bacteria. Therefore, for development of any predictive model for cholera, it is important to quantify the spatial and temporal variability of phytoplankton in the BoB. Satellite remote sensing is the most effective way to quantify this variability over a range of space and time scales. Using ten years (1998-2007) of daily, weekly and monthly SeaWiFs chlorophyll, a surrogate variable for measuring phytoplankton, imagery we explore the spatial pattern and dominant temporal variability of chlorophyll over the BoB region. We find that chlorophyll in the coastal waters has more variability, both in temporal and spatial scales, than the offshore waters. Mechanism of production and space-time variability of coastal chlorophyll is different from those of offshore chlorophyll. While coastal chlorophyll is dominated by influx of terrestrial nutrients through river discharge, chlorophyll in the offshore region is primarily controlled by oceanic processes. We will also explore issues related to dominant space and time scales of chlorophyll variations in the entire bay.

  3. Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays.

    Science.gov (United States)

    Honkela, Antti; Peltonen, Jaakko; Topa, Hande; Charapitsa, Iryna; Matarese, Filomena; Grote, Korbinian; Stunnenberg, Hendrik G; Reid, George; Lawrence, Neil D; Rattray, Magnus

    2015-10-20

    Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles because of differences in transcription time, degradation rate, and RNA-processing kinetics. Recent studies have shown that a splicing-associated RNA production delay can be significant. To investigate this issue more generally, it is useful to develop methods applicable to genome-wide datasets. We introduce a joint model of transcriptional activation and mRNA accumulation that can be used for inference of transcription rate, RNA production delay, and degradation rate given data from high-throughput sequencing time course experiments. We combine a mechanistic differential equation model with a nonparametric statistical modeling approach allowing us to capture a broad range of activation kinetics, and we use Bayesian parameter estimation to quantify the uncertainty in estimates of the kinetic parameters. We apply the model to data from estrogen receptor α activation in the MCF-7 breast cancer cell line. We use RNA polymerase II ChIP-Seq time course data to characterize transcriptional activation and mRNA-Seq time course data to quantify mature transcripts. We find that 11% of genes with a good signal in the data display a delay of more than 20 min between completing transcription and mature mRNA production. The genes displaying these long delays are significantly more likely to be short. We also find a statistical association between high delay and late intron retention in pre-mRNA data, indicating significant splicing-associated production delays in many genes.

  4. Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues.

    Science.gov (United States)

    Anafi, Ron C; Pellegrino, Renata; Shockley, Keith R; Romer, Micah; Tufik, Sergio; Pack, Allan I

    2013-05-30

    Many have assumed that the primary function of sleep is for the brain. We evaluated the molecular consequences of sleep and sleep deprivation outside the brain, in heart and lung. Using microarrays we compared gene expression in tissue from sleeping and sleep deprived mice euthanized at the same diurnal times. In each tissue, nearly two thousand genes demonstrated statistically significant differential expression as a function of sleep/wake behavioral state. To mitigate the influence of an artificial deprivation protocol, we identified a subset of these transcripts as specifically sleep-enhanced or sleep-repressed by requiring that their expression also change over the course of unperturbed sleep. 3% and 6% of the assayed transcripts showed "sleep specific" changes in the lung and heart respectively. Sleep specific transcripts in these tissues demonstrated highly significant overlap and shared temporal dynamics. Markers of cellular stress and the unfolded protein response were reduced during sleep in both tissues. These results mirror previous findings in brain. Sleep-enhanced pathways reflected the unique metabolic functions of each tissue. Transcripts related to carbohydrate and sulfur metabolic processes were enhanced by sleep in the lung, and collectively favor buffering from oxidative stress. DNA repair and protein metabolism annotations were significantly enriched among the sleep-enhanced transcripts in the heart. Our results also suggest that sleep may provide a Zeitgeber, or synchronizing cue, in the lung as a large cluster of transcripts demonstrated systematic changes in inter-animal variability as a function of both sleep duration and circadian time. Our data support the notion that the molecular consequences of sleep/wake behavioral state extend beyond the brain to include peripheral tissues. Sleep state induces a highly overlapping response in both heart and lung. We conclude that sleep enhances organ specific molecular functions and that it has a

  5. Analysis of the transcriptional responses in inflorescence buds of Jatropha curcas exposed to cytokinin treatment.

    Science.gov (United States)

    Chen, Mao-Sheng; Pan, Bang-Zhen; Wang, Gui-Juan; Ni, Jun; Niu, Longjian; Xu, Zeng-Fu

    2014-11-30

    Jatropha curcas L. is a potential biofuel plant. Application of exogenous cytokinin (6-benzyladenine, BA) on its inflorescence buds can significantly increase the number of female flowers, thereby improving seed yield. To investigate which genes and signal pathways are involved in the response to cytokinin in J. curcas inflorescence buds, we monitored transcriptional activity in inflorescences at 0, 3, 12, 24, and 48 h after BA treatment using a microarray. We detected 5,555 differentially expressed transcripts over the course of the experiment, which could be grouped into 12 distinct temporal expression patterns. We also identified 31 and 131 transcripts in J. curcas whose homologs in model plants function in flowering and phytohormonal signaling pathways, respectively. According to the transcriptional analysis of genes involved in flower development, we hypothesized that BA treatment delays floral organ formation by inhibiting the transcription of the A, B and E classes of floral organ-identity genes, which would allow more time to generate more floral primordia in inflorescence meristems, thereby enhancing inflorescence branching and significantly increasing flower number per inflorescence. BA treatment might also play an important role in maintaining the flowering signals by activating the transcription of GIGANTEA (GI) and inactivating the transcription of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and TERMINAL FLOWER 1b (TFL1b). In addition, exogenous cytokinin treatment could regulate the expression of genes involved in the metabolism and signaling of other phytohormones, indicating that cytokinin and other phytohormones jointly regulate flower development in J. curcas inflorescence buds. Our study provides a framework to better understand the molecular mechanisms underlying changes in flowering traits in response to cytokinin treatment in J. curcas inflorescence buds. The results provide valuable information related to the mechanisms of cross-talk among

  6. Evolving Temporal Association Rules with Genetic Algorithms

    Science.gov (United States)

    Matthews, Stephen G.; Gongora, Mario A.; Hopgood, Adrian A.

    A novel framework for mining temporal association rules by discovering itemsets with a genetic algorithm is introduced. Metaheuristics have been applied to association rule mining, we show the efficacy of extending this to another variant - temporal association rule mining. Our framework is an enhancement to existing temporal association rule mining methods as it employs a genetic algorithm to simultaneously search the rule space and temporal space. A methodology for validating the ability of the proposed framework isolates target temporal itemsets in synthetic datasets. The Iterative Rule Learning method successfully discovers these targets in datasets with varying levels of difficulty.

  7. Exploration and Mining Roadmap

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2002-09-01

    This Exploration and Mining Technology Roadmap represents the third roadmap for the Mining Industry of the Future. It is based upon the results of the Exploration and Mining Roadmap Workshop held May 10 ñ 11, 2001.

  8. 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.

  9. Dissecting dynamic genetic variation that controls temporal gene response in yeast.

    Directory of Open Access Journals (Sweden)

    Avital Brodt

    2014-12-01

    Full Text Available Inter-individual variation in regulatory circuits controlling gene expression is a powerful source of functional information. The study of associations among genetic variants and gene expression provides important insights about cell circuitry but cannot specify whether and when potential variants dynamically alter their genetic effect during the course of response. Here we develop a computational procedure that captures temporal changes in genetic effects, and apply it to analyze transcription during inhibition of the TOR signaling pathway in segregating yeast cells. We found a high-order coordination of gene modules: sets of genes co-associated with the same genetic variant and sharing a common temporal genetic effect pattern. The temporal genetic effects of some modules represented a single state-transitioning pattern; for example, at 10-30 minutes following stimulation, genetic effects in the phosphate utilization module attained a characteristic transition to a new steady state. In contrast, another module showed an impulse pattern of genetic effects; for example, in the poor nitrogen sources utilization module, a spike up of a genetic effect at 10-20 minutes following stimulation reflected inter-individual variation in the timing (rather than magnitude of response. Our analysis suggests that the same mechanism typically leads to both inter-individual variation and the temporal genetic effect pattern in a module. Our methodology provides a quantitative genetic approach to studying the molecular mechanisms that shape dynamic changes in transcriptional responses.

  10. Temporal Reasoning and Default Logics.

    Science.gov (United States)

    1985-10-01

    OCOPY RESOLUTION TEST CHART NATIONAL BUJREAU OF 5TANDAROS - 963 - ET VERIT TEMPRAL EASNINGAND EFALT LGIC Stev Rans an Dre Mc~rmot YALE UIVERIT DEATETO...couch the ab example in temporal terms. Consider the successor predicate to indicate fatherhood -(s x y) is intended to mean "x is the father of y...11.111j.W IL. &6I 1.1 ~ 2.0 111.8 MICROCOPY RESOLUTION TEST CHART NATIONAL BLREAU OF STANDARDS - 1965~ A 36 h . • ,% V. end point), and n is a nonnegative

  11. Brd4 bridges the transcriptional regulators, Aire and P-TEFb, to promote elongation of peripheral-tissue antigen transcripts in thymic stromal cells.

    Science.gov (United States)

    Yoshida, Hideyuki; Bansal, Kushagra; Schaefer, Uwe; Chapman, Trevor; Rioja, Inmaculada; Proekt, Irina; Anderson, Mark S; Prinjha, Rab K; Tarakhovsky, Alexander; Benoist, Christophe; Mathis, Diane

    2015-08-11

    Aire controls immunologic tolerance by inducing a battery of thymic transcripts encoding proteins characteristic of peripheral tissues. Its unusually broad effect is achieved by releasing RNA polymerase II paused just downstream of transcriptional start sites. We explored Aire's collaboration with the bromodomain-containing protein, Brd4, uncovering an astonishing correspondence between those genes induced by Aire and those inhibited by a small-molecule bromodomain blocker. Aire:Brd4 binding depended on an orchestrated series of posttranslational modifications within Aire's caspase activation and recruitment domain. This interaction attracted P-TEFb, thereby mobilizing downstream transcriptional elongation and splicing machineries. Aire:Brd4 association was critical for tolerance induction, and its disruption could account for certain point mutations that provoke human autoimmune disease. Our findings evoke the possibility of unanticipated immunologic mechanisms subtending the potent antitumor effects of bromodomain blockers.

  12. Botanical Exploration Of Sinai

    OpenAIRE

    Batanouny, K. H. [كمال الدين حسن البتانوني

    1985-01-01

    The history of the botanical exploration of Sinai has been reviewed. It has been divided into the following periods: I. Expeditions in the eighteenth century. II. Exploration from 1800 till the publication of "Florula Sinaica". III. Exploration from 1835 till the publication of "Flora Orientalis". IV. A decade of intensive exploration (1861-1871). V. An era of extensive floristic studies (1871-1929) with the publication of the Flora of Egypt. VI. A period of updating. VII...

  13. Exploration cost-cutting

    Energy Technology Data Exchange (ETDEWEB)

    Huttrer, J.

    1996-12-31

    This presentation by Jerry Huttrer, President, Geothermal Management Company, discusses the general state of exploration in the geothermal industry today, and mentions some ways to economize and perhaps save costs of geothermal exploration in the future. He suggests an increased use of satellite imagery in the mapping of geothermal resources and the identification of hot spots. Also, coordinating with oil and gas exploration efforts, the efficiency of the exploration task could be optimized.

  14. Globally-Perceived Experiences of Online Instructors: A Preliminary Exploration

    Science.gov (United States)

    Hsieh, Pei-Hsuan

    2010-01-01

    This paper explores online instructors' perceptions on teaching experiences occurring in their own countries. The interviewees are instructors who have taught online courses for more than two years. Eleven interview transcripts, obtained from online instructors from six countries (Australia, Canada, China, United Kingdom, United States and Taiwan)…

  15. Morphosyntactic annotation of CHILDES transcripts*

    Science.gov (United States)

    SAGAE, KENJI; DAVIS, ERIC; LAVIE, ALON; MACWHINNEY, BRIAN; WINTNER, SHULY

    2014-01-01

    Corpora of child language are essential for research in child language acquisition and psycholinguistics. Linguistic annotation of the corpora provides researchers with better means for exploring the development of grammatical constructions and their usage. We describe a project whose goal is to annotate the English section of the CHILDES database with grammatical relations in the form of labeled dependency structures. We have produced a corpus of over 18,800 utterances (approximately 65,000 words) with manually curated gold-standard grammatical relation annotations. Using this corpus, we have developed a highly accurate data-driven parser for the English CHILDES data, which we used to automatically annotate the remainder of the English section of CHILDES. We have also extended the parser to Spanish, and are currently working on supporting more languages. The parser and the manually and automatically annotated data are freely available for research purposes. PMID:20334720

  16. A mixed-effects model of the dynamic response of muscle gene transcript expression to endurance exercise.

    Science.gov (United States)

    Busso, Thierry; Flück, Martin

    2013-05-01

    Altered expression of a broad range of gene transcripts after exercise reflects the specific adjustment of skeletal muscle makeup to endurance training. Towards a quantitative understanding of this molecular regulation, we aimed to build a mixed-effects model of the dynamics of co-related transcript responses to exercise. It was built on the assumption that transcript levels after exercise varied because of changes in the balance between transcript synthesis and degradation. It was applied to microarray data of 231 gene transcripts in vastus lateralis muscle of six subjects 1, 8 and 24 h after endurance exercise and 6-week training on a stationary bicycle. Cluster analysis was used to select groups of transcripts having highest co-correlation of their expression (r > 0.70): Group 1 comprised 45 transcripts including factors defining the oxidative and contractile phenotype and Group 2 included 39 transcripts mainly defined by factors found at the cell periphery and the extracellular space. Data from six subjects were pooled to filter experimental noise. The model fitted satisfactorily the responses of Group 1 (r (2) = 0.62 before and 0.85 after training, P < 0.001) and Group 2 (r (2) = 0.75 and 0.79, P < 0.001). Predicted variation in transcription rate induced by exercise yielded a difference in amplitude and time-to-peak response of gene transcripts between the two groups before training and with training in Group 2. The findings illustrate that a mixed-effects model of transcript responses to exercise is suitable to explore the regulation of muscle plasticity by training at the transcriptional level and indicate critical experiments needed to consolidate model parameters empirically.

  17. Genetic alphabet expansion transcription generating functional RNA molecules containing a five-letter alphabet including modified unnatural and natural base nucleotides by thermostable T7 RNA polymerase variants.

    Science.gov (United States)

    Kimoto, Michiko; Meyer, Adam J; Hirao, Ichiro; Ellington, Andrew D

    2017-11-14

    Thermostable T7 RNA polymerase variants were explored for genetic alphabet expansion transcription involving the unnatural Ds-Pa pair. One variant exhibited high incorporation efficiencies of functionally modified Pa substrates and enabled the simultaneous incorporation of 2'-fluoro-nucleoside triphosphates of pyrimidines into transcripts, allowing the generation of novel, highly functional RNA molecules.

  18. Surface water - groundwater interactions at different spatial and temporal scales

    DEFF Research Database (Denmark)

    Sebök, Éva

    As there is a growing demand for the protection and optimal management of both the surface water and groundwater resources, the understanding of their exchange processes is of great importance. This PhD study aimed at describing the natural spatial and temporal variability of these interactions...... in lowland catchments, mainly exploring and assessing Distributed Temperature Sensing (DTS) which by detecting variability in temperatures at the Sediment-Water Interface (SWI) can indirectly map variability in groundwater discharge at several spatial and temporal scales. On the small-scale (... streambeds which were shown to influence DTS data by sedimentation and scouring processes. A new methodology was therefore developed for the long-term monitoring of surface water-groundwater exchanges in soft-bedded streams....

  19. little sister: An Afro-Temporal Solo-Play.

    Science.gov (United States)

    De Berry, Misty

    2017-07-03

    little sister: An Afro-Temporal Solo-Play is at once a memory-scape and a mytho-biography set to poetry, movement, and mixed media. A performance poem spanning from the Antebellum South to present-moment Chicago, it tells the story of a nomadic spirit named little-she who shape-shifts through the memories and imaginings of her sister, the narrator. Through the characters little-she and the narrator, the solo-performance explores embodied ways to rupture and relieve the impact of macro forms of violence in the micro realm of the everyday. To this end, little sister witnesses and disrupts the legacy of violence in the lives of queer Black women through a trans-temporal navigation of everyday encounters within familial, small groups and intimate partner spaces.

  20. Awareness of temporal lag is necessary for motor–visual temporal recalibration

    Directory of Open Access Journals (Sweden)

    Masaki eTsujita

    2016-01-01

    Full Text Available Consistent exposure to a temporal lag between observers’ voluntary action and its visual feedback induced recalibration of temporal order perception between a motor action and a visual stimulus. It remains unclear what kinds of processing underlie this motor–visual temporal recalibration. This study examined the necessity of motor–visual temporal recalibration for awareness of a temporal lag between a motor action and its visual feedback. In Experiment 1, we allocated observers to either the multiple-step or single-step lag conditions. In the multiple-step lag condition, we first inserted a small temporal lag and subsequently increased it with progress of the adaptation period, to make observers unaware of the temporal lag during the adaptation period. In the single-step lag condition, we instructed observers about the temporal lag before adaptation, and inserted a substantial temporal lag from the beginning of the adaptation period to ensure that they were aware of the temporal lag. We found significant recalibration only in the single-step lag condition. In Experiment 2, we exposed all observers to a substantial temporal lag from the beginning of adaptation period with no instruction about insertion of the temporal lag. We asked observers at the end of the experiment whether they were aware of the temporal lag. We found significant recalibration for only observers who were aware of the lag. These results suggest that awareness of the temporal lag plays a crucial role in motor–visual temporal recalibration.

  1. 22 CFR 1500.9 - Transcripts, recording of closed meetings.

    Science.gov (United States)

    2010-04-01

    ... cost of duplication or transcription. The Foundation shall maintain a complete verbatim copy of the... contain information which may be withheld under § 1500.5. Copies of such transcript, or a transcription of...

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

    NARCIS (Netherlands)

    Hestand, Matthew Scott

    2010-01-01

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

  3. A chromatin-based mechanism for limiting divergent noncoding transcription

    DEFF Research Database (Denmark)

    Marquardt, Sebastian; Escalante-Chong, Renan; Pho, Nam

    2014-01-01

    In addition to their annotated transcript, many eukaryotic mRNA promoters produce divergent noncoding transcripts. To define determinants of divergent promoter directionality, we used genomic replacement experiments. Sequences within noncoding transcripts specified their degradation pathways, and...

  4. Optimizing memory function in temporal lobe epilepsy.

    Science.gov (United States)

    Thompson, P J; Conn, H; Baxendale, S A; Donnachie, E; McGrath, K; Geraldi, C; Duncan, J S

    2016-05-01

    The study aimed to assess whether engagement in a memory training programme and performing internet brain training exercises improve memory function in people with temporal lobe epilepsy (TLE). Seventy-seven people with TLE, complaining of memory difficulties, completed the study. Participants ranged in age from 19 to 67 years and 40 had left TLE. Participants were randomised to one of four conditions; Group 1: traditional memory training, Group 2: Lumosity, an on-line cognitive training programme, Group 3: traditional memory training and Lumosity, and Group 4: no training. Memory efficiency and mood were assessed at baseline and three months later. Group analyses indicated improved verbal recall after training (pLumosity use was not associated with changes in the memory outcome measures but there was a relationship with depression ratings and the number of memory games played (pLumosity the on-line cognitive training programme had specific advantages. Positive change was not universal and larger studies will be required to explore factors associated with successful outcomes. Copyright © 2016 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

  5. High throughput assays for analyzing transcription factors.

    Science.gov (United States)

    Li, Xianqiang; Jiang, Xin; Yaoi, Takuro

    2006-06-01

    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.

  6. Transcriptional events defining plant immune responses.

    Science.gov (United States)

    Birkenbihl, Rainer P; Liu, Shouan; Somssich, Imre E

    2017-08-01

    Rapid and massive transcriptional reprogramming upon pathogen recognition is the decisive step in plant-phytopathogen interactions. Plant transcription factors (TFs) are key players in this process but they require a suite of other context-specific co-regulators to establish sensory transcription regulatory networks to bring about host immunity. Molecular, genetic and biochemical studies, particularly in the model plants Arabidopsis and rice, are continuously uncovering new components of the transcriptional machinery that can selectively impact host resistance toward a diverse range of pathogens. Moreover, detailed studies on key immune regulators, such as WRKY TFs and NPR1, are beginning to reveal the underlying mechanisms by which defense hormones influence the function of these factors. Here we provide a short update on such recent developments. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    African Journals Online (AJOL)

    , and the probable mechanism. Methods: After ... Keywords: Mitochondrial transcription factor A, NF-κB, Hypoxia, Human retinal endothelial cell,. Diabetic retinopathy ..... choice for diabetic retinopathy therapy, as TFAM activity clearly affects the ...

  8. Transcriptional Responses to the Auxin Hormone.

    Science.gov (United States)

    Weijers, Dolf; Wagner, Doris

    2016-04-29

    Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.

  9. Promoter proximal polyadenylation sites reduce transcription activity

    DEFF Research Database (Denmark)

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

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site......, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites...... RNA polymerase II-transcribed genes use specialized termination mechanisms to maintain high transcription levels....

  10. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    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...

  11. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

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

  12. Automatic Phonetic Transcription for Danish Speech Recognition

    DEFF Research Database (Denmark)

    Kirkedal, Andreas Søeborg

    to acquire and expensive to create. For languages with productive compounding or agglutinative languages like German and Finnish, respectively, phonetic dictionaries are also hard to maintain. For this reason, automatic phonetic transcription tools have been produced for many languages. The quality...... of automatic phonetic transcriptions vary greatly with respect to language and transcription strategy. For some languages where the difference between the graphemic and phonetic representations are small, graphemic transcriptions can be used to create ASR systems with acceptable performance. In other languages...... for English and now extended to cover 50 languages. Due to the nature of open source software, the quality of language support depends greatly on who encoded them. The Danish version was created by a Danish native speaker and contains more than 8,600 spelling-to-phoneme rules and more than 11,000 rules...

  13. Targeted HIV-1 Latency Reversal Using CRISPR/Cas9-Derived Transcriptional Activator Systems.

    Directory of Open Access Journals (Sweden)

    Julia K Bialek

    Full Text Available CRISPR/Cas9 technology is currently considered the most advanced tool for targeted genome engineering. Its sequence-dependent specificity has been explored for locus-directed transcriptional modulation. Such modulation, in particular transcriptional activation, has been proposed as key approach to overcome silencing of dormant HIV provirus in latently infected cellular reservoirs. Currently available agents for provirus activation, so-called latency reversing agents (LRAs, act indirectly through cellular pathways to induce viral transcription. However, their clinical performance remains suboptimal, possibly because reservoirs have diverse cellular identities and/or proviral DNA is intractable to the induced pathways. We have explored two CRISPR/Cas9-derived activator systems as targeted approaches to induce dormant HIV-1 proviral DNA. These systems recruit multiple transcriptional activation domains to the HIV 5' long terminal repeat (LTR, for which we have identified an optimal target region within the LTR U3 sequence. Using this target region, we demonstrate transcriptional activation of proviral genomes via the synergistic activation mediator complex in various in culture model systems for HIV latency. Observed levels of induction are comparable or indeed higher than treatment with established LRAs. Importantly, activation is complete, leading to production of infective viral particles. Our data demonstrate that CRISPR/Cas9-derived technologies can be applied to counteract HIV latency and may therefore represent promising novel approaches in the quest for HIV elimination.

  14. Transcription Factors in Xylem Development. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Sederoff, Ronald; Whetten, Ross; O' Malley, David; Campbell, Malcolm

    1999-07-01

    Answers to the following questions are answered in this report. do the two pine Byb proteins previously identified as candidate transcription factors bind to DNA and activate transcription? In what cell types are tehse Myb proteins expressed? Are these proteins localized to the nucleus? Do other proteins in pine xylem interact with these Myb proteins? Does altered expression of these genes have an impact on xylogenesis, specifically the expression of monolignol biosynthetic genes?

  15. A unified architecture of transcriptional regulatory elements

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  16. Exploring cattle movements in Belgium.

    Science.gov (United States)

    Ensoy, Chellafe; Faes, Christel; Welby, Sarah; Van der Stede, Yves; Aerts, Marc

    2014-09-01

    Movement of animals from one farm to another is a potential risk and can lead to the spreading of livestock diseases. Therefore, in order to implement effective control measures, it is important to understand the movement network in a given area. Using the SANITEL data from 2005 to 2009, around 2 million cattle movements in Belgium were traced. Exploratory analysis revealed different spatial structures for the movement of different cattle types: fattening calves are mostly moved to the Antwerp region, adult cattle are moved to different parts in Belgium. Based on these differences, movement of cattle would more likely cause a spread of disease to a larger number of areas in Belgium as compared to the fattening calves. A closer inspection of the spatial and temporal patterns of cattle movement using a weighted negative binomial model, revealed a significant short-distance movement of bovine which could be an important factor contributing to the local spreading of a disease. The model however revealed hot spot areas of movement in Belgium; four areas in the Walloon region (Luxembourg, Hainaut, Namur and Liege) were found as hot spot areas while East and West Flanders are important "receivers" of movement. This implies that an introduction of a disease to these Walloon regions could result in a spread toward the East and West Flanders regions, as what happened in the case of Bluetongue BTV-8 outbreak in 2006. The temporal component in the model also revealed a linear trend and short- and long-term seasonality in the cattle movement with a peak around spring and autumn. The result of this explorative analysis enabled the identification of "hot spots" in time and space which is important in enhancing any existing monitoring and surveillance system. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Urban Space Explorer: A Visual Analytics System for Urban Planning.

    Science.gov (United States)

    Karduni, Alireza; Cho, Isaac; Wessel, Ginette; Ribarsky, William; Sauda, Eric; Dou, Wenwen

    2017-01-01

    Understanding people's behavior is fundamental to many planning professions (including transportation, community development, economic development, and urban design) that rely on data about frequently traveled routes, places, and social and cultural practices. Based on the results of a practitioner survey, the authors designed Urban Space Explorer, a visual analytics system that utilizes mobile social media to enable interactive exploration of public-space-related activity along spatial, temporal, and semantic dimensions.

  18. Treating autism by targeting the temporal lobes.

    Science.gov (United States)

    Chi, Richard P; Snyder, Allan W

    2014-11-01

    Compelling new findings suggest that an early core signature of autism is a deficient left anterior temporal lobe response to language and an atypical over-activation of the right anterior temporal lobe. Intriguingly, our recent results from an entirely different line of reasoning and experiments also show that applying cathodal stimulation (suppressing) at the left anterior temporal lobe together with anodal stimulation (facilitating) at the right anterior temporal lobe, by transcranial direct current stimulation (tDCS), can induce some autistic-like cognitive abilities in otherwise normal adults. If we could briefly induce autistic like cognitive abilities in healthy individuals, it follows that we might be able to mitigate some autistic traits by reversing the above stimulation protocol, in an attempt to restore the typical dominance of the left anterior temporal lobe. Accordingly, we hypothesize that at least some autistic traits can be mitigated, by applying anodal stimulation (facilitating) at the left anterior temporal lobe together with cathodal stimulation (suppressing) at the right anterior temporal lobe. Our hypothesis is supported by strong convergent evidence that autistic symptoms can emerge and later reverse due to the onset and subsequent recovery of various temporal lobe (predominantly the left) pathologies. It is also consistent with evidence that the temporal lobes (especially the left) are a conceptual hub, critical for extracting meaning from lower level sensory information to form a coherent representation, and that a deficit in the temporal lobes underlies autistic traits. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Vesicular stomatitis virus polymerase's strong affinity to its template suggests exotic transcription models.

    Directory of Open Access Journals (Sweden)

    Xiaolin Tang

    2014-12-01

    Full Text Available Vesicular stomatitis virus (VSV is the prototype for negative sense non segmented (NNS RNA viruses which include potent human and animal pathogens such as Rabies, Ebola and measles. The polymerases of NNS RNA viruses only initiate transcription at or near the 3' end of their genome template. We measured the dissociation constant of VSV polymerases from their whole genome template to be 20 pM. Given this low dissociation constant, initiation and sustainability of transcription becomes nontrivial. To explore possible mechanisms, we simulated the first hour of transcription using Monte Carlo methods and show that a one-time initial dissociation of all polymerases during entry is not sufficient to sustain transcription. We further show that efficient transcription requires a sliding mechanism for non-transcribing polymerases and can be realized with different polymerase-polymerase interactions and distinct template topologies. In conclusion, we highlight a model in which collisions between transcribing and sliding non-transcribing polymerases result in release of the non-transcribing polymerases allowing for redistribution of polymerases between separate templates during transcription and suggest specific experiments to further test these mechanisms.

  20. Targeted inactivation of transcription factors by overexpression of their truncated forms in plants.

    Science.gov (United States)

    Seo, Pil Joon; Hong, Shin-Young; Ryu, Jae Yong; Jeong, Eun-Young; Kim, Sang-Gyu; Baldwin, Ian T; Park, Chung-Mo

    2012-10-01

    Transcription factors are central constituents of gene regulatory networks that control diverse aspects of plant development and environmental adaptability. Therefore they have been explored for decades as primary targets for agricultural biotechnology. A gene of interest can readily be introduced into many crop plants, whereas targeted gene inactivation is practically difficult in many cases. Here, we developed an artificial small interfering peptide (a-siPEP) approach, which is based on overexpression of specific protein domains, and evaluated its application for the targeted inactivation of transcription factors in the dicot model, Arabidopsis, and monocot model, Brachypodium. We designed potential a-siPEPs of two representative MADS box transcription factors, SUPPRESSOR OF OVEREXPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS (AG), and a MYB transcription factor, LATE ELONGATED HYPOCOTYL (LHY). Transgenic plants overproducing the a-siPEPs displayed phenotypes comparable to those of gene-deficient mutants. The a-siPEPs attenuate nuclear import and DNA-binding of target transcription factors. Our data demonstrate that the a-siPEP tool is an efficient genetic means of inactivating specific transcription factors in plants. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  1. Spectro-Temporal Weighting of Loudness

    Science.gov (United States)

    Oberfeld, Daniel; Heeren, Wiebke; Rennies, Jan; Verhey, Jesko

    2012-01-01

    Real-world sounds like speech or traffic noise typically exhibit spectro-temporal variability because the energy in different spectral regions evolves differently as a sound unfolds in time. However, it is currently not well understood how the energy in different spectral and temporal portions contributes to loudness. This study investigated how listeners weight different temporal and spectral components of a sound when judging its overall loudness. Spectral weights were measured for the combination of three loudness-matched narrowband noises with different center frequencies. To measure temporal weights, 1,020-ms stimuli were presented, which randomly changed in level every 100 ms. Temporal weights were measured for each narrowband noise separately, and for a broadband noise containing the combination of the three noise bands. Finally, spectro-temporal weights were measured with stimuli where the level of the three narrowband noises randomly and independently changed every 100 ms. The data consistently showed that (i) the first 300 ms of the sounds had a greater influence on overall loudness perception than later temporal portions (primacy effect), and (ii) the lowest noise band contributed significantly more to overall loudness than the higher bands. The temporal weights did not differ between the three frequency bands. Notably, the spectral weights and temporal weights estimated from the conditions with only spectral or only temporal variability were very similar to the corresponding weights estimated in the spectro-temporal condition. The results indicate that the temporal and the spectral weighting of the loudness of a time-varying sound are independent processes. The spectral weights remain constant across time, and the temporal weights do not change across frequency. The results are discussed in the context of current loudness models. PMID:23209670

  2. Spectro-temporal weighting of loudness.

    Directory of Open Access Journals (Sweden)

    Daniel Oberfeld

    Full Text Available Real-world sounds like speech or traffic noise typically exhibit spectro-temporal variability because the energy in different spectral regions evolves differently as a sound unfolds in time. However, it is currently not well understood how the energy in different spectral and temporal portions contributes to loudness. This study investigated how listeners weight different temporal and spectral components of a sound when judging its overall loudness. Spectral weights were measured for the combination of three loudness-matched narrowband noises with different center frequencies. To measure temporal weights, 1,020-ms stimuli were presented, which randomly changed in level every 100 ms. Temporal weights were measured for each narrowband noise separately, and for a broadband noise containing the combination of the three noise bands. Finally, spectro-temporal weights were measured with stimuli where the level of the three narrowband noises randomly and independently changed every 100 ms. The data consistently showed that (i the first 300 ms of the sounds had a greater influence on overall loudness perception than later temporal portions (primacy effect, and (ii the lowest noise band contributed significantly more to overall loudness than the higher bands. The temporal weights did not differ between the three frequency bands. Notably, the spectral weights and temporal weights estimated from the conditions with only spectral or only temporal variability were very similar to the corresponding weights estimated in the spectro-temporal condition. The results indicate that the temporal and the spectral weighting of the loudness of a time-varying sound are independent processes. The spectral weights remain constant across time, and the temporal weights do not change across frequency. The results are discussed in the context of current loudness models.

  3. Temporal regulation of foregut development by HTZ-1/H2A.Z and PHA-4/FoxA.

    Directory of Open Access Journals (Sweden)

    Dustin L Updike

    2006-09-01

    Full Text Available The histone variant H2A.Z is evolutionarily conserved and plays an essential role in mice, Drosophila, and Tetrahymena. The essential function of H2A.Z is unknown, with some studies suggesting a role in transcriptional repression and others in activation. Here we show that Caenorhabditis elegans HTZ-1/H2A.Z and the remodeling complex MYS-1/ESA1-SSL-1/SWR1 synergize with the FoxA transcription factor PHA-4 to coordinate temporal gene expression during foregut development. We observe dramatic genetic interactions between pha-4 and htz-1, mys-1, and ssl-1. A survey of transcription factors reveals that this interaction is specific, and thus pha-4 is acutely sensitive to reductions in these three proteins. Using a nuclear spot assay to visualize HTZ-1 in living embryos as organogenesis proceeds, we show that HTZ-1 is recruited to foregut promoters at the time of transcriptional onset, and this recruitment requires PHA-4. Loss of htz-1 by RNAi is lethal and leads to delayed expression of a subset of foregut genes. Thus, the effects of PHA-4 on temporal regulation can be explained in part by recruitment of HTZ-1 to target promoters. We suggest PHA-4 and HTZ-1 coordinate temporal gene expression by modulating the chromatin environment.

  4. Auditory evoked fields elicited by spectral, temporal, and spectral-temporal changes in human cerebral cortex

    Directory of Open Access Journals (Sweden)

    Hidehiko eOkamoto

    2012-05-01

    Full Text Available Natural sounds contain complex spectral components, which are temporally modulated as time-varying signals. Recent studies have suggested that the auditory system encodes spectral and temporal sound information differently. However, it remains unresolved how the human brain processes sounds containing both spectral and temporal changes. In the present study, we investigated human auditory evoked responses elicited by spectral, temporal, and spectral-temporal sound changes by means of magnetoencephalography (MEG. The auditory evoked responses elicited by the spectral-temporal change were very similar to those elicited by the spectral change, but those elicited by the temporal change were delayed by 30 – 50 ms and differed from the others in morphology. The results suggest that human brain responses corresponding to spectral sound changes precede those corresponding to temporal sound changes, even when the spectral and temporal changes occur simultaneously.

  5. Temporal sensitivity. [time dependent human perception of visual stimuli

    Science.gov (United States)

    Watson, Andrew B.

    1986-01-01

    Human visual temporal sensitivity is examined. The stimuli used to measure temporal sensitivity are described and the linear systems theory is reviewed in terms of temporal sensitivity. A working model which represents temporal sensitivity is proposed. The visibility of a number of temporal wave forms, sinusoids, rectangular pulses, and pulse pairs, is analyzed. The relation between spatial and temporal effects is studied. Temporal variations induced by image motion and the effects of light adaptation on temporal sensitivity are considered.

  6. When transcription goes on Holliday: Double Holliday junctions block RNA polymerase II transcription in vitro.

    Science.gov (United States)

    Pipathsouk, Anne; Belotserkovskii, Boris P; Hanawalt, Philip C

    2017-02-01

    Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJs), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact. Thus, the DHJ structure should strongly resist transient unwinding during transcription; consequently, it is predicted to cause significantly stronger blockage than single HJ structures. The patterns of transcription blockage obtained for RNA polymerase II transcription in HeLa cell nuclear extracts were in accordance with this prediction. However, we did not detect transcription blockage with purified T7 phage RNA polymerase; we discuss a possible explanation for this difference. In general, our findings implicate naturally occurring Holliday junctions in transcription arrest. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Dynamic analysis of stochastic transcription cycles.

    Directory of Open Access Journals (Sweden)

    Claire V Harper

    2011-04-01

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

  8. Hourly temporal distribution of wind

    Science.gov (United States)

    Deligiannis, Ilias; Dimitriadis, Panayiotis; Koutsoyiannis, Demetris

    2016-04-01

    The wind process is essential for hydrometeorology and additionally, is one of the basic renewable energy resources. Most stochastic forecast models are limited up to daily scales disregarding the hourly scale which is significant for renewable energy management. Here, we analyze hourly wind timeseries giving emphasis on the temporal distribution of wind within the day. We finally present a periodic model based on statistical as well as hydrometeorological reasoning that shows good agreement with data. Acknowledgement: This research is conducted within the frame of the undergraduate course "Stochastic Methods in Water Resources" of the National Technical University of Athens (NTUA). The School of Civil Engineering of NTUA provided moral support for the participation of the students in the Assembly.

  9. Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases.

    Science.gov (United States)

    Lavysh, Daria; Sokolova, Maria; Slashcheva, Marina; Förstner, Konrad U; Severinov, Konstantin

    2017-02-14

    Bacteriophage AR9 is a recently sequenced jumbo phage that encodes two multisubunit RNA polymerases. Here we investigated the AR9 transcription strategy and the effect of AR9 infection on the transcription of its host, Bacillus subtilis Analysis of whole-genome transcription revealed early, late, and continuously expressed AR9 genes. Alignment of sequences upstream of the 5' ends of AR9 transcripts revealed consensus sequences that define early and late phage promoters. Continuously expressed AR9 genes have both early and late promoters in front of them. Early AR9 transcription is independent of protein synthesis and must be determined by virion RNA polymerase injected together with viral DNA. During infection, the overall amount of host mRNAs is significantly decreased. Analysis of relative amounts of host transcripts revealed notable differences in the levels of some mRNAs. The physiological significance of up- or downregulation of host genes for AR9 phage infection remains to be established. AR9 infection is significantly affected by rifampin, an inhibitor of host RNA polymerase transcription. The effect is likely caused by the antibiotic-induced killing of host cells, while phage genome transcription is solely performed by viral RNA polymerases.IMPORTANCE Phages regulate the timing of the expression of their own genes to coordinate processes in the infected cell and maximize the release of viral progeny. Phages also alter the levels of host transcripts. Here we present the results of a temporal analysis of the host and viral transcriptomes of Bacillus subtilis infected with a giant phage, AR9. We identify viral promoters recognized by two virus-encoded RNA polymerases that are a unique feature of the phiKZ-related group of phages to which AR9 belongs. Our results set the stage for future analyses of highly unusual RNA polymerases encoded by AR9 and other phiKZ-related phages. Copyright © 2017 Lavysh et al.

  10. A Temporal Map of Coaching

    Science.gov (United States)

    Theeboom, Tim; Van Vianen, Annelies E. M.; Beersma, Bianca

    2017-01-01

    Economic pressures on companies, technological developments, and less stable career paths pose potential threats to the well-being of employees (e.g., stress, burn-out) and require constant adaptation. In the light of these challenges, it is not surprising that employees often seek the support of a coach. The role of a coach is to foster change by facilitating a coachees’ movement through a self-regulatory cycle with the ultimate aim of stimulating sustained well-being and functioning. While meta-analytic research indicates that coaching interventions can be effectively applied to assist employees in dealing with change, the current literature on coaching lacks solid theoretical frameworks that are needed to build a cumulative knowledge-base and to inspire evidence-based practice. In this conceptual analysis, we examine the coaching process through a temporal lens. By doing so, we provide an integrated theoretical framework: a temporal map of coaching. In this framework, we link seminal concepts in psychology to the coaching process, and describe which competencies of coachees are crucial in the different stages of change that coaching aims to bring about. During the preparatory contemplation stage, targeting coachees’ awareness by enhancing their mindfulness and environmental receptiveness is important. During the contemplation stage, coachees’ willingness and perceived ability to change are central competencies. We propose that coaches should therefore foster intrinsic goal orientation and self-efficacy during this stage. During the planning stage, coaches should focus on goal-setting and implementation intentions. Finally, during the maintenance/termination stage, stimulating coachees’ reflection is especially important in order to help them to integrate their learning experiences. The framework delineated in this paper contributes to the understanding of coaching as a tool to assist employees in dealing with the challenges of an increasingly dynamic

  11. Motor Activity Improves Temporal Expectancy

    Science.gov (United States)

    Fautrelle, Lilian; Mareschal, Denis; French, Robert; Addyman, Caspar; Thomas, Elizabeth

    2015-01-01

    Certain brain areas involved in interval timing are also important in motor activity. This raises the possibility that motor activity might influence interval timing. To test this hypothesis, we assessed interval timing in healthy adults following different types of training. The pre- and post-training tasks consisted of a button press in response to the presentation of a rhythmic visual stimulus. Alterations in temporal expectancy were evaluated by measuring response times. Training consisted of responding to the visual presentation of regularly appearing stimuli by either: (1) pointing with a whole-body movement, (2) pointing only with the arm, (3) imagining pointing with a whole-body movement, (4) simply watching the stimulus presentation, (5) pointing with a whole-body movement in response to a target that appeared at irregular intervals (6) reading a newspaper. Participants performing a motor activity in response to the regular target showed significant improvements in judgment times compared to individuals with no associated motor activity. Individuals who only imagined pointing with a whole-body movement also showed significant improvements. No improvements were observed in the group that trained with a motor response to an irregular stimulus, hence eliminating the explanation that the improved temporal expectations of the other motor training groups was purely due to an improved motor capacity to press the response button. All groups performed a secondary task equally well, hence indicating that our results could not simply be attributed to differences in attention between the groups. Our results show that motor activity, even when it does not play a causal or corrective role, can lead to improved interval timing judgments. PMID:25806813

  12. A Temporal Map of Coaching

    Directory of Open Access Journals (Sweden)

    Tim Theeboom

    2017-08-01

    Full Text Available Economic pressures on companies, technological developments, and less stable career paths pose potential threats to the well-being of employees (e.g., stress, burn-out and require constant adaptation. In the light of these challenges, it is not surprising that employees often seek the support of a coach. The role of a coach is to foster change by facilitating a coachees’ movement through a self-regulatory cycle with the ultimate aim of stimulating sustained well-being and functioning. While meta-analytic research indicates that coaching interventions can be effectively applied to assist employees in dealing with change, the current literature on coaching lacks solid theoretical frameworks that are needed to build a cumulative knowledge-base and to inspire evidence-based practice. In this conceptual analysis, we examine the coaching process through a temporal lens. By doing so, we provide an integrated theoretical framework: a temporal map of coaching. In this framework, we link seminal concepts in psychology to the coaching process, and describe which competencies of coachees are crucial in the different stages of change that coaching aims to bring about. During the preparatory contemplation stage, targeting coachees’ awareness by enhancing their mindfulness and environmental receptiveness is important. During the contemplation stage, coachees’ willingness and perceived ability to change are central competencies. We propose that coaches should therefore foster intrinsic goal orientation and self-efficacy during this stage. During the planning stage, coaches should focus on goal-setting and implementation intentions. Finally, during the maintenance/termination stage, stimulating coachees’ reflection is especially important in order to help them to integrate their learning experiences. The framework delineated in this paper contributes to the understanding of coaching as a tool to assist employees in dealing with the challenges of an

  13. Memory for temporally dynamic scenes.

    Science.gov (United States)

    Ferguson, Ryan; Homa, Donald; Ellis, Derek

    2017-07-01

    Recognition memory was investigated for individual frames extracted from temporally continuous, visually rich film segments of 5-15 min. Participants viewed a short clip from a film in either a coherent or a jumbled order, followed by a recognition test of studied frames. Foils came either from an earlier or a later part of the film (Experiment 1) or from deleted segments selected from random cuts of varying duration (0.5 to 30 s) within the film itself (Experiment 2). When the foils came from an earlier or later part of the film (Experiment 1), recognition was excellent, with the hit rate far exceeding the false-alarm rate (.78 vs. 18). In Experiment 2, recognition was far worse, with the hit rate (.76) exceeding the false-alarm rate only for foils drawn from the longest cuts (15 and 30 s) and matching the false-alarm rate for the 5 s segments. When the foils were drawn from the briefest cuts (0.5 and 1.0 s), the false-alarm rate exceeded the hit rate. Unexpectedly, jumbling had no effect on recognition in either experiment. These results are consistent with the view that memory for complex visually temporal events is excellent, with the integrity unperturbed by disruption of the global structure of the visual stream. Disruption of memory was observed only when foils were drawn from embedded segments of duration less than 5 s, an outcome consistent with the view that memory at these shortest durations are consolidated with expectations drawn from the previous stream.

  14. SST: Single-Stream Temporal Action Proposals

    KAUST Repository

    Buch, Shyamal

    2017-11-09

    Our paper presents a new approach for temporal detection of human actions in long, untrimmed video sequences. We introduce Single-Stream Temporal Action Proposals (SST), a new effective and efficient deep architecture for the generation of temporal action proposals. Our network can run continuously in a single stream over very long input video sequences, without the need to divide input into short overlapping clips or temporal windows for batch processing. We demonstrate empirically that our model outperforms the state-of-the-art on the task of temporal action proposal generation, while achieving some of the fastest processing speeds in the literature. Finally, we demonstrate that using SST proposals in conjunction with existing action classifiers results in improved state-of-the-art temporal action detection performance.

  15. Binding motifs in bacterial gene promoters modulate transcriptional effect of global regulators

    Energy Technology Data Exchange (ETDEWEB)

    Leuze, Michael Rex [ORNL; Karpinets, Tatiana V [ORNL; Syed, Mustafa H [ORNL; Beliaev, Alexander S [ORNL; Uberbacher, Edward C [ORNL

    2012-01-01

    Bacterial gene regulation involves transcription factors (TFs) that influence the expression of many genes. Global regulators, including CRP (cAMP Receptor Protein), ArcA, and FNR, can modulate the transcriptional activity of multiple operons. The similarity of a regulatory element s sequence to a TF s consensus binding site (BS) and the position of the regulatory element in an operon promoter are considered the most important determinants of this TF s regulatory influence. In this study we explore the hypothesis that the number of TFBS half-sites (where a half-site is one half of the palindromic BS consensus sequence, which we shall refer to as a binding motif or a BM) of a global regulator in an operon s promoter plays an important role in the operon s transcriptional regulation. We examine empirical data from transcriptional profiling of the CRP regulon in Shewanella oneidenses MR 1 and Escherichia coli, and of the ArcA regulon in S. oneidenses MR 1. We compare the power of CRP BM counts and of full, symmetrical CRP TFBS characteristics, namely similarity to consensus and location, to predict CRP-induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full-length TFBS quality or location. Regression analysis indicates that IHF (Integration Host Factor) and ArcA have synergistic effects on CRP-induced gene transcription, positive and negative, respectively. Based on these results, we propose that the fine-tuning of bacterial transcriptional activity by CRP may involves not only the bending of the operon promoter, facilitated by CRP in cooperation with the histone-like protein IHF, but also the cumulative binding affinity of multiple weak BMs.

  16. Extraction of transcript diversity from scientific literature.

    Directory of Open Access Journals (Sweden)

    Parantu K Shah

    2005-06-01

    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 http://www.bork.embl.de/LSAT/.

  17. Visual explorer facilitator's guide

    CERN Document Server

    Palus, Charles J

    2010-01-01

    Grounded in research and practice, the Visual Explorer™ Facilitator's Guide provides a method for supporting collaborative, creative conversations about complex issues through the power of images. The guide is available as a component in the Visual Explorer Facilitator's Letter-sized Set, Visual Explorer Facilitator's Post card-sized Set, Visual Explorer Playing Card-sized Set, and is also available as a stand-alone title for purchase to assist multiple tool users in an organization.

  18. Pattern Recognition by Hierarchical Temporal Memory

    OpenAIRE

    Maltoni, Prof. Davide

    2011-01-01

    Hierarchical Temporal Memory (HTM) is still largely unknown by the pattern recognition community and only a few studies have been published in the scientific literature. This paper reviews HTM architecture and related learning algorithms by using formal notation and pseudocode description. Novel approaches are then proposed to encode coincidence-group membership (fuzzy grouping) and to derive temporal groups (maxstab temporal clustering). Systematic experiments on three line-drawing datasets ...

  19. Induction of Linear Temporal Logic Programs

    OpenAIRE

    Kolter, Robert

    2017-01-01

    We propose a framework for the synthesis of temporal logic programs which are formulated in a simple temporal logic programming language from both positive and negative examples. First we will prove that results from the theory of first order inductive logic programming carry over to the domain of temporal logic. After this we will show how programs formulated in the presented language can be generalized or specialized in order to satisfy the specification induced by the sets of examples.

  20. Temporal Feature Integration for Music Organisation

    OpenAIRE

    Meng, Anders; Larsen, Jan; Hansen, Lars Kai

    2006-01-01

    This Ph.D. thesis focuses on temporal feature integration for music organisation. Temporal feature integration is the process of combining all the feature vectors of a given time-frame into a single new feature vector in order to capture relevant information in the frame. Several existing methods for handling sequences of features are formulated in the temporal feature integration framework. Two datasets for music genre classification have been considered as valid test-beds for music organisa...

  1. Regulatory elements and transcriptional control of chickenvasahomologue (CVH) promoter in chicken primordial germ cells.

    Science.gov (United States)

    Jin, So Dam; Lee, Bo Ram; Hwang, Young Sun; Lee, Hong Jo; Rim, Jong Seop; Han, Jae Yong

    2017-01-01

    Primordial germ cells (PGCs), the precursors of functional gametes, have distinct characteristics and exhibit several unique molecular mechanisms to maintain pluripotency and germness in comparison to somatic cells. They express germ cell-specific RNA binding proteins (RBPs) by modulating tissue-specific cis - and trans -regulatory elements. Studies on gene structures of chicken vasa homologue ( CVH ), a chicken RNA binding protein, involved in temporal and spatial regulation are thus important not only for understanding the molecular mechanisms that regulate germ cell fate, but also for practical applications of primordial germ cells. However, very limited studies are available on regulatory elements that control germ cell-specific expression in chicken. Therefore, we investigated the intricate regulatory mechanism(s) that governs transcriptional control of CVH . We constructed green fluorescence protein (GFP) or luciferase reporter vectors containing the various 5' flanking regions of CVH gene. From the 5' deletion and fragmented assays in chicken PGCs, we have identified a CVH promoter that locates at -316 to +275 base pair fragment with the highest luciferase activity. Additionally, we confirmed for the first time that the 5' untranslated region (UTR) containing intron 1 is required for promoter activity of the CVH gene in chicken PGCs. Furthermore, using a transcription factor binding prediction, transcriptome analysis and siRNA-mediated knockdown, we have identified that a set of transcription factors play a role in the PGC-specific CVH gene expression. These results demonstrate that cis -elements and transcription factors localizing in the 5' flanking region including the 5' UTR and an intron are important for transcriptional regulation of the CVH gene in chicken PGCs. Finally, this information will contribute to research studies in areas of reproductive biology, constructing of germ cell-specific synthetic promoter for tracing primordial germ cells as well

  2. Host Transcription Factors in the Immediate Pro-Inflammatory Response to the Parasitic Mite Psoroptes ovis

    Science.gov (United States)

    Burgess, Stewart T. G.; McNeilly, Tom N.; Watkins, Craig A.; Nisbet, Alasdair J.; Huntley, John F.

    2011-01-01

    Background Sheep scab, caused by infestation with the ectoparasitic mite Psoroptes ovis, results in the rapid development of cutaneous inflammation and leads to the crusted skin lesions characteristic of the disease. We described previously the global host transcriptional response to infestation with P. ovis, elucidating elements of the inflammatory processes which lead to the development of a rapid and profound immune response. However, the mechanisms by which this response is instigated remain unclear. To identify novel methods of intervention a better understanding of the early events involved in triggering the immune response is essential. The objective of this study was to gain a clearer understanding of the mechanisms and signaling pathways involved in the instigation of the immediate pro-inflammatory response. Results Through a combination of transcription factor binding site enrichment and pathway analysis we identified key roles for a number of transcription factors in the instigation of cutaneous inflammation. In particular, defined roles were elucidated for the transcription factors NF-kB and AP-1 in the orchestration of the early pro-inflammatory response, with these factors being implicated in the activation of a suite of inflammatory mediators. Conclusions Interrogation of the host temporal response to P. ovis infestation has enabled the further identification of the mechanisms underlying the development of the immediate host pro-inflammatory response. This response involves key regulatory roles for the transcription factors NF-kB and AP-1. Pathway analysis demonstrated that the activation of these transcription factors may be triggered following a host LPS-type response, potentially involving TLR4-signalling and also lead to the intriguing possibility that this could be triggered by a P. ovis allergen. PMID:21915322

  3. Host transcription factors in the immediate pro-inflammatory response to the parasitic mite Psoroptes ovis.

    Directory of Open Access Journals (Sweden)

    Stewart T G Burgess

    Full Text Available BACKGROUND: Sheep scab, caused by infestation with the ectoparasitic mite Psoroptes ovis, results in the rapid development of cutaneous inflammation and leads to the crusted skin lesions characteristic of the disease. We described previously the global host transcriptional response to infestation with P. ovis, elucidating elements of the inflammatory processes which lead to the development of a rapid and profound immune response. However, the mechanisms by which this response is instigated remain unclear. To identify novel methods of intervention a better understanding of the early events involved in triggering the immune response is essential. The objective of this study was to gain a clearer understanding of the mechanisms and signaling pathways involved in the instigation of the immediate pro-inflammatory response. RESULTS: Through a combination of transcription factor binding site enrichment and pathway analysis we identified key roles for a number of transcription factors in the instigation of cutaneous inflammation. In particular, defined roles were elucidated for the transcription factors NF-kB and AP-1 in the orchestration of the early pro-inflammatory response, with these factors being implicated in the activation of a suite of inflammatory mediators. CONCLUSIONS: Interrogation of the host temporal response to P. ovis infestation has enabled the further identification of the mechanisms underlying the development of the immediate host pro-inflammatory response. This response involves key regulatory roles for the transcription factors NF-kB and AP-1. Pathway analysis demonstrated that the activation of these transcription factors may be triggered following a host LPS-type response, potentially involving TLR4-signalling and also lead to the intriguing possibility that this could be triggered by a P. ovis allergen.

  4. Optimization of temporal networks under uncertainty

    CERN Document Server

    Wiesemann, Wolfram

    2012-01-01

    Many decision problems in Operations Research are defined on temporal networks, that is, workflows of time-consuming tasks whose processing order is constrained by precedence relations. For example, temporal networks are used to model projects, computer applications, digital circuits and production processes. Optimization problems arise in temporal networks when a decision maker wishes to determine a temporal arrangement of the tasks and/or a resource assignment that optimizes some network characteristic (e.g. the time required to complete all tasks). The parameters of these optimization probl

  5. Resting state networks in temporal lobe epilepsy

    National Research Council Canada - National Science Library

    Cataldi, Mauro; Avoli, Massimo; Villers‐Sidani, Etienne

    2013-01-01

    Temporal lobe epilepsy ( TLE ) is typically described as a neurologic disorder affecting a cerebral network comprising the hippocampus proper and several anatomically related extrahippocampal regions...

  6. Methyl jasmonate, gibberellic acid, and auxin affect transcription and transcript accumulation of chloroplast genes in barley.

    Science.gov (United States)

    Zubo, Yan O; Yamburenko, Maria V; Kusnetsov, Viktor V; Börner, Thomas

    2011-08-15

    Phytohormones control growth and development of plants. Their effects on the expression of nuclear genes are well investigated. Although they influence plastid-related processes, it is largely unknown whether phytohormones exert their control also by regulating the expression of plastid/chloroplast genes. We have therefore studied the effects of methyl jasmonate (MeJA), gibberellic acid (GA(3)), an auxin (indole-3-acetic acid, IAA), a brassinosteroid (24-epibrassinolide, BR) and a cytokinin (6-benzyladenine) on transcription (run-on assays) and transcript levels (RNA blot hybridization) of chloroplast genes after incubation of detached barley leaves in hormone solutions. BR was the only hormone without significant influence on chloroplast transcription. It showed, however, a weak reducing effect on transcript accumulation. MeJA, IAA and GA(3) repressed both transcription and transcript accumulation, while BA counteracted the effects of the other hormones. Effects of phytohormones on transcription differed in several cases from their influence on transcript levels suggesting that hormones may act via separate signaling pathways on transcription and transcript accumulation in chloroplasts. We observed striking differences in the response of chloroplast gene expression on phytohormones between the lower (young cells) and the upper segments (oldest cells) of barley leaves. Quantity and quality of the hormone effects on chloroplast gene expression seem to depend therefore on the age and/or developmental stage of the cells. As the individual chloroplast genes responded in different ways on phytohormone treatment, gene- and transcript-specific factors should be involved. Our data suggest that phytohormones adjust gene expression in the nucleo-cytoplasmic compartment and in plastids/chloroplasts in response to internal and external cues. Copyright © 2011 Elsevier GmbH. All rights reserved.

  7. Temporal discounting rates and their relation to exercise behavior in older adults.

    Science.gov (United States)

    Tate, Linda M; Tsai, Pao-Feng; Landes, Reid D; Rettiganti, Mallikarjuna; Lefler, Leanne L

    2015-12-01

    As our nation's population ages, the rates of chronic illness and disability are expected to increase significantly. Despite the knowledge that exercise may prevent chronic disease and promote health among older adults, many still are inactive. Factors related to exercise behaviors have been explored in recent years. However, temporal discounting is a motivational concept that has not been explored in regard to exercise in older adults. Temporal discounting is a decision making process by which an individual chooses a smaller more immediate reward over a larger delayed reward. The aim of this study was to determine if temporal discounting rates vary between exercising and non-exercising older adults. This study used cross-sectional survey of 137 older adults living in the community. Older adults were recruited from 11 rural Arkansas churches. The Kirby delay-discounting Monetary Choice Questionnaire was used to collect discounting rates and then bivariate analysis was performed to compare temporal discounting rate between the exercisers and non-exercisers. Finally, multivariate analysis was used to compare discounting rate controlling for other covariates. The results indicated that exercising older adults display lower temporal discounting rates than non-exercising older adults. After controlling for education, exercisers still have lower temporal discounting rates than non-exercisers (polder adults. This research suggests that if we can find appropriate incentives for discounting individuals, some type of immediate reward, then potentially we can design programs to engage and retain older adults in exercise. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Dynamic transcriptional signature and cell fate analysis reveals plasticity of individual neural plate border cells.

    Science.gov (United States)

    Roellig, Daniela; Tan-Cabugao, Johanna; Esaian, Sevan; Bronner, Marianne E

    2017-03-29

    The 'neural plate border' of vertebrate embryos contains precursors of neural crest and placode cells, both defining vertebrate characteristics. How these lineages segregate from neural and epidermal fates has been a matter of debate. We address this by performing a fine-scale quantitative temporal analysis of transcription factor expression in the neural plate border of chick embryos. The results reveal significant overlap of transcription factors characteristic of multiple lineages in individual border cells from gastrula through neurula stages. Cell fate analysis using a Sox2 (neural) enhancer reveals that cells that are initially Sox2+ cells can contribute not only to neural tube but also to neural crest and epidermis. Moreover, modulating levels of Sox2 or Pax7 alters the apportionment of neural tube versus neural crest fates. Our results resolve a long-standing question and suggest that many individual border cells maintain ability to contribute to multiple ectodermal lineages until or beyond neural tube closure.

  9. Transcription Elongation by RNA Polymerase I Is Linked to Efficient rRNA Processing and Ribosome Assembly

    OpenAIRE

    Schneider, David A.; Michel, Antje; Sikes, Martha L.; Vu, Loan; Dodd, Jonathan A.; Salgia, Shilpa; Osheim, Yvonne N.; Beyer, Ann L.; Nomura, Masayasu

    2007-01-01

    The synthesis of ribosomes in eukaryotic cells is a complex process involving many nonribosomal protein factors and snoRNAs. In general, the processes of rRNA transcription and ribosome assembly are treated as temporally or spatially distinct. Here, we describe the identification of a point mutation in the second largest subunit of RNA polymerase I near the active center of the enzyme that results in an elongation-defective enzyme in the yeast Saccharomyces cerevisiae. In vivo, this mutant sh...

  10. Transcript patterns associated with ectomycorrhiza development in Eucalyptus globulus and Pisolithus microcarpus.

    Science.gov (United States)

    Duplessis, Sébastien; Courty, Pierre-Emmanuel; Tagu, Denis; Martin, Francis

    2005-02-01

    Regulated gene expression is an important mechanism for controlling ectomycorrhizal symbiosis development. This study aimed to elucidate the coordination between development of mycorrhiza and the differential gene expression in both partners. We analysed RNA levels from sequential samples of symbiotic tissues of Eucalyptus globulus bicostata and the basidiomycete Pisolithus microcarpus progressing through ectomycorrhiza development using cDNA arrays. We derived groups of coordinately expressed genes using hierarchical and nonhierarchical clustering algorithms. Five major distinct temporal patterns of induction/repression were observed with distinct groups of early, middle-, and late-transcriptionally responsive genes to symbiosis formation. At earliest stages, the differentially expressed fungal genes included cell wall symbiosis-regulated proteins, hydrophobins and mannoproteins, whereas transcripts coding for defense-related proteins were upregulated in plant tissues. Middle- and late-transcriptionally responsive genes coded enzymes of glycolysis, tricarboxylic acid cycle and amino acid biosynthesis, as well as protein synthesis, hormone metabolism and signal transduction components. This investigation confirms and extends earlier results which found that changes in morphology associated with mycorrhizal development were accompanied by changes in transcript patterns, but no ectomycorrhiza-specific genes were detected.

  11. Non-Equilibrium Thermodynamics of Transcriptional Bursts

    Science.gov (United States)

    Hernández-Lemus, Enrique

    Gene transcription or Gene Expression (GE) is the process which transforms the information encoded in DNA into a functional RNA message. It is known that GE can occur in bursts or pulses. Transcription is irregular, with strong periods of activity, interspersed by long periods of inactivity. If we consider the average behavior over millions of cells, this process appears to be continuous. But at the individual cell level, there is considerable variability, and for most genes, very little activity at any one time. Some have claimed that GE bursting can account for the high variability in gene expression occurring between cells in isogenic populations. This variability has a big impact on cell behavior and thus on phenotypic conditions and disease. In view of these facts, the development of a thermodynamic framework to study gene expression and transcriptional regulation to integrate the vast amount of molecular biophysical GE data is appealing. Application of such thermodynamic formalism is useful to observe various dissipative phenomena in GE regulatory dynamics. In this chapter we will examine at some detail the complex phenomena of transcriptional bursts (specially of a certain class of anomalous bursts) in the context of a non-equilibrium thermodynamics formalism and will make some initial comments on the relevance of some irreversible processes that may be connected to anomalous transcriptional bursts.

  12. Manuscript Transcription by Crowdsourcing: Transcribe Bentham

    Directory of Open Access Journals (Sweden)

    Martin Moyle

    2011-02-01

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

  13. Transcriptional features of genomic regulatory blocks.

    Science.gov (United States)

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

    2009-01-01

    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.

  14. Transcriptional profiling of fetal hypothalamic TRH neurons.

    Science.gov (United States)

    Guerra-Crespo, Magdalena; Pérez-Monter, Carlos; Janga, Sarath Chandra; Castillo-Ramírez, Santiago; Gutiérrez-Rios, Rosa María; Joseph-Bravo, Patricia; Pérez-Martínez, Leonor; Charli, Jean-Louis

    2011-05-10

    During murine hypothalamic development, different neuroendocrine cell phenotypes are generated in overlapping periods; this suggests that cell-type specific developmental programs operate to achieve complete maturation. A balance between programs that include cell proliferation, cell cycle withdrawal as well as epigenetic regulation of gene expression characterizes neurogenesis. Thyrotropin releasing hormone (TRH) is a peptide that regulates energy homeostasis and autonomic responses. To better understand the molecular mechanisms underlying TRH neuron development, we performed a genome wide study of its transcriptome during fetal hypothalamic development. In primary cultures, TRH cells constitute 2% of the total fetal hypothalamic cell population. To purify these cells, we took advantage of the fact that the segment spanning -774 to +84 bp of the Trh gene regulatory region confers specific expression of the green fluorescent protein (GFP) in the TRH cells. Transfected TRH cells were purified by fluorescence activated cell sorting, various cell preparations pooled, and their transcriptome compared to that of GFP- hypothalamic cells. TRH cells undergoing the terminal phase of differentiation, expressed genes implicated in protein biosynthesis, intracellular signaling and transcriptional control. Among the transcription-associated transcripts, we identified the transcription factors Klf4, Klf10 and Atf3, which were previously uncharacterized within the hypothalamus. To our knowledge, this is one of the first reports identifying transcripts with a potentially important role during the development of a specific hypothalamic neuronal phenotype. This genome-scale study forms a rational foundation for identifying genes that might participate in the development and function of hypothalamic TRH neurons.

  15. The adenovirus E1A N-terminal repression domain represses transcription from a chromatin template in vitro.

    Science.gov (United States)

    Loewenstein, Paul M; Wu, Shwu-Yuan; Chiang, Cheng-Ming; Green, Maurice

    2012-06-20

    The adenovirus repression domain of E1A 243R at the E1A N-terminus (E1A 1-80) transcriptionally represses genes involved in differentiation and cell cycle progression. E1A 1-80 represses transcription in vitro from naked DNA templates through its interaction with p300 and TFIID. E1A 1-80 can also interact with several chromatin remodeling factors and associates with chromatin in vivo. We show here that E1A 243R and E1A 1-80 can repress transcription from a reconstituted chromatin template in vitro. Temporal analysis reveals strong repression by E1A 1-80 when added at pre-activation, activation and early transcription stages. Interestingly, E1A 1-80 can greatly enhance transcription from chromatin templates, but not from naked DNA, when added at pre-initiation complex (PIC) formation and transcription-initiation stages. These data reveal a new dimension for E1A 1-80's interface with chromatin and may reflect its interaction with key players in PIC formation, p300 and TFIID, and/or possibly a role in chromatin remodeling. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. The exploration metaphor

    Science.gov (United States)

    Mcgreevy, Michael W.

    1991-01-01

    NASA's experience in planetary exploration has demonstrated that the desktop workstation is inadequate for many visualization situations. The primary mission displays for the unmanned Surveyor missions to the moon during the mid-1960's, for example, were environmental images assembled on the inside surfaces of spherical shells. Future exploration missions will greatly benefit from advances in digital computer and display technology, but there remain unmet user interface needs. Alternative user interfaces and metaphors are needed for planetary exploration and other interactions with complex spatial environments. These interfaces and metaphors would enable the user to directly explore environments and naturally manipulate objects in those environments. Personal simulators, virtual workstations, and telepresence user interfaces are systems capable of providing this integration of user space and task space. The Exploration Metaphor is a useful concept for guiding the design of user interfaces for virtual environments and telepresence. To apply the Exploration Metaphor is to assert that computing is like exploration, and to support objects, operations, and contexts comparable to those encountered in the exploration of natural environments. The Exploration Metaphor, under development for user interfaces in support of NASA's planetary exploration missions and goals, will also benefit other applications where complex spatial information must be visualized. Visualization methods and systems for planetary exploration are becoming increasingly integrated and interactive as computing technology improves. These advances will benefit from virtual environment and telepresence interface technology. A key development has been the processing of multiple images and other sensor data to create detailed digital models of the planets and moons. Data from images of the Earth, Mars, and Miranda, for example, have been converted into 3D models, and dynamic virtual fly-overs have been

  17. Systematic analysis of transcription start sites in avian development.

    Directory of Open Access Journals (Sweden)

    Marina Lizio

    2017-09-01

    Full Text Available Cap Analysis of Gene Expression (CAGE in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM] were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals. By facilitating promoter-based molecular analysis and genetic

  18. Characterization of neurons in the cortical white matter in human temporal lobe epilepsy.

    Science.gov (United States)

    Richter, Zsófia; Janszky, József; Sétáló, György; Horváth, Réka; Horváth, Zsolt; Dóczi, Tamás; Seress, László; Ábrahám, Hajnalka

    2016-10-01

    The aim of the present work was to characterize neurons in the archi- and neocortical white matter, and to investigate their distribution in mesial temporal sclerosis. Immunohistochemistry and quantification of neurons were performed on surgically resected tissue sections of patients with therapy-resistant temporal lobe epilepsy. Temporal lobe tissues of patients with tumor but without epilepsy and that from autopsy were used as controls. Neurons were identified with immunohistochemistry using antibodies against NeuN, calcium-binding proteins, transcription factor Tbr1 and neurofilaments. We found significantly higher density of neurons in the archi- and neocortical white matter of patients with temporal lobe epilepsy than in that of controls. Based on their morphology and neurochemical content, both excitatory and inhibitory cells were present among these neurons. A subset of neurons in the white matter was Tbr-1-immunoreactive and these neurons coexpressed NeuN and neurofilament marker SMI311R. No colocalization of Tbr1 was observed with the inhibitory neuronal markers, calcium-binding proteins. We suggest that a large population of white matter neurons comprises remnants of the subplate. Furthermore, we propose that a subset of white matter neurons was arrested during migration, highlighting the role of cortical maldevelopment in epilepsy associated with mesial temporal sclerosis. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

  19. Beyond Transcription Factors: The Role of Chromatin Modifying Enzymes in Regulating Transcription Required for Memory

    Science.gov (United States)

    Barrett, Ruth M.; Wood, Marcelo A.

    2008-01-01

    One of the alluring aspects of examining chromatin modifications in the role of modulating transcription required for long-term memory processes is that these modifications may provide transient and potentially stable epigenetic marks in the service of activating and/or maintaining transcriptional processes. These, in turn, may ultimately…

  20. Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription.

    Science.gov (United States)

    Josefowicz, Steven Z; Shimada, Miho; Armache, Anja; Li, Charles H; Miller, Rand M; Lin, Shu; Yang, Aerin; Dill, Brian D; Molina, Henrik; Park, Hee-Sung; Garcia, Benjamin A; Taunton, Jack; Roeder, Robert G; Allis, C David

    2016-10-20

    The inflammatory response requires coordinated activation of both transcription factors and chromatin to induce transcription for defense against pathogens and environmental insults. We sought to elucidate the connections between inflammatory signaling pathways and chromatin through genomic footprinting of kinase activity and unbiased identification of prominent histone phosphorylation events. We identified H3 serine 28 phosphorylation (H3S28ph) as the principal stimulation-dependent histone modification and observed its enrichment at induced genes in mouse macrophages stimulated with bacterial lipopolysaccharide. Using pharmacological and genetic approaches, we identified mitogen- and stress-activated protein kinases (MSKs) as primary mediators of H3S28ph in macrophages. Cell-free transcription assays demonstrated that H3S28ph directly promotes p300/CBP-dependent transcription. Further, MSKs can activate both signal-responsive transcription factors and the chromatin template with additive effects on transcription. Specific inhibition of MSKs in macrophages selectively reduced transcription of stimulation-induced genes. Our results suggest that MSKs incorporate upstream signaling inputs and control multiple downstream regulators of inducible transcription. Copyright © 2016 Elsevier Inc. All rights reserved.