WorldWideScience

Sample records for large-scale rnai screens

  1. RNAi Screening in Spodoptera frugiperda.

    Science.gov (United States)

    Ghosh, Subhanita; Singh, Gatikrushna; Sachdev, Bindiya; Kumar, Ajit; Malhotra, Pawan; Mukherjee, Sunil K; Bhatnagar, Raj K

    2016-01-01

    RNA interference is a potent and precise reverse genetic approach to carryout large-scale functional genomic studies in a given organism. During the past decade, RNAi has also emerged as an important investigative tool to understand the process of viral pathogenesis. Our laboratory has successfully generated transgenic reporter and RNAi sensor line of Spodoptera frugiperda (Sf21) cells and developed a reversal of silencing assay via siRNA or shRNA guided screening to investigate RNAi factors or viral pathogenic factors with extraordinary fidelity. Here we describe empirical approaches and conceptual understanding to execute successful RNAi screening in Spodoptera frugiperda 21-cell line.

  2. Automated microscopy for high-content RNAi screening

    Science.gov (United States)

    2010-01-01

    Fluorescence microscopy is one of the most powerful tools to investigate complex cellular processes such as cell division, cell motility, or intracellular trafficking. The availability of RNA interference (RNAi) technology and automated microscopy has opened the possibility to perform cellular imaging in functional genomics and other large-scale applications. Although imaging often dramatically increases the content of a screening assay, it poses new challenges to achieve accurate quantitative annotation and therefore needs to be carefully adjusted to the specific needs of individual screening applications. In this review, we discuss principles of assay design, large-scale RNAi, microscope automation, and computational data analysis. We highlight strategies for imaging-based RNAi screening adapted to different library and assay designs. PMID:20176920

  3. In Vivo RNAi-Based Screens: Studies in Model Organisms

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    Miki Yamamoto-Hino

    2013-11-01

    Full Text Available RNA interference (RNAi is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA and target mRNA molecules. Numerous cell-based genome-wide screens have successfully identified novel genes involved in various biological processes, including signal transduction, cell viability/death, and cell morphology. However, cell-based screens cannot address cellular processes such as development, behavior, and immunity. Drosophila and Caenorhabditis elegans are two model organisms whose whole bodies and individual body parts have been subjected to RNAi-based genome-wide screening. Moreover, Drosophila RNAi allows the manipulation of gene function in a spatiotemporal manner when it is implemented using the Gal4/UAS system. Using this inducible RNAi technique, various large-scale screens have been performed in Drosophila, demonstrating that the method is straightforward and valuable. However, accumulated results reveal that the results of RNAi-based screens have relatively high levels of error, such as false positives and negatives. Here, we review in vivo RNAi screens in Drosophila and the methods that could be used to remove ambiguity from screening results.

  4. iScreen: Image-Based High-Content RNAi Screening Analysis Tools.

    Science.gov (United States)

    Zhong, Rui; Dong, Xiaonan; Levine, Beth; Xie, Yang; Xiao, Guanghua

    2015-09-01

    High-throughput RNA interference (RNAi) screening has opened up a path to investigating functional genomics in a genome-wide pattern. However, such studies are often restricted to assays that have a single readout format. Recently, advanced image technologies have been coupled with high-throughput RNAi screening to develop high-content screening, in which one or more cell image(s), instead of a single readout, were generated from each well. This image-based high-content screening technology has led to genome-wide functional annotation in a wider spectrum of biological research studies, as well as in drug and target discovery, so that complex cellular phenotypes can be measured in a multiparametric format. Despite these advances, data analysis and visualization tools are still largely lacking for these types of experiments. Therefore, we developed iScreen (image-Based High-content RNAi Screening Analysis Tool), an R package for the statistical modeling and visualization of image-based high-content RNAi screening. Two case studies were used to demonstrate the capability and efficiency of the iScreen package. iScreen is available for download on CRAN (http://cran.cnr.berkeley.edu/web/packages/iScreen/index.html). The user manual is also available as a supplementary document. © 2014 Society for Laboratory Automation and Screening.

  5. A Computational model for compressed sensing RNAi cellular screening

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    Tan Hua

    2012-12-01

    Full Text Available Abstract Background RNA interference (RNAi becomes an increasingly important and effective genetic tool to study the function of target genes by suppressing specific genes of interest. This system approach helps identify signaling pathways and cellular phase types by tracking intensity and/or morphological changes of cells. The traditional RNAi screening scheme, in which one siRNA is designed to knockdown one specific mRNA target, needs a large library of siRNAs and turns out to be time-consuming and expensive. Results In this paper, we propose a conceptual model, called compressed sensing RNAi (csRNAi, which employs a unique combination of group of small interfering RNAs (siRNAs to knockdown a much larger size of genes. This strategy is based on the fact that one gene can be partially bound with several small interfering RNAs (siRNAs and conversely, one siRNA can bind to a few genes with distinct binding affinity. This model constructs a multi-to-multi correspondence between siRNAs and their targets, with siRNAs much fewer than mRNA targets, compared with the conventional scheme. Mathematically this problem involves an underdetermined system of equations (linear or nonlinear, which is ill-posed in general. However, the recently developed compressed sensing (CS theory can solve this problem. We present a mathematical model to describe the csRNAi system based on both CS theory and biological concerns. To build this model, we first search nucleotide motifs in a target gene set. Then we propose a machine learning based method to find the effective siRNAs with novel features, such as image features and speech features to describe an siRNA sequence. Numerical simulations show that we can reduce the siRNA library to one third of that in the conventional scheme. In addition, the features to describe siRNAs outperform the existing ones substantially. Conclusions This csRNAi system is very promising in saving both time and cost for large-scale RNAi

  6. The Sheffield RNAi Screening Facility (SRSF): portfolio growth and technology development.

    Science.gov (United States)

    Brown, Stephen

    2014-05-01

    The Sheffield RNAi Screening Facility (SRSF) (www.rnai.group.shef.ac.uk) was established in 2008 with Wellcome Trust and University of Sheffield funding, with the task to provide the first UK RNAi screening resource for academic groups interested in identifying genes required in a diverse range of biological processes using Drosophila cell culture. The SRSF has carried out a wide range of screens varying in sizes from bespoke small-scale libraries, targeting a few hundred genes, to high-throughput, genome-wide studies. The SRSF has grown and improved with a dedicated partnership of its academic customers based mainly in the UK. We are part of the UK Academics Functional Genomics Network, participating in organizing an annual meeting in London and are part of the University of Sheffield's D3N (www.d3n.org.uk), connecting academics, biotech and pharmaceutical companies with a multidisciplinary network in Drug Discovery and Development. Recently, the SRSF has been funded by the Yorkshire Cancer Research Fund to perform genome-wide RNAi screens using human cells as part of a core facility for regional Yorkshire Universities and screens are now underway. Overall the SRSF has carried out more than 40 screens from Drosophila and human cell culture experiments.

  7. GenomeRNAi: a database for cell-based RNAi phenotypes.

    Science.gov (United States)

    Horn, Thomas; Arziman, Zeynep; Berger, Juerg; Boutros, Michael

    2007-01-01

    RNA interference (RNAi) has emerged as a powerful tool to generate loss-of-function phenotypes in a variety of organisms. Combined with the sequence information of almost completely annotated genomes, RNAi technologies have opened new avenues to conduct systematic genetic screens for every annotated gene in the genome. As increasing large datasets of RNAi-induced phenotypes become available, an important challenge remains the systematic integration and annotation of functional information. Genome-wide RNAi screens have been performed both in Caenorhabditis elegans and Drosophila for a variety of phenotypes and several RNAi libraries have become available to assess phenotypes for almost every gene in the genome. These screens were performed using different types of assays from visible phenotypes to focused transcriptional readouts and provide a rich data source for functional annotation across different species. The GenomeRNAi database provides access to published RNAi phenotypes obtained from cell-based screens and maps them to their genomic locus, including possible non-specific regions. The database also gives access to sequence information of RNAi probes used in various screens. It can be searched by phenotype, by gene, by RNAi probe or by sequence and is accessible at http://rnai.dkfz.de.

  8. Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway

    Science.gov (United States)

    2012-01-01

    Background Genome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as library design and post-screening bioinformatics may be effecting the data generated. Results Here we present a new genome-wide RNAi screen of the Drosophila JAK/STAT signalling pathway undertaken in the Sheffield RNAi Screening Facility (SRSF). This screen was carried out using a second-generation, computationally optimised dsRNA library and analysed using current methods and bioinformatic tools. To examine advances in RNAi screening technology, we compare this screen to a biologically very similar screen undertaken in 2005 with a first-generation library. Both screens used the same cell line, reporters and experimental design, with the SRSF screen identifying 42 putative regulators of JAK/STAT signalling, 22 of which verified in a secondary screen and 16 verified with an independent probe design. Following reanalysis of the original screen data, comparisons of the two gene lists allows us to make estimates of false discovery rates in the SRSF data and to conduct an assessment of off-target effects (OTEs) associated with both libraries. We discuss the differences and similarities between the resulting data sets and examine the relative improvements in gene discovery protocols. Conclusions Our work represents one of the first direct comparisons between first- and second-generation libraries and shows that modern library designs together with methodological advances have had a significant influence on genome-scale RNAi screens. PMID:23006893

  9. An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme

    Science.gov (United States)

    Wiles, Amy M.; Ravi, Dashnamoorthy; Bhavani, Selvaraj; Bishop, Alexander J.R.

    2010-01-01

    Genome-wide RNAi screening is a powerful, yet relatively immature technology that allows investigation into the role of individual genes in a process of choice. Most RNAi screens identify a large number of genes with a continuous gradient in the assessed phenotype. Screeners must then decide whether to examine just those genes with the most robust phenotype or to examine the full gradient of genes that cause an effect and how to identify the candidate genes to be validated. We have used RNAi in Drosophila cells to examine viability in a 384-well plate format and compare two screens, untreated control and treatment. We compare multiple normalization methods, which take advantage of different features within the data, including quantile normalization, background subtraction, scaling, cellHTS2 1, and interquartile range measurement. Considering the false-positive potential that arises from RNAi technology, a robust validation method was designed for the purpose of gene selection for future investigations. In a retrospective analysis, we describe the use of validation data to evaluate each normalization method. While no normalization method worked ideally, we found that a combination of two methods, background subtraction followed by quantile normalization and cellHTS2, at different thresholds, captures the most dependable and diverse candidate genes. Thresholds are suggested depending on whether a few candidate genes are desired or a more extensive systems level analysis is sought. In summary, our normalization approaches and experimental design to perform validation experiments are likely to apply to those high-throughput screening systems attempting to identify genes for systems level analysis. PMID:18753689

  10. Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy.

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    Allan, Kristina J; Mahoney, Douglas J; Baird, Stephen D; Lefebvre, Charles A; Stojdl, David F

    2018-04-03

    High-throughput genome-wide RNAi (RNA interference) screening technology has been widely used for discovering host factors that impact virus replication. Here we present the application of this technology to uncovering host targets that specifically modulate the replication of Maraba virus, an oncolytic rhabdovirus, and vaccinia virus with the goal of enhancing therapy. While the protocol has been tested for use with oncolytic Maraba virus and oncolytic vaccinia virus, this approach is applicable to other oncolytic viruses and can also be utilized for identifying host targets that modulate virus replication in mammalian cells in general. This protocol describes the development and validation of an assay for high-throughput RNAi screening in mammalian cells, the key considerations and preparation steps important for conducting a primary high-throughput RNAi screen, and a step-by-step guide for conducting a primary high-throughput RNAi screen; in addition, it broadly outlines the methods for conducting secondary screen validation and tertiary validation studies. The benefit of high-throughput RNAi screening is that it allows one to catalogue, in an extensive and unbiased fashion, host factors that modulate any aspect of virus replication for which one can develop an in vitro assay such as infectivity, burst size, and cytotoxicity. It has the power to uncover biotherapeutic targets unforeseen based on current knowledge.

  11. Kinase profiling of liposarcomas using RNAi and drug screening assays identified druggable targets

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    Deepika Kanojia

    2017-11-01

    Full Text Available Abstract Background Liposarcoma, the most common soft tissue tumor, is understudied cancer, and limited progress has been made in the treatment of metastatic disease. The Achilles heel of cancer often is their kinases that are excellent therapeutic targets. However, very limited knowledge exists of therapeutic critical kinase targets in liposarcoma that could be potentially used in disease management. Methods Large RNAi and small-molecule tyrosine kinase inhibitor screens were performed against the proliferative capacity of liposarcoma cell lines of different subtypes. Each small molecule inhibitor was either FDA approved or in a clinical trial. Results Screening assays identified several previously unrecognized targets including PTK2 and KIT in liposarcoma. We also observed that ponatinib, multi-targeted tyrosine kinase inhibitor, was the most effective drug with anti-growth effects against all cell lines. In vitro assays showed that ponatinib inhibited the clonogenic proliferation of liposarcoma, and this anti-growth effect was associated with apoptosis and cell cycle arrest at the G0/G1 phase as well as a decrease in the KIT signaling pathway. In addition, ponatinib inhibited in vivo growth of liposarcoma in a xenograft model. Conclusions Two large-scale kinase screenings identified novel liposarcoma targets and a FDA-approved inhibitor, ponatinib with clear anti-liposarcoma activity highlighting its potential therapy for treatment of this deadly tumor.

  12. A genome scale RNAi screen identifies GLI1 as a novel gene regulating vorinostat sensitivity.

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    Falkenberg, K J; Newbold, A; Gould, C M; Luu, J; Trapani, J A; Matthews, G M; Simpson, K J; Johnstone, R W

    2016-07-01

    Vorinostat is an FDA-approved histone deacetylase inhibitor (HDACi) that has proven clinical success in some patients; however, it remains unclear why certain patients remain unresponsive to this agent and other HDACis. Constitutive STAT (signal transducer and activator of transcription) activation, overexpression of prosurvival Bcl-2 proteins and loss of HR23B have been identified as potential biomarkers of HDACi resistance; however, none have yet been used to aid the clinical utility of HDACi. Herein, we aimed to further elucidate vorinostat-resistance mechanisms through a functional genomics screen to identify novel genes that when knocked down by RNA interference (RNAi) sensitized cells to vorinostat-induced apoptosis. A synthetic lethal functional screen using a whole-genome protein-coding RNAi library was used to identify genes that when knocked down cooperated with vorinostat to induce tumor cell apoptosis in otherwise resistant cells. Through iterative screening, we identified 10 vorinostat-resistance candidate genes that sensitized specifically to vorinostat. One of these vorinostat-resistance genes was GLI1, an oncogene not previously known to regulate the activity of HDACi. Treatment of vorinostat-resistant cells with the GLI1 small-molecule inhibitor, GANT61, phenocopied the effect of GLI1 knockdown. The mechanism by which GLI1 loss of function sensitized tumor cells to vorinostat-induced apoptosis is at least in part through interactions with vorinostat to alter gene expression in a manner that favored apoptosis. Upon GLI1 knockdown and vorinostat treatment, BCL2L1 expression was repressed and overexpression of BCL2L1 inhibited GLI1-knockdown-mediated vorinostat sensitization. Taken together, we present the identification and characterization of GLI1 as a new HDACi resistance gene, providing a strong rationale for development of GLI1 inhibitors for clinical use in combination with HDACi therapy.

  13. Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons.

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    Lejeune, François-Xavier; Mesrob, Lilia; Parmentier, Frédéric; Bicep, Cedric; Vazquez-Manrique, Rafael P; Parker, J Alex; Vert, Jean-Philippe; Tourette, Cendrine; Neri, Christian

    2012-03-13

    A central goal in Huntington's disease (HD) research is to identify and prioritize candidate targets for neuroprotective intervention, which requires genome-scale information on the modifiers of early-stage neuron injury in HD. Here, we performed a large-scale RNA interference screen in C. elegans strains that express N-terminal huntingtin (htt) in touch receptor neurons. These neurons control the response to light touch. Their function is strongly impaired by expanded polyglutamines (128Q) as shown by the nearly complete loss of touch response in adult animals, providing an in vivo model in which to manipulate the early phases of expanded-polyQ neurotoxicity. In total, 6034 genes were examined, revealing 662 gene inactivations that either reduce or aggravate defective touch response in 128Q animals. Several genes were previously implicated in HD or neurodegenerative disease, suggesting that this screen has effectively identified candidate targets for HD. Network-based analysis emphasized a subset of high-confidence modifier genes in pathways of interest in HD including metabolic, neurodevelopmental and pro-survival pathways. Finally, 49 modifiers of 128Q-neuron dysfunction that are dysregulated in the striatum of either R/2 or CHL2 HD mice, or both, were identified. Collectively, these results highlight the relevance to HD pathogenesis, providing novel information on the potential therapeutic targets for neuroprotection in HD. © 2012 Lejeune et al; licensee BioMed Central Ltd.

  14. RNAi Screening Facility

    Data.gov (United States)

    Federal Laboratory Consortium — Small interfering RNA (siRNA) molecules are pieces of RNA that block the activity of genes through a natural process called RNA interference (RNAi). This process has...

  15. A forward genetic screen reveals essential and non-essential RNAi factors in Paramecium tetraurelia

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    Marker, Simone; Carradec, Quentin; Tanty, Véronique; Arnaiz, Olivier; Meyer, Eric

    2014-01-01

    In most eukaryotes, small RNA-mediated gene silencing pathways form complex interacting networks. In the ciliate Paramecium tetraurelia, at least two RNA interference (RNAi) mechanisms coexist, involving distinct but overlapping sets of protein factors and producing different types of short interfering RNAs (siRNAs). One is specifically triggered by high-copy transgenes, and the other by feeding cells with double-stranded RNA (dsRNA)-producing bacteria. In this study, we designed a forward genetic screen for mutants deficient in dsRNA-induced silencing, and a powerful method to identify the relevant mutations by whole-genome sequencing. We present a set of 47 mutant alleles for five genes, revealing two previously unknown RNAi factors: a novel Paramecium-specific protein (Pds1) and a Cid1-like nucleotidyl transferase. Analyses of allelic diversity distinguish non-essential and essential genes and suggest that the screen is saturated for non-essential, single-copy genes. We show that non-essential genes are specifically involved in dsRNA-induced RNAi while essential ones are also involved in transgene-induced RNAi. One of the latter, the RNA-dependent RNA polymerase RDR2, is further shown to be required for all known types of siRNAs, as well as for sexual reproduction. These results open the way for the dissection of the genetic complexity, interconnection, mechanisms and natural functions of RNAi pathways in P. tetraurelia. PMID:24860163

  16. Identification of neural outgrowth genes using genome-wide RNAi.

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    Katharine J Sepp

    2008-07-01

    Full Text Available While genetic screens have identified many genes essential for neurite outgrowth, they have been limited in their ability to identify neural genes that also have earlier critical roles in the gastrula, or neural genes for which maternally contributed RNA compensates for gene mutations in the zygote. To address this, we developed methods to screen the Drosophila genome using RNA-interference (RNAi on primary neural cells and present the results of the first full-genome RNAi screen in neurons. We used live-cell imaging and quantitative image analysis to characterize the morphological phenotypes of fluorescently labelled primary neurons and glia in response to RNAi-mediated gene knockdown. From the full genome screen, we focused our analysis on 104 evolutionarily conserved genes that when downregulated by RNAi, have morphological defects such as reduced axon extension, excessive branching, loss of fasciculation, and blebbing. To assist in the phenotypic analysis of the large data sets, we generated image analysis algorithms that could assess the statistical significance of the mutant phenotypes. The algorithms were essential for the analysis of the thousands of images generated by the screening process and will become a valuable tool for future genome-wide screens in primary neurons. Our analysis revealed unexpected, essential roles in neurite outgrowth for genes representing a wide range of functional categories including signalling molecules, enzymes, channels, receptors, and cytoskeletal proteins. We also found that genes known to be involved in protein and vesicle trafficking showed similar RNAi phenotypes. We confirmed phenotypes of the protein trafficking genes Sec61alpha and Ran GTPase using Drosophila embryo and mouse embryonic cerebral cortical neurons, respectively. Collectively, our results showed that RNAi phenotypes in primary neural culture can parallel in vivo phenotypes, and the screening technique can be used to identify many new

  17. Neuron-specific feeding RNAi in C. elegans and its use in a screen for essential genes required for GABA neuron function.

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    Firnhaber, Christopher; Hammarlund, Marc

    2013-11-01

    Forward genetic screens are important tools for exploring the genetic requirements for neuronal function. However, conventional forward screens often have difficulty identifying genes whose relevant functions are masked by pleiotropy. In particular, if loss of gene function results in sterility, lethality, or other severe pleiotropy, neuronal-specific functions cannot be readily analyzed. Here we describe a method in C. elegans for generating cell-specific knockdown in neurons using feeding RNAi and its application in a screen for the role of essential genes in GABAergic neurons. We combine manipulations that increase the sensitivity of select neurons to RNAi with manipulations that block RNAi in other cells. We produce animal strains in which feeding RNAi results in restricted gene knockdown in either GABA-, acetylcholine-, dopamine-, or glutamate-releasing neurons. In these strains, we observe neuron cell-type specific behavioral changes when we knock down genes required for these neurons to function, including genes encoding the basal neurotransmission machinery. These reagents enable high-throughput, cell-specific knockdown in the nervous system, facilitating rapid dissection of the site of gene action and screening for neuronal functions of essential genes. Using the GABA-specific RNAi strain, we screened 1,320 RNAi clones targeting essential genes on chromosomes I, II, and III for their effect on GABA neuron function. We identified 48 genes whose GABA cell-specific knockdown resulted in reduced GABA motor output. This screen extends our understanding of the genetic requirements for continued neuronal function in a mature organism.

  18. RNAi screening for characterisation of ER-associated degradation pathways in mammalian cells

    DEFF Research Database (Denmark)

    Månsson, Mats David Joakim

    in a process termed ER-associated degradation (ERAD). This mechanism proceeds through four steps involving recognition, dislocation, ubiquitination and proteasomal degradation. This report describes a high-throughput screening method for identification of hitherto unknown pathways for degradation. We present...... fluorescence-based RNAi screens in mammalian cells on TCR-α-GFP and HANSκLC, for identification of ERAD pathways. By validating the obtained screening hits we concluded that UBE2J2 is involved in TCR-α-GFP degradation, possibly by ubiquitination of C-terminal serine residues in TCR-α-GFP. Additionally, we also...

  19. Large-scale field application of RNAi technology reducing Israeli acute paralysis virus disease in honey bees (Apis mellifera, Hymenoptera: Apidae.

    Directory of Open Access Journals (Sweden)

    Wayne Hunter

    Full Text Available The importance of honey bees to the world economy far surpasses their contribution in terms of honey production; they are responsible for up to 30% of the world's food production through pollination of crops. Since fall 2006, honey bees in the U.S. have faced a serious population decline, due in part to a phenomenon called Colony Collapse Disorder (CCD, which is a disease syndrome that is likely caused by several factors. Data from an initial study in which investigators compared pathogens in honey bees affected by CCD suggested a putative role for Israeli Acute Paralysis Virus, IAPV. This is a single stranded RNA virus with no DNA stage placed taxonomically within the family Dicistroviridae. Although subsequent studies have failed to find IAPV in all CCD diagnosed colonies, IAPV has been shown to cause honey bee mortality. RNA interference technology (RNAi has been used successfully to silence endogenous insect (including honey bee genes both by injection and feeding. Moreover, RNAi was shown to prevent bees from succumbing to infection from IAPV under laboratory conditions. In the current study IAPV specific homologous dsRNA was used in the field, under natural beekeeping conditions in order to prevent mortality and improve the overall health of bees infected with IAPV. This controlled study included a total of 160 honey bee hives in two discrete climates, seasons and geographical locations (Florida and Pennsylvania. To our knowledge, this is the first successful large-scale real world use of RNAi for disease control.

  20. iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum.

    Science.gov (United States)

    Dönitz, Jürgen; Schmitt-Engel, Christian; Grossmann, Daniela; Gerischer, Lizzy; Tech, Maike; Schoppmeier, Michael; Klingler, Martin; Bucher, Gregor

    2015-01-01

    The iBeetle-Base (http://ibeetle-base.uni-goettingen.de) makes available annotations of RNAi phenotypes, which were gathered in a large scale RNAi screen in the red flour beetle Tribolium castaneum (iBeetle screen). In addition, it provides access to sequence information and links for all Tribolium castaneum genes. The iBeetle-Base contains the annotations of phenotypes of several thousands of genes knocked down during embryonic and metamorphic epidermis and muscle development in addition to phenotypes linked to oogenesis and stink gland biology. The phenotypes are described according to the EQM (entity, quality, modifier) system using controlled vocabularies and the Tribolium morphological ontology (TrOn). Furthermore, images linked to the respective annotations are provided. The data are searchable either for specific phenotypes using a complex 'search for morphological defects' or a 'quick search' for gene names and IDs. The red flour beetle Tribolium castaneum has become an important model system for insect functional genetics and is a representative of the most species rich taxon, the Coleoptera, which comprise several devastating pests. It is used for studying insect typical development, the evolution of development and for research on metabolism and pest control. Besides Drosophila, Tribolium is the first insect model organism where large scale unbiased screens have been performed. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Automated cell analysis tool for a genome-wide RNAi screen with support vector machine based supervised learning

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    Remmele, Steffen; Ritzerfeld, Julia; Nickel, Walter; Hesser, Jürgen

    2011-03-01

    RNAi-based high-throughput microscopy screens have become an important tool in biological sciences in order to decrypt mostly unknown biological functions of human genes. However, manual analysis is impossible for such screens since the amount of image data sets can often be in the hundred thousands. Reliable automated tools are thus required to analyse the fluorescence microscopy image data sets usually containing two or more reaction channels. The herein presented image analysis tool is designed to analyse an RNAi screen investigating the intracellular trafficking and targeting of acylated Src kinases. In this specific screen, a data set consists of three reaction channels and the investigated cells can appear in different phenotypes. The main issue of the image processing task is an automatic cell segmentation which has to be robust and accurate for all different phenotypes and a successive phenotype classification. The cell segmentation is done in two steps by segmenting the cell nuclei first and then using a classifier-enhanced region growing on basis of the cell nuclei to segment the cells. The classification of the cells is realized by a support vector machine which has to be trained manually using supervised learning. Furthermore, the tool is brightness invariant allowing different staining quality and it provides a quality control that copes with typical defects during preparation and acquisition. A first version of the tool has already been successfully applied for an RNAi-screen containing three hundred thousand image data sets and the SVM extended version is designed for additional screens.

  2. Screensaver: an open source lab information management system (LIMS for high throughput screening facilities

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    Nale Jennifer

    2010-05-01

    Full Text Available Abstract Background Shared-usage high throughput screening (HTS facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. Results We have developed Screensaver, a free, open source, web-based lab information management system (LIMS, to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. Conclusions The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.

  3. Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.

    Science.gov (United States)

    Tolopko, Andrew N; Sullivan, John P; Erickson, Sean D; Wrobel, David; Chiang, Su L; Rudnicki, Katrina; Rudnicki, Stewart; Nale, Jennifer; Selfors, Laura M; Greenhouse, Dara; Muhlich, Jeremy L; Shamu, Caroline E

    2010-05-18

    Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.

  4. A Genome-wide multidimensional RNAi screen reveals pathways controlling MHC class II antigen presentation

    NARCIS (Netherlands)

    Paul, Petra; van den Hoorn, Tineke; Jongsma, Marlieke L. M.; Bakker, Mark J.; Hengeveld, Rutger; Janssen, Lennert; Cresswell, Peter; Egan, David A.; van Ham, Marieke; ten Brinke, Anja; Ovaa, Huib; Beijersbergen, Roderick L.; Kuijl, Coenraad; Neefjes, Jacques

    2011-01-01

    MHC class II molecules (MHC-II) present peptides to T helper cells to facilitate immune responses and are strongly linked to autoimmune diseases. To unravel processes controlling MHC-II antigen presentation, we performed a genome-wide flow cytometry-based RNAi screen detecting MHC-II expression and

  5. Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens.

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    Lyons, Eli; Sheridan, Paul; Tremmel, Georg; Miyano, Satoru; Sugano, Sumio

    2017-10-24

    High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications.

  6. FUN-L: gene prioritization for RNAi screens.

    Science.gov (United States)

    Lees, Jonathan G; Hériché, Jean-Karim; Morilla, Ian; Fernández, José M; Adler, Priit; Krallinger, Martin; Vilo, Jaak; Valencia, Alfonso; Ellenberg, Jan; Ranea, Juan A; Orengo, Christine

    2015-06-15

    Most biological processes remain only partially characterized with many components still to be identified. Given that a whole genome can usually not be tested in a functional assay, identifying the genes most likely to be of interest is of critical importance to avoid wasting resources. Given a set of known functionally related genes and using a state-of-the-art approach to data integration and mining, our Functional Lists (FUN-L) method provides a ranked list of candidate genes for testing. Validation of predictions from FUN-L with independent RNAi screens confirms that FUN-L-produced lists are enriched in genes with the expected phenotypes. In this article, we describe a website front end to FUN-L. The website is freely available to use at http://funl.org © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. A Tendon Cell Specific RNAi Screen Reveals Novel Candidates Essential for Muscle Tendon Interaction.

    Directory of Open Access Journals (Sweden)

    Prabhat Tiwari

    Full Text Available Tendons are fibrous connective tissue which connect muscles to the skeletal elements thus acting as passive transmitters of force during locomotion and provide appropriate body posture. Tendon-derived cues, albeit poorly understood, are necessary for proper muscle guidance and attachment during development. In the present study, we used dorsal longitudinal muscles of Drosophila and their tendon attachment sites to unravel the molecular nature of interactions between muscles and tendons. We performed a genetic screen using RNAi-mediated knockdown in tendon cells to find out molecular players involved in the formation and maintenance of myotendinous junction and found 21 candidates out of 2507 RNAi lines screened. Of these, 19 were novel molecules in context of myotendinous system. Integrin-βPS and Talin, picked as candidates in this screen, are known to play important role in the cell-cell interaction and myotendinous junction formation validating our screen. We have found candidates with enzymatic function, transcription activity, cell adhesion, protein folding and intracellular transport function. Tango1, an ER exit protein involved in collagen secretion was identified as a candidate molecule involved in the formation of myotendinous junction. Tango1 knockdown was found to affect development of muscle attachment sites and formation of myotendinous junction. Tango1 was also found to be involved in secretion of Viking (Collagen type IV and BM-40 from hemocytes and fat cells.

  8. GUItars: a GUI tool for analysis of high-throughput RNA interference screening data.

    Directory of Open Access Journals (Sweden)

    Asli N Goktug

    Full Text Available High-throughput RNA interference (RNAi screening has become a widely used approach to elucidating gene functions. However, analysis and annotation of large data sets generated from these screens has been a challenge for researchers without a programming background. Over the years, numerous data analysis methods were produced for plate quality control and hit selection and implemented by a few open-access software packages. Recently, strictly standardized mean difference (SSMD has become a widely used method for RNAi screening analysis mainly due to its better control of false negative and false positive rates and its ability to quantify RNAi effects with a statistical basis. We have developed GUItars to enable researchers without a programming background to use SSMD as both a plate quality and a hit selection metric to analyze large data sets.The software is accompanied by an intuitive graphical user interface for easy and rapid analysis workflow. SSMD analysis methods have been provided to the users along with traditionally-used z-score, normalized percent activity, and t-test methods for hit selection. GUItars is capable of analyzing large-scale data sets from screens with or without replicates. The software is designed to automatically generate and save numerous graphical outputs known to be among the most informative high-throughput data visualization tools capturing plate-wise and screen-wise performances. Graphical outputs are also written in HTML format for easy access, and a comprehensive summary of screening results is written into tab-delimited output files.With GUItars, we demonstrated robust SSMD-based analysis workflow on a 3840-gene small interfering RNA (siRNA library and identified 200 siRNAs that increased and 150 siRNAs that decreased the assay activities with moderate to stronger effects. GUItars enables rapid analysis and illustration of data from large- or small-scale RNAi screens using SSMD and other traditional analysis

  9. ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling | Office of Cancer Genomics

    Science.gov (United States)

    Functional genomics (FG) screens, using RNAi or CRISPR technology, have become a standard tool for systematic, genome-wide loss-of-function studies for therapeutic target discovery. As in many large-scale assays, however, off-target effects, variable reagents' potency and experimental noise must be accounted for appropriately control for false positives.

  10. Combined Gene Expression and RNAi Screening to Identify Alkylation Damage Survival Pathways from Fly to Human.

    Science.gov (United States)

    Zanotto-Filho, Alfeu; Dashnamoorthy, Ravi; Loranc, Eva; de Souza, Luis H T; Moreira, José C F; Suresh, Uthra; Chen, Yidong; Bishop, Alexander J R

    2016-01-01

    Alkylating agents are a key component of cancer chemotherapy. Several cellular mechanisms are known to be important for its survival, particularly DNA repair and xenobiotic detoxification, yet genomic screens indicate that additional cellular components may be involved. Elucidating these components has value in either identifying key processes that can be modulated to improve chemotherapeutic efficacy or may be altered in some cancers to confer chemoresistance. We therefore set out to reevaluate our prior Drosophila RNAi screening data by comparison to gene expression arrays in order to determine if we could identify any novel processes in alkylation damage survival. We noted a consistent conservation of alkylation survival pathways across platforms and species when the analysis was conducted on a pathway/process level rather than at an individual gene level. Better results were obtained when combining gene lists from two datasets (RNAi screen plus microarray) prior to analysis. In addition to previously identified DNA damage responses (p53 signaling and Nucleotide Excision Repair), DNA-mRNA-protein metabolism (transcription/translation) and proteasome machinery, we also noted a highly conserved cross-species requirement for NRF2, glutathione (GSH)-mediated drug detoxification and Endoplasmic Reticulum stress (ER stress)/Unfolded Protein Responses (UPR) in cells exposed to alkylation. The requirement for GSH, NRF2 and UPR in alkylation survival was validated by metabolomics, protein studies and functional cell assays. From this we conclude that RNAi/gene expression fusion is a valid strategy to rapidly identify key processes that may be extendable to other contexts beyond damage survival.

  11. Combined Gene Expression and RNAi Screening to Identify Alkylation Damage Survival Pathways from Fly to Human.

    Directory of Open Access Journals (Sweden)

    Alfeu Zanotto-Filho

    Full Text Available Alkylating agents are a key component of cancer chemotherapy. Several cellular mechanisms are known to be important for its survival, particularly DNA repair and xenobiotic detoxification, yet genomic screens indicate that additional cellular components may be involved. Elucidating these components has value in either identifying key processes that can be modulated to improve chemotherapeutic efficacy or may be altered in some cancers to confer chemoresistance. We therefore set out to reevaluate our prior Drosophila RNAi screening data by comparison to gene expression arrays in order to determine if we could identify any novel processes in alkylation damage survival. We noted a consistent conservation of alkylation survival pathways across platforms and species when the analysis was conducted on a pathway/process level rather than at an individual gene level. Better results were obtained when combining gene lists from two datasets (RNAi screen plus microarray prior to analysis. In addition to previously identified DNA damage responses (p53 signaling and Nucleotide Excision Repair, DNA-mRNA-protein metabolism (transcription/translation and proteasome machinery, we also noted a highly conserved cross-species requirement for NRF2, glutathione (GSH-mediated drug detoxification and Endoplasmic Reticulum stress (ER stress/Unfolded Protein Responses (UPR in cells exposed to alkylation. The requirement for GSH, NRF2 and UPR in alkylation survival was validated by metabolomics, protein studies and functional cell assays. From this we conclude that RNAi/gene expression fusion is a valid strategy to rapidly identify key processes that may be extendable to other contexts beyond damage survival.

  12. The RNAi Inheritance Machinery of Caenorhabditis elegans.

    Science.gov (United States)

    Spracklin, George; Fields, Brandon; Wan, Gang; Becker, Diveena; Wallig, Ashley; Shukla, Aditi; Kennedy, Scott

    2017-07-01

    Gene silencing mediated by dsRNA (RNAi) can persist for multiple generations in Caenorhabditis elegans (termed RNAi inheritance). Here we describe the results of a forward genetic screen in C. elegans that has identified six factors required for RNAi inheritance: GLH-1/VASA, PUP-1/CDE-1, MORC-1, SET-32, and two novel nematode-specific factors that we term here (heritable RNAi defective) HRDE-2 and HRDE-4 The new RNAi inheritance factors exhibit mortal germline (Mrt) phenotypes, which we show is likely caused by epigenetic deregulation in germ cells. We also show that HRDE-2 contributes to RNAi inheritance by facilitating the binding of small RNAs to the inheritance Argonaute (Ago) HRDE-1 Together, our results identify additional components of the RNAi inheritance machinery whose conservation provides insights into the molecular mechanism of RNAi inheritance, further our understanding of how the RNAi inheritance machinery promotes germline immortality, and show that HRDE-2 couples the inheritance Ago HRDE-1 with the small RNAs it needs to direct RNAi inheritance and germline immortality. Copyright © 2017 by the Genetics Society of America.

  13. ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling.

    Science.gov (United States)

    Yu, Jiyang; Silva, Jose; Califano, Andrea

    2016-01-15

    Functional genomics (FG) screens, using RNAi or CRISPR technology, have become a standard tool for systematic, genome-wide loss-of-function studies for therapeutic target discovery. As in many large-scale assays, however, off-target effects, variable reagents' potency and experimental noise must be accounted for appropriately control for false positives. Indeed, rigorous statistical analysis of high-throughput FG screening data remains challenging, particularly when integrative analyses are used to combine multiple sh/sgRNAs targeting the same gene in the library. We use large RNAi and CRISPR repositories that are publicly available to evaluate a novel meta-analysis approach for FG screens via Bayesian hierarchical modeling, Screening Bayesian Evaluation and Analysis Method (ScreenBEAM). Results from our analysis show that the proposed strategy, which seamlessly combines all available data, robustly outperforms classical algorithms developed for microarray data sets as well as recent approaches designed for next generation sequencing technologies. Remarkably, the ScreenBEAM algorithm works well even when the quality of FG screens is relatively low, which accounts for about 80-95% of the public datasets. R package and source code are available at: https://github.com/jyyu/ScreenBEAM. ac2248@columbia.edu, jose.silva@mssm.edu, yujiyang@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. RNAi screen of DAF-16/FOXO target genes in C. elegans links pathogenesis and dauer formation.

    Directory of Open Access Journals (Sweden)

    Victor L Jensen

    2010-12-01

    Full Text Available The DAF-16/FOXO transcription factor is the major downstream output of the insulin/IGF1R signaling pathway controlling C. elegans dauer larva development and aging. To identify novel downstream genes affecting dauer formation, we used RNAi to screen candidate genes previously identified to be regulated by DAF-16. We used a sensitized genetic background [eri-1(mg366; sdf-9(m708], which enhances both RNAi efficiency and constitutive dauer formation (Daf-c. Among 513 RNAi clones screened, 21 displayed a synthetic Daf-c (SynDaf phenotype with sdf-9. One of these genes, srh-100, was previously identified to be SynDaf, but twenty have not previously been associated with dauer formation. Two of the latter genes, lys-1 and cpr-1, are known to participate in innate immunity and six more are predicted to do so, suggesting that the immune response may contribute to the dauer decision. Indeed, we show that two of these genes, lys-1 and clc-1, are required for normal resistance to Staphylococcus aureus. clc-1 is predicted to function in epithelial cohesion. Dauer formation exhibited by daf-8(m85, sdf-9(m708, and the wild-type N2 (at 27°C were all enhanced by exposure to pathogenic bacteria, while not enhanced in a daf-22(m130 background. We conclude that knockdown of the genes required for proper pathogen resistance increases pathogenic infection, leading to increased dauer formation in our screen. We propose that dauer larva formation is a behavioral response to pathogens mediated by increased dauer pheromone production.

  15. RNAi-Mediated Reverse Genetic Screen Identified Drosophila Chaperones Regulating Eye and Neuromuscular Junction Morphology

    Directory of Open Access Journals (Sweden)

    Sandeep Raut

    2017-07-01

    Full Text Available Accumulation of toxic proteins in neurons has been linked with the onset of neurodegenerative diseases, which in many cases are characterized by altered neuronal function and synapse loss. Molecular chaperones help protein folding and the resolubilization of unfolded proteins, thereby reducing the protein aggregation stress. While most of the chaperones are expressed in neurons, their functional relevance remains largely unknown. Here, using bioinformatics analysis, we identified 95 Drosophila chaperones and classified them into seven different classes. Ubiquitous actin5C-Gal4-mediated RNAi knockdown revealed that ∼50% of the chaperones are essential in Drosophila. Knocking down these genes in eyes revealed that ∼30% of the essential chaperones are crucial for eye development. Using neuron-specific knockdown, immunocytochemistry, and robust behavioral assays, we identified a new set of chaperones that play critical roles in the regulation of Drosophila NMJ structural organization. Together, our data present the first classification and comprehensive analysis of Drosophila chaperones. Our screen identified a new set of chaperones that regulate eye and NMJ morphogenesis. The outcome of the screen reported here provides a useful resource for further elucidating the role of individual chaperones in Drosophila eye morphogenesis and synaptic development.

  16. Investigating ER-Associated Degradation with RNAi Screening - and Searching for Model Proteins to Do It with

    DEFF Research Database (Denmark)

    Jensen, Njal Winther

    Abstract In eukaryotes, secretory proteins are translocated into the endoplasmic reticulum (ER) for folding assistance, acquisition of posttranslational modifications and sorting. Proteins that do not obtain their native conformation are eliminated by ER-associated degradation (ERAD). ERAD...... is a sophisticated pathway that recognizes misfolded proteins and targets them for degradation by the 26S proteasome residing in the cytosol. More than 60 diseases including Alzheimer’s disease, Huntington’s disease and Parkinson’s disease have been linked to the ERAD pathway underscoring its crucial role...... for cellular homeostasis. The aim of this thesis has been to gain insight into ERAD. The experimental approach was RNAi screening, which is a fast and efficient method for initial evaluation of a large pool of genes. Since relatively few proteins routinely are used as ERAD substrates, the first goal...

  17. The Transgenic RNAi Project at Harvard Medical School: Resources and Validation.

    Science.gov (United States)

    Perkins, Lizabeth A; Holderbaum, Laura; Tao, Rong; Hu, Yanhui; Sopko, Richelle; McCall, Kim; Yang-Zhou, Donghui; Flockhart, Ian; Binari, Richard; Shim, Hye-Seok; Miller, Audrey; Housden, Amy; Foos, Marianna; Randkelv, Sakara; Kelley, Colleen; Namgyal, Pema; Villalta, Christians; Liu, Lu-Ping; Jiang, Xia; Huan-Huan, Qiao; Wang, Xia; Fujiyama, Asao; Toyoda, Atsushi; Ayers, Kathleen; Blum, Allison; Czech, Benjamin; Neumuller, Ralph; Yan, Dong; Cavallaro, Amanda; Hibbard, Karen; Hall, Don; Cooley, Lynn; Hannon, Gregory J; Lehmann, Ruth; Parks, Annette; Mohr, Stephanie E; Ueda, Ryu; Kondo, Shu; Ni, Jian-Quan; Perrimon, Norbert

    2015-11-01

    To facilitate large-scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome-scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently composed of 11,491 lines and covering 71% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated website, the RNAi Stock Validation and Phenotypes Project (RSVP, http://www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (United States), National Institute of Genetics (Japan), and TsingHua Fly Center (China). Copyright © 2015 by the Genetics Society of America.

  18. The Transgenic RNAi Project at Harvard Medical School: Resources and Validation

    Science.gov (United States)

    Perkins, Lizabeth A.; Holderbaum, Laura; Tao, Rong; Hu, Yanhui; Sopko, Richelle; McCall, Kim; Yang-Zhou, Donghui; Flockhart, Ian; Binari, Richard; Shim, Hye-Seok; Miller, Audrey; Housden, Amy; Foos, Marianna; Randkelv, Sakara; Kelley, Colleen; Namgyal, Pema; Villalta, Christians; Liu, Lu-Ping; Jiang, Xia; Huan-Huan, Qiao; Wang, Xia; Fujiyama, Asao; Toyoda, Atsushi; Ayers, Kathleen; Blum, Allison; Czech, Benjamin; Neumuller, Ralph; Yan, Dong; Cavallaro, Amanda; Hibbard, Karen; Hall, Don; Cooley, Lynn; Hannon, Gregory J.; Lehmann, Ruth; Parks, Annette; Mohr, Stephanie E.; Ueda, Ryu; Kondo, Shu; Ni, Jian-Quan; Perrimon, Norbert

    2015-01-01

    To facilitate large-scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome-scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT–qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently composed of 11,491 lines and covering 71% of Drosophila genes. Data on the characterization of the lines either by RT–qPCR or phenotype is available on a dedicated website, the RNAi Stock Validation and Phenotypes Project (RSVP, http://www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (United States), National Institute of Genetics (Japan), and TsingHua Fly Center (China). PMID:26320097

  19. Genome-wide RNAi screening identifies genes inhibiting the migration of glioblastoma cells.

    Directory of Open Access Journals (Sweden)

    Jian Yang

    Full Text Available Glioblastoma Multiforme (GBM cells are highly invasive, infiltrating into the surrounding normal brain tissue, making it impossible to completely eradicate GBM tumors by surgery or radiation. Increasing evidence also shows that these migratory cells are highly resistant to cytotoxic reagents, but decreasing their migratory capability can re-sensitize them to chemotherapy. These evidences suggest that the migratory cell population may serve as a better therapeutic target for more effective treatment of GBM. In order to understand the regulatory mechanism underlying the motile phenotype, we carried out a genome-wide RNAi screen for genes inhibiting the migration of GBM cells. The screening identified a total of twenty-five primary hits; seven of them were confirmed by secondary screening. Further study showed that three of the genes, FLNA, KHSRP and HCFC1, also functioned in vivo, and knocking them down caused multifocal tumor in a mouse model. Interestingly, two genes, KHSRP and HCFC1, were also found to be correlated with the clinical outcome of GBM patients. These two genes have not been previously associated with cell migration.

  20. RNAi Screen in Drosophila melanogastor Identifies Regulators of Steroidogenesis and Developmental Maturation

    DEFF Research Database (Denmark)

    Danielsen, Erik Thomas

    and duration required for juvenile-adult transition. This PhD project demonstrates the power of Drosophila genetics by taking an in vivo genome-wide RNAi screening approach to uncover genes required for the function of steroid producing tissue and developmental maturation. In total, 1909 genes were found...... to be required for the prothoracic gland function and affected the developmental timing for the juvenile-adult transition. Among the screen hits, we focused on an uncharacterized gene, sit (CG5278), which is highly expressed in the gland and is required for ecdysone production. Sit is a homolog of mammalian very...... flux of cholesterol uptake in the gland cells and affected the endosomal trafficking. Therefore this gene was suggested to be named stuck in traffic (sit). Sit’s role in cholesterol uptake was also supported by the observation that the developmental delayed phenotype from loss of sit expression...

  1. Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens

    Directory of Open Access Journals (Sweden)

    Sun Youxian

    2008-06-01

    image-based datasets derived from a wide spectrum of experimental conditions and is suitable to adaptively process new images which are continuously added to existing datasets. Validations were carried out on different dataset, including published RNAi screening using Drosophila embryos [Additional files 1, 2], dataset for cell cycle phase identification using HeLa cells [Additional files 1, 3, 4] and synthetic dataset using polygons, our methods tackled three aforementioned tasks effectively with an accuracy range of 85%–90%. When our method is implemented in the context of a Drosophila genome-scale RNAi image-based screening of cultured cells aimed to identifying the contribution of individual genes towards the regulation of cell-shape, it efficiently discovers meaningful new phenotypes and provides novel biological insight. We also propose a two-step procedure to modify the novelty detection method based on one-class SVM, so that it can be used to online phenotype discovery. In different conditions, we compared the SVM based method with our method using various datasets and our methods consistently outperformed SVM based method in at least two of three tasks by 2% to 5%. These results demonstrate that our methods can be used to better identify novel phenotypes in image-based datasets from a wide range of conditions and organisms. Conclusion We demonstrate that our method can detect various novel phenotypes effectively in complex datasets. Experiment results also validate that our method performs consistently under different order of image input, variation of starting conditions including the number and composition of existing phenotypes, and dataset from different screens. In our findings, the proposed method is suitable for online phenotype discovery in diverse high-throughput image-based genetic and chemical screens.

  2. Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis

    Directory of Open Access Journals (Sweden)

    Enright Anton J

    2010-03-01

    Full Text Available Abstract Background RNA inhibition by siRNAs is a frequently used approach to identify genes required for specific biological processes. However RNAi screening using siRNAs is hampered by non-specific or off target effects of the siRNAs, making it difficult to separate genuine hits from false positives. It is thought that many of the off-target effects seen in RNAi experiments are due to siRNAs acting as microRNAs (miRNAs, causing a reduction in gene expression of unintended targets via matches to the 6 or 7 nt 'seed' sequence. We have conducted a careful examination of off-target effects during an siRNA screen for novel regulators of the TRAIL apoptosis induction pathway(s. Results We identified 3 hexamers and 3 heptamer seed sequences that appeared multiple times in the top twenty siRNAs in the TRAIL apoptosis screen. Using a novel statistical enrichment approach, we systematically identified a further 17 hexamer and 13 heptamer seed sequences enriched in high scoring siRNAs. The presence of one of these seeds sequences (which could explain 6 of 8 confirmed off-target effects is sufficient to elicit a phenotype. Three of these seed sequences appear in the human miRNAs miR-26a, miR-145 and miR-384. Transfection of mimics of these miRNAs protects several cell types from TRAIL-induced cell death. Conclusions We have demonstrated a role for miR-26a, miR-145 and miR-26a in TRAIL-induced apoptosis. Further these results show that RNAi screening enriches for siRNAs with relevant off-target effects. Some of these effects can be identified by the over-representation of certain seed sequences in high-scoring siRNAs and we demonstrate the usefulness of such systematic analysis of enriched seed sequences.

  3. Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae

    OpenAIRE

    Xiao, Han; Zhao, Huimin

    2014-01-01

    Background Furfural is a major growth inhibitor in lignocellulosic hydrolysates and improving furfural tolerance of microorganisms is critical for rapid and efficient fermentation of lignocellulosic biomass. In this study, we used the RNAi-Assisted Genome Evolution (RAGE) method to select for furfural resistant mutants of Saccharomyces cerevisiae, and identified a new determinant of furfural tolerance. Results By using a genome-wide RNAi (RNA-interference) screen in S. cerevisiae for genes in...

  4. The health system and population health implications of large-scale diabetes screening in India: a microsimulation model of alternative approaches.

    Directory of Open Access Journals (Sweden)

    Sanjay Basu

    2015-05-01

    Full Text Available Like a growing number of rapidly developing countries, India has begun to develop a system for large-scale community-based screening for diabetes. We sought to identify the implications of using alternative screening instruments to detect people with undiagnosed type 2 diabetes among diverse populations across India.We developed and validated a microsimulation model that incorporated data from 58 studies from across the country into a nationally representative sample of Indians aged 25-65 y old. We estimated the diagnostic and health system implications of three major survey-based screening instruments and random glucometer-based screening. Of the 567 million Indians eligible for screening, depending on which of four screening approaches is utilized, between 158 and 306 million would be expected to screen as "high risk" for type 2 diabetes, and be referred for confirmatory testing. Between 26 million and 37 million of these people would be expected to meet international diagnostic criteria for diabetes, but between 126 million and 273 million would be "false positives." The ratio of false positives to true positives varied from 3.9 (when using random glucose screening to 8.2 (when using a survey-based screening instrument in our model. The cost per case found would be expected to be from US$5.28 (when using random glucose screening to US$17.06 (when using a survey-based screening instrument, presenting a total cost of between US$169 and US$567 million. The major limitation of our analysis is its dependence on published cohort studies that are unlikely fully to capture the poorest and most rural areas of the country. Because these areas are thought to have the lowest diabetes prevalence, this may result in overestimation of the efficacy and health benefits of screening.Large-scale community-based screening is anticipated to produce a large number of false-positive results, particularly if using currently available survey-based screening

  5. Screening and large-scale expression of membrane proteins in mammalian cells for structural studies.

    Science.gov (United States)

    Goehring, April; Lee, Chia-Hsueh; Wang, Kevin H; Michel, Jennifer Carlisle; Claxton, Derek P; Baconguis, Isabelle; Althoff, Thorsten; Fischer, Suzanne; Garcia, K Christopher; Gouaux, Eric

    2014-11-01

    Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in overexpression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient production of baculovirus and robust expression of the target protein. In this protocol, we show how to use small-scale transient transfection and fluorescence-detection size-exclusion chromatography (FSEC) experiments using a GFP-His8-tagged candidate protein to screen for monodispersity and expression level. Once promising candidates are identified, we describe how to generate baculovirus, transduce HEK293S GnTI(-) (N-acetylglucosaminyltransferase I-negative) cells in suspension culture and overexpress the candidate protein. We have used these methods to prepare pure samples of chicken acid-sensing ion channel 1a (cASIC1) and Caenorhabditis elegans glutamate-gated chloride channel (GluCl) for X-ray crystallography, demonstrating how to rapidly and efficiently screen hundreds of constructs and accomplish large-scale expression in 4-6 weeks.

  6. Development of RNAi method for screening candidate genes to control emerald ash borer, Agrilus planipennis.

    Science.gov (United States)

    Rodrigues, Thais B; Rieske, Lynne K; J Duan, Jian; Mogilicherla, Kanakachari; Palli, Subba R

    2017-08-07

    The ingestion of double-strand RNAs (dsRNA) targeting essential genes in an insect could cause mortality. Based on this principle, a new generation of insect control methods using RNA interference (RNAi) are being developed. In this work, we developed a bioassay for oral delivery of dsRNA to an invasive forest and urban tree pest, the emerald ash borer (EAB, Agrilus planipennis). EAB feeds and develops beneath the bark, killing trees rapidly. This behavior, coupled with the lack of a reliable artificial diet for rearing larvae and adults, make them difficult to study. We found that dsRNA is transported and processed to siRNAs by EAB larvae within 72 h after ingestion. Also, feeding neonate larvae with IAP (inhibitor of apoptosis) or COP (COPI coatomer, β subunit) dsRNA silenced their target genes and caused mortality. Both an increase in the concentration of dsRNA fed and sequential feeding of two different dsRNAs increased mortality. Here we provide evidence for successful RNAi in EAB, and demonstrate the development of a rapid and effective bioassay for oral delivery of dsRNA to screen additional genes.

  7. A genome-wide RNAi screen to dissect centriole duplication and centrosome maturation in Drosophila.

    Directory of Open Access Journals (Sweden)

    Jeroen Dobbelaere

    2008-09-01

    Full Text Available Centrosomes comprise a pair of centrioles surrounded by an amorphous pericentriolar material (PCM. Here, we have performed a microscopy-based genome-wide RNA interference (RNAi screen in Drosophila cells to identify proteins required for centriole duplication and mitotic PCM recruitment. We analysed 92% of the Drosophila genome (13,059 genes and identified 32 genes involved in centrosome function. An extensive series of secondary screens classified these genes into four categories: (1 nine are required for centriole duplication, (2 11 are required for centrosome maturation, (3 nine are required for both functions, and (4 three genes regulate centrosome separation. These 32 hits include several new centrosomal components, some of which have human homologs. In addition, we find that the individual depletion of only two proteins, Polo and Centrosomin (Cnn can completely block centrosome maturation. Cnn is phosphorylated during mitosis in a Polo-dependent manner, suggesting that the Polo-dependent phosphorylation of Cnn initiates centrosome maturation in flies.

  8. Environmental RNAi in herbivorous insects.

    Science.gov (United States)

    Ivashuta, Sergey; Zhang, Yuanji; Wiggins, B Elizabeth; Ramaseshadri, Partha; Segers, Gerrit C; Johnson, Steven; Meyer, Steve E; Kerstetter, Randy A; McNulty, Brian C; Bolognesi, Renata; Heck, Gregory R

    2015-05-01

    Environmental RNAi (eRNAi) is a sequence-specific regulation of endogenous gene expression in a receptive organism by exogenous double-stranded RNA (dsRNA). Although demonstrated under artificial dietary conditions and via transgenic plant presentations in several herbivorous insects, the magnitude and consequence of exogenous dsRNA uptake and the role of eRNAi remains unknown under natural insect living conditions. Our analysis of coleopteran insects sensitive to eRNAi fed on wild-type plants revealed uptake of plant endogenous long dsRNAs, but not small RNAs. Subsequently, the dsRNAs were processed into 21 nt siRNAs by insects and accumulated in high quantities in insect cells. No accumulation of host plant-derived siRNAs was observed in lepidopteran larvae that are recalcitrant to eRNAi. Stability of ingested dsRNA in coleopteran larval gut followed by uptake and transport from the gut to distal tissues appeared to be enabling factors for eRNAi. Although a relatively large number of distinct coleopteran insect-processed plant-derived siRNAs had sequence complementarity to insect transcripts, the vast majority of the siRNAs were present in relatively low abundance, and RNA-seq analysis did not detect a significant effect of plant-derived siRNAs on insect transcriptome. In summary, we observed a broad genome-wide uptake of plant endogenous dsRNA and subsequent processing of ingested dsRNA into 21 nt siRNAs in eRNAi-sensitive insects under natural feeding conditions. In addition to dsRNA stability in gut lumen and uptake, dosage of siRNAs targeting a given insect transcript is likely an important factor in order to achieve measurable eRNAi-based regulation in eRNAi-competent insects that lack an apparent silencing amplification mechanism. © 2015 Ivashuta et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  9. Reliability analysis of the Ahringer Caenorhabditis elegans RNAi feeding library: a guide for genome-wide screens

    Directory of Open Access Journals (Sweden)

    Lu Yiming

    2011-03-01

    Full Text Available Abstract Background The Ahringer C. elegans RNAi feeding library prepared by cloning genomic DNA fragments has been widely used in genome-wide analysis of gene function. However, the library has not been thoroughly validated by direct sequencing, and there are potential errors, including: 1 mis-annotation (the clone with the retired gene name should be remapped to the actual target gene; 2 nonspecific PCR amplification; 3 cross-RNAi; 4 mis-operation such as sample loading error, etc. Results Here we performed a reliability analysis on the Ahringer C. elegans RNAi feeding library, which contains 16,256 bacterial strains, using a bioinformatics approach. Results demonstrated that most (98.3% of the bacterial strains in the library are reliable. However, we also found that 2,851 (17.54% bacterial strains need to be re-annotated even they are reliable. Most of these bacterial strains are the clones having the retired gene names. Besides, 28 strains are grouped into unreliable category and 226 strains are marginal because of probably expressing unrelated double-stranded RNAs (dsRNAs. The accuracy of the prediction was further confirmed by direct sequencing analysis of 496 bacterial strains. Finally, a freely accessible database named CelRNAi (http://biocompute.bmi.ac.cn/CelRNAi/ was developed as a valuable complement resource for the feeding RNAi library by providing the predicted information on all bacterial strains. Moreover, submission of the direct sequencing result or any other annotations for the bacterial strains to the database are allowed and will be integrated into the CelRNAi database to improve the accuracy of the library. In addition, we provide five candidate primer sets for each of the unreliable and marginal bacterial strains for users to construct an alternative vector for their own RNAi studies. Conclusions Because of the potential unreliability of the Ahringer C. elegans RNAi feeding library, we strongly suggest the user examine

  10. Chemically intuited, large-scale screening of MOFs by machine learning techniques

    Science.gov (United States)

    Borboudakis, Giorgos; Stergiannakos, Taxiarchis; Frysali, Maria; Klontzas, Emmanuel; Tsamardinos, Ioannis; Froudakis, George E.

    2017-10-01

    A novel computational methodology for large-scale screening of MOFs is applied to gas storage with the use of machine learning technologies. This approach is a promising trade-off between the accuracy of ab initio methods and the speed of classical approaches, strategically combined with chemical intuition. The results demonstrate that the chemical properties of MOFs are indeed predictable (stochastically, not deterministically) using machine learning methods and automated analysis protocols, with the accuracy of predictions increasing with sample size. Our initial results indicate that this methodology is promising to apply not only to gas storage in MOFs but in many other material science projects.

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

    Directory of Open Access Journals (Sweden)

    Firnhaber Christopher B

    2010-10-01

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

  12. A genome-wide RNAi screen identifies novel targets of neratinib resistance leading to identification of potential drug resistant genetic markers.

    Science.gov (United States)

    Seyhan, Attila A; Varadarajan, Usha; Choe, Sung; Liu, Wei; Ryan, Terence E

    2012-04-01

    Neratinib (HKI-272) is a small molecule tyrosine kinase inhibitor of the ErbB receptor family currently in Phase III clinical trials. Despite its efficacy, the mechanism of potential cellular resistance to neratinib and genes involved with it remains unknown. We have used a pool-based lentiviral genome-wide functional RNAi screen combined with a lethal dose of neratinib to discover chemoresistant interactions with neratinib. Our screen has identified a collection of genes whose inhibition by RNAi led to neratinib resistance including genes involved in oncogenesis (e.g. RAB33A, RAB6A and BCL2L14), transcription factors (e.g. FOXP4, TFEC, ZNF), cellular ion transport (e.g. CLIC3, TRAPPC2P1, P2RX2), protein ubiquitination (e.g. UBL5), cell cycle (e.g. CCNF), and genes known to interact with breast cancer-associated genes (e.g. CCNF, FOXP4, TFEC, several ZNF factors, GNA13, IGFBP1, PMEPA1, SOX5, RAB33A, RAB6A, FXR1, DDO, TFEC, OLFM2). The identification of novel mediators of cellular resistance to neratinib could lead to the identification of new or neoadjuvant drug targets. Their use as patient or treatment selection biomarkers could make the application of anti-ErbB therapeutics more clinically effective.

  13. RNAi screen reveals an Abl kinase-dependent host cell pathway involved in Pseudomonas aeruginosa internalization.

    Directory of Open Access Journals (Sweden)

    Julia F Pielage

    2008-03-01

    Full Text Available Internalization of the pathogenic bacterium Pseudomonas aeruginosa by non-phagocytic cells is promoted by rearrangements of the actin cytoskeleton, but the host pathways usurped by this bacterium are not clearly understood. We used RNAi-mediated gene inactivation of approximately 80 genes known to regulate the actin cytoskeleton in Drosophila S2 cells to identify host molecules essential for entry of P. aeruginosa. This work revealed Abl tyrosine kinase, the adaptor protein Crk, the small GTPases Rac1 and Cdc42, and p21-activated kinase as components of a host signaling pathway that leads to internalization of P. aeruginosa. Using a variety of complementary approaches, we validated the role of this pathway in mammalian cells. Remarkably, ExoS and ExoT, type III secreted toxins of P. aeruginosa, target this pathway by interfering with GTPase function and, in the case of ExoT, by abrogating P. aeruginosa-induced Abl-dependent Crk phosphorylation. Altogether, this work reveals that P. aeruginosa utilizes the Abl pathway for entering host cells and reveals unexpected complexity by which the P. aeruginosa type III secretion system modulates this internalization pathway. Our results furthermore demonstrate the applicability of using RNAi screens to identify host signaling cascades usurped by microbial pathogens that may be potential targets for novel therapies directed against treatment of antibiotic-resistant infections.

  14. Optimization of a Fluorescence-Based Assay for Large-Scale Drug Screening against Babesia and Theileria Parasites.

    Science.gov (United States)

    Rizk, Mohamed Abdo; El-Sayed, Shimaa Abd El-Salam; Terkawi, Mohamed Alaa; Youssef, Mohamed Ahmed; El Said, El Said El Shirbini; Elsayed, Gehad; El-Khodery, Sabry; El-Ashker, Maged; Elsify, Ahmed; Omar, Mosaab; Salama, Akram; Yokoyama, Naoaki; Igarashi, Ikuo

    2015-01-01

    A rapid and accurate assay for evaluating antibabesial drugs on a large scale is required for the discovery of novel chemotherapeutic agents against Babesia parasites. In the current study, we evaluated the usefulness of a fluorescence-based assay for determining the efficacies of antibabesial compounds against bovine and equine hemoparasites in in vitro cultures. Three different hematocrits (HCTs; 2.5%, 5%, and 10%) were used without daily replacement of the medium. The results of a high-throughput screening assay revealed that the best HCT was 2.5% for bovine Babesia parasites and 5% for equine Babesia and Theileria parasites. The IC50 values of diminazene aceturate obtained by fluorescence and microscopy did not differ significantly. Likewise, the IC50 values of luteolin, pyronaridine tetraphosphate, nimbolide, gedunin, and enoxacin did not differ between the two methods. In conclusion, our fluorescence-based assay uses low HCT and does not require daily replacement of culture medium, making it highly suitable for in vitro large-scale drug screening against Babesia and Theileria parasites that infect cattle and horses.

  15. Optimization of a Fluorescence-Based Assay for Large-Scale Drug Screening against Babesia and Theileria Parasites.

    Directory of Open Access Journals (Sweden)

    Mohamed Abdo Rizk

    Full Text Available A rapid and accurate assay for evaluating antibabesial drugs on a large scale is required for the discovery of novel chemotherapeutic agents against Babesia parasites. In the current study, we evaluated the usefulness of a fluorescence-based assay for determining the efficacies of antibabesial compounds against bovine and equine hemoparasites in in vitro cultures. Three different hematocrits (HCTs; 2.5%, 5%, and 10% were used without daily replacement of the medium. The results of a high-throughput screening assay revealed that the best HCT was 2.5% for bovine Babesia parasites and 5% for equine Babesia and Theileria parasites. The IC50 values of diminazene aceturate obtained by fluorescence and microscopy did not differ significantly. Likewise, the IC50 values of luteolin, pyronaridine tetraphosphate, nimbolide, gedunin, and enoxacin did not differ between the two methods. In conclusion, our fluorescence-based assay uses low HCT and does not require daily replacement of culture medium, making it highly suitable for in vitro large-scale drug screening against Babesia and Theileria parasites that infect cattle and horses.

  16. A Large-Scale RNAi Screen Identifies SGK1 as a Key Survival Kinase for GBM Stem Cells.

    Science.gov (United States)

    Kulkarni, Shreya; Goel-Bhattacharya, Surbhi; Sengupta, Sejuti; Cochran, Brent H

    2018-01-01

    Glioblastoma multiforme (GBM) is the most common type of primary malignant brain cancer and has a very poor prognosis. A subpopulation of cells known as GBM stem-like cells (GBM-SC) have the capacity to initiate and sustain tumor growth and possess molecular characteristics similar to the parental tumor. GBM-SCs are known to be enriched in hypoxic niches and may contribute to therapeutic resistance. Therefore, to identify genetic determinants important for the proliferation and survival of GBM stem cells, an unbiased pooled shRNA screen of 10,000 genes was conducted under normoxic as well as hypoxic conditions. A number of essential genes were identified that are required for GBM-SC growth, under either or both oxygen conditions, in two different GBM-SC lines. Interestingly, only about a third of the essential genes were common to both cell lines. The oxygen environment significantly impacts the cellular genetic dependencies as 30% of the genes required under hypoxia were not required under normoxic conditions. In addition to identifying essential genes already implicated in GBM such as CDK4, KIF11 , and RAN , the screen also identified new genes that have not been previously implicated in GBM stem cell biology. The importance of the serum and glucocorticoid-regulated kinase 1 (SGK1) for cellular survival was validated in multiple patient-derived GBM stem cell lines using shRNA, CRISPR, and pharmacologic inhibitors. However, SGK1 depletion and inhibition has little effect on traditional serum grown glioma lines and on differentiated GBM-SCs indicating its specific importance in GBM stem cell survival. Implications: This study identifies genes required for the growth and survival of GBM stem cells under both normoxic and hypoxic conditions and finds SGK1 as a novel potential drug target for GBM. Mol Cancer Res; 16(1); 103-14. ©2017 AACR . ©2017 American Association for Cancer Research.

  17. Isolating genes involved with genotoxic drug response in the nematode Caenorhabditis elegans using genome-wide RNAi screening

    DEFF Research Database (Denmark)

    Schøler, Lone Vedel; Møller, Tine Hørning; Nørgaard, Steffen

    2012-01-01

    The soil nematode Caenorhabditis elegans has become a popular genetic model organism used to study a broad range of complex biological processes, including development, aging, apoptosis, and DNA damage responses. Many genetic tools and tricks have been developed in C. elegans including knock down...... of gene expression via RNA interference (RNAi). In C. elegans RNAi can effectively be administrated via feeding the nematodes bacteria expressing double-stranded RNA targeting the gene of interest. Several commercial C. elegans RNAi libraries are available and hence gene inactivation using RNAi can...

  18. A genome-wide RNAi screen identifies novel targets of neratinib sensitivity leading to neratinib and paclitaxel combination drug treatments.

    Science.gov (United States)

    Seyhan, Attila A; Varadarajan, Usha; Choe, Sung; Liu, Yan; McGraw, John; Woods, Matthew; Murray, Stuart; Eckert, Amy; Liu, Wei; Ryan, Terence E

    2011-06-01

    ErbB2 is frequently activated in tumors, and influences a wide array of cellular functions, including proliferation, apoptosis, cell motility and adhesion. HKI-272 (neratinib) is a small molecule pan-kinase inhibitor of the ErbB family of receptor tyrosine kinases, and shows strong antiproliferative activity in ErbB2-overexpressing breast cancer cells. We undertook a genome-wide pooled lentiviral RNAi screen to identify synthetic lethal or enhancer (synthetic modulator screen) genes that interact with neratinib in a human breast cancer cell line (SKBR-3). These genes upon knockdown would modulate cell viability in the presence of subeffective concentrations of neratinib. We discovered a diverse set of genes whose depletion selectively impaired or enhanced the viability of SKBR-3 cells in the presence of neratinib. We observed diverse pathways including EGFR, hypoxia, cAMP, and protein ubiquitination that, when co-treated with RNAi and neratinib, resulted in arrest of cell proliferation. Examining the changes of these genes and their protein products also led to a rationale for clinically relevant drug combination treatments. Treatment of cells with either paclitaxel or cytarabine in combination with neratinib resulted in a strong antiproliferative effect. The identification of novel mediators of cellular response to neratinib and the development of potential drug combination treatments have expanded our understanding of neratinib's mode-of-action for the development of more effective therapeutic regimens. Notably, our findings support a paclitaxel and neratinib phase III clinical trial in breast cancer patients.

  19. A Kinome RNAi Screen in Drosophila Identifies Novel Genes Interacting with Lgl, aPKC, and Crb Cell Polarity Genes in Epithelial Tissues.

    Science.gov (United States)

    Parsons, Linda M; Grzeschik, Nicola A; Amaratunga, Kasun; Burke, Peter; Quinn, Leonie M; Richardson, Helena E

    2017-08-07

    In both Drosophila melanogaster and mammalian systems, epithelial structure and underlying cell polarity are essential for proper tissue morphogenesis and organ growth. Cell polarity interfaces with multiple cellular processes that are regulated by the phosphorylation status of large protein networks. To gain insight into the molecular mechanisms that coordinate cell polarity with tissue growth, we screened a boutique collection of RNAi stocks targeting the kinome for their capacity to modify Drosophila "cell polarity" eye and wing phenotypes. Initially, we identified kinase or phosphatase genes whose depletion modified adult eye phenotypes associated with the manipulation of cell polarity complexes (via overexpression of Crb or aPKC). We next conducted a secondary screen to test whether these cell polarity modifiers altered tissue overgrowth associated with depletion of Lgl in the wing. These screens identified Hippo, Jun kinase (JNK), and Notch signaling pathways, previously linked to cell polarity regulation of tissue growth. Furthermore, novel pathways not previously connected to cell polarity regulation of tissue growth were identified, including Wingless (Wg/Wnt), Ras, and lipid/Phospho-inositol-3-kinase (PI3K) signaling pathways. Additionally, we demonstrated that the "nutrient sensing" kinases Salt Inducible Kinase 2 and 3 ( SIK2 and 3 ) are potent modifiers of cell polarity phenotypes and regulators of tissue growth. Overall, our screen has revealed novel cell polarity-interacting kinases and phosphatases that affect tissue growth, providing a platform for investigating molecular mechanisms coordinating cell polarity and tissue growth during development. Copyright © 2017 Parsons et al.

  20. web cellHTS2: A web-application for the analysis of high-throughput screening data

    Directory of Open Access Journals (Sweden)

    Boutros Michael

    2010-04-01

    Full Text Available Abstract Background The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2. Results The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats. Conclusions The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at http://web-cellHTS2.dkfz.de. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.

  1. Genome-wide RNAi Screen Identifies Networks Involved in Intestinal Stem Cell Regulation in Drosophila

    Directory of Open Access Journals (Sweden)

    Xiankun Zeng

    2015-02-01

    Full Text Available The intestinal epithelium is the most rapidly self-renewing tissue in adult animals and maintained by intestinal stem cells (ISCs in both Drosophila and mammals. To comprehensively identify genes and pathways that regulate ISC fates, we performed a genome-wide transgenic RNAi screen in adult Drosophila intestine and identified 405 genes that regulate ISC maintenance and lineage-specific differentiation. By integrating these genes into publicly available interaction databases, we further developed functional networks that regulate ISC self-renewal, ISC proliferation, ISC maintenance of diploid status, ISC survival, ISC-to-enterocyte (EC lineage differentiation, and ISC-to-enteroendocrine (EE lineage differentiation. By comparing regulators among ISCs, female germline stem cells, and neural stem cells, we found that factors related to basic stem cell cellular processes are commonly required in all stem cells, and stem-cell-specific, niche-related signals are required only in the unique stem cell type. Our findings provide valuable insights into stem cell maintenance and lineage-specific differentiation.

  2. Current issues of RNAi therapeutics delivery and development.

    Science.gov (United States)

    Haussecker, D

    2014-12-10

    the applications of RNAi therapeutics are rather limited. This is largely based on the observation that the biodistribution of RNAi formulations is typically more limited compared to small molecules and oral administration is not possible with current technologies. Similarly, the utility of a given RNAi formulation is limited to a few cell types and tissues at most and a universal delivery strategy should remain elusive for the foreseeable future. Therefore, to further expand on the therapeutic utility and patient convenience of RNAi, it is important to overcome a number of delivery-related technical and scientific challenges which will be discussed in this presentation. For systemic applications, these include the necessity for extended blood circulation times, vascular escape (probably the most rewarding inquiry currently), tissue penetration, cellular uptake, and escape into the cytoplasm. In terms of safety, it is important that these formulations do not accumulate in the body, do not cause excessive off-targeting due to 'chemical stickiness' (often useful for purposes of biodistribution), and overcome the physical/biological barriers in a controlled manner. The time for realizing the therapeutic potential of RNAi has come. At the same time, it is important to lay the foundations for the next leg of value creation by overcoming the challenges of delivering RNAi to new cell types. Based on results from exploratory research, the renewed interest in RNAi therapeutics and capital infusion, there is a reason to be optimistic that this can be achieved. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Feasibility of large-scale screening using N-ERC/mesothelin levels in the blood for the early diagnosis of malignant mesothelioma.

    Science.gov (United States)

    Imashimizu, Kohta; Shiomi, Kazu; Maeda, Masahiro; Aoki, Naoko; Igarashi, Kiyoko; Suzuki, Fumio; Koizumi, Mitsuru; Suzuki, Kenji; Hino, Okio

    2011-05-01

    A large-scale screening involving the measurement of N-ERC/mesothelin levels in blood using an ELISA system for the early diagnosis of malignant mesothelioma (MM) was carried out in individuals with a history of employment at construction sites. Approximately 30,000 subjects were screened. Of the 80 subjects with high-risk values, one male patient was diagnosed as having MM based on a PET study and histopathology. This is the first report of the pre-clinical diagnosis of MM based on blood test screening. In addition, plasma levels of N-ERC/mesothelin may be effectively used for monitoring relapse after surgery.

  4. RNAi effector diversity in nematodes.

    Directory of Open Access Journals (Sweden)

    Johnathan J Dalzell

    2011-06-01

    Full Text Available While RNA interference (RNAi has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (dsRNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii The Argonautes (AGOs responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii Secondary Argonautes (SAGOs are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research

  5. Large-scale Topographical Screen for Investigation of Physical Neural-Guidance Cues

    Science.gov (United States)

    Li, Wei; Tang, Qing Yuan; Jadhav, Amol D.; Narang, Ankit; Qian, Wei Xian; Shi, Peng; Pang, Stella W.

    2015-03-01

    A combinatorial approach was used to present primary neurons with a large library of topographical features in the form of micropatterned substrate for high-throughput screening of physical neural-guidance cues that can effectively promote different aspects of neuronal development, including axon and dendritic outgrowth. Notably, the neuronal-guidance capability of specific features was automatically identified using a customized image processing software, thus significantly increasing the screening throughput with minimal subjective bias. Our results indicate that the anisotropic topographies promote axonal and in some cases dendritic extension relative to the isotropic topographies, while dendritic branching showed preference to plain substrates over the microscale features. The results from this work can be readily applied towards engineering novel biomaterials with precise surface topography that can serve as guidance conduits for neuro-regenerative applications. This novel topographical screening strategy combined with the automated processing capability can also be used for high-throughput screening of chemical or genetic regulatory factors in primary neurons.

  6. Genome-wide RNAi screen reveals ALK1 mediates LDL uptake and transcytosis in endothelial cells

    Science.gov (United States)

    Kraehling, Jan R.; Chidlow, John H.; Rajagopal, Chitra; Sugiyama, Michael G.; Fowler, Joseph W.; Lee, Monica Y.; Zhang, Xinbo; Ramírez, Cristina M.; Park, Eon Joo; Tao, Bo; Chen, Keyang; Kuruvilla, Leena; Larriveé, Bruno; Folta-Stogniew, Ewa; Ola, Roxana; Rotllan, Noemi; Zhou, Wenping; Nagle, Michael W.; Herz, Joachim; Williams, Kevin Jon; Eichmann, Anne; Lee, Warren L.; Fernández-Hernando, Carlos; Sessa, William C.

    2016-01-01

    In humans and animals lacking functional LDL receptor (LDLR), LDL from plasma still readily traverses the endothelium. To identify the pathways of LDL uptake, a genome-wide RNAi screen was performed in endothelial cells and cross-referenced with GWAS-data sets. Here we show that the activin-like kinase 1 (ALK1) mediates LDL uptake into endothelial cells. ALK1 binds LDL with lower affinity than LDLR and saturates only at hypercholesterolemic concentrations. ALK1 mediates uptake of LDL into endothelial cells via an unusual endocytic pathway that diverts the ligand from lysosomal degradation and promotes LDL transcytosis. The endothelium-specific genetic ablation of Alk1 in Ldlr-KO animals leads to less LDL uptake into the aortic endothelium, showing its physiological role in endothelial lipoprotein metabolism. In summary, identification of pathways mediating LDLR-independent uptake of LDL may provide unique opportunities to block the initiation of LDL accumulation in the vessel wall or augment hepatic LDLR-dependent clearance of LDL. PMID:27869117

  7. RNAi Therapeutics in Autoimmune Disease

    Directory of Open Access Journals (Sweden)

    Seunghee Cha

    2013-03-01

    Full Text Available Since the discovery of RNA interference (RNAi, excitement has grown over its potential therapeutic uses. Targeting RNAi pathways provides a powerful tool to change biological processes post-transcriptionally in various health conditions such as cancer or autoimmune diseases. Optimum design of shRNA, siRNA, and miRNA enhances stability and specificity of RNAi-based approaches whereas it has to reduce or prevent undesirable immune responses or off-target effects. Recent advances in understanding pathogenesis of autoimmune diseases have allowed application of these tools in vitro as well as in vivo with some degree of success. Further research on the design and delivery of effectors of RNAi pathway and underlying molecular basis of RNAi would warrant practical use of RNAi-based therapeutics in human applications. This review will focus on the approaches used for current therapeutics and their applications in autoimmune diseases, including rheumatoid arthritis and Sjögren’s syndrome.

  8. RNAi phenotype profiling of kinases identifies potential therapeutic targets in Ewing's sarcoma.

    Science.gov (United States)

    Arora, Shilpi; Gonzales, Irma M; Hagelstrom, R Tanner; Beaudry, Christian; Choudhary, Ashish; Sima, Chao; Tibes, Raoul; Mousses, Spyro; Azorsa, David O

    2010-08-18

    Ewing's sarcomas are aggressive musculoskeletal tumors occurring most frequently in the long and flat bones as a solitary lesion mostly during the teen-age years of life. With current treatments, significant number of patients relapse and survival is poor for those with metastatic disease. As part of novel target discovery in Ewing's sarcoma, we applied RNAi mediated phenotypic profiling to identify kinase targets involved in growth and survival of Ewing's sarcoma cells. Four Ewing's sarcoma cell lines TC-32, TC-71, SK-ES-1 and RD-ES were tested in high throughput-RNAi screens using a siRNA library targeting 572 kinases. Knockdown of 25 siRNAs reduced the growth of all four Ewing's sarcoma cell lines in replicate screens. Of these, 16 siRNA were specific and reduced proliferation of Ewing's sarcoma cells as compared to normal fibroblasts. Secondary validation and preliminary mechanistic studies highlighted the kinases STK10 and TNK2 as having important roles in growth and survival of Ewing's sarcoma cells. Furthermore, knockdown of STK10 and TNK2 by siRNA showed increased apoptosis. In summary, RNAi-based phenotypic profiling proved to be a powerful gene target discovery strategy, leading to successful identification and validation of STK10 and TNK2 as two novel potential therapeutic targets for Ewing's sarcoma.

  9. Identification of ER Proteins Involved in the Functional Organisation of the Early Secretory Pathway in Drosophila Cells by a Targeted RNAi Screen

    Science.gov (United States)

    Kondylis, Vangelis; Tang, Yang; Fuchs, Florian; Boutros, Michael; Rabouille, Catherine

    2011-01-01

    Background In Drosophila, the early secretory apparatus comprises discrete paired Golgi stacks in close proximity to exit sites from the endoplasmic reticulum (tER sites), thus forming tER-Golgi units. Although many components involved in secretion have been identified, the structural components sustaining its organisation are less known. Here we set out to identify novel ER resident proteins involved in the of tER-Golgi unit organisation. Results To do so, we designed a novel screening strategy combining a bioinformatics pre-selection with an RNAi screen. We first selected 156 proteins exhibiting known or related ER retention/retrieval signals from a list of proteins predicted to have a signal sequence. We then performed a microscopy-based primary and confirmation RNAi screen in Drosophila S2 cells directly scoring the organisation of the tER-Golgi units. We identified 49 hits, most of which leading to an increased number of smaller tER-Golgi units (MG for “more and smaller Golgi”) upon depletion. 16 of them were validated and characterised, showing that this phenotype was not due to an inhibition in secretion, a block in G2, or ER stress. Interestingly, the MG phenotype was often accompanied by an increase in the cell volume. Out of 6 proteins, 4 were localised to the ER. Conclusions This work has identified novel proteins involved in the organisation of the Drosophila early secretory pathway. It contributes to the effort of assigning protein functions to gene annotation in the secretory pathway, and analysis of the MG hits revealed an enrichment of ER proteins. These results suggest a link between ER localisation, aspects of cell metabolism and tER-Golgi structural organisation. PMID:21383842

  10. Large scale statistical inference of signaling pathways from RNAi and microarray data

    Directory of Open Access Journals (Sweden)

    Poustka Annemarie

    2007-10-01

    Full Text Available Abstract Background The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain insights into signaling pathways by observing downstream effects of individual knock-downs on gene expression. These secondary effects can be used to computationally reverse engineer features of the upstream signaling pathway. Results In this paper we address this challenging problem by extending previous work by Markowetz et al., who proposed a statistical framework to score networks hypotheses in a Bayesian manner. Our extensions go in three directions: First, we introduce a way to omit the data discretization step needed in the original framework via a calculation based on p-values instead. Second, we show how prior assumptions on the network structure can be incorporated into the scoring scheme using regularization techniques. Third and most important, we propose methods to scale up the original approach, which is limited to around 5 genes, to large scale networks. Conclusion Comparisons of these methods on artificial data are conducted. Our proposed module network is employed to infer the signaling network between 13 genes in the ER-α pathway in human MCF-7 breast cancer cells. Using a bootstrapping approach this reconstruction can be found with good statistical stability. The code for the module network inference method is available in the latest version of the R-package nem, which can be obtained from the Bioconductor homepage.

  11. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia.

    Science.gov (United States)

    Zuber, Johannes; Shi, Junwei; Wang, Eric; Rappaport, Amy R; Herrmann, Harald; Sison, Edward A; Magoon, Daniel; Qi, Jun; Blatt, Katharina; Wunderlich, Mark; Taylor, Meredith J; Johns, Christopher; Chicas, Agustin; Mulloy, James C; Kogan, Scott C; Brown, Patrick; Valent, Peter; Bradner, James E; Lowe, Scott W; Vakoc, Christopher R

    2011-08-03

    Epigenetic pathways can regulate gene expression by controlling and interpreting chromatin modifications. Cancer cells are characterized by altered epigenetic landscapes, and commonly exploit the chromatin regulatory machinery to enforce oncogenic gene expression programs. Although chromatin alterations are, in principle, reversible and often amenable to drug intervention, the promise of targeting such pathways therapeutically has been limited by an incomplete understanding of cancer-specific dependencies on epigenetic regulators. Here we describe a non-biased approach to probe epigenetic vulnerabilities in acute myeloid leukaemia (AML), an aggressive haematopoietic malignancy that is often associated with aberrant chromatin states. By screening a custom library of small hairpin RNAs (shRNAs) targeting known chromatin regulators in a genetically defined AML mouse model, we identify the protein bromodomain-containing 4 (Brd4) as being critically required for disease maintenance. Suppression of Brd4 using shRNAs or the small-molecule inhibitor JQ1 led to robust antileukaemic effects in vitro and in vivo, accompanied by terminal myeloid differentiation and elimination of leukaemia stem cells. Similar sensitivities were observed in a variety of human AML cell lines and primary patient samples, revealing that JQ1 has broad activity in diverse AML subtypes. The effects of Brd4 suppression are, at least in part, due to its role in sustaining Myc expression to promote aberrant self-renewal, which implicates JQ1 as a pharmacological means to suppress MYC in cancer. Our results establish small-molecule inhibition of Brd4 as a promising therapeutic strategy in AML and, potentially, other cancers, and highlight the utility of RNA interference (RNAi) screening for revealing epigenetic vulnerabilities that can be exploited for direct pharmacological intervention.

  12. The Caenorhabditis elegans RDE-10/RDE-11 complex regulates RNAi by promoting secondary siRNA amplification.

    Science.gov (United States)

    Zhang, Chi; Montgomery, Taiowa A; Fischer, Sylvia E J; Garcia, Susana M D A; Riedel, Christian G; Fahlgren, Noah; Sullivan, Christopher M; Carrington, James C; Ruvkun, Gary

    2012-05-22

    In nematodes, plants, and fungi, RNAi is remarkably potent and persistent due to the amplification of initial silencing signals by RNA-dependent RNA polymerases (RdRPs). In Caenorhabditis elegans (C. elegans), the interaction between the RNA-induced silencing complex (RISC) loaded with primary small interfering RNAs (siRNAs) and the target messenger RNA (mRNA) leads to the recruitment of RdRPs and synthesis of secondary siRNAs using the target mRNA as the template. The mechanism and genetic requirements for secondary siRNA accumulation are not well understood. From a forward genetic screen for C. elegans genes required for RNAi, we identified rde-10, and through proteomic analysis of RDE-10-interacting proteins, we identified a protein complex containing the new RNAi factor RDE-11, the known RNAi factors RSD-2 and ERGO-1, and other candidate RNAi factors. The RNAi defective genes rde-10 and rde-11 encode a novel protein and a RING-type zinc finger domain protein, respectively. Mutations in rde-10 and rde-11 genes cause dosage-sensitive RNAi deficiencies: these mutants are resistant to low dosage but sensitive to high dosage of double-stranded RNAs. We assessed the roles of rde-10, rde-11, and other dosage-sensitive RNAi-defective genes rsd-2, rsd-6, and haf-6 in both exogenous and endogenous small RNA pathways using high-throughput sequencing and qRT-PCR. These genes are required for the accumulation of secondary siRNAs in both exogenous and endogenous RNAi pathways. The RDE-10/RDE-11 complex is essential for the amplification of RNAi in C. elegans by promoting secondary siRNA accumulation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. In vivo RNAi screen reveals neddylation genes as novel regulators of Hedgehog signaling.

    Directory of Open Access Journals (Sweden)

    Juan Du

    Full Text Available Hedgehog (Hh signaling is highly conserved in all metazoan animals and plays critical roles in many developmental processes. Dysregulation of the Hh signaling cascade has been implicated in many diseases, including cancer. Although key components of the Hh pathway have been identified, significant gaps remain in our understanding of the regulation of individual Hh signaling molecules. Here, we report the identification of novel regulators of the Hh pathway, obtained from an in vivo RNA interference (RNAi screen in Drosophila. By selectively targeting critical genes functioning in post-translational modification systems utilizing ubiquitin (Ub and Ub-like proteins, we identify two novel genes (dUba3 and dUbc12 that negatively regulate Hh signaling activity. We provide in vivo and in vitro evidence illustrating that dUba3 and dUbc12 are essential components of the neddylation pathway; they function in an enzyme cascade to conjugate the ubiquitin-like NEDD8 modifier to Cullin proteins. Neddylation activates the Cullin-containing ubiquitin ligase complex, which in turn promotes the degradation of Cubitus interruptus (Ci, the downstream transcription factor of the Hh pathway. Our study reveals a conserved molecular mechanism of the neddylation pathway in Drosophila and sheds light on the complex post-translational regulations in Hh signaling.

  14. A genome-wide RNAi screen identifies regulators of cholesterol-modified hedgehog secretion in Drosophila.

    Directory of Open Access Journals (Sweden)

    Reid Aikin

    Full Text Available Hedgehog (Hh proteins are secreted molecules that function as organizers in animal development. In addition to being palmitoylated, Hh is the only metazoan protein known to possess a covalently-linked cholesterol moiety. The absence of either modification severely disrupts the organization of numerous tissues during development. It is currently not known how lipid-modified Hh is secreted and released from producing cells. We have performed a genome-wide RNAi screen in Drosophila melanogaster cells to identify regulators of Hh secretion. We found that cholesterol-modified Hh secretion is strongly dependent on coat protein complex I (COPI but not COPII vesicles, suggesting that cholesterol modification alters the movement of Hh through the early secretory pathway. We provide evidence that both proteolysis and cholesterol modification are necessary for the efficient trafficking of Hh through the ER and Golgi. Finally, we identified several putative regulators of protein secretion and demonstrate a role for some of these genes in Hh and Wingless (Wg morphogen secretion in vivo. These data open new perspectives for studying how morphogen secretion is regulated, as well as provide insight into regulation of lipid-modified protein secretion.

  15. Considering RNAi experimental design in parasitic helminths.

    Science.gov (United States)

    Dalzell, Johnathan J; Warnock, Neil D; McVeigh, Paul; Marks, Nikki J; Mousley, Angela; Atkinson, Louise; Maule, Aaron G

    2012-04-01

    Almost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.

  16. Achieving efficient RNAi therapy: progress and challenges

    Directory of Open Access Journals (Sweden)

    Kun Gao

    2013-07-01

    Full Text Available RNA interference (RNAi has been harnessed to produce a new class of drugs for treatment of various diseases. This review summarizes the most important parameters that govern the silencing efficiency and duration of the RNAi effect such as small interfering RNA (siRNA stability and modification, the type of delivery system and particle sizing methods. It also discusses the predominant barriers for siRNA delivery, such as off-target effects and introduces internalization, endosomal escape and mathematical modeling in RNAi therapy and combinatorial RNAi. At present, effective delivery of RNAi therapeutics in vivo remains a challenge although significant progress has been made in this field.

  17. Application of RNAi to Genomic Drug Target Validation in Schistosomes.

    Directory of Open Access Journals (Sweden)

    Alessandra Guidi

    2015-05-01

    Full Text Available Concerns over the possibility of resistance developing to praziquantel (PZQ, has stimulated efforts to develop new drugs for schistosomiasis. In addition to the development of improved whole organism screens, the success of RNA interference (RNAi in schistosomes offers great promise for the identification of potential drug targets to initiate drug discovery. In this study we set out to contribute to RNAi based validation of putative drug targets. Initially a list of 24 target candidates was compiled based on the identification of putative essential genes in schistosomes orthologous of C. elegans essential genes. Knockdown of Calmodulin (Smp_026560.2 (Sm-Calm, that topped this list, produced a phenotype characterised by waves of contraction in adult worms but no phenotype in schistosomula. Knockdown of the atypical Protein Kinase C (Smp_096310 (Sm-aPKC resulted in loss of viability in both schistosomula and adults and led us to focus our attention on other kinase genes that were identified in the above list and through whole organism screening of known kinase inhibitor sets followed by chemogenomic evaluation. RNAi knockdown of these kinase genes failed to affect adult worm viability but, like Sm-aPKC, knockdown of Polo-like kinase 1, Sm-PLK1 (Smp_009600 and p38-MAPK, Sm-MAPK p38 (Smp_133020 resulted in an increased mortality of schistosomula after 2-3 weeks, an effect more marked in the presence of human red blood cells (hRBC. For Sm-PLK-1 the same effects were seen with the specific inhibitor, BI2536, which also affected viable egg production in adult worms. For Sm-PLK-1 and Sm-aPKC the in vitro effects were reflected in lower recoveries in vivo. We conclude that the use of RNAi combined with culture with hRBC is a reliable method for evaluating genes important for larval development. However, in view of the slow manifestation of the effects of Sm-aPKC knockdown in adults and the lack of effects of Sm-PLK-1 and Sm-MAPK p38 on adult viability

  18. RNAi suppressors encoded by pathogenic human viruses

    NARCIS (Netherlands)

    de Vries, Walter; Berkhout, Ben

    2008-01-01

    RNA silencing or RNAi interference (RNAi) serves as an innate antiviral mechanism in plants, fungi and animals. Human viruses, like plant viruses, encode suppressor proteins or RNAs that block or modulate the RNAi pathway. This review summarizes the mechanisms by which pathogenic human viruses

  19. Study on the millimeter-wave scale absorber based on the Salisbury screen

    Science.gov (United States)

    Yuan, Liming; Dai, Fei; Xu, Yonggang; Zhang, Yuan

    2018-03-01

    In order to solve the problem on the millimeter-wave scale absorber, the Salisbury screen absorber is employed and designed based on the RL. By optimizing parameters including the sheet resistance of the surface resistive layer, the permittivity and the thickness of the grounded dielectric layer, the RL of the Salisbury screen absorber could be identical with that of the theoretical scale absorber. An example is given to verify the effectiveness of the method, where the Salisbury screen absorber is designed by the proposed method and compared with the theoretical scale absorber. Meanwhile, plate models and tri-corner reflector (TCR) models are constructed according to the designed result and their scattering properties are simulated by FEKO. Results reveal that the deviation between the designed Salisbury screen absorber and the theoretical scale absorber falls within the tolerance of radar Cross section (RCS) measurement. The work in this paper has important theoretical and practical significance in electromagnetic measurement of large scale ratio.

  20. Asian citrus psyllid RNAi pathway - RNAi evidence

    Science.gov (United States)

    In silico analyses of the draft genome of Diaphorina citri, the Asian citrus psyllid, for genes within the Ribonucleic acid interference(RNAi), pathway was successful. The psyllid is the vector of the plant-infecting bacterium, Candidatus Liberibacter asiaticus (CLas), which is linked to citrus gree...

  1. A large-scale RNA interference screen identifies genes that regulate autophagy at different stages.

    Science.gov (United States)

    Guo, Sujuan; Pridham, Kevin J; Virbasius, Ching-Man; He, Bin; Zhang, Liqing; Varmark, Hanne; Green, Michael R; Sheng, Zhi

    2018-02-12

    Dysregulated autophagy is central to the pathogenesis and therapeutic development of cancer. However, how autophagy is regulated in cancer is not well understood and genes that modulate cancer autophagy are not fully defined. To gain more insights into autophagy regulation in cancer, we performed a large-scale RNA interference screen in K562 human chronic myeloid leukemia cells using monodansylcadaverine staining, an autophagy-detecting approach equivalent to immunoblotting of the autophagy marker LC3B or fluorescence microscopy of GFP-LC3B. By coupling monodansylcadaverine staining with fluorescence-activated cell sorting, we successfully isolated autophagic K562 cells where we identified 336 short hairpin RNAs. After candidate validation using Cyto-ID fluorescence spectrophotometry, LC3B immunoblotting, and quantitative RT-PCR, 82 genes were identified as autophagy-regulating genes. 20 genes have been reported previously and the remaining 62 candidates are novel autophagy mediators. Bioinformatic analyses revealed that most candidate genes were involved in molecular pathways regulating autophagy, rather than directly participating in the autophagy process. Further autophagy flux assays revealed that 57 autophagy-regulating genes suppressed autophagy initiation, whereas 21 candidates promoted autophagy maturation. Our RNA interference screen identifies identified genes that regulate autophagy at different stages, which helps decode autophagy regulation in cancer and offers novel avenues to develop autophagy-related therapies for cancer.

  2. RNAi High-Throughput Screening of Single- and Multi-Cell-Type Tumor Spheroids: A Comprehensive Analysis in Two and Three Dimensions.

    Science.gov (United States)

    Fu, Jiaqi; Fernandez, Daniel; Ferrer, Marc; Titus, Steven A; Buehler, Eugen; Lal-Nag, Madhu A

    2017-06-01

    The widespread use of two-dimensional (2D) monolayer cultures for high-throughput screening (HTS) to identify targets in drug discovery has led to attrition in the number of drug targets being validated. Solid tumors are complex, aberrantly growing microenvironments that harness structural components from stroma, nutrients fed through vasculature, and immunosuppressive factors. Increasing evidence of stromally-derived signaling broadens the complexity of our understanding of the tumor microenvironment while stressing the importance of developing better models that reflect these interactions. Three-dimensional (3D) models may be more sensitive to certain gene-silencing events than 2D models because of their components of hypoxia, nutrient gradients, and increased dependence on cell-cell interactions and therefore are more representative of in vivo interactions. Colorectal cancer (CRC) and breast cancer (BC) models composed of epithelial cells only, deemed single-cell-type tumor spheroids (SCTS) and multi-cell-type tumor spheroids (MCTS), containing fibroblasts were developed for RNAi HTS in 384-well microplates with flat-bottom wells for 2D screening and round-bottom, ultra-low-attachment wells for 3D screening. We describe the development of a high-throughput assay platform that can assess physiologically relevant phenotypic differences between screening 2D versus 3D SCTS, 3D SCTS, and MCTS in the context of different cancer subtypes. This assay platform represents a paradigm shift in how we approach drug discovery that can reduce the attrition rate of drugs that enter the clinic.

  3. Conditional RNAi: towards a silent gene therapy.

    Science.gov (United States)

    Lee, Sang-Kyung; Kumar, Priti

    2009-07-02

    RNA interference (RNAi) has the potential to permit the downregulation of virtually any gene. While transgenic RNAi enables stable propagation of the resulting phenotype to progeny, the dominant nature of RNAi limits its use to applications where the continued suppression of gene expression does not disturb normal cell functioning. This is of particular importance when the target gene product is essential for cell survival, development or differentiation. It is therefore desirable that knockdown be externally regulatable. This review is aimed at providing an overview of the approaches for conditional RNAi in mammalian systems, with a special mention of studies employing these approaches to target therapeutically/biologically relevant molecules, their advantages and disadvantages, and a pointer towards approaches best suited for RNAi-based gene therapy.

  4. Flavivirus RNAi suppression: decoding non-coding RNA.

    Science.gov (United States)

    Pijlman, Gorben P

    2014-08-01

    Flaviviruses are important human pathogens that are transmitted by invertebrate vectors, mostly mosquitoes and ticks. During replication in their vector, flaviviruses are subject to a potent innate immune response known as antiviral RNA interference (RNAi). This defense mechanism is associated with the production of small interfering (si)RNA that lead to degradation of viral RNA. To what extent flaviviruses would benefit from counteracting antiviral RNAi is subject of debate. Here, the experimental evidence to suggest the existence of flavivirus RNAi suppressors is discussed. I will highlight the putative role of non-coding, subgenomic flavivirus RNA in suppression of RNAi in insect and mammalian cells. Novel insights from ongoing research will reveal how arthropod-borne viruses modulate innate immunity including antiviral RNAi. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Digital radiography with a large-scale electronic flat-panel detector vs screen-film radiography: observer preference in clinical skeletal diagnostics

    International Nuclear Information System (INIS)

    Hamers, S.; Freyschmidt, J.; Neitzel, U.

    2001-01-01

    The imaging performance of a recently developed digital flat-panel detector system was compared with conventional screen-film imaging in an observer preference study. In total, 34 image pairs of various regions of the skeleton were obtained in 24 patients; 30 image pairs were included in the study. The conventional images were acquired with 250- and 400-speed screen-film combinations, using the standard technique of our department. Within hours, the digital images were obtained using identical exposure parameters. The digital system employed a large-area (43 x 43 cm) flat-panel detector based on amorphous silicon (Trixell Pixium 4600), integrated in a Bucky table. Six radiologists independently evaluated the image pairs with respect to image latitude, soft tissue rendition, rendition of the periosteal and enosteal border of cortical bone, rendition of cancellous bone and the visibility of potentially present pathological changes, using a subjective five-point scale. The digital images were rated significantly (p=0.001) better than the screen-film images with respect to soft tissue rendition and image latitude. Also the rendition of the cancellous bone and the periosteal and enosteal border of the cortical bone was rated significantly (p=0.05) better for the flat-panel detector. The visibility of pathological lesions was equivalent; only large-area sclerotic lesions (n=2) were seen superiorly on screen-film images. The new digital flat-panel detector based on amorphous silicon appears to be at least equivalent to conventional screen-film combinations for skeletal examinations, and in most respects even superior. (orig.)

  6. Large Scale Screening of Low Cost Ferritic Steel Designs For Advanced Ultra Supercritical Boiler Using First Principles Methods

    Energy Technology Data Exchange (ETDEWEB)

    Ouyang, Lizhi [Tennessee State Univ. Nashville, TN (United States)

    2016-11-29

    Advanced Ultra Supercritical Boiler (AUSC) requires materials that can operate in corrosive environment at temperature and pressure as high as 760°C (or 1400°F) and 5000psi, respectively, while at the same time maintain good ductility at low temperature. We develop automated simulation software tools to enable fast large scale screening studies of candidate designs. While direct evaluation of creep rupture strength and ductility are currently not feasible, properties such as energy, elastic constants, surface energy, interface energy, and stack fault energy can be used to assess their relative ductility and creeping strength. We implemented software to automate the complex calculations to minimize human inputs in the tedious screening studies which involve model structures generation, settings for first principles calculations, results analysis and reporting. The software developed in the project and library of computed mechanical properties of phases found in ferritic steels, many are complex solid solutions estimated for the first time, will certainly help the development of low cost ferritic steel for AUSC.

  7. Emerging strategies for RNA interference (RNAi) applications in insects.

    Science.gov (United States)

    Nandety, Raja Sekhar; Kuo, Yen-Wen; Nouri, Shahideh; Falk, Bryce W

    2015-01-01

    RNA interference (RNAi) in insects is a gene regulatory process that also plays a vital role in the maintenance and in the regulation of host defenses against invading viruses. Small RNAs determine the specificity of the RNAi through precise recognition of their targets. These small RNAs in insects comprise small interfering RNAs (siRNAs), micro RNAs (miRNAs) and Piwi interacting RNAs (piRNAs) of various lengths. In this review, we have explored different forms of the RNAi inducers that are presently in use, and their applications for an effective and efficient fundamental and practical RNAi research with insects. Further, we reviewed trends in next generation sequencing (NGS) technologies and their importance for insect RNAi, including the identification of novel insect targets as well as insect viruses. Here we also describe a rapidly emerging trend of using plant viruses to deliver the RNAi inducer molecules into insects for an efficient RNAi response.

  8. RNAi dynamics in Juvenile Fasciola spp. Liver flukes reveals the persistence of gene silencing in vitro.

    Directory of Open Access Journals (Sweden)

    Paul McVeigh

    2014-09-01

    Full Text Available Fasciola spp. liver fluke cause pernicious disease in humans and animals. Whilst current control is unsustainable due to anthelmintic resistance, gene silencing (RNA interference, RNAi has the potential to contribute to functional validation of new therapeutic targets. The susceptibility of juvenile Fasciola hepatica to double stranded (dsRNA-induced RNAi has been reported. To exploit this we probe RNAi dynamics, penetrance and persistence with the aim of building a robust platform for reverse genetics in liver fluke. We describe development of standardised RNAi protocols for a commercially-available liver fluke strain (the US Pacific North West Wild Strain, validated via robust transcriptional silencing of seven virulence genes, with in-depth experimental optimisation of three: cathepsin L (FheCatL and B (FheCatB cysteine proteases, and a σ-class glutathione transferase (FheσGST.Robust transcriptional silencing of targets in both F. hepatica and Fasciola gigantica juveniles is achievable following exposure to long (200-320 nt dsRNAs or 27 nt short interfering (siRNAs. Although juveniles are highly RNAi-susceptible, they display slower transcript and protein knockdown dynamics than those reported previously. Knockdown was detectable following as little as 4h exposure to trigger (target-dependent and in all cases silencing persisted for ≥25 days following long dsRNA exposure. Combinatorial silencing of three targets by mixing multiple long dsRNAs was similarly efficient. Despite profound transcriptional suppression, we found a significant time-lag before the occurrence of protein suppression; FheσGST and FheCatL protein suppression were only detectable after 9 and 21 days, respectively.In spite of marked variation in knockdown dynamics, we find that a transient exposure to long dsRNA or siRNA triggers robust RNAi penetrance and persistence in liver fluke NEJs supporting the development of multiple-throughput phenotypic screens for control

  9. A high-throughput screening system for barley/powdery mildew interactions based on automated analysis of light micrographs.

    Science.gov (United States)

    Ihlow, Alexander; Schweizer, Patrick; Seiffert, Udo

    2008-01-23

    To find candidate genes that potentially influence the susceptibility or resistance of crop plants to powdery mildew fungi, an assay system based on transient-induced gene silencing (TIGS) as well as transient over-expression in single epidermal cells of barley has been developed. However, this system relies on quantitative microscopic analysis of the barley/powdery mildew interaction and will only become a high-throughput tool of phenomics upon automation of the most time-consuming steps. We have developed a high-throughput screening system based on a motorized microscope which evaluates the specimens fully automatically. A large-scale double-blind verification of the system showed an excellent agreement of manual and automated analysis and proved the system to work dependably. Furthermore, in a series of bombardment experiments an RNAi construct targeting the Mlo gene was included, which is expected to phenocopy resistance mediated by recessive loss-of-function alleles such as mlo5. In most cases, the automated analysis system recorded a shift towards resistance upon RNAi of Mlo, thus providing proof of concept for its usefulness in detecting gene-target effects. Besides saving labor and enabling a screening of thousands of candidate genes, this system offers continuous operation of expensive laboratory equipment and provides a less subjective analysis as well as a complete and enduring documentation of the experimental raw data in terms of digital images. In general, it proves the concept of enabling available microscope hardware to handle challenging screening tasks fully automatically.

  10. Gene silencing in Tribolium castaneum as a tool for the targeted identification of candidate RNAi targets in crop pests.

    Science.gov (United States)

    Knorr, Eileen; Fishilevich, Elane; Tenbusch, Linda; Frey, Meghan L F; Rangasamy, Murugesan; Billion, Andre; Worden, Sarah E; Gandra, Premchand; Arora, Kanika; Lo, Wendy; Schulenberg, Greg; Valverde-Garcia, Pablo; Vilcinskas, Andreas; Narva, Kenneth E

    2018-02-01

    RNAi shows potential as an agricultural technology for insect control, yet, a relatively low number of robust lethal RNAi targets have been demonstrated to control insects of agricultural interest. In the current study, a selection of lethal RNAi target genes from the iBeetle (Tribolium castaneum) screen were used to demonstrate efficacy of orthologous targets in the economically important coleopteran pests Diabrotica virgifera virgifera and Meligethes aeneus. Transcript orthologs of 50 selected genes were analyzed in D. v. virgifera diet-based RNAi bioassays; 21 of these RNAi targets showed mortality and 36 showed growth inhibition. Low dose injection- and diet-based dsRNA assays in T. castaneum and D. v. virgifera, respectively, enabled the identification of the four highly potent RNAi target genes: Rop, dre4, ncm, and RpII140. Maize was genetically engineered to express dsRNA directed against these prioritized candidate target genes. T 0 plants expressing Rop, dre4, or RpII140 RNA hairpins showed protection from D. v. virgifera larval feeding damage. dsRNA targeting Rop, dre4, ncm, and RpII140 in M. aeneus also caused high levels of mortality both by injection and feeding. In summary, high throughput systems for model organisms can be successfully used to identify potent RNA targets for difficult-to-work with agricultural insect pests.

  11. Screen-Space Normal Distribution Function Caching for Consistent Multi-Resolution Rendering of Large Particle Data

    KAUST Repository

    Ibrahim, Mohamed

    2017-08-28

    Molecular dynamics (MD) simulations are crucial to investigating important processes in physics and thermodynamics. The simulated atoms are usually visualized as hard spheres with Phong shading, where individual particles and their local density can be perceived well in close-up views. However, for large-scale simulations with 10 million particles or more, the visualization of large fields-of-view usually suffers from strong aliasing artifacts, because the mismatch between data size and output resolution leads to severe under-sampling of the geometry. Excessive super-sampling can alleviate this problem, but is prohibitively expensive. This paper presents a novel visualization method for large-scale particle data that addresses aliasing while enabling interactive high-quality rendering. We introduce the novel concept of screen-space normal distribution functions (S-NDFs) for particle data. S-NDFs represent the distribution of surface normals that map to a given pixel in screen space, which enables high-quality re-lighting without re-rendering particles. In order to facilitate interactive zooming, we cache S-NDFs in a screen-space mipmap (S-MIP). Together, these two concepts enable interactive, scale-consistent re-lighting and shading changes, as well as zooming, without having to re-sample the particle data. We show how our method facilitates the interactive exploration of real-world large-scale MD simulation data in different scenarios.

  12. Screen-Space Normal Distribution Function Caching for Consistent Multi-Resolution Rendering of Large Particle Data

    KAUST Repository

    Ibrahim, Mohamed; Wickenhauser, Patrick; Rautek, Peter; Reina, Guido; Hadwiger, Markus

    2017-01-01

    Molecular dynamics (MD) simulations are crucial to investigating important processes in physics and thermodynamics. The simulated atoms are usually visualized as hard spheres with Phong shading, where individual particles and their local density can be perceived well in close-up views. However, for large-scale simulations with 10 million particles or more, the visualization of large fields-of-view usually suffers from strong aliasing artifacts, because the mismatch between data size and output resolution leads to severe under-sampling of the geometry. Excessive super-sampling can alleviate this problem, but is prohibitively expensive. This paper presents a novel visualization method for large-scale particle data that addresses aliasing while enabling interactive high-quality rendering. We introduce the novel concept of screen-space normal distribution functions (S-NDFs) for particle data. S-NDFs represent the distribution of surface normals that map to a given pixel in screen space, which enables high-quality re-lighting without re-rendering particles. In order to facilitate interactive zooming, we cache S-NDFs in a screen-space mipmap (S-MIP). Together, these two concepts enable interactive, scale-consistent re-lighting and shading changes, as well as zooming, without having to re-sample the particle data. We show how our method facilitates the interactive exploration of real-world large-scale MD simulation data in different scenarios.

  13. Large scale electrolysers

    International Nuclear Information System (INIS)

    B Bello; M Junker

    2006-01-01

    Hydrogen production by water electrolysis represents nearly 4 % of the world hydrogen production. Future development of hydrogen vehicles will require large quantities of hydrogen. Installation of large scale hydrogen production plants will be needed. In this context, development of low cost large scale electrolysers that could use 'clean power' seems necessary. ALPHEA HYDROGEN, an European network and center of expertise on hydrogen and fuel cells, has performed for its members a study in 2005 to evaluate the potential of large scale electrolysers to produce hydrogen in the future. The different electrolysis technologies were compared. Then, a state of art of the electrolysis modules currently available was made. A review of the large scale electrolysis plants that have been installed in the world was also realized. The main projects related to large scale electrolysis were also listed. Economy of large scale electrolysers has been discussed. The influence of energy prices on the hydrogen production cost by large scale electrolysis was evaluated. (authors)

  14. RNAi and retroviruses: are they in RISC?

    Science.gov (United States)

    Vasselon, Thierry; Bouttier, Manuella; Saumet, Anne; Lecellier, Charles-Henri

    2013-02-01

    RNA interference (RNAi) is a potent cellular system against viruses in various organisms. Although common traits are observed in plants, insects, and nematodes, the situation observed in mammals appears more complex. In mammalian somatic cells, RNAi is implicated in endonucleolytic cleavage mediated by artificially delivered small interfering RNAs (siRNAs) as well as in translation repression mediated by microRNAs (miRNAs). Because siRNAs and miRNAs recognize viral mRNAs, RNAi inherently limits virus production and participates in antiviral defense. However, several observations made in the cases of hepatitis C virus and retroviruses (including the human immunodeficiency virus and the primate foamy virus) bring evidence that this relationship is much more complex and that certain components of the RNAi effector complex [called the RNA-induced silencing complex (RISC)], such as AGO2, are also required for viral replication. Here, we summarize recent discoveries that have revealed this dual implication in virus biology. We further discuss their potential implications for the functions of RNAi-related proteins, with special emphasis on retrotransposition and genome stability.

  15. A cell spot microarray method for production of high density siRNA transfection microarrays

    Directory of Open Access Journals (Sweden)

    Mpindi John-Patrick

    2011-03-01

    Full Text Available Abstract Background High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible. Results Here, we describe the optimization of a miniaturized cell spot microarray (CSMA method, which facilitates utilization of the transfection microarray technique for disparate RNAi analyses. To promote rapid adaptation of the method, the concept has been tested with a panel of 92 adherent cell types, including primary human cells. We demonstrate the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells. Conclusions The CSMA method facilitates reproducible preparation of highly parallel cell microarrays for large-scale gene knockdown analyses. This will be critical towards expanding the cell based functional genetic screens to include more RNAi constructs, allow combinatorial RNAi analyses, multi-parametric phenotypic readouts or comparative analysis of many different cell types.

  16. Repression of germline RNAi pathways in somatic cells by retinoblastoma pathway chromatin complexes.

    Directory of Open Access Journals (Sweden)

    Xiaoyun Wu

    Full Text Available The retinoblastoma (Rb tumor suppressor acts with a number of chromatin cofactors in a wide range of species to suppress cell proliferation. The Caenorhabditis elegans retinoblastoma gene and many of these cofactors, called synMuv B genes, were identified in genetic screens for cell lineage defects caused by growth factor misexpression. Mutations in many synMuv B genes, including lin-35/Rb, also cause somatic misexpression of the germline RNA processing P granules and enhanced RNAi. We show here that multiple small RNA components, including a set of germline-specific Argonaute genes, are misexpressed in the soma of many synMuv B mutant animals, revealing one node for enhanced RNAi. Distinct classes of synMuv B mutants differ in the subcellular architecture of their misexpressed P granules, their profile of misexpressed small RNA and P granule genes, as well as their enhancement of RNAi and the related silencing of transgenes. These differences define three classes of synMuv B genes, representing three chromatin complexes: a LIN-35/Rb-containing DRM core complex, a SUMO-recruited Mec complex, and a synMuv B heterochromatin complex, suggesting that intersecting chromatin pathways regulate the repression of small RNA and P granule genes in the soma and the potency of RNAi. Consistent with this, the DRM complex and the synMuv B heterochromatin complex were genetically additive and displayed distinct antagonistic interactions with the MES-4 histone methyltransferase and the MRG-1 chromodomain protein, two germline chromatin regulators required for the synMuv phenotype and the somatic misexpression of P granule components. Thus intersecting synMuv B chromatin pathways conspire with synMuv B suppressor chromatin factors to regulate the expression of small RNA pathway genes, which enables heightened RNAi response. Regulation of small RNA pathway genes by human retinoblastoma may also underlie its role as a tumor suppressor gene.

  17. New genes tied to endocrine, metabolic, and dietary regulation of lifespan from a Caenorhabditis elegans genomic RNAi screen.

    Directory of Open Access Journals (Sweden)

    Malene Hansen

    2005-07-01

    Full Text Available Most of our knowledge about the regulation of aging comes from mutants originally isolated for other phenotypes. To ask whether our current view of aging has been affected by selection bias, and to deepen our understanding of known longevity pathways, we screened a genomic Caenorhabditis elegans RNAi library for clones that extend lifespan. We identified 23 new longevity genes affecting signal transduction, the stress response, gene expression, and metabolism and assigned these genes to specific longevity pathways. Our most important findings are (i that dietary restriction extends C. elegans' lifespan by down-regulating expression of key genes, including a gene required for methylation of many macromolecules, (ii that integrin signaling is likely to play a general, evolutionarily conserved role in lifespan regulation, and (iii that specific lipophilic hormones may influence lifespan in a DAF-16/FOXO-dependent fashion. Surprisingly, of the new genes that have conserved sequence domains, only one could not be associated with a known longevity pathway. Thus, our current view of the genetics of aging has probably not been distorted substantially by selection bias.

  18. New Genes Tied to Endocrine, Metabolic, and Dietary Regulation of Lifespan from a Caenorhabditis elegans Genomic RNAi Screen.

    Directory of Open Access Journals (Sweden)

    2005-07-01

    Full Text Available Most of our knowledge about the regulation of aging comes from mutants originally isolated for other phenotypes. To ask whether our current view of aging has been affected by selection bias, and to deepen our understanding of known longevity pathways, we screened a genomic Caenorhabditis elegans RNAi library for clones that extend lifespan. We identified 23 new longevity genes affecting signal transduction, the stress response, gene expression, and metabolism and assigned these genes to specific longevity pathways. Our most important findings are (i that dietary restriction extends C. elegans' lifespan by down-regulating expression of key genes, including a gene required for methylation of many macromolecules, (ii that integrin signaling is likely to play a general, evolutionarily conserved role in lifespan regulation, and (iii that specific lipophilic hormones may influence lifespan in a DAF-16/FOXO-dependent fashion. Surprisingly, of the new genes that have conserved sequence domains, only one could not be associated with a known longevity pathway. Thus, our current view of the genetics of aging has probably not been distorted substantially by selection bias.

  19. Towards a durable RNAi gene therapy for HIV-AIDS

    NARCIS (Netherlands)

    Berkhout, Ben; ter Brake, Olivier

    2009-01-01

    Background: RNA interference (RNAi) can be employed as a potent antiviral mechanism Objective: To discuss RNAi approaches to target pathogenic human viruses causing acute or chronic infections, in particular RNAi gene therapy against HIV-1. Methods: A review of relevant literature.

  20. Identifiability in N-mixture models: a large-scale screening test with bird data.

    Science.gov (United States)

    Kéry, Marc

    2018-02-01

    Binomial N-mixture models have proven very useful in ecology, conservation, and monitoring: they allow estimation and modeling of abundance separately from detection probability using simple counts. Recently, doubts about parameter identifiability have been voiced. I conducted a large-scale screening test with 137 bird data sets from 2,037 sites. I found virtually no identifiability problems for Poisson and zero-inflated Poisson (ZIP) binomial N-mixture models, but negative-binomial (NB) models had problems in 25% of all data sets. The corresponding multinomial N-mixture models had no problems. Parameter estimates under Poisson and ZIP binomial and multinomial N-mixture models were extremely similar. Identifiability problems became a little more frequent with smaller sample sizes (267 and 50 sites), but were unaffected by whether the models did or did not include covariates. Hence, binomial N-mixture model parameters with Poisson and ZIP mixtures typically appeared identifiable. In contrast, NB mixtures were often unidentifiable, which is worrying since these were often selected by Akaike's information criterion. Identifiability of binomial N-mixture models should always be checked. If problems are found, simpler models, integrated models that combine different observation models or the use of external information via informative priors or penalized likelihoods, may help. © 2017 by the Ecological Society of America.

  1. A genome-scale RNA-interference screen identifies RRAS signaling as a pathologic feature of Huntington's disease.

    Directory of Open Access Journals (Sweden)

    John P Miller

    Full Text Available A genome-scale RNAi screen was performed in a mammalian cell-based assay to identify modifiers of mutant huntingtin toxicity. Ontology analysis of suppressor data identified processes previously implicated in Huntington's disease, including proteolysis, glutamate excitotoxicity, and mitochondrial dysfunction. In addition to established mechanisms, the screen identified multiple components of the RRAS signaling pathway as loss-of-function suppressors of mutant huntingtin toxicity in human and mouse cell models. Loss-of-function in orthologous RRAS pathway members also suppressed motor dysfunction in a Drosophila model of Huntington's disease. Abnormal activation of RRAS and a down-stream effector, RAF1, was observed in cellular models and a mouse model of Huntington's disease. We also observe co-localization of RRAS and mutant huntingtin in cells and in mouse striatum, suggesting that activation of R-Ras may occur through protein interaction. These data indicate that mutant huntingtin exerts a pathogenic effect on this pathway that can be corrected at multiple intervention points including RRAS, FNTA/B, PIN1, and PLK1. Consistent with these results, chemical inhibition of farnesyltransferase can also suppress mutant huntingtin toxicity. These data suggest that pharmacological inhibition of RRAS signaling may confer therapeutic benefit in Huntington's disease.

  2. Role of optometry school in single day large scale school vision testing

    Science.gov (United States)

    Anuradha, N; Ramani, Krishnakumar

    2015-01-01

    Background: School vision testing aims at identification and management of refractive errors. Large-scale school vision testing using conventional methods is time-consuming and demands a lot of chair time from the eye care professionals. A new strategy involving a school of optometry in single day large scale school vision testing is discussed. Aim: The aim was to describe a new approach of performing vision testing of school children on a large scale in a single day. Materials and Methods: A single day vision testing strategy was implemented wherein 123 members (20 teams comprising optometry students and headed by optometrists) conducted vision testing for children in 51 schools. School vision testing included basic vision screening, refraction, frame measurements, frame choice and referrals for other ocular problems. Results: A total of 12448 children were screened, among whom 420 (3.37%) were identified to have refractive errors. 28 (1.26%) children belonged to the primary, 163 to middle (9.80%), 129 (4.67%) to secondary and 100 (1.73%) to the higher secondary levels of education respectively. 265 (2.12%) children were referred for further evaluation. Conclusion: Single day large scale school vision testing can be adopted by schools of optometry to reach a higher number of children within a short span. PMID:25709271

  3. RNAi technology: a new platform for crop pest control.

    Science.gov (United States)

    Mamta, B; Rajam, M V

    2017-07-01

    The insect pests are big threat in meeting the food demands for future generation. The present pest control strategies, including the existing transgenic approaches show certain limitations and are not completely successful in limiting the insect pests. However, the sequence-specific gene silencing via RNA interference (RNAi) holds a great promise for effective management of agricultural pests. RNAi is naturally occurring conserved process responsible for gene regulation and defense against pathogens. The efficacy of RNAi varies among different insect orders and also depends upon various factors, including the target gene selection, method of dsRNAs delivery, expression of dsRNAs and presence of off-target effects. RNAi-mediated silencing of different insect genes involved in various physiological processes was found to be detrimental to insects growth, development and survival. In this article, we have reviewed the potential of RNAi-based strategies for effective management of insect pests. We have also discussed the various parameters, which are to be considered for host-induced RNAi-mediated control of insect pests without producing any effect on non-target organisms and environment.

  4. An RNAi-mediated screen identifies novel targets for next-generation antiepileptic drugs based on increased expression of the homeostatic regulator pumilio.

    Science.gov (United States)

    Lin, Wei-Hsiang; He, Miaomiao; Fan, Yuen Ngan; Baines, Richard A

    2018-05-02

    Despite availability of a diverse range of anti-epileptic drugs (AEDs), only about two-thirds of epilepsy patients respond well to drug treatment. Thus, novel targets are required to catalyse the design of next-generation AEDs. Manipulation of neuron firing-rate homoeostasis, through enhancing Pumilio (Pum) activity, has been shown to be potently anticonvulsant in Drosophila. In this study, we performed a genome-wide RNAi screen in S2R + cells, using a luciferase-based dPum activity reporter and identified 1166 genes involved in dPum regulation. Of these genes, we focused on 699 genes that, on knock-down, potentiate dPum activity/expression. Of this subgroup, 101 genes are activity-dependent based on comparison with genes previously identified as activity-dependent by RNA-sequencing. Functional cluster analysis shows these genes are enriched in pathways involved in DNA damage, regulation of cell cycle and proteasomal protein catabolism. To test for anticonvulsant activity, we utilised an RNA-interference approach in vivo. RNAi-mediated knockdown showed that 57/101 genes (61%) are sufficient to significantly reduce seizure duration in the characterized seizure mutant, para bss . We further show that chemical inhibitors of protein products of some of the genes targeted are similarly anticonvulsant. Finally, to establish whether the anticonvulsant activity of identified compounds results from increased dpum transcription, we performed a luciferase-based assay to monitor dpum promoter activity. Third instar larvae exposed to sodium fluoride, gemcitabine, metformin, bestatin, WP1066 or valproic acid all showed increased dpum promoter activity. Thus, this study validates Pum as a favourable target for AED design and, moreover, identifies a number of lead compounds capable of increasing the expression of this homeostatic regulator.

  5. Decision aid on breast cancer screening reduces attendance rate: results of a large-scale, randomized, controlled study by the DECIDEO group

    Science.gov (United States)

    Bourmaud, Aurelie; Soler-Michel, Patricia; Oriol, Mathieu; Regnier, Véronique; Tinquaut, Fabien; Nourissat, Alice; Bremond, Alain; Moumjid, Nora; Chauvin, Franck

    2016-01-01

    Controversies regarding the benefits of breast cancer screening programs have led to the promotion of new strategies taking into account individual preferences, such as decision aid. The aim of this study was to assess the impact of a decision aid leaflet on the participation of women invited to participate in a national breast cancer screening program. This Randomized, multicentre, controlled trial. Women aged 50 to 74 years, were randomly assigned to receive either a decision aid or the usual invitation letter. Primary outcome was the participation rate 12 months after the invitation. 16 000 women were randomized and 15 844 included in the modified intention-to-treat analysis. The participation rate in the intervention group was 40.25% (3174/7885 women) compared with 42.13% (3353/7959) in the control group (p = 0.02). Previous attendance for screening (RR = 6.24; [95%IC: 5.75-6.77]; p < 0.0001) and medium household income (RR = 1.05; [95%IC: 1.01-1.09]; p = 0.0074) were independently associated with attendance for screening. This large-scale study demonstrates that the decision aid reduced the participation rate. The decision aid activate the decision making process of women toward non-attendance to screening. These results show the importance of promoting informed patient choices, especially when those choices cannot be anticipated. PMID:26883201

  6. RNAiFold: a web server for RNA inverse folding and molecular design.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

    2013-07-01

    Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

  7. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells

    OpenAIRE

    Hummon Amanda B; Pitt Jason J; Camps Jordi; Emons Georg; Skube Susan B; Huppi Konrad; Jones Tamara L; Beissbarth Tim; Kramer Frank; Grade Marian; Difilippantonio Michael J; Ried Thomas; Caplen Natasha J

    2012-01-01

    Abstract Background Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. Results A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently C...

  8. Progress on RNAi-based molecular medicines

    OpenAIRE

    Chen, Jing; Xie, Jianping

    2012-01-01

    Jing Chen, Jianping XieInstitute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, ChinaAbstract: RNA interference (RNAi) is a promising strategy to suppress the expression of disease-relevant genes and induce post-transcriptional gene silencing. Their simplicity and stability endow RNAi with great advantages in molecular medicine. Several RNA...

  9. Vitellogenin RNAi halts ovarian growth and diverts reproductive proteins and lipids in young grasshoppers.

    Science.gov (United States)

    Tokar, Derek R; Veleta, Katherine A; Canzano, Joseph; Hahn, Daniel A; Hatle, John D

    2014-11-01

    Reduced reproduction extends lifespan of females in many animals. To test the effects of reproduction on storage of macronutrients, we block reproductive output in the lubber grasshopper by injecting RNAi against the precursor to egg-yolk protein, vitellogenin, in early adulthood. Controls were injected with either buffer or RNAi against the major storage protein in the hemolymph, hexamerin-90. Vitellogenin RNAi greatly reduced both levels of mRNA for vitellogenin and ovarian growth, in comparison to both controls. Fat body mass was increased upon vitellogenin RNAi, but concentrations of the three hexameric storage proteins from the hemolymph were not. Surprisingly, hemolymph vitellogenin levels were increased upon vitellogenin RNAi. Total reproductive protein (hemolymph vitellogenin plus ovarian vitellin) was unchanged by vitellogenin RNAi, as reproductive protein was diverted to the hemolymph. Similarly, the increased lipid storage upon vitellogenin RNAi was largely attributable to the reduction in lipid in the ovary, due to decreased ovarian growth. A BLAST search revealed that the 515 bp sequence of vitellogenin used for RNAi had three 11 bp regions identical to the vitellogenin receptor of the cockroach Leucophaea maderae. This suggests that our treatment, in addition to reducing levels of vitellogenin transcript, may have also blocked transport of vitellogenin from the hemolymph to the ovary. This would be consistent with halted ovarian growth simultaneous with high levels of vitellogenin in the hemolymph. Nonetheless, the accumulation of vitellogenin, instead of hexameric storage proteins, is inconsistent with a simple model of the trade-off between reproduction and storage. This was observed in young females; future studies will address whether investment of proteins may shift to the soma as individuals age. Overall, our results suggest that blockage of reproduction in young grasshoppers redirects lipids to storage and reproductive proteins to the hemolymph

  10. Evaluation of a large-scale tuberculosis contact investigation in the Netherlands

    NARCIS (Netherlands)

    Borgen, K.; Koster, B.; Meijer, H.; Kuyvenhoven, V.; van der Sande, M.; Cobelens, F.

    2008-01-01

    The aim of the present study was to evaluate yield and effectiveness of a large-scale contact investigation around a supermarket employee with infectious tuberculosis. Supermarket customers were screened by tuberculin skin test (TST) and/or radiography, depending on individual characteristics. The

  11. Disinformative data in large-scale hydrological modelling

    Directory of Open Access Journals (Sweden)

    A. Kauffeldt

    2013-07-01

    Full Text Available Large-scale hydrological modelling has become an important tool for the study of global and regional water resources, climate impacts, and water-resources management. However, modelling efforts over large spatial domains are fraught with problems of data scarcity, uncertainties and inconsistencies between model forcing and evaluation data. Model-independent methods to screen and analyse data for such problems are needed. This study aimed at identifying data inconsistencies in global datasets using a pre-modelling analysis, inconsistencies that can be disinformative for subsequent modelling. The consistency between (i basin areas for different hydrographic datasets, and (ii between climate data (precipitation and potential evaporation and discharge data, was examined in terms of how well basin areas were represented in the flow networks and the possibility of water-balance closure. It was found that (i most basins could be well represented in both gridded basin delineations and polygon-based ones, but some basins exhibited large area discrepancies between flow-network datasets and archived basin areas, (ii basins exhibiting too-high runoff coefficients were abundant in areas where precipitation data were likely affected by snow undercatch, and (iii the occurrence of basins exhibiting losses exceeding the potential-evaporation limit was strongly dependent on the potential-evaporation data, both in terms of numbers and geographical distribution. Some inconsistencies may be resolved by considering sub-grid variability in climate data, surface-dependent potential-evaporation estimates, etc., but further studies are needed to determine the reasons for the inconsistencies found. Our results emphasise the need for pre-modelling data analysis to identify dataset inconsistencies as an important first step in any large-scale study. Applying data-screening methods before modelling should also increase our chances to draw robust conclusions from subsequent

  12. RNAi strategies to suppress insects of fruit and tree crops

    Science.gov (United States)

    Use of ribonucleic acid interference, RNAi, to reduce plant feeding Hemiptera in fruit tree and grapevines. The successful use of RNAi strategies to reduce insect pests, psyllids and leafhoppers was demonstrated. An RNAi bioassay which absorbs dsRNA into plant tissues provided up to 40 days of act...

  13. Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

    Science.gov (United States)

    Schneider, Nadine; Hindle, Sally; Lange, Gudrun; Klein, Robert; Albrecht, Jürgen; Briem, Hans; Beyer, Kristin; Claußen, Holger; Gastreich, Marcus; Lemmen, Christian; Rarey, Matthias

    2012-06-01

    The HYDE scoring function consistently describes hydrogen bonding, the hydrophobic effect and desolvation. It relies on HYdration and DEsolvation terms which are calibrated using octanol/water partition coefficients of small molecules. We do not use affinity data for calibration, therefore HYDE is generally applicable to all protein targets. HYDE reflects the Gibbs free energy of binding while only considering the essential interactions of protein-ligand complexes. The greatest benefit of HYDE is that it yields a very intuitive atom-based score, which can be mapped onto the ligand and protein atoms. This allows the direct visualization of the score and consequently facilitates analysis of protein-ligand complexes during the lead optimization process. In this study, we validated our new scoring function by applying it in large-scale docking experiments. We could successfully predict the correct binding mode in 93% of complexes in redocking calculations on the Astex diverse set, while our performance in virtual screening experiments using the DUD dataset showed significant enrichment values with a mean AUC of 0.77 across all protein targets with little or no structural defects. As part of these studies, we also carried out a very detailed analysis of the data that revealed interesting pitfalls, which we highlight here and which should be addressed in future benchmark datasets.

  14. Phylogenetic origin and diversification of RNAi pathway genes in insects

    DEFF Research Database (Denmark)

    Dowling, Daniel; Pauli, Thomas; Donath, Alexander

    2016-01-01

    RNAinterference (RNAi) refers tothe set ofmolecular processes foundin eukaryotic organisms in which smallRNAmolecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense...... against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes...... across 100 insect species, encompassing all currently recognized insect orders. We inferred the phylogenetic origin of insect-specific RNAi pathway genes and also identified several hitherto unrecorded gene expansions using whole-body transcriptome data from the international 1KITE (1000 Insect...

  15. The status of RNAi-based transgenic research in plant nematology

    Directory of Open Access Journals (Sweden)

    Tushar Kanti Dutta

    2015-01-01

    Full Text Available With the understanding of nematode-plant interactions at the molecular level, new avenues for engineering resistance have opened up, with RNA interference being one of them. Induction of RNAi by delivering double-stranded RNA (dsRNA has been very successful in the model non-parasitic nematode, Caenorhabditis elegans, while in plant nematodes, dsRNA delivery has been accomplished by soaking nematodes with dsRNA solution mixed with synthetic neurostimulants. The success of in vitro RNAi of target genes has inspired the use of in planta delivery of dsRNA to feeding nematodes. The most convincing success of host-delivered RNAi has been achieved against root-knot nematodes. Plant-mediated RNAi has been shown to lead to the specific down-regulation of target genes in invading nematodes, which had a profound effect on nematode development. RNAi-based transgenics are advantageous as they do not produce any functional foreign proteins and target organisms in a sequence-specific manner. Although the development of RNAi-based transgenics against plant nematodes is still in the preliminary stage, they offer novel management strategy for the future.

  16. Liver diseases: A major, neglected global public health problem requiring urgent actions and large-scale screening.

    Science.gov (United States)

    Marcellin, Patrick; Kutala, Blaise K

    2018-02-01

    CLDs represent an important, and certainly underestimated, global public health problem. CLDs are highly prevalent and silent, related to different, sometimes associated causes. The distribution of the causes of these diseases is slowly changing, and within the next decade, the proportion of virus-induced CLDs will certainly decrease significantly while the proportion of NASH will increase. There is an urgent need for effective global actions including education, prevention and early diagnosis to manage and treat CLDs, thus preventing cirrhosis-related morbidity and mortality. Our role is to increase the awareness of the public, healthcare professionals and public health authorities to encourage active policies for early management that will decrease the short- and long-term public health burden of these diseases. Because necroinflammation is the key mechanism in the progression of CLDs, it should be detected early. Thus, large-scale screening for CLDs is needed. ALT levels are an easy and inexpensive marker of liver necroinflammation and could be the first-line tool in this process. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  17. Beyond insects: current status, achievements and future perspectives of RNAi in mite pests.

    Science.gov (United States)

    Niu, Jinzhi; Shen, Guangmao; Christiaens, Olivier; Smagghe, Guy; He, Lin; Wang, Jinjun

    2018-05-11

    Mites comprise a group of key agricultural pests on a wide range of crops. They cause harm through feeding on the plant and transferring dangerous pathogens, and the rapid evolution of pesticide resistance in mites highlights the need for novel control methods. Currently, RNA interference (RNAi) shows a great potential for insect pest control. Here, we review the literature associated with RNAi in mite pests. We discuss different target genes and RNAi efficiency in various mite species, a promising Varroa control program through RNAi, the synergy of RNAi with plant defense mechanisms and microorganisms, and the current understandings of systemic movement of dsRNA. Based on this, we can conclude that there is a clear potential for an RNAi-based mite control application but further research on several aspects is needed, including: (i) the factors influencing the RNAi efficiency, (ii) the mechanism of environmental RNAi and cross-kingdom dsRNA trafficking, (iii) the mechanism of possible systemic and parental RNAi, and (iv) non-target effects, specifically in predatory mites, should be considered during the RNAi target selection. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  18. The effectiveness of RNAi in Caenorhabditis elegans is maintained during spaceflight.

    Directory of Open Access Journals (Sweden)

    Timothy Etheridge

    Full Text Available BACKGROUND: Overcoming spaceflight-induced (pathophysiologic adaptations is a major challenge preventing long-term deep space exploration. RNA interference (RNAi has emerged as a promising therapeutic for combating diseases on Earth; however the efficacy of RNAi in space is currently unknown. METHODS: Caenorhabditis elegans were prepared in liquid media on Earth using standard techniques and treated acutely with RNAi or a vector control upon arrival in Low Earth Orbit. After culturing during 4 and 8 d spaceflight, experiments were stopped by freezing at -80°C until analysis by mRNA and microRNA array chips, microscopy and Western blot on return to Earth. Ground controls (GC on Earth were simultaneously grown under identical conditions. RESULTS: After 8 d spaceflight, mRNA expression levels of components of the RNAi machinery were not different from that in GC (e.g., Dicer, Argonaute, Piwi; P>0.05. The expression of 228 microRNAs, of the 232 analysed, were also unaffected during 4 and 8 d spaceflight (P>0.05. In spaceflight, RNAi against green fluorescent protein (gfp reduced chromosomal gfp expression in gonad tissue, which was not different from GC. RNAi against rbx-1 also induced abnormal chromosome segregation in the gonad during spaceflight as on Earth. Finally, culture in RNAi against lysosomal cathepsins prevented degradation of the muscle-specific α-actin protein in both spaceflight and GC conditions. CONCLUSIONS: Treatment with RNAi works as effectively in the space environment as on Earth within multiple tissues, suggesting RNAi may provide an effective tool for combating spaceflight-induced pathologies aboard future long-duration space missions. Furthermore, this is the first demonstration that RNAi can be utilised to block muscle protein degradation, both on Earth and in space.

  19. RNAi technology extends its reach: Engineering plant resistance ...

    African Journals Online (AJOL)

    RNA interference (RNAi) is a homology-dependent gene silencing technology that is initiated by double stranded RNA (dsRNA). It has emerged as a genetic tool for engineering plants resistance against prokaryotic pathogens such as virus and bacteria. Recent studies broaden the role of RNAi, and many successful ...

  20. The Role of RNA Interference (RNAi in Arbovirus-Vector Interactions

    Directory of Open Access Journals (Sweden)

    Carol D. Blair

    2015-02-01

    Full Text Available RNA interference (RNAi was shown over 18 years ago to be a mechanism by which arbovirus replication and transmission could be controlled in arthropod vectors. During the intervening period, research on RNAi has defined many of the components and mechanisms of this antiviral pathway in arthropods, yet a number of unexplored questions remain. RNAi refers to RNA-mediated regulation of gene expression. Originally, the term described silencing of endogenous genes by introduction of exogenous double-stranded (dsRNA with the same sequence as the gene to be silenced. Further research has shown that RNAi comprises three gene regulation pathways that are mediated by small RNAs: the small interfering (siRNA, micro (miRNA, and Piwi-interacting (piRNA pathways. The exogenous (exo-siRNA pathway is now recognized as a major antiviral innate immune response of arthropods. More recent studies suggest that the piRNA and miRNA pathways might also have important roles in arbovirus-vector interactions. This review will focus on current knowledge of the role of the exo-siRNA pathway as an arthropod vector antiviral response and on emerging research into vector piRNA and miRNA pathway modulation of arbovirus-vector interactions. Although it is assumed that arboviruses must evade the vector’s antiviral RNAi response in order to maintain their natural transmission cycles, the strategies by which this is accomplished are not well defined. RNAi is also an important tool for arthropod gene knock-down in functional genomics studies and in development of arbovirus-resistant mosquito populations. Possible arbovirus strategies for evasion of RNAi and applications of RNAi in functional genomics analysis and arbovirus transmission control will also be reviewed.

  1. RNAi nanomedicines: challenges and opportunities within the immune system

    International Nuclear Information System (INIS)

    Weinstein, Shiri; Peer, Dan

    2010-01-01

    RNAi, as a novel therapeutic modality, has an enormous potential to bring the era of personalized medicine one step further from notion into reality. However, delivery of RNAi effector molecules into their target tissues and cells remain extremely challenging. Major attempts have been made in recent years to develop sophisticated nanocarriers that could overcome these hurdles. This review will present the recent progress with the challenges and opportunities in this emerging field, focusing mostly on the in vivo applications with special emphasis on the strategies for RNAi delivery into immune cells. (topical review)

  2. RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe

    International Nuclear Information System (INIS)

    Smialowska, Agata; Djupedal, Ingela; Wang, Jingwen; Kylsten, Per; Swoboda, Peter; Ekwall, Karl

    2014-01-01

    Highlights: • Protein coding genes accumulate anti-sense sRNAs in fission yeast S. pombe. • RNAi represses protein-coding genes in S. pombe. • RNAi-mediated gene repression is post-transcriptional. - Abstract: RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe

  3. RNAi technologies in agricultural biotechnology: The Toxicology Forum 40th Annual Summer Meeting.

    Science.gov (United States)

    Sherman, James H; Munyikwa, Tichafa; Chan, Stephen Y; Petrick, Jay S; Witwer, Kenneth W; Choudhuri, Supratim

    2015-11-01

    During the 40th Annual Meeting of The Toxicology Forum, the current and potential future science, regulations, and politics of agricultural biotechnology were presented and discussed. The meeting session described herein focused on the technology of RNA interference (RNAi) in agriculture. The general process by which RNAi works, currently registered RNAi-based plant traits, example RNAi-based traits in development, potential use of double stranded RNA (dsRNA) as topically applied pesticide active ingredients, research related to the safety of RNAi, biological barriers to ingested dsRNA, recent regulatory RNAi science reviews, and regulatory considerations related to the use of RNAi in agriculture were discussed. Participants generally agreed that the current regulatory framework is robust and appropriate for evaluating the safety of RNAi employed in agricultural biotechnology and were also supportive of the use of RNAi to develop improved crop traits. However, as with any emerging technology, the potential range of future products, potential future regulatory frameworks, and public acceptance of the technology will continue to evolve. As such, continuing dialogue was encouraged to promote education of consumers and science-based regulations. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Citrus tristeza virus-based RNAi in citrus plants induces gene silencing in Diaphorina citri, a phloem-sap sucking insect vector of citrus greening disease (Huanglongbing).

    Science.gov (United States)

    Hajeri, Subhas; Killiny, Nabil; El-Mohtar, Choaa; Dawson, William O; Gowda, Siddarame

    2014-04-20

    A transient expression vector based on Citrus tristeza virus (CTV) is unusually stable. Because of its stability it is being considered for use in the field to control Huanglongbing (HLB), which is caused by Candidatus Liberibacter asiaticus (CLas) and vectored by Asian citrus psyllid, Diaphorina citri. In the absence of effective control strategies for CLas, emphasis has been on control of D. citri. Coincident cohabitation in phloem tissue by CLas, D. citri and CTV was exploited to develop a novel method to mitigate HLB through RNA interference (RNAi). Since CTV has three RNA silencing suppressors, it was not known if CTV-based vector could induce RNAi in citrus. Yet, expression of sequences targeting citrus phytoene desaturase gene by CTV-RNAi resulted in photo-bleaching phenotype. CTV-RNAi vector, engineered with truncated abnormal wing disc (Awd) gene of D. citri, induced altered Awd expression when silencing triggers ingested by feeding D. citri nymphs. Decreased Awd in nymphs resulted in malformed-wing phenotype in adults and increased adult mortality. This impaired ability of D. citri to fly would potentially limit the successful vectoring of CLas bacteria between citrus trees in the grove. CTV-RNAi vector would be relevant for fast-track screening of candidate sequences for RNAi-mediated pest control. Copyright © 2014. Published by Elsevier B.V.

  5. Large Scale Gaussian Processes for Atmospheric Parameter Retrieval and Cloud Screening

    Science.gov (United States)

    Camps-Valls, G.; Gomez-Chova, L.; Mateo, G.; Laparra, V.; Perez-Suay, A.; Munoz-Mari, J.

    2017-12-01

    Current Earth-observation (EO) applications for image classification have to deal with an unprecedented big amount of heterogeneous and complex data sources. Spatio-temporally explicit classification methods are a requirement in a variety of Earth system data processing applications. Upcoming missions such as the super-spectral Copernicus Sentinels EnMAP and FLEX will soon provide unprecedented data streams. Very high resolution (VHR) sensors like Worldview-3 also pose big challenges to data processing. The challenge is not only attached to optical sensors but also to infrared sounders and radar images which increased in spectral, spatial and temporal resolution. Besides, we should not forget the availability of the extremely large remote sensing data archives already collected by several past missions, such ENVISAT, Cosmo-SkyMED, Landsat, SPOT, or Seviri/MSG. These large-scale data problems require enhanced processing techniques that should be accurate, robust and fast. Standard parameter retrieval and classification algorithms cannot cope with this new scenario efficiently. In this work, we review the field of large scale kernel methods for both atmospheric parameter retrieval and cloud detection using infrared sounding IASI data and optical Seviri/MSG imagery. We propose novel Gaussian Processes (GPs) to train problems with millions of instances and high number of input features. Algorithms can cope with non-linearities efficiently, accommodate multi-output problems, and provide confidence intervals for the predictions. Several strategies to speed up algorithms are devised: random Fourier features and variational approaches for cloud classification using IASI data and Seviri/MSG, and engineered randomized kernel functions and emulation in temperature, moisture and ozone atmospheric profile retrieval from IASI as a proxy to the upcoming MTG-IRS sensor. Excellent compromise between accuracy and scalability are obtained in all applications.

  6. RNAi-based silencing of genes encoding the vacuolar- ATPase ...

    African Journals Online (AJOL)

    RNAi-based silencing of genes encoding the vacuolar- ATPase subunits a and c in pink bollworm (Pectinophora gossypiella). Ahmed M. A. Mohammed. Abstract. RNA interference is a post- transcriptional gene regulation mechanism that is predominantly found in eukaryotic organisms. RNAi demonstrated a successful ...

  7. Large-scale solar purchasing

    International Nuclear Information System (INIS)

    1999-01-01

    The principal objective of the project was to participate in the definition of a new IEA task concerning solar procurement (''the Task'') and to assess whether involvement in the task would be in the interest of the UK active solar heating industry. The project also aimed to assess the importance of large scale solar purchasing to UK active solar heating market development and to evaluate the level of interest in large scale solar purchasing amongst potential large scale purchasers (in particular housing associations and housing developers). A further aim of the project was to consider means of stimulating large scale active solar heating purchasing activity within the UK. (author)

  8. A comprehensive platform for highly multiplexed mammalian functional genetic screens

    Directory of Open Access Journals (Sweden)

    Cheung-Ong Kahlin

    2011-05-01

    Full Text Available Abstract Background Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens. Results Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens. Conclusion Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray based deconvolution methods.

  9. RNAi and Antiviral Defense in the Honey Bee

    Science.gov (United States)

    Brutscher, Laura M.; Flenniken, Michelle L.

    2015-01-01

    Honey bees play an important agricultural and ecological role as pollinators of numerous agricultural crops and other plant species. Therefore, investigating the factors associated with high annual losses of honey bee colonies in the US is an important and active area of research. Pathogen incidence and abundance correlate with Colony Collapse Disorder- (CCD-) affected colonies in the US and colony losses in the US and in some European countries. Honey bees are readily infected by single-stranded positive sense RNA viruses. Largely dependent on the host immune response, virus infections can either remain asymptomatic or result in deformities, paralysis, or death of adults or larvae. RNA interference (RNAi) is an important antiviral defense mechanism in insects, including honey bees. Herein, we review the role of RNAi in honey bee antiviral defense and highlight some parallels between insect and mammalian immune systems. A more thorough understanding of the role of pathogens on honey bee health and the immune mechanisms bees utilize to combat infectious agents may lead to the development of strategies that enhance honey bee health and result in the discovery of additional mechanisms of immunity in metazoans. PMID:26798663

  10. RNAi and Antiviral Defense in the Honey Bee

    Directory of Open Access Journals (Sweden)

    Laura M. Brutscher

    2015-01-01

    Full Text Available Honey bees play an important agricultural and ecological role as pollinators of numerous agricultural crops and other plant species. Therefore, investigating the factors associated with high annual losses of honey bee colonies in the US is an important and active area of research. Pathogen incidence and abundance correlate with Colony Collapse Disorder- (CCD- affected colonies in the US and colony losses in the US and in some European countries. Honey bees are readily infected by single-stranded positive sense RNA viruses. Largely dependent on the host immune response, virus infections can either remain asymptomatic or result in deformities, paralysis, or death of adults or larvae. RNA interference (RNAi is an important antiviral defense mechanism in insects, including honey bees. Herein, we review the role of RNAi in honey bee antiviral defense and highlight some parallels between insect and mammalian immune systems. A more thorough understanding of the role of pathogens on honey bee health and the immune mechanisms bees utilize to combat infectious agents may lead to the development of strategies that enhance honey bee health and result in the discovery of additional mechanisms of immunity in metazoans.

  11. Defense and counterdefense in the RNAi-based antiviral immune system in insects

    NARCIS (Netherlands)

    van Mierlo, J.T.; van Cleef, K.W.; Rij, R.P. van

    2011-01-01

    RNA interference (RNAi) is an important pathway to combat virus infections in insects and plants. Hallmarks of antiviral RNAi in these organisms are: (1) an increase in virus replication after inactivation of major actors in the RNAi pathway, (2) production of virus-derived small interfering RNAs

  12. Assessing the Accuracy of the Modified Chinese Autism Spectrum Rating Scale and Social Responsiveness Scale for Screening Autism Spectrum Disorder in Chinese Children

    Institute of Scientific and Technical Information of China (English)

    Bingrui Zhou; Hao Zhou; Lijie Wu; Xiaobing Zou; Xuerong Luo; Eric Fombonne; Yi Wang; Weili Yan; Xiu Xu

    2017-01-01

    The reported prevalence of autism spectrum disorder (ASD) has been increasing rapidly in many parts of the world.However,data on its prevalence in China are largely missing.Here,we assessed the suitability of the modified Chinese version of a newly-developed ASD screening tool,the Modified Chinese Autism Spectrum Rating Scales (MC-ASRS) in screening for ASD in Chinese children aged 6-12 years,through comparison with the Social Responsiveness Scale (SRS) that has been widely used for ASD screening.We recruited the parents/caregivers of 1588 typically-developing children and 190 children with ASD aged 6-12 years to complete the MC-ASRS and SRS,and evaluated the validity of both scales in discriminating children with ASD from those developing typically.The results showed that MC-ASRS performed as well as SRS in sensitivity,specificity,and area-under-the-curve (both >0.95) in receiver operating characteristic analysis,with a fair false-negative rate.These results suggest that MC-ASRS is a promising tool for screening for children with ASD in the general Chinese population.

  13. Nymphal RNAi: systemic RNAi mediated gene knockdown in juvenile grasshopper

    Directory of Open Access Journals (Sweden)

    Dong Ying

    2005-10-01

    Full Text Available Abstract Background Grasshopper serves as important model system in neuroscience, development and evolution. Representatives of this primitive insect group are also highly relevant targets of pest control efforts. Unfortunately, the lack of genetics or gene specific molecular manipulation imposes major limitations to the study of grasshopper biology. Results We investigated whether juvenile instars of the grasshopper species Schistocerca americana are conducive to gene silencing via the systemic RNAi pathway. Injection of dsRNA corresponding to the eye colour gene vermilion into first instar nymphs triggered suppression of ommochrome formation in the eye lasting through two instars equivalent to 10–14 days in absolute time. QRT-PCR analysis revealed a two fold decrease of target transcript levels in affected animals. Control injections of EGFP dsRNA did not result in detectable phenotypic changes. RT-PCR and in situ hybridization detected ubiquitous expression of the grasshopper homolog of the dsRNA channel protein gene sid-1 in embryos, nymphs and adults. Conclusion Our results demonstrate that systemic dsRNA application elicits specific and long-term gene silencing in juvenile grasshopper instars. The conservation of systemic RNAi in the grasshopper suggests that this pathway can be exploited for gene specific manipulation of juvenile and adult instars in a wide range of primitive insects.

  14. RNA Interference in the Age of CRISPR: Will CRISPR Interfere with RNAi?

    Directory of Open Access Journals (Sweden)

    Unnikrishnan Unniyampurath

    2016-02-01

    Full Text Available The recent emergence of multiple technologies for modifying gene structure has revolutionized mammalian biomedical research and enhanced the promises of gene therapy. Over the past decade, RNA interference (RNAi based technologies widely dominated various research applications involving experimental modulation of gene expression at the post-transcriptional level. Recently, a new gene editing technology, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR and the CRISPR-associated protein 9 (Cas9 (CRISPR/Cas9 system, has received unprecedented acceptance in the scientific community for a variety of genetic applications. Unlike RNAi, the CRISPR/Cas9 system is bestowed with the ability to introduce heritable precision insertions and deletions in the eukaryotic genome. The combination of popularity and superior capabilities of CRISPR/Cas9 system raises the possibility that this technology may occupy the roles currently served by RNAi and may even make RNAi obsolete. We performed a comparative analysis of the technical aspects and applications of the CRISPR/Cas9 system and RNAi in mammalian systems, with the purpose of charting out a predictive picture on whether the CRISPR/Cas9 system will eclipse the existence and future of RNAi. The conclusion drawn from this analysis is that RNAi will still occupy specific domains of biomedical research and clinical applications, under the current state of development of these technologies. However, further improvements in CRISPR/Cas9 based technology may ultimately enable it to dominate RNAi in the long term.

  15. A Novel Yeast Surface Display Method for Large-Scale Screen Inhibitors of Sortase A.

    Science.gov (United States)

    Wu, Lin; Li, Huijun; Tang, Tianle

    2017-01-24

    high-throughput analysis, but the conventional method is much more sensitive. The method described in this paper is expected to lead to large-scale screening of sortase A inhibitors which can be used to decrease the risk of drug resistance development.

  16. A Novel Yeast Surface Display Method for Large-Scale Screen Inhibitors of Sortase A

    Directory of Open Access Journals (Sweden)

    Lin Wu

    2017-01-01

    suitable for high-throughput analysis, but the conventional method is much more sensitive. The method described in this paper is expected to lead to large-scale screening of sortase A inhibitors which can be used to decrease the risk of drug resistance development.

  17. RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming

    Directory of Open Access Journals (Sweden)

    Cheng-Xu Delon Toh

    2016-06-01

    Full Text Available Incomplete knowledge of the mechanisms at work continues to hamper efforts to maximize reprogramming efficiency. Here, we present a systematic genome-wide RNAi screen to determine the global regulators during the early stages of human reprogramming. Our screen identifies functional repressors and effectors that act to impede or promote the reprogramming process. Repressors and effectors form close interacting networks in pathways, including RNA processing, G protein signaling, protein ubiquitination, and chromatin modification. Combinatorial knockdown of five repressors (SMAD3, ZMYM2, SFRS11, SAE1, and ESET synergistically resulted in ∼85% TRA-1-60-positive cells. Removal of the novel splicing factor SFRS11 during reprogramming is accompanied by rapid acquisition of pluripotency-specific spliced forms. Mechanistically, SFRS11 regulates exon skipping and mutually exclusive splicing of transcripts in genes involved in cell differentiation, mRNA splicing, and chromatin modification. Our study provides insights into the reprogramming process, which comprises comprehensive and multi-layered transcriptional, splicing, and epigenetic machineries.

  18. RNAi Technique in Stem Cell Research: Current Status and Future Perspectives.

    Science.gov (United States)

    Zou, Gang-Ming

    2017-01-01

    RNAi is a mechanism displayed by most eukaryotic cells to rid themselves of foreign double-strand RNA molecules. In the 18 years since the initial report, RNAi has now been demonstrated to function in mammalian cells to alter gene expression and has been used as a means for genetic discovery as well as a possible strategy for genetic correction and genetic therapy in cancer and other disease. The aim of this review is to provide a general overview of how RNAi suppresses gene expression and to examine some published RNAi approaches that have resulted in changes in stem cell function and suggest the possible clinical relevance of this work in cancer therapy through targeting cancer stem cells.

  19. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments.

    Science.gov (United States)

    Sastry, Madhavi; Lowrie, Jeffrey F; Dixon, Steven L; Sherman, Woody

    2010-05-24

    A systematic virtual screening study on 11 pharmaceutically relevant targets has been conducted to investigate the interrelation between 8 two-dimensional (2D) fingerprinting methods, 13 atom-typing schemes, 13 bit scaling rules, and 12 similarity metrics using the new cheminformatics package Canvas. In total, 157 872 virtual screens were performed to assess the ability of each combination of parameters to identify actives in a database screen. In general, fingerprint methods, such as MOLPRINT2D, Radial, and Dendritic that encode information about local environment beyond simple linear paths outperformed other fingerprint methods. Atom-typing schemes with more specific information, such as Daylight, Mol2, and Carhart were generally superior to more generic atom-typing schemes. Enrichment factors across all targets were improved considerably with the best settings, although no single set of parameters performed optimally on all targets. The size of the addressable bit space for the fingerprints was also explored, and it was found to have a substantial impact on enrichments. Small bit spaces, such as 1024, resulted in many collisions and in a significant degradation in enrichments compared to larger bit spaces that avoid collisions.

  20. Investigating Engineered Ribonucleoprotein Particles to Improve Oral RNAi Delivery in Crop Insect Pests.

    Science.gov (United States)

    Gillet, François-Xavier; Garcia, Rayssa A; Macedo, Leonardo L P; Albuquerque, Erika V S; Silva, Maria C M; Grossi-de-Sa, Maria F

    2017-01-01

    Genetically modified (GM) crops producing double-stranded RNAs (dsRNAs) are being investigated largely as an RNA interference (RNAi)-based resistance strategy against crop insect pests. However, limitations of this strategy include the sensitivity of dsRNA to insect gut nucleases and its poor insect cell membrane penetration. Working with the insect pest cotton boll weevil ( Anthonomus grandis ), we showed that the chimeric protein PTD-DRBD (peptide transduction domain-dsRNA binding domain) combined with dsRNA forms a ribonucleoprotein particle (RNP) that improves the effectiveness of the RNAi mechanism in the insect. The RNP slows down nuclease activity, probably by masking the dsRNA. Furthermore, PTD-mediated internalization in insect gut cells is achieved within minutes after plasma membrane contact, limiting the exposure time of the RNPs to gut nucleases. Therefore, the RNP provides an approximately 2-fold increase in the efficiency of insect gene silencing upon oral delivery when compared to naked dsRNA. Taken together, these data demonstrate the role of engineered RNPs in improving dsRNA stability and cellular entry, representing a path toward the design of enhanced RNAi strategies in GM plants against crop insect pests.

  1. Investigating Engineered Ribonucleoprotein Particles to Improve Oral RNAi Delivery in Crop Insect Pests

    Directory of Open Access Journals (Sweden)

    François-Xavier Gillet

    2017-04-01

    Full Text Available Genetically modified (GM crops producing double-stranded RNAs (dsRNAs are being investigated largely as an RNA interference (RNAi-based resistance strategy against crop insect pests. However, limitations of this strategy include the sensitivity of dsRNA to insect gut nucleases and its poor insect cell membrane penetration. Working with the insect pest cotton boll weevil (Anthonomus grandis, we showed that the chimeric protein PTD-DRBD (peptide transduction domain—dsRNA binding domain combined with dsRNA forms a ribonucleoprotein particle (RNP that improves the effectiveness of the RNAi mechanism in the insect. The RNP slows down nuclease activity, probably by masking the dsRNA. Furthermore, PTD-mediated internalization in insect gut cells is achieved within minutes after plasma membrane contact, limiting the exposure time of the RNPs to gut nucleases. Therefore, the RNP provides an approximately 2-fold increase in the efficiency of insect gene silencing upon oral delivery when compared to naked dsRNA. Taken together, these data demonstrate the role of engineered RNPs in improving dsRNA stability and cellular entry, representing a path toward the design of enhanced RNAi strategies in GM plants against crop insect pests.

  2. Human factors guidelines for large-screen displays

    International Nuclear Information System (INIS)

    Collier, Steve

    2005-09-01

    Any control-room project (including upgrades or evolutionary improvements to existing control-rooms) is well advised at the outset first to gather and update related background material for the design. This information-gathering exercise should also take into account experience from similar projects and operating experience. For these reasons, we decided to use our research, and experience in large-screen display design with several clients to update human factors guidance for large-screen displays, to take into account new ergonomics guidelines, operating experience, and work from similar projects. To write the updated guidelines, we drew on much of our experience across several departments at IFE, including research funded by the HRP programme, and experience with individual clients. Guidance here is accordingly focused mainly on recent areas of technical and human innovations in the man-machine interface. One particular area of focus was on the increasing use of large-screen display systems in modern control-rooms, and on how guidelines could be adapted and supplemented for their design. Guidance or reference to recommended sources is also given for control suite arrangement and layout, control-room layout, workstation layout, design of displays and controls, and design of the work environment, especially insofar as these ergonomic issues interact with the effectiveness of modern displays, in particular large screen displays. The work shows that there can be synergy between HRP research and bilateral activities: the one side offers a capability to develop tools and guidelines, while the other side gives an opportunity to test and refine these in practice, to the benefit of both parties. (Author)

  3. Human factors guidelines for large-screen displays

    Energy Technology Data Exchange (ETDEWEB)

    Collier, Steve

    2005-09-15

    Any control-room project (including upgrades or evolutionary improvements to existing control-rooms) is well advised at the outset first to gather and update related background material for the design. This information-gathering exercise should also take into account experience from similar projects and operating experience. For these reasons, we decided to use our research, and experience in large-screen display design with several clients to update human factors guidance for large-screen displays, to take into account new ergonomics guidelines, operating experience, and work from similar projects. To write the updated guidelines, we drew on much of our experience across several departments at IFE, including research funded by the HRP programme, and experience with individual clients. Guidance here is accordingly focused mainly on recent areas of technical and human innovations in the man-machine interface. One particular area of focus was on the increasing use of large-screen display systems in modern control-rooms, and on how guidelines could be adapted and supplemented for their design. Guidance or reference to recommended sources is also given for control suite arrangement and layout, control-room layout, workstation layout, design of displays and controls, and design of the work environment, especially insofar as these ergonomic issues interact with the effectiveness of modern displays, in particular large screen displays. The work shows that there can be synergy between HRP research and bilateral activities: the one side offers a capability to develop tools and guidelines, while the other side gives an opportunity to test and refine these in practice, to the benefit of both parties. (Author)

  4. Identification of highly effective target genes for RNAi-mediated control of emerald ash borer, Agrilus planipennis.

    Science.gov (United States)

    Rodrigues, Thais B; Duan, Jian J; Palli, Subba R; Rieske, Lynne K

    2018-03-22

    Recent study has shown that RNA interference (RNAi) is efficient in emerald ash borer (EAB), Agrilus planipennis, and that ingestion of double-stranded RNA (dsRNA) targeting specific genes causes gene silencing and mortality in neonates. Here, we report on the identification of highly effective target genes for RNAi-mediated control of EAB. We screened 13 candidate genes in neonate larvae and selected the most effective target genes for further investigation, including their effect on EAB adults and on a non-target organism, Tribolium castaneum. The two most efficient target genes selected, hsp (heat shock 70-kDa protein cognate 3) and shi (shibire), caused up to 90% mortality of larvae and adults. In EAB eggs, larvae, and adults, the hsp is expressed at higher levels when compared to that of shi. Ingestion of dsHSP and dsSHI caused mortality in both neonate larvae and adults. Administration of a mixture of both dsRNAs worked better than either dsRNA by itself. In contrast, injection of EAB.dsHSP and EAB.dsSHI did not cause mortality in T. castaneum. Thus, the two genes identified cause high mortality in the EAB with no apparent phenotype effects in a non-target organism, the red flour beetle, and could be used in RNAi-mediated control of this invasive pest.

  5. The RNAi Universe in Fungi: A Varied Landscape of Small RNAs and Biological Functions.

    Science.gov (United States)

    Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M

    2017-09-08

    RNA interference (RNAi) is a conserved eukaryotic mechanism that uses small RNA molecules to suppress gene expression through sequence-specific messenger RNA degradation, translational repression, or transcriptional inhibition. In filamentous fungi, the protective function of RNAi in the maintenance of genome integrity is well known. However, knowledge of the regulatory role of RNAi in fungi has had to wait until the recent identification of different endogenous small RNA classes, which are generated by distinct RNAi pathways. In addition, RNAi research on new fungal models has uncovered the role of small RNAs and RNAi pathways in the regulation of diverse biological functions. In this review, we give an up-to-date overview of the different classes of small RNAs and RNAi pathways in fungi and their roles in the defense of genome integrity and regulation of fungal physiology and development, as well as in the interaction of fungi with biotic and abiotic environments.

  6. Energy transfers in large-scale and small-scale dynamos

    Science.gov (United States)

    Samtaney, Ravi; Kumar, Rohit; Verma, Mahendra

    2015-11-01

    We present the energy transfers, mainly energy fluxes and shell-to-shell energy transfers in small-scale dynamo (SSD) and large-scale dynamo (LSD) using numerical simulations of MHD turbulence for Pm = 20 (SSD) and for Pm = 0.2 on 10243 grid. For SSD, we demonstrate that the magnetic energy growth is caused by nonlocal energy transfers from the large-scale or forcing-scale velocity field to small-scale magnetic field. The peak of these energy transfers move towards lower wavenumbers as dynamo evolves, which is the reason for the growth of the magnetic fields at the large scales. The energy transfers U2U (velocity to velocity) and B2B (magnetic to magnetic) are forward and local. For LSD, we show that the magnetic energy growth takes place via energy transfers from large-scale velocity field to large-scale magnetic field. We observe forward U2U and B2B energy flux, similar to SSD.

  7. Differential RNAi responses of Nicotiana benthamiana individuals transformed with a hairpin-inducing construct during Plum pox virus challenge.

    Science.gov (United States)

    Montes, Christian; Castro, Álvaro; Barba, Paola; Rubio, Julia; Sánchez, Evelyn; Carvajal, Denisse; Aguirre, Carlos; Tapia, Eduardo; DelÍ Orto, Paola; Decroocq, Veronique; Prieto, Humberto

    2014-10-01

    Gene silencing and large-scale small RNA analysis can be used to develop RNA interference (RNAi)-based resistance strategies for Plum pox virus (PPV), a high impact disease of Prunus spp. In this study, a pPPViRNA hairpin-inducing vector harboring two silencing motif-rich regions of the PPV coat protein (CP) gene was evaluated in transgenic Nicotiana benthamiana (NB) plants. Wild-type NB plants infected with a chimeric PPV virus (PPV::GFP) exhibited affected leaves with mosaic chlorosis congruent to GFP fluorescence at 21 day post-inoculation; transgenic lines depicted a range of phenotypes from fully resistant to susceptible. ELISA values and GFP fluorescence intensities were used to select transgenic-resistant (TG-R) and transgenic-susceptible (TG-S) lines for further characterization of small interfering RNAs (siRNAs) by large-scale small RNA sequencing. In infected TG-S and untransformed (WT) plants, the observed siRNAs were nearly exclusively 21- and 22-nt siRNAs that targeted the whole PPV::GFP genome; 24-nt siRNAs were absent in these individuals. Challenged TG-R plants accumulated a full set of 21- to 24-nt siRNAs that were primarily associated with the selected motif-rich regions, indicating that a trans-acting siRNAs process prevented viral multiplication. BLAST analysis identified 13 common siRNA clusters targeting the CP gene. 21-nt siRNA sequences were associated with the 22-nt siRNAs and the scarce 23- and 24-nt molecules in TG-S plants and with most of the observed 22-, 23-, and 24-nt siRNAs in TG-R individuals. These results validate the use of a multi-hot spot silencing vector against PPV and elucidate the molecules by which hairpin-inducing vectors initiate RNAi in vivo.

  8. Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi-SlPH tomato line with reduced fruit acidity and higher pH.

    Science.gov (United States)

    Barad, Shiri; Sela, Noa; Dubey, Amit K; Kumar, Dilip; Luria, Neta; Ment, Dana; Cohen, Shahar; Schaffer, Arthur A; Prusky, Dov

    2017-08-04

    The destructive phytopathogen Colletotrichum gloeosporioides causes anthracnose disease in fruit. During host colonization, it secretes ammonia, which modulates environmental pH and regulates gene expression, contributing to pathogenicity. However, the effect of host pH environment on pathogen colonization has never been evaluated. Development of an isogenic tomato line with reduced expression of the gene for acidity, SlPH (Solyc10g074790.1.1), enabled this analysis. Total RNA from C. gloeosporioides colonizing wild-type (WT) and RNAi-SlPH tomato lines was sequenced and gene-expression patterns were compared. C. gloeosporioides inoculation of the RNAi-SlPH line with pH 5.96 compared to the WT line with pH 4.2 showed 30% higher colonization and reduced ammonia accumulation. Large-scale comparative transcriptome analysis of the colonized RNAi-SlPH and WT lines revealed their different mechanisms of colonization-pattern activation: whereas the WT tomato upregulated 13-LOX (lipoxygenase), jasmonic acid and glutamate biosynthesis pathways, it downregulated processes related to chlorogenic acid biosynthesis II, phenylpropanoid biosynthesis and hydroxycinnamic acid tyramine amide biosynthesis; the RNAi-SlPH line upregulated UDP-D-galacturonate biosynthesis I and free phenylpropanoid acid biosynthesis, but mainly downregulated pathways related to sugar metabolism, such as the glyoxylate cycle and L-arabinose degradation II. Comparison of C. gloeosporioides gene expression during colonization of the WT and RNAi-SlPH lines showed that the fungus upregulates ammonia and nitrogen transport and the gamma-aminobutyric acid metabolic process during colonization of the WT, while on the RNAi-SlPH tomato, it mainly upregulates the nitrate metabolic process. Modulation of tomato acidity and pH had significant phenotypic effects on C. gloeosporioides development. The fungus showed increased colonization on the neutral RNAi-SlPH fruit, and limited colonization on the WT acidic fruit

  9. A regulatory network of Drosophila germline stem cell self-renewal

    OpenAIRE

    Yan, Dong; Neumüller, Ralph A.; Buckner, Michael; Ayers, Kathleen; Li, Hua; Hu, Yanhui; Yang-Zhou, Donghui; Pan, Lei; Wang, Xiaoxi; Kelley, Colleen; Vinayagam, Arunachalam; Binari, Richard; Randklev, Sakara; Perkins, Lizabeth A.; Xie, Ting

    2014-01-01

    Stem cells possess the capacity to generate two cells of distinct fate upon division; one cell retaining stem cell identity and the other cell destined to differentiate. These cell fates are established by cell-type-specific genetic networks. To comprehensively identify components of these networks, we performed a large-scale RNAi screen in Drosophila female germline stem cells (GSCs) covering ~25% of the genome. The screen identified 366 genes that affect GSC maintenance, differentiation or ...

  10. [Expression analysis of a transformer gene in Daphnia pulex after RNAi].

    Science.gov (United States)

    Guo, C Y; Chen, P; Zhang, M M; Ning, J J; Wang, С L; Wang, D L; Zhao, Y L

    2016-01-01

    In order to explore the importance of the transformer (tra) gene in reproductive mode switching in Daphnia pulex, we studied the effect of silencing of this gene using RNA interference (RNAi). We obtained Dptra dsRNA by constructing and using a dsRNA expression vector and transcription method in vitro. D. pulex individuals in different reproductive modes were treated by soaking in a solution of Dptra dsRNA. We then assayed the expression of the endogenous Dptra mRNA after RNAi treatment using RT-PCR and obtained the suppression ratio. Expression of the tra gene in the RNAi groups was down-regulated compared with the controls after 16 h (p < 0.05). We also analyzed the effect of RNAi on the expression of the TRA protein using Western blot, which showed that the expression level of the TRA protein was reduced after RNAi treatment. Our experimental results showed that soaking of D. pulex adults in tra-specific dsRNA transcribed in vitro can specifically reduce the level of tra mRNA and also reduce the expression of the TRA protein, demonstrating effective in vivo silencing of the tra gene.

  11. Large-scale data analytics

    CERN Document Server

    Gkoulalas-Divanis, Aris

    2014-01-01

    Provides cutting-edge research in large-scale data analytics from diverse scientific areas Surveys varied subject areas and reports on individual results of research in the field Shares many tips and insights into large-scale data analytics from authors and editors with long-term experience and specialization in the field

  12. Pre-clinical Safety and Off-Target Studies to Support Translation of AAV-Mediated RNAi Therapy for FSHD.

    Science.gov (United States)

    Wallace, Lindsay M; Saad, Nizar Y; Pyne, Nettie K; Fowler, Allison M; Eidahl, Jocelyn O; Domire, Jacqueline S; Griffin, Danielle A; Herman, Adam C; Sahenk, Zarife; Rodino-Klapac, Louise R; Harper, Scott Q

    2018-03-16

    RNAi emerged as a prospective molecular therapy nearly 15 years ago. Since then, two major RNAi platforms have been under development: oligonucleotides and gene therapy. Oligonucleotide-based approaches have seen more advancement, with some promising therapies that may soon reach market. In contrast, vector-based approaches for RNAi therapy have remained largely in the pre-clinical realm, with limited clinical safety and efficacy data to date. We are developing a gene therapy approach to treat the autosomal-dominant disorder facioscapulohumeral muscular dystrophy. Our strategy involves silencing the myotoxic gene DUX4 using adeno-associated viral vectors to deliver targeted microRNA expression cassettes (miDUX4s). We previously demonstrated proof of concept for this approach in mice, and we are now taking additional steps here to assess safety issues related to miDUX4 overexpression and sequence-specific off-target silencing. In this study, we describe improvements in vector design and expansion of our miDUX4 sequence repertoire and report differential toxicity elicited by two miDUX4 sequences, of which one was toxic and the other was not. This study provides important data to help advance our goal of translating RNAi gene therapy for facioscapulohumeral muscular dystrophy.

  13. Large-scale grid management

    International Nuclear Information System (INIS)

    Langdal, Bjoern Inge; Eggen, Arnt Ove

    2003-01-01

    The network companies in the Norwegian electricity industry now have to establish a large-scale network management, a concept essentially characterized by (1) broader focus (Broad Band, Multi Utility,...) and (2) bigger units with large networks and more customers. Research done by SINTEF Energy Research shows so far that the approaches within large-scale network management may be structured according to three main challenges: centralization, decentralization and out sourcing. The article is part of a planned series

  14. Psychometric properties of the Vulnerability to Abuse Screening Scale for screening abuse of older adults

    Directory of Open Access Journals (Sweden)

    Raquel Batista Dantas

    Full Text Available ABSTRACT OBJECTIVE Adapt and evaluate the psychometric properties of the Vulnerability to Abuse Screening Scale to identify risk of domestic violence against older adults in Brazil. METHODS The instrument was adapted and validated in a sample of 151 older adults from a geriatric reference center in the municipality of Belo Horizonte, State of Minas Gerais, in 2014. We collected sociodemographic, clinical, and abuse-related information, and verified reliability by reproducibility in a sample of 55 older people, who underwent re-testing of the instrument seven days after the first application. Descriptive and comparative analyses were performed for all variables, with a significance level of 5%. The construct validity was analyzed by the principal components method with a tetrachoric correlation matrix, the reliability of the scale by the weighted Kappa (Kp statistic, and the internal consistency by the Kuder-Richardson estimator formula 20 (KR-20. RESULTS The average age of the participants was 72.1 years (DP = 6.96; 95%CI 70.94–73.17, with a maximum of 92 years, and they were predominantly female (76.2%; 95%CI 69.82–83.03. When analyzing the relationship between the scores of the Vulnerability to Abuse Screening Scale, categorized by presence (score > 3 or absence (score < 3 of vulnerability to abuse, with clinical and health conditions, we found statistically significant differences for self-perception of health (p = 0.002, depressive symptoms (p = 0.000, and presence of rheumatism (p = 0.003. There were no statistically significant differences between sexes. The Vulnerability to Abuse Screening Scale acceptably evaluated validity in the transcultural adaptation process, demonstrating dimensionality coherent with the original proposal (four factors. In the internal consistency analysis, the instrument presented good results (KR-20 = 0.69 and the reliability via reproducibility was considered excellent for the global scale (Kp = 0

  15. Miniature short hairpin RNA screens to characterize antiproliferative drugs.

    Science.gov (United States)

    Kittanakom, Saranya; Arnoldo, Anthony; Brown, Kevin R; Wallace, Iain; Kunavisarut, Tada; Torti, Dax; Heisler, Lawrence E; Surendra, Anuradha; Moffat, Jason; Giaever, Guri; Nislow, Corey

    2013-08-07

    The application of new proteomics and genomics technologies support a view in which few drugs act solely by inhibiting a single cellular target. Indeed, drug activity is modulated by complex, often incompletely understood cellular mechanisms. Therefore, efforts to decipher mode of action through genetic perturbation such as RNAi typically yields "hits" that fall into several categories. Of particular interest to the present study, we aimed to characterize secondary activities of drugs on cells. Inhibiting a known target can result in clinically relevant synthetic phenotypes. In one scenario, drug perturbation could, for example, improperly activate a protein that normally inhibits a particular kinase. In other cases, additional, lower affinity targets can be inhibited as in the example of inhibition of c-Kit observed in Bcr-Abl-positive cells treated with Gleevec. Drug transport and metabolism also play an important role in the way any chemicals act within the cells. Finally, RNAi per se can also affect cell fitness by more general off-target effects, e.g., via the modulation of apoptosis or DNA damage repair. Regardless of the root cause of these unwanted effects, understanding the scope of a drug's activity and polypharmacology is essential for better understanding its mechanism(s) of action, and such information can guide development of improved therapies. We describe a rapid, cost-effective approach to characterize primary and secondary effects of small-molecules by using small-scale libraries of virally integrated short hairpin RNAs. We demonstrate this principle using a "minipool" composed of shRNAs that target the genes encoding the reported protein targets of approved drugs. Among the 28 known reported drug-target pairs, we successfully identify 40% of the targets described in the literature and uncover several unanticipated drug-target interactions based on drug-induced synthetic lethality. We provide a detailed protocol for performing such screens and for

  16. Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen

    Science.gov (United States)

    Suratanee, Apichat; Schaefer, Martin H.; Betts, Matthew J.; Soons, Zita; Mannsperger, Heiko; Harder, Nathalie; Oswald, Marcus; Gipp, Markus; Ramminger, Ellen; Marcus, Guillermo; Männer, Reinhard; Rohr, Karl; Wanker, Erich; Russell, Robert B.; Andrade-Navarro, Miguel A.; Eils, Roland; König, Rainer

    2014-01-01

    Characterizing the activating and inhibiting effect of protein-protein interactions (PPI) is fundamental to gain insight into the complex signaling system of a human cell. A plethora of methods has been suggested to infer PPI from data on a large scale, but none of them is able to characterize the effect of this interaction. Here, we present a novel computational development that employs mitotic phenotypes of a genome-wide RNAi knockdown screen and enables identifying the activating and inhibiting effects of PPIs. Exemplarily, we applied our technique to a knockdown screen of HeLa cells cultivated at standard conditions. Using a machine learning approach, we obtained high accuracy (82% AUC of the receiver operating characteristics) by cross-validation using 6,870 known activating and inhibiting PPIs as gold standard. We predicted de novo unknown activating and inhibiting effects for 1,954 PPIs in HeLa cells covering the ten major signaling pathways of the Kyoto Encyclopedia of Genes and Genomes, and made these predictions publicly available in a database. We finally demonstrate that the predicted effects can be used to cluster knockdown genes of similar biological processes in coherent subgroups. The characterization of the activating or inhibiting effect of individual PPIs opens up new perspectives for the interpretation of large datasets of PPIs and thus considerably increases the value of PPIs as an integrated resource for studying the detailed function of signaling pathways of the cellular system of interest. PMID:25255318

  17. Ethics of large-scale change

    OpenAIRE

    Arler, Finn

    2006-01-01

      The subject of this paper is long-term large-scale changes in human society. Some very significant examples of large-scale change are presented: human population growth, human appropriation of land and primary production, the human use of fossil fuels, and climate change. The question is posed, which kind of attitude is appropriate when dealing with large-scale changes like these from an ethical point of view. Three kinds of approaches are discussed: Aldo Leopold's mountain thinking, th...

  18. C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation.

    Science.gov (United States)

    Liu, Ying; Ye, Xuecheng; Jiang, Feng; Liang, Chunyang; Chen, Dongmei; Peng, Junmin; Kinch, Lisa N; Grishin, Nick V; Liu, Qinghua

    2009-08-07

    The catalytic engine of RNA interference (RNAi) is the RNA-induced silencing complex (RISC), wherein the endoribonuclease Argonaute and single-stranded small interfering RNA (siRNA) direct target mRNA cleavage. We reconstituted long double-stranded RNA- and duplex siRNA-initiated RISC activities with the use of recombinant Drosophila Dicer-2, R2D2, and Ago2 proteins. We used this core reconstitution system to purify an RNAi regulator that we term C3PO (component 3 promoter of RISC), a complex of Translin and Trax. C3PO is a Mg2+-dependent endoribonuclease that promotes RISC activation by removing siRNA passenger strand cleavage products. These studies establish an in vitro RNAi reconstitution system and identify C3PO as a key activator of the core RNAi machinery.

  19. The application of RNAi-based treatments for inflammatory bowel disease

    DEFF Research Database (Denmark)

    Olesen, Morten Tobias Jarlstad; Gonzalez, Borja Ballarin; Howard, Ken

    2014-01-01

    in which small interfering RNA (siRNA) mediates specific downregulation of key molecular targets of the IBD inflammatory process may offer a precise, potent and safer alternative to conventional treatments. This review describes the aetiology of Crohn’s disease and ulcerative colitis and the cellular...... and molecular basis for current treatments to highlight target candidates for an RNAi-based approach. Promising preclinical studies support an RNAi application; however, optimal siRNA designs that maximise potency and development of enabling technologies for site- and cellular-specific delivery......Inflammatory bowel disease (IBD) is a chronic, relapsing, idiopathic inflammation of the gastrointestinal tract with no permanent cure. Present immunosuppressive and anti-inflammatory therapies are often ineffective and associated with severe side effects. An RNA interference (RNAi)-based approach...

  20. Biotechnological uses of RNAi in plants: risk assessment considerations.

    Science.gov (United States)

    Casacuberta, Josep M; Devos, Yann; du Jardin, Patrick; Ramon, Matthew; Vaucheret, Hervé; Nogué, Fabien

    2015-03-01

    RNAi offers opportunities to generate new traits in genetically modified (GM) plants. Instead of expressing novel proteins, RNAi-based GM plants reduce target gene expression. Silencing of off-target genes may trigger unintended effects, and identifying these genes would facilitate risk assessment. However, using bioinformatics alone is not reliable, due to the lack of genomic data and insufficient knowledge of mechanisms governing mRNA-small (s)RNA interactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Limited agreement of independent RNAi screens for virus-required host genes owes more to false-negative than false-positive factors.

    Directory of Open Access Journals (Sweden)

    Linhui Hao

    Full Text Available Systematic, genome-wide RNA interference (RNAi analysis is a powerful approach to identify gene functions that support or modulate selected biological processes. An emerging challenge shared with some other genome-wide approaches is that independent RNAi studies often show limited agreement in their lists of implicated genes. To better understand this, we analyzed four genome-wide RNAi studies that identified host genes involved in influenza virus replication. These studies collectively identified and validated the roles of 614 cell genes, but pair-wise overlap among the four gene lists was only 3% to 15% (average 6.7%. However, a number of functional categories were overrepresented in multiple studies. The pair-wise overlap of these enriched-category lists was high, ∼19%, implying more agreement among studies than apparent at the gene level. Probing this further, we found that the gene lists implicated by independent studies were highly connected in interacting networks by independent functional measures such as protein-protein interactions, at rates significantly higher than predicted by chance. We also developed a general, model-based approach to gauge the effects of false-positive and false-negative factors and to estimate, from a limited number of studies, the total number of genes involved in a process. For influenza virus replication, this novel statistical approach estimates the total number of cell genes involved to be ∼2,800. This and multiple other aspects of our experimental and computational results imply that, when following good quality control practices, the low overlap between studies is primarily due to false negatives rather than false-positive gene identifications. These results and methods have implications for and applications to multiple forms of genome-wide analysis.

  2. Transcriptome Analysis and Screening for Potential Target Genes for RNAi-Mediated Pest Control of the Beet Armyworm, Spodoptera exigua.

    Science.gov (United States)

    Li, Hang; Jiang, Weihua; Zhang, Zan; Xing, Yanru; Li, Fei

    2013-01-01

    The beet armyworm, Spodoptera exigua (Hübner), is a serious pest worldwide that causes significant losses in crops. Unfortunately, genetic resources for the beet armyworm is extremely scarce. To improve these resources we sequenced the transcriptome of S. exigua representing all stages including eggs, 1(st) to 5(th) instar larvae, pupae, male and female adults using the Illumina Solexa platform. We assembled the transcriptome with Trinity that yielded 31,414 contigs. Of these contigs, 18,592 were annotated as protein coding genes by Blast searches against the NCBI nr database. It has been shown that knockdown of important insect genes by dsRNAs or siRNAs is a feasible mechanism to control insect pests. The first key step towards developing an efficient RNAi-mediated pest control technique is to find suitable target genes. To screen for effective target genes in the beet armyworm, we selected nine candidate genes. The sequences of these genes were amplified using the RACE strategy. Then, siRNAs were designed and chemically synthesized. We injected 2 µl siRNA (2 µg/µl) into the 4(th) instar larvae to knock down the respective target genes. The mRNA abundance of target genes decreased to different levels (∼20-94.3%) after injection of siRNAs. Knockdown of eight genes including chitinase7, PGCP, chitinase1, ATPase, tubulin1, arf2, tubulin2 and arf1 caused a significantly high level of mortality compared to the negative control (Ppest control.

  3. A protocol for assessment of direct effects of RNAi to earthworms

    DEFF Research Database (Denmark)

    de Pinto, Roberta; Strandberg, Morten Tune; Kostov, Kaloyan

    both how to study fate and effects of the RNAi molecules. If COI or another gene apt for silencing will be successful in the earthworm L. terrestris, this could become a suggested positive control agent for future non-target studies of RNAi. The testing of environmental effects of NBT require...

  4. Role of RNA interference (RNAi) in the moss Physcomitrella patens

    KAUST Repository

    Arif, Muhammad Asif; Frank, Wolfgang; Khraiwesh, Basel

    2013-01-01

    RNA interference (RNAi) is a mechanism that regulates genes by either transcriptional (TGS) or posttranscriptional gene silencing (PTGS), required for genome maintenance and proper development of an organism. Small non-coding RNAs are the key players in RNAi and have been intensively studied in eukaryotes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs are synthesized from a short hairpin structure while siRNAs are derived from long double-stranded RNAs (dsRNA). Both miRNA and siRNAs control the expression of cognate target RNAs by binding to reverse complementary sequences mediating cleavage or translational inhibition of the target RNA. They also act on the DNA and cause epigenetic changes such as DNA methylation and histone modifications. In the last years, the analysis of plant RNAi pathways was extended to the bryophyte Physcomitrella patens, a non-flowering, non-vascular ancient land plant that diverged from the lineage of seed plants approximately 450 million years ago. Based on a number of characteristic features and its phylogenetic key position in land plant evolution P. patens emerged as a plant model species to address basic as well as applied topics in plant biology. Here we summarize the current knowledge on the role of RNAi in P. patens that shows functional overlap with RNAi pathways from seed plants, and also unique features specific to this species. 2013 by the authors; licensee MDPI, Basel, Switzerland.

  5. Role of RNA interference (RNAi) in the moss Physcomitrella patens

    KAUST Repository

    Arif, Muhammad Asif

    2013-01-14

    RNA interference (RNAi) is a mechanism that regulates genes by either transcriptional (TGS) or posttranscriptional gene silencing (PTGS), required for genome maintenance and proper development of an organism. Small non-coding RNAs are the key players in RNAi and have been intensively studied in eukaryotes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs are synthesized from a short hairpin structure while siRNAs are derived from long double-stranded RNAs (dsRNA). Both miRNA and siRNAs control the expression of cognate target RNAs by binding to reverse complementary sequences mediating cleavage or translational inhibition of the target RNA. They also act on the DNA and cause epigenetic changes such as DNA methylation and histone modifications. In the last years, the analysis of plant RNAi pathways was extended to the bryophyte Physcomitrella patens, a non-flowering, non-vascular ancient land plant that diverged from the lineage of seed plants approximately 450 million years ago. Based on a number of characteristic features and its phylogenetic key position in land plant evolution P. patens emerged as a plant model species to address basic as well as applied topics in plant biology. Here we summarize the current knowledge on the role of RNAi in P. patens that shows functional overlap with RNAi pathways from seed plants, and also unique features specific to this species. 2013 by the authors; licensee MDPI, Basel, Switzerland.

  6. Enhancement of allele discrimination by introduction of nucleotide mismatches into siRNA in allele-specific gene silencing by RNAi.

    Directory of Open Access Journals (Sweden)

    Yusuke Ohnishi

    Full Text Available Allele-specific gene silencing by RNA interference (RNAi is therapeutically useful for specifically inhibiting the expression of disease-associated alleles without suppressing the expression of corresponding wild-type alleles. To realize such allele-specific RNAi (ASP-RNAi, the design and assessment of small interfering RNA (siRNA duplexes conferring ASP-RNAi is vital; however, it is also difficult. In a previous study, we developed an assay system to assess ASP-RNAi with mutant and wild-type reporter alleles encoding the Photinus and Renilla luciferase genes. In line with experiments using the system, we realized that it is necessary and important to enhance allele discrimination between mutant and corresponding wild-type alleles. Here, we describe the improvement of ASP-RNAi against mutant alleles carrying single nucleotide variations by introducing base substitutions into siRNA sequences, where original variations are present in the central position. Artificially mismatched siRNAs or short-hairpin RNAs (shRNAs against mutant alleles of the human Prion Protein (PRNP gene, which appear to be associated with susceptibility to prion diseases, were examined using this assessment system. The data indicates that introduction of a one-base mismatch into the siRNAs and shRNAs was able to enhance discrimination between the mutant and wild-type alleles. Interestingly, the introduced mismatches that conferred marked improvement in ASP-RNAi, appeared to be largely present in the guide siRNA elements, corresponding to the 'seed region' of microRNAs. Due to the essential role of the 'seed region' of microRNAs in their association with target RNAs, it is conceivable that disruption of the base-pairing interactions in the corresponding seed region, as well as the central position (involved in cleavage of target RNAs, of guide siRNA elements could influence allele discrimination. In addition, we also suggest that nucleotide mismatches at the 3'-ends of sense

  7. Host-induced silencing of essential genes in Puccinia triticina through transgenic expression of RNAi sequences reduces severity of leaf rust infection in wheat.

    Science.gov (United States)

    Panwar, Vinay; Jordan, Mark; McCallum, Brent; Bakkeren, Guus

    2018-05-01

    Leaf rust, caused by the pathogenic fungus Puccinia triticina (Pt), is one of the most serious biotic threats to sustainable wheat production worldwide. This obligate biotrophic pathogen is prevalent worldwide and is known for rapid adaptive evolution to overcome resistant wheat varieties. Novel disease control approaches are therefore required to minimize the yield losses caused by Pt. Having shown previously the potential of host-delivered RNA interference (HD-RNAi) in functional screening of Pt genes involved in pathogenesis, we here evaluated the use of this technology in transgenic wheat plants as a method to achieve protection against wheat leaf rust (WLR) infection. Stable expression of hairpin RNAi constructs with sequence homology to Pt MAP-kinase (PtMAPK1) or a cyclophilin (PtCYC1) encoding gene in susceptible wheat plants showed efficient silencing of the corresponding genes in the interacting fungus resulting in disease resistance throughout the T 2 generation. Inhibition of Pt proliferation in transgenic lines by in planta-induced RNAi was associated with significant reduction in target fungal transcript abundance and reduced fungal biomass accumulation in highly resistant plants. Disease protection was correlated with the presence of siRNA molecules specific to targeted fungal genes in the transgenic lines harbouring the complementary HD-RNAi construct. This work demonstrates that generating transgenic wheat plants expressing RNAi-inducing transgenes to silence essential genes in rust fungi can provide effective disease resistance, thus opening an alternative way for developing rust-resistant crops. © 2017 Her Majesty the Queen in Right of Canada. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  8. Reduction of adenovirus E1A mRNA by RNAi results in enhanced recombinant protein expression in transiently transfected HEK293 cells.

    Science.gov (United States)

    Hacker, David L; Bertschinger, Martin; Baldi, Lucia; Wurm, Florian M

    2004-10-27

    Human embryonic kidney 293 (HEK293) cells, a widely used host for large-scale transient expression of recombinant proteins, are transformed with the adenovirus E1A and E1B genes. Because the E1A proteins function as transcriptional activators or repressors, they may have a positive or negative effect on transient transgene expression in this cell line. Suspension cultures of HEK293 EBNA (HEK293E) cells were co-transfected with a reporter plasmid expressing the GFP gene and a plasmid expressing a short hairpin RNA (shRNA) targeting the E1A mRNAs for degradation by RNA interference (RNAi). The presence of the shRNA in HEK293E cells reduced the steady state level of E1A mRNA up to 75% and increased transient GFP expression from either the elongation factor-1alpha (EF-1alpha) promoter or the human cytomegalovirus (HCMV) immediate early promoter up to twofold. E1A mRNA depletion also resulted in a twofold increase in transient expression of a recombinant IgG in both small- and large-scale suspension cultures when the IgG light and heavy chain genes were controlled by the EF-1alpha promoter. Finally, transient IgG expression was enhanced 2.5-fold when the anti-E1A shRNA was expressed from the same vector as the IgG light chain gene. These results demonstrated that E1A has a negative effect on transient gene expression in HEK293E cells, and they established that RNAi can be used to enhance recombinant protein expression in mammalian cells.

  9. Non-destructive screening method for radiation hardened performance of large scale integration

    International Nuclear Information System (INIS)

    Zhou Dong; Xi Shanbin; Guo Qi; Ren Diyuan; Li Yudong; Sun Jing; Wen Lin

    2013-01-01

    The space radiation environment could induce radiation damage on the electronic devices. As the performance of commercial devices is generally superior to that of radiation hardened devices, it is necessary to screen out the devices with good radiation hardened performance from the commercial devices and applying these devices to space systems could improve the reliability of the systems. Combining the mathematical regression analysis with the different physical stressing experiments, we investigated the non-destructive screening method for radiation hardened performance of the integrated circuit. The relationship between the change of typical parameters and the radiation performance of the circuit was discussed. The irradiation-sensitive parameters were confirmed. The pluralistic linear regression equation toward the prediction of the radiation performance was established. Finally, the regression equations under stress conditions were verified by practical irradiation. The results show that the reliability and accuracy of the non-destructive screening method can be elevated by combining the mathematical regression analysis with the practical stressing experiment. (authors)

  10. Political consultation and large-scale research

    International Nuclear Information System (INIS)

    Bechmann, G.; Folkers, H.

    1977-01-01

    Large-scale research and policy consulting have an intermediary position between sociological sub-systems. While large-scale research coordinates science, policy, and production, policy consulting coordinates science, policy and political spheres. In this very position, large-scale research and policy consulting lack of institutional guarantees and rational back-ground guarantee which are characteristic for their sociological environment. This large-scale research can neither deal with the production of innovative goods under consideration of rentability, nor can it hope for full recognition by the basis-oriented scientific community. Policy consulting knows neither the competence assignment of the political system to make decisions nor can it judge succesfully by the critical standards of the established social science, at least as far as the present situation is concerned. This intermediary position of large-scale research and policy consulting has, in three points, a consequence supporting the thesis which states that this is a new form of institutionalization of science: These are: 1) external control, 2) the organization form, 3) the theoretical conception of large-scale research and policy consulting. (orig.) [de

  11. Nanoparticle-Based Delivery System for Biomedical Applications of RNAi

    DEFF Research Database (Denmark)

    Yang, Chuanxu

    RNA interference (RNAi) is a post-transcriptional gene silencing process triggered by double-strand RNA, including synthetic short interfering RNA (siRNA) and endogenous microRNA (miRNA). RNAi has attracted great attention for developing a new class of therapeutics, due to its capability to speci......RNA/miRNA and transport them to the action site in the target cells. This thesis describes the development of various nanocarriers for siRNA/miRNA delivery and investigate their potential biomedical applications including: anti-inflammation, tissue engineering and cancer...

  12. Large-scale multimedia modeling applications

    International Nuclear Information System (INIS)

    Droppo, J.G. Jr.; Buck, J.W.; Whelan, G.; Strenge, D.L.; Castleton, K.J.; Gelston, G.M.

    1995-08-01

    Over the past decade, the US Department of Energy (DOE) and other agencies have faced increasing scrutiny for a wide range of environmental issues related to past and current practices. A number of large-scale applications have been undertaken that required analysis of large numbers of potential environmental issues over a wide range of environmental conditions and contaminants. Several of these applications, referred to here as large-scale applications, have addressed long-term public health risks using a holistic approach for assessing impacts from potential waterborne and airborne transport pathways. Multimedia models such as the Multimedia Environmental Pollutant Assessment System (MEPAS) were designed for use in such applications. MEPAS integrates radioactive and hazardous contaminants impact computations for major exposure routes via air, surface water, ground water, and overland flow transport. A number of large-scale applications of MEPAS have been conducted to assess various endpoints for environmental and human health impacts. These applications are described in terms of lessons learned in the development of an effective approach for large-scale applications

  13. A genome-wide gene function prediction resource for Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Han Yan

    2010-08-01

    Full Text Available Predicting gene functions by integrating large-scale biological data remains a challenge for systems biology. Here we present a resource for Drosophila melanogaster gene function predictions. We trained function-specific classifiers to optimize the influence of different biological datasets for each functional category. Our model predicted GO terms and KEGG pathway memberships for Drosophila melanogaster genes with high accuracy, as affirmed by cross-validation, supporting literature evidence, and large-scale RNAi screens. The resulting resource of prioritized associations between Drosophila genes and their potential functions offers a guide for experimental investigations.

  14. The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides.

    Science.gov (United States)

    Nicolás, Francisco E; Vila, Ana; Moxon, Simon; Cascales, María D; Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M; Garre, Victoriano

    2015-03-25

    RNA interference (RNAi) is a conserved mechanism of genome defence that can also have a role in the regulation of endogenous functions through endogenous small RNAs (esRNAs). In fungi, knowledge of the functions regulated by esRNAs has been hampered by lack of clear phenotypes in most mutants affected in the RNAi machinery. Mutants of Mucor circinelloides affected in RNAi genes show defects in physiological and developmental processes, thus making Mucor an outstanding fungal model for studying endogenous functions regulated by RNAi. Some classes of Mucor esRNAs map to exons (ex-siRNAs) and regulate expression of the genes from which they derive. To have a broad picture of genes regulated by the silencing machinery during vegetative growth, we have sequenced and compared the mRNA profiles of mutants in the main RNAi genes by using RNA-seq. In addition, we have achieved a more complete phenotypic characterization of silencing mutants. Deletion of any main RNAi gene provoked a deep impact in mRNA accumulation at exponential and stationary growth. Genes showing increased mRNA levels, as expected for direct ex-siRNAs targets, but also genes with decreased expression were detected, suggesting that, most probably, the initial ex-siRNA targets regulate the expression of other genes, which can be up- or down-regulated. Expression of 50% of the genes was dependent on more than one RNAi gene in agreement with the existence of several classes of ex-siRNAs produced by different combinations of RNAi proteins. These combinations of proteins have also been involved in the regulation of different cellular processes. Besides genes regulated by the canonical RNAi pathway, this analysis identified processes, such as growth at low pH and sexual interaction that are regulated by a dicer-independent non-canonical RNAi pathway. This work shows that the RNAi pathways play a relevant role in the regulation of a significant number of endogenous genes in M. circinelloides during exponential

  15. Pilot study of large-scale production of mutant pigs by ENU mutagenesis.

    Science.gov (United States)

    Hai, Tang; Cao, Chunwei; Shang, Haitao; Guo, Weiwei; Mu, Yanshuang; Yang, Shulin; Zhang, Ying; Zheng, Qiantao; Zhang, Tao; Wang, Xianlong; Liu, Yu; Kong, Qingran; Li, Kui; Wang, Dayu; Qi, Meng; Hong, Qianlong; Zhang, Rui; Wang, Xiupeng; Jia, Qitao; Wang, Xiao; Qin, Guosong; Li, Yongshun; Luo, Ailing; Jin, Weiwu; Yao, Jing; Huang, Jiaojiao; Zhang, Hongyong; Li, Menghua; Xie, Xiangmo; Zheng, Xuejuan; Guo, Kenan; Wang, Qinghua; Zhang, Shibin; Li, Liang; Xie, Fei; Zhang, Yu; Weng, Xiaogang; Yin, Zhi; Hu, Kui; Cong, Yimei; Zheng, Peng; Zou, Hailong; Xin, Leilei; Xia, Jihan; Ruan, Jinxue; Li, Hegang; Zhao, Weiming; Yuan, Jing; Liu, Zizhan; Gu, Weiwang; Li, Ming; Wang, Yong; Wang, Hongmei; Yang, Shiming; Liu, Zhonghua; Wei, Hong; Zhao, Jianguo; Zhou, Qi; Meng, Anming

    2017-06-22

    N-ethyl-N-nitrosourea (ENU) mutagenesis is a powerful tool to generate mutants on a large scale efficiently, and to discover genes with novel functions at the whole-genome level in Caenorhabditis elegans, flies, zebrafish and mice, but it has never been tried in large model animals. We describe a successful systematic three-generation ENU mutagenesis screening in pigs with the establishment of the Chinese Swine Mutagenesis Consortium. A total of 6,770 G1 and 6,800 G3 pigs were screened, 36 dominant and 91 recessive novel pig families with various phenotypes were established. The causative mutations in 10 mutant families were further mapped. As examples, the mutation of SOX10 (R109W) in pig causes inner ear malfunctions and mimics human Mondini dysplasia, and upregulated expression of FBXO32 is associated with congenital splay legs. This study demonstrates the feasibility of artificial random mutagenesis in pigs and opens an avenue for generating a reservoir of mutants for agricultural production and biomedical research.

  16. RNAi: An emerging field of molecular research

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-29

    Dec 29, 2008 ... structure and genome integrity (Hannon, 2002; Grewal and Moazed ... function. COMPONENTS OF RNAi. Among the components of gene silencing process, some serve as .... PTGS technology has many advantages: It is.

  17. Large-scale biophysical evaluation of protein PEGylation effects

    DEFF Research Database (Denmark)

    Vernet, Erik; Popa, Gina; Pozdnyakova, Irina

    2016-01-01

    PEGylation is the most widely used method to chemically modify protein biopharmaceuticals, but surprisingly limited public data is available on the biophysical effects of protein PEGylation. Here we report the first large-scale study, with site-specific mono-PEGylation of 15 different proteins...... of PEGylation on the thermal stability of a protein based on data generated by circular dichroism (CD), differential scanning calorimetry (DSC), or differential scanning fluorimetry (DSF). In addition, DSF was validated as a fast and inexpensive screening method for thermal unfolding studies of PEGylated...... proteins. Multivariate data analysis revealed clear trends in biophysical properties upon PEGylation for a subset of proteins, although no universal trends were found. Taken together, these findings are important in the consideration of biophysical methods and evaluation of second...

  18. Sensitivity of 2-[18F]fluoro-2-deoxyglucose positron emission tomography for advanced colorectal neoplasms: a large-scale analysis of 7505 asymptomatic screening individuals.

    Science.gov (United States)

    Sekiguchi, Masau; Kakugawa, Yasuo; Terauchi, Takashi; Matsumoto, Minori; Saito, Hiroshi; Muramatsu, Yukio; Saito, Yutaka; Matsuda, Takahisa

    2016-12-01

    The sensitivity of 2-[ 18 F]fluoro-2-deoxyglucose positron emission tomography (FDG-PET) for advanced colorectal neoplasms among healthy subjects is not yet fully understood. The present study aimed to clarify the sensitivity by analyzing large-scale data from an asymptomatic screening population. A total of 7505 asymptomatic screenees who underwent both FDG-PET and colonoscopy at our Cancer Screening Division between February 2004 and March 2013 were analyzed. FDG-PET and colonoscopy were performed on consecutive days, and each examination was interpreted in a blinded fashion. The results of the two examinations were compared for each of the divided six colonic segments, with those from colonoscopy being set as the reference. The relationships between the sensitivity of FDG-PET and clinicopathological features of advanced neoplasms were also evaluated. Two hundred ninety-one advanced neoplasms, including 24 invasive cancers, were detected in 262 individuals. Thirteen advanced neoplasms (advanced adenomas) were excluded from the analysis because of the coexistence of lesions in the same colonic segment. The sensitivity, specificity, and positive and negative predictive values of FDG-PET for advanced neoplasms were 16.9 % [95 % confidence interval (CI) 12.7-21.8 %], 99.3 % (95 % CI 99.2-99.4 %), 13.5 % (95 % CI 10.1-17.6 %), and 99.4 % (95 % CI 99.3-99.5 %), respectively. The sensitivity was lower for lesions with less advanced histological grade, of smaller size, and flat-type morphology, and for those located in the proximal part of the colon. FDG-PET is believed to be difficult to use as a primary screening tool in population-based colorectal cancer screening because of its low sensitivity for advanced neoplasms. Even when it is used in opportunistic cancer screening, the limit of its sensitivity should be considered.

  19. Decentralized Large-Scale Power Balancing

    DEFF Research Database (Denmark)

    Halvgaard, Rasmus; Jørgensen, John Bagterp; Poulsen, Niels Kjølstad

    2013-01-01

    problem is formulated as a centralized large-scale optimization problem but is then decomposed into smaller subproblems that are solved locally by each unit connected to an aggregator. For large-scale systems the method is faster than solving the full problem and can be distributed to include an arbitrary...

  20. A large-scale study of epilepsy in Ecuador: methodological aspects.

    Science.gov (United States)

    Placencia, M; Suarez, J; Crespo, F; Sander, J W; Shorvon, S D; Ellison, R H; Cascante, S M

    1992-01-01

    The methodology is presented of a large-scale study of epilepsy carried out in a highland area in northern Ecuador, South America, covering a population of 72,121 people; The study was carried out in two phases, the first, a cross-sectional phase, consisted of a house-to-house survey of all persons in this population, screening for epileptic seizures using a specially designed questionnaire. Possible cases identified in screening were assessed in a cascade diagnostic procedure applied by general doctors and neurologists. Its objectives were: to establish a comprehensive epidemiological profile of epileptic seizures; to describe the clinical phenomenology of this condition in the community; to validate methods for diagnosis and classification of epileptic seizures by a non-specialised team; and to ascertain the community's knowledge, attitudes and practices regarding epilepsy. A sample was selected in this phase in order to study the social aspects of epilepsy in this community. The second phase, which was longitudinal, assessed the ability of non-specialist care in the treatment of epilepsy. It consisted of a prospective clinical trial of antiepileptic therapy in untreated patients using two standard anti-epileptic drugs. Patients were followed for 12 months by a multidisciplinary team consisting of a primary health worker, rural doctor, neurologist, anthropologist, and psychologist. Standardised, reproducible instruments and methods were used. This study was carried out through co-operation between the medical profession, political agencies and the pharmaceutical industry, at an international level. We consider this a model for further large-scale studies of this type.

  1. The insect ecdysone receptor is a good potential target for RNAi-based pest control.

    Science.gov (United States)

    Yu, Rong; Xu, Xinping; Liang, Yongkang; Tian, Honggang; Pan, Zhanqing; Jin, Shouheng; Wang, Na; Zhang, Wenqing

    2014-01-01

    RNA interference (RNAi) has great potential for use in insect pest control. However, some significant challenges must be overcome before RNAi-based pest control can become a reality. One challenge is the proper selection of a good target gene for RNAi. Here, we report that the insect ecdysone receptor (EcR) is a good potential target for RNAi-based pest control in the brown planthopper Nilaparvata lugens, a serious insect pest of rice plants. We demonstrated that the use of a 360 bp fragment (NlEcR-c) that is common between NlEcR-A and NlEcR-B for feeding RNAi experiments significantly decreased the relative mRNA expression levels of NlEcR compared with those in the dsGFP control. Feeding RNAi also resulted in a significant reduction in the number of offspring per pair of N. lugens. Consequently, a transgenic rice line expressing NlEcR dsRNA was constructed by Agrobacterium- mediated transformation. The results of qRT-PCR showed that the total copy number of the target gene in all transgenic rice lines was 2. Northern blot analysis showed that the small RNA of the hairpin dsNlEcR-c was successfully expressed in the transgenic rice lines. After newly hatched nymphs of N. lugens fed on the transgenic rice lines, effective RNAi was observed. The NlEcR expression levels in all lines examined were decreased significantly compared with the control. In all lines, the survival rate of the nymphs was nearly 90%, and the average number of offspring per pair in the treated groups was significantly less than that observed in the control, with a decrease of 44.18-66.27%. These findings support an RNAi-based pest control strategy and are also important for the management of rice insect pests.

  2. A genome-wide siRNA screen in mammalian cells for regulators of S6 phosphorylation.

    Directory of Open Access Journals (Sweden)

    Angela Papageorgiou

    Full Text Available mTOR complex1, the major regulator of mRNA translation in all eukaryotic cells, is strongly activated in most cancers. We performed a genome-wide RNAi screen in a human cancer cell line, seeking genes that regulate S6 phosphorylation, readout of mTORC1 activity. Applying a stringent selection, we retrieved nearly 600 genes wherein at least two RNAis gave significant reduction in S6-P. This cohort contains known regulators of mTOR complex 1 and is significantly enriched in genes whose depletion affects the proliferation/viability of the large set of cancer cell lines in the Achilles database in a manner paralleling that caused by mTOR depletion. We next examined the effect of RNAi pools directed at 534 of these gene products on S6-P in TSC1 null mouse embryo fibroblasts. 76 RNAis reduced S6 phosphorylation significantly in 2 or 3 replicates. Surprisingly, among this cohort of genes the only elements previously associated with the maintenance of mTORC1 activity are two subunits of the vacuolar ATPase and the CUL4 subunit DDB1. RNAi against a second set of 84 targets reduced S6-P in only one of three replicates. However, an indication that this group also bears attention is the presence of rpS6KB1 itself, Rac1 and MAP4K3, a protein kinase that supports amino acid signaling to rpS6KB1. The finding that S6 phosphorylation requires a previously unidentified, functionally diverse cohort of genes that participate in fundamental cellular processes such as mRNA translation, RNA processing, DNA repair and metabolism suggests the operation of feedback pathways in the regulation of mTORC1 operating through novel mechanisms.

  3. Automating large-scale reactor systems

    International Nuclear Information System (INIS)

    Kisner, R.A.

    1985-01-01

    This paper conveys a philosophy for developing automated large-scale control systems that behave in an integrated, intelligent, flexible manner. Methods for operating large-scale systems under varying degrees of equipment degradation are discussed, and a design approach that separates the effort into phases is suggested. 5 refs., 1 fig

  4. The use of saliva as a practical and feasible alternative to urine in large-scale screening for congenital cytomegalovirus infection increasesinclusion and detection rates

    Directory of Open Access Journals (Sweden)

    Emanuelle Santos de Carvalho Cardoso

    2015-04-01

    Full Text Available INTRODUCTION: Although urine is considered the gold-standard material for the detection of congenital cytomegalovirus (CMV infection, it can be difficult to obtain in newborns. The aim of this study was to compare the efficiency of detection of congenital CMV infection in saliva and urine samples. METHODS: One thousand newborns were included in the study. Congenital cytomegalovirus deoxyribonucleic acid (DNA was detected by polymerase chain reaction (PCR. RESULTS: Saliva samples were obtained from all the newborns, whereas urine collection was successful in only 333 cases. There was no statistically significant difference between the use of saliva alone or saliva and urine collected simultaneously for the detection of CMV infection. CONCLUSIONS: Saliva samples can be used in large-scale neonatal screening for CMV infection.

  5. Large scale meta-analysis of fragment-based screening campaigns: privileged fragments and complementary technologies.

    Science.gov (United States)

    Kutchukian, Peter S; Wassermann, Anne Mai; Lindvall, Mika K; Wright, S Kirk; Ottl, Johannes; Jacob, Jaison; Scheufler, Clemens; Marzinzik, Andreas; Brooijmans, Natasja; Glick, Meir

    2015-06-01

    A first step in fragment-based drug discovery (FBDD) often entails a fragment-based screen (FBS) to identify fragment "hits." However, the integration of conflicting results from orthogonal screens remains a challenge. Here we present a meta-analysis of 35 fragment-based campaigns at Novartis, which employed a generic 1400-fragment library against diverse target families using various biophysical and biochemical techniques. By statistically interrogating the multidimensional FBS data, we sought to investigate three questions: (1) What makes a fragment amenable for FBS? (2) How do hits from different fragment screening technologies and target classes compare with each other? (3) What is the best way to pair FBS assay technologies? In doing so, we identified substructures that were privileged for specific target classes, as well as fragments that were privileged for authentic activity against many targets. We also revealed some of the discrepancies between technologies. Finally, we uncovered a simple rule of thumb in screening strategy: when choosing two technologies for a campaign, pairing a biochemical and biophysical screen tends to yield the greatest coverage of authentic hits. © 2014 Society for Laboratory Automation and Screening.

  6. RNAi-based GM plants: food for thought for risk assessors.

    Science.gov (United States)

    Ramon, Matthew; Devos, Yann; Lanzoni, Anna; Liu, Yi; Gomes, Ana; Gennaro, Andrea; Waigmann, Elisabeth

    2014-12-01

    RNA interference (RNAi) is an emerging technology that offers new opportunities for the generation of new traits in genetically modified (GM) plants. Potential risks associated with RNAi-based GM plants and issues specific to their risk assessment were discussed during an international scientific workshop (June 2014) organized by the European Food Safety Authority (EFSA). Selected key outcomes of the workshop are reported here. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  7. Spanish-language screening scales: A critical review.

    Science.gov (United States)

    Torres-Castro, S; Mena-Montes, B; González-Ambrosio, G; Zubieta-Zavala, A; Torres-Carrillo, N M; Acosta-Castillo, G I; Espinel-Bermúdez, M C

    2018-05-09

    Dementia is a chronic, degenerative disease with a strong impact on families and health systems. The instruments currently in use for measuring cognitive impairment have different psychometric characteristics in terms of application time, cut-off point, reliability, and validity. The objective of this review is to describe the characteristics of the validated, Spanish-language versions of the Mini-Cog, Clock-Drawing Test, and Mini-Mental State Examination scales for cognitive impairment screening. We performed a three-stage literature search of articles published on Medline since 1953. We selected articles on validated, Spanish-language versions of the scales that included data on reliability, validity, sensitivity, and specificity. The 3 screening tools assessed in this article provide support for primary care professionals. Timely identification of mild cognitive impairment and dementia is crucial for the prognosis of these patients. Copyright © 2018 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

  8. RNAi screen reveals host cell kinases specifically involved in Listeria monocytogenes spread from cell to cell.

    Directory of Open Access Journals (Sweden)

    Ryan Chong

    Full Text Available Intracellular bacterial pathogens, such as Listeria monocytogenes and Rickettsia conorii display actin-based motility in the cytosol of infected cells and spread from cell to cell through the formation of membrane protrusions at the cell cortex. Whereas the mechanisms supporting cytosolic actin-based motility are fairly well understood, it is unclear whether specific host factors may be required for supporting the formation and resolution of membrane protrusions. To address this gap in knowledge, we have developed high-throughput fluorescence microscopy and computer-assisted image analysis procedures to quantify pathogen spread in human epithelial cells. We used the approach to screen a siRNA library covering the human kinome and identified 7 candidate kinases whose depletion led to severe spreading defects in cells infected with L. monocytogenes. We conducted systematic validation procedures with redundant silencing reagents and confirmed the involvement of the serine/threonine kinases, CSNK1A1 and CSNK2B. We conducted secondary assays showing that, in contrast with the situation observed in CSNK2B-depleted cells, L. monocytogenes formed wild-type cytosolic tails and displayed wild-type actin-based motility in the cytosol of CSNK1A1-depleted cells. Furthermore, we developed a protrusion formation assay and showed that the spreading defect observed in CSNK1A1-depleted cells correlated with the formation of protrusion that did not resolve into double-membrane vacuoles. Moreover, we developed sending and receiving cell-specific RNAi procedures and showed that CSNK1A was required in the sending cells, but was dispensable in the receiving cells, for protrusion resolution. Finally, we showed that the observed defects were specific to Listeria monocytogenes, as Rickettsia conorii displayed wild-type cell-to-cell spread in CSNK1A1- and CSNK2B-depleted cells. We conclude that, in addition to the specific host factors supporting cytosolic actin

  9. The Software Reliability of Large Scale Integration Circuit and Very Large Scale Integration Circuit

    OpenAIRE

    Artem Ganiyev; Jan Vitasek

    2010-01-01

    This article describes evaluation method of faultless function of large scale integration circuits (LSI) and very large scale integration circuits (VLSI). In the article there is a comparative analysis of factors which determine faultless of integrated circuits, analysis of already existing methods and model of faultless function evaluation of LSI and VLSI. The main part describes a proposed algorithm and program for analysis of fault rate in LSI and VLSI circuits.

  10. RNAi Technology for Insect Management and Protection of Beneficial Insects from Diseases: Lessons, Challenges and Risk Assessments.

    Science.gov (United States)

    Zotti, M J; Smagghe, G

    2015-06-01

    The time has passed for us to wonder whether RNA interference (RNAi) effectively controls pest insects or protects beneficial insects from diseases. The RNAi era in insect science began with studies of gene function and genetics that paved the way for the development of novel and highly specific approaches for the management of pest insects and, more recently, for the treatment and prevention of diseases in beneficial insects. The slight differences in components of RNAi pathways are sufficient to provide a high degree of variation in responsiveness among insects. The current framework to assess the negative effects of genetically modified (GM) plants on human health is adequate for RNAi-based GM plants. Because of the mode of action of RNAi and the lack of genomic data for most exposed non-target organisms, it becomes difficult to determine the environmental risks posed by RNAi-based technologies and the benefits provided for the protection of crops. A better understanding of the mechanisms that determine the variability in the sensitivity of insects would accelerate the worldwide release of commercial RNAi-based approaches.

  11. Large-scale generation of human iPSC-derived neural stem cells/early neural progenitor cells and their neuronal differentiation.

    Science.gov (United States)

    D'Aiuto, Leonardo; Zhi, Yun; Kumar Das, Dhanjit; Wilcox, Madeleine R; Johnson, Jon W; McClain, Lora; MacDonald, Matthew L; Di Maio, Roberto; Schurdak, Mark E; Piazza, Paolo; Viggiano, Luigi; Sweet, Robert; Kinchington, Paul R; Bhattacharjee, Ayantika G; Yolken, Robert; Nimgaonka, Vishwajit L; Nimgaonkar, Vishwajit L

    2014-01-01

    Induced pluripotent stem cell (iPSC)-based technologies offer an unprecedented opportunity to perform high-throughput screening of novel drugs for neurological and neurodegenerative diseases. Such screenings require a robust and scalable method for generating large numbers of mature, differentiated neuronal cells. Currently available methods based on differentiation of embryoid bodies (EBs) or directed differentiation of adherent culture systems are either expensive or are not scalable. We developed a protocol for large-scale generation of neuronal stem cells (NSCs)/early neural progenitor cells (eNPCs) and their differentiation into neurons. Our scalable protocol allows robust and cost-effective generation of NSCs/eNPCs from iPSCs. Following culture in neurobasal medium supplemented with B27 and BDNF, NSCs/eNPCs differentiate predominantly into vesicular glutamate transporter 1 (VGLUT1) positive neurons. Targeted mass spectrometry analysis demonstrates that iPSC-derived neurons express ligand-gated channels and other synaptic proteins and whole-cell patch-clamp experiments indicate that these channels are functional. The robust and cost-effective differentiation protocol described here for large-scale generation of NSCs/eNPCs and their differentiation into neurons paves the way for automated high-throughput screening of drugs for neurological and neurodegenerative diseases.

  12. An optimized lentiviral vector system for conditional RNAi and efficient cloning of microRNA embedded short hairpin RNA libraries.

    Science.gov (United States)

    Adams, Felix F; Heckl, Dirk; Hoffmann, Thomas; Talbot, Steven R; Kloos, Arnold; Thol, Felicitas; Heuser, Michael; Zuber, Johannes; Schambach, Axel; Schwarzer, Adrian

    2017-09-01

    RNA interference (RNAi) and CRISPR-Cas9-based screening systems have emerged as powerful and complementary tools to unravel genetic dependencies through systematic gain- and loss-of-function studies. In recent years, a series of technical advances helped to enhance the performance of virally delivered RNAi. For instance, the incorporation of short hairpin RNAs (shRNAs) into endogenous microRNA contexts (shRNAmiRs) allows the use of Tet-regulated promoters for synchronous onset of gene knockdown and precise interrogation of gene dosage effects. However, remaining challenges include lack of efficient cloning strategies, inconsistent knockdown potencies and leaky expression. Here, we present a simple, one-step cloning approach for rapid and efficient cloning of miR-30 shRNAmiR libraries. We combined a human miR-30 backbone retaining native flanking sequences with an optimized all-in-one lentiviral vector system for conditional RNAi to generate a versatile toolbox characterized by higher doxycycline sensitivity, reduced leakiness and enhanced titer. Furthermore, refinement of existing shRNA design rules resulted in substantially improved prediction of powerful shRNAs. Our approach was validated by accurate quantification of the knockdown potency of over 250 single shRNAmiRs. To facilitate access and use by the scientific community, an online tool was developed for the automated design of refined shRNA-coding oligonucleotides ready for cloning into our system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Phylogenetic distribution of large-scale genome patchiness

    Directory of Open Access Journals (Sweden)

    Hackenberg Michael

    2008-04-01

    Full Text Available Abstract Background The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level. Results The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best-sequenced genome assemblies from eleven eukaryotic genomes: mammals (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris, birds (Gallus gallus, fishes (Danio rerio, invertebrates (Drosophila melanogaster and Caenorhabditis elegans, plants (Arabidopsis thaliana and yeasts (Saccharomyces cerevisiae. We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range. Conclusion Large-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level.

  14. Managing large-scale models: DBS

    International Nuclear Information System (INIS)

    1981-05-01

    A set of fundamental management tools for developing and operating a large scale model and data base system is presented. Based on experience in operating and developing a large scale computerized system, the only reasonable way to gain strong management control of such a system is to implement appropriate controls and procedures. Chapter I discusses the purpose of the book. Chapter II classifies a broad range of generic management problems into three groups: documentation, operations, and maintenance. First, system problems are identified then solutions for gaining management control are disucssed. Chapters III, IV, and V present practical methods for dealing with these problems. These methods were developed for managing SEAS but have general application for large scale models and data bases

  15. Large Scale Self-Organizing Information Distribution System

    National Research Council Canada - National Science Library

    Low, Steven

    2005-01-01

    This project investigates issues in "large-scale" networks. Here "large-scale" refers to networks with large number of high capacity nodes and transmission links, and shared by a large number of users...

  16. CrossCheck: an open-source web tool for high-throughput screen data analysis.

    Science.gov (United States)

    Najafov, Jamil; Najafov, Ayaz

    2017-07-19

    Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis. CrossCheck is a centralized database that allows effortless comparison of the user-entered list of gene symbols with 16,231 published datasets. These datasets include published data from genome-wide RNAi and CRISPR screens, interactome proteomics and phosphoproteomics screens, cancer mutation databases, low-throughput studies of major cell signaling mediators, such as kinases, E3 ubiquitin ligases and phosphatases, and gene ontological information. Moreover, CrossCheck includes a novel database of predicted protein kinase substrates, which was developed using proteome-wide consensus motif searches. CrossCheck dramatically simplifies high-throughput screen data analysis and enables researchers to dig deep into the published literature and streamline data-driven hypothesis generation. CrossCheck is freely accessible as a web-based application at http://proteinguru.com/crosscheck.

  17. Flavivirus RNAi suppression: decoding non-coding RNA

    NARCIS (Netherlands)

    Pijlman, G.P.

    2014-01-01

    Flaviviruses are important human pathogens that are transmitted by invertebrate vectors, mostly mosquitoes and ticks. During replication in their vector, flaviviruses are subject to a potent innate immune response known as antiviral RNA interference (RNAi). This defense mechanism is associated with

  18. Core RNAi machinery and gene knockdown in the emerald ash borer (Agrilus planipennis).

    Science.gov (United States)

    Zhao, Chaoyang; Alvarez Gonzales, Miguel A; Poland, Therese M; Mittapalli, Omprakash

    2015-01-01

    The RNA interference (RNAi) technology has been widely used in insect functional genomics research and provides an alternative approach for insect pest management. To understand whether the emerald ash borer (Agrilus planipennis), an invasive and destructive coleopteran insect pest of ash tree (Fraxinus spp.), possesses a strong RNAi machinery that is capable of degrading target mRNA as a response to exogenous double-stranded RNA (dsRNA) induction, we identified three RNAi pathway core component genes, Dicer-2, Argonaute-2 and R2D2, from the A. planipennis genome sequence. Characterization of these core components revealed that they contain conserved domains essential for the proteins to function in the RNAi pathway. Phylogenetic analyses showed that they are closely related to homologs derived from other coleopteran species. We also delivered the dsRNA fragment of AplaScrB-2, a β-fructofuranosidase-encoding gene horizontally acquired by A. planipennis as we reported previously, into A. planipennis adults through microinjection. Quantitative real-time PCR analysis on the dsRNA-treated beetles demonstrated a significantly decreased gene expression level of AplaScrB-2 appearing on day 2 and lasting until at least day 6. This study is the first record of RNAi applied in A. planipennis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Large scale structure and baryogenesis

    International Nuclear Information System (INIS)

    Kirilova, D.P.; Chizhov, M.V.

    2001-08-01

    We discuss a possible connection between the large scale structure formation and the baryogenesis in the universe. An update review of the observational indications for the presence of a very large scale 120h -1 Mpc in the distribution of the visible matter of the universe is provided. The possibility to generate a periodic distribution with the characteristic scale 120h -1 Mpc through a mechanism producing quasi-periodic baryon density perturbations during inflationary stage, is discussed. The evolution of the baryon charge density distribution is explored in the framework of a low temperature boson condensate baryogenesis scenario. Both the observed very large scale of a the visible matter distribution in the universe and the observed baryon asymmetry value could naturally appear as a result of the evolution of a complex scalar field condensate, formed at the inflationary stage. Moreover, for some model's parameters a natural separation of matter superclusters from antimatter ones can be achieved. (author)

  20. State-of-the-art of large scale biogas plants

    International Nuclear Information System (INIS)

    Prisum, J.M.; Noergaard, P.

    1992-01-01

    A survey of the technological state of large scale biogas plants in Europe treating manure is given. 83 plants are in operation at present. Of these, 16 are centralised digestion plants. Transport costs at centralised digestion plants amounts to between 25 and 40 percent of the total operational costs. Various transport equipment is used. Most large scale digesters are CSTRs, but serial, contact, 2-step, and plug-flow digesters are also found. Construction materials are mostly steel and concrete. Mesophilic digestion is most common (56%), thermophilic digestion is used in 17% of the plants, combined mesophilic and thermophilic digestion is used in 28% of the centralised plants. Mixing of digester content is performed with gas injection, propellers, and gas-liquid displacement. Heating is carried out using external or internal heat exchangers. Heat recovery is only used in Denmark. Gas purification equipment is commonplace, but not often needed. Several plants use separation of the digested manure, often as part of a post-treatment/-purification process or for the production of 'compost'. Screens, sieve belt separaters, centrifuges and filter presses are employed. The use of biogas varies considerably. In some cases, combined heat and power stations are supplying the grid and district heating systems. Other plants use only either the electricity or heat. (au)

  1. Automatic management software for large-scale cluster system

    International Nuclear Information System (INIS)

    Weng Yunjian; Chinese Academy of Sciences, Beijing; Sun Gongxing

    2007-01-01

    At present, the large-scale cluster system faces to the difficult management. For example the manager has large work load. It needs to cost much time on the management and the maintenance of large-scale cluster system. The nodes in large-scale cluster system are very easy to be chaotic. Thousands of nodes are put in big rooms so that some managers are very easy to make the confusion with machines. How do effectively carry on accurate management under the large-scale cluster system? The article introduces ELFms in the large-scale cluster system. Furthermore, it is proposed to realize the large-scale cluster system automatic management. (authors)

  2. GPU-based large-scale visualization

    KAUST Repository

    Hadwiger, Markus

    2013-11-19

    Recent advances in image and volume acquisition as well as computational advances in simulation have led to an explosion of the amount of data that must be visualized and analyzed. Modern techniques combine the parallel processing power of GPUs with out-of-core methods and data streaming to enable the interactive visualization of giga- and terabytes of image and volume data. A major enabler for interactivity is making both the computational and the visualization effort proportional to the amount of data that is actually visible on screen, decoupling it from the full data size. This leads to powerful display-aware multi-resolution techniques that enable the visualization of data of almost arbitrary size. The course consists of two major parts: An introductory part that progresses from fundamentals to modern techniques, and a more advanced part that discusses details of ray-guided volume rendering, novel data structures for display-aware visualization and processing, and the remote visualization of large online data collections. You will learn how to develop efficient GPU data structures and large-scale visualizations, implement out-of-core strategies and concepts such as virtual texturing that have only been employed recently, as well as how to use modern multi-resolution representations. These approaches reduce the GPU memory requirements of extremely large data to a working set size that fits into current GPUs. You will learn how to perform ray-casting of volume data of almost arbitrary size and how to render and process gigapixel images using scalable, display-aware techniques. We will describe custom virtual texturing architectures as well as recent hardware developments in this area. We will also describe client/server systems for distributed visualization, on-demand data processing and streaming, and remote visualization. We will describe implementations using OpenGL as well as CUDA, exploiting parallelism on GPUs combined with additional asynchronous

  3. Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens.

    Science.gov (United States)

    de Groot, Reinoud; Lüthi, Joel; Lindsay, Helen; Holtackers, René; Pelkmans, Lucas

    2018-01-23

    High-content imaging using automated microscopy and computer vision allows multivariate profiling of single-cell phenotypes. Here, we present methods for the application of the CISPR-Cas9 system in large-scale, image-based, gene perturbation experiments. We show that CRISPR-Cas9-mediated gene perturbation can be achieved in human tissue culture cells in a timeframe that is compatible with image-based phenotyping. We developed a pipeline to construct a large-scale arrayed library of 2,281 sequence-verified CRISPR-Cas9 targeting plasmids and profiled this library for genes affecting cellular morphology and the subcellular localization of components of the nuclear pore complex (NPC). We conceived a machine-learning method that harnesses genetic heterogeneity to score gene perturbations and identify phenotypically perturbed cells for in-depth characterization of gene perturbation effects. This approach enables genome-scale image-based multivariate gene perturbation profiling using CRISPR-Cas9. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  4. Rod-coating: towards large-area fabrication of uniform reduced graphene oxide films for flexible touch screens.

    Science.gov (United States)

    Wang, Jie; Liang, Minghui; Fang, Yan; Qiu, Tengfei; Zhang, Jin; Zhi, Linjie

    2012-06-05

    A novel strategy is developed for the large-scale fabrication of reduced graphene oxide films directly on flexible substrates in a controlled manner by the combination of a rod-coating technique and room-temperature reduction of graphene oxide. The as-prepared films display excellent uniformity, good transparency and conductivity, and great flexibility in a touch screen. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Vitellogenin-RNAi and ovariectomy each increase lifespan, increase protein storage, and decrease feeding, but are not additive in grasshoppers.

    Science.gov (United States)

    Tetlak, Alicia G; Burnett, Jacob B; Hahn, Daniel A; Hatle, John D

    2015-12-01

    Reduced reproduction has been shown to increase lifespan in many animals, yet the mechanisms behind this trade-off are unclear. We addressed this question by combining two distinct, direct means of life-extension via reduced reproduction, to test whether they were additive. In the lubber grasshopper, Romalea microptera, ovariectomized (OVX) individuals had a ~20% increase in lifespan and a doubling of storage relative to controls (Sham operated). Similarly, young female grasshoppers treated with RNAi against vitellogenin (the precursor to egg yolk protein) had increased fat body mass and halted ovarian growth. In this study, we compared VgRNAi to two control groups that do not reduce reproduction, namely buffer injection (Buffer) and injection with RNAi against a hexameric storage protein (Hex90RNAi). Each injection treatment was tested with and without ovariectomy. Hence, we tested feeding, storage, and lifespans in six groups: OVX and Buffer, OVX and Hex90RNAi, OVX and VgRNAi, Sham and Buffer, Sham and Hex90RNAi, and Sham and VgRNAi. Ovariectomized grasshoppers and VgRNAi grasshoppers each had similar reductions in feeding (~40%), increases in protein storage in the hemolymph (150-300%), and extensions in lifespan (13-21%). Ovariectomized grasshoppers had higher vitellogenin protein levels than did VgRNAi grasshoppers. Last but not least, when ovariectomy and VgRNAi were applied together, there was no greater effect on feeding, protein storage, or longevity. Hence, feeding regulation, and protein storage in insects, may be conserved components of life-extension via reduced reproduction.

  6. Expression profiling and cross-species RNA interference (RNAi of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae

    Directory of Open Access Journals (Sweden)

    Culleton Bridget A

    2010-01-01

    Full Text Available Abstract Background Some organisms can survive extreme desiccation by entering a state of suspended animation known as anhydrobiosis. The free-living mycophagous nematode Aphelenchus avenae can be induced to enter anhydrobiosis by pre-exposure to moderate reductions in relative humidity (RH prior to extreme desiccation. This preconditioning phase is thought to allow modification of the transcriptome by activation of genes required for desiccation tolerance. Results To identify such genes, a panel of expressed sequence tags (ESTs enriched for sequences upregulated in A. avenae during preconditioning was created. A subset of 30 genes with significant matches in databases, together with a number of apparently novel sequences, were chosen for further study. Several of the recognisable genes are associated with water stress, encoding, for example, two new hydrophilic proteins related to the late embryogenesis abundant (LEA protein family. Expression studies confirmed EST panel members to be upregulated by evaporative water loss, and the majority of genes was also induced by osmotic stress and cold, but rather fewer by heat. We attempted to use RNA interference (RNAi to demonstrate the importance of this gene set for anhydrobiosis, but found A. avenae to be recalcitrant with the techniques used. Instead, therefore, we developed a cross-species RNAi procedure using A. avenae sequences in another anhydrobiotic nematode, Panagrolaimus superbus, which is amenable to gene silencing. Of 20 A. avenae ESTs screened, a significant reduction in survival of desiccation in treated P. superbus populations was observed with two sequences, one of which was novel, while the other encoded a glutathione peroxidase. To confirm a role for glutathione peroxidases in anhydrobiosis, RNAi with cognate sequences from P. superbus was performed and was also shown to reduce desiccation tolerance in this species. Conclusions This study has identified and characterised the

  7. Large scale network-centric distributed systems

    CERN Document Server

    Sarbazi-Azad, Hamid

    2014-01-01

    A highly accessible reference offering a broad range of topics and insights on large scale network-centric distributed systems Evolving from the fields of high-performance computing and networking, large scale network-centric distributed systems continues to grow as one of the most important topics in computing and communication and many interdisciplinary areas. Dealing with both wired and wireless networks, this book focuses on the design and performance issues of such systems. Large Scale Network-Centric Distributed Systems provides in-depth coverage ranging from ground-level hardware issu

  8. The high throughput biomedicine unit at the institute for molecular medicine Finland: high throughput screening meets precision medicine.

    Science.gov (United States)

    Pietiainen, Vilja; Saarela, Jani; von Schantz, Carina; Turunen, Laura; Ostling, Paivi; Wennerberg, Krister

    2014-05-01

    The High Throughput Biomedicine (HTB) unit at the Institute for Molecular Medicine Finland FIMM was established in 2010 to serve as a national and international academic screening unit providing access to state of the art instrumentation for chemical and RNAi-based high throughput screening. The initial focus of the unit was multiwell plate based chemical screening and high content microarray-based siRNA screening. However, over the first four years of operation, the unit has moved to a more flexible service platform where both chemical and siRNA screening is performed at different scales primarily in multiwell plate-based assays with a wide range of readout possibilities with a focus on ultraminiaturization to allow for affordable screening for the academic users. In addition to high throughput screening, the equipment of the unit is also used to support miniaturized, multiplexed and high throughput applications for other types of research such as genomics, sequencing and biobanking operations. Importantly, with the translational research goals at FIMM, an increasing part of the operations at the HTB unit is being focused on high throughput systems biological platforms for functional profiling of patient cells in personalized and precision medicine projects.

  9. Large-Scale Outflows in Seyfert Galaxies

    Science.gov (United States)

    Colbert, E. J. M.; Baum, S. A.

    1995-12-01

    \\catcode`\\@=11 \\ialign{m @th#1hfil ##hfil \\crcr#2\\crcr\\sim\\crcr}}} \\catcode`\\@=12 Highly collimated outflows extend out to Mpc scales in many radio-loud active galaxies. In Seyfert galaxies, which are radio-quiet, the outflows extend out to kpc scales and do not appear to be as highly collimated. In order to study the nature of large-scale (>~1 kpc) outflows in Seyferts, we have conducted optical, radio and X-ray surveys of a distance-limited sample of 22 edge-on Seyfert galaxies. Results of the optical emission-line imaging and spectroscopic survey imply that large-scale outflows are present in >~{{1} /{4}} of all Seyferts. The radio (VLA) and X-ray (ROSAT) surveys show that large-scale radio and X-ray emission is present at about the same frequency. Kinetic luminosities of the outflows in Seyferts are comparable to those in starburst-driven superwinds. Large-scale radio sources in Seyferts appear diffuse, but do not resemble radio halos found in some edge-on starburst galaxies (e.g. M82). We discuss the feasibility of the outflows being powered by the active nucleus (e.g. a jet) or a circumnuclear starburst.

  10. SCALE INTERACTION IN A MIXING LAYER. THE ROLE OF THE LARGE-SCALE GRADIENTS

    KAUST Repository

    Fiscaletti, Daniele

    2015-08-23

    The interaction between scales is investigated in a turbulent mixing layer. The large-scale amplitude modulation of the small scales already observed in other works depends on the crosswise location. Large-scale positive fluctuations correlate with a stronger activity of the small scales on the low speed-side of the mixing layer, and a reduced activity on the high speed-side. However, from physical considerations we would expect the scales to interact in a qualitatively similar way within the flow and across different turbulent flows. Therefore, instead of the large-scale fluctuations, the large-scale gradients modulation of the small scales has been additionally investigated.

  11. The 5'-end heterogeneity of adenovirus virus-associated RNAI contributes to the asymmetric guide strand incorporation into the RNA-induced silencing complex.

    Science.gov (United States)

    Xu, Ning; Gkountela, Sofia; Saeed, Khalid; Akusjärvi, Göran

    2009-11-01

    Human Adenovirus type 5 encodes two short RNA polymerase III transcripts, the virus-associated (VA) RNAI and VA RNAII, which can adopt stable hairpin structures that resemble micro-RNA precursors. The terminal stems of the VA RNAs are processed into small RNAs (mivaRNAs) that are incorporated into RISC. It has been reported that VA RNAI has two transcription initiation sites, which produce two VA RNAI species; a major species, VA RNAI(G), which accounts for 75% of the VA RNAI pool, and a minor species, VA RNAI(A), which initiates transcription three nucleotides upstream compared to VA RNAI(G). We show that this 5'-heterogeneity results in a dramatic difference in RISC assembly. Thus, both VA RNAI(G) and VA RNAI(A) are processed by Dicer at the same position in the terminal stem generating the same 3'-strand mivaRNA. This mivaRNA is incorporated into RISC with 200-fold higher efficiency compared to the 5'-strand of mivaRNAI. Of the small number of 5'-strands used in RISC assembly only VA RNAI(A) generated active RISC complexes. We also show that the 3'-strand of mivaRNAI, although being the preferred substrate for RISC assembly, generates unstable RISC complexes with a low in vitro cleavage activity, only around 2% compared to RISC assembled on the VA RNAI(A) 5'-strand.

  12. Dissecting the large-scale galactic conformity

    Science.gov (United States)

    Seo, Seongu

    2018-01-01

    Galactic conformity is an observed phenomenon that galaxies located in the same region have similar properties such as star formation rate, color, gas fraction, and so on. The conformity was first observed among galaxies within in the same halos (“one-halo conformity”). The one-halo conformity can be readily explained by mutual interactions among galaxies within a halo. Recent observations however further witnessed a puzzling connection among galaxies with no direct interaction. In particular, galaxies located within a sphere of ~5 Mpc radius tend to show similarities, even though the galaxies do not share common halos with each other ("two-halo conformity" or “large-scale conformity”). Using a cosmological hydrodynamic simulation, Illustris, we investigate the physical origin of the two-halo conformity and put forward two scenarios. First, back-splash galaxies are likely responsible for the large-scale conformity. They have evolved into red galaxies due to ram-pressure stripping in a given galaxy cluster and happen to reside now within a ~5 Mpc sphere. Second, galaxies in strong tidal field induced by large-scale structure also seem to give rise to the large-scale conformity. The strong tides suppress star formation in the galaxies. We discuss the importance of the large-scale conformity in the context of galaxy evolution.

  13. Experimental study of tissue-engineered cartilage allograft with RNAi chondrocytes in vivo

    Directory of Open Access Journals (Sweden)

    Wang ZH

    2014-05-01

    Full Text Available Zhenghui Wang,1 Xiaoli Li,2 Xi-Jing He,3 Xianghong Zhang,1 Zhuangqun Yang,4 Min Xu,1 Baojun Wu,1 Junbo Tu,5 Huanan Luo,1 Jing Yan11Department of Otolaryngology – Head and Neck Surgery, 2Department of Dermatology, 3Department of Orthopedics, The Second Hospital, Xi’an Jiaotong University, 4Department of Plastic and Burns Surgery, The First Hospital, Xi’an Jiaotong University, 5Department of Oral and Maxillofacial Plastic Surgery, The Stomatological Hospital, Xi’an Jiaotong University, Xi’an, People’s Republic of ChinaPurpose: To determine the effects of RNA interference (RNAi on chondrocyte proliferation, function, and immunological rejection after allogenic tissue-engineered cartilage transplantation within bone matrix gelatin scaffolds.Methods: Seven million rat normal and RNAi chondrocytes were harvested and separately composited with fibrin glue to make the cell suspension, and then transplanted subcutaneously into the back of Sprague Dawley rats after being cultured for 10 days in vitro. Untransplanted animals served as the control group. The allograft and immunological response were examined at 1, 2, 4, 8, and 12 months postoperatively with hematoxylin and eosin histochemical staining, immunohistochemical staining (aggrecan, type II collagen, class I and II major histocompatibility complex, and flow cytometry for peripheral blood cluster of differentiation 4+ (CD4+ and CD8+ T-cells.Results: There was no infection or death in the rats except one, which died in the first week. Compared to the control group, the RNAi group had fewer eukomonocytes infiltrated, which were only distributed around the graft. The ratio of CD4+/CD8+ T-cells in the RNAi group was significantly lower than the normal one (P<0.05. There were many more positively stained chondrocytes and positively stained areas around the cells in the RNAi group, which were not found in the control group.Conclusion: The aggrecanase-1 and aggrecanase-2 RNAi for chondrocytes

  14. Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward?

    DEFF Research Database (Denmark)

    Shi, Leming; Haibe-Kains, Benjamin; Birkbak, Nicolai Juul

    2014-01-01

    Large-scale pharmacogenomic high-throughput screening (HTS) studies hold great potential for generating robust genomic predictors of drug response. Two recent large-scale HTS studies have reported results of such screens, revealing several known and novel drug sensitivities and biomarkers...

  15. Large-scale perspective as a challenge

    NARCIS (Netherlands)

    Plomp, M.G.A.

    2012-01-01

    1. Scale forms a challenge for chain researchers: when exactly is something ‘large-scale’? What are the underlying factors (e.g. number of parties, data, objects in the chain, complexity) that determine this? It appears to be a continuum between small- and large-scale, where positioning on that

  16. Algorithm 896: LSA: Algorithms for Large-Scale Optimization

    Czech Academy of Sciences Publication Activity Database

    Lukšan, Ladislav; Matonoha, Ctirad; Vlček, Jan

    2009-01-01

    Roč. 36, č. 3 (2009), 16-1-16-29 ISSN 0098-3500 R&D Pro jects: GA AV ČR IAA1030405; GA ČR GP201/06/P397 Institutional research plan: CEZ:AV0Z10300504 Keywords : algorithms * design * large-scale optimization * large-scale nonsmooth optimization * large-scale nonlinear least squares * large-scale nonlinear minimax * large-scale systems of nonlinear equations * sparse pro blems * partially separable pro blems * limited-memory methods * discrete Newton methods * quasi-Newton methods * primal interior-point methods Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 1.904, year: 2009

  17. Scale interactions in a mixing layer – the role of the large-scale gradients

    KAUST Repository

    Fiscaletti, D.

    2016-02-15

    © 2016 Cambridge University Press. The interaction between the large and the small scales of turbulence is investigated in a mixing layer, at a Reynolds number based on the Taylor microscale of , via direct numerical simulations. The analysis is performed in physical space, and the local vorticity root-mean-square (r.m.s.) is taken as a measure of the small-scale activity. It is found that positive large-scale velocity fluctuations correspond to large vorticity r.m.s. on the low-speed side of the mixing layer, whereas, they correspond to low vorticity r.m.s. on the high-speed side. The relationship between large and small scales thus depends on position if the vorticity r.m.s. is correlated with the large-scale velocity fluctuations. On the contrary, the correlation coefficient is nearly constant throughout the mixing layer and close to unity if the vorticity r.m.s. is correlated with the large-scale velocity gradients. Therefore, the small-scale activity appears closely related to large-scale gradients, while the correlation between the small-scale activity and the large-scale velocity fluctuations is shown to reflect a property of the large scales. Furthermore, the vorticity from unfiltered (small scales) and from low pass filtered (large scales) velocity fields tend to be aligned when examined within vortical tubes. These results provide evidence for the so-called \\'scale invariance\\' (Meneveau & Katz, Annu. Rev. Fluid Mech., vol. 32, 2000, pp. 1-32), and suggest that some of the large-scale characteristics are not lost at the small scales, at least at the Reynolds number achieved in the present simulation.

  18. Validation of RNAi by real time PCR

    DEFF Research Database (Denmark)

    Josefsen, Knud; Lee, Ying Chiu

    2011-01-01

    Real time PCR is the analytic tool of choice for quantification of gene expression, while RNAi is concerned with downregulation of gene expression. Together, they constitute a powerful approach in any loss of function studies of selective genes. We illustrate here the use of real time PCR to verify...

  19. Large-scale matrix-handling subroutines 'ATLAS'

    International Nuclear Information System (INIS)

    Tsunematsu, Toshihide; Takeda, Tatsuoki; Fujita, Keiichi; Matsuura, Toshihiko; Tahara, Nobuo

    1978-03-01

    Subroutine package ''ATLAS'' has been developed for handling large-scale matrices. The package is composed of four kinds of subroutines, i.e., basic arithmetic routines, routines for solving linear simultaneous equations and for solving general eigenvalue problems and utility routines. The subroutines are useful in large scale plasma-fluid simulations. (auth.)

  20. Large-scale solar heat

    Energy Technology Data Exchange (ETDEWEB)

    Tolonen, J.; Konttinen, P.; Lund, P. [Helsinki Univ. of Technology, Otaniemi (Finland). Dept. of Engineering Physics and Mathematics

    1998-12-31

    In this project a large domestic solar heating system was built and a solar district heating system was modelled and simulated. Objectives were to improve the performance and reduce costs of a large-scale solar heating system. As a result of the project the benefit/cost ratio can be increased by 40 % through dimensioning and optimising the system at the designing stage. (orig.)

  1. Large-Area Cross-Aligned Silver Nanowire Electrodes for Flexible, Transparent, and Force-Sensitive Mechanochromic Touch Screens.

    Science.gov (United States)

    Cho, Seungse; Kang, Saewon; Pandya, Ashish; Shanker, Ravi; Khan, Ziyauddin; Lee, Youngsu; Park, Jonghwa; Craig, Stephen L; Ko, Hyunhyub

    2017-04-25

    Silver nanowire (AgNW) networks are considered to be promising structures for use as flexible transparent electrodes for various optoelectronic devices. One important application of AgNW transparent electrodes is the flexible touch screens. However, the performances of flexible touch screens are still limited by the large surface roughness and low electrical to optical conductivity ratio of random network AgNW electrodes. In addition, although the perception of writing force on the touch screen enables a variety of different functions, the current technology still relies on the complicated capacitive force touch sensors. This paper demonstrates a simple and high-throughput bar-coating assembly technique for the fabrication of large-area (>20 × 20 cm 2 ), highly cross-aligned AgNW networks for transparent electrodes with the sheet resistance of 21.0 Ω sq -1 at 95.0% of optical transmittance, which compares favorably with that of random AgNW networks (sheet resistance of 21.0 Ω sq -1 at 90.4% of optical transmittance). As a proof of concept demonstration, we fabricate flexible, transparent, and force-sensitive touch screens using cross-aligned AgNW electrodes integrated with mechanochromic spiropyran-polydimethylsiloxane composite film. Our force-sensitive touch screens enable the precise monitoring of dynamic writings, tracing and drawing of underneath pictures, and perception of handwriting patterns with locally different writing forces. The suggested technique provides a robust and powerful platform for the controllable assembly of nanowires beyond the scale of conventional fabrication techniques, which can find diverse applications in multifunctional flexible electronic and optoelectronic devices.

  2. Gene Network Polymorphism Illuminates Loss and Retention of Novel RNAi Silencing Components in the Cryptococcus Pathogenic Species Complex.

    Directory of Open Access Journals (Sweden)

    Marianna Feretzaki

    2016-03-01

    Full Text Available RNAi is a ubiquitous pathway that serves central functions throughout eukaryotes, including maintenance of genome stability and repression of transposon expression and movement. However, a number of organisms have lost their RNAi pathways, including the model yeast Saccharomyces cerevisiae, the maize pathogen Ustilago maydis, the human pathogen Cryptococcus deuterogattii, and some human parasite pathogens, suggesting there may be adaptive benefits associated with both retention and loss of RNAi. By comparing the RNAi-deficient genome of the Pacific Northwest Outbreak C. deuterogattii strain R265 with the RNAi-proficient genomes of the Cryptococcus pathogenic species complex, we identified a set of conserved genes that were lost in R265 and all other C. deuterogattii isolates examined. Genetic and molecular analyses reveal several of these lost genes play roles in RNAi pathways. Four novel components were examined further. Znf3 (a zinc finger protein and Qip1 (a homolog of N. crassa Qip were found to be essential for RNAi, while Cpr2 (a constitutive pheromone receptor and Fzc28 (a transcription factor are involved in sex-induced but not mitosis-induced silencing. Our results demonstrate that the mitotic and sex-induced RNAi pathways rely on the same core components, but sex-induced silencing may be a more specific, highly induced variant that involves additional specialized or regulatory components. Our studies further illustrate how gene network polymorphisms involving known components of key cellular pathways can inform identification of novel elements and suggest that RNAi loss may have been a core event in the speciation of C. deuterogattii and possibly contributed to its pathogenic trajectory.

  3. Probes of large-scale structure in the Universe

    International Nuclear Information System (INIS)

    Suto, Yasushi; Gorski, K.; Juszkiewicz, R.; Silk, J.

    1988-01-01

    Recent progress in observational techniques has made it possible to confront quantitatively various models for the large-scale structure of the Universe with detailed observational data. We develop a general formalism to show that the gravitational instability theory for the origin of large-scale structure is now capable of critically confronting observational results on cosmic microwave background radiation angular anisotropies, large-scale bulk motions and large-scale clumpiness in the galaxy counts. (author)

  4. Screening for Adolescent Problematic Internet Use: Validation of the Problematic and Risky Internet Use Screening Scale (PRIUSS).

    Science.gov (United States)

    Jelenchick, Lauren A; Eickhoff, Jens; Zhang, Chong; Kraninger, Kristina; Christakis, Dimitri A; Moreno, Megan A

    2015-01-01

    Problematic Internet use (PIU) is an emerging health concern that lacks screening measures validated for use with adolescents and young adults. This study aimed to validate the Problematic and Risky Internet Use Screening Scale (PRIUSS) for use with older adolescents and to increase its clinical utility by determining scoring guidelines and assessing the relationship between PIU and other mental health conditions. This cross-sectional survey study took place at a large, public Midwestern university among 330 older adolescents aged 18 to 25 years. Confirmatory factor analysis and Spearman's correlations were used to assess the PRIUSS' structural and construct validity, respectively. A risk-based scoring cutoff was estimated using a Bayesian latent class modeling approach to computing a receiver operating characteristic curve. The confirmatory factor analysis indices for the 3-factor model indicated an acceptable fit (goodness-of-fit index 0.89, root mean square error of approximation 0.07). A cutoff of 25 (sensitivity 0.80, 95% confidence interval [CI] 0.47-0.99; specificity 0.79, 95% CI 0.73-0.84) is proposed for identifying those at risk for PIU. Participants at risk for PIU were at significantly greater odds of also reporting symptoms of attention-deficit/hyperactivity disorder (odds ratio [OR] 2.36 95% CI 1.21-4.62, P = .009), depression (OR 3.25, 95% CI 1.65-6.42, P = .008), and social anxiety (OR 3.77, 95% CI 2.06-6.89, P < .000). The PRIUSS demonstrated validity as a PIU screening instrument for adolescents and young adults. Screening for PIU may also help to identify those at high reciprocal risk for other mental health conditions. Copyright © 2015. Published by Elsevier Inc.

  5. Large-scale grid management; Storskala Nettforvaltning

    Energy Technology Data Exchange (ETDEWEB)

    Langdal, Bjoern Inge; Eggen, Arnt Ove

    2003-07-01

    The network companies in the Norwegian electricity industry now have to establish a large-scale network management, a concept essentially characterized by (1) broader focus (Broad Band, Multi Utility,...) and (2) bigger units with large networks and more customers. Research done by SINTEF Energy Research shows so far that the approaches within large-scale network management may be structured according to three main challenges: centralization, decentralization and out sourcing. The article is part of a planned series.

  6. Japanese large-scale interferometers

    CERN Document Server

    Kuroda, K; Miyoki, S; Ishizuka, H; Taylor, C T; Yamamoto, K; Miyakawa, O; Fujimoto, M K; Kawamura, S; Takahashi, R; Yamazaki, T; Arai, K; Tatsumi, D; Ueda, A; Fukushima, M; Sato, S; Shintomi, T; Yamamoto, A; Suzuki, T; Saitô, Y; Haruyama, T; Sato, N; Higashi, Y; Uchiyama, T; Tomaru, T; Tsubono, K; Ando, M; Takamori, A; Numata, K; Ueda, K I; Yoneda, H; Nakagawa, K; Musha, M; Mio, N; Moriwaki, S; Somiya, K; Araya, A; Kanda, N; Telada, S; Sasaki, M; Tagoshi, H; Nakamura, T; Tanaka, T; Ohara, K

    2002-01-01

    The objective of the TAMA 300 interferometer was to develop advanced technologies for kilometre scale interferometers and to observe gravitational wave events in nearby galaxies. It was designed as a power-recycled Fabry-Perot-Michelson interferometer and was intended as a step towards a final interferometer in Japan. The present successful status of TAMA is presented. TAMA forms a basis for LCGT (large-scale cryogenic gravitational wave telescope), a 3 km scale cryogenic interferometer to be built in the Kamioka mine in Japan, implementing cryogenic mirror techniques. The plan of LCGT is schematically described along with its associated R and D.

  7. Transgenic RNAi in mouse oocytes: The first decade

    Czech Academy of Sciences Publication Activity Database

    Malík, Radek; Svoboda, Petr

    2012-01-01

    Roč. 134, 1-2 (2012), s. 64-68 ISSN 0378-4320 Institutional research plan: CEZ:AV0Z50520514 Institutional support: RVO:68378050 Keywords : RNAi * oocyte * transgene * silencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.897, year: 2012

  8. Virtual screening methods as tools for drug lead discovery from large chemical libraries.

    Science.gov (United States)

    Ma, X H; Zhu, F; Liu, X; Shi, Z; Zhang, J X; Yang, S Y; Wei, Y Q; Chen, Y Z

    2012-01-01

    Virtual screening methods have been developed and explored as useful tools for searching drug lead compounds from chemical libraries, including large libraries that have become publically available. In this review, we discussed the new developments in exploring virtual screening methods for enhanced performance in searching large chemical libraries, their applications in screening libraries of ~ 1 million or more compounds in the last five years, the difficulties in their applications, and the strategies for further improving these methods.

  9. GRAPHICS-IMAGE MIXED METHOD FOR LARGE-SCALE BUILDINGS RENDERING

    Directory of Open Access Journals (Sweden)

    Y. Zhou

    2018-05-01

    Full Text Available Urban 3D model data is huge and unstructured, LOD and Out-of-core algorithm are usually used to reduce the amount of data that drawn in each frame to improve the rendering efficiency. When the scene is large enough, even the complex optimization algorithm is difficult to achieve better results. Based on the traditional study, a novel idea was developed. We propose a graphics and image mixed method for large-scale buildings rendering. Firstly, the view field is divided into several regions, the graphics-image mixed method used to render the scene on both screen and FBO, then blending the FBO with scree. The algorithm is tested on the huge CityGML model data in the urban areas of New York which contained 188195 public building models, and compared with the Cesium platform. The experiment result shows the system was running smoothly. The experimental results confirm that the algorithm can achieve more massive building scene roaming under the same hardware conditions, and can rendering the scene without vision loss.

  10. Screening and large-scale expression of membrane proteins in mammalian cells for structural studies

    OpenAIRE

    Goehring, April; Lee, Chia-Hsueh; Wang, Kevin H.; Michel, Jennifer Carlisle; Claxton, Derek P.; Baconguis, Isabelle; Althoff, Thorsten; Fischer, Suzanne; Garcia, K. Christopher; Gouaux, Eric

    2014-01-01

    Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in over-expression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient productio...

  11. Visual analysis of inter-process communication for large-scale parallel computing.

    Science.gov (United States)

    Muelder, Chris; Gygi, Francois; Ma, Kwan-Liu

    2009-01-01

    In serial computation, program profiling is often helpful for optimization of key sections of code. When moving to parallel computation, not only does the code execution need to be considered but also communication between the different processes which can induce delays that are detrimental to performance. As the number of processes increases, so does the impact of the communication delays on performance. For large-scale parallel applications, it is critical to understand how the communication impacts performance in order to make the code more efficient. There are several tools available for visualizing program execution and communications on parallel systems. These tools generally provide either views which statistically summarize the entire program execution or process-centric views. However, process-centric visualizations do not scale well as the number of processes gets very large. In particular, the most common representation of parallel processes is a Gantt char t with a row for each process. As the number of processes increases, these charts can become difficult to work with and can even exceed screen resolution. We propose a new visualization approach that affords more scalability and then demonstrate it on systems running with up to 16,384 processes.

  12. The CSR-1 endogenous RNAi pathway ensures accurate transcriptional reprogramming during the oocyte-to-embryo transition in Caenorhabditis elegans.

    Science.gov (United States)

    Fassnacht, Christina; Tocchini, Cristina; Kumari, Pooja; Gaidatzis, Dimos; Stadler, Michael B; Ciosk, Rafal

    2018-03-01

    Endogenous RNAi (endoRNAi) is a conserved mechanism for fine-tuning gene expression. In the nematode Caenorhabditis elegans, several endoRNAi pathways are required for the successful development of reproductive cells. The CSR-1 endoRNAi pathway promotes germ cell development, primarily by facilitating the expression of germline genes. In this study, we report a novel function for the CSR-1 pathway in preventing premature activation of embryonic transcription in the developing oocytes, which is accompanied by a general Pol II activation. This CSR-1 function requires its RNase activity, suggesting that, by controlling the levels of maternal mRNAs, CSR-1-dependent endoRNAi contributes to an orderly reprogramming of transcription during the oocyte-to-embryo transition.

  13. CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.

    Science.gov (United States)

    Flobak, Åsmund; Vazquez, Miguel; Lægreid, Astrid; Valencia, Alfonso

    2017-08-01

    Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required. CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experimental mathematical models describing dose response relationships. CImbinator is written in Ruby and R. It uses the R package drc for advanced drug response modeling. CImbinator is available at http://cimbinator.bioinfo.cnio.es , the source-code is open and available at https://github.com/Rbbt-Workflows/combination_index . A Docker image is also available at https://hub.docker.com/r/mikisvaz/rbbt-ci_mbinator/ . asmund.flobak@ntnu.no or miguel.vazquez@cnio.es. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  14. Large scale model testing

    International Nuclear Information System (INIS)

    Brumovsky, M.; Filip, R.; Polachova, H.; Stepanek, S.

    1989-01-01

    Fracture mechanics and fatigue calculations for WWER reactor pressure vessels were checked by large scale model testing performed using large testing machine ZZ 8000 (with a maximum load of 80 MN) at the SKODA WORKS. The results are described from testing the material resistance to fracture (non-ductile). The testing included the base materials and welded joints. The rated specimen thickness was 150 mm with defects of a depth between 15 and 100 mm. The results are also presented of nozzles of 850 mm inner diameter in a scale of 1:3; static, cyclic, and dynamic tests were performed without and with surface defects (15, 30 and 45 mm deep). During cyclic tests the crack growth rate in the elastic-plastic region was also determined. (author). 6 figs., 2 tabs., 5 refs

  15. Why small-scale cannabis growers stay small: five mechanisms that prevent small-scale growers from going large scale.

    Science.gov (United States)

    Hammersvik, Eirik; Sandberg, Sveinung; Pedersen, Willy

    2012-11-01

    Over the past 15-20 years, domestic cultivation of cannabis has been established in a number of European countries. New techniques have made such cultivation easier; however, the bulk of growers remain small-scale. In this study, we explore the factors that prevent small-scale growers from increasing their production. The study is based on 1 year of ethnographic fieldwork and qualitative interviews conducted with 45 Norwegian cannabis growers, 10 of whom were growing on a large-scale and 35 on a small-scale. The study identifies five mechanisms that prevent small-scale indoor growers from going large-scale. First, large-scale operations involve a number of people, large sums of money, a high work-load and a high risk of detection, and thus demand a higher level of organizational skills than for small growing operations. Second, financial assets are needed to start a large 'grow-site'. Housing rent, electricity, equipment and nutrients are expensive. Third, to be able to sell large quantities of cannabis, growers need access to an illegal distribution network and knowledge of how to act according to black market norms and structures. Fourth, large-scale operations require advanced horticultural skills to maximize yield and quality, which demands greater skills and knowledge than does small-scale cultivation. Fifth, small-scale growers are often embedded in the 'cannabis culture', which emphasizes anti-commercialism, anti-violence and ecological and community values. Hence, starting up large-scale production will imply having to renegotiate or abandon these values. Going from small- to large-scale cannabis production is a demanding task-ideologically, technically, economically and personally. The many obstacles that small-scale growers face and the lack of interest and motivation for going large-scale suggest that the risk of a 'slippery slope' from small-scale to large-scale growing is limited. Possible political implications of the findings are discussed. Copyright

  16. Distributed large-scale dimensional metrology new insights

    CERN Document Server

    Franceschini, Fiorenzo; Maisano, Domenico

    2011-01-01

    Focuses on the latest insights into and challenges of distributed large scale dimensional metrology Enables practitioners to study distributed large scale dimensional metrology independently Includes specific examples of the development of new system prototypes

  17. Soaking RNAi in Bombyx mori BmN4-SID1 Cells Arrests Cell Cycle Progression

    Science.gov (United States)

    Mon, Hiroaki; Li, Zhiqing; Kobayashi, Isao; Tomita, Shuichiro; Lee, JaeMan; Sezutsu, Hideki; Tamura, Toshiki; Kusakabe, Takahiro

    2013-01-01

    RNA interference (RNAi) is an evolutionarily conserved mechanism for sequence-specific gene silencing. Previously, the BmN4-SID1 cell expressing Caenorhabditis ele gans SID-1 was established, in which soaking RNAi could induce effective gene silencing. To establish its utility, 6 cell cycle progression related cDNAs, CDK1, MYC, MYB, RNRS, CDT1, and GEMININ, were isolated from the silkworm, Bombyx mori L. (Lepidoptera: Bombycidae), and their expressions were further silenced by soaking RNAi in the BmN4-SID1 cells. The cell cycle progression analysis using flow cytometer demonstrated that the small amount of double stranded RNA was enough to arrest cell cycle progression at the specific cell phases. These data suggest that RNAi in the BmN4-SID1 cells can be used as a powerful tool for loss-of-function analysis of B. mori genes. PMID:24773378

  18. Hydroxychloroquine screening practice patterns within a large multispecialty ophthalmic practice.

    Science.gov (United States)

    Au, Adrian; Parikh, Vishal; Modi, Yasha S; Ehlers, Justis P; Schachat, Andrew P; Singh, Rishi P

    2015-09-01

    To determine provider compliance with hydroxychloroquine screening following the revised recommendations published in 2011 by the American Academy of Ophthalmology. Evaluation of adherence to a screening protocol. Subjects were identified with hydroxychloroquine as a medication by electronic query at a large multispecialty ophthalmic practice. Patients were excluded if patients: (1) were screened by an outside physician; (2) lacked recorded height, weight, start date, or dosing; or (3) took hydroxychloroquine for malaria prophylaxis. Screening tests were stratified by ophthalmic subspecialty. Guidelines define proper screening as 1 subjective test-Humphrey visual field (HVF), and 1 objective test-spectral-domain optical coherence tomography (SD OCT), fundus autofluorescence (FAF), or multifocal electroretinography (mfERG). Adherence to guidelines was determined by categorizing practices as: (1) "appropriate"-consistent with guidelines; (2) "underscreened"-insufficient testing; or (3) "inappropriate"-no testing. The study comprised 756 patients with a mean age of 56 years undergoing 1294 screening visits. Twenty-one patients received initial screenings outside the institution. Most common screening tests employed included SD OCT (56.6%), 10-2 HVF (55.0%), and Amsler grid (40.0%). Of the 735 initial screenings, 341 (46.4%) were appropriately screened, 204 (27.8%) underscreened, and 190 (25.9%) inappropriately screened. Of those who presented solely for screening (560), 307 (54.8%) were appropriately screened, 144 (25.7%) underscreened, and 109 (19.5%) inappropriately screened. Of patients presenting for hydroxychloroquine screening, 54.8% of patients received appropriate evaluation, indicating lack of adherence to guidelines. Overall, SD OCT and 10-2 HVF were the preferred screening modalities, with FAF and mfERG less frequently ordered. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. SCALE INTERACTION IN A MIXING LAYER. THE ROLE OF THE LARGE-SCALE GRADIENTS

    KAUST Repository

    Fiscaletti, Daniele; Attili, Antonio; Bisetti, Fabrizio; Elsinga, Gerrit E.

    2015-01-01

    from physical considerations we would expect the scales to interact in a qualitatively similar way within the flow and across different turbulent flows. Therefore, instead of the large-scale fluctuations, the large-scale gradients modulation of the small scales has been additionally investigated.

  20. Late extraembryonic morphogenesis and its zen(RNAi)-induced failure in the milkweed bug Oncopeltus fasciatus.

    Science.gov (United States)

    Panfilio, Kristen A

    2009-09-15

    Many insects undergo katatrepsis, essential reorganization by the extraembryonic membranes that repositions the embryo. Knockdown of the zen gene by RNA interference (RNAi) prevents katatrepsis in the milkweed bug Oncopeltus fasciatus. However, the precise morphogenetic defect has been uncertain, and katatrepsis itself has not been characterized in detail. The dynamics of wild type and zen(RNAi) eggs were analyzed from time-lapse movies, supplemented by analysis of fixed specimens. These investigations identify three zen(RNAi) defects. First, a reduced degree of tissue contraction implies a role for zen in baseline compression prior to katatrepsis. Subsequently, a characteristic 'bouncing' activity commences, leading to the initiation of katatrepsis in wild type eggs. The second zen(RNAi) defect is a delay in this activity, suggesting that a temporal window of opportunity is missed after zen knockdown. Ultimately, the extraembryonic membranes fail to rupture in zen(RNAi) eggs: the third defect. Nevertheless, the outer serosal membrane manages to contract, albeit in an aberrant fashion with additional phenotypic consequences for the embryo. These data identify a novel epithelial morphogenetic event - rupture of the 'serosal window' structure - as the ultimate site of defect. Overall, Oncopeltus zen seems to have a role in coordinating a number of pre-katatreptic events during mid embryogenesis.

  1. RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Dotu, Ivan; Clote, Peter

    2015-07-01

    Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Prostate Cancer Screening Results from PLCO

    Science.gov (United States)

    Learn the results of the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial, a large-scale clinical trial to determine whether certain cancer screening tests can help reduce deaths from prostate, lung, colorectal, and ovarian cancer.

  3. Trends in large-scale testing of reactor structures

    International Nuclear Information System (INIS)

    Blejwas, T.E.

    2003-01-01

    Large-scale tests of reactor structures have been conducted at Sandia National Laboratories since the late 1970s. This paper describes a number of different large-scale impact tests, pressurization tests of models of containment structures, and thermal-pressure tests of models of reactor pressure vessels. The advantages of large-scale testing are evident, but cost, in particular limits its use. As computer models have grown in size, such as number of degrees of freedom, the advent of computer graphics has made possible very realistic representation of results - results that may not accurately represent reality. A necessary condition to avoiding this pitfall is the validation of the analytical methods and underlying physical representations. Ironically, the immensely larger computer models sometimes increase the need for large-scale testing, because the modeling is applied to increasing more complex structural systems and/or more complex physical phenomena. Unfortunately, the cost of large-scale tests is a disadvantage that will likely severely limit similar testing in the future. International collaborations may provide the best mechanism for funding future programs with large-scale tests. (author)

  4. Chinese version of the Postpartum Depression Screening Scale: translation and validation.

    Science.gov (United States)

    Li, Lezhi; Liu, Fang; Zhang, Huilin; Wang, Li; Chen, Xiaofang

    2011-01-01

    Postpartum depression is an important public health problem in China. Although 10%-20% of Chinese women having recently given birth are affected by postpartum depression, only 10% receive treatment due to the lack of proper screening. The aims of this study were to translate the Postpartum Depression Screening Scale into Chinese (C-PDSS) and establish the psychometric properties of the C-PDSS. The study was undertaken in three phases, composed of forward and backward translation of the Postpartum Depression Screening Scale into Chinese, examination of content validity, and field testing to establish the reliability, validity, and optimal cutoff score of the C-PDSS along with its sensitivity, specificity, and predictive values. A total sample of 387 mothers within 12 weeks postpartum participated in the study. Each mother was asked to complete the C-PDSS and the Chinese version of the Edinburgh Postnatal Depression Scale and then was interviewed by an experienced researcher using the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition, Text Revision. The Cronbach's alpha coefficient was .96 for the total C-PDSS, and the overall intraclass correlation was .79. Factor analysis of the scale revealed that it was composed of 7 factors with eigenvalues >1, accounting for 74.25% of the total variance. There was a significantly positive correlation between the C-PDSS and the Chinese version of the Edinburgh Postnatal Depression Scale (r = .66, p confirmatory factor analysis and generalization of the C-PDSS to a different sample in China.

  5. The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans.

    Science.gov (United States)

    Yang, Huan; Vallandingham, Jim; Shiu, Philip; Li, Hua; Hunter, Craig P; Mak, Ho Yi

    2014-04-14

    RNAi is a potent mechanism for downregulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi, and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary small interfering RNAs (siRNAs). Exogenous double-stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA-dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear whether the subcellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved phenylalanine-glycine (FG) domain-containing DEAD box helicase, localizes in P granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA-targeted mRNA in distinct cytoplasmic compartments. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. The Bergen Shopping Addiction Scale: reliability and validity of a brief screening test

    Science.gov (United States)

    Andreassen, Cecilie S.; Griffiths, Mark D.; Pallesen, Ståle; Bilder, Robert M.; Torsheim, Torbjørn; Aboujaoude, Elias

    2015-01-01

    Although excessive and compulsive shopping has been increasingly placed within the behavioral addiction paradigm in recent years, items in existing screens arguably do not assess the core criteria and components of addiction. To date, assessment screens for shopping disorders have primarily been rooted within the impulse-control or obsessive-compulsive disorder paradigms. Furthermore, existing screens use the terms ‘shopping,’ ‘buying,’ and ‘spending’ interchangeably, and do not necessarily reflect contemporary shopping habits. Consequently, a new screening tool for assessing shopping addiction was developed. Initially, 28 items, four for each of seven addiction criteria (salience, mood modification, conflict, tolerance, withdrawal, relapse, and problems), were constructed. These items and validated scales (i.e., Compulsive Buying Measurement Scale, Mini-International Personality Item Pool, Hospital Anxiety and Depression Scale, Rosenberg Self-Esteem Scale) were then administered to 23,537 participants (Mage = 35.8 years, SDage = 13.3). The highest loading item from each set of four pooled items reflecting the seven addiction criteria were retained in the final scale, The Bergen Shopping Addiction Scale (BSAS). The factor structure of the BSAS was good (RMSEA = 0.064, CFI = 0.983, TLI = 0.973) and coefficient alpha was 0.87. The scores on the BSAS converged with scores on the Compulsive Buying Measurement Scale (CBMS; 0.80), and were positively correlated with extroversion and neuroticism, and negatively with conscientiousness, agreeableness, and intellect/imagination. The scores of the BSAS were positively associated with anxiety, depression, and low self-esteem and inversely related to age. Females scored higher than males on the BSAS. The BSAS is the first scale to fully embed shopping addiction within an addiction paradigm. A recommended cutoff score for the new scale and future research directions are discussed. PMID:26441749

  7. The Bergen Shopping Addiction Scale: Reliability and validity of a brief screening test

    Directory of Open Access Journals (Sweden)

    Cecilie Schou Andreassen

    2015-09-01

    Full Text Available Although excessive and compulsive shopping has been increasingly placed within the behavioral addiction paradigm in recent years, items in existing screens arguably do not assess the core criteria and components of addiction. To date, assessment screens for shopping disorders have primarily been rooted within the impulse-control or obsessive-compulsive disorder paradigms. Furthermore, existing screens use the terms ‘shopping’, ‘buying’, and ‘spending’ interchangeably, and do not necessarily reflect contemporary shopping habits. Consequently, a new screening tool for assessing shopping addiction was developed. Initially, 28 items, four for each of seven addiction criteria (salience, mood modification, conflict, tolerance, withdrawal, relapse, and problems, were constructed. These items and validated scales (i.e., Compulsive Buying Measurement Scale, Mini-International Personality Item Pool, Hospital Anxiety and Depression Scale, Rosenberg Self-Esteem Scale were then administered to 23,537 participants (Mage=35.8 years, SDage=13.3. The highest loading item from each set of four pooled items reflecting the seven addiction criteria were retained in the final scale, The Bergen Shopping Addiction Scale (BSAS. The factor structure of the BSAS was good (RMSEA=.064, CFI=.983, TLI=.973 and coefficient alpha was .87. The scores on the BSAS converged with scores on the Compulsive Buying Measurement Scale (.80, and were positively correlated with extroversion and neuroticism, and negatively with conscientiousness, agreeableness, and intellect/imagination. The scores of the BSAS were positively associated with anxiety, depression, and low self-esteem and inversely related to age. Females scored higher than males on the BSAS. The BSAS is the first scale to fully embed shopping addiction within an addiction paradigm. A recommended cutoff score for the new scale and future research directions are discussed.

  8. The Bergen Shopping Addiction Scale: reliability and validity of a brief screening test.

    Science.gov (United States)

    Andreassen, Cecilie S; Griffiths, Mark D; Pallesen, Ståle; Bilder, Robert M; Torsheim, Torbjørn; Aboujaoude, Elias

    2015-01-01

    Although excessive and compulsive shopping has been increasingly placed within the behavioral addiction paradigm in recent years, items in existing screens arguably do not assess the core criteria and components of addiction. To date, assessment screens for shopping disorders have primarily been rooted within the impulse-control or obsessive-compulsive disorder paradigms. Furthermore, existing screens use the terms 'shopping,' 'buying,' and 'spending' interchangeably, and do not necessarily reflect contemporary shopping habits. Consequently, a new screening tool for assessing shopping addiction was developed. Initially, 28 items, four for each of seven addiction criteria (salience, mood modification, conflict, tolerance, withdrawal, relapse, and problems), were constructed. These items and validated scales (i.e., Compulsive Buying Measurement Scale, Mini-International Personality Item Pool, Hospital Anxiety and Depression Scale, Rosenberg Self-Esteem Scale) were then administered to 23,537 participants (M age = 35.8 years, SD age = 13.3). The highest loading item from each set of four pooled items reflecting the seven addiction criteria were retained in the final scale, The Bergen Shopping Addiction Scale (BSAS). The factor structure of the BSAS was good (RMSEA = 0.064, CFI = 0.983, TLI = 0.973) and coefficient alpha was 0.87. The scores on the BSAS converged with scores on the Compulsive Buying Measurement Scale (CBMS; 0.80), and were positively correlated with extroversion and neuroticism, and negatively with conscientiousness, agreeableness, and intellect/imagination. The scores of the BSAS were positively associated with anxiety, depression, and low self-esteem and inversely related to age. Females scored higher than males on the BSAS. The BSAS is the first scale to fully embed shopping addiction within an addiction paradigm. A recommended cutoff score for the new scale and future research directions are discussed.

  9. Simulator comparison of thumball, thumb switch, and touch screen input concepts for interaction with a large screen cockpit display format

    Science.gov (United States)

    Jones, Denise R.; Parrish, Russell V.

    1990-01-01

    A piloted simulation study was conducted comparing three different input methods for interfacing to a large screen, multiwindow, whole flight deck display for management of transport aircraft systems. The thumball concept utilized a miniature trackball embedded in a conventional side arm controller. The multifunction control throttle and stick (MCTAS) concept employed a thumb switch located in the throttle handle. The touch screen concept provided data entry through a capacitive touch screen installed on the display surface. The objective and subjective results obtained indicate that, with present implementations, the thumball concept was the most appropriate for interfacing with aircraft systems/subsystems presented on a large screen display. Not unexpectedly, the completion time differences between the three concepts varied with the task being performed, although the thumball implementation consistently outperformed the other two concepts. However, pilot suggestions for improved implementations of the MCTAS and touch screen concepts could reduce some of these differences.

  10. The validity of military screening for mental health problems: diagnostic accuracy of the PCL, K10 and AUDIT scales in an entire military population.

    Science.gov (United States)

    Searle, Amelia K; Van Hooff, Miranda; McFarlane, Alexander C; Davies, Christopher E; Fairweather-Schmidt, A Kate; Hodson, Stephanie E; Benassi, Helen; Steele, Nicole

    2015-03-01

    Depression, alcohol use disorders and post-traumatic stress disorder (PTSD) are serious issues among military personnel due to their impact on operational capability and individual well-being. Several military forces screen for these disorders using scales including the Kessler Psychological Distress Scale (K10), Alcohol Use Disorders Identification Test (AUDIT), and Post-traumatic Stress Disorder Checklist (PCL). However, it is unknown whether established cutoffs apply to military populations. This study is the first to test the diagnostic accuracy of these three scales in a population-based military cohort. A large sample of currently-serving Australian Defence Force (ADF) Navy, Army and Air Force personnel (n = 24,481) completed the K10, AUDIT and PCL-C (civilian version). Then, a stratified sub-sample (n = 1798) completed a structured diagnostic interview detecting 30-day disorder. Data were weighted to represent the ADF population (n = 50,049). Receiver operating characteristic (ROC) analyses suggested all three scales had acceptable sensitivity and specificity, with areas under the curve from 0.75 to 0.93. AUDIT and K10 screening cutoffs closely paralleled established cutoffs, whereas the PCL-C screening cutoff resembled that recommended for US military personnel. These self-report scales represent a cost-effective and clinically-useful means of screening personnel for disorder. Military populations may need lower cutoffs than civilians to screen for PTSD. Copyright © 2014 John Wiley & Sons, Ltd.

  11. Biosafety considerations of RNAi-mediated virus resistance in fruit-tree cultivars and in rootstock.

    Science.gov (United States)

    Lemgo, Godwin Nana Yaw; Sabbadini, Silvia; Pandolfini, Tiziana; Mezzetti, Bruno

    2013-12-01

    A major application of RNA interference (RNAi) is envisaged for the production of virus-resistant transgenic plants. For fruit trees, this remains the most, if not the only, viable option for the control of plant viral disease outbreaks in cultivated orchards, due to the difficulties associated with the use of traditional and conventional disease-control measures. The use of RNAi might provide an additional benefit for woody crops if silenced rootstock can efficiently transmit the silencing signal to non-transformed scions, as has already been demonstrated in herbaceous plants. This would provide a great opportunity to produce non-transgenic fruit from transgenic rootstock. In this review, we scrutinise some of the concerns that might arise with the use of RNAi for engineering virus-resistant plants, and we speculate that this virus resistance has fewer biosafety concerns. This is mainly because RNAi-eliciting constructs only express small RNA molecules rather than proteins, and because this technology can be applied using plant rootstock that can confer virus resistance to the scion, leaving the scion untransformed. We discuss the main biosafety concerns related to the release of new types of virus-resistant plants and the risk assessment approaches in the application of existing regulatory systems (in particular, those of the European Union, the USA, and Canada) for the evaluation and approval of RNAi-mediated virus-resistant plants, either as transgenic varieties or as plant virus resistance induced by transgenic rootstock.

  12. Large Scale Computations in Air Pollution Modelling

    DEFF Research Database (Denmark)

    Zlatev, Z.; Brandt, J.; Builtjes, P. J. H.

    Proceedings of the NATO Advanced Research Workshop on Large Scale Computations in Air Pollution Modelling, Sofia, Bulgaria, 6-10 July 1998......Proceedings of the NATO Advanced Research Workshop on Large Scale Computations in Air Pollution Modelling, Sofia, Bulgaria, 6-10 July 1998...

  13. Large-Scale 3D Printing: The Way Forward

    Science.gov (United States)

    Jassmi, Hamad Al; Najjar, Fady Al; Ismail Mourad, Abdel-Hamid

    2018-03-01

    Research on small-scale 3D printing has rapidly evolved, where numerous industrial products have been tested and successfully applied. Nonetheless, research on large-scale 3D printing, directed to large-scale applications such as construction and automotive manufacturing, yet demands a great a great deal of efforts. Large-scale 3D printing is considered an interdisciplinary topic and requires establishing a blended knowledge base from numerous research fields including structural engineering, materials science, mechatronics, software engineering, artificial intelligence and architectural engineering. This review article summarizes key topics of relevance to new research trends on large-scale 3D printing, particularly pertaining (1) technological solutions of additive construction (i.e. the 3D printers themselves), (2) materials science challenges, and (3) new design opportunities.

  14. Growth Limits in Large Scale Networks

    DEFF Research Database (Denmark)

    Knudsen, Thomas Phillip

    limitations. The rising complexity of network management with the convergence of communications platforms is shown as problematic for both automatic management feasibility and for manpower resource management. In the fourth step the scope is extended to include the present society with the DDN project as its......The Subject of large scale networks is approached from the perspective of the network planner. An analysis of the long term planning problems is presented with the main focus on the changing requirements for large scale networks and the potential problems in meeting these requirements. The problems...... the fundamental technological resources in network technologies are analysed for scalability. Here several technological limits to continued growth are presented. The third step involves a survey of major problems in managing large scale networks given the growth of user requirements and the technological...

  15. Accelerating sustainability in large-scale facilities

    CERN Multimedia

    Marina Giampietro

    2011-01-01

    Scientific research centres and large-scale facilities are intrinsically energy intensive, but how can big science improve its energy management and eventually contribute to the environmental cause with new cleantech? CERN’s commitment to providing tangible answers to these questions was sealed in the first workshop on energy management for large scale scientific infrastructures held in Lund, Sweden, on the 13-14 October.   Participants at the energy management for large scale scientific infrastructures workshop. The workshop, co-organised with the European Spallation Source (ESS) and  the European Association of National Research Facilities (ERF), tackled a recognised need for addressing energy issues in relation with science and technology policies. It brought together more than 150 representatives of Research Infrastrutures (RIs) and energy experts from Europe and North America. “Without compromising our scientific projects, we can ...

  16. Visual coherence for large-scale line-plot visualizations

    KAUST Repository

    Muigg, Philipp

    2011-06-01

    Displaying a large number of lines within a limited amount of screen space is a task that is common to many different classes of visualization techniques such as time-series visualizations, parallel coordinates, link-node diagrams, and phase-space diagrams. This paper addresses the challenging problems of cluttering and overdraw inherent to such visualizations. We generate a 2x2 tensor field during line rasterization that encodes the distribution of line orientations through each image pixel. Anisotropic diffusion of a noise texture is then used to generate a dense, coherent visualization of line orientation. In order to represent features of different scales, we employ a multi-resolution representation of the tensor field. The resulting technique can easily be applied to a wide variety of line-based visualizations. We demonstrate this for parallel coordinates, a time-series visualization, and a phase-space diagram. Furthermore, we demonstrate how to integrate a focus+context approach by incorporating a second tensor field. Our approach achieves interactive rendering performance for large data sets containing millions of data items, due to its image-based nature and ease of implementation on GPUs. Simulation results from computational fluid dynamics are used to evaluate the performance and usefulness of the proposed method. © 2011 The Author(s).

  17. Visual coherence for large-scale line-plot visualizations

    KAUST Repository

    Muigg, Philipp; Hadwiger, Markus; Doleisch, Helmut; Grö ller, Eduard M.

    2011-01-01

    Displaying a large number of lines within a limited amount of screen space is a task that is common to many different classes of visualization techniques such as time-series visualizations, parallel coordinates, link-node diagrams, and phase-space diagrams. This paper addresses the challenging problems of cluttering and overdraw inherent to such visualizations. We generate a 2x2 tensor field during line rasterization that encodes the distribution of line orientations through each image pixel. Anisotropic diffusion of a noise texture is then used to generate a dense, coherent visualization of line orientation. In order to represent features of different scales, we employ a multi-resolution representation of the tensor field. The resulting technique can easily be applied to a wide variety of line-based visualizations. We demonstrate this for parallel coordinates, a time-series visualization, and a phase-space diagram. Furthermore, we demonstrate how to integrate a focus+context approach by incorporating a second tensor field. Our approach achieves interactive rendering performance for large data sets containing millions of data items, due to its image-based nature and ease of implementation on GPUs. Simulation results from computational fluid dynamics are used to evaluate the performance and usefulness of the proposed method. © 2011 The Author(s).

  18. Development of a Novel Targeted RNAi Delivery Technology inTherapies for Metabolic Diseases

    Science.gov (United States)

    2017-10-01

    report Impact on other disciplines: Nothing to report Impact on technology transfer: Nothing to report Impact on society : Nothing to report 5. CHANGES...AWARD NUMBER: W81XWH-15-1-0569 TITLE: Development of a Novel Targeted RNAi Delivery Technology in Therapies for Metabolic Diseases PRINCIPAL...COVERED 30Sep2016 - 29Sep2017 4. TITLE AND SUBTITLE Development of a Novel Targeted RNAi Delivery Technology in Therapies for Metabolic Diseases 5a

  19. Large scale reflood test

    International Nuclear Information System (INIS)

    Hirano, Kemmei; Murao, Yoshio

    1980-01-01

    The large-scale reflood test with a view to ensuring the safety of light water reactors was started in fiscal 1976 based on the special account act for power source development promotion measures by the entrustment from the Science and Technology Agency. Thereafter, to establish the safety of PWRs in loss-of-coolant accidents by joint international efforts, the Japan-West Germany-U.S. research cooperation program was started in April, 1980. Thereupon, the large-scale reflood test is now included in this program. It consists of two tests using a cylindrical core testing apparatus for examining the overall system effect and a plate core testing apparatus for testing individual effects. Each apparatus is composed of the mock-ups of pressure vessel, primary loop, containment vessel and ECCS. The testing method, the test results and the research cooperation program are described. (J.P.N.)

  20. Distinct RNAi Pathways in the Regulation of Physiology and Development in the Fungus Mucor circinelloides.

    Science.gov (United States)

    Ruiz-Vázquez, Rosa M; Nicolás, Francisco E; Torres-Martínez, Santiago; Garre, Victoriano

    2015-01-01

    The basal fungus Mucor circinelloides has become, in recent years, a valuable model to study RNA-mediated gene silencing or RNA interference (RNAi). Serendipitously discovered in the late 1900s, the gene silencing in M. circinelloides is a landscape of consensus and dissents. Although similar to other classical fungal models in the basic design of the essential machinery that is responsible for silencing of gene expression, the existence of small RNA molecules of different sizes generated during this process and the presence of a mechanism that amplifies the silencing signal, give it a unique identity. In addition, M. circinelloides combines the components of RNAi machinery to carry out functions that not only limit themselves to the defense against foreign genetic material, but it uses some of these elements to regulate the expression of its own genes. Thus, different combinations of RNAi elements produce distinct classes of endogenous small RNAs (esRNAs) that regulate different physiological and developmental processes in response to environmental signals. The recent discovery of a new RNAi pathway involved in the specific degradation of endogenous mRNAs, using a novel RNase protein, adds one more element to the exciting puzzle of the gene silencing in M. circinelloides, in addition to providing hints about the evolutionary origin of the RNAi mechanism. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Large Scale Cosmological Anomalies and Inhomogeneous Dark Energy

    Directory of Open Access Journals (Sweden)

    Leandros Perivolaropoulos

    2014-01-01

    Full Text Available A wide range of large scale observations hint towards possible modifications on the standard cosmological model which is based on a homogeneous and isotropic universe with a small cosmological constant and matter. These observations, also known as “cosmic anomalies” include unexpected Cosmic Microwave Background perturbations on large angular scales, large dipolar peculiar velocity flows of galaxies (“bulk flows”, the measurement of inhomogenous values of the fine structure constant on cosmological scales (“alpha dipole” and other effects. The presence of the observational anomalies could either be a large statistical fluctuation in the context of ΛCDM or it could indicate a non-trivial departure from the cosmological principle on Hubble scales. Such a departure is very much constrained by cosmological observations for matter. For dark energy however there are no significant observational constraints for Hubble scale inhomogeneities. In this brief review I discuss some of the theoretical models that can naturally lead to inhomogeneous dark energy, their observational constraints and their potential to explain the large scale cosmic anomalies.

  2. RNAi-mediated resistance to rice black-streaked dwarf virus in transgenic rice.

    Science.gov (United States)

    Ahmed, Mohamed M S; Bian, Shiquan; Wang, Muyue; Zhao, Jing; Zhang, Bingwei; Liu, Qiaoquan; Zhang, Changquan; Tang, Shuzhu; Gu, Minghong; Yu, Hengxiu

    2017-04-01

    Rice black-streaked dwarf virus (RBSDV), a member of the genus Fijivirus in the family Reoviridae, causes significant economic losses in rice production in China and many other Asian countries. Development of resistant varieties by using conventional breeding methods is limited, as germplasm with high level of resistance to RBSDV have not yet been found. One of the most promising methods to confer resistance against RBSDV is the use of RNA interference (RNAi) technology. RBSDV non-structural protein P7-2, encoded by S7-2 gene, is a potential F-box protein and involved in the plant-virus interaction through the ubiquitination pathway. P8, encoded by S8 gene, is the minor core protein that possesses potent active transcriptional repression activity. In this study, we transformed rice calli using a mini-twin T-DNA vector harboring RNAi constructs of the RBSDV genes S7-2 or S8, and obtained plants harboring the target gene constructs and the selectable marker gene, hygromycin phosphotransferase (HPT). From the offspring of these transgenic plants, we obtained selectable marker (HPT gene)-free plants. Homozygous T 5 transgenic lines which harbored either S7-2-RNAi or S8-RNAi exhibited high level resistance against RBSDV under field infection pressure from indigenous viruliferous small brown planthoppers. Thus, our results showed that RNA interference with the expression of S7-2 or S8 genes seemed an effective way to induce high level resistance in rice against RBSD disease.

  3. Large-scale patterns in Rayleigh-Benard convection

    International Nuclear Information System (INIS)

    Hardenberg, J. von; Parodi, A.; Passoni, G.; Provenzale, A.; Spiegel, E.A.

    2008-01-01

    Rayleigh-Benard convection at large Rayleigh number is characterized by the presence of intense, vertically moving plumes. Both laboratory and numerical experiments reveal that the rising and descending plumes aggregate into separate clusters so as to produce large-scale updrafts and downdrafts. The horizontal scales of the aggregates reported so far have been comparable to the horizontal extent of the containers, but it has not been clear whether that represents a limitation imposed by domain size. In this work, we present numerical simulations of convection at sufficiently large aspect ratio to ascertain whether there is an intrinsic saturation scale for the clustering process when that ratio is large enough. From a series of simulations of Rayleigh-Benard convection with Rayleigh numbers between 10 5 and 10 8 and with aspect ratios up to 12π, we conclude that the clustering process has a finite horizontal saturation scale with at most a weak dependence on Rayleigh number in the range studied

  4. Molecular Characterization and the Function of Argonaute3 in RNAi Pathway of Plutella xylostella.

    Science.gov (United States)

    Hameed, Muhammad Salman; Wang, Zhengbing; Vasseur, Liette; Yang, Guang

    2018-04-20

    Argonaute (Ago) protein family plays a key role in the RNA interference (RNAi) process in different insects including Lepidopteran. However, the role of Ago proteins in the RNAi pathway of Plutella xylostella is still unknown. We cloned an Argonaute3 gene in P. xylostella ( PxAgo3 ) with the complete coding sequence of 2832 bp. The encoded protein had 935 amino acids with an expected molecular weight of 108.9 kDa and an isoelectric point of 9.29. It contained a PAZ (PIWI/Argonaute/Zwile) domain and PIWI (P-element-induced whimpy testes) domain. PxAgo3 was classified into the Piwi subfamily of Ago proteins with a high similarity of 93.0% with Bombyx mori Ago3 (BmAgo3). The suppression of PxAgo3 by dsPxAgo3 was observed 3 h after treatment and was maintained until 24 h. Knockdown of PxAgo3 decreased the suppression level of PxActin by dsPxActin in P. xylostella cells, while overexpression of PxAgo3 increased the RNAi efficiency. Our results suggest that PxAgo3 play a key role in the double stranded RNA (dsRNA)-regulated RNAi pathway in P. xylostella .

  5. Biosafety research for non-target organism risk assessment of RNAi-based GE plants

    Science.gov (United States)

    Roberts, Andrew F.; Devos, Yann; Lemgo, Godwin N. Y.; Zhou, Xuguo

    2015-01-01

    RNA interference, or RNAi, refers to a set of biological processes that make use of conserved cellular machinery to silence genes. Although there are several variations in the source and mechanism, they are all triggered by double stranded RNA (dsRNA) which is processed by a protein complex into small, single stranded RNA, referred to as small interfering RNAs (siRNA) with complementarity to sequences in genes targeted for silencing. The use of the RNAi mechanism to develop new traits in plants has fueled a discussion about the environmental safety of the technology for these applications, and this was the subject of a symposium session at the 13th ISBGMO in Cape Town, South Africa. This paper continues that discussion by proposing research areas that may be beneficial for future environmental risk assessments of RNAi-based genetically modified plants, with a particular focus on non-target organism assessment. PMID:26594220

  6. Manufacturing test of large scale hollow capsule and long length cladding in the large scale oxide dispersion strengthened (ODS) martensitic steel

    International Nuclear Information System (INIS)

    Narita, Takeshi; Ukai, Shigeharu; Kaito, Takeji; Ohtsuka, Satoshi; Fujiwara, Masayuki

    2004-04-01

    Mass production capability of oxide dispersion strengthened (ODS) martensitic steel cladding (9Cr) has being evaluated in the Phase II of the Feasibility Studies on Commercialized Fast Reactor Cycle System. The cost for manufacturing mother tube (raw materials powder production, mechanical alloying (MA) by ball mill, canning, hot extrusion, and machining) is a dominant factor in the total cost for manufacturing ODS ferritic steel cladding. In this study, the large-sale 9Cr-ODS martensitic steel mother tube which is made with a large-scale hollow capsule, and long length claddings were manufactured, and the applicability of these processes was evaluated. Following results were obtained in this study. (1) Manufacturing the large scale mother tube in the dimension of 32 mm OD, 21 mm ID, and 2 m length has been successfully carried out using large scale hollow capsule. This mother tube has a high degree of accuracy in size. (2) The chemical composition and the micro structure of the manufactured mother tube are similar to the existing mother tube manufactured by a small scale can. And the remarkable difference between the bottom and top sides in the manufactured mother tube has not been observed. (3) The long length cladding has been successfully manufactured from the large scale mother tube which was made using a large scale hollow capsule. (4) For reducing the manufacturing cost of the ODS steel claddings, manufacturing process of the mother tubes using a large scale hollow capsules is promising. (author)

  7. Amplification of large-scale magnetic field in nonhelical magnetohydrodynamics

    KAUST Repository

    Kumar, Rohit

    2017-08-11

    It is typically assumed that the kinetic and magnetic helicities play a crucial role in the growth of large-scale dynamo. In this paper, we demonstrate that helicity is not essential for the amplification of large-scale magnetic field. For this purpose, we perform nonhelical magnetohydrodynamic (MHD) simulation, and show that the large-scale magnetic field can grow in nonhelical MHD when random external forcing is employed at scale 1/10 the box size. The energy fluxes and shell-to-shell transfer rates computed using the numerical data show that the large-scale magnetic energy grows due to the energy transfers from the velocity field at the forcing scales.

  8. Reply: Comparison of slope instability screening tools following a large storm event and application to forest management and policy

    Science.gov (United States)

    Whittaker, Kara A.; McShane, Dan

    2013-02-01

    A large storm event in southwest Washington State triggered over 2500 landslides and provided an opportunity to assess two slope stability screening tools. The statistical analysis conducted demonstrated that both screening tools are effective at predicting where landslides were likely to take place (Whittaker and McShane, 2012). Here we reply to two discussions of this article related to the development of the slope stability screening tools and the accuracy and scale of the spatial data used. Neither of the discussions address our statistical analysis or results. We provide greater detail on our sampling criteria and also elaborate on the policy and management implications of our findings and how they complement those of a separate investigation of landslides resulting from the same storm. The conclusions made in Whittaker and McShane (2012) stand as originally published unless future analysis indicates otherwise.

  9. Hydrometeorological variability on a large french catchment and its relation to large-scale circulation across temporal scales

    Science.gov (United States)

    Massei, Nicolas; Dieppois, Bastien; Fritier, Nicolas; Laignel, Benoit; Debret, Maxime; Lavers, David; Hannah, David

    2015-04-01

    In the present context of global changes, considerable efforts have been deployed by the hydrological scientific community to improve our understanding of the impacts of climate fluctuations on water resources. Both observational and modeling studies have been extensively employed to characterize hydrological changes and trends, assess the impact of climate variability or provide future scenarios of water resources. In the aim of a better understanding of hydrological changes, it is of crucial importance to determine how and to what extent trends and long-term oscillations detectable in hydrological variables are linked to global climate oscillations. In this work, we develop an approach associating large-scale/local-scale correlation, enmpirical statistical downscaling and wavelet multiresolution decomposition of monthly precipitation and streamflow over the Seine river watershed, and the North Atlantic sea level pressure (SLP) in order to gain additional insights on the atmospheric patterns associated with the regional hydrology. We hypothesized that: i) atmospheric patterns may change according to the different temporal wavelengths defining the variability of the signals; and ii) definition of those hydrological/circulation relationships for each temporal wavelength may improve the determination of large-scale predictors of local variations. The results showed that the large-scale/local-scale links were not necessarily constant according to time-scale (i.e. for the different frequencies characterizing the signals), resulting in changing spatial patterns across scales. This was then taken into account by developing an empirical statistical downscaling (ESD) modeling approach which integrated discrete wavelet multiresolution analysis for reconstructing local hydrometeorological processes (predictand : precipitation and streamflow on the Seine river catchment) based on a large-scale predictor (SLP over the Euro-Atlantic sector) on a monthly time-step. This approach

  10. Superconducting materials for large scale applications

    International Nuclear Information System (INIS)

    Dew-Hughes, D.

    1975-01-01

    Applications of superconductors capable of carrying large current densities in large-scale electrical devices are examined. Discussions are included on critical current density, superconducting materials available, and future prospects for improved superconducting materials. (JRD)

  11. Large-scale influences in near-wall turbulence.

    Science.gov (United States)

    Hutchins, Nicholas; Marusic, Ivan

    2007-03-15

    Hot-wire data acquired in a high Reynolds number facility are used to illustrate the need for adequate scale separation when considering the coherent structure in wall-bounded turbulence. It is found that a large-scale motion in the log region becomes increasingly comparable in energy to the near-wall cycle as the Reynolds number increases. Through decomposition of fluctuating velocity signals, it is shown that this large-scale motion has a distinct modulating influence on the small-scale energy (akin to amplitude modulation). Reassessment of DNS data, in light of these results, shows similar trends, with the rate and intensity of production due to the near-wall cycle subject to a modulating influence from the largest-scale motions.

  12. Identification of a novel Drosophila gene, beltless, using injectable embryonic and adult RNA interference (RNAi

    Directory of Open Access Journals (Sweden)

    Manev Hari

    2003-08-01

    Full Text Available Abstract Background RNA interference (RNAi is a process triggered by a double-stranded RNA that leads to targeted down-regulation/silencing of gene expression and can be used for functional genomics; i.e. loss-of-function studies. Here we report on the use of RNAi in the identification of a developmentally important novel Drosophila (fruit fly gene (corresponding to a putative gene CG5652/GM06434, that we named beltless based on an embryonic loss-of-function phenotype. Results Beltless mRNA is expressed in all developmental stages except in 0–6 h embryos. In situ RT-PCR localized beltless mRNA in the ventral cord and brain of late stage embryos and in the nervous system, ovaries, and the accessory glands of adult flies. RNAi was induced by injection of short (22 bp beltless double-stranded RNAs into embryos or into adult flies. Embryonic RNAi altered cuticular phenotypes ranging from partially-formed to missing denticle belts (thus beltless of the abdominal segments A2–A4. Embryonic beltless RNAi was lethal. Adult RNAi resulted in the shrinkage of the ovaries by half and reduced the number of eggs laid. We also examined Df(1RK4 flies in which deletion removes 16 genes, including beltless. In some embryos, we observed cuticular abnormalities similar to our findings with beltless RNAi. After differentiating Df(1RK4 embryos into those with visible denticle belts and those missing denticle belts, we assayed the presence of beltless mRNA; no beltless mRNA was detectable in embryos with missing denticle belts. Conclusions We have identified a developmentally important novel Drosophila gene, beltless, which has been characterized in loss-of-function studies using RNA interference. The putative beltless protein shares homologies with the C. elegans nose resistant to fluoxetine (NRF NRF-6 gene, as well as with several uncharacterized C. elegans and Drosophila melanogaster genes, some with prominent acyltransferase domains. Future studies should

  13. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells

    Directory of Open Access Journals (Sweden)

    Hummon Amanda B

    2012-01-01

    Full Text Available Abstract Background Colorectal carcinomas (CRC carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. Results A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH, a protein recently linked to regulation of the AKT1/ß-catenin pathway. Conclusions We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of

  14. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells.

    Science.gov (United States)

    Hummon, Amanda B; Pitt, Jason J; Camps, Jordi; Emons, Georg; Skube, Susan B; Huppi, Konrad; Jones, Tamara L; Beissbarth, Tim; Kramer, Frank; Grade, Marian; Difilippantonio, Michael J; Ried, Thomas; Caplen, Natasha J

    2012-01-04

    Colorectal carcinomas (CRC) carry massive genetic and transcriptional alterations that influence multiple cellular pathways. The study of proteins whose loss-of-function (LOF) alters the growth of CRC cells can be used to further understand the cellular processes cancer cells depend upon for survival. A small-scale RNAi screen of ~400 genes conducted in SW480 CRC cells identified several candidate genes as required for the viability of CRC cells, most prominently CASP8AP2/FLASH. To understand the function of this gene in maintaining the viability of CRC cells in an unbiased manner, we generated gene specific expression profiles following RNAi. Silencing of CASP8AP2/FLASH resulted in altered expression of over 2500 genes enriched for genes associated with cellular growth and proliferation. Loss of CASP8AP2/FLASH function was significantly associated with altered transcription of the genes encoding the replication-dependent histone proteins as a result of the expression of the non-canonical polyA variants of these transcripts. Silencing of CASP8AP2/FLASH also mediated enrichment of changes in the expression of targets of the NFκB and MYC transcription factors. These findings were confirmed by whole transcriptome analysis of CASP8AP2/FLASH silenced cells at multiple time points. Finally, we identified and validated that CASP8AP2/FLASH LOF increases the expression of neurofilament heavy polypeptide (NEFH), a protein recently linked to regulation of the AKT1/ß-catenin pathway. We have used unbiased RNAi based approaches to identify and characterize the function of CASP8AP2/FLASH, a protein not previously reported as required for cell survival. This study further defines the role CASP8AP2/FLASH plays in the regulating expression of the replication-dependent histones and shows that its LOF results in broad and reproducible effects on the transcriptome of colorectal cancer cells including the induction of expression of the recently described tumor suppressor gene NEFH.

  15. TAF11 assembles RISC loading complex to enhance RNAi efficiency

    Science.gov (United States)

    Liang, Chunyang; Wang, Yibing; Murota, Yukiko; Liu, Xiang; Smith, Dean; Siomi, Mikiko C.; Liu, Qinghua

    2015-01-01

    SUMMARY Assembly of the RNA-induced silencing complex (RISC) requires formation of the RISC loading complex (RLC), which contains Dicer-2(Dcr-2)-R2D2 complex and recruits duplex siRNA to Ago2 in Drosophila melanogaster. However, the precise composition and action mechanism of Drosophila RLC remain unclear. Here, we identified the missing factor of RLC as TATA-binding protein associated factor 11 (TAF11) by genetic screen. Although an annotated nuclear transcription factor, we found that TAF11 also associated with Dcr-2/R2D2 and localized to cytoplasmic D2 bodies. Consistent with defective RLC assembly in taf11−/− ovary extract, we reconstituted the RLC in vitro using recombinant Dcr-2-R2D2 complex, TAF11, and duplex siRNA. Furthermore, we showed that TAF11 tetramer facilitates Dcr-2-R2D2 tetramerization to enhance siRNA binding and RISC loading activities. Together, our genetic and biochemical studies define the molecular nature of Drosophila RLC and elucidate a novel cytoplasmic function of TAF11 in organizing RLC assembly to enhance RNAi efficiency. PMID:26257286

  16. Optimization of a Fluorescence-Based Assay for Large-Scale Drug Screening against Babesia and Theileria Parasites

    OpenAIRE

    Rizk, Mohamed Abdo; El-Sayed, Shimaa Abd El-Salam; Terkawi, Mohamed Alaa; Youssef, Mohamed Ahmed; El Said, El Said El Shirbini; Elsayed, Gehad; El-Khodery, Sabry; El-Ashker, Maged; Elsify, Ahmed; Omar, Mosaab; Salama, Akram; Yokoyama, Naoaki; Igarashi, Ikuo

    2015-01-01

    A rapid and accurate assay for evaluating antibabesial drugs on a large scale is required for the discovery of novel chemotherapeutic agents against Babesia parasites. In the current study, we evaluated the usefulness of a fluorescence-based assay for determining the efficacies of antibabesial compounds against bovine and equine hemoparasites in in vitro cultures. Three different hematocrits (HCTs; 2.5%, 5%, and 10%) were used without daily replacement of the medium. The results of a high-thr...

  17. PKI security in large-scale healthcare networks.

    Science.gov (United States)

    Mantas, Georgios; Lymberopoulos, Dimitrios; Komninos, Nikos

    2012-06-01

    During the past few years a lot of PKI (Public Key Infrastructures) infrastructures have been proposed for healthcare networks in order to ensure secure communication services and exchange of data among healthcare professionals. However, there is a plethora of challenges in these healthcare PKI infrastructures. Especially, there are a lot of challenges for PKI infrastructures deployed over large-scale healthcare networks. In this paper, we propose a PKI infrastructure to ensure security in a large-scale Internet-based healthcare network connecting a wide spectrum of healthcare units geographically distributed within a wide region. Furthermore, the proposed PKI infrastructure facilitates the trust issues that arise in a large-scale healthcare network including multi-domain PKI infrastructures.

  18. Emerging large-scale solar heating applications

    International Nuclear Information System (INIS)

    Wong, W.P.; McClung, J.L.

    2009-01-01

    Currently the market for solar heating applications in Canada is dominated by outdoor swimming pool heating, make-up air pre-heating and domestic water heating in homes, commercial and institutional buildings. All of these involve relatively small systems, except for a few air pre-heating systems on very large buildings. Together these applications make up well over 90% of the solar thermal collectors installed in Canada during 2007. These three applications, along with the recent re-emergence of large-scale concentrated solar thermal for generating electricity, also dominate the world markets. This paper examines some emerging markets for large scale solar heating applications, with a focus on the Canadian climate and market. (author)

  19. Emerging large-scale solar heating applications

    Energy Technology Data Exchange (ETDEWEB)

    Wong, W.P.; McClung, J.L. [Science Applications International Corporation (SAIC Canada), Ottawa, Ontario (Canada)

    2009-07-01

    Currently the market for solar heating applications in Canada is dominated by outdoor swimming pool heating, make-up air pre-heating and domestic water heating in homes, commercial and institutional buildings. All of these involve relatively small systems, except for a few air pre-heating systems on very large buildings. Together these applications make up well over 90% of the solar thermal collectors installed in Canada during 2007. These three applications, along with the recent re-emergence of large-scale concentrated solar thermal for generating electricity, also dominate the world markets. This paper examines some emerging markets for large scale solar heating applications, with a focus on the Canadian climate and market. (author)

  20. Construction of RNAi lentiviral vector targeting mouse Islet-1 gene

    Directory of Open Access Journals (Sweden)

    Shen-shen ZHI

    2011-02-01

    Full Text Available Objective To construct and select RNAi lentiviral vectors that can silence mouse Islet-1 gene effectively.Methods Three groups of RNAi-target of mouse Islet-1 gene were designed,and corresponding shRNA oligo(sh1,sh2 and sh3 were synthesized,and then they were respectively inserted to the PLVTHM vector that had been digested by endonuclease.Agarose gel electrophoresis and sequencing were used to select and indentify the positive clones.The positive clones were extracted and then mixed with E.coli to amplify positive clones.The amplified clones were then infected into 293T along with the other 3 helper plasmids to produce lentiviral vector.After the construction of the lentiviral vector,plaque formation test was performed to determine the titer of lentiviral vector.The lentiviral vectors were then infected into C3H10T1/2 cells.The transfect efficiency of the lentiviral vectors was determined with flow cytometry with detection of green fluorescent protein(GFP.Q-PCR was employed to detect the RNAi efficiency of the lentiviral vectors.Results Agarose gel electrophoresis analysis showed that the clones with right gene at the target size were successfully established;gene sequencing showed that the right DNA fragments had been inserted;plaque formation test showed that the titer of the virus solution was 3.87×108TU/ml;the transfect efficiency of the lentiviral vector infected into C3H10T1/2 cells was 90.36%.All the 3 groups of shRNA targets(sh1,sh2 and sh3 showed an inhibitory effect on Islet-1 gene,and the sh1 showed the highest inhibitory effect(76.8%,as compared with that of normal cells(P < 0.05.Conclusion The RNAi lentiviral vector that can effectively silence the mouse Islet-1 gene has been constructed successfully,which may lay a foundation for further investigation of Islet-1 gene.

  1. New insights into siRNA amplification and RNAi.

    Science.gov (United States)

    Zhang, Chi; Ruvkun, Gary

    2012-08-01

    In the nematode Caenorhabditis elegans (C. elegans), gene inactivation by RNA interference can achieve remarkable potency due to the amplification of initial silencing triggers by RNA-dependent RNA polymerases (RdRPs). RdRPs catalyze the biogenesis of an abundant species of secondary small interfering RNAs (siRNAs) using the target mRNA as template. The interaction between primary siRNAs derived from the exogenous double-stranded RNA (dsRNA) trigger and the target mRNA is required for the recruitment of RdRPs. Other genetic requirements for RdRP activities have not been characterized. Recent studies have identified the RDE-10/RDE-11 complex which interacts with the primary siRNA bound target mRNA and acts upstream of the RdRPs. rde-10 and rde-11 mutants show an RNAi defective phenotype because the biogenesis of secondary siRNAs is completely abolished. In addition, the RDE-10/RDE-11 complex plays a similar role in the endogenous RNAi pathway for the biogenesis of a subset of siRNAs targeting recently acquired, duplicated genes.

  2. Molecular Characterization and the Function of Argonaute3 in RNAi Pathway of Plutella xylostella

    Directory of Open Access Journals (Sweden)

    Muhammad Salman Hameed

    2018-04-01

    Full Text Available Argonaute (Ago protein family plays a key role in the RNA interference (RNAi process in different insects including Lepidopteran. However, the role of Ago proteins in the RNAi pathway of Plutella xylostella is still unknown. We cloned an Argonaute3 gene in P. xylostella (PxAgo3 with the complete coding sequence of 2832 bp. The encoded protein had 935 amino acids with an expected molecular weight of 108.9 kDa and an isoelectric point of 9.29. It contained a PAZ (PIWI/Argonaute/Zwile domain and PIWI (P-element-induced whimpy testes domain. PxAgo3 was classified into the Piwi subfamily of Ago proteins with a high similarity of 93.0% with Bombyx mori Ago3 (BmAgo3. The suppression of PxAgo3 by dsPxAgo3 was observed 3 h after treatment and was maintained until 24 h. Knockdown of PxAgo3 decreased the suppression level of PxActin by dsPxActin in P. xylostella cells, while overexpression of PxAgo3 increased the RNAi efficiency. Our results suggest that PxAgo3 play a key role in the double stranded RNA (dsRNA-regulated RNAi pathway in P. xylostella.

  3. A directed RNAi screen based on larval growth arrest reveals new modifiers of C. elegans insulin signaling.

    Directory of Open Access Journals (Sweden)

    Ola Billing

    Full Text Available Genes regulating Caenorhabditis elegans insulin/IGF signaling (IIS have largely been identified on the basis of their involvement in dauer development or longevity. A third IIS phenotype is the first larval stage (L1 diapause, which is also influenced by asna-1, a regulator of DAF-28/insulin secretion. We reasoned that new regulators of IIS strength might be identified in screens based on the L1 diapause and the asna-1 phenotype. Eighty- six genes were selected for analysis by virtue of their predicted interaction with ASNA-1 and screened for asna-1-like larval arrest. ykt-6, mrps-2, mrps-10 and mrpl-43 were identified as genes which, when inactivated, caused larval arrest without any associated feeding defects. Several tests indicated that IIS strength was weaker and that insulin secretion was defective in these animals. This study highlights the role of the Golgi network and the mitochondria in insulin secretion and provides a new list of genes that modulate IIS in C. elegans.

  4. Large-scale regions of antimatter

    International Nuclear Information System (INIS)

    Grobov, A. V.; Rubin, S. G.

    2015-01-01

    Amodified mechanism of the formation of large-scale antimatter regions is proposed. Antimatter appears owing to fluctuations of a complex scalar field that carries a baryon charge in the inflation era

  5. Large-scale regions of antimatter

    Energy Technology Data Exchange (ETDEWEB)

    Grobov, A. V., E-mail: alexey.grobov@gmail.com; Rubin, S. G., E-mail: sgrubin@mephi.ru [National Research Nuclear University MEPhI (Russian Federation)

    2015-07-15

    Amodified mechanism of the formation of large-scale antimatter regions is proposed. Antimatter appears owing to fluctuations of a complex scalar field that carries a baryon charge in the inflation era.

  6. Large-Scale Analysis of Art Proportions

    DEFF Research Database (Denmark)

    Jensen, Karl Kristoffer

    2014-01-01

    While literature often tries to impute mathematical constants into art, this large-scale study (11 databases of paintings and photos, around 200.000 items) shows a different truth. The analysis, consisting of the width/height proportions, shows a value of rarely if ever one (square) and with majo......While literature often tries to impute mathematical constants into art, this large-scale study (11 databases of paintings and photos, around 200.000 items) shows a different truth. The analysis, consisting of the width/height proportions, shows a value of rarely if ever one (square...

  7. The Expanded Large Scale Gap Test

    Science.gov (United States)

    1987-03-01

    NSWC TR 86-32 DTIC THE EXPANDED LARGE SCALE GAP TEST BY T. P. LIDDIARD D. PRICE RESEARCH AND TECHNOLOGY DEPARTMENT ’ ~MARCH 1987 Ap~proved for public...arises, to reduce the spread in the LSGT 50% gap value.) The worst charges, such as those with the highest or lowest densities, the largest re-pressed...Arlington, VA 22217 PE 62314N INS3A 1 RJ14E31 7R4TBK 11 TITLE (Include Security CIlmsilficatiorn The Expanded Large Scale Gap Test . 12. PEIRSONAL AUTHOR() T

  8. Large scale and big data processing and management

    CERN Document Server

    Sakr, Sherif

    2014-01-01

    Large Scale and Big Data: Processing and Management provides readers with a central source of reference on the data management techniques currently available for large-scale data processing. Presenting chapters written by leading researchers, academics, and practitioners, it addresses the fundamental challenges associated with Big Data processing tools and techniques across a range of computing environments.The book begins by discussing the basic concepts and tools of large-scale Big Data processing and cloud computing. It also provides an overview of different programming models and cloud-bas

  9. Reconfiguring Cooperative Work by Visualizing EPR on Large Projected Screens

    DEFF Research Database (Denmark)

    Simonsen, Jesper

    Simonsen, J. (2006): Reconfiguring Cooperative Work by Visualizing EPR on Large Projected Screens, Paper presented at the PDC 2006 workshop on: Reconfiguring Healthcare: Issues in Computer Supported Cooperative Work in Healthcare Environments. Participatory Design Conference, Trento, Italy, August...

  10. Large scale cluster computing workshop

    International Nuclear Information System (INIS)

    Dane Skow; Alan Silverman

    2002-01-01

    Recent revolutions in computer hardware and software technologies have paved the way for the large-scale deployment of clusters of commodity computers to address problems heretofore the domain of tightly coupled SMP processors. Near term projects within High Energy Physics and other computing communities will deploy clusters of scale 1000s of processors and be used by 100s to 1000s of independent users. This will expand the reach in both dimensions by an order of magnitude from the current successful production facilities. The goals of this workshop were: (1) to determine what tools exist which can scale up to the cluster sizes foreseen for the next generation of HENP experiments (several thousand nodes) and by implication to identify areas where some investment of money or effort is likely to be needed. (2) To compare and record experimences gained with such tools. (3) To produce a practical guide to all stages of planning, installing, building and operating a large computing cluster in HENP. (4) To identify and connect groups with similar interest within HENP and the larger clustering community

  11. Large-scale testing of women in Copenhagen has not reduced the prevalence of Chlamydia trachomatis infections

    DEFF Research Database (Denmark)

    Westh, Henrik Torkil; Kolmos, H J

    2003-01-01

    OBJECTIVE: To examine the impact of a stable, large-scale enzyme immunoassay (EIA) Chlamydia trachomatis testing situation in Copenhagen, and to estimate the impact of introducing a genomic-based assay with higher sensitivity and specificity. METHODS: Over a five-year study period, 25 305-28 505...... and negative predictive values of the Chlamydia test result, new screening strategies for both men and women in younger age groups will be necessary if chlamydial infections are to be curtailed....

  12. Large-Scale Agriculture and Outgrower Schemes in Ethiopia

    DEFF Research Database (Denmark)

    Wendimu, Mengistu Assefa

    , the impact of large-scale agriculture and outgrower schemes on productivity, household welfare and wages in developing countries is highly contentious. Chapter 1 of this thesis provides an introduction to the study, while also reviewing the key debate in the contemporary land ‘grabbing’ and historical large...... sugarcane outgrower scheme on household income and asset stocks. Chapter 5 examines the wages and working conditions in ‘formal’ large-scale and ‘informal’ small-scale irrigated agriculture. The results in Chapter 2 show that moisture stress, the use of untested planting materials, and conflict over land...... commands a higher wage than ‘formal’ large-scale agriculture, while rather different wage determination mechanisms exist in the two sectors. Human capital characteristics (education and experience) partly explain the differences in wages within the formal sector, but play no significant role...

  13. Economically viable large-scale hydrogen liquefaction

    Science.gov (United States)

    Cardella, U.; Decker, L.; Klein, H.

    2017-02-01

    The liquid hydrogen demand, particularly driven by clean energy applications, will rise in the near future. As industrial large scale liquefiers will play a major role within the hydrogen supply chain, production capacity will have to increase by a multiple of today’s typical sizes. The main goal is to reduce the total cost of ownership for these plants by increasing energy efficiency with innovative and simple process designs, optimized in capital expenditure. New concepts must ensure a manageable plant complexity and flexible operability. In the phase of process development and selection, a dimensioning of key equipment for large scale liquefiers, such as turbines and compressors as well as heat exchangers, must be performed iteratively to ensure technological feasibility and maturity. Further critical aspects related to hydrogen liquefaction, e.g. fluid properties, ortho-para hydrogen conversion, and coldbox configuration, must be analysed in detail. This paper provides an overview on the approach, challenges and preliminary results in the development of efficient as well as economically viable concepts for large-scale hydrogen liquefaction.

  14. The World Health Organization Adult Attention-Deficit/Hyperactivity Disorder Self-Report Screening Scale for DSM-5.

    Science.gov (United States)

    Ustun, Berk; Adler, Lenard A; Rudin, Cynthia; Faraone, Stephen V; Spencer, Thomas J; Berglund, Patricia; Gruber, Michael J; Kessler, Ronald C

    2017-05-01

    Recognition that adult attention-deficit/hyperactivity disorder (ADHD) is common, seriously impairing, and usually undiagnosed has led to the development of adult ADHD screening scales for use in community, workplace, and primary care settings. However, these scales are all calibrated to DSM-IV criteria, which are narrower than the recently developed DSM-5 criteria. To update for DSM-5 criteria and improve the operating characteristics of the widely used World Health Organization Adult ADHD Self-Report Scale (ASRS) for screening. Probability subsamples of participants in 2 general population surveys (2001-2003 household survey [n = 119] and 2004-2005 managed care subscriber survey [n = 218]) who completed the full 29-question self-report ASRS, with both subsamples over-sampling ASRS-screened positives, were blindly administered a semistructured research diagnostic interview for DSM-5 adult ADHD. In 2016, the Risk-Calibrated Supersparse Linear Integer Model, a novel machine-learning algorithm designed to create screening scales with optimal integer weights and limited numbers of screening questions, was applied to the pooled data to create a DSM-5 version of the ASRS screening scale. The accuracy of the new scale was then confirmed in an independent 2011-2012 clinical sample of patients seeking evaluation at the New York University Langone Medical Center Adult ADHD Program (NYU Langone) and 2015-2016 primary care controls (n = 300). Data analysis was conducted from April 4, 2016, to September 22, 2016. The sensitivity, specificity, area under the curve (AUC), and positive predictive value (PPV) of the revised ASRS. Of the total 637 participants, 44 (37.0%) household survey respondents, 51 (23.4%) managed care respondents, and 173 (57.7%) NYU Langone respondents met DSM-5 criteria for adult ADHD in the semistructured diagnostic interview. Of the respondents who met DSM-5 criteria for adult ADHD, 123 were male (45.9%); mean (SD) age was 33.1 (11.4) years

  15. The World Health Organization Adult Attention-Deficit/Hyperactivity Disorder Self-Report Screening Scale for DSM-5

    Science.gov (United States)

    Ustun, Berk; Adler, Lenard A.; Rudin, Cynthia; Faraone, Stephen V.; Spencer, Thomas J.; Berglund, Patricia; Gruber, Michael J.

    2017-01-01

    Importance Recognition that adult attention-deficit/hyperactivity disorder (ADHD) is common, seriously impairing, and usually undiagnosed has led to the development of adult ADHD screening scales for use in community, workplace, and primary care settings. However, these scales are all calibrated to DSM-IV criteria, which are narrower than the recently developed DSM-5 criteria. Objectives To update for DSM-5 criteria and improve the operating characteristics of the widely used World Health Organization Adult ADHD Self-Report Scale (ASRS) for screening. Design, Setting, and Participants Probability subsamples of participants in 2 general population surveys (2001-2003 household survey [n = 119] and 2004-2005 managed care subscriber survey [n = 218]) who completed the full 29-question self-report ASRS, with both subsamples over-sampling ASRS-screened positives, were blindly administered a semistructured research diagnostic interview for DSM-5 adult ADHD. In 2016, the Risk-Calibrated Supersparse Linear Integer Model, a novel machine-learning algorithm designed to create screening scales with optimal integer weights and limited numbers of screening questions, was applied to the pooled data to create a DSM-5 version of the ASRS screening scale. The accuracy of the new scale was then confirmed in an independent 2011-2012 clinical sample of patients seeking evaluation at the New York University Langone Medical Center Adult ADHD Program (NYU Langone) and 2015-2016 primary care controls (n = 300). Data analysis was conducted from April 4, 2016, to September 22, 2016. Main Outcomes and Measures The sensitivity, specificity, area under the curve (AUC), and positive predictive value (PPV) of the revised ASRS. Results Of the total 637 participants, 44 (37.0%) household survey respondents, 51 (23.4%) managed care respondents, and 173 (57.7%) NYU Langone respondents met DSM-5 criteria for adult ADHD in the semistructured diagnostic interview. Of the respondents who met

  16. Large scale chromatographic separations using continuous displacement chromatography (CDC)

    International Nuclear Information System (INIS)

    Taniguchi, V.T.; Doty, A.W.; Byers, C.H.

    1988-01-01

    A process for large scale chromatographic separations using a continuous chromatography technique is described. The process combines the advantages of large scale batch fixed column displacement chromatography with conventional analytical or elution continuous annular chromatography (CAC) to enable large scale displacement chromatography to be performed on a continuous basis (CDC). Such large scale, continuous displacement chromatography separations have not been reported in the literature. The process is demonstrated with the ion exchange separation of a binary lanthanide (Nd/Pr) mixture. The process is, however, applicable to any displacement chromatography separation that can be performed using conventional batch, fixed column chromatography

  17. Screening wells by multi-scale grids for multi-stage Markov Chain Monte Carlo simulation

    DEFF Research Database (Denmark)

    Akbari, Hani; Engsig-Karup, Allan Peter

    2018-01-01

    /production wells, aiming at accurate breakthrough capturing as well as above mentioned efficiency goals. However this short time simulation needs fine-scale structure of the geological model around wells and running a fine-scale model is not as cheap as necessary for screening steps. On the other hand applying...... it on a coarse-scale model declines important data around wells and causes inaccurate results, particularly accurate breakthrough capturing which is important for prediction applications. Therefore we propose a multi-scale grid which preserves the fine-scale model around wells (as well as high permeable regions...... and fractures) and coarsens rest of the field and keeps efficiency and accuracy for the screening well stage and coarse-scale simulation, as well. A discrete wavelet transform is used as a powerful tool to generate the desired unstructured multi-scale grid efficiently. Finally an accepted proposal on coarse...

  18. Large Scale Processes and Extreme Floods in Brazil

    Science.gov (United States)

    Ribeiro Lima, C. H.; AghaKouchak, A.; Lall, U.

    2016-12-01

    Persistent large scale anomalies in the atmospheric circulation and ocean state have been associated with heavy rainfall and extreme floods in water basins of different sizes across the world. Such studies have emerged in the last years as a new tool to improve the traditional, stationary based approach in flood frequency analysis and flood prediction. Here we seek to advance previous studies by evaluating the dominance of large scale processes (e.g. atmospheric rivers/moisture transport) over local processes (e.g. local convection) in producing floods. We consider flood-prone regions in Brazil as case studies and the role of large scale climate processes in generating extreme floods in such regions is explored by means of observed streamflow, reanalysis data and machine learning methods. The dynamics of the large scale atmospheric circulation in the days prior to the flood events are evaluated based on the vertically integrated moisture flux and its divergence field, which are interpreted in a low-dimensional space as obtained by machine learning techniques, particularly supervised kernel principal component analysis. In such reduced dimensional space, clusters are obtained in order to better understand the role of regional moisture recycling or teleconnected moisture in producing floods of a given magnitude. The convective available potential energy (CAPE) is also used as a measure of local convection activities. We investigate for individual sites the exceedance probability in which large scale atmospheric fluxes dominate the flood process. Finally, we analyze regional patterns of floods and how the scaling law of floods with drainage area responds to changes in the climate forcing mechanisms (e.g. local vs large scale).

  19. Computing in Large-Scale Dynamic Systems

    NARCIS (Netherlands)

    Pruteanu, A.S.

    2013-01-01

    Software applications developed for large-scale systems have always been difficult to de- velop due to problems caused by the large number of computing devices involved. Above a certain network size (roughly one hundred), necessary services such as code updating, topol- ogy discovery and data

  20. Fires in large scale ventilation systems

    International Nuclear Information System (INIS)

    Gregory, W.S.; Martin, R.A.; White, B.W.; Nichols, B.D.; Smith, P.R.; Leslie, I.H.; Fenton, D.L.; Gunaji, M.V.; Blythe, J.P.

    1991-01-01

    This paper summarizes the experience gained simulating fires in large scale ventilation systems patterned after ventilation systems found in nuclear fuel cycle facilities. The series of experiments discussed included: (1) combustion aerosol loading of 0.61x0.61 m HEPA filters with the combustion products of two organic fuels, polystyrene and polymethylemethacrylate; (2) gas dynamic and heat transport through a large scale ventilation system consisting of a 0.61x0.61 m duct 90 m in length, with dampers, HEPA filters, blowers, etc.; (3) gas dynamic and simultaneous transport of heat and solid particulate (consisting of glass beads with a mean aerodynamic diameter of 10μ) through the large scale ventilation system; and (4) the transport of heat and soot, generated by kerosene pool fires, through the large scale ventilation system. The FIRAC computer code, designed to predict fire-induced transients in nuclear fuel cycle facility ventilation systems, was used to predict the results of experiments (2) through (4). In general, the results of the predictions were satisfactory. The code predictions for the gas dynamics, heat transport, and particulate transport and deposition were within 10% of the experimentally measured values. However, the code was less successful in predicting the amount of soot generation from kerosene pool fires, probably due to the fire module of the code being a one-dimensional zone model. The experiments revealed a complicated three-dimensional combustion pattern within the fire room of the ventilation system. Further refinement of the fire module within FIRAC is needed. (orig.)

  1. Large-Scale Spacecraft Fire Safety Tests

    Science.gov (United States)

    Urban, David; Ruff, Gary A.; Ferkul, Paul V.; Olson, Sandra; Fernandez-Pello, A. Carlos; T'ien, James S.; Torero, Jose L.; Cowlard, Adam J.; Rouvreau, Sebastien; Minster, Olivier; hide

    2014-01-01

    An international collaborative program is underway to address open issues in spacecraft fire safety. Because of limited access to long-term low-gravity conditions and the small volume generally allotted for these experiments, there have been relatively few experiments that directly study spacecraft fire safety under low-gravity conditions. Furthermore, none of these experiments have studied sample sizes and environment conditions typical of those expected in a spacecraft fire. The major constraint has been the size of the sample, with prior experiments limited to samples of the order of 10 cm in length and width or smaller. This lack of experimental data forces spacecraft designers to base their designs and safety precautions on 1-g understanding of flame spread, fire detection, and suppression. However, low-gravity combustion research has demonstrated substantial differences in flame behavior in low-gravity. This, combined with the differences caused by the confined spacecraft environment, necessitates practical scale spacecraft fire safety research to mitigate risks for future space missions. To address this issue, a large-scale spacecraft fire experiment is under development by NASA and an international team of investigators. This poster presents the objectives, status, and concept of this collaborative international project (Saffire). The project plan is to conduct fire safety experiments on three sequential flights of an unmanned ISS re-supply spacecraft (the Orbital Cygnus vehicle) after they have completed their delivery of cargo to the ISS and have begun their return journeys to earth. On two flights (Saffire-1 and Saffire-3), the experiment will consist of a flame spread test involving a meter-scale sample ignited in the pressurized volume of the spacecraft and allowed to burn to completion while measurements are made. On one of the flights (Saffire-2), 9 smaller (5 x 30 cm) samples will be tested to evaluate NASAs material flammability screening tests

  2. Large-scale Complex IT Systems

    OpenAIRE

    Sommerville, Ian; Cliff, Dave; Calinescu, Radu; Keen, Justin; Kelly, Tim; Kwiatkowska, Marta; McDermid, John; Paige, Richard

    2011-01-01

    This paper explores the issues around the construction of large-scale complex systems which are built as 'systems of systems' and suggests that there are fundamental reasons, derived from the inherent complexity in these systems, why our current software engineering methods and techniques cannot be scaled up to cope with the engineering challenges of constructing such systems. It then goes on to propose a research and education agenda for software engineering that identifies the major challen...

  3. Large-scale complex IT systems

    OpenAIRE

    Sommerville, Ian; Cliff, Dave; Calinescu, Radu; Keen, Justin; Kelly, Tim; Kwiatkowska, Marta; McDermid, John; Paige, Richard

    2012-01-01

    12 pages, 2 figures This paper explores the issues around the construction of large-scale complex systems which are built as 'systems of systems' and suggests that there are fundamental reasons, derived from the inherent complexity in these systems, why our current software engineering methods and techniques cannot be scaled up to cope with the engineering challenges of constructing such systems. It then goes on to propose a research and education agenda for software engineering that ident...

  4. First Mile Challenges for Large-Scale IoT

    KAUST Repository

    Bader, Ahmed; Elsawy, Hesham; Gharbieh, Mohammad; Alouini, Mohamed-Slim; Adinoyi, Abdulkareem; Alshaalan, Furaih

    2017-01-01

    The Internet of Things is large-scale by nature. This is not only manifested by the large number of connected devices, but also by the sheer scale of spatial traffic intensity that must be accommodated, primarily in the uplink direction. To that end

  5. Repurposing CRISPR/Cas9 for in situ functional assays

    NARCIS (Netherlands)

    Malina, Abba; Mills, John R; Cencic, Regina; Yan, Yifei; Fraser, James; Schippers, Laura M; Paquet, Marilène; Dostie, Josée; Pelletier, Jerry

    2013-01-01

    RNAi combined with next-generation sequencing has proven to be a powerful and cost-effective genetic screening platform in mammalian cells. Still, this technology has its limitations and is incompatible with in situ mutagenesis screens on a genome-wide scale. Using p53 as a proof-of-principle

  6. Prospects for large scale electricity storage in Denmark

    DEFF Research Database (Denmark)

    Krog Ekman, Claus; Jensen, Søren Højgaard

    2010-01-01

    In a future power systems with additional wind power capacity there will be an increased need for large scale power management as well as reliable balancing and reserve capabilities. Different technologies for large scale electricity storage provide solutions to the different challenges arising w...

  7. RNAi Experiments in D. melanogaster : Solutions to the Overlooked Problem of Off-Targets Shared by Independent dsRNAs

    NARCIS (Netherlands)

    Seinen, Erwin; Burgerhof, Johannes G. M.; Jansen, Ritsert C.; Sibon, Ody C. M.; Polymenis, Michael

    2010-01-01

    Background: RNAi technology is widely used to downregulate specific gene products. Investigating the phenotype induced by downregulation of gene products provides essential information about the function of the specific gene of interest. When RNAi is applied in Drosophila melanogaster or

  8. Evolution of scaling emergence in large-scale spatial epidemic spreading.

    Science.gov (United States)

    Wang, Lin; Li, Xiang; Zhang, Yi-Qing; Zhang, Yan; Zhang, Kan

    2011-01-01

    Zipf's law and Heaps' law are two representatives of the scaling concepts, which play a significant role in the study of complexity science. The coexistence of the Zipf's law and the Heaps' law motivates different understandings on the dependence between these two scalings, which has still hardly been clarified. In this article, we observe an evolution process of the scalings: the Zipf's law and the Heaps' law are naturally shaped to coexist at the initial time, while the crossover comes with the emergence of their inconsistency at the larger time before reaching a stable state, where the Heaps' law still exists with the disappearance of strict Zipf's law. Such findings are illustrated with a scenario of large-scale spatial epidemic spreading, and the empirical results of pandemic disease support a universal analysis of the relation between the two laws regardless of the biological details of disease. Employing the United States domestic air transportation and demographic data to construct a metapopulation model for simulating the pandemic spread at the U.S. country level, we uncover that the broad heterogeneity of the infrastructure plays a key role in the evolution of scaling emergence. The analyses of large-scale spatial epidemic spreading help understand the temporal evolution of scalings, indicating the coexistence of the Zipf's law and the Heaps' law depends on the collective dynamics of epidemic processes, and the heterogeneity of epidemic spread indicates the significance of performing targeted containment strategies at the early time of a pandemic disease.

  9. Large-Scale Structure and Hyperuniformity of Amorphous Ices

    Science.gov (United States)

    Martelli, Fausto; Torquato, Salvatore; Giovambattista, Nicolas; Car, Roberto

    2017-09-01

    We investigate the large-scale structure of amorphous ices and transitions between their different forms by quantifying their large-scale density fluctuations. Specifically, we simulate the isothermal compression of low-density amorphous ice (LDA) and hexagonal ice to produce high-density amorphous ice (HDA). Both HDA and LDA are nearly hyperuniform; i.e., they are characterized by an anomalous suppression of large-scale density fluctuations. By contrast, in correspondence with the nonequilibrium phase transitions to HDA, the presence of structural heterogeneities strongly suppresses the hyperuniformity and the system becomes hyposurficial (devoid of "surface-area fluctuations"). Our investigation challenges the largely accepted "frozen-liquid" picture, which views glasses as structurally arrested liquids. Beyond implications for water, our findings enrich our understanding of pressure-induced structural transformations in glasses.

  10. Large-screen display industry: market and technology trends for direct view and projection displays

    Science.gov (United States)

    Castellano, Joseph A.; Mentley, David E.

    1996-03-01

    Large screen information displays are defined as dynamic electronic displays that can be viewed by more than one person and are at least 2-feet wide. These large area displays for public viewing provide convenience, entertainment, security, and efficiency to the viewers. There are numerous uses for large screen information displays including those in advertising, transportation, traffic control, conference room presentations, computer aided design, banking, and military command/control. A noticeable characteristic of the large screen display market is the interchangeability of display types. For any given application, the user can usually choose from at least three alternative technologies, and sometimes from many more. Some display types have features that make them suitable for specific applications due to temperature, brightness, power consumption, or other such characteristic. The overall worldwide unit consumption of large screen information displays of all types and for all applications (excluding consumer TV) will increase from 401,109 units in 1995 to 655,797 units in 2002. On a unit consumption basis, applications in business and education represent the largest share of unit consumption over this time period; in 1995, this application represented 69.7% of the total. The market (value of shipments) will grow from DOL3.1 billion in 1995 to DOL3.9 billion in 2002. The market will be dominated by front LCD projectors and LCD overhead projector plates.

  11. Scaling behaviour of Fisher and Shannon entropies for the exponential-cosine screened coulomb potential

    Science.gov (United States)

    Abdelmonem, M. S.; Abdel-Hady, Afaf; Nasser, I.

    2017-07-01

    The scaling laws are given for the entropies in the information theory, including the Shannon's entropy, its power, the Fisher's information and the Fisher-Shannon product, using the exponential-cosine screened Coulomb potential. The scaling laws are specified, in the r-space, as a function of |μ - μc, nℓ|, where μ is the screening parameter and μc, nℓ its critical value for the specific quantum numbers n and ℓ. Scaling laws for other physical quantities, such as energy eigenvalues, the moments, static polarisability, transition probabilities, etc. are also given. Some of these are reported for the first time. The outcome is compared with the available literatures' results.

  12. TAF11 Assembles the RISC Loading Complex to Enhance RNAi Efficiency.

    Science.gov (United States)

    Liang, Chunyang; Wang, Yibing; Murota, Yukiko; Liu, Xiang; Smith, Dean; Siomi, Mikiko C; Liu, Qinghua

    2015-09-03

    Assembly of the RNA-induced silencing complex (RISC) requires formation of the RISC loading complex (RLC), which contains the Dicer-2 (Dcr-2)-R2D2 complex and recruits duplex siRNA to Ago2 in Drosophila melanogaster. However, the precise composition and action mechanism of Drosophila RLC remain unclear. Here we identified the missing factor of RLC as TATA-binding protein-associated factor 11 (TAF11) by genetic screen. Although it is an annotated nuclear transcription factor, we found that TAF11 also associated with Dcr-2/R2D2 and localized to cytoplasmic D2 bodies. Consistent with defective RLC assembly in taf11(-/-) ovary extract, we reconstituted the RLC in vitro using the recombinant Dcr-2-R2D2 complex, TAF11, and duplex siRNA. Furthermore, we showed that TAF11 tetramer facilitates Dcr-2-R2D2 tetramerization to enhance siRNA binding and RISC loading activities. Together, our genetic and biochemical studies define the molecular nature of the Drosophila RLC and elucidate a cytoplasmic function of TAF11 in organizing RLC assembly to enhance RNAi efficiency. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Effective and specific in planta RNAi in cyst nematodes: expression interference of four parasitism genes reduces parasitic success.

    Science.gov (United States)

    Sindhu, Anoop S; Maier, Tom R; Mitchum, Melissa G; Hussey, Richard S; Davis, Eric L; Baum, Thomas J

    2009-01-01

    Cyst nematodes are highly evolved sedentary plant endoparasites that use parasitism proteins injected through the stylet into host tissues to successfully parasitize plants. These secretory proteins likely are essential for parasitism as they are involved in a variety of parasitic events leading to the establishment of specialized feeding cells required by the nematode to obtain nourishment. With the advent of RNA interference (RNAi) technology and the demonstration of host-induced gene silencing in parasites, a new strategy to control pests and pathogens has become available, particularly in root-knot nematodes. Plant host-induced silencing of cyst nematode genes so far has had only limited success but similarly should disrupt the parasitic cycle and render the host plant resistant. Additional in planta RNAi data for cyst nematodes are being provided by targeting four parasitism genes through host-induced RNAi gene silencing in transgenic Arabidopsis thaliana, which is a host for the sugar beet cyst nematode Heterodera schachtii. Here it is reported that mRNA abundances of targeted nematode genes were specifically reduced in nematodes feeding on plants expressing corresponding RNAi constructs. Furthermore, this host-induced RNAi of all four nematode parasitism genes led to a reduction in the number of mature nematode females. Although no complete resistance was observed, the reduction of developing females ranged from 23% to 64% in different RNAi lines. These observations demonstrate the relevance of the targeted parasitism genes during the nematode life cycle and, potentially more importantly, suggest that a viable level of resistance in crop plants may be accomplished in the future using this technology against cyst nematodes.

  14. Double inflation: A possible resolution of the large-scale structure problem

    International Nuclear Information System (INIS)

    Turner, M.S.; Villumsen, J.V.; Vittorio, N.; Silk, J.; Juszkiewicz, R.

    1986-11-01

    A model is presented for the large-scale structure of the universe in which two successive inflationary phases resulted in large small-scale and small large-scale density fluctuations. This bimodal density fluctuation spectrum in an Ω = 1 universe dominated by hot dark matter leads to large-scale structure of the galaxy distribution that is consistent with recent observational results. In particular, large, nearly empty voids and significant large-scale peculiar velocity fields are produced over scales of ∼100 Mpc, while the small-scale structure over ≤ 10 Mpc resembles that in a low density universe, as observed. Detailed analytical calculations and numerical simulations are given of the spatial and velocity correlations. 38 refs., 6 figs

  15. Large-scale fracture mechancis testing -- requirements and possibilities

    International Nuclear Information System (INIS)

    Brumovsky, M.

    1993-01-01

    Application of fracture mechanics to very important and/or complicated structures, like reactor pressure vessels, brings also some questions about the reliability and precision of such calculations. These problems become more pronounced in cases of elastic-plastic conditions of loading and/or in parts with non-homogeneous materials (base metal and austenitic cladding, property gradient changes through material thickness) or with non-homogeneous stress fields (nozzles, bolt threads, residual stresses etc.). For such special cases some verification by large-scale testing is necessary and valuable. This paper discusses problems connected with planning of such experiments with respect to their limitations, requirements to a good transfer of received results to an actual vessel. At the same time, an analysis of possibilities of small-scale model experiments is also shown, mostly in connection with application of results between standard, small-scale and large-scale experiments. Experience from 30 years of large-scale testing in SKODA is used as an example to support this analysis. 1 fig

  16. Ethics of large-scale change

    DEFF Research Database (Denmark)

    Arler, Finn

    2006-01-01

    , which kind of attitude is appropriate when dealing with large-scale changes like these from an ethical point of view. Three kinds of approaches are discussed: Aldo Leopold's mountain thinking, the neoclassical economists' approach, and finally the so-called Concentric Circle Theories approach...

  17. Comparison Between Overtopping Discharge in Small and Large Scale Models

    DEFF Research Database (Denmark)

    Helgason, Einar; Burcharth, Hans F.

    2006-01-01

    The present paper presents overtopping measurements from small scale model test performed at the Haudraulic & Coastal Engineering Laboratory, Aalborg University, Denmark and large scale model tests performed at the Largde Wave Channel,Hannover, Germany. Comparison between results obtained from...... small and large scale model tests show no clear evidence of scale effects for overtopping above a threshold value. In the large scale model no overtopping was measured for waveheights below Hs = 0.5m as the water sunk into the voids between the stones on the crest. For low overtopping scale effects...

  18. A microliter-scale high-throughput screening system with quantum-dot nanoprobes for amyloid-β aggregation inhibitors.

    Directory of Open Access Journals (Sweden)

    Yukako Ishigaki

    Full Text Available The aggregation of amyloid β protein (Aβ is a key step in the pathogenesis of Alzheimer's disease (AD, and therefore inhibitory substances for Aβ aggregation may have preventive and/or therapeutic potential for AD. Here we report a novel microliter-scale high-throughput screening system for Aβ aggregation inhibitors based on fluorescence microscopy-imaging technology with quantum-dot Nanoprobes. This screening system could be analyzed with a 5-µl sample volume when a 1536-well plate was used, and the inhibitory activity could be estimated as half-maximal effective concentrations (EC50. We attempted to comprehensively screen Aβ aggregation inhibitors from 52 spices using this system to assess whether this novel screening system is actually useful for screening inhibitors. Screening results indicate that approximately 90% of the ethanolic extracts from the spices showed inhibitory activity for Aβ aggregation. Interestingly, spices belonging to the Lamiaceae, the mint family, showed significantly higher activity than the average of tested spices. Furthermore, we tried to isolate the main inhibitory compound from Saturejahortensis, summer savory, a member of the Lamiaceae, using this system, and revealed that the main active compound was rosmarinic acid. These results demonstrate that this novel microliter-scale high-throughput screening system could be applied to the actual screening of Aβ aggregation inhibitors. Since this system can analyze at a microscopic scale, it is likely that further minimization of the system would easily be possible such as protein microarray technology.

  19. Automated NMR fragment based screening identified a novel interface blocker to the LARG/RhoA complex.

    Directory of Open Access Journals (Sweden)

    Jia Gao

    Full Text Available The small GTPase cycles between the inactive GDP form and the activated GTP form, catalyzed by the upstream guanine exchange factors. The modulation of such process by small molecules has been proven to be a fruitful route for therapeutic intervention to prevent the over-activation of the small GTPase. The fragment based approach emerging in the past decade has demonstrated its paramount potential in the discovery of inhibitors targeting such novel and challenging protein-protein interactions. The details regarding the procedure of NMR fragment screening from scratch have been rarely disclosed comprehensively, thus restricts its wider applications. To achieve a consistent screening applicable to a number of targets, we developed a highly automated protocol to cover every aspect of NMR fragment screening as possible, including the construction of small but diverse libray, determination of the aqueous solubility by NMR, grouping compounds with mutual dispersity to a cocktail, and the automated processing and visualization of the ligand based screening spectra. We exemplified our streamlined screening in RhoA alone and the complex of the small GTPase RhoA and its upstream guanine exchange factor LARG. Two hits were confirmed from the primary screening in cocktail and secondary screening over individual hits for LARG/RhoA complex, while one of them was also identified from the screening for RhoA alone. HSQC titration of the two hits over RhoA and LARG alone, respectively, identified one compound binding to RhoA.GDP at a 0.11 mM affinity, and perturbed the residues at the switch II region of RhoA. This hit blocked the formation of the LARG/RhoA complex, validated by the native gel electrophoresis, and the titration of RhoA to ¹⁵N labeled LARG in the absence and presence the compound, respectively. It therefore provides us a starting point toward a more potent inhibitor to RhoA activation catalyzed by LARG.

  20. RNAi: An emerging field of molecular research | Kabir | African ...

    African Journals Online (AJOL)

    RNA interference (RNAi) is a specific technique using only a few double stranded RNA (dsRNA) molecules to stop the expression which has made it one of the important areas in molecular biology. By introducing a gene into the host genome which is highly homologous to an endogenous gene, the RNA silencing is ...

  1. Increased RNAi Efficacy in Spodoptera exigua via the Formulation of dsRNA With Guanylated Polymers

    Directory of Open Access Journals (Sweden)

    Olivier Christiaens

    2018-04-01

    Full Text Available Lepidoptera comprise some of the most devastating herbivorous pest insects worldwide. One of the most promising novel pest control strategies is exploiting the RNA interference (RNAi mechanism to target essential genes for knockdown and incite toxic effects in the target species without harming other organisms in the ecosystem. However, many insects are refractory to oral RNAi, often due to rapid degradation of ingested dsRNA in their digestive system. This is the case for many lepidopteran insects, including the beet armyworm Spodoptera exigua, which is characterized by a very alkaline gut environment (pH > 9.0 and a strong intestinal nucleolytic activity. In this research, guanidine-containing polymers were developed to protect dsRNA against nucleolytic degradation, specifically in high pH environments. First, their ability to protect dsRNA against nucleolytic degradation in gut juice of the beet armyworm S. exigua was investigated ex vivo. Polymers with high guanidine content provided a strong protection against nucleolytic degradation at pH 11, protecting the dsRNA for up to 30 h. Next, cellular uptake of the dsRNA and the polyplexes in lepidopteran CF203 midgut cells was investigated by confocal microscopy, showing that the polymer also enhanced cellular uptake of the dsRNA. Finally, in vivo feeding RNAi bioassays demonstrated that using these guanidine-containing polymer nanoparticles led to an increased RNAi efficiency in S. exigua. Targeting the essential gene chitin synthase B, we observed that the mortality increased to 53% in the polymer-protected dsRNA treatment compared to only 16% with the naked dsRNA and found that polymer-protected dsRNA completely halted the development of the caterpillars. These results show that using guanylated polymers as a formulation strategy can prevent degradation of dsRNA in the alkaline and strongly nucleolytic gut of lepidopteran insects. Furthermore, the polymer also enhances cellular uptake in

  2. Large-scale community echocardiographic screening reveals a major burden of undiagnosed valvular heart disease in older people: the OxVALVE Population Cohort Study†

    Science.gov (United States)

    d'Arcy, Joanna L.; Coffey, Sean; Loudon, Margaret A.; Kennedy, Andrew; Pearson-Stuttard, Jonathan; Birks, Jacqueline; Frangou, Eleni; Farmer, Andrew J.; Mant, David; Wilson, Jo; Myerson, Saul G.; Prendergast, Bernard D.

    2016-01-01

    Background Valvular heart disease (VHD) is expected to become more common as the population ages. However, current estimates of its natural history and prevalence are based on historical studies with potential sources of bias. We conducted a cross-sectional analysis of the clinical and epidemiological characteristics of VHD identified at recruitment of a large cohort of older people. Methods and results We enrolled 2500 individuals aged ≥65 years from a primary care population and screened for undiagnosed VHD using transthoracic echocardiography. Newly identified (predominantly mild) VHD was detected in 51% of participants. The most common abnormalities were aortic sclerosis (34%), mitral regurgitation (22%), and aortic regurgitation (15%). Aortic stenosis was present in 1.3%. The likelihood of undiagnosed VHD was two-fold higher in the two most deprived socioeconomic quintiles than in the most affluent quintile, and three-fold higher in individuals with atrial fibrillation. Clinically significant (moderate or severe) undiagnosed VHD was identified in 6.4%. In addition, 4.9% of the cohort had pre-existing VHD (a total prevalence of 11.3%). Projecting these findings using population data, we estimate that the prevalence of clinically significant VHD will double before 2050. Conclusions Previously undetected VHD affects 1 in 2 of the elderly population and is more common in lower socioeconomic classes. These unique data demonstrate the contemporary clinical and epidemiological characteristics of VHD in a large population-based cohort of older people and confirm the scale of the emerging epidemic of VHD, with widespread implications for clinicians and healthcare resources. PMID:27354049

  3. Needs, opportunities, and options for large scale systems research

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, G.L.

    1984-10-01

    The Office of Energy Research was recently asked to perform a study of Large Scale Systems in order to facilitate the development of a true large systems theory. It was decided to ask experts in the fields of electrical engineering, chemical engineering and manufacturing/operations research for their ideas concerning large scale systems research. The author was asked to distribute a questionnaire among these experts to find out their opinions concerning recent accomplishments and future research directions in large scale systems research. He was also requested to convene a conference which included three experts in each area as panel members to discuss the general area of large scale systems research. The conference was held on March 26--27, 1984 in Pittsburgh with nine panel members, and 15 other attendees. The present report is a summary of the ideas presented and the recommendations proposed by the attendees.

  4. Large-scale structure of the Universe

    International Nuclear Information System (INIS)

    Doroshkevich, A.G.

    1978-01-01

    The problems, discussed at the ''Large-scale Structure of the Universe'' symposium are considered on a popular level. Described are the cell structure of galaxy distribution in the Universe, principles of mathematical galaxy distribution modelling. The images of cell structures, obtained after reprocessing with the computer are given. Discussed are three hypothesis - vortical, entropic, adiabatic, suggesting various processes of galaxy and galaxy clusters origin. A considerable advantage of the adiabatic hypothesis is recognized. The relict radiation, as a method of direct studying the processes taking place in the Universe is considered. The large-scale peculiarities and small-scale fluctuations of the relict radiation temperature enable one to estimate the turbance properties at the pre-galaxy stage. The discussion of problems, pertaining to studying the hot gas, contained in galaxy clusters, the interactions within galaxy clusters and with the inter-galaxy medium, is recognized to be a notable contribution into the development of theoretical and observational cosmology

  5. The RDE-10/RDE-11 complex triggers RNAi-induced mRNA degradation by association with target mRNA in C. elegans.

    Science.gov (United States)

    Yang, Huan; Zhang, Ying; Vallandingham, Jim; Li, Hua; Li, Hau; Florens, Laurence; Mak, Ho Yi

    2012-04-15

    The molecular mechanisms for target mRNA degradation in Caenorhabditis elegans undergoing RNAi are not fully understood. Using a combination of genetic, proteomic, and biochemical approaches, we report a divergent RDE-10/RDE-11 complex that is required for RNAi in C. elegans. Genetic analysis indicates that the RDE-10/RDE-11 complex acts in parallel to nuclear RNAi. Association of the complex with target mRNA is dependent on RDE-1 but not RRF-1, suggesting that target mRNA recognition depends on primary but not secondary siRNA. Furthermore, RDE-11 is required for mRNA degradation subsequent to target engagement. Deep sequencing reveals a fivefold decrease in secondary siRNA abundance in rde-10 and rde-11 mutant animals, while primary siRNA and microRNA biogenesis is normal. Therefore, the RDE-10/RDE-11 complex is critical for amplifying the exogenous RNAi response. Our work uncovers an essential output of the RNAi pathway in C. elegans.

  6. Seismic safety in conducting large-scale blasts

    Science.gov (United States)

    Mashukov, I. V.; Chaplygin, V. V.; Domanov, V. P.; Semin, A. A.; Klimkin, M. A.

    2017-09-01

    In mining enterprises to prepare hard rocks for excavation a drilling and blasting method is used. With the approach of mining operations to settlements the negative effect of large-scale blasts increases. To assess the level of seismic impact of large-scale blasts the scientific staff of Siberian State Industrial University carried out expertise for coal mines and iron ore enterprises. Determination of the magnitude of surface seismic vibrations caused by mass explosions was performed using seismic receivers, an analog-digital converter with recording on a laptop. The registration results of surface seismic vibrations during production of more than 280 large-scale blasts at 17 mining enterprises in 22 settlements are presented. The maximum velocity values of the Earth’s surface vibrations are determined. The safety evaluation of seismic effect was carried out according to the permissible value of vibration velocity. For cases with exceedance of permissible values recommendations were developed to reduce the level of seismic impact.

  7. Single-field consistency relations of large scale structure part III: test of the equivalence principle

    Energy Technology Data Exchange (ETDEWEB)

    Creminelli, Paolo [Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, Trieste, 34151 (Italy); Gleyzes, Jérôme; Vernizzi, Filippo [CEA, Institut de Physique Théorique, Gif-sur-Yvette cédex, F-91191 France (France); Hui, Lam [Physics Department and Institute for Strings, Cosmology and Astroparticle Physics, Columbia University, New York, NY, 10027 (United States); Simonović, Marko, E-mail: creminel@ictp.it, E-mail: jerome.gleyzes@cea.fr, E-mail: lhui@astro.columbia.edu, E-mail: msimonov@sissa.it, E-mail: filippo.vernizzi@cea.fr [SISSA, via Bonomea 265, Trieste, 34136 (Italy)

    2014-06-01

    The recently derived consistency relations for Large Scale Structure do not hold if the Equivalence Principle (EP) is violated. We show it explicitly in a toy model with two fluids, one of which is coupled to a fifth force. We explore the constraints that galaxy surveys can set on EP violation looking at the squeezed limit of the 3-point function involving two populations of objects. We find that one can explore EP violations of order 10{sup −3}÷10{sup −4} on cosmological scales. Chameleon models are already very constrained by the requirement of screening within the Solar System and only a very tiny region of the parameter space can be explored with this method. We show that no violation of the consistency relations is expected in Galileon models.

  8. Image-based Exploration of Large-Scale Pathline Fields

    KAUST Repository

    Nagoor, Omniah H.

    2014-05-27

    While real-time applications are nowadays routinely used in visualizing large nu- merical simulations and volumes, handling these large-scale datasets requires high-end graphics clusters or supercomputers to process and visualize them. However, not all users have access to powerful clusters. Therefore, it is challenging to come up with a visualization approach that provides insight to large-scale datasets on a single com- puter. Explorable images (EI) is one of the methods that allows users to handle large data on a single workstation. Although it is a view-dependent method, it combines both exploration and modification of visual aspects without re-accessing the original huge data. In this thesis, we propose a novel image-based method that applies the concept of EI in visualizing large flow-field pathlines data. The goal of our work is to provide an optimized image-based method, which scales well with the dataset size. Our approach is based on constructing a per-pixel linked list data structure in which each pixel contains a list of pathlines segments. With this view-dependent method it is possible to filter, color-code and explore large-scale flow data in real-time. In addition, optimization techniques such as early-ray termination and deferred shading are applied, which further improves the performance and scalability of our approach.

  9. A population study comparing screening performance of prototypes for depression and anxiety with standard scales

    Directory of Open Access Journals (Sweden)

    Christensen Helen

    2011-11-01

    Full Text Available Abstract Background Screening instruments for mental disorders need to be short, engaging, and valid. Current screening instruments are usually questionnaire-based and may be opaque to the user. A prototype approach where individuals identify with a description of an individual with typical symptoms of depression, anxiety, social phobia or panic may be a shorter, faster and more acceptable method for screening. The aim of the study was to evaluate the accuracy of four new prototype screeners for predicting depression and anxiety disorders and to compare their performance with existing scales. Methods Short and ultra-short prototypes were developed for Major Depressive Disorder (MDD, Generalised Anxiety Disorder (GAD, Panic Disorder (PD and Social Phobia (SP. Prototypes were compared to typical short and ultra-short self-report screening scales, such as the Centre for Epidemiology Scale, CES-D and the GAD-7, and their short forms. The Mini International Neuropsychiatric Interview (MINI version 6 1 was used as the gold standard for obtaining clinical criteria through a telephone interview. From a population sample, 225 individuals who endorsed a prototype and 101 who did not were administered the MINI. Receiver operating characteristic (ROC curves were plotted for the short and ultra short prototypes and for the short and ultra short screening scales. Results The study found that the rates of endorsement of the prototypes were commensurate with prevalence estimates. The short-form and ultra short scales outperformed the short and ultra short prototypes for every disorder except GAD, where the GAD prototype outperformed the GAD 7. Conclusions The findings suggest that people may be able to self-identify generalised anxiety more accurately than depression based on a description of a prototypical case. However, levels of identification were lower than expected. Considerable benefits from this method of screening may ensue if our prototypes can be

  10. Homogenization of Large-Scale Movement Models in Ecology

    Science.gov (United States)

    Garlick, M.J.; Powell, J.A.; Hooten, M.B.; McFarlane, L.R.

    2011-01-01

    A difficulty in using diffusion models to predict large scale animal population dispersal is that individuals move differently based on local information (as opposed to gradients) in differing habitat types. This can be accommodated by using ecological diffusion. However, real environments are often spatially complex, limiting application of a direct approach. Homogenization for partial differential equations has long been applied to Fickian diffusion (in which average individual movement is organized along gradients of habitat and population density). We derive a homogenization procedure for ecological diffusion and apply it to a simple model for chronic wasting disease in mule deer. Homogenization allows us to determine the impact of small scale (10-100 m) habitat variability on large scale (10-100 km) movement. The procedure generates asymptotic equations for solutions on the large scale with parameters defined by small-scale variation. The simplicity of this homogenization procedure is striking when compared to the multi-dimensional homogenization procedure for Fickian diffusion,and the method will be equally straightforward for more complex models. ?? 2010 Society for Mathematical Biology.

  11. RNAi-mediated resistance to SMV and BYMV in transgenic tobacco

    Directory of Open Access Journals (Sweden)

    Lo Thi Mai Thu

    2016-09-01

    Full Text Available Soybean mosaic virus (SMV and bean yellow mosaic virus (BYMV are two typical types of viruses that cause mosaic in soybean plants. Multiple viral infections at the same site can lead to 66% to 80% yield reduction. We have aimed to improve SMV and BYMV resistance in Vietnamese soybeans using gene transfer techniques under the mechanism of RNAi. In this study, we present newly generated transgenic tobacco plants carrying RNAi [CPi (SMV-BYMV] resistance to the two types of viruses; 73.08% of transgenic tobacco lines proved to be fully resistant to SMV and BYMV. In addition, the number of virus copies in transgenic tobacco plants was reduced on average by more than 51% compared to the control plants (wild type. This promising result shows the potential of transerring the CPi (SMV-BYMV structure in soybean to increase resistance of soybean to SMV and BYMV and advance the aims of antiviral soybean breeding in Vietnam.

  12. The role of large-scale, extratropical dynamics in climate change

    Energy Technology Data Exchange (ETDEWEB)

    Shepherd, T.G. [ed.

    1994-02-01

    The climate modeling community has focused recently on improving our understanding of certain processes, such as cloud feedbacks and ocean circulation, that are deemed critical to climate-change prediction. Although attention to such processes is warranted, emphasis on these areas has diminished a general appreciation of the role played by the large-scale dynamics of the extratropical atmosphere. Lack of interest in extratropical dynamics may reflect the assumption that these dynamical processes are a non-problem as far as climate modeling is concerned, since general circulation models (GCMs) calculate motions on this scale from first principles. Nevertheless, serious shortcomings in our ability to understand and simulate large-scale dynamics exist. Partly due to a paucity of standard GCM diagnostic calculations of large-scale motions and their transports of heat, momentum, potential vorticity, and moisture, a comprehensive understanding of the role of large-scale dynamics in GCM climate simulations has not been developed. Uncertainties remain in our understanding and simulation of large-scale extratropical dynamics and their interaction with other climatic processes, such as cloud feedbacks, large-scale ocean circulation, moist convection, air-sea interaction and land-surface processes. To address some of these issues, the 17th Stanstead Seminar was convened at Bishop`s University in Lennoxville, Quebec. The purpose of the Seminar was to promote discussion of the role of large-scale extratropical dynamics in global climate change. Abstracts of the talks are included in this volume. On the basis of these talks, several key issues emerged concerning large-scale extratropical dynamics and their climatic role. Individual records are indexed separately for the database.

  13. The role of large-scale, extratropical dynamics in climate change

    International Nuclear Information System (INIS)

    Shepherd, T.G.

    1994-02-01

    The climate modeling community has focused recently on improving our understanding of certain processes, such as cloud feedbacks and ocean circulation, that are deemed critical to climate-change prediction. Although attention to such processes is warranted, emphasis on these areas has diminished a general appreciation of the role played by the large-scale dynamics of the extratropical atmosphere. Lack of interest in extratropical dynamics may reflect the assumption that these dynamical processes are a non-problem as far as climate modeling is concerned, since general circulation models (GCMs) calculate motions on this scale from first principles. Nevertheless, serious shortcomings in our ability to understand and simulate large-scale dynamics exist. Partly due to a paucity of standard GCM diagnostic calculations of large-scale motions and their transports of heat, momentum, potential vorticity, and moisture, a comprehensive understanding of the role of large-scale dynamics in GCM climate simulations has not been developed. Uncertainties remain in our understanding and simulation of large-scale extratropical dynamics and their interaction with other climatic processes, such as cloud feedbacks, large-scale ocean circulation, moist convection, air-sea interaction and land-surface processes. To address some of these issues, the 17th Stanstead Seminar was convened at Bishop's University in Lennoxville, Quebec. The purpose of the Seminar was to promote discussion of the role of large-scale extratropical dynamics in global climate change. Abstracts of the talks are included in this volume. On the basis of these talks, several key issues emerged concerning large-scale extratropical dynamics and their climatic role. Individual records are indexed separately for the database

  14. Screening for depressive disorders using the MASQ anhedonic depression scale: A receiver-operator characteristic analysis

    Science.gov (United States)

    Bredemeier, Keith; Spielberg, Jeffrey M.; Silton, Rebecca Levin; Berenbaum, Howard; Heller, Wendy; Miller, Gregory A.

    2010-01-01

    The present study examined the utility of the anhedonic depression scale from the Mood and Anxiety Symptoms Questionnaire (MASQ-AD) as a way to screen for depressive disorders. Using receiver-operator characteristic analysis, the sensitivity and specificity of the full 22-item MASQ-AD scale, as well as the 8 and 14-item subscales, were examined in relation to both current and lifetime DSM-IV depressive disorder diagnoses in two nonpatient samples. As a means of comparison, the sensitivity and specificity of a measure of a relevant personality dimension, neuroticism, was also examined. Results from both samples support the clinical utility of the MASQ-AD scale as a means of screening for depressive disorders. Findings were strongest for the MASQ-AD 8-item subscale and when predicting current depression status. Furthermore, the MASQ-AD 8-item subscale outperformed the neuroticism measure under certain conditions. The overall usefulness of the MASQ-AD scale as a screening device is discussed, as well as possible cutoff scores for use in research. PMID:20822283

  15. Large-scale functional purification of recombinant HIV-1 capsid.

    Directory of Open Access Journals (Sweden)

    Magdeleine Hung

    Full Text Available During human immunodeficiency virus type-1 (HIV-1 virion maturation, capsid proteins undergo a major rearrangement to form a conical core that protects the viral nucleoprotein complexes. Mutations in the capsid sequence that alter the stability of the capsid core are deleterious to viral infectivity and replication. Recently, capsid assembly has become an attractive target for the development of a new generation of anti-retroviral agents. Drug screening efforts and subsequent structural and mechanistic studies require gram quantities of active, homogeneous and pure protein. Conventional means of laboratory purification of Escherichia coli expressed recombinant capsid protein rely on column chromatography steps that are not amenable to large-scale production. Here we present a function-based purification of wild-type and quadruple mutant capsid proteins, which relies on the inherent propensity of capsid protein to polymerize and depolymerize. This method does not require the packing of sizable chromatography columns and can generate double-digit gram quantities of functionally and biochemically well-behaved proteins with greater than 98% purity. We have used the purified capsid protein to characterize two known assembly inhibitors in our in-house developed polymerization assay and to measure their binding affinities. Our capsid purification procedure provides a robust method for purifying large quantities of a key protein in the HIV-1 life cycle, facilitating identification of the next generation anti-HIV agents.

  16. Status: Large-scale subatmospheric cryogenic systems

    International Nuclear Information System (INIS)

    Peterson, T.

    1989-01-01

    In the late 1960's and early 1970's an interest in testing and operating RF cavities at 1.8K motivated the development and construction of four large (300 Watt) 1.8K refrigeration systems. in the past decade, development of successful superconducting RF cavities and interest in obtaining higher magnetic fields with the improved Niobium-Titanium superconductors has once again created interest in large-scale 1.8K refrigeration systems. The L'Air Liquide plant for Tore Supra is a recently commissioned 300 Watt 1.8K system which incorporates new technology, cold compressors, to obtain the low vapor pressure for low temperature cooling. CEBAF proposes to use cold compressors to obtain 5KW at 2.0K. Magnetic refrigerators of 10 Watt capacity or higher at 1.8K are now being developed. The state of the art of large-scale refrigeration in the range under 4K will be reviewed. 28 refs., 4 figs., 7 tabs

  17. Large-scale weakly supervised object localization via latent category learning.

    Science.gov (United States)

    Chong Wang; Kaiqi Huang; Weiqiang Ren; Junge Zhang; Maybank, Steve

    2015-04-01

    Localizing objects in cluttered backgrounds is challenging under large-scale weakly supervised conditions. Due to the cluttered image condition, objects usually have large ambiguity with backgrounds. Besides, there is also a lack of effective algorithm for large-scale weakly supervised localization in cluttered backgrounds. However, backgrounds contain useful latent information, e.g., the sky in the aeroplane class. If this latent information can be learned, object-background ambiguity can be largely reduced and background can be suppressed effectively. In this paper, we propose the latent category learning (LCL) in large-scale cluttered conditions. LCL is an unsupervised learning method which requires only image-level class labels. First, we use the latent semantic analysis with semantic object representation to learn the latent categories, which represent objects, object parts or backgrounds. Second, to determine which category contains the target object, we propose a category selection strategy by evaluating each category's discrimination. Finally, we propose the online LCL for use in large-scale conditions. Evaluation on the challenging PASCAL Visual Object Class (VOC) 2007 and the large-scale imagenet large-scale visual recognition challenge 2013 detection data sets shows that the method can improve the annotation precision by 10% over previous methods. More importantly, we achieve the detection precision which outperforms previous results by a large margin and can be competitive to the supervised deformable part model 5.0 baseline on both data sets.

  18. Large-scale networks in engineering and life sciences

    CERN Document Server

    Findeisen, Rolf; Flockerzi, Dietrich; Reichl, Udo; Sundmacher, Kai

    2014-01-01

    This edited volume provides insights into and tools for the modeling, analysis, optimization, and control of large-scale networks in the life sciences and in engineering. Large-scale systems are often the result of networked interactions between a large number of subsystems, and their analysis and control are becoming increasingly important. The chapters of this book present the basic concepts and theoretical foundations of network theory and discuss its applications in different scientific areas such as biochemical reactions, chemical production processes, systems biology, electrical circuits, and mobile agents. The aim is to identify common concepts, to understand the underlying mathematical ideas, and to inspire discussions across the borders of the various disciplines.  The book originates from the interdisciplinary summer school “Large Scale Networks in Engineering and Life Sciences” hosted by the International Max Planck Research School Magdeburg, September 26-30, 2011, and will therefore be of int...

  19. Evaluating usability of the Halden Reactor Large Screen Display. Is the Information Rich Design concept suitable for real-world installations?

    International Nuclear Information System (INIS)

    Braseth, Alf Ove

    2013-01-01

    Large Screen Displays (LSDs) are beginning to supplement desktop displays in modern control rooms, having the potential to display the big picture of complex processes. Information Rich Design (IRD) is a LSD concept used in many real-life installations in the petroleum domain, and more recently in nuclear research applications. The objectives of IRD are to provide the big picture, avoiding keyhole related problems while supporting fast visual perception of larger data sets. Two LSDs based on the IRD concept have been developed for large-scale nuclear simulators for research purposes; they have however suffered from unsatisfying user experience. The new Halden Reactor LSD, used to monitor a nuclear research reactor, was designed according to recent proposed Design Principles compiled in this paper to mitigate previously experienced problems. This paper evaluates the usability of the Halden Reactor LSD, comparing usability data with the replaced analogue panel, and data for an older IRD large screen display. The results suggest that the IRD concept is suitable for use in real-life applications from a user experience point of view, and that the recently proposed Design Principles have had a positive effect on usability. (author)

  20. An Novel Architecture of Large-scale Communication in IOT

    Science.gov (United States)

    Ma, Wubin; Deng, Su; Huang, Hongbin

    2018-03-01

    In recent years, many scholars have done a great deal of research on the development of Internet of Things and networked physical systems. However, few people have made the detailed visualization of the large-scale communications architecture in the IOT. In fact, the non-uniform technology between IPv6 and access points has led to a lack of broad principles of large-scale communications architectures. Therefore, this paper presents the Uni-IPv6 Access and Information Exchange Method (UAIEM), a new architecture and algorithm that addresses large-scale communications in the IOT.

  1. Benefits of transactive memory systems in large-scale development

    OpenAIRE

    Aivars, Sablis

    2016-01-01

    Context. Large-scale software development projects are those consisting of a large number of teams, maybe even spread across multiple locations, and working on large and complex software tasks. That means that neither a team member individually nor an entire team holds all the knowledge about the software being developed and teams have to communicate and coordinate their knowledge. Therefore, teams and team members in large-scale software development projects must acquire and manage expertise...

  2. Towards RNAi based therapy of liver diseases : diversity and complexity of shRNA and miRNA processing and functions

    NARCIS (Netherlands)

    Maczuga, Piotr

    2013-01-01

    Familial hypercholesterolemia (FH) is a genetic disorder characterized by high levels of low density lipoprotein cholesterol (LDL-C) and increasing the risk of cardio vascular diseases. FH and many other liver diseases can possibly be treated with RNA interference (RNAi). RNAi is a natural process

  3. Validation of the Arab Youth Mental Health scale as a screening tool for depression/anxiety in Lebanese children

    Directory of Open Access Journals (Sweden)

    Nakkash Rima

    2011-03-01

    Full Text Available Abstract Background Early detection of common mental disorders, such as depression and anxiety, among children and adolescents requires the use of validated, culturally sensitive, and developmentally appropriate screening instruments. The Arab region has a high proportion of youth, yet Arabic-language screening instruments for mental disorders among this age group are virtually absent. Methods We carried out construct and clinical validation on the recently-developed Arab Youth Mental Health (AYMH scale as a screening tool for depression/anxiety. The scale was administered with 10-14 year old children attending a social service center in Beirut, Lebanon (N = 153. The clinical assessment was conducted by a child and adolescent clinical psychiatrist employing the DSM IV criteria. We tested the scale's sensitivity, specificity, and internal consistency. Results Scale scores were generally significantly associated with how participants responded to standard questions on health, mental health, and happiness, indicating good construct validity. The results revealed that the scale exhibited good internal consistency (Cronbach's alpha = 0.86 and specificity (79%. However, it exhibited moderate sensitivity for girls (71% and poor sensitivity for boys (50%. Conclusions The AYMH scale is useful as a screening tool for general mental health states and a valid screening instrument for common mental disorders among girls. It is not a valid instrument for detecting depression and anxiety among boys in an Arab culture.

  4. Study of a large scale neutron measurement channel

    International Nuclear Information System (INIS)

    Amarouayache, Anissa; Ben Hadid, Hayet.

    1982-12-01

    A large scale measurement channel allows the processing of the signal coming from an unique neutronic sensor, during three different running modes: impulses, fluctuations and current. The study described in this note includes three parts: - A theoretical study of the large scale channel and its brief description are given. The results obtained till now in that domain are presented. - The fluctuation mode is thoroughly studied and the improvements to be done are defined. The study of a fluctuation linear channel with an automatic commutation of scales is described and the results of the tests are given. In this large scale channel, the method of data processing is analogical. - To become independent of the problems generated by the use of a an analogical processing of the fluctuation signal, a digital method of data processing is tested. The validity of that method is improved. The results obtained on a test system realized according to this method are given and a preliminary plan for further research is defined [fr

  5. Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries.

    Science.gov (United States)

    Ma, Xiao H; Jia, Jia; Zhu, Feng; Xue, Ying; Li, Ze R; Chen, Yu Z

    2009-05-01

    Machine learning methods have been explored as ligand-based virtual screening tools for facilitating drug lead discovery. These methods predict compounds of specific pharmacodynamic, pharmacokinetic or toxicological properties based on their structure-derived structural and physicochemical properties. Increasing attention has been directed at these methods because of their capability in predicting compounds of diverse structures and complex structure-activity relationships without requiring the knowledge of target 3D structure. This article reviews current progresses in using machine learning methods for virtual screening of pharmacodynamically active compounds from large compound libraries, and analyzes and compares the reported performances of machine learning tools with those of structure-based and other ligand-based (such as pharmacophore and clustering) virtual screening methods. The feasibility to improve the performance of machine learning methods in screening large libraries is discussed.

  6. Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation.

    Science.gov (United States)

    Li, Jian-Feng; Bush, Jenifer; Xiong, Yan; Li, Lei; McCormack, Matthew

    2011-01-01

    Protein-protein interactions (PPIs) constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been successfully used for large-scale surveys of PPIs in plants, each having advantages and disadvantages. Here we present split firefly luciferase complementation (SFLC) as a highly sensitive and noninvasive technique for in planta PPI investigation. In this assay, the separate halves of a firefly luciferase can come into close proximity and transiently restore its catalytic activity only when their fusion partners, namely the two proteins of interest, interact with each other. This assay was conferred with quantitativeness and high throughput potential when the Arabidopsis mesophyll protoplast system and a microplate luminometer were employed for protein expression and luciferase measurement, respectively. Using the SFLC assay, we could monitor the dynamics of rapamycin-induced and ascomycin-disrupted interaction between Arabidopsis FRB and human FKBP proteins in a near real-time manner. As a proof of concept for large-scale PPI survey, we further applied the SFLC assay to testing 132 binary PPIs among 8 auxin response factors (ARFs) and 12 Aux/IAA proteins from Arabidopsis. Our results demonstrated that the SFLC assay is ideal for in vivo quantitative PPI analysis in plant cells and is particularly powerful for large-scale binary PPI screens.

  7. Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation.

    Directory of Open Access Journals (Sweden)

    Jian-Feng Li

    Full Text Available Protein-protein interactions (PPIs constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been successfully used for large-scale surveys of PPIs in plants, each having advantages and disadvantages. Here we present split firefly luciferase complementation (SFLC as a highly sensitive and noninvasive technique for in planta PPI investigation. In this assay, the separate halves of a firefly luciferase can come into close proximity and transiently restore its catalytic activity only when their fusion partners, namely the two proteins of interest, interact with each other. This assay was conferred with quantitativeness and high throughput potential when the Arabidopsis mesophyll protoplast system and a microplate luminometer were employed for protein expression and luciferase measurement, respectively. Using the SFLC assay, we could monitor the dynamics of rapamycin-induced and ascomycin-disrupted interaction between Arabidopsis FRB and human FKBP proteins in a near real-time manner. As a proof of concept for large-scale PPI survey, we further applied the SFLC assay to testing 132 binary PPIs among 8 auxin response factors (ARFs and 12 Aux/IAA proteins from Arabidopsis. Our results demonstrated that the SFLC assay is ideal for in vivo quantitative PPI analysis in plant cells and is particularly powerful for large-scale binary PPI screens.

  8. Capabilities of the Large-Scale Sediment Transport Facility

    Science.gov (United States)

    2016-04-01

    pump flow meters, sediment trap weigh tanks , and beach profiling lidar. A detailed discussion of the original LSTF features and capabilities can be...ERDC/CHL CHETN-I-88 April 2016 Approved for public release; distribution is unlimited. Capabilities of the Large-Scale Sediment Transport...describes the Large-Scale Sediment Transport Facility (LSTF) and recent upgrades to the measurement systems. The purpose of these upgrades was to increase

  9. C. elegans bicd-1, homolog of the Drosophila dynein accessory factor Bicaudal D, regulates the branching of PVD sensory neuron dendrites.

    Science.gov (United States)

    Aguirre-Chen, Cristina; Bülow, Hannes E; Kaprielian, Zaven

    2011-02-01

    The establishment of cell type-specific dendritic arborization patterns is a key phase in the assembly of neuronal circuitry that facilitates the integration and processing of synaptic and sensory input. Although studies in Drosophila and vertebrate systems have identified a variety of factors that regulate dendrite branch formation, the molecular mechanisms that control this process remain poorly defined. Here, we introduce the use of the Caenorhabditis elegans PVD neurons, a pair of putative nociceptors that elaborate complex dendritic arbors, as a tractable model for conducting high-throughput RNAi screens aimed at identifying key regulators of dendritic branch formation. By carrying out two separate RNAi screens, a small-scale candidate-based screen and a large-scale screen of the ~3000 genes on chromosome IV, we retrieved 11 genes that either promote or suppress the formation of PVD-associated dendrites. We present a detailed functional characterization of one of the genes, bicd-1, which encodes a microtubule-associated protein previously shown to modulate the transport of mRNAs and organelles in a variety of organisms. Specifically, we describe a novel role for bicd-1 in regulating dendrite branch formation and show that bicd-1 is likely to be expressed, and primarily required, in PVD neurons to control dendritic branching. We also present evidence that bicd-1 operates in a conserved pathway with dhc-1 and unc-116, components of the dynein minus-end-directed and kinesin-1 plus-end-directed microtubule-based motor complexes, respectively, and interacts genetically with the repulsive guidance receptor unc-5.

  10. Clathrin Heavy Chain Is Important for Viability, Oviposition, Embryogenesis and, Possibly, Systemic RNAi Response in the Predatory Mite Metaseiulus occidentalis

    Science.gov (United States)

    Wu, Ke; Hoy, Marjorie A.

    2014-01-01

    Clathrin heavy chain has been shown to be important for viability, embryogenesis, and RNA interference (RNAi) in arthropods such as Drosophila melanogaster. However, the functional roles of clathrin heavy chain in chelicerate arthropods, such as the predatory mite Metaseiulus occidentalis, remain unknown. We previously showed that dsRNA ingestion, followed by feeding on spider mites, induced systemic and robust RNAi in M. occidentalis females. In the current study, we performed a loss-of-function analysis of the clathrin heavy chain gene in M. occidentalis using RNAi. We showed that ingestion of clathrin heavy chain dsRNA by M. occidentalis females resulted in gene knockdown and reduced longevity. In addition, clathrin heavy chain dsRNA treatment almost completely abolished oviposition by M. occidentalis females and the few eggs produced did not hatch. Finally, we demonstrated that clathrin heavy chain gene knockdown in M. occidentalis females significantly reduced a subsequent RNAi response induced by ingestion of cathepsin L dsRNA. The last finding suggests that clathrin heavy chain may be involved in systemic RNAi responses mediated by orally delivered dsRNAs in M. occidentalis. PMID:25329675

  11. Spatiotemporal property and predictability of large-scale human mobility

    Science.gov (United States)

    Zhang, Hai-Tao; Zhu, Tao; Fu, Dongfei; Xu, Bowen; Han, Xiao-Pu; Chen, Duxin

    2018-04-01

    Spatiotemporal characteristics of human mobility emerging from complexity on individual scale have been extensively studied due to the application potential on human behavior prediction and recommendation, and control of epidemic spreading. We collect and investigate a comprehensive data set of human activities on large geographical scales, including both websites browse and mobile towers visit. Numerical results show that the degree of activity decays as a power law, indicating that human behaviors are reminiscent of scale-free random walks known as Lévy flight. More significantly, this study suggests that human activities on large geographical scales have specific non-Markovian characteristics, such as a two-segment power-law distribution of dwelling time and a high possibility for prediction. Furthermore, a scale-free featured mobility model with two essential ingredients, i.e., preferential return and exploration, and a Gaussian distribution assumption on the exploration tendency parameter is proposed, which outperforms existing human mobility models under scenarios of large geographical scales.

  12. Problems of large-scale vertically-integrated aquaculture

    Energy Technology Data Exchange (ETDEWEB)

    Webber, H H; Riordan, P F

    1976-01-01

    The problems of vertically-integrated aquaculture are outlined; they are concerned with: species limitations (in the market, biological and technological); site selection, feed, manpower needs, and legal, institutional and financial requirements. The gaps in understanding of, and the constraints limiting, large-scale aquaculture are listed. Future action is recommended with respect to: types and diversity of species to be cultivated, marketing, biotechnology (seed supply, disease control, water quality and concerted effort), siting, feed, manpower, legal and institutional aids (granting of water rights, grants, tax breaks, duty-free imports, etc.), and adequate financing. The last of hard data based on experience suggests that large-scale vertically-integrated aquaculture is a high risk enterprise, and with the high capital investment required, banks and funding institutions are wary of supporting it. Investment in pilot projects is suggested to demonstrate that large-scale aquaculture can be a fully functional and successful business. Construction and operation of such pilot farms is judged to be in the interests of both the public and private sector.

  13. Item response theory analysis of the Lichtenberg Financial Decision Screening Scale.

    Science.gov (United States)

    Teresi, Jeanne A; Ocepek-Welikson, Katja; Lichtenberg, Peter A

    2017-01-01

    The focus of these analyses was to examine the psychometric properties of the Lichtenberg Financial Decision Screening Scale (LFDSS). The purpose of the screen was to evaluate the decisional abilities and vulnerability to exploitation of older adults. Adults aged 60 and over were interviewed by social, legal, financial, or health services professionals who underwent in-person training on the administration and scoring of the scale. Professionals provided a rating of the decision-making abilities of the older adult. The analytic sample included 213 individuals with an average age of 76.9 (SD = 10.1). The majority (57%) were female. Data were analyzed using item response theory (IRT) methodology. The results supported the unidimensionality of the item set. Several IRT models were tested. Ten ordinal and binary items evidenced a slightly higher reliability estimate (0.85) than other versions and better coverage in terms of the range of reliable measurement across the continuum of financial incapacity.

  14. Large-scale computing with Quantum Espresso

    International Nuclear Information System (INIS)

    Giannozzi, P.; Cavazzoni, C.

    2009-01-01

    This paper gives a short introduction to Quantum Espresso: a distribution of software for atomistic simulations in condensed-matter physics, chemical physics, materials science, and to its usage in large-scale parallel computing.

  15. RNAi-mediated silencing of MAP kinase signalling genes (Fmk1, Hog1, and Pbs2) in Fusarium oxysporum reduces pathogenesis on tomato plants.

    Science.gov (United States)

    Pareek, Manish; Rajam, Manchikatla Venkat

    2017-09-01

    Fusarium oxysporum is a soil-borne plant fungal pathogen, and causes colossal losses in several crop plants including tomato. Effective control measures include the use of harmful fungicides and resistant cultivars, but these methods have shown limited success. Conventional methods to validate fungal pathogenic genes are labour intensive. Therefore, an alternative strategy is required to efficiently characterize unknown pathogenic genes. RNA interference (RNAi) has emerged as a potential tool to functionally characterize novel fungal pathogenic genes and also to control fungal diseases. Here, we report an efficient method to produce stable RNAi transformants of F. oxysporum using Agrobacterium-mediated transformation (AMT). We have transformed F. oxysporum spores using RNAi constructs of Fmk1, Hog1, and Pbs2 MAP kinase signalling genes. Fmk1 RNAi fungal transformants showed loss of surface hydrophobicity, reduced invasive growth on tomato fruits and hypo-virulence on tomato seedlings. Hog1 and Pbs2 RNAi transformants showed altered conidial size, and reduced invasive growth and pathogenesis. These results showed that AMT using RNAi constructs is an effective approach for dissecting the role of genes involved in pathogenesis in F. oxysporum and this could be extended for other fungal systems. The obtained knowledge can be easily translated for developing fungal resistant crops by RNAi. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  16. The effect of Interaction Anxiousness Scale and Brief Social Phobia Scale for screening social anxiety disorder in college students: a study on discriminative validity.

    Science.gov (United States)

    Cao, Jianqin; Yang, Jinwei; Zhou, Yuqiu; Chu, Fuliu; Zhao, Xiwu; Wang, Weiren; Wang, Yunlong; Peng, Tao

    2016-12-01

    Social anxiety disorder (SAD) is one of the most prevalent mental health problems, but there is little research concerning the effective screening instruments in practice. This study was designed to examine the discriminative validity of Interaction Anxiousness Scale (IAS) and Brief Social Phobia Scale (BSPS) for the screening of SAD through the compared and combined analysis. Firstly, 421 Chinese undergraduates were screened by the IAS and BSPS. Secondly, in the follow-up stage, 248 students were interviewed by the Structured Clinical Interview for DSM-IV. Receiver operating characteristic (ROC) analysis was used, and the related psychometric characters were checked. The results indicated that the ROC in these two scales demonstrated discrimination is in satisfactory level (range: 0.7-0.8). However, the highest agreement (92.17%) was identified when a cut-off point of 50 measured by the IAS and a cut-off point of 34 by the BSPS were combined, also with higher PPV, SENS, SPEC and OA than that reached when BSPS was used individually, as well as PPV, SPEC and OA in IAS. The findings indicate that the combination of these two scales is valid as the general screening instrument for SAD in maximizing the discriminative validity.

  17. Maximally efficient two-stage screening: Determining intellectual disability in Taiwanese military conscripts.

    Science.gov (United States)

    Chien, Chia-Chang; Huang, Shu-Fen; Lung, For-Wey

    2009-01-27

    The purpose of this study was to apply a two-stage screening method for the large-scale intelligence screening of military conscripts. We collected 99 conscripted soldiers whose educational levels were senior high school level or lower to be the participants. Every participant was required to take the Wisconsin Card Sorting Test (WCST) and the Wechsler Adult Intelligence Scale-Revised (WAIS-R) assessments. Logistic regression analysis showed the conceptual level responses (CLR) index of the WCST was the most significant index for determining intellectual disability (ID; FIQ ≤ 84). We used the receiver operating characteristic curve to determine the optimum cut-off point of CLR. The optimum one cut-off point of CLR was 66; the two cut-off points were 49 and 66. Comparing the two-stage window screening with the two-stage positive screening, the area under the curve and the positive predictive value increased. Moreover, the cost of the two-stage window screening decreased by 59%. The two-stage window screening is more accurate and economical than the two-stage positive screening. Our results provide an example for the use of two-stage screening and the possibility of the WCST to replace WAIS-R in large-scale screenings for ID in the future.

  18. Assessment of potential risks of dietary RNAi to a soil micro-arthropod, Sinella curviseta Brook (Collembola: Entomobryidae

    Directory of Open Access Journals (Sweden)

    Huipeng Pan

    2016-07-01

    Full Text Available RNAi-based genetically engineered (GE crops for the management of insect pests are likely to be commercialized by the end of this decade. Without a workable framework for conducting the ecological risk assessment (ERA and a standardized ERA protocol, however, the utility of RNAi transgenic crops in pest management remains uncertain. The overall goal of this study is to assess the risks of RNAi-based GE crops on a non-target soil micro-arthropod, Sinella curviseta, which could be exposed to plant-protected dsRNAs deposited in crop residues. Based on the preliminary research, we hypothesized that insecticidal dsRNAs targeting at the western corn rootworm, Diabrotica virgifera virgifera, a billion-dollar insect pest, has no adverse impacts on S. curviseta, a soil decomposer. Following a tiered approach, we tested this risk hypothesis using a well-designed dietary RNAi toxicity assay. To create the worst-case scenario, the full-length cDNA of v-ATPase subunit A from S. curviseta were cloned and a 400 bp fragment representing the highest sequence similarity between target pest and non-target arthropods was selected as the template to synthesize insecticidal dsRNAs. Specifically, 10-day old S. curviseta larvae were subjected to artificial diets containing v-ATPase A dsRNAs from both D. v. virgifera (dsDVV and S. curviseta (dsSC, respectively, a dsRNA control, β-glucuronidase, from plant (dsGUS, and a vehicle control, H2O. The endpoint measurements included gene expression profiles, survival, and life history traits, such as developmental time, fecundity, hatching rate, and body length. Although S. curviseta larvae developed significantly faster under the treatments of dsDVV and dsSC than the vehicle control, the combined results from both temporal RNAi effect study and dietary RNAi toxicity assay support the risk hypothesis, suggesting that the impacts of ingested arthropod-active dsRNAs on this representative soil decomposer are negligible.

  19. Development of marker-free transgenic Jatropha curcas producing curcin-deficient seeds through endosperm-specific RNAi-mediated gene silencing.

    Science.gov (United States)

    Gu, Keyu; Tian, Dongsheng; Mao, Huizhu; Wu, Lifang; Yin, Zhongchao

    2015-10-08

    Jatropha curcas L. is a potential biofuel plant and its seed oil is suitable for biodiesel production. Despite this promising application, jatropha seeds contain two major toxic components, namely phorbol esters and curcins. These compounds would reduce commercial value of seed cake and raise safety and environment concerns on jatropha plantation and processing. Curcins are Type I ribosome inactivating proteins. Several curcin genes have been identified in the jatropha genome. Among which, the Curcin 1 (C1) gene is identified to be specifically expressed in endosperm, whereas the Curcin 2A (C2A) is mainly expressed in young leaves. A marker-free RNAi construct carrying a β-estradiol-regulated Cre/loxP system and a C1 promoter-driven RNAi cassette for C1 gene was made and used to generate marker-free transgenic RNAi plants to specifically silence the C1 gene in the endosperm of J. curcas. Plants of transgenic line L1, derived from T0-1, carry two copies of marker-free RNAi cassette, whereas plants of L35, derived from T0-35, harbored one copy of marker-free RNAi cassette and three copies of closely linked and yet truncated Hpt genes. The C1 protein content in endosperm of L1 and L35 seeds was greatly reduced or undetectable, while the C2A proteins in young leaves of T0-1 and T0-35 plants were unaffected. In addition, the C1 mRNA transcripts were undetectable in the endosperm of T3 seeds of L1 and L35. The results demonstrated that the expression of the C1 gene was specifically down-regulated or silenced by the double-stranded RNA-mediated RNA interference generated from the RNAi cassette. The C1 promoter-driven RNAi cassette for the C1 gene in transgenic plants was functional and heritable. Both C1 transcripts and C1 proteins were greatly down-regulated or silenced in the endosperm of transgenic J. curcas. The marker-free transgenic plants and curcin-deficient seeds developed in this study provided a solution for the toxicity of curcins in jatropha seeds and

  20. VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

    Directory of Open Access Journals (Sweden)

    Andrew E. Webb

    2017-06-01

    Full Text Available Background Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these analyses can represent significant challenges, particularly when working with entire proteomes (all protein coding sequences in a genome from a large number of species. Methods We present VESPA, software capable of automating a selective pressure analysis using codeML in addition to the preparatory analyses and summary statistics. VESPA is written in python and Perl and is designed to run within a UNIX environment. Results We have benchmarked VESPA and our results show that the method is consistent, performs well on both large scale and smaller scale datasets, and produces results in line with previously published datasets. Discussion Large-scale gene family identification, sequence alignment, and phylogeny reconstruction are all important aspects of large-scale molecular evolutionary analyses. VESPA provides flexible software for simplifying these processes along with downstream selective pressure variation analyses. The software automatically interprets results from codeML and produces simplified summary files to assist the user in better understanding the results. VESPA may be found at the following website: http://www.mol-evol.org/VESPA.

  1. Large-scale community echocardiographic screening reveals a major burden of undiagnosed valvular heart disease in older people: the OxVALVE Population Cohort Study.

    Science.gov (United States)

    d'Arcy, Joanna L; Coffey, Sean; Loudon, Margaret A; Kennedy, Andrew; Pearson-Stuttard, Jonathan; Birks, Jacqueline; Frangou, Eleni; Farmer, Andrew J; Mant, David; Wilson, Jo; Myerson, Saul G; Prendergast, Bernard D

    2016-12-14

    Valvular heart disease (VHD) is expected to become more common as the population ages. However, current estimates of its natural history and prevalence are based on historical studies with potential sources of bias. We conducted a cross-sectional analysis of the clinical and epidemiological characteristics of VHD identified at recruitment of a large cohort of older people. We enrolled 2500 individuals aged ≥65 years from a primary care population and screened for undiagnosed VHD using transthoracic echocardiography. Newly identified (predominantly mild) VHD was detected in 51% of participants. The most common abnormalities were aortic sclerosis (34%), mitral regurgitation (22%), and aortic regurgitation (15%). Aortic stenosis was present in 1.3%. The likelihood of undiagnosed VHD was two-fold higher in the two most deprived socioeconomic quintiles than in the most affluent quintile, and three-fold higher in individuals with atrial fibrillation. Clinically significant (moderate or severe) undiagnosed VHD was identified in 6.4%. In addition, 4.9% of the cohort had pre-existing VHD (a total prevalence of 11.3%). Projecting these findings using population data, we estimate that the prevalence of clinically significant VHD will double before 2050. Previously undetected VHD affects 1 in 2 of the elderly population and is more common in lower socioeconomic classes. These unique data demonstrate the contemporary clinical and epidemiological characteristics of VHD in a large population-based cohort of older people and confirm the scale of the emerging epidemic of VHD, with widespread implications for clinicians and healthcare resources. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions please email: journals.permissions@oup.com.

  2. RESTRUCTURING OF THE LARGE-SCALE SPRINKLERS

    Directory of Open Access Journals (Sweden)

    Paweł Kozaczyk

    2016-09-01

    Full Text Available One of the best ways for agriculture to become independent from shortages of precipitation is irrigation. In the seventies and eighties of the last century a number of large-scale sprinklers in Wielkopolska was built. At the end of 1970’s in the Poznan province 67 sprinklers with a total area of 6400 ha were installed. The average size of the sprinkler reached 95 ha. In 1989 there were 98 sprinklers, and the area which was armed with them was more than 10 130 ha. The study was conducted on 7 large sprinklers with the area ranging from 230 to 520 hectares in 1986÷1998. After the introduction of the market economy in the early 90’s and ownership changes in agriculture, large-scale sprinklers have gone under a significant or total devastation. Land on the State Farms of the State Agricultural Property Agency has leased or sold and the new owners used the existing sprinklers to a very small extent. This involved a change in crop structure, demand structure and an increase in operating costs. There has also been a threefold increase in electricity prices. Operation of large-scale irrigation encountered all kinds of barriers in practice and limitations of system solutions, supply difficulties, high levels of equipment failure which is not inclined to rational use of available sprinklers. An effect of a vision of the local area was to show the current status of the remaining irrigation infrastructure. The adopted scheme for the restructuring of Polish agriculture was not the best solution, causing massive destruction of assets previously invested in the sprinkler system.

  3. Large-scale synthesis of YSZ nanopowder by Pechini method

    Indian Academy of Sciences (India)

    Administrator

    structure and chemical purity of 99⋅1% by inductively coupled plasma optical emission spectroscopy on a large scale. Keywords. Sol–gel; yttria-stabilized zirconia; large scale; nanopowder; Pechini method. 1. Introduction. Zirconia has attracted the attention of many scientists because of its tremendous thermal, mechanical ...

  4. RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans.

    Science.gov (United States)

    Steiner, Florian A; Okihara, Kristy L; Hoogstrate, Suzanne W; Sijen, Titia; Ketting, René F

    2009-02-01

    RNA interference (RNAi) is a process in which double-stranded RNA is cleaved into small interfering RNAs (siRNAs) that induce the destruction of homologous single-stranded mRNAs. Argonaute proteins are essential components of this silencing process; they bind siRNAs directly and can cleave RNA targets using a conserved RNase H motif. In Caenorhabditis elegans, the Argonaute protein RDE-1 has a central role in RNAi. In animals lacking RDE-1, the introduction of double-stranded RNA does not trigger any detectable level of RNAi. Here we show that RNase H activity of RDE-1 is required only for efficient removal of the passenger strand of the siRNA duplex and not for triggering the silencing response at the target-mRNA level. These results uncouple the role of the RDE-1 RNase H activity in small RNA maturation from its role in target-mRNA silencing in vivo.

  5. Large Scale Screening of Ethnomedicinal Plants for Identification of Potential Antibacterial Compounds

    Directory of Open Access Journals (Sweden)

    Sujogya Kumar Panda

    2016-03-01

    Full Text Available The global burden of bacterial infections is very high and has been exacerbated by increasing resistance to multiple antibiotics. Antibiotic resistance leads to failed treatment of infections, which can ultimately lead to death. To overcome antibiotic resistance, it is necessary to identify new antibacterial agents. In this study, a total of 662 plant extracts (diverse parts from 222 plant species (82 families, 177 genera were screened for antibacterial activity using the agar cup plate method. The aqueous and methanolic extracts were prepared from diverse plant parts and screened against eight bacterial (two Gram-positive and six Gram-negative species, most of which are involved in common infections with multiple antibiotic resistance. The methanolic extracts of several plants were shown to have zones of inhibition ≥ 12 mm against both Gram-positive and Gram-negative bacteria. The minimum inhibitory concentration was calculated only with methanolic extracts of selected plants, those showed zone of inhibition ≥ 12 mm against both Gram-positive and Gram-negative bacteria. Several extracts had minimum inhibitory concentration ≤ 1 mg/mL. Specifically Adhatoda vasica, Ageratum conyzoides, Alangium salvifolium, Alpinia galanga, Andrographis paniculata, Anogeissus latifolia, Annona squamosa, A. reticulate, Azadirachta indica, Buchanania lanzan, Cassia fistula, Celastrus paniculatus, Centella asiatica, Clausena excavate, Cleome viscosa, Cleistanthus collinus, Clerodendrum indicum, Croton roxburghii, Diospyros melanoxylon, Eleutherine bulbosa, Erycibe paniculata, Eryngium foetidum, Garcinia cowa, Helicteres isora, Hemidesmus indicus, Holarrhena antidysenterica, Lannea coromandelica, Millettia extensa, Mimusops elengi, Nyctanthes arbor-tristis, Oroxylum indicum, Paederia foetida, Pterospermum acerifolium, Punica granatum, Semecarpus anacardium, Spondias pinnata, Terminalia alata and Vitex negundo were shown to have significant antimicrobial

  6. Large Scale Screening of Ethnomedicinal Plants for Identification of Potential Antibacterial Compounds.

    Science.gov (United States)

    Panda, Sujogya Kumar; Mohanta, Yugal Kishore; Padhi, Laxmipriya; Park, Young-Hwan; Mohanta, Tapan Kumar; Bae, Hanhong

    2016-03-14

    The global burden of bacterial infections is very high and has been exacerbated by increasing resistance to multiple antibiotics. Antibiotic resistance leads to failed treatment of infections, which can ultimately lead to death. To overcome antibiotic resistance, it is necessary to identify new antibacterial agents. In this study, a total of 662 plant extracts (diverse parts) from 222 plant species (82 families, 177 genera) were screened for antibacterial activity using the agar cup plate method. The aqueous and methanolic extracts were prepared from diverse plant parts and screened against eight bacterial (two Gram-positive and six Gram-negative) species, most of which are involved in common infections with multiple antibiotic resistance. The methanolic extracts of several plants were shown to have zones of inhibition ≥ 12 mm against both Gram-positive and Gram-negative bacteria. The minimum inhibitory concentration was calculated only with methanolic extracts of selected plants, those showed zone of inhibition ≥ 12 mm against both Gram-positive and Gram-negative bacteria. Several extracts had minimum inhibitory concentration ≤ 1 mg/mL. Specifically Adhatoda vasica, Ageratum conyzoides, Alangium salvifolium, Alpinia galanga, Andrographis paniculata, Anogeissus latifolia, Annona squamosa, A. reticulate, Azadirachta indica, Buchanania lanzan, Cassia fistula, Celastrus paniculatus, Centella asiatica, Clausena excavate, Cleome viscosa, Cleistanthus collinus, Clerodendrum indicum, Croton roxburghii, Diospyros melanoxylon, Eleutherine bulbosa, Erycibe paniculata, Eryngium foetidum, Garcinia cowa, Helicteres isora, Hemidesmus indicus, Holarrhena antidysenterica, Lannea coromandelica, Millettia extensa, Mimusops elengi, Nyctanthes arbor-tristis, Oroxylum indicum, Paederia foetida, Pterospermum acerifolium, Punica granatum, Semecarpus anacardium, Spondias pinnata, Terminalia alata and Vitex negundo were shown to have significant antimicrobial activity. The species

  7. The Phoenix series large scale LNG pool fire experiments.

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Richard B.; Jensen, Richard Pearson; Demosthenous, Byron; Luketa, Anay Josephine; Ricks, Allen Joseph; Hightower, Marion Michael; Blanchat, Thomas K.; Helmick, Paul H.; Tieszen, Sheldon Robert; Deola, Regina Anne; Mercier, Jeffrey Alan; Suo-Anttila, Jill Marie; Miller, Timothy J.

    2010-12-01

    The increasing demand for natural gas could increase the number and frequency of Liquefied Natural Gas (LNG) tanker deliveries to ports across the United States. Because of the increasing number of shipments and the number of possible new facilities, concerns about the potential safety of the public and property from an accidental, and even more importantly intentional spills, have increased. While improvements have been made over the past decade in assessing hazards from LNG spills, the existing experimental data is much smaller in size and scale than many postulated large accidental and intentional spills. Since the physics and hazards from a fire change with fire size, there are concerns about the adequacy of current hazard prediction techniques for large LNG spills and fires. To address these concerns, Congress funded the Department of Energy (DOE) in 2008 to conduct a series of laboratory and large-scale LNG pool fire experiments at Sandia National Laboratories (Sandia) in Albuquerque, New Mexico. This report presents the test data and results of both sets of fire experiments. A series of five reduced-scale (gas burner) tests (yielding 27 sets of data) were conducted in 2007 and 2008 at Sandia's Thermal Test Complex (TTC) to assess flame height to fire diameter ratios as a function of nondimensional heat release rates for extrapolation to large-scale LNG fires. The large-scale LNG pool fire experiments were conducted in a 120 m diameter pond specially designed and constructed in Sandia's Area III large-scale test complex. Two fire tests of LNG spills of 21 and 81 m in diameter were conducted in 2009 to improve the understanding of flame height, smoke production, and burn rate and therefore the physics and hazards of large LNG spills and fires.

  8. Examination of the lumbar vertebral column using large-screen image intensifier photofluorography

    Energy Technology Data Exchange (ETDEWEB)

    Soimakallio, S.; Manninen, H.; Mahlamaeki, S.

    1985-01-01

    The OPTILUX 57 device with its large image intensifying screen is very efficient in visualizing the lumbar vertebrae. The article explains the techniques and summarizes results obtained in the examination of young sportsmen.

  9. A Quantitative RNAi Screen for JNK Modifiers Identifies Pvr as a Novel Regulator of Drosophila Immune Signaling

    Science.gov (United States)

    Bond, David; Foley, Edan

    2009-01-01

    Drosophila melanogaster responds to gram-negative bacterial challenges through the IMD pathway, a signal transduction cassette that is driven by the coordinated activities of JNK, NF-κB and caspase modules. While many modifiers of NF-κB activity were identified in cell culture and in vivo assays, the regulatory apparatus that determines JNK inputs into the IMD pathway is relatively unexplored. In this manuscript, we present the first quantitative screen of the entire genome of Drosophila for novel regulators of JNK activity in the IMD pathway. We identified a large number of gene products that negatively or positively impact on JNK activation in the IMD pathway. In particular, we identified the Pvr receptor tyrosine kinase as a potent inhibitor of JNK activation. In a series of in vivo and cell culture assays, we demonstrated that activation of the IMD pathway drives JNK-dependent expression of the Pvr ligands, Pvf2 and Pvf3, which in turn act through the Pvr/ERK MAP kinase pathway to attenuate the JNK and NF-κB arms of the IMD pathway. Our data illuminate a poorly understood arm of a critical and evolutionarily conserved innate immune response. Furthermore, given the pleiotropic involvement of JNK in eukaryotic cell biology, we believe that many of the novel regulators identified in this screen are of interest beyond immune signaling. PMID:19893628

  10. RNAi screening of subtracted transcriptomes reveals tumor suppression by taurine-activated GABAA receptors involved in volume regulation

    Science.gov (United States)

    van Nierop, Pim; Vormer, Tinke L.; Foijer, Floris; Verheij, Joanne; Lodder, Johannes C.; Andersen, Jesper B.; Mansvelder, Huibert D.; te Riele, Hein

    2018-01-01

    To identify coding and non-coding suppressor genes of anchorage-independent proliferation by efficient loss-of-function screening, we have developed a method for enzymatic production of low complexity shRNA libraries from subtracted transcriptomes. We produced and screened two LEGO (Low-complexity by Enrichment for Genes shut Off) shRNA libraries that were enriched for shRNA vectors targeting coding and non-coding polyadenylated transcripts that were reduced in transformed Mouse Embryonic Fibroblasts (MEFs). The LEGO shRNA libraries included ~25 shRNA vectors per transcript which limited off-target artifacts. Our method identified 79 coding and non-coding suppressor transcripts. We found that taurine-responsive GABAA receptor subunits, including GABRA5 and GABRB3, were induced during the arrest of non-transformed anchor-deprived MEFs and prevented anchorless proliferation. We show that taurine activates chloride currents through GABAA receptors on MEFs, causing seclusion of cell volume in large membrane protrusions. Volume seclusion from cells by taurine correlated with reduced proliferation and, conversely, suppression of this pathway allowed anchorage-independent proliferation. In human cholangiocarcinomas, we found that several proteins involved in taurine signaling via GABAA receptors were repressed. Low GABRA5 expression typified hyperproliferative tumors, and loss of taurine signaling correlated with reduced patient survival, suggesting this tumor suppressive mechanism operates in vivo. PMID:29787571

  11. Geospatial Optimization of Siting Large-Scale Solar Projects

    Energy Technology Data Exchange (ETDEWEB)

    Macknick, Jordan [National Renewable Energy Lab. (NREL), Golden, CO (United States); Quinby, Ted [National Renewable Energy Lab. (NREL), Golden, CO (United States); Caulfield, Emmet [Stanford Univ., CA (United States); Gerritsen, Margot [Stanford Univ., CA (United States); Diffendorfer, Jay [U.S. Geological Survey, Boulder, CO (United States); Haines, Seth [U.S. Geological Survey, Boulder, CO (United States)

    2014-03-01

    Recent policy and economic conditions have encouraged a renewed interest in developing large-scale solar projects in the U.S. Southwest. However, siting large-scale solar projects is complex. In addition to the quality of the solar resource, solar developers must take into consideration many environmental, social, and economic factors when evaluating a potential site. This report describes a proof-of-concept, Web-based Geographical Information Systems (GIS) tool that evaluates multiple user-defined criteria in an optimization algorithm to inform discussions and decisions regarding the locations of utility-scale solar projects. Existing siting recommendations for large-scale solar projects from governmental and non-governmental organizations are not consistent with each other, are often not transparent in methods, and do not take into consideration the differing priorities of stakeholders. The siting assistance GIS tool we have developed improves upon the existing siting guidelines by being user-driven, transparent, interactive, capable of incorporating multiple criteria, and flexible. This work provides the foundation for a dynamic siting assistance tool that can greatly facilitate siting decisions among multiple stakeholders.

  12. State-of-the-Art in GPU-Based Large-Scale Volume Visualization

    KAUST Repository

    Beyer, Johanna

    2015-05-01

    This survey gives an overview of the current state of the art in GPU techniques for interactive large-scale volume visualization. Modern techniques in this field have brought about a sea change in how interactive visualization and analysis of giga-, tera- and petabytes of volume data can be enabled on GPUs. In addition to combining the parallel processing power of GPUs with out-of-core methods and data streaming, a major enabler for interactivity is making both the computational and the visualization effort proportional to the amount and resolution of data that is actually visible on screen, i.e. \\'output-sensitive\\' algorithms and system designs. This leads to recent output-sensitive approaches that are \\'ray-guided\\', \\'visualization-driven\\' or \\'display-aware\\'. In this survey, we focus on these characteristics and propose a new categorization of GPU-based large-scale volume visualization techniques based on the notions of actual output-resolution visibility and the current working set of volume bricks-the current subset of data that is minimally required to produce an output image of the desired display resolution. Furthermore, we discuss the differences and similarities of different rendering and data traversal strategies in volume rendering by putting them into a common context-the notion of address translation. For our purposes here, we view parallel (distributed) visualization using clusters as an orthogonal set of techniques that we do not discuss in detail but that can be used in conjunction with what we present in this survey. © 2015 The Eurographics Association and John Wiley & Sons Ltd.

  13. State-of-the-Art in GPU-Based Large-Scale Volume Visualization

    KAUST Repository

    Beyer, Johanna; Hadwiger, Markus; Pfister, Hanspeter

    2015-01-01

    This survey gives an overview of the current state of the art in GPU techniques for interactive large-scale volume visualization. Modern techniques in this field have brought about a sea change in how interactive visualization and analysis of giga-, tera- and petabytes of volume data can be enabled on GPUs. In addition to combining the parallel processing power of GPUs with out-of-core methods and data streaming, a major enabler for interactivity is making both the computational and the visualization effort proportional to the amount and resolution of data that is actually visible on screen, i.e. 'output-sensitive' algorithms and system designs. This leads to recent output-sensitive approaches that are 'ray-guided', 'visualization-driven' or 'display-aware'. In this survey, we focus on these characteristics and propose a new categorization of GPU-based large-scale volume visualization techniques based on the notions of actual output-resolution visibility and the current working set of volume bricks-the current subset of data that is minimally required to produce an output image of the desired display resolution. Furthermore, we discuss the differences and similarities of different rendering and data traversal strategies in volume rendering by putting them into a common context-the notion of address translation. For our purposes here, we view parallel (distributed) visualization using clusters as an orthogonal set of techniques that we do not discuss in detail but that can be used in conjunction with what we present in this survey. © 2015 The Eurographics Association and John Wiley & Sons Ltd.

  14. Large-scale Agricultural Land Acquisitions in West Africa | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    This project will examine large-scale agricultural land acquisitions in nine West African countries -Burkina Faso, Guinea-Bissau, Guinea, Benin, Mali, Togo, Senegal, Niger, and Côte d'Ivoire. ... They will use the results to increase public awareness and knowledge about the consequences of large-scale land acquisitions.

  15. Large-scale motions in the universe: a review

    International Nuclear Information System (INIS)

    Burstein, D.

    1990-01-01

    The expansion of the universe can be retarded in localised regions within the universe both by the presence of gravity and by non-gravitational motions generated in the post-recombination universe. The motions of galaxies thus generated are called 'peculiar motions', and the amplitudes, size scales and coherence of these peculiar motions are among the most direct records of the structure of the universe. As such, measurements of these properties of the present-day universe provide some of the severest tests of cosmological theories. This is a review of the current evidence for large-scale motions of galaxies out to a distance of ∼5000 km s -1 (in an expanding universe, distance is proportional to radial velocity). 'Large-scale' in this context refers to motions that are correlated over size scales larger than the typical sizes of groups of galaxies, up to and including the size of the volume surveyed. To orient the reader into this relatively new field of study, a short modern history is given together with an explanation of the terminology. Careful consideration is given to the data used to measure the distances, and hence the peculiar motions, of galaxies. The evidence for large-scale motions is presented in a graphical fashion, using only the most reliable data for galaxies spanning a wide range in optical properties and over the complete range of galactic environments. The kinds of systematic errors that can affect this analysis are discussed, and the reliability of these motions is assessed. The predictions of two models of large-scale motion are compared to the observations, and special emphasis is placed on those motions in which our own Galaxy directly partakes. (author)

  16. State of the Art in Large-Scale Soil Moisture Monitoring

    Science.gov (United States)

    Ochsner, Tyson E.; Cosh, Michael Harold; Cuenca, Richard H.; Dorigo, Wouter; Draper, Clara S.; Hagimoto, Yutaka; Kerr, Yan H.; Larson, Kristine M.; Njoku, Eni Gerald; Small, Eric E.; hide

    2013-01-01

    Soil moisture is an essential climate variable influencing land atmosphere interactions, an essential hydrologic variable impacting rainfall runoff processes, an essential ecological variable regulating net ecosystem exchange, and an essential agricultural variable constraining food security. Large-scale soil moisture monitoring has advanced in recent years creating opportunities to transform scientific understanding of soil moisture and related processes. These advances are being driven by researchers from a broad range of disciplines, but this complicates collaboration and communication. For some applications, the science required to utilize large-scale soil moisture data is poorly developed. In this review, we describe the state of the art in large-scale soil moisture monitoring and identify some critical needs for research to optimize the use of increasingly available soil moisture data. We review representative examples of 1) emerging in situ and proximal sensing techniques, 2) dedicated soil moisture remote sensing missions, 3) soil moisture monitoring networks, and 4) applications of large-scale soil moisture measurements. Significant near-term progress seems possible in the use of large-scale soil moisture data for drought monitoring. Assimilation of soil moisture data for meteorological or hydrologic forecasting also shows promise, but significant challenges related to model structures and model errors remain. Little progress has been made yet in the use of large-scale soil moisture observations within the context of ecological or agricultural modeling. Opportunities abound to advance the science and practice of large-scale soil moisture monitoring for the sake of improved Earth system monitoring, modeling, and forecasting.

  17. Tracking and tracing of participants in two large cancer screening trials.

    Science.gov (United States)

    Marcus, Pamela M; Childs, Jeffery; Gahagan, Betsy; Gren, Lisa H

    2012-07-01

    Many clinical trials rely on participant report to first learn about study events. It is therefore important to have current contact information and the ability to locate participants should information become outdated. The Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO) and the Lung Screening Study (LSS) component of the National Lung Screening Trial, two large randomized cancer screening trials, enrolled almost 190,000 participants on whom annual contact was necessary. Ten screening centers participated in both trials. Centers developed methods to track participants and trace them when necessary. We describe the methods used to keep track of participants and trace them when lost, and the extent to which each method was used. Screening center coordinators were asked, using a self-administered paper questionnaire, to rate the extent to which specific tracking and tracing methods were used. Many methods were used by the screening centers, including telephone calls, mail, and internet searches. The most extensively used methods involved telephoning the participant on his or her home or cell phone, or telephoning a person identified by the participant as someone who would know about the participant's whereabouts. Internet searches were used extensively as well; these included searches on names, reverse-lookup searches (on addresses or telephone numbers) and searches of the Social Security Death Index. Over time, the percentage of participants requiring tracing decreased. Telephone communication and internet services were useful in keeping track of PLCO and LSS participants and tracing them when contact information was no longer valid. Published by Elsevier Inc.

  18. Evaluation of French version of the Vulnerability to abuse screen scale (VASS), a elder abuse screening tool.

    Science.gov (United States)

    Grenier, Florian; Capriz, Françoise; Lacroix-Hugues, Virginie; Paysant, François; Pradier, Christian; Franco, Alain

    2016-06-01

    The elder abuse is a major public health problem. In the world, almost 4 to 10% of people of more than 65 years would be abuse. The generalist practitioners report only 2% of the elder abuse. Furthermore, the evaluations of elder abuse screenings test found in the scientist literature were unsatisfactory. Evaluate the elder abuse screening capacities of the Vulnerability to abuse screen scale (VASS) in order to propose it to the doctors. VASS was translated in French. It's a quantitative and a forward-looking study whose the answers of people of more than 65 years old were analysed and compared in blind way to the answers of socials workers. 200 patients were included between March and May 2012 in the CHU of Cimiez, Nice. We found 104 patients in danger of abuse, 40 cases of abuse revealed by the socials workers, so 20% of abuses were reported by the gold standard. It means a sensibility of 90,9%, a specificity of 49,7% and a predictive value of 96,1% to a score of 1 to the test. The screening test VASS shown it useful to detect elder people in danger of abuse but a few discriminants and not adapted to patients who have cognitive pathologies. It's a screening tool usable by default, more sensitive than others tests in the scientist literature. However, these results ask the question of the useful of these tools of elder abuse screening in comparison with the education of doctors which made proofs of success in this subject.

  19. Examination of the lumbar vertebral column using large-screen image intensifier photofluorography

    International Nuclear Information System (INIS)

    Soimakallio, S.; Manninen, H.; Mahlamaeki, S.; Kuopio Central Hospital

    1985-01-01

    The OPTILUX 57 device with its large image intensifying screen is very efficient in visualizing the lumbar vertebrae. The article explains the techniques and summarizes results obtained in the examination of young sportsmen. (orig.) [de

  20. A route to explosive large-scale magnetic reconnection in a super-ion-scale current sheet

    Directory of Open Access Journals (Sweden)

    K. G. Tanaka

    2009-01-01

    Full Text Available How to trigger magnetic reconnection is one of the most interesting and important problems in space plasma physics. Recently, electron temperature anisotropy (αeo=Te⊥/Te|| at the center of a current sheet and non-local effect of the lower-hybrid drift instability (LHDI that develops at the current sheet edges have attracted attention in this context. In addition to these effects, here we also study the effects of ion temperature anisotropy (αio=Ti⊥/Ti||. Electron anisotropy effects are known to be helpless in a current sheet whose thickness is of ion-scale. In this range of current sheet thickness, the LHDI effects are shown to weaken substantially with a small increase in thickness and the obtained saturation level is too low for a large-scale reconnection to be achieved. Then we investigate whether introduction of electron and ion temperature anisotropies in the initial stage would couple with the LHDI effects to revive quick triggering of large-scale reconnection in a super-ion-scale current sheet. The results are as follows. (1 The initial electron temperature anisotropy is consumed very quickly when a number of minuscule magnetic islands (each lateral length is 1.5~3 times the ion inertial length form. These minuscule islands do not coalesce into a large-scale island to enable large-scale reconnection. (2 The subsequent LHDI effects disturb the current sheet filled with the small islands. This makes the triggering time scale to be accelerated substantially but does not enhance the saturation level of reconnected flux. (3 When the ion temperature anisotropy is added, it survives through the small island formation stage and makes even quicker triggering to happen when the LHDI effects set-in. Furthermore the saturation level is seen to be elevated by a factor of ~2 and large-scale reconnection is achieved only in this case. Comparison with two-dimensional simulations that exclude the LHDI effects confirms that the saturation level

  1. Large-scale Labeled Datasets to Fuel Earth Science Deep Learning Applications

    Science.gov (United States)

    Maskey, M.; Ramachandran, R.; Miller, J.

    2017-12-01

    Deep learning has revolutionized computer vision and natural language processing with various algorithms scaled using high-performance computing. However, generic large-scale labeled datasets such as the ImageNet are the fuel that drives the impressive accuracy of deep learning results. Large-scale labeled datasets already exist in domains such as medical science, but creating them in the Earth science domain is a challenge. While there are ways to apply deep learning using limited labeled datasets, there is a need in the Earth sciences for creating large-scale labeled datasets for benchmarking and scaling deep learning applications. At the NASA Marshall Space Flight Center, we are using deep learning for a variety of Earth science applications where we have encountered the need for large-scale labeled datasets. We will discuss our approaches for creating such datasets and why these datasets are just as valuable as deep learning algorithms. We will also describe successful usage of these large-scale labeled datasets with our deep learning based applications.

  2. A heritable antiviral RNAi response limits Orsay virus infection in Caenorhabditis elegans N2.

    Directory of Open Access Journals (Sweden)

    Mark G Sterken

    Full Text Available Orsay virus (OrV is the first virus known to be able to complete a full infection cycle in the model nematode species Caenorhabditis elegans. OrV is transmitted horizontally and its infection is limited by antiviral RNA interference (RNAi. However, we have no insight into the kinetics of OrV replication in C. elegans. We developed an assay that infects worms in liquid, allowing precise monitoring of the infection. The assay revealed a dual role for the RNAi response in limiting Orsay virus infection in C. elegans. Firstly, it limits the progression of the initial infection at the step of recognition of dsRNA. Secondly, it provides an inherited protection against infection in the offspring. This establishes the heritable RNAi response as anti-viral mechanism during OrV infections in C. elegans. Our results further illustrate that the inheritance of the anti-viral response is important in controlling the infection in the canonical wild type Bristol N2. The OrV replication kinetics were established throughout the worm life-cycle, setting a standard for further quantitative assays with the OrV-C. elegans infection model.

  3. Functional analysis of pathogenicity proteins of the potato cyst nematode Globodera rostochiensis using RNAi.

    Science.gov (United States)

    Chen, Qing; Rehman, S; Smant, G; Jones, John T

    2005-07-01

    RNA interference (RNAi) has been used widely as a tool for examining gene function and a method that allows its use with plant-parasitic nematodes recently has been described. Here, we use a modified method to analyze the function of secreted beta-1,4, endoglucanases of the potato cyst nematode Globodera rostochiensis, the first in vivo functional analysis of a pathogenicity protein of a plant-parasitic nematode. Knockout of the beta-1,4, endoglucanases reduced the ability of the nematodes to invade roots. We also use RNAi to show that gr-ams-1, a secreted protein of the main sense organs (the amphids), is essential for host location.

  4. Large-scale structure observables in general relativity

    International Nuclear Information System (INIS)

    Jeong, Donghui; Schmidt, Fabian

    2015-01-01

    We review recent studies that rigorously define several key observables of the large-scale structure of the Universe in a general relativistic context. Specifically, we consider (i) redshift perturbation of cosmic clock events; (ii) distortion of cosmic rulers, including weak lensing shear and magnification; and (iii) observed number density of tracers of the large-scale structure. We provide covariant and gauge-invariant expressions of these observables. Our expressions are given for a linearly perturbed flat Friedmann–Robertson–Walker metric including scalar, vector, and tensor metric perturbations. While we restrict ourselves to linear order in perturbation theory, the approach can be straightforwardly generalized to higher order. (paper)

  5. Fatigue Analysis of Large-scale Wind turbine

    Directory of Open Access Journals (Sweden)

    Zhu Yongli

    2017-01-01

    Full Text Available The paper does research on top flange fatigue damage of large-scale wind turbine generator. It establishes finite element model of top flange connection system with finite element analysis software MSC. Marc/Mentat, analyzes its fatigue strain, implements load simulation of flange fatigue working condition with Bladed software, acquires flange fatigue load spectrum with rain-flow counting method, finally, it realizes fatigue analysis of top flange with fatigue analysis software MSC. Fatigue and Palmgren-Miner linear cumulative damage theory. The analysis result indicates that its result provides new thinking for flange fatigue analysis of large-scale wind turbine generator, and possesses some practical engineering value.

  6. Real-time simulation of large-scale floods

    Science.gov (United States)

    Liu, Q.; Qin, Y.; Li, G. D.; Liu, Z.; Cheng, D. J.; Zhao, Y. H.

    2016-08-01

    According to the complex real-time water situation, the real-time simulation of large-scale floods is very important for flood prevention practice. Model robustness and running efficiency are two critical factors in successful real-time flood simulation. This paper proposed a robust, two-dimensional, shallow water model based on the unstructured Godunov- type finite volume method. A robust wet/dry front method is used to enhance the numerical stability. An adaptive method is proposed to improve the running efficiency. The proposed model is used for large-scale flood simulation on real topography. Results compared to those of MIKE21 show the strong performance of the proposed model.

  7. [Adverse Effect Predictions Based on Computational Toxicology Techniques and Large-scale Databases].

    Science.gov (United States)

    Uesawa, Yoshihiro

    2018-01-01

     Understanding the features of chemical structures related to the adverse effects of drugs is useful for identifying potential adverse effects of new drugs. This can be based on the limited information available from post-marketing surveillance, assessment of the potential toxicities of metabolites and illegal drugs with unclear characteristics, screening of lead compounds at the drug discovery stage, and identification of leads for the discovery of new pharmacological mechanisms. This present paper describes techniques used in computational toxicology to investigate the content of large-scale spontaneous report databases of adverse effects, and it is illustrated with examples. Furthermore, volcano plotting, a new visualization method for clarifying the relationships between drugs and adverse effects via comprehensive analyses, will be introduced. These analyses may produce a great amount of data that can be applied to drug repositioning.

  8. A genome-wide screen identifies conserved protein hubs required for cadherin-mediated cell–cell adhesion

    Science.gov (United States)

    Toret, Christopher P.; D’Ambrosio, Michael V.; Vale, Ronald D.; Simon, Michael A.

    2014-01-01

    Cadherins and associated catenins provide an important structural interface between neighboring cells, the actin cytoskeleton, and intracellular signaling pathways in a variety of cell types throughout the Metazoa. However, the full inventory of the proteins and pathways required for cadherin-mediated adhesion has not been established. To this end, we completed a genome-wide (∼14,000 genes) ribonucleic acid interference (RNAi) screen that targeted Ca2+-dependent adhesion in DE-cadherin–expressing Drosophila melanogaster S2 cells in suspension culture. This novel screen eliminated Ca2+-independent cell–cell adhesion, integrin-based adhesion, cell spreading, and cell migration. We identified 17 interconnected regulatory hubs, based on protein functions and protein–protein interactions that regulate the levels of the core cadherin–catenin complex and coordinate cadherin-mediated cell–cell adhesion. Representative proteins from these hubs were analyzed further in Drosophila oogenesis, using targeted germline RNAi, and adhesion was analyzed in Madin–Darby canine kidney mammalian epithelial cell–cell adhesion. These experiments reveal roles for a diversity of cellular pathways that are required for cadherin function in Metazoa, including cytoskeleton organization, cell–substrate interactions, and nuclear and cytoplasmic signaling. PMID:24446484

  9. Large-scale numerical simulations of plasmas

    International Nuclear Information System (INIS)

    Hamaguchi, Satoshi

    2004-01-01

    The recent trend of large scales simulations of fusion plasma and processing plasmas is briefly summarized. Many advanced simulation techniques have been developed for fusion plasmas and some of these techniques are now applied to analyses of processing plasmas. (author)

  10. Breast cancer screening halves the risk of breast cancer death: a case-referent study

    NARCIS (Netherlands)

    Paap, Ellen; Verbeek, André L. M.; Botterweck, Anita A. M.; van Doorne-Nagtegaal, Heidi J.; Imhof-Tas, Mechli; de Koning, Harry J.; Otto, Suzie J.; de Munck, Linda; van der Steen, Annemieke; Holland, Roland; den Heeten, Gerard J.; Broeders, Mireille J. M.

    2014-01-01

    Large-scale epidemiologic studies have consistently demonstrated the effectiveness of mammographic screening programs, however the benefits are still subject to debate. We estimated the effect of the Dutch screening program on breast cancer mortality. In a large multi-region case-referent study, we

  11. Nearly incompressible fluids: Hydrodynamics and large scale inhomogeneity

    International Nuclear Information System (INIS)

    Hunana, P.; Zank, G. P.; Shaikh, D.

    2006-01-01

    A system of hydrodynamic equations in the presence of large-scale inhomogeneities for a high plasma beta solar wind is derived. The theory is derived under the assumption of low turbulent Mach number and is developed for the flows where the usual incompressible description is not satisfactory and a full compressible treatment is too complex for any analytical studies. When the effects of compressibility are incorporated only weakly, a new description, referred to as 'nearly incompressible hydrodynamics', is obtained. The nearly incompressible theory, was originally applied to homogeneous flows. However, large-scale gradients in density, pressure, temperature, etc., are typical in the solar wind and it was unclear how inhomogeneities would affect the usual incompressible and nearly incompressible descriptions. In the homogeneous case, the lowest order expansion of the fully compressible equations leads to the usual incompressible equations, followed at higher orders by the nearly incompressible equations, as introduced by Zank and Matthaeus. With this work we show that the inclusion of large-scale inhomogeneities (in this case time-independent and radially symmetric background solar wind) modifies the leading-order incompressible description of solar wind flow. We find, for example, that the divergence of velocity fluctuations is nonsolenoidal and that density fluctuations can be described to leading order as a passive scalar. Locally (for small lengthscales), this system of equations converges to the usual incompressible equations and we therefore use the term 'locally incompressible' to describe the equations. This term should be distinguished from the term 'nearly incompressible', which is reserved for higher-order corrections. Furthermore, we find that density fluctuations scale with Mach number linearly, in contrast to the original homogeneous nearly incompressible theory, in which density fluctuations scale with the square of Mach number. Inhomogeneous nearly

  12. Genome-Wide RNAi Ionomics Screen Reveals New Genes and Regulation of Human Trace Element Metabolism

    OpenAIRE

    Malinouski, Mikalai; Hasan, Nesrin M.; Zhang, Yan; Seravalli, Javier; Lin, Jie; Avanesov, Andrei; Lutsenko, Svetlana; Gladyshev, Vadim N.

    2017-01-01

    Trace elements are essential for human metabolism and dysregulation of their homeostasis is associated with numerous disorders. Here we characterize mechanisms that regulate trace elements in human cells by designing and performing a genome-wide high-throughput siRNA/ionomics screen, and examining top hits in cellular and biochemical assays. The screen reveals high stability of the ionomes, especially the zinc ionome, and yields known regulators and novel candidates. We further uncover fundam...

  13. Performance Health Monitoring of Large-Scale Systems

    Energy Technology Data Exchange (ETDEWEB)

    Rajamony, Ram [IBM Research, Austin, TX (United States)

    2014-11-20

    This report details the progress made on the ASCR funded project Performance Health Monitoring for Large Scale Systems. A large-­scale application may not achieve its full performance potential due to degraded performance of even a single subsystem. Detecting performance faults, isolating them, and taking remedial action is critical for the scale of systems on the horizon. PHM aims to develop techniques and tools that can be used to identify and mitigate such performance problems. We accomplish this through two main aspects. The PHM framework encompasses diagnostics, system monitoring, fault isolation, and performance evaluation capabilities that indicates when a performance fault has been detected, either due to an anomaly present in the system itself or due to contention for shared resources between concurrently executing jobs. Software components called the PHM Control system then build upon the capabilities provided by the PHM framework to mitigate degradation caused by performance problems.

  14. Decreasing erucic acid level by RNAi-mediated silencing of fatty ...

    African Journals Online (AJOL)

    To develop low level of erucic acid in rapeseeds by intron-spliced hairpin RNA, an inverted repeat unit of a partial BnFAE1.1 gene interrupted by a spliceable intron ... In conclusion, the expression of endogenous BnFAE1.1 was efficiently silenced by the designed RNAi silencer, causing a significant down-regulation in the ...

  15. The impact of new forms of large-scale general practice provider collaborations on England's NHS: a systematic review.

    Science.gov (United States)

    Pettigrew, Luisa M; Kumpunen, Stephanie; Mays, Nicholas; Rosen, Rebecca; Posaner, Rachel

    2018-03-01

    Over the past decade, collaboration between general practices in England to form new provider networks and large-scale organisations has been driven largely by grassroots action among GPs. However, it is now being increasingly advocated for by national policymakers. Expectations of what scaling up general practice in England will achieve are significant. To review the evidence of the impact of new forms of large-scale general practice provider collaborations in England. Systematic review. Embase, MEDLINE, Health Management Information Consortium, and Social Sciences Citation Index were searched for studies reporting the impact on clinical processes and outcomes, patient experience, workforce satisfaction, or costs of new forms of provider collaborations between general practices in England. A total of 1782 publications were screened. Five studies met the inclusion criteria and four examined the same general practice networks, limiting generalisability. Substantial financial investment was required to establish the networks and the associated interventions that were targeted at four clinical areas. Quality improvements were achieved through standardised processes, incentives at network level, information technology-enabled performance dashboards, and local network management. The fifth study of a large-scale multisite general practice organisation showed that it may be better placed to implement safety and quality processes than conventional practices. However, unintended consequences may arise, such as perceptions of disenfranchisement among staff and reductions in continuity of care. Good-quality evidence of the impacts of scaling up general practice provider organisations in England is scarce. As more general practice collaborations emerge, evaluation of their impacts will be important to understand which work, in which settings, how, and why. © British Journal of General Practice 2018.

  16. Data management in large-scale collaborative toxicity studies: how to file experimental data for automated statistical analysis.

    Science.gov (United States)

    Stanzel, Sven; Weimer, Marc; Kopp-Schneider, Annette

    2013-06-01

    High-throughput screening approaches are carried out for the toxicity assessment of a large number of chemical compounds. In such large-scale in vitro toxicity studies several hundred or thousand concentration-response experiments are conducted. The automated evaluation of concentration-response data using statistical analysis scripts saves time and yields more consistent results in comparison to data analysis performed by the use of menu-driven statistical software. Automated statistical analysis requires that concentration-response data are available in a standardised data format across all compounds. To obtain consistent data formats, a standardised data management workflow must be established, including guidelines for data storage, data handling and data extraction. In this paper two procedures for data management within large-scale toxicological projects are proposed. Both procedures are based on Microsoft Excel files as the researcher's primary data format and use a computer programme to automate the handling of data files. The first procedure assumes that data collection has not yet started whereas the second procedure can be used when data files already exist. Successful implementation of the two approaches into the European project ACuteTox is illustrated. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. DISE: A Seed-Dependent RNAi Off-Target Effect That Kills Cancer Cells.

    Science.gov (United States)

    Putzbach, William; Gao, Quan Q; Patel, Monal; Haluck-Kangas, Ashley; Murmann, Andrea E; Peter, Marcus E

    2018-01-01

    Off-target effects (OTEs) represent a significant caveat for RNAi caused by substantial complementarity between siRNAs and unintended mRNAs. We now discuss the existence of three types of seed-dependent OTEs (sOTEs). Type I involves unintended targeting through the guide strand seed of an siRNA. Type II is caused by the activity of the seed on the designated siRNA passenger strand when loaded into the RNA-induced silencing complex (RISC). Both type I and II sOTEs will elicit unpredictable cellular responses. By contrast, in sOTE type III the guide strand seed preferentially targets essential survival genes resulting in death induced by survival gene elimination (DISE). In this Opinion article, we discuss DISE as a consequence of RNAi that may preferentially affect cancer cells. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Learning from large scale neural simulations

    DEFF Research Database (Denmark)

    Serban, Maria

    2017-01-01

    Large-scale neural simulations have the marks of a distinct methodology which can be fruitfully deployed to advance scientific understanding of the human brain. Computer simulation studies can be used to produce surrogate observational data for better conceptual models and new how...

  19. Phenomenology of two-dimensional stably stratified turbulence under large-scale forcing

    KAUST Repository

    Kumar, Abhishek; Verma, Mahendra K.; Sukhatme, Jai

    2017-01-01

    In this paper, we characterise the scaling of energy spectra, and the interscale transfer of energy and enstrophy, for strongly, moderately and weakly stably stratified two-dimensional (2D) turbulence, restricted in a vertical plane, under large-scale random forcing. In the strongly stratified case, a large-scale vertically sheared horizontal flow (VSHF) coexists with small scale turbulence. The VSHF consists of internal gravity waves and the turbulent flow has a kinetic energy (KE) spectrum that follows an approximate k−3 scaling with zero KE flux and a robust positive enstrophy flux. The spectrum of the turbulent potential energy (PE) also approximately follows a k−3 power-law and its flux is directed to small scales. For moderate stratification, there is no VSHF and the KE of the turbulent flow exhibits Bolgiano–Obukhov scaling that transitions from a shallow k−11/5 form at large scales, to a steeper approximate k−3 scaling at small scales. The entire range of scales shows a strong forward enstrophy flux, and interestingly, large (small) scales show an inverse (forward) KE flux. The PE flux in this regime is directed to small scales, and the PE spectrum is characterised by an approximate k−1.64 scaling. Finally, for weak stratification, KE is transferred upscale and its spectrum closely follows a k−2.5 scaling, while PE exhibits a forward transfer and its spectrum shows an approximate k−1.6 power-law. For all stratification strengths, the total energy always flows from large to small scales and almost all the spectral indicies are well explained by accounting for the scale-dependent nature of the corresponding flux.

  20. Phenomenology of two-dimensional stably stratified turbulence under large-scale forcing

    KAUST Repository

    Kumar, Abhishek

    2017-01-11

    In this paper, we characterise the scaling of energy spectra, and the interscale transfer of energy and enstrophy, for strongly, moderately and weakly stably stratified two-dimensional (2D) turbulence, restricted in a vertical plane, under large-scale random forcing. In the strongly stratified case, a large-scale vertically sheared horizontal flow (VSHF) coexists with small scale turbulence. The VSHF consists of internal gravity waves and the turbulent flow has a kinetic energy (KE) spectrum that follows an approximate k−3 scaling with zero KE flux and a robust positive enstrophy flux. The spectrum of the turbulent potential energy (PE) also approximately follows a k−3 power-law and its flux is directed to small scales. For moderate stratification, there is no VSHF and the KE of the turbulent flow exhibits Bolgiano–Obukhov scaling that transitions from a shallow k−11/5 form at large scales, to a steeper approximate k−3 scaling at small scales. The entire range of scales shows a strong forward enstrophy flux, and interestingly, large (small) scales show an inverse (forward) KE flux. The PE flux in this regime is directed to small scales, and the PE spectrum is characterised by an approximate k−1.64 scaling. Finally, for weak stratification, KE is transferred upscale and its spectrum closely follows a k−2.5 scaling, while PE exhibits a forward transfer and its spectrum shows an approximate k−1.6 power-law. For all stratification strengths, the total energy always flows from large to small scales and almost all the spectral indicies are well explained by accounting for the scale-dependent nature of the corresponding flux.

  1. Exploring the large-scale structure of Taylor–Couette turbulence through Large-Eddy Simulations

    Science.gov (United States)

    Ostilla-Mónico, Rodolfo; Zhu, Xiaojue; Verzicco, Roberto

    2018-04-01

    Large eddy simulations (LES) of Taylor-Couette (TC) flow, the flow between two co-axial and independently rotating cylinders are performed in an attempt to explore the large-scale axially-pinned structures seen in experiments and simulations. Both static and dynamic LES models are used. The Reynolds number is kept fixed at Re = 3.4 · 104, and the radius ratio η = ri /ro is set to η = 0.909, limiting the effects of curvature and resulting in frictional Reynolds numbers of around Re τ ≈ 500. Four rotation ratios from Rot = ‑0.0909 to Rot = 0.3 are simulated. First, the LES of TC is benchmarked for different rotation ratios. Both the Smagorinsky model with a constant of cs = 0.1 and the dynamic model are found to produce reasonable results for no mean rotation and cyclonic rotation, but deviations increase for increasing rotation. This is attributed to the increasing anisotropic character of the fluctuations. Second, “over-damped” LES, i.e. LES with a large Smagorinsky constant is performed and is shown to reproduce some features of the large-scale structures, even when the near-wall region is not adequately modeled. This shows the potential for using over-damped LES for fast explorations of the parameter space where large-scale structures are found.

  2. Large-scale preparation of hollow graphitic carbon nanospheres

    International Nuclear Information System (INIS)

    Feng, Jun; Li, Fu; Bai, Yu-Jun; Han, Fu-Dong; Qi, Yong-Xin; Lun, Ning; Lu, Xi-Feng

    2013-01-01

    Hollow graphitic carbon nanospheres (HGCNSs) were synthesized on large scale by a simple reaction between glucose and Mg at 550 °C in an autoclave. Characterization by X-ray diffraction, Raman spectroscopy and transmission electron microscopy demonstrates the formation of HGCNSs with an average diameter of 10 nm or so and a wall thickness of a few graphenes. The HGCNSs exhibit a reversible capacity of 391 mAh g −1 after 60 cycles when used as anode materials for Li-ion batteries. -- Graphical abstract: Hollow graphitic carbon nanospheres could be prepared on large scale by the simple reaction between glucose and Mg at 550 °C, which exhibit superior electrochemical performance to graphite. Highlights: ► Hollow graphitic carbon nanospheres (HGCNSs) were prepared on large scale at 550 °C ► The preparation is simple, effective and eco-friendly. ► The in situ yielded MgO nanocrystals promote the graphitization. ► The HGCNSs exhibit superior electrochemical performance to graphite.

  3. Accelerating large-scale phase-field simulations with GPU

    Directory of Open Access Journals (Sweden)

    Xiaoming Shi

    2017-10-01

    Full Text Available A new package for accelerating large-scale phase-field simulations was developed by using GPU based on the semi-implicit Fourier method. The package can solve a variety of equilibrium equations with different inhomogeneity including long-range elastic, magnetostatic, and electrostatic interactions. Through using specific algorithm in Compute Unified Device Architecture (CUDA, Fourier spectral iterative perturbation method was integrated in GPU package. The Allen-Cahn equation, Cahn-Hilliard equation, and phase-field model with long-range interaction were solved based on the algorithm running on GPU respectively to test the performance of the package. From the comparison of the calculation results between the solver executed in single CPU and the one on GPU, it was found that the speed on GPU is enormously elevated to 50 times faster. The present study therefore contributes to the acceleration of large-scale phase-field simulations and provides guidance for experiments to design large-scale functional devices.

  4. First Mile Challenges for Large-Scale IoT

    KAUST Repository

    Bader, Ahmed

    2017-03-16

    The Internet of Things is large-scale by nature. This is not only manifested by the large number of connected devices, but also by the sheer scale of spatial traffic intensity that must be accommodated, primarily in the uplink direction. To that end, cellular networks are indeed a strong first mile candidate to accommodate the data tsunami to be generated by the IoT. However, IoT devices are required in the cellular paradigm to undergo random access procedures as a precursor to resource allocation. Such procedures impose a major bottleneck that hinders cellular networks\\' ability to support large-scale IoT. In this article, we shed light on the random access dilemma and present a case study based on experimental data as well as system-level simulations. Accordingly, a case is built for the latent need to revisit random access procedures. A call for action is motivated by listing a few potential remedies and recommendations.

  5. Influence of Speed and Rainfall on Large-Scale Wheat Lodging from 2007 to 2014 in China.

    Directory of Open Access Journals (Sweden)

    Liyuan Niu

    Full Text Available Strong wind and heavy rain remain the two most important causes of large acreage wheat (Triticum aestivum L. lodging in China. For research the influence of wind speed and rainfall-separately as well as together-on the extent and degree of lodging, five levels of the severity of lodging were defined based on a combination of the lodging area and the degree of tilting. Detailed meteorological information was studied on 52 instances of large-scale lodging that occurred from 2007 to 2014. The results showed that strong wind's lodging accounted for 8% of the instances studied, continuous rainfall's lodging accounted for 19% and strong winds-heavy rainfall's accounted for 73%. The minimum instantaneous wind speed that could cause large-scale lodging was closely related to rainfall. Without rainfall, the wind speed that resulted in lodging ranging in severity from slight to severe (Level 2 to Level 5 was 14.9 m/s, 19.3 m/s, 21.5 m/s, and 26.5 m/s, respectively; when accompanied by rainfall, the wind speed that resulted in lodging of the same severity decreased linearly with the increase of rainfall. These results will be particularly useful in preventing and alleviating wheat lodging as well screening wheat varieties with good lodging resistance.

  6. Thermal power generation projects ``Large Scale Solar Heating``; EU-Thermie-Projekte ``Large Scale Solar Heating``

    Energy Technology Data Exchange (ETDEWEB)

    Kuebler, R.; Fisch, M.N. [Steinbeis-Transferzentrum Energie-, Gebaeude- und Solartechnik, Stuttgart (Germany)

    1998-12-31

    The aim of this project is the preparation of the ``Large-Scale Solar Heating`` programme for an Europe-wide development of subject technology. The following demonstration programme was judged well by the experts but was not immediately (1996) accepted for financial subsidies. In November 1997 the EU-commission provided 1,5 million ECU which allowed the realisation of an updated project proposal. By mid 1997 a small project was approved, that had been requested under the lead of Chalmes Industriteteknik (CIT) in Sweden and is mainly carried out for the transfer of technology. (orig.) [Deutsch] Ziel dieses Vorhabens ist die Vorbereitung eines Schwerpunktprogramms `Large Scale Solar Heating`, mit dem die Technologie europaweit weiterentwickelt werden sollte. Das daraus entwickelte Demonstrationsprogramm wurde von den Gutachtern positiv bewertet, konnte jedoch nicht auf Anhieb (1996) in die Foerderung aufgenommen werden. Im November 1997 wurden von der EU-Kommission dann kurzfristig noch 1,5 Mio ECU an Foerderung bewilligt, mit denen ein aktualisierter Projektvorschlag realisiert werden kann. Bereits Mitte 1997 wurde ein kleineres Vorhaben bewilligt, das unter Federfuehrung von Chalmers Industriteknik (CIT) in Schweden beantragt worden war und das vor allem dem Technologietransfer dient. (orig.)

  7. Large-scale retrieval for medical image analytics: A comprehensive review.

    Science.gov (United States)

    Li, Zhongyu; Zhang, Xiaofan; Müller, Henning; Zhang, Shaoting

    2018-01-01

    Over the past decades, medical image analytics was greatly facilitated by the explosion of digital imaging techniques, where huge amounts of medical images were produced with ever-increasing quality and diversity. However, conventional methods for analyzing medical images have achieved limited success, as they are not capable to tackle the huge amount of image data. In this paper, we review state-of-the-art approaches for large-scale medical image analysis, which are mainly based on recent advances in computer vision, machine learning and information retrieval. Specifically, we first present the general pipeline of large-scale retrieval, summarize the challenges/opportunities of medical image analytics on a large-scale. Then, we provide a comprehensive review of algorithms and techniques relevant to major processes in the pipeline, including feature representation, feature indexing, searching, etc. On the basis of existing work, we introduce the evaluation protocols and multiple applications of large-scale medical image retrieval, with a variety of exploratory and diagnostic scenarios. Finally, we discuss future directions of large-scale retrieval, which can further improve the performance of medical image analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. [Psychometric attributes of the Spanish version of A-TAC screening scale for autism spectrum disorders].

    Science.gov (United States)

    Cubo, E; Sáez Velasco, S; Delgado Benito, V; Ausín Villaverde, V; García Soto, X R; Trejo Gabriel Y Galán, J M; Martín Santidrián, A; Macarrón, J V; Cordero Guevara, J; Benito-León, J; Louis, E D

    2011-07-01

    As there are no biological markers for Autism Spectrum Disorders (ASD), screening must focus on behaviour and the presence of a markedly abnormal development or a deficiency in verbal and non-verbal social interaction and communication. To evaluate the psychometric attributes of a Spanish version of the autism domain of the Autism-Tics, AD/HD and other Comorbidities Inventory (A-TAC) scale for ASD screening. A total of 140 subjects (43% male, 57% female) aged 6-16, with ASD (n=15), Mental Retardation (n=40), Psychiatric Illness (n=22), Tics (n=12) and controls (n=51), were included for ASD screening. The predictive validity, acceptability, scale assumptions, internal consistency, and precision were analysed. The internal consistency was high (α=0.93), and the standard error was adequate (1.13 [95% CI, -1.08 a 3.34]). The mean scores of the Autism module were higher in patients diagnosed with ASD and mental disability compared to the rest of the patients (P<.001). The area under the curve was 0.96 for the ASD group. The autism domain of the A-TAC scale seems to be a reliable, valid and precise tool for ASD screening in the Spanish school population. Copyright © 2010 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.

  9. Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway*

    Science.gov (United States)

    Foda, Bardees M.; Singh, Upinder

    2015-01-01

    RNA interference (RNAi) is a fundamental biological process that plays a crucial role in regulation of gene expression in many organisms. Transcriptional gene silencing (TGS) is one of the important nuclear roles of RNAi. Our previous data show that Entamoeba histolytica has a robust RNAi pathway that links to TGS via Argonaute 2-2 (Ago2-2) associated 27-nucleotide small RNAs with 5′-polyphosphate termini. Here, we report the first repressive histone mark to be identified in E. histolytica, dimethylation of H3K27 (H3K27Me2), and demonstrate that it is enriched at genes that are silenced by RNAi-mediated TGS. An RNAi-silencing trigger can induce H3K27Me2 deposits at both episomal and chromosomal loci, mediating gene silencing. Our data support two phases of RNAi-mediated TGS: an active silencing phase where the RNAi trigger is present and both H3K27Me2 and Ago2-2 concurrently enrich at chromosomal loci; and an established silencing phase in which the RNAi trigger is removed, but gene silencing with H3K27Me2 enrichment persist independently of Ago2-2 deposition. Importantly, some genes display resistance to chromosomal silencing despite induction of functional small RNAs. In those situations, the RNAi-triggering plasmid that is maintained episomally gets partially silenced and has H3K27Me2 enrichment, but the chromosomal copy displays no repressive histone enrichment. Our data are consistent with a model in which H3K27Me2 is a repressive histone modification, which is strongly associated with transcriptional repression. This is the first example of an epigenetic histone modification that functions to mediate RNAi-mediated TGS in the deep-branching eukaryote E. histolytica. PMID:26149683

  10. Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway.

    Science.gov (United States)

    Foda, Bardees M; Singh, Upinder

    2015-08-21

    RNA interference (RNAi) is a fundamental biological process that plays a crucial role in regulation of gene expression in many organisms. Transcriptional gene silencing (TGS) is one of the important nuclear roles of RNAi. Our previous data show that Entamoeba histolytica has a robust RNAi pathway that links to TGS via Argonaute 2-2 (Ago2-2) associated 27-nucleotide small RNAs with 5'-polyphosphate termini. Here, we report the first repressive histone mark to be identified in E. histolytica, dimethylation of H3K27 (H3K27Me2), and demonstrate that it is enriched at genes that are silenced by RNAi-mediated TGS. An RNAi-silencing trigger can induce H3K27Me2 deposits at both episomal and chromosomal loci, mediating gene silencing. Our data support two phases of RNAi-mediated TGS: an active silencing phase where the RNAi trigger is present and both H3K27Me2 and Ago2-2 concurrently enrich at chromosomal loci; and an established silencing phase in which the RNAi trigger is removed, but gene silencing with H3K27Me2 enrichment persist independently of Ago2-2 deposition. Importantly, some genes display resistance to chromosomal silencing despite induction of functional small RNAs. In those situations, the RNAi-triggering plasmid that is maintained episomally gets partially silenced and has H3K27Me2 enrichment, but the chromosomal copy displays no repressive histone enrichment. Our data are consistent with a model in which H3K27Me2 is a repressive histone modification, which is strongly associated with transcriptional repression. This is the first example of an epigenetic histone modification that functions to mediate RNAi-mediated TGS in the deep-branching eukaryote E. histolytica. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Photorealistic large-scale urban city model reconstruction.

    Science.gov (United States)

    Poullis, Charalambos; You, Suya

    2009-01-01

    The rapid and efficient creation of virtual environments has become a crucial part of virtual reality applications. In particular, civil and defense applications often require and employ detailed models of operations areas for training, simulations of different scenarios, planning for natural or man-made events, monitoring, surveillance, games, and films. A realistic representation of the large-scale environments is therefore imperative for the success of such applications since it increases the immersive experience of its users and helps reduce the difference between physical and virtual reality. However, the task of creating such large-scale virtual environments still remains a time-consuming and manual work. In this work, we propose a novel method for the rapid reconstruction of photorealistic large-scale virtual environments. First, a novel, extendible, parameterized geometric primitive is presented for the automatic building identification and reconstruction of building structures. In addition, buildings with complex roofs containing complex linear and nonlinear surfaces are reconstructed interactively using a linear polygonal and a nonlinear primitive, respectively. Second, we present a rendering pipeline for the composition of photorealistic textures, which unlike existing techniques, can recover missing or occluded texture information by integrating multiple information captured from different optical sensors (ground, aerial, and satellite).

  12. Prototype Vector Machine for Large Scale Semi-Supervised Learning

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Kai; Kwok, James T.; Parvin, Bahram

    2009-04-29

    Practicaldataminingrarelyfalls exactlyinto the supervisedlearning scenario. Rather, the growing amount of unlabeled data poses a big challenge to large-scale semi-supervised learning (SSL). We note that the computationalintensivenessofgraph-based SSLarises largely from the manifold or graph regularization, which in turn lead to large models that are dificult to handle. To alleviate this, we proposed the prototype vector machine (PVM), a highlyscalable,graph-based algorithm for large-scale SSL. Our key innovation is the use of"prototypes vectors" for effcient approximation on both the graph-based regularizer and model representation. The choice of prototypes are grounded upon two important criteria: they not only perform effective low-rank approximation of the kernel matrix, but also span a model suffering the minimum information loss compared with the complete model. We demonstrate encouraging performance and appealing scaling properties of the PVM on a number of machine learning benchmark data sets.

  13. COLA with scale-dependent growth: applications to screened modified gravity models

    Energy Technology Data Exchange (ETDEWEB)

    Winther, Hans A.; Koyama, Kazuya; Wright, Bill S. [Institute of Cosmology and Gravitation, University of Portsmouth, Dennis Sciama Building, Burnaby Road, Portsmouth, PO1 3FX (United Kingdom); Manera, Marc [Centre for Theoretical Cosmology, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom); Zhao, Gong-Bo, E-mail: hans.a.winther@gmail.com, E-mail: kazuya.koyama@port.ac.uk, E-mail: manera.work@gmail.com, E-mail: bill.wright@port.ac.uk, E-mail: gong-bo.Zhao@port.ac.uk [National Astronomy Observatories, Chinese Academy of Science, Beijing, 100012 (China)

    2017-08-01

    We present a general parallelized and easy-to-use code to perform numerical simulations of structure formation using the COLA (COmoving Lagrangian Acceleration) method for cosmological models that exhibit scale-dependent growth at the level of first and second order Lagrangian perturbation theory. For modified gravity theories we also include screening using a fast approximate method that covers all the main examples of screening mechanisms in the literature. We test the code by comparing it to full simulations of two popular modified gravity models, namely f ( R ) gravity and nDGP, and find good agreement in the modified gravity boost-factors relative to ΛCDM even when using a fairly small number of COLA time steps.

  14. Screening older adults at risk of falling with the Tinetti balance scale.

    Science.gov (United States)

    Raîche, M; Hébert, R; Prince, F; Corriveau, H

    2000-09-16

    In a prospective study of 225 community dwelling people 75 years and older, we tested the validity of the Tinetti balance scale to predict individuals who will fall at least once during the following year. A score of 36 or less identified 7 of 10 fallers with 70% sensitivity and 52% specificity. With this cut-off score, 53% of the individuals were screened positive and presented a two-fold risk of falling. These characteristics support the use of this test to screen older people at risk of falling in order to include them in a preventive intervention.

  15. Disrupted coupling of large-scale networks is associated with relapse behaviour in heroin-dependent men

    Science.gov (United States)

    Li, Qiang; Liu, Jierong; Wang, Wei; Wang, Yarong; Li, Wei; Chen, Jiajie; Zhu, Jia; Yan, Xuejiao; Li, Yongbin; Li, Zhe; Ye, Jianjun; Wang, Wei

    2018-01-01

    Background It is unknown whether impaired coupling among 3 core large-scale brain networks (salience [SN], default mode [DMN] and executive control networks [ECN]) is associated with relapse behaviour in treated heroin-dependent patients. Methods We conducted a prospective resting-state functional MRI study comparing the functional connectivity strength among healthy controls and heroin-dependent men who had either relapsed or were in early remission. Men were considered to be either relapsed or in early remission based on urine drug screens during a 3-month follow-up period. We also examined how the coupling of large-scale networks correlated with relapse behaviour among heroin-dependent men. Results We included 20 controls and 50 heroin-dependent men (26 relapsed and 24 early remission) in our analyses. The relapsed men showed greater connectivity than the early remission and control groups between the dorsal anterior cingulate cortex (key node of the SN) and the dorsomedial prefrontal cortex (included in the DMN). The relapsed men and controls showed lower connectivity than the early remission group between the left dorsolateral prefrontal cortex (key node of the left ECN) and the dorsomedial prefrontal cortex. The percentage of positive urine drug screens positively correlated with the coupling between the dorsal anterior cingulate cortex and dorsomedial prefrontal cortex, but negatively correlated with the coupling between the left dorsolateral prefrontal cortex and dorsomedial prefrontal cortex. Limitations We examined deficits in only 3 core networks leading to relapse behaviour. Other networks may also contribute to relapse. Conclusion Greater coupling between the SN and DMN and lower coupling between the left ECN and DMN is associated with relapse behaviour. These findings may shed light on the development of new treatments for heroin addiction. PMID:29252165

  16. Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions.

    Science.gov (United States)

    diCenzo, George C; Finan, Turlough M

    2018-01-01

    The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration. Subsequent expression of the site-specific recombinase mediates recombination between the two target sequences, resulting in the excision of the intervening region and its loss from the genome. We further illustrate how this deletion system can be readily adapted to function as a large-scale in vivo cloning procedure, in which the region excised from the genome is captured as a replicative plasmid. We next provide a procedure for the metabolic analysis of bacterial large-scale genome deletion mutants using the Biolog Phenotype MicroArray™ system. Finally, a pipeline is described, and a sample Matlab script is provided, for the integration of the obtained data with a draft metabolic reconstruction for the refinement of the reactions and gene-protein-reaction relationships in a metabolic reconstruction.

  17. Accelerating Relevance Vector Machine for Large-Scale Data on Spark

    Directory of Open Access Journals (Sweden)

    Liu Fang

    2017-01-01

    Full Text Available Relevance vector machine (RVM is a machine learning algorithm based on a sparse Bayesian framework, which performs well when running classification and regression tasks on small-scale datasets. However, RVM also has certain drawbacks which restricts its practical applications such as (1 slow training process, (2 poor performance on training large-scale datasets. In order to solve these problem, we propose Discrete AdaBoost RVM (DAB-RVM which incorporate ensemble learning in RVM at first. This method performs well with large-scale low-dimensional datasets. However, as the number of features increases, the training time of DAB-RVM increases as well. To avoid this phenomenon, we utilize the sufficient training samples of large-scale datasets and propose all features boosting RVM (AFB-RVM, which modifies the way of obtaining weak classifiers. In our experiments we study the differences between various boosting techniques with RVM, demonstrating the performance of the proposed approaches on Spark. As a result of this paper, two proposed approaches on Spark for different types of large-scale datasets are available.

  18. Insecticidal potency of RNAi-based catalase knockdown in Rhynchophorus ferrugineus (Oliver) (Coleoptera: Curculionidae).

    Science.gov (United States)

    Al-Ayedh, Hassan; Rizwan-Ul-Haq, Muhammad; Hussain, Abid; Aljabr, Ahmed M

    2016-11-01

    Palm trees around the world are prone to notorious Rhynchophorus ferrugineus, which causes heavy losses of palm plantations. In Middle Eastern countries, this pest is a major threat to date palm orchards. Conventional pest control measures with the major share of synthetic insecticides have resulted in insect resistance and environmental issues. Therefore, in order to explore better alternatives, the RNAi approach was employed to knock down the catalase gene in fifth and tenth larval instars with different dsRNA application methods, and their insecticidal potency was studied. dsRNA of 444 bp was prepared to knock down catalase in R. ferrugineus. Out of the three dsRNA application methods, dsRNA injection into larvae was the most effective, followed by dsRNA application by artificial feeding. Both methods resulted in significant catalase knockdown in various tissues, especially the midgut. As a result, the highest growth inhibition of 123.49 and 103.47% and larval mortality of 80 and 40% were observed in fifth-instar larvae, whereas larval growth inhibition remained at 86.83 and 69.08% with larval mortality at 30 and 10% in tenth-instar larvae after dsRNA injection and artificial diet treatment. The topical application method was the least efficient, with the lowest larval growth inhibition of 57.23 and 45.61% and 0% mortality in fifth- and tenth-instar larvae. Generally, better results were noted at the high dsRNA dose of 5 µL. Catalase enzyme is found in most insect body tissues, and thus its dsRNA can cause broad-scale gene knockdown within the insect body, depending upon the application method. Significant larval mortality and growth inhibition after catalase knockdown in R. ferrugineus confirms its insecticidal potency and suggests a bright future for RNAi-based bioinsecticides in pest control. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  19. Neuronal migration is regulated by endogenous RNAi and chromatin-binding factor ZFP-1/AF10 in Caenorhabditis elegans.

    Science.gov (United States)

    Kennedy, Lisa M; Grishok, Alla

    2014-05-01

    Endogenous short RNAs and the conserved plant homeodomain (PHD) zinc-finger protein ZFP-1/AF10 regulate overlapping sets of genes in Caenorhabditis elegans, which suggests that they control common biological pathways. We have shown recently that the RNAi factor RDE-4 and ZFP-1 negatively modulate transcription of the insulin/PI3 signaling-dependent kinase PDK-1 to promote C. elegans fitness. Moreover, we have demonstrated that the insulin/IGF-1-PI3K-signaling pathway regulates the activity of the DAF-16/FOXO transcription factor in the hypodermis to nonautonomously promote the anterior migrations of the hermaphrodite-specific neurons (HSNs) during embryogenesis of C. elegans. In this study, we implicate the PHD-containing isoform of ZFP-1 and endogenous RNAi in the regulation of HSN migration. ZFP-1 affects HSN migration in part through its negative effect on pdk-1 transcription and modulation of downstream DAF-16 activity. We also identify a novel role for ZFP-1 and RNAi pathway components, including RDE-4, in the regulation of HSN migration in parallel with DAF-16. Therefore, the coordinated activities of DAF-16, ZFP-1, and endogenous RNAi contribute to gene regulation during development to ensure proper neuronal positioning.

  20. Bayesian hierarchical model for large-scale covariance matrix estimation.

    Science.gov (United States)

    Zhu, Dongxiao; Hero, Alfred O

    2007-12-01

    Many bioinformatics problems implicitly depend on estimating large-scale covariance matrix. The traditional approaches tend to give rise to high variance and low accuracy due to "overfitting." We cast the large-scale covariance matrix estimation problem into the Bayesian hierarchical model framework, and introduce dependency between covariance parameters. We demonstrate the advantages of our approaches over the traditional approaches using simulations and OMICS data analysis.

  1. Short-term cytotoxic effects and long-term instability of RNAi delivered using lentiviral vectors

    Directory of Open Access Journals (Sweden)

    Kruithof Egbert KO

    2004-08-01

    Full Text Available Abstract Background RNA interference (RNAi can potently reduce target gene expression in mammalian cells and is in wide use for loss-of-function studies. Several recent reports have demonstrated that short double-stranded RNAs (dsRNAs, used to mediate RNAi, can also induce an interferon-based response resulting in changes in the expression of many interferon-responsive genes. Off-target gene silencing has also been described, bringing into question the validity of certain RNAi-based approaches for studying gene function. We have targeted the plasminogen activator inhibitor-2 (PAI-2 or SERPINB2 mRNA using lentiviral vectors for delivery of U6 promoter-driven PAI-2-targeted short hairpin RNA (shRNA expression. PAI-2 is reported to have anti-apoptotic activity, thus reduction of endogenous expression may be expected to make cells more sensitive to programmed cell death. Results As expected, we encountered a cytotoxic phenotype when targeting the PAI-2 mRNA with vector-derived shRNA. However, this predicted phenotype was a potent non-specific effect of shRNA expression, as functional overexpression of the target protein failed to rescue the phenotype. By decreasing the shRNA length or modifying its sequence we maintained PAI-2 silencing and reduced, but did not eliminate, cytotoxicity. ShRNA of 21 complementary nucleotides (21 mers or more increased expression of the oligoadenylate synthase-1 (OAS1 interferon-responsive gene. 19 mer shRNA had no effect on OAS1 expression but long-term selective pressure on cell growth was observed. By lowering lentiviral vector titre we were able to reduce both expression of shRNA and induction of OAS1, without a major impact on the efficacy of gene silencing. Conclusions Our data demonstrate a rapid cytotoxic effect of shRNAs expressed in human tumor cell lines. There appears to be a cut-off of 21 complementary nucleotides below which there is no interferon response while target gene silencing is maintained

  2. Concurrent Driving Method with Fast Scan Rate for Large Mutual Capacitance Touch Screens

    Directory of Open Access Journals (Sweden)

    Mohamed Gamal Ahmed Mohamed

    2015-01-01

    Full Text Available A novel touch screen control technique is introduced, which scans each frame in two steps of concurrent multichannel driving and differential sensing. The proposed technique substantially increases the scan rate and reduces the ambient noise effectively. It is also extended to a multichip architecture to support excessively large touch screens with great scan rate improvement. The proposed method has been implemented using 0.18 μm CMOS TowerJazz process and tested with FPGA and AFE board connecting a 23-inch touch screen. Experimental results show a scan rate improvement of up to 23.8 times and an SNR improvement of 24.6 dB over the conventional method.

  3. Creating Large Scale Database Servers

    International Nuclear Information System (INIS)

    Becla, Jacek

    2001-01-01

    The BaBar experiment at the Stanford Linear Accelerator Center (SLAC) is designed to perform a high precision investigation of the decays of the B-meson produced from electron-positron interactions. The experiment, started in May 1999, will generate approximately 300TB/year of data for 10 years. All of the data will reside in Objectivity databases accessible via the Advanced Multi-threaded Server (AMS). To date, over 70TB of data have been placed in Objectivity/DB, making it one of the largest databases in the world. Providing access to such a large quantity of data through a database server is a daunting task. A full-scale testbed environment had to be developed to tune various software parameters and a fundamental change had to occur in the AMS architecture to allow it to scale past several hundred terabytes of data. Additionally, several protocol extensions had to be implemented to provide practical access to large quantities of data. This paper will describe the design of the database and the changes that we needed to make in the AMS for scalability reasons and how the lessons we learned would be applicable to virtually any kind of database server seeking to operate in the Petabyte region

  4. Creating Large Scale Database Servers

    Energy Technology Data Exchange (ETDEWEB)

    Becla, Jacek

    2001-12-14

    The BaBar experiment at the Stanford Linear Accelerator Center (SLAC) is designed to perform a high precision investigation of the decays of the B-meson produced from electron-positron interactions. The experiment, started in May 1999, will generate approximately 300TB/year of data for 10 years. All of the data will reside in Objectivity databases accessible via the Advanced Multi-threaded Server (AMS). To date, over 70TB of data have been placed in Objectivity/DB, making it one of the largest databases in the world. Providing access to such a large quantity of data through a database server is a daunting task. A full-scale testbed environment had to be developed to tune various software parameters and a fundamental change had to occur in the AMS architecture to allow it to scale past several hundred terabytes of data. Additionally, several protocol extensions had to be implemented to provide practical access to large quantities of data. This paper will describe the design of the database and the changes that we needed to make in the AMS for scalability reasons and how the lessons we learned would be applicable to virtually any kind of database server seeking to operate in the Petabyte region.

  5. Large-scale pool fires

    Directory of Open Access Journals (Sweden)

    Steinhaus Thomas

    2007-01-01

    Full Text Available A review of research into the burning behavior of large pool fires and fuel spill fires is presented. The features which distinguish such fires from smaller pool fires are mainly associated with the fire dynamics at low source Froude numbers and the radiative interaction with the fire source. In hydrocarbon fires, higher soot levels at increased diameters result in radiation blockage effects around the perimeter of large fire plumes; this yields lower emissive powers and a drastic reduction in the radiative loss fraction; whilst there are simplifying factors with these phenomena, arising from the fact that soot yield can saturate, there are other complications deriving from the intermittency of the behavior, with luminous regions of efficient combustion appearing randomly in the outer surface of the fire according the turbulent fluctuations in the fire plume. Knowledge of the fluid flow instabilities, which lead to the formation of large eddies, is also key to understanding the behavior of large-scale fires. Here modeling tools can be effectively exploited in order to investigate the fluid flow phenomena, including RANS- and LES-based computational fluid dynamics codes. The latter are well-suited to representation of the turbulent motions, but a number of challenges remain with their practical application. Massively-parallel computational resources are likely to be necessary in order to be able to adequately address the complex coupled phenomena to the level of detail that is necessary.

  6. RNAi-derived transgenic resistance to Mungbean yellow mosaic India virus in cowpea.

    Science.gov (United States)

    Kumar, Sanjeev; Tanti, Bhaben; Patil, Basavaprabhu L; Mukherjee, Sunil Kumar; Sahoo, Lingaraj

    2017-01-01

    Cowpea is an important grain legume crop of Africa, Latin America, and Southeast Asia. Leaf curl and golden mosaic diseases caused by Mungbean yellow mosaic India virus (MYMIV) have emerged as most devastating viral diseases of cowpea in Southeast Asia. In this study, we employed RNA interference (RNAi) strategy to control cowpea-infecting MYMIV. For this, we generated transgenic cowpea plants harbouring three different intron hairpin RNAi constructs, containing the AC2, AC4 and fusion of AC2 and AC4 (AC2+AC4) of seven cowpea-infecting begomoviruses. The T0 and T1 transgenic cowpea lines of all the three constructs accumulated transgene-specific siRNAs. Transgenic plants were further assayed up to T1 generations, for resistance to MYMIV using agro-infectious clones. Nearly 100% resistance against MYMIV infection was observed in transgenic lines, expressing AC2-hp and AC2+AC4-hp RNA, when compared with untransformed controls and plants transformed with empty vectors, which developed severe viral disease symptoms within 3 weeks. The AC4-hp RNA expressing lines displayed appearance of milder symptoms after 5 weeks of MYMIV-inoculation. Northern blots revealed a positive correlation between the level of transgene-specific siRNAs accumulation and virus resistance. The MYMIV-resistant transgenic lines accumulated nearly zero or very low titres of viral DNA. The transgenic cowpea plants had normal phenotype with no yield penalty in greenhouse conditions. This is the first demonstration of RNAi-derived resistance to MYMIV in cowpea.

  7. Confirming the RNAi-mediated mechanism of action of siRNA-based cancer therapeutics in mice.

    Science.gov (United States)

    Judge, Adam D; Robbins, Marjorie; Tavakoli, Iran; Levi, Jasna; Hu, Lina; Fronda, Anna; Ambegia, Ellen; McClintock, Kevin; MacLachlan, Ian

    2009-03-01

    siRNAs that specifically silence the expression of cancer-related genes offer a therapeutic approach in oncology. However, it remains critical to determine the true mechanism of their therapeutic effects. Here, we describe the preclinical development of chemically modified siRNA targeting the essential cell-cycle proteins polo-like kinase 1 (PLK1) and kinesin spindle protein (KSP) in mice. siRNA formulated in stable nucleic acid lipid particles (SNALP) displayed potent antitumor efficacy in both hepatic and subcutaneous tumor models. This was correlated with target gene silencing following a single intravenous administration that was sufficient to cause extensive mitotic disruption and tumor cell apoptosis. Our siRNA formulations induced no measurable immune response, minimizing the potential for nonspecific effects. Additionally, RNAi-specific mRNA cleavage products were found in tumor cells, and their presence correlated with the duration of target mRNA silencing. Histological biomarkers confirmed that RNAi-mediated gene silencing effectively inhibited the target's biological activity. This report supports an RNAi-mediated mechanism of action for siRNA antitumor effects, suggesting a new methodology for targeting other key genes in cancer development with siRNA-based therapeutics.

  8. Decentralised stabilising controllers for a class of large-scale linear ...

    Indian Academy of Sciences (India)

    subsystems resulting from a new aggregation-decomposition technique. The method has been illustrated through a numerical example of a large-scale linear system consisting of three subsystems each of the fourth order. Keywords. Decentralised stabilisation; large-scale linear systems; optimal feedback control; algebraic ...

  9. Large Scale Survey Data in Career Development Research

    Science.gov (United States)

    Diemer, Matthew A.

    2008-01-01

    Large scale survey datasets have been underutilized but offer numerous advantages for career development scholars, as they contain numerous career development constructs with large and diverse samples that are followed longitudinally. Constructs such as work salience, vocational expectations, educational expectations, work satisfaction, and…

  10. Maximally efficient two-stage screening: Determining intellectual disability in Taiwanese military conscripts

    Directory of Open Access Journals (Sweden)

    Chia-Chang Chien

    2009-01-01

    Full Text Available Chia-Chang Chien1, Shu-Fen Huang1,2,3,4, For-Wey Lung1,2,3,41Department of Psychiatry, Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan; 2Graduate Institute of Behavioral Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan; 3Department of Psychiatry, National Defense Medical Center, Taipei, Taiwan; 4Calo Psychiatric Center, Pingtung County, TaiwanObjective: The purpose of this study was to apply a two-stage screening method for the large-scale intelligence screening of military conscripts.Methods: We collected 99 conscripted soldiers whose educational levels were senior high school level or lower to be the participants. Every participant was required to take the Wisconsin Card Sorting Test (WCST and the Wechsler Adult Intelligence Scale-Revised (WAIS-R assessments.Results: Logistic regression analysis showed the conceptual level responses (CLR index of the WCST was the most significant index for determining intellectual disability (ID; FIQ ≤ 84. We used the receiver operating characteristic curve to determine the optimum cut-off point of CLR. The optimum one cut-off point of CLR was 66; the two cut-off points were 49 and 66. Comparing the two-stage window screening with the two-stage positive screening, the area under the curve and the positive predictive value increased. Moreover, the cost of the two-stage window screening decreased by 59%.Conclusion: The two-stage window screening is more accurate and economical than the two-stage positive screening. Our results provide an example for the use of two-stage screening and the possibility of the WCST to replace WAIS-R in large-scale screenings for ID in the future.Keywords: intellectual disability, intelligence screening, two-stage positive screening, Wisconsin Card Sorting Test, Wechsler Adult Intelligence Scale-Revised

  11. Similitude and scaling of large structural elements: Case study

    Directory of Open Access Journals (Sweden)

    M. Shehadeh

    2015-06-01

    Full Text Available Scaled down models are widely used for experimental investigations of large structures due to the limitation in the capacities of testing facilities along with the expenses of the experimentation. The modeling accuracy depends upon the model material properties, fabrication accuracy and loading techniques. In the present work the Buckingham π theorem is used to develop the relations (i.e. geometry, loading and properties between the model and a large structural element as that is present in the huge existing petroleum oil drilling rigs. The model is to be designed, loaded and treated according to a set of similitude requirements that relate the model to the large structural element. Three independent scale factors which represent three fundamental dimensions, namely mass, length and time need to be selected for designing the scaled down model. Numerical prediction of the stress distribution within the model and its elastic deformation under steady loading is to be made. The results are compared with those obtained from the full scale structure numerical computations. The effect of scaled down model size and material on the accuracy of the modeling technique is thoroughly examined.

  12. Collaborative Work without Large, Shared Displays: Looking for “the Big Picture” on a Small Screen?

    DEFF Research Database (Denmark)

    Hertzum, Morten

    2017-01-01

    Large, shared displays – such as electronic whiteboards – have proven successful in supporting actors in forming and maintaining an overview of tightly coupled collaborative activities. However, in many developing countries the technology of choice is mobile phones, which have neither a large nor...... a shared screen. It therefore appears relevant to ask: How may mobile devices with small screens support, or fail to support, actors in forming and maintaining an overview of their collaborative activities?...

  13. Interference RNA (RNAi)-based silencing of endogenous thrombopoietin receptor (Mpl) in Dami cells resulted in decreased hNUDC-mediated megakaryocyte proliferation and differentiation

    International Nuclear Information System (INIS)

    Pang, Shi-Feng; Li, Xiao-Kun; Zhang, Qiang; Yang, Fang; Xu, Peilin

    2009-01-01

    Recently our laboratory reported evidence showing that hNUDC acts as an additional cytokine for thrombopoietin receptor (Mpl). Previously known as the human homolog of a fungal nuclear migration protein, hNUDC plays a critical role in megakaryocyte differentiation and maturation. Here we sought to further clarify the hNUDC-Mpl ligand-receptor relationship by utilizing interference RNA (RNAi) to knockdown Mpl expression in a megakaryocyte cell line. We created U6 promoter driven constructs to express short hairpin RNAs (shRNA) with affinity for different sites on Mpl mRNA. By including Mpl-EGFP fusion protein in these constructs, we were able to effectively screen the shRNA that was most efficient in inhibiting Mpl mRNA expression. This shRNA was subsequently transferred into a lentivirus vector and transduced into Dami cells, a cell line which constitutively expresses endogenous Mpl. This lentiviral vector was also designed to simultaneously express EGFP to monitor transfection efficiency. Our results show that lentivirus can be used to effectively deliver shRNAs into Dami cells and cause specific inhibition of Mpl protein expression after transduction. Furthermore, we show the functional effects of shRNA-mediated Mpl silencing by demonstrating reduced hNUDC stimulated megakaryocyte proliferation and differentiation. Thus, the use of a RNAi knockdown strategy has allowed us to pinpoint the connection of hNUDC with Mpl in the regulation of megakaryocyte maturation.

  14. Large-scale preparation of hollow graphitic carbon nanospheres

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Jun; Li, Fu [Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Bai, Yu-Jun, E-mail: byj97@126.com [Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); State Key laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Han, Fu-Dong; Qi, Yong-Xin; Lun, Ning [Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Lu, Xi-Feng [Lunan Institute of Coal Chemical Engineering, Jining 272000 (China)

    2013-01-15

    Hollow graphitic carbon nanospheres (HGCNSs) were synthesized on large scale by a simple reaction between glucose and Mg at 550 Degree-Sign C in an autoclave. Characterization by X-ray diffraction, Raman spectroscopy and transmission electron microscopy demonstrates the formation of HGCNSs with an average diameter of 10 nm or so and a wall thickness of a few graphenes. The HGCNSs exhibit a reversible capacity of 391 mAh g{sup -1} after 60 cycles when used as anode materials for Li-ion batteries. -- Graphical abstract: Hollow graphitic carbon nanospheres could be prepared on large scale by the simple reaction between glucose and Mg at 550 Degree-Sign C, which exhibit superior electrochemical performance to graphite. Highlights: Black-Right-Pointing-Pointer Hollow graphitic carbon nanospheres (HGCNSs) were prepared on large scale at 550 Degree-Sign C Black-Right-Pointing-Pointer The preparation is simple, effective and eco-friendly. Black-Right-Pointing-Pointer The in situ yielded MgO nanocrystals promote the graphitization. Black-Right-Pointing-Pointer The HGCNSs exhibit superior electrochemical performance to graphite.

  15. Large-scale impact cratering on the terrestrial planets

    International Nuclear Information System (INIS)

    Grieve, R.A.F.

    1982-01-01

    The crater densities on the earth and moon form the basis for a standard flux-time curve that can be used in dating unsampled planetary surfaces and constraining the temporal history of endogenic geologic processes. Abundant evidence is seen not only that impact cratering was an important surface process in planetary history but also that large imapact events produced effects that were crucial in scale. By way of example, it is noted that the formation of multiring basins on the early moon was as important in defining the planetary tectonic framework as plate tectonics is on the earth. Evidence from several planets suggests that the effects of very-large-scale impacts go beyond the simple formation of an impact structure and serve to localize increased endogenic activity over an extended period of geologic time. Even though no longer occurring with the frequency and magnitude of early solar system history, it is noted that large scale impact events continue to affect the local geology of the planets. 92 references

  16. Optical interconnect for large-scale systems

    Science.gov (United States)

    Dress, William

    2013-02-01

    This paper presents a switchless, optical interconnect module that serves as a node in a network of identical distribution modules for large-scale systems. Thousands to millions of hosts or endpoints may be interconnected by a network of such modules, avoiding the need for multi-level switches. Several common network topologies are reviewed and their scaling properties assessed. The concept of message-flow routing is discussed in conjunction with the unique properties enabled by the optical distribution module where it is shown how top-down software control (global routing tables, spanning-tree algorithms) may be avoided.

  17. The Nonmydriatic Fundus Camera in Diabetic Retinopathy Screening: A Cost-Effective Study with Evaluation for Future Large-Scale Application

    Directory of Open Access Journals (Sweden)

    Giuseppe Scarpa

    2016-01-01

    Full Text Available Aims. The study aimed to present the experience of a screening programme for early detection of diabetic retinopathy (DR using a nonmydriatic fundus camera, evaluating the feasibility in terms of validity, resources absorption, and future advantages of a potential application, in an Italian local health authority. Methods. Diabetic patients living in the town of Ponzano, Veneto Region (Northern Italy, were invited to be enrolled in the screening programme. The “no prevention strategy” with the inclusion of the estimation of blindness related costs was compared with screening costs in order to evaluate a future extensive and feasible implementation of the procedure, through a budget impact approach. Results. Out of 498 diabetic patients eligible, 80% was enrolled in the screening programme. 115 patients (34% were referred to an ophthalmologist and 9 cases required prompt treatment for either proliferative DR or macular edema. Based on the pilot data, it emerged that an extensive use of the investigated screening programme, within the Greater Treviso area, could prevent 6 cases of blindness every year, resulting in a saving of €271,543.32 (−13.71%. Conclusions. Fundus images obtained with a nonmydriatic fundus camera could be considered an effective, cost-sparing, and feasible screening tool for the early detection of DR, preventing blindness as a result of diabetes.

  18. Attitude stabilization of a spacecraft equipped with large electrostatic protection screens

    Science.gov (United States)

    Nikitin, D. Yu.; Tikhonov, A. A.

    2018-05-01

    A satellite with a system of three electrostatic radiation protection (ERP) screens is under consideration. The screens are constructed as electrostatically charged toroidal shields with characteristic size of order equal to 100 m. The interaction of electric charge with the Earth's magnetic field (EMF) give rise to the Lorentz torque acting upon a satellite attitude motion. As the sizes of ERP system are large, we derive the Lorentz torque taking into account the complex form of ERP screens and gradient of the EMF in the screen volume. It is assumed that the satellite center of charge coincides with the satellite mass center. The EMF is modeled by the straight magnetic dipole. In the paper we investigate the usage of Lorentz torque for passive attitude stabilization for satellite in a circular equatorial orbit. Mathematical model for attitude dynamics of a satellite equipped with ERP interacting with the EMF is derived and first integral of corresponding differential equations is constructed. The straight equilibrium position of the satellite in the orbital frame is found. Sufficient conditions for stability of satellite equilibrium position are constructed with the use of the first integral. The gravity gradient torque is taken into account. The satellite equilibrium stability domain is constructed.

  19. [A large-scale accident in Alpine terrain].

    Science.gov (United States)

    Wildner, M; Paal, P

    2015-02-01

    Due to the geographical conditions, large-scale accidents amounting to mass casualty incidents (MCI) in Alpine terrain regularly present rescue teams with huge challenges. Using an example incident, specific conditions and typical problems associated with such a situation are presented. The first rescue team members to arrive have the elementary tasks of qualified triage and communication to the control room, which is required to dispatch the necessary additional support. Only with a clear "concept", to which all have to adhere, can the subsequent chaos phase be limited. In this respect, a time factor confounded by adverse weather conditions or darkness represents enormous pressure. Additional hazards are frostbite and hypothermia. If priorities can be established in terms of urgency, then treatment and procedure algorithms have proven successful. For evacuation of causalities, a helicopter should be strived for. Due to the low density of hospitals in Alpine regions, it is often necessary to distribute the patients over a wide area. Rescue operations in Alpine terrain have to be performed according to the particular conditions and require rescue teams to have specific knowledge and expertise. The possibility of a large-scale accident should be considered when planning events. With respect to optimization of rescue measures, regular training and exercises are rational, as is the analysis of previous large-scale Alpine accidents.

  20. Hierarchical Cantor set in the large scale structure with torus geometry

    Energy Technology Data Exchange (ETDEWEB)

    Murdzek, R. [Physics Department, ' Al. I. Cuza' University, Blvd. Carol I, Nr. 11, Iassy 700506 (Romania)], E-mail: rmurdzek@yahoo.com

    2008-12-15

    The formation of large scale structures is considered within a model with string on toroidal space-time. Firstly, the space-time geometry is presented. In this geometry, the Universe is represented by a string describing a torus surface. Thereafter, the large scale structure of the Universe is derived from the string oscillations. The results are in agreement with the cellular structure of the large scale distribution and with the theory of a Cantorian space-time.

  1. Large-scale Motion of Solar Filaments

    Indian Academy of Sciences (India)

    tribpo

    Large-scale Motion of Solar Filaments. Pavel Ambrož, Astronomical Institute of the Acad. Sci. of the Czech Republic, CZ-25165. Ondrejov, The Czech Republic. e-mail: pambroz@asu.cas.cz. Alfred Schroll, Kanzelhöehe Solar Observatory of the University of Graz, A-9521 Treffen,. Austria. e-mail: schroll@solobskh.ac.at.

  2. Sensitivity analysis for large-scale problems

    Science.gov (United States)

    Noor, Ahmed K.; Whitworth, Sandra L.

    1987-01-01

    The development of efficient techniques for calculating sensitivity derivatives is studied. The objective is to present a computational procedure for calculating sensitivity derivatives as part of performing structural reanalysis for large-scale problems. The scope is limited to framed type structures. Both linear static analysis and free-vibration eigenvalue problems are considered.

  3. Data-driven process decomposition and robust online distributed modelling for large-scale processes

    Science.gov (United States)

    Shu, Zhang; Lijuan, Li; Lijuan, Yao; Shipin, Yang; Tao, Zou

    2018-02-01

    With the increasing attention of networked control, system decomposition and distributed models show significant importance in the implementation of model-based control strategy. In this paper, a data-driven system decomposition and online distributed subsystem modelling algorithm was proposed for large-scale chemical processes. The key controlled variables are first partitioned by affinity propagation clustering algorithm into several clusters. Each cluster can be regarded as a subsystem. Then the inputs of each subsystem are selected by offline canonical correlation analysis between all process variables and its controlled variables. Process decomposition is then realised after the screening of input and output variables. When the system decomposition is finished, the online subsystem modelling can be carried out by recursively block-wise renewing the samples. The proposed algorithm was applied in the Tennessee Eastman process and the validity was verified.

  4. Topology Optimization of Large Scale Stokes Flow Problems

    DEFF Research Database (Denmark)

    Aage, Niels; Poulsen, Thomas Harpsøe; Gersborg-Hansen, Allan

    2008-01-01

    This note considers topology optimization of large scale 2D and 3D Stokes flow problems using parallel computations. We solve problems with up to 1.125.000 elements in 2D and 128.000 elements in 3D on a shared memory computer consisting of Sun UltraSparc IV CPUs.......This note considers topology optimization of large scale 2D and 3D Stokes flow problems using parallel computations. We solve problems with up to 1.125.000 elements in 2D and 128.000 elements in 3D on a shared memory computer consisting of Sun UltraSparc IV CPUs....

  5. Development of a first-principles code based on the screened KKR method for large super-cells

    International Nuclear Information System (INIS)

    Doi, S; Ogura, M; Akai, H

    2013-01-01

    The procedures of performing first-principles electronic structure calculation using the Korringa-Kohn-Rostoker (KKR) and the screened KKR methods are reviewed with an emphasis put on their numerical efficiency. It is shown that an iterative matrix inversion combined with a suitable preconditioning greatly improves the computational time of screened KKR method. The method is well parallelized and also has an O(N) scaling property

  6. The Cosmology Large Angular Scale Surveyor

    Science.gov (United States)

    Harrington, Kathleen; Marriage, Tobias; Ali, Aamir; Appel, John; Bennett, Charles; Boone, Fletcher; Brewer, Michael; Chan, Manwei; Chuss, David T.; Colazo, Felipe; hide

    2016-01-01

    The Cosmology Large Angular Scale Surveyor (CLASS) is a four telescope array designed to characterize relic primordial gravitational waves from inflation and the optical depth to reionization through a measurement of the polarized cosmic microwave background (CMB) on the largest angular scales. The frequencies of the four CLASS telescopes, one at 38 GHz, two at 93 GHz, and one dichroic system at 145217 GHz, are chosen to avoid spectral regions of high atmospheric emission and span the minimum of the polarized Galactic foregrounds: synchrotron emission at lower frequencies and dust emission at higher frequencies. Low-noise transition edge sensor detectors and a rapid front-end polarization modulator provide a unique combination of high sensitivity, stability, and control of systematics. The CLASS site, at 5200 m in the Chilean Atacama desert, allows for daily mapping of up to 70% of the sky and enables the characterization of CMB polarization at the largest angular scales. Using this combination of a broad frequency range, large sky coverage, control over systematics, and high sensitivity, CLASS will observe the reionization and recombination peaks of the CMB E- and B-mode power spectra. CLASS will make a cosmic variance limited measurement of the optical depth to reionization and will measure or place upper limits on the tensor-to-scalar ratio, r, down to a level of 0.01 (95% C.L.).

  7. Prehospital Acute Stroke Severity Scale to Predict Large Artery Occlusion: Design and Comparison With Other Scales.

    Science.gov (United States)

    Hastrup, Sidsel; Damgaard, Dorte; Johnsen, Søren Paaske; Andersen, Grethe

    2016-07-01

    We designed and validated a simple prehospital stroke scale to identify emergent large vessel occlusion (ELVO) in patients with acute ischemic stroke and compared the scale to other published scales for prediction of ELVO. A national historical test cohort of 3127 patients with information on intracranial vessel status (angiography) before reperfusion therapy was identified. National Institutes of Health Stroke Scale (NIHSS) items with the highest predictive value of occlusion of a large intracranial artery were identified, and the most optimal combination meeting predefined criteria to ensure usefulness in the prehospital phase was determined. The predictive performance of Prehospital Acute Stroke Severity (PASS) scale was compared with other published scales for ELVO. The PASS scale was composed of 3 NIHSS scores: level of consciousness (month/age), gaze palsy/deviation, and arm weakness. In derivation of PASS 2/3 of the test cohort was used and showed accuracy (area under the curve) of 0.76 for detecting large arterial occlusion. Optimal cut point ≥2 abnormal scores showed: sensitivity=0.66 (95% CI, 0.62-0.69), specificity=0.83 (0.81-0.85), and area under the curve=0.74 (0.72-0.76). Validation on 1/3 of the test cohort showed similar performance. Patients with a large artery occlusion on angiography with PASS ≥2 had a median NIHSS score of 17 (interquartile range=6) as opposed to PASS <2 with a median NIHSS score of 6 (interquartile range=5). The PASS scale showed equal performance although more simple when compared with other scales predicting ELVO. The PASS scale is simple and has promising accuracy for prediction of ELVO in the field. © 2016 American Heart Association, Inc.

  8. 1001 Ways to run AutoDock Vina for virtual screening

    NARCIS (Netherlands)

    Jaghoori, Mohammad Mahdi; Bleijlevens, Boris; Olabarriaga, Silvia D.

    2016-01-01

    Large-scale computing technologies have enabled high-throughput virtual screening involving thousands to millions of drug candidates. It is not trivial, however, for biochemical scientists to evaluate the technical alternatives and their implications for running such large experiments. Besides

  9. Proportional incidence and radiological review of large (T2+) breast cancers as surrogate indicators of screening programme performance

    International Nuclear Information System (INIS)

    Ciatto, S.; Bernardi, D.; Pellegrini, M.; Borsato, G.; Peterlongo, P.; Gentilini, M.A.; Caumo, F.; Frigerio, A.; Houssami, N.

    2012-01-01

    Surrogate measures of screening performance [e.g. interval cancer (IC) proportional incidence] allow timely monitoring of sensitivity and quality. This study explored measures using large (T2+) breast cancers as potential indicators of screening performance. The proportional incidence of T2+ cancers (observed/expected cases) in a population-based screening programme (Trento, 2001-2009) was estimated. A parallel review of 'negative' preceding mammograms for screen-detected T2+ and for all ICs, using 'blinded' independent readings and case-mixes (54 T2+, 50 ICs, 170 controls) was also performed. T2+ cancers were observed in 168 screening participants: 48 at first screen, 67 at repeat screening and 53 ICs. The T2+ estimated proportional incidence was 68% (observed/expected = 168/247), corresponding to an estimated 32% reduction in the rate of T2+ cancers in screening participants relative to that expected without screening. Majority review classified 27.8% (15/54) of T2+ and 28% (14/50) of ICs as screening error (P = 0.84), with variable recall rates amongst radiologists (8.8-15.2%). T2+ review could be integrated as part of quality monitoring and potentially prove more feasible than IC review for some screening services. circle Interval breast cancers, assumed as screening failures, are monitored to estimate screening performance circle Large (T2+) cancers at screening may also represent failed prior screening detection circle Analysis of T2+ lesions may be more feasible than assessing interval cancers circle Analysis of T2+ cancers is a potential further measure of screening performance. (orig.)

  10. Proportional incidence and radiological review of large (T2+) breast cancers as surrogate indicators of screening programme performance

    Energy Technology Data Exchange (ETDEWEB)

    Ciatto, S.; Bernardi, D.; Pellegrini, M.; Borsato, G.; Peterlongo, P. [APSS, U.O. Senologia Clinica e Screening Mammografico, Dipartimento di Radiodiagnostica, Trento (Italy); Gentilini, M.A. [APSS, Servizio Osservatorio Epidemiologico, Direzione promozione ed educazione alla salute, Trento (Italy); Caumo, F. [Centro di Prevenzione Senologica, Verona (Italy); Frigerio, A. [CRR, Centro di Riferimento Regionale per lo Screening Mammografico, Torino (Italy); Houssami, N. [University of Sydney, Screening and Test Evaluation Program, School of Public Health, Sydney Medical School, Sydney (Australia)

    2012-06-15

    Surrogate measures of screening performance [e.g. interval cancer (IC) proportional incidence] allow timely monitoring of sensitivity and quality. This study explored measures using large (T2+) breast cancers as potential indicators of screening performance. The proportional incidence of T2+ cancers (observed/expected cases) in a population-based screening programme (Trento, 2001-2009) was estimated. A parallel review of 'negative' preceding mammograms for screen-detected T2+ and for all ICs, using 'blinded' independent readings and case-mixes (54 T2+, 50 ICs, 170 controls) was also performed. T2+ cancers were observed in 168 screening participants: 48 at first screen, 67 at repeat screening and 53 ICs. The T2+ estimated proportional incidence was 68% (observed/expected = 168/247), corresponding to an estimated 32% reduction in the rate of T2+ cancers in screening participants relative to that expected without screening. Majority review classified 27.8% (15/54) of T2+ and 28% (14/50) of ICs as screening error (P = 0.84), with variable recall rates amongst radiologists (8.8-15.2%). T2+ review could be integrated as part of quality monitoring and potentially prove more feasible than IC review for some screening services. circle Interval breast cancers, assumed as screening failures, are monitored to estimate screening performance circle Large (T2+) cancers at screening may also represent failed prior screening detection circle Analysis of T2+ lesions may be more feasible than assessing interval cancers circle Analysis of T2+ cancers is a potential further measure of screening performance. (orig.)

  11. Analysis using large-scale ringing data

    Directory of Open Access Journals (Sweden)

    Baillie, S. R.

    2004-06-01

    Full Text Available Birds are highly mobile organisms and there is increasing evidence that studies at large spatial scales are needed if we are to properly understand their population dynamics. While classical metapopulation models have rarely proved useful for birds, more general metapopulation ideas involving collections of populations interacting within spatially structured landscapes are highly relevant (Harrison, 1994. There is increasing interest in understanding patterns of synchrony, or lack of synchrony, between populations and the environmental and dispersal mechanisms that bring about these patterns (Paradis et al., 2000. To investigate these processes we need to measure abundance, demographic rates and dispersal at large spatial scales, in addition to gathering data on relevant environmental variables. There is an increasing realisation that conservation needs to address rapid declines of common and widespread species (they will not remain so if such trends continue as well as the management of small populations that are at risk of extinction. While the knowledge needed to support the management of small populations can often be obtained from intensive studies in a few restricted areas, conservation of widespread species often requires information on population trends and processes measured at regional, national and continental scales (Baillie, 2001. While management prescriptions for widespread populations may initially be developed from a small number of local studies or experiments, there is an increasing need to understand how such results will scale up when applied across wider areas. There is also a vital role for monitoring at large spatial scales both in identifying such population declines and in assessing population recovery. Gathering data on avian abundance and demography at large spatial scales usually relies on the efforts of large numbers of skilled volunteers. Volunteer studies based on ringing (for example Constant Effort Sites [CES

  12. A Genome-Wide Screen for Dendritically Localized RNAs Identifies Genes Required for Dendrite Morphogenesis

    Directory of Open Access Journals (Sweden)

    Mala Misra

    2016-08-01

    Full Text Available Localizing messenger RNAs at specific subcellular sites is a conserved mechanism for targeting the synthesis of cytoplasmic proteins to distinct subcellular domains, thereby generating the asymmetric protein distributions necessary for cellular and developmental polarity. However, the full range of transcripts that are asymmetrically distributed in specialized cell types, and the significance of their localization, especially in the nervous system, are not known. We used the EP-MS2 method, which combines EP transposon insertion with the MS2/MCP in vivo fluorescent labeling system, to screen for novel localized transcripts in polarized cells, focusing on the highly branched Drosophila class IV dendritic arborization neurons. Of a total of 541 lines screened, we identified 55 EP-MS2 insertions producing transcripts that were enriched in neuronal processes, particularly in dendrites. The 47 genes identified by these insertions encode molecularly diverse proteins, and are enriched for genes that function in neuronal development and physiology. RNAi-mediated knockdown confirmed roles for many of the candidate genes in dendrite morphogenesis. We propose that the transport of mRNAs encoded by these genes into the dendrites allows their expression to be regulated on a local scale during the dynamic developmental processes of dendrite outgrowth, branching, and/or remodeling.

  13. Large screen mimic display design research for advanced main control room in nuclear power plant

    International Nuclear Information System (INIS)

    Zheng Mingguang; Yang Yanhua; Xu Jijun; Zhang Qinshun; Ning Zhonghe

    2002-01-01

    Firstly the evolution of mimic diagrams or displays used in the main control room of nuclear power plant was introduced. The active functions of mimic diagrams were analyzed on the release of operator psychological burden and pressure, the assistance of operator for the information searching, status understanding, manual actuation, correct decision making as well as the safe and reliable operation of the nuclear power plant. The importance and necessity to use the (large screen) mimic diagrams in advanced main control room of nuclear power plant, the design principle, design details and verification measures of large screen mimic display are also described

  14. Fast Simulation of Large-Scale Floods Based on GPU Parallel Computing

    OpenAIRE

    Qiang Liu; Yi Qin; Guodong Li

    2018-01-01

    Computing speed is a significant issue of large-scale flood simulations for real-time response to disaster prevention and mitigation. Even today, most of the large-scale flood simulations are generally run on supercomputers due to the massive amounts of data and computations necessary. In this work, a two-dimensional shallow water model based on an unstructured Godunov-type finite volume scheme was proposed for flood simulation. To realize a fast simulation of large-scale floods on a personal...

  15. Managing Risk and Uncertainty in Large-Scale University Research Projects

    Science.gov (United States)

    Moore, Sharlissa; Shangraw, R. F., Jr.

    2011-01-01

    Both publicly and privately funded research projects managed by universities are growing in size and scope. Complex, large-scale projects (over $50 million) pose new management challenges and risks for universities. This paper explores the relationship between project success and a variety of factors in large-scale university projects. First, we…

  16. Parallel clustering algorithm for large-scale biological data sets.

    Science.gov (United States)

    Wang, Minchao; Zhang, Wu; Ding, Wang; Dai, Dongbo; Zhang, Huiran; Xie, Hao; Chen, Luonan; Guo, Yike; Xie, Jiang

    2014-01-01

    Recent explosion of biological data brings a great challenge for the traditional clustering algorithms. With increasing scale of data sets, much larger memory and longer runtime are required for the cluster identification problems. The affinity propagation algorithm outperforms many other classical clustering algorithms and is widely applied into the biological researches. However, the time and space complexity become a great bottleneck when handling the large-scale data sets. Moreover, the similarity matrix, whose constructing procedure takes long runtime, is required before running the affinity propagation algorithm, since the algorithm clusters data sets based on the similarities between data pairs. Two types of parallel architectures are proposed in this paper to accelerate the similarity matrix constructing procedure and the affinity propagation algorithm. The memory-shared architecture is used to construct the similarity matrix, and the distributed system is taken for the affinity propagation algorithm, because of its large memory size and great computing capacity. An appropriate way of data partition and reduction is designed in our method, in order to minimize the global communication cost among processes. A speedup of 100 is gained with 128 cores. The runtime is reduced from serval hours to a few seconds, which indicates that parallel algorithm is capable of handling large-scale data sets effectively. The parallel affinity propagation also achieves a good performance when clustering large-scale gene data (microarray) and detecting families in large protein superfamilies.

  17. Adaptive visualization for large-scale graph

    International Nuclear Information System (INIS)

    Nakamura, Hiroko; Shinano, Yuji; Ohzahata, Satoshi

    2010-01-01

    We propose an adoptive visualization technique for representing a large-scale hierarchical dataset within limited display space. A hierarchical dataset has nodes and links showing the parent-child relationship between the nodes. These nodes and links are described using graphics primitives. When the number of these primitives is large, it is difficult to recognize the structure of the hierarchical data because many primitives are overlapped within a limited region. To overcome this difficulty, we propose an adaptive visualization technique for hierarchical datasets. The proposed technique selects an appropriate graph style according to the nodal density in each area. (author)

  18. Stabilization Algorithms for Large-Scale Problems

    DEFF Research Database (Denmark)

    Jensen, Toke Koldborg

    2006-01-01

    The focus of the project is on stabilization of large-scale inverse problems where structured models and iterative algorithms are necessary for computing approximate solutions. For this purpose, we study various iterative Krylov methods and their abilities to produce regularized solutions. Some......-curve. This heuristic is implemented as a part of a larger algorithm which is developed in collaboration with G. Rodriguez and P. C. Hansen. Last, but not least, a large part of the project has, in different ways, revolved around the object-oriented Matlab toolbox MOORe Tools developed by PhD Michael Jacobsen. New...

  19. Screening for anxiety, depression, and anxious depression in primary care

    DEFF Research Database (Denmark)

    Goldberg, David P.; Reed, Geoffrey M.; Robles, Rebeca

    2017-01-01

    Background In this field study of WHO's revised classification of mental disorders for primary care settings, the ICD-11 PHC, we tested the usefulness of two five-item screening scales for anxiety and depression to be administered in primary care settings. Methods The study was conducted in primary...... in primary care settings. Conclusions The two five-item screening scales for anxiety and depression provide a practical way for PCPs to evaluate the likelihood of mood and anxiety disorders without paper and pencil measures that are not feasible in many settings. These scales may provide substantially...... care settings in four large middle-income countries. Primary care physicians (PCPs) referred individuals who they suspected might be psychologically distressed to the study. Screening scales as well as a structured diagnostic interview, the revised Clinical Interview Schedule (CIS-R), adapted...

  20. Design study on sodium cooled large-scale reactor

    International Nuclear Information System (INIS)

    Murakami, Tsutomu; Hishida, Masahiko; Kisohara, Naoyuki

    2004-07-01

    In Phase 1 of the 'Feasibility Studies on Commercialized Fast Reactor Cycle Systems (F/S)', an advanced loop type reactor has been selected as a promising concept of sodium-cooled large-scale reactor, which has a possibility to fulfill the design requirements of the F/S. In Phase 2, design improvement for further cost reduction of establishment of the plant concept has been performed. This report summarizes the results of the design study on the sodium-cooled large-scale reactor performed in JFY2003, which is the third year of Phase 2. In the JFY2003 design study, critical subjects related to safety, structural integrity and thermal hydraulics which found in the last fiscal year has been examined and the plant concept has been modified. Furthermore, fundamental specifications of main systems and components have been set and economy has been evaluated. In addition, as the interim evaluation of the candidate concept of the FBR fuel cycle is to be conducted, cost effectiveness and achievability for the development goal were evaluated and the data of the three large-scale reactor candidate concepts were prepared. As a results of this study, the plant concept of the sodium-cooled large-scale reactor has been constructed, which has a prospect to satisfy the economic goal (construction cost: less than 200,000 yens/kWe, etc.) and has a prospect to solve the critical subjects. From now on, reflecting the results of elemental experiments, the preliminary conceptual design of this plant will be preceded toward the selection for narrowing down candidate concepts at the end of Phase 2. (author)

  1. Design study on sodium-cooled large-scale reactor

    International Nuclear Information System (INIS)

    Shimakawa, Yoshio; Nibe, Nobuaki; Hori, Toru

    2002-05-01

    In Phase 1 of the 'Feasibility Study on Commercialized Fast Reactor Cycle Systems (F/S)', an advanced loop type reactor has been selected as a promising concept of sodium-cooled large-scale reactor, which has a possibility to fulfill the design requirements of the F/S. In Phase 2 of the F/S, it is planed to precede a preliminary conceptual design of a sodium-cooled large-scale reactor based on the design of the advanced loop type reactor. Through the design study, it is intended to construct such a plant concept that can show its attraction and competitiveness as a commercialized reactor. This report summarizes the results of the design study on the sodium-cooled large-scale reactor performed in JFY2001, which is the first year of Phase 2. In the JFY2001 design study, a plant concept has been constructed based on the design of the advanced loop type reactor, and fundamental specifications of main systems and components have been set. Furthermore, critical subjects related to safety, structural integrity, thermal hydraulics, operability, maintainability and economy have been examined and evaluated. As a result of this study, the plant concept of the sodium-cooled large-scale reactor has been constructed, which has a prospect to satisfy the economic goal (construction cost: less than 200,000yens/kWe, etc.) and has a prospect to solve the critical subjects. From now on, reflecting the results of elemental experiments, the preliminary conceptual design of this plant will be preceded toward the selection for narrowing down candidate concepts at the end of Phase 2. (author)

  2. Large scale CMB anomalies from thawing cosmic strings

    Energy Technology Data Exchange (ETDEWEB)

    Ringeval, Christophe [Centre for Cosmology, Particle Physics and Phenomenology, Institute of Mathematics and Physics, Louvain University, 2 Chemin du Cyclotron, 1348 Louvain-la-Neuve (Belgium); Yamauchi, Daisuke; Yokoyama, Jun' ichi [Research Center for the Early Universe (RESCEU), Graduate School of Science, The University of Tokyo, Tokyo 113-0033 (Japan); Bouchet, François R., E-mail: christophe.ringeval@uclouvain.be, E-mail: yamauchi@resceu.s.u-tokyo.ac.jp, E-mail: yokoyama@resceu.s.u-tokyo.ac.jp, E-mail: bouchet@iap.fr [Institut d' Astrophysique de Paris, UMR 7095-CNRS, Université Pierre et Marie Curie, 98bis boulevard Arago, 75014 Paris (France)

    2016-02-01

    Cosmic strings formed during inflation are expected to be either diluted over super-Hubble distances, i.e., invisible today, or to have crossed our past light cone very recently. We discuss the latter situation in which a few strings imprint their signature in the Cosmic Microwave Background (CMB) Anisotropies after recombination. Being almost frozen in the Hubble flow, these strings are quasi static and evade almost all of the previously derived constraints on their tension while being able to source large scale anisotropies in the CMB sky. Using a local variance estimator on thousand of numerically simulated Nambu-Goto all sky maps, we compute the expected signal and show that it can mimic a dipole modulation at large angular scales while being negligible at small angles. Interestingly, such a scenario generically produces one cold spot from the thawing of a cosmic string loop. Mixed with anisotropies of inflationary origin, we find that a few strings of tension GU = O(1) × 10{sup −6} match the amplitude of the dipole modulation reported in the Planck satellite measurements and could be at the origin of other large scale anomalies.

  3. Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse.

    Directory of Open Access Journals (Sweden)

    Tia DiTommaso

    2014-10-01

    Full Text Available The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP. A total of 562 different mouse lines were subjected to a variety of tests assessing cutaneous expression, macroscopic clinical disease, histological change, hair follicle cycling, and aberrant marker expression. Cutaneous lesions were associated with mutations in 23 different genes. Many of these were not previously associated with skin disease in the organ (Mysm1, Vangl1, Trpc4ap, Nom1, Sparc, Farp2, and Prkab1, while others were ascribed new cutaneous functions on the basis of the screening approach (Krt76, Lrig1, Myo5a, Nsun2, and Nf1. The integration of these skin specific screening protocols into the Sanger-MGP primary phenotyping pipelines marks the largest reported reverse genetic screen undertaken in any organ and defines approaches to maximise the productivity of future projects of this nature, while flagging genes for further characterisation.

  4. Recent advances in therapeutic recruitment of mammalian RNAi and bacterial CRISPR-Cas DNA interference pathways as emerging antiviral strategies.

    Science.gov (United States)

    Chin, Wei-Xin; Ang, Swee Kim; Chu, Justin Jang Hann

    2017-01-01

    In invertebrate eukaryotes and prokaryotes, respectively, the RNAi and clustered regularly interspaced short palindromic repeats-CRISPR-associated (CRISPR-Cas) pathways are highly specific and efficient RNA and DNA interference systems, and are well characterised as potent antiviral systems. It has become possible to recruit or reconstitute these pathways in mammalian cells, where they can be directed against desired host or viral targets. The RNAi and CRISPR-Cas systems can therefore yield ideal antiviral therapeutics, capable of specific and efficient viral inhibition with minimal off-target effects, but development of such therapeutics can be slow. This review covers recent advances made towards developing RNAi or CRISPR-Cas strategies for clinical use. These studies address the delivery, toxicity or target design issues that typically plague the in vivo or clinical use of these technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Penile Dysmorphic Disorder: Development of a Screening Scale.

    Science.gov (United States)

    Veale, David; Miles, Sarah; Read, Julie; Troglia, Andrea; Carmona, Lina; Fiorito, Chiara; Wells, Hannah; Wylie, Kevan; Muir, Gordon

    2015-11-01

    Penile dysmorphic disorder (PDD) is shorthand for men diagnosed with body dysmorphic disorder, in whom the size or shape of the penis is their main, if not their exclusive, preoccupation causing significant shame or handicap. There are no specific measures for identifying men with PDD compared to men who are anxious about the size of their penis but do not have PDD. Such a measure might be helpful for treatment planning, reducing unrealistic expectations, and measuring outcome after any psychological or physical intervention. Our aim was, therefore, to validate a specific measure, termed the Cosmetic Procedure Screening Scale for PDD (COPS-P). Eighty-one male participants were divided into three groups: a PDD group (n = 21), a small penis anxiety group (n = 37), and a control group (n = 23). All participants completed the COPS-P as well as standardized measures of depression, anxiety, social phobia, body image, quality of life, and erectile function. Penis size was also measured. The final COPS-P was based on nine items. The scale had good internal reliability and significant convergent validity with measures of related constructs. It discriminated between the PDD group, the small penis anxiety group, and the control group. This is the first study to develop a scale able to discriminate between those with PDD and men anxious about their size who did not have PDD. Clinicians and researchers may use the scale as part of an assessment for men presenting with anxiety about penis size and as an audit or outcome measure after any intervention for this population.

  6. Exploiting multi-scale parallelism for large scale numerical modelling of laser wakefield accelerators

    International Nuclear Information System (INIS)

    Fonseca, R A; Vieira, J; Silva, L O; Fiuza, F; Davidson, A; Tsung, F S; Mori, W B

    2013-01-01

    A new generation of laser wakefield accelerators (LWFA), supported by the extreme accelerating fields generated in the interaction of PW-Class lasers and underdense targets, promises the production of high quality electron beams in short distances for multiple applications. Achieving this goal will rely heavily on numerical modelling to further understand the underlying physics and identify optimal regimes, but large scale modelling of these scenarios is computationally heavy and requires the efficient use of state-of-the-art petascale supercomputing systems. We discuss the main difficulties involved in running these simulations and the new developments implemented in the OSIRIS framework to address these issues, ranging from multi-dimensional dynamic load balancing and hybrid distributed/shared memory parallelism to the vectorization of the PIC algorithm. We present the results of the OASCR Joule Metric program on the issue of large scale modelling of LWFA, demonstrating speedups of over 1 order of magnitude on the same hardware. Finally, scalability to over ∼10 6 cores and sustained performance over ∼2 P Flops is demonstrated, opening the way for large scale modelling of LWFA scenarios. (paper)

  7. Balancing modern Power System with large scale of wind power

    DEFF Research Database (Denmark)

    Basit, Abdul; Altin, Müfit; Hansen, Anca Daniela

    2014-01-01

    Power system operators must ensure robust, secure and reliable power system operation even with a large scale integration of wind power. Electricity generated from the intermittent wind in large propor-tion may impact on the control of power system balance and thus deviations in the power system...... frequency in small or islanded power systems or tie line power flows in interconnected power systems. Therefore, the large scale integration of wind power into the power system strongly concerns the secure and stable grid operation. To ensure the stable power system operation, the evolving power system has...... to be analysed with improved analytical tools and techniques. This paper proposes techniques for the active power balance control in future power systems with the large scale wind power integration, where power balancing model provides the hour-ahead dispatch plan with reduced planning horizon and the real time...

  8. Immobilized metal-affinity chromatography protein-recovery screening is predictive of crystallographic structure success

    International Nuclear Information System (INIS)

    Choi, Ryan; Kelley, Angela; Leibly, David; Nakazawa Hewitt, Stephen; Napuli, Alberto; Van Voorhis, Wesley

    2011-01-01

    An overview of the methods used for high-throughput cloning and protein-expression screening of SSGCID hexahistidine recombinant proteins is provided. It is demonstrated that screening for recombinant proteins that are highly recoverable from immobilized metal-affinity chromatography improves the likelihood that a protein will produce a structure. The recombinant expression of soluble proteins in Escherichia coli continues to be a major bottleneck in structural genomics. The establishment of reliable protocols for the performance of small-scale expression and solubility testing is an essential component of structural genomic pipelines. The SSGCID Protein Production Group at the University of Washington (UW-PPG) has developed a high-throughput screening (HTS) protocol for the measurement of protein recovery from immobilized metal-affinity chromatography (IMAC) which predicts successful purification of hexahistidine-tagged proteins. The protocol is based on manual transfer of samples using multichannel pipettors and 96-well plates and does not depend on the use of robotic platforms. This protocol has been applied to evaluate the expression and solubility of more than 4000 proteins expressed in E. coli. The UW-PPG also screens large-scale preparations for recovery from IMAC prior to purification. Analysis of these results show that our low-cost non-automated approach is a reliable method for the HTS demands typical of large structural genomic projects. This paper provides a detailed description of these protocols and statistical analysis of the SSGCID screening results. The results demonstrate that screening for proteins that yield high recovery after IMAC, both after small-scale and large-scale expression, improves the selection of proteins that can be successfully purified and will yield a crystal structure

  9. Large-Scale Graph Processing Using Apache Giraph

    KAUST Repository

    Sakr, Sherif

    2017-01-07

    This book takes its reader on a journey through Apache Giraph, a popular distributed graph processing platform designed to bring the power of big data processing to graph data. Designed as a step-by-step self-study guide for everyone interested in large-scale graph processing, it describes the fundamental abstractions of the system, its programming models and various techniques for using the system to process graph data at scale, including the implementation of several popular and advanced graph analytics algorithms.

  10. Large-Scale Graph Processing Using Apache Giraph

    KAUST Repository

    Sakr, Sherif; Orakzai, Faisal Moeen; Abdelaziz, Ibrahim; Khayyat, Zuhair

    2017-01-01

    This book takes its reader on a journey through Apache Giraph, a popular distributed graph processing platform designed to bring the power of big data processing to graph data. Designed as a step-by-step self-study guide for everyone interested in large-scale graph processing, it describes the fundamental abstractions of the system, its programming models and various techniques for using the system to process graph data at scale, including the implementation of several popular and advanced graph analytics algorithms.

  11. An interactive display system for large-scale 3D models

    Science.gov (United States)

    Liu, Zijian; Sun, Kun; Tao, Wenbing; Liu, Liman

    2018-04-01

    With the improvement of 3D reconstruction theory and the rapid development of computer hardware technology, the reconstructed 3D models are enlarging in scale and increasing in complexity. Models with tens of thousands of 3D points or triangular meshes are common in practical applications. Due to storage and computing power limitation, it is difficult to achieve real-time display and interaction with large scale 3D models for some common 3D display software, such as MeshLab. In this paper, we propose a display system for large-scale 3D scene models. We construct the LOD (Levels of Detail) model of the reconstructed 3D scene in advance, and then use an out-of-core view-dependent multi-resolution rendering scheme to realize the real-time display of the large-scale 3D model. With the proposed method, our display system is able to render in real time while roaming in the reconstructed scene and 3D camera poses can also be displayed. Furthermore, the memory consumption can be significantly decreased via internal and external memory exchange mechanism, so that it is possible to display a large scale reconstructed scene with over millions of 3D points or triangular meshes in a regular PC with only 4GB RAM.

  12. Large-scale hydrology in Europe : observed patterns and model performance

    Energy Technology Data Exchange (ETDEWEB)

    Gudmundsson, Lukas

    2011-06-15

    In a changing climate, terrestrial water storages are of great interest as water availability impacts key aspects of ecosystem functioning. Thus, a better understanding of the variations of wet and dry periods will contribute to fully grasp processes of the earth system such as nutrient cycling and vegetation dynamics. Currently, river runoff from small, nearly natural, catchments is one of the few variables of the terrestrial water balance that is regularly monitored with detailed spatial and temporal coverage on large scales. River runoff, therefore, provides a foundation to approach European hydrology with respect to observed patterns on large scales, with regard to the ability of models to capture these.The analysis of observed river flow from small catchments, focused on the identification and description of spatial patterns of simultaneous temporal variations of runoff. These are dominated by large-scale variations of climatic variables but also altered by catchment processes. It was shown that time series of annual low, mean and high flows follow the same atmospheric drivers. The observation that high flows are more closely coupled to large scale atmospheric drivers than low flows, indicates the increasing influence of catchment properties on runoff under dry conditions. Further, it was shown that the low-frequency variability of European runoff is dominated by two opposing centres of simultaneous variations, such that dry years in the north are accompanied by wet years in the south.Large-scale hydrological models are simplified representations of our current perception of the terrestrial water balance on large scales. Quantification of the models strengths and weaknesses is the prerequisite for a reliable interpretation of simulation results. Model evaluations may also enable to detect shortcomings with model assumptions and thus enable a refinement of the current perception of hydrological systems. The ability of a multi model ensemble of nine large-scale

  13. Detection of large scale 3' deletions in the PMS2 gene amongst Colon-CFR participants: have we been missing anything?

    Science.gov (United States)

    Clendenning, Mark; Walsh, Michael D; Gelpi, Judith Balmana; Thibodeau, Stephen N; Lindor, Noralane; Potter, John D; Newcomb, Polly; LeMarchand, Loic; Haile, Robert; Gallinger, Steve; Hopper, John L; Jenkins, Mark A; Rosty, Christophe; Young, Joanne P; Buchanan, Daniel D

    2013-09-01

    Current screening practices have been able to identify PMS2 mutations in 78 % of cases of colorectal cancer from the Colorectal Cancer Family Registry (Colon CFR) which showed solitary loss of the PMS2 protein. However the detection of large-scale deletions in the 3' end of the PMS2 gene has not been possible due to technical difficulties associated with pseudogene sequences. Here, we utilised a recently described MLPA/long-range PCR-based approach to screen the remaining 22 % (n = 16) of CRC-affected probands for mutations in the 3' end of the PMS2 gene. No deletions encompassing any or all of exons 12 through 15 were identified; therefore, our results suggest that 3' deletions in PMS2 are not a frequent occurrence in such families.

  14. Large-scale perturbations from the waterfall field in hybrid inflation

    International Nuclear Information System (INIS)

    Fonseca, José; Wands, David; Sasaki, Misao

    2010-01-01

    We estimate large-scale curvature perturbations from isocurvature fluctuations in the waterfall field during hybrid inflation, in addition to the usual inflaton field perturbations. The tachyonic instability at the end of inflation leads to an explosive growth of super-Hubble scale perturbations, but they retain the steep blue spectrum characteristic of vacuum fluctuations in a massive field during inflation. The power spectrum thus peaks around the Hubble-horizon scale at the end of inflation. We extend the usual δN formalism to include the essential role of these small fluctuations when estimating the large-scale curvature perturbation. The resulting curvature perturbation due to fluctuations in the waterfall field is second-order and the spectrum is expected to be of order 10 −54 on cosmological scales

  15. In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4.

    Science.gov (United States)

    Habig, Jeffrey W; Aruscavage, P Joseph; Bass, Brenda L

    2008-01-01

    C. elegans Dicer requires an accessory double-stranded RNA binding protein, RDE-4, to enact the first step of RNA interference, the cleavage of dsRNA to produce siRNA. While RDE-4 is typically essential for RNAi, we report that in the presence of high concentrations of trigger dsRNA, rde-4 deficient animals are capable of silencing a transgene. By multiple criteria the silencing occurs by the canonical RNAi pathway. For example, silencing is RDE-1 dependent and exhibits a decrease in the targeted mRNA in response to an increase in siRNA. We also find that high concentrations of dsRNA trigger lead to increased accumulation of primary siRNAs, consistent with the existence of a rate-limiting step during the conversion of primary to secondary siRNAs. Our studies also revealed that transgene silencing occurs at low levels in the soma, even in the presence of ADARs, and that at least some siRNAs accumulate in a temperature-dependent manner. We conclude that an RNAi response varies with different conditions, and this may allow an organism to tailor a response to specific environmental signals.

  16. Autoantigen La promotes efficient RNAi, antiviral response, and transposon silencing by facilitating multiple-turnover RISC catalysis.

    Science.gov (United States)

    Liu, Ying; Tan, Huiling; Tian, Hui; Liang, Chunyang; Chen, She; Liu, Qinghua

    2011-11-04

    The effector of RNA interference (RNAi) is the RNA-induced silencing complex (RISC). C3PO promotes the activation of RISC by degrading the Argonaute2 (Ago2)-nicked passenger strand of duplex siRNA. Active RISC is a multiple-turnover enzyme that uses the guide strand of siRNA to direct the Ago2-mediated sequence-specific cleavage of complementary mRNA. How this effector step of RNAi is regulated is currently unknown. Here, we used the human Ago2 minimal RISC system to purify Sjögren's syndrome antigen B (SSB)/autoantigen La as an activator of the RISC-mediated mRNA cleavage activity. Our reconstitution studies showed that La could promote multiple-turnover RISC catalysis by facilitating the release of cleaved mRNA from RISC. Moreover, we demonstrated that La was required for efficient RNAi, antiviral defense, and transposon silencing in vivo. Taken together, the findings of C3PO and La reveal a general concept that regulatory factors are required to remove Ago2-cleaved products to assemble or restore active RISC. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. RNAi trigger fragment truncation attenuates soybean FAD2-1 transcript suppression and yields intermediate oil phenotypes.

    Science.gov (United States)

    Wagner, Nicholas; Mroczka, Andrew; Roberts, Peter D; Schreckengost, William; Voelker, Toni

    2011-09-01

    Suppression of the microsomal ω6 oleate desaturase during the seed development of soybean (Glycine max) with the 420-bp soybean FAD2-1A intron as RNAi trigger shifts the conventional fatty acid composition of soybean oil from 20% oleic and 60% polyunsaturates to one containing greater than 80% oleic acid and less than 10% polyunsaturates. To determine whether RNAi could be attenuated by reducing the trigger fragment length, transgenic plants were generated to express successively shorter 5' or 3' deletion derivatives of the FAD2-1A intron. We observed a gradual reduction in transcript suppression with shorter trigger fragments. Fatty acid composition was less affected with shorter triggers, and triggers less than 60 bp had no phenotypic effect. No trigger sequences conferring significantly higher or lower suppression efficiencies were found, and the primary determinant of suppression effect was sequence length. The observed relationship of transcript suppression with the induced fatty acid phenotype indicates that RNAi is a saturation process and not a step change between suppressed and nonsuppressed states and intermediate suppression states can be achieved. © 2010 Monsanto. Plant Biotechnology Journal © 2010 Society for Experimental Biology and Blackwell Publishing Ltd.

  18. In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4.

    Directory of Open Access Journals (Sweden)

    Jeffrey W Habig

    Full Text Available C. elegans Dicer requires an accessory double-stranded RNA binding protein, RDE-4, to enact the first step of RNA interference, the cleavage of dsRNA to produce siRNA. While RDE-4 is typically essential for RNAi, we report that in the presence of high concentrations of trigger dsRNA, rde-4 deficient animals are capable of silencing a transgene. By multiple criteria the silencing occurs by the canonical RNAi pathway. For example, silencing is RDE-1 dependent and exhibits a decrease in the targeted mRNA in response to an increase in siRNA. We also find that high concentrations of dsRNA trigger lead to increased accumulation of primary siRNAs, consistent with the existence of a rate-limiting step during the conversion of primary to secondary siRNAs. Our studies also revealed that transgene silencing occurs at low levels in the soma, even in the presence of ADARs, and that at least some siRNAs accumulate in a temperature-dependent manner. We conclude that an RNAi response varies with different conditions, and this may allow an organism to tailor a response to specific environmental signals.

  19. Decoupling local mechanics from large-scale structure in modular metamaterials

    Science.gov (United States)

    Yang, Nan; Silverberg, Jesse L.

    2017-04-01

    A defining feature of mechanical metamaterials is that their properties are determined by the organization of internal structure instead of the raw fabrication materials. This shift of attention to engineering internal degrees of freedom has coaxed relatively simple materials into exhibiting a wide range of remarkable mechanical properties. For practical applications to be realized, however, this nascent understanding of metamaterial design must be translated into a capacity for engineering large-scale structures with prescribed mechanical functionality. Thus, the challenge is to systematically map desired functionality of large-scale structures backward into a design scheme while using finite parameter domains. Such “inverse design” is often complicated by the deep coupling between large-scale structure and local mechanical function, which limits the available design space. Here, we introduce a design strategy for constructing 1D, 2D, and 3D mechanical metamaterials inspired by modular origami and kirigami. Our approach is to assemble a number of modules into a voxelized large-scale structure, where the module’s design has a greater number of mechanical design parameters than the number of constraints imposed by bulk assembly. This inequality allows each voxel in the bulk structure to be uniquely assigned mechanical properties independent from its ability to connect and deform with its neighbors. In studying specific examples of large-scale metamaterial structures we show that a decoupling of global structure from local mechanical function allows for a variety of mechanically and topologically complex designs.

  20. Calcium/calmodulin kinase1 and its relation to thermotolerance and HSP90 in Sporothrix schenckii: an RNAi and yeast two-hybrid study

    Directory of Open Access Journals (Sweden)

    Gonzalez-Mendez Ricardo

    2011-07-01

    Full Text Available Abstract Background Sporothrix schenckii is a pathogenic dimorphic fungus of worldwide distribution. It grows in the saprophytic form with hyaline, regularly septated hyphae and pyriform conidia at 25°C and as the yeast or parasitic form at 35°C. Previously, we characterized a calcium/calmodulin kinase in this fungus. Inhibitors of this kinase were observed to inhibit the yeast cell cycle in S. schenckii. Results The presence of RNA interference (RNAi mechanism in this fungus was confirmed by the identification of a Dicer-1 homologue in S. schenckii DNA. RNAi technology was used to corroborate the role of calcium/calmodulin kinase I in S. schenckii dimorphism. Yeast cells were transformed with the pSilent-Dual2G (pSD2G plasmid w/wo inserts of the coding region of the calcium/calmodulin kinase I (sscmk1 gene. Transformants were selected at 35°C using resistance to geneticin. Following transfer to liquid medium at 35°C, RNAi transformants developed as abnormal mycelium clumps and not as yeast cells as would be expected. The level of sscmk1 gene expression in RNAi transformants at 35°C was less than that of cells transformed with the empty pSD2G at this same temperature. Yeast two-hybrid analysis of proteins that interact with SSCMK1 identified a homologue of heat shock protein 90 (HSP90 as interacting with this kinase. Growth of the fungus similar to that of the RNAi transformants was observed in medium with geldanamycin (GdA, 10 μM, an inhibitor of HSP90. Conclusions Using the RNAi technology we silenced the expression of sscmk1 gene in this fungus. RNAi transformants were unable to grow as yeast cells at 35°C showing decreased tolerance to this temperature. The interaction of SSCMK1 with HSP90, observed using the yeast two-hybrid assay suggests that this kinase is involved in thermotolerance through its interaction with HSP90. SSCMK1 interacted with the C terminal domain of HSP90 where effector proteins and co-chaperones interact. These

  1. The origin of large scale cosmic structure

    International Nuclear Information System (INIS)

    Jones, B.J.T.; Palmer, P.L.

    1985-01-01

    The paper concerns the origin of large scale cosmic structure. The evolution of density perturbations, the nonlinear regime (Zel'dovich's solution and others), the Gott and Rees clustering hierarchy, the spectrum of condensations, and biassed galaxy formation, are all discussed. (UK)

  2. A practical process for light-water detritiation at large scales

    Energy Technology Data Exchange (ETDEWEB)

    Boniface, H.A. [Atomic Energy of Canada Limited, Chalk River, ON (Canada); Robinson, J., E-mail: jr@tyne-engineering.com [Tyne Engineering, Burlington, ON (Canada); Gnanapragasam, N.V.; Castillo, I.; Suppiah, S. [Atomic Energy of Canada Limited, Chalk River, ON (Canada)

    2014-07-01

    AECL and Tyne Engineering have recently completed a preliminary engineering design for a modest-scale tritium removal plant for light water, intended for installation at AECL's Chalk River Laboratories (CRL). This plant design was based on the Combined Electrolysis and Catalytic Exchange (CECE) technology developed at CRL over many years and demonstrated there and elsewhere. The general features and capabilities of this design have been reported as well as the versatility of the design for separating any pair of the three hydrogen isotopes. The same CECE technology could be applied directly to very large-scale wastewater detritiation, such as the case at Fukushima Daiichi Nuclear Power Station. However, since the CECE process scales linearly with throughput, the required capital and operating costs are substantial for such large-scale applications. This paper discusses some options for reducing the costs of very large-scale detritiation. Options include: Reducing tritium removal effectiveness; Energy recovery; Improving the tolerance of impurities; Use of less expensive or more efficient equipment. A brief comparison with alternative processes is also presented. (author)

  3. OffshoreDC DC grids for integration of large scale wind power

    DEFF Research Database (Denmark)

    Zeni, Lorenzo; Endegnanew, Atsede Gualu; Stamatiou, Georgios

    The present report summarizes the main findings of the Nordic Energy Research project “DC grids for large scale integration of offshore wind power – OffshoreDC”. The project is been funded by Nordic Energy Research through the TFI programme and was active between 2011 and 2016. The overall...... objective of the project was to drive the development of the VSC based HVDC technology for future large scale offshore grids, supporting a standardised and commercial development of the technology, and improving the opportunities for the technology to support power system integration of large scale offshore...

  4. Low-Complexity Transmit Antenna Selection and Beamforming for Large-Scale MIMO Communications

    Directory of Open Access Journals (Sweden)

    Kun Qian

    2014-01-01

    Full Text Available Transmit antenna selection plays an important role in large-scale multiple-input multiple-output (MIMO communications, but optimal large-scale MIMO antenna selection is a technical challenge. Exhaustive search is often employed in antenna selection, but it cannot be efficiently implemented in large-scale MIMO communication systems due to its prohibitive high computation complexity. This paper proposes a low-complexity interactive multiple-parameter optimization method for joint transmit antenna selection and beamforming in large-scale MIMO communication systems. The objective is to jointly maximize the channel outrage capacity and signal-to-noise (SNR performance and minimize the mean square error in transmit antenna selection and minimum variance distortionless response (MVDR beamforming without exhaustive search. The effectiveness of all the proposed methods is verified by extensive simulation results. It is shown that the required antenna selection processing time of the proposed method does not increase along with the increase of selected antennas, but the computation complexity of conventional exhaustive search method will significantly increase when large-scale antennas are employed in the system. This is particularly useful in antenna selection for large-scale MIMO communication systems.

  5. Large-scale exploration and analysis of drug combinations.

    Science.gov (United States)

    Li, Peng; Huang, Chao; Fu, Yingxue; Wang, Jinan; Wu, Ziyin; Ru, Jinlong; Zheng, Chunli; Guo, Zihu; Chen, Xuetong; Zhou, Wei; Zhang, Wenjuan; Li, Yan; Chen, Jianxin; Lu, Aiping; Wang, Yonghua

    2015-06-15

    Drug combinations are a promising strategy for combating complex diseases by improving the efficacy and reducing corresponding side effects. Currently, a widely studied problem in pharmacology is to predict effective drug combinations, either through empirically screening in clinic or pure experimental trials. However, the large-scale prediction of drug combination by a systems method is rarely considered. We report a systems pharmacology framework to predict drug combinations (PreDCs) on a computational model, termed probability ensemble approach (PEA), for analysis of both the efficacy and adverse effects of drug combinations. First, a Bayesian network integrating with a similarity algorithm is developed to model the combinations from drug molecular and pharmacological phenotypes, and the predictions are then assessed with both clinical efficacy and adverse effects. It is illustrated that PEA can predict the combination efficacy of drugs spanning different therapeutic classes with high specificity and sensitivity (AUC = 0.90), which was further validated by independent data or new experimental assays. PEA also evaluates the adverse effects (AUC = 0.95) quantitatively and detects the therapeutic indications for drug combinations. Finally, the PreDC database includes 1571 known and 3269 predicted optimal combinations as well as their potential side effects and therapeutic indications. The PreDC database is available at http://sm.nwsuaf.edu.cn/lsp/predc.php. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. The effective field theory of cosmological large scale structures

    Energy Technology Data Exchange (ETDEWEB)

    Carrasco, John Joseph M. [Stanford Univ., Stanford, CA (United States); Hertzberg, Mark P. [Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States); Senatore, Leonardo [Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2012-09-20

    Large scale structure surveys will likely become the next leading cosmological probe. In our universe, matter perturbations are large on short distances and small at long scales, i.e. strongly coupled in the UV and weakly coupled in the IR. To make precise analytical predictions on large scales, we develop an effective field theory formulated in terms of an IR effective fluid characterized by several parameters, such as speed of sound and viscosity. These parameters, determined by the UV physics described by the Boltzmann equation, are measured from N-body simulations. We find that the speed of sound of the effective fluid is c2s ≈ 10–6c2 and that the viscosity contributions are of the same order. The fluid describes all the relevant physics at long scales k and permits a manifestly convergent perturbative expansion in the size of the matter perturbations δ(k) for all the observables. As an example, we calculate the correction to the power spectrum at order δ(k)4. As a result, the predictions of the effective field theory are found to be in much better agreement with observation than standard cosmological perturbation theory, already reaching percent precision at this order up to a relatively short scale k ≃ 0.24h Mpc–1.

  7. Temporal flexibility and careers: The role of large-scale organizations for physicians

    OpenAIRE

    Forrest Briscoe

    2006-01-01

    Temporal flexibility and careers: The role of large-scale organizations for physicians. Forrest Briscoe Briscoe This study investigates how employment in large-scale organizations affects the work lives of practicing physicians. Well-established theory associates larger organizations with bureaucratic constraint, loss of workplace control, and dissatisfaction, but this author finds that large scale is also associated with greater schedule and career flexibility. Ironically, the bureaucratic p...

  8. The role of large scale motions on passive scalar transport

    Science.gov (United States)

    Dharmarathne, Suranga; Araya, Guillermo; Tutkun, Murat; Leonardi, Stefano; Castillo, Luciano

    2014-11-01

    We study direct numerical simulation (DNS) of turbulent channel flow at Reτ = 394 to investigate effect of large scale motions on fluctuating temperature field which forms a passive scalar field. Statistical description of the large scale features of the turbulent channel flow is obtained using two-point correlations of velocity components. Two-point correlations of fluctuating temperature field is also examined in order to identify possible similarities between velocity and temperature fields. The two-point cross-correlations betwen the velocity and temperature fluctuations are further analyzed to establish connections between these two fields. In addition, we use proper orhtogonal decompotion (POD) to extract most dominant modes of the fields and discuss the coupling of large scale features of turbulence and the temperature field.

  9. Signatures of non-universal large scales in conditional structure functions from various turbulent flows

    International Nuclear Information System (INIS)

    Blum, Daniel B; Voth, Greg A; Bewley, Gregory P; Bodenschatz, Eberhard; Gibert, Mathieu; Xu Haitao; Gylfason, Ármann; Mydlarski, Laurent; Yeung, P K

    2011-01-01

    We present a systematic comparison of conditional structure functions in nine turbulent flows. The flows studied include forced isotropic turbulence simulated on a periodic domain, passive grid wind tunnel turbulence in air and in pressurized SF 6 , active grid wind tunnel turbulence (in both synchronous and random driving modes), the flow between counter-rotating discs, oscillating grid turbulence and the flow in the Lagrangian exploration module (in both constant and random driving modes). We compare longitudinal Eulerian second-order structure functions conditioned on the instantaneous large-scale velocity in each flow to assess the ways in which the large scales affect the small scales in a variety of turbulent flows. Structure functions are shown to have larger values when the large-scale velocity significantly deviates from the mean in most flows, suggesting that dependence on the large scales is typical in many turbulent flows. The effects of the large-scale velocity on the structure functions can be quite strong, with the structure function varying by up to a factor of 2 when the large-scale velocity deviates from the mean by ±2 standard deviations. In several flows, the effects of the large-scale velocity are similar at all the length scales we measured, indicating that the large-scale effects are scale independent. In a few flows, the effects of the large-scale velocity are larger on the smallest length scales. (paper)

  10. Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers.

    Science.gov (United States)

    Deng, Xiang; Zhironkina, Oxana A; Cherepanynets, Varvara D; Strelkova, Olga S; Kireev, Igor I; Belmont, Andrew S

    2016-09-26

    In higher eukaryotic interphase nuclei, the 100- to >1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significant changes in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change in the overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Evaluation of drought propagation in an ensemble mean of large-scale hydrological models

    NARCIS (Netherlands)

    Loon, van A.F.; Huijgevoort, van M.H.J.; Lanen, van H.A.J.

    2012-01-01

    Hydrological drought is increasingly studied using large-scale models. It is, however, not sure whether large-scale models reproduce the development of hydrological drought correctly. The pressing question is how well do large-scale models simulate the propagation from meteorological to hydrological

  12. Configuration management in large scale infrastructure development

    NARCIS (Netherlands)

    Rijn, T.P.J. van; Belt, H. van de; Los, R.H.

    2000-01-01

    Large Scale Infrastructure (LSI) development projects such as the construction of roads, rail-ways and other civil engineering (water)works is tendered differently today than a decade ago. Traditional workflow requested quotes from construction companies for construction works where the works to be

  13. Dual Decomposition for Large-Scale Power Balancing

    DEFF Research Database (Denmark)

    Halvgaard, Rasmus; Jørgensen, John Bagterp; Vandenberghe, Lieven

    2013-01-01

    Dual decomposition is applied to power balancing of exible thermal storage units. The centralized large-scale problem is decomposed into smaller subproblems and solved locallyby each unit in the Smart Grid. Convergence is achieved by coordinating the units consumption through a negotiation...

  14. Generation of large-scale vortives in compressible helical turbulence

    International Nuclear Information System (INIS)

    Chkhetiani, O.G.; Gvaramadze, V.V.

    1989-01-01

    We consider generation of large-scale vortices in compressible self-gravitating turbulent medium. The closed equation describing evolution of the large-scale vortices in helical turbulence with finite correlation time is obtained. This equation has the form similar to the hydromagnetic dynamo equation, which allows us to call the vortx genertation effect the vortex dynamo. It is possible that principally the same mechanism is responsible both for amplification and maintenance of density waves and magnetic fields in gaseous disks of spiral galaxies. (author). 29 refs

  15. Dipolar modulation of Large-Scale Structure

    Science.gov (United States)

    Yoon, Mijin

    For the last two decades, we have seen a drastic development of modern cosmology based on various observations such as the cosmic microwave background (CMB), type Ia supernovae, and baryonic acoustic oscillations (BAO). These observational evidences have led us to a great deal of consensus on the cosmological model so-called LambdaCDM and tight constraints on cosmological parameters consisting the model. On the other hand, the advancement in cosmology relies on the cosmological principle: the universe is isotropic and homogeneous on large scales. Testing these fundamental assumptions is crucial and will soon become possible given the planned observations ahead. Dipolar modulation is the largest angular anisotropy of the sky, which is quantified by its direction and amplitude. We measured a huge dipolar modulation in CMB, which mainly originated from our solar system's motion relative to CMB rest frame. However, we have not yet acquired consistent measurements of dipolar modulations in large-scale structure (LSS), as they require large sky coverage and a number of well-identified objects. In this thesis, we explore measurement of dipolar modulation in number counts of LSS objects as a test of statistical isotropy. This thesis is based on two papers that were published in peer-reviewed journals. In Chapter 2 [Yoon et al., 2014], we measured a dipolar modulation in number counts of WISE matched with 2MASS sources. In Chapter 3 [Yoon & Huterer, 2015], we investigated requirements for detection of kinematic dipole in future surveys.

  16. Impact of large-scale tides on cosmological distortions via redshift-space power spectrum

    Science.gov (United States)

    Akitsu, Kazuyuki; Takada, Masahiro

    2018-03-01

    Although large-scale perturbations beyond a finite-volume survey region are not direct observables, these affect measurements of clustering statistics of small-scale (subsurvey) perturbations in large-scale structure, compared with the ensemble average, via the mode-coupling effect. In this paper we show that a large-scale tide induced by scalar perturbations causes apparent anisotropic distortions in the redshift-space power spectrum of galaxies in a way depending on an alignment between the tide, wave vector of small-scale modes and line-of-sight direction. Using the perturbation theory of structure formation, we derive a response function of the redshift-space power spectrum to large-scale tide. We then investigate the impact of large-scale tide on estimation of cosmological distances and the redshift-space distortion parameter via the measured redshift-space power spectrum for a hypothetical large-volume survey, based on the Fisher matrix formalism. To do this, we treat the large-scale tide as a signal, rather than an additional source of the statistical errors, and show that a degradation in the parameter is restored if we can employ the prior on the rms amplitude expected for the standard cold dark matter (CDM) model. We also discuss whether the large-scale tide can be constrained at an accuracy better than the CDM prediction, if the effects up to a larger wave number in the nonlinear regime can be included.

  17. Large-scale Intelligent Transporation Systems simulation

    Energy Technology Data Exchange (ETDEWEB)

    Ewing, T.; Canfield, T.; Hannebutte, U.; Levine, D.; Tentner, A.

    1995-06-01

    A prototype computer system has been developed which defines a high-level architecture for a large-scale, comprehensive, scalable simulation of an Intelligent Transportation System (ITS) capable of running on massively parallel computers and distributed (networked) computer systems. The prototype includes the modelling of instrumented ``smart`` vehicles with in-vehicle navigation units capable of optimal route planning and Traffic Management Centers (TMC). The TMC has probe vehicle tracking capabilities (display position and attributes of instrumented vehicles), and can provide 2-way interaction with traffic to provide advisories and link times. Both the in-vehicle navigation module and the TMC feature detailed graphical user interfaces to support human-factors studies. The prototype has been developed on a distributed system of networked UNIX computers but is designed to run on ANL`s IBM SP-X parallel computer system for large scale problems. A novel feature of our design is that vehicles will be represented by autonomus computer processes, each with a behavior model which performs independent route selection and reacts to external traffic events much like real vehicles. With this approach, one will be able to take advantage of emerging massively parallel processor (MPP) systems.

  18. The Hamburg large scale geostrophic ocean general circulation model. Cycle 1

    International Nuclear Information System (INIS)

    Maier-Reimer, E.; Mikolajewicz, U.

    1992-02-01

    The rationale for the Large Scale Geostrophic ocean circulation model (LSG-OGCM) is based on the observations that for a large scale ocean circulation model designed for climate studies, the relevant characteristic spatial scales are large compared with the internal Rossby radius throughout most of the ocean, while the characteristic time scales are large compared with the periods of gravity modes and barotropic Rossby wave modes. In the present version of the model, the fast modes have been filtered out by a conventional technique of integrating the full primitive equations, including all terms except the nonlinear advection of momentum, by an implicit time integration method. The free surface is also treated prognostically, without invoking a rigid lid approximation. The numerical scheme is unconditionally stable and has the additional advantage that it can be applied uniformly to the entire globe, including the equatorial and coastal current regions. (orig.)

  19. Assessment of RNAi-induced silencing in banana (Musa spp.).

    Science.gov (United States)

    Dang, Tuong Vi T; Windelinckx, Saskia; Henry, Isabelle M; De Coninck, Barbara; Cammue, Bruno P A; Swennen, Rony; Remy, Serge

    2014-09-18

    In plants, RNA- based gene silencing mediated by small RNAs functions at the transcriptional or post-transcriptional level to negatively regulate target genes, repetitive sequences, viral RNAs and/or transposon elements. Post-transcriptional gene silencing (PTGS) or the RNA interference (RNAi) approach has been achieved in a wide range of plant species for inhibiting the expression of target genes by generating double-stranded RNA (dsRNA). However, to our knowledge, successful RNAi-application to knock-down endogenous genes has not been reported in the important staple food crop banana. Using embryogenic cell suspension (ECS) transformed with ß-glucuronidase (GUS) as a model system, we assessed silencing of gusAINT using three intron-spliced hairpin RNA (ihpRNA) constructs containing gusAINT sequences of 299-nt, 26-nt and 19-nt, respectively. Their silencing potential was analysed in 2 different experimental set-ups. In the first, Agrobacterium-mediated co-transformation of banana ECS with a gusAINT containing vector and an ihpRNA construct resulted in a significantly reduced GUS enzyme activity 6-8 days after co-cultivation with either the 299-nt and 19-nt ihpRNA vectors. In the second approach, these ihpRNA constructs were transferred to stable GUS-expressing ECS and their silencing potential was evaluated in the regenerated in vitro plants. In comparison to control plants, transgenic plants transformed with the 299-nt gusAINT targeting sequence showed a 4.5 fold down-regulated gusA mRNA expression level, while GUS enzyme activity was reduced by 9 fold. Histochemical staining of plant tissues confirmed these findings. Northern blotting used to detect the expression of siRNA in the 299-nt ihpRNA vector transgenic in vitro plants revealed a negative relationship between siRNA expression and GUS enzyme activity. In contrast, no reduction in GUS activity or GUS mRNA expression occurred in the regenerated lines transformed with either of the two gusAINT oligo target

  20. Soft X-ray Emission from Large-Scale Galactic Outflows in Seyfert Galaxies

    Science.gov (United States)

    Colbert, E. J. M.; Baum, S.; O'Dea, C.; Veilleux, S.

    1998-01-01

    Kiloparsec-scale soft X-ray nebulae extend along the galaxy minor axes in several Seyfert galaxies, including NGC 2992, NGC 4388 and NGC 5506. In these three galaxies, the extended X-ray emission observed in ROSAT HRI images has 0.2-2.4 keV X-ray luminosities of 0.4-3.5 x 10(40) erg s(-1) . The X-ray nebulae are roughly co-spatial with the large-scale radio emission, suggesting that both are produced by large-scale galactic outflows. Assuming pressure balance between the radio and X-ray plasmas, the X-ray filling factor is >~ 10(4) times as large as the radio plasma filling factor, suggesting that large-scale outflows in Seyfert galaxies are predominantly winds of thermal X-ray emitting gas. We favor an interpretation in which large-scale outflows originate as AGN-driven jets that entrain and heat gas on kpc scales as they make their way out of the galaxy. AGN- and starburst-driven winds are also possible explanations if the winds are oriented along the rotation axis of the galaxy disk. Since large-scale outflows are present in at least 50 percent of Seyfert galaxies, the soft X-ray emission from the outflowing gas may, in many cases, explain the ``soft excess" X-ray feature observed below 2 keV in X-ray spectra of many Seyfert 2 galaxies.